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RhizoWheat_ms2_references.bib
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RhizoWheat_ms2_references.bib
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@article{Adesina2009,
abstract = {The rhizosphere competence of 15 in vitro antagonists of Rhizoctonia solani was determined 4 weeks after sowing inoculated lettuce seeds into nonsterile soil. Based on the colonization ability determined by selective plating, eight strains were selected for growth chamber experiments to determine their efficacy in controlling bottom rot caused by R. solani on lettuce. Although in the first experiment all antagonists colonized the rhizosphere of lettuce with CFU counts above 2 × 106 g-1 of root fresh weight, only four isolates significantly reduced disease severity. In subsequent experiments involving these four antagonists, only Pseudomonas jessenii RU47 showed effective and consistent disease suppression. Plate counts and denaturing gradient gel electrophoresis (DGGE) fingerprints of Pseudomonas-specific gacA genes amplified from total community DNA confirmed that RU47 established as the dominant Pseudomonas population in the rhizosphere of inoculated lettuce plants. Furthermore, the DGGE fingerprint revealed that R. solani AG1-IB inoculation severely affected the bacterial and fungal community structure in the rhizosphere of lettuce and that these effects were much less pronounced in the presence of RU47. Although the exact mechanism of antagonistic activity and the ecology of RU47 remain to be further explored, our results suggest that RU47 is a promising agent to control bottom rot of lettuce. © 2009 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.},
author = {Modupe F. Adesina and Rita Grosch and Antje Lembke and Tzenko D. Vatchev and Kornelia Smalla},
doi = {10.1111/j.1574-6941.2009.00685.x},
issn = {01686496},
issue = {1},
journal = {FEMS Microbiology Ecology},
keywords = {Antagonists,Biocontrol,Lettuce,Microbial communities,Rhizoctonia solani,Rhizosphere competence},
month = {7},
pages = {62-74},
pmid = {19486156},
title = {In vitro antagonists of Rhizoctonia solani tested on lettuce: Rhizosphere competence, biocontrol efficiency and rhizosphere microbial community response: Research article},
volume = {69},
year = {2009},
}
@article{Adesina2007,
abstract = {A cultivation-based approach was used to determine the in vitro antagonistic potential of soil bacteria towards Rhizoctonia solani AG3 and Fusarium oxysporum f. sp. lini (Foln3). Four composite soil samples were collected from four agricultural sites with previous documentation of disease suppression, located in France (FR), the Netherlands (NL), Sweden (SE) and the United Kingdom (UK). Similarly, two sites from Germany (Berlin, G-BR; and Braunschweig, G-BS) without documentation of disease suppression were sampled. Total bacterial counts were determined by plating serial dilutions from the composite soil samples onto R2A, AGS and King's B media. A total of 1,788 isolates (approximately 100 isolates per medium and site) was screened for antifungal activity, and in vitro antagonists (327 isolates) were found amongst the dominant culturable bacteria isolated from all six soils. The overall proportion of antagonists and the number of isolates with inhibitory activity against F. oxysporum were highest in three of the suppressive soils (FR, NL and SE). Characterization of antagonistic bacteria revealed a high phenotypic and genotypic diversity. Siderophore and protease activity were the most prominent phenotypic traits amongst the antagonists. The composition and diversity of antagonists in each soil was site-specific. Nevertheless, none of the antimicrobial traits of bacteria potentially contributing to soil suppressiveness analyzed in this study could be regarded as specific to a given site. © 2007 Elsevier Ltd. All rights reserved.},
author = {Modupe F. Adesina and Antje Lembke and Rodrigo Costa and Arjen Speksnijder and Kornelia Smalla},
doi = {10.1016/j.soilbio.2007.06.004},
issn = {00380717},
issue = {11},
journal = {Soil Biology and Biochemistry},
keywords = {Biocontrol,Fusarium oxysporum,Lytic enzymes,Rhizoctonia solani,Siderophores,Suppressive soils},
month = {11},
pages = {2818-2828},
title = {Screening of bacterial isolates from various European soils for in vitro antagonistic activity towards Rhizoctonia solani and Fusarium oxysporum: Site-dependent composition and diversity revealed},
volume = {39},
year = {2007},
}
@article{Ahmad2022,
abstract = {Community composition and recruitment are important elements of plant-microbe interactions and may provide insights for plant development and resilience. The results of 16S rRNA amplicon sequencing from four rhizocompartments for four wheat cultivars grown under controlled conditions and sampled after flag leaf emergence are provided. Data demonstrate differences in microbial communities according to rhizocompartment.Community composition and recruitment are important elements of plant-microbe interactions and may provide insights for plant development and resilience. The results of 16S rRNA amplicon sequencing from four rhizocompartments for four wheat cultivars grown under controlled conditions and sampled after flag leaf emergence are provided. Data demonstrate differences in microbial communities according to rhizocompartment.},
author = {J Ahmad and A Zervas and L Ellegaard-Jensen and RC Hennessy and I Carbone and V Cornish and DS Müller-Stöver and A Grunden and CS Jacobsen and MH Nicolaisen},
doi = {10.1128/mra.00663-22},
issn = {2576098X},
issue = {11},
journal = {Microbiology Resource Announcements},
month = {11},
publisher = {American Society for Microbiology},
title = {Microbial Diversity in Four Rhizocompartments (Bulk Soil, Rhizosphere, Rhizoplane, and Endosphere) of Four Winter Wheat Varieties at the Fully Emerged Flag Leaf Growth Stage},
volume = {11},
year = {2022},
}
@article{,
abstract = {The microbiota inhabiting the rhizosphere, the thin layer of soil surrounding plant roots, can promote the growth, development, and health of their host plants. Previous research indicated that differences in the genetic composition of the host plant coincide with variations in the composition of the rhizosphere microbiota.The microbiota populating the rhizosphere, the interface between roots and soil, can modulate plant growth, development, and health. These microbial communities are not stochastically assembled from the surrounding soil, but their composition and putative function are controlled, at least partially, by the host plant. Here, we use the staple cereal barley as a model to gain novel insights into the impact of differential applications of nitrogen, a rate-limiting step for global crop production, on the host genetic control of the rhizosphere microbiota. Using a high-throughput amplicon sequencing survey, we determined that nitrogen availability for plant uptake is a factor promoting the selective enrichment of individual taxa in the rhizosphere of wild and domesticated barley genotypes. Shotgun sequencing and metagenome-assembled genomes revealed that this taxonomic diversification is mirrored by a functional specialization, manifested by the differential enrichment of multiple Gene Ontology terms, of the microbiota of plants exposed to nitrogen conditions limiting barley growth. Finally, a plant soil feedback experiment revealed that host control of the barley microbiota underpins the assembly of a phylogenetically diverse group of bacteria putatively required to sustain plant performance under nitrogen-limiting supplies. Taken together, our observations indicate that under nitrogen conditions limiting plant growth, host-microbe and microbe-microbe interactions fine-tune the host genetic selection of the barley microbiota at both taxonomic and functional levels. The disruption of these recruitment cues negatively impacts plant growth. IMPORTANCE The microbiota inhabiting the rhizosphere, the thin layer of soil surrounding plant roots, can promote the growth, development, and health of their host plants. Previous research indicated that differences in the genetic composition of the host plant coincide with variations in the composition of the rhizosphere microbiota. This is particularly evident when looking at the microbiota associated with input-demanding modern cultivated varieties and their wild relatives, which have evolved under marginal conditions. However, the functional significance of these differences remains to be fully elucidated. We investigated the rhizosphere microbiota of wild and cultivated genotypes of the global crop barley and determined that nutrient conditions limiting plant growth amplify the host control on microbes at the root-soil interface. This is reflected in a plant- and genotype-dependent functional specialization of the rhizosphere microbiota, which appears to be required for optimal plant growth. These findings provide novel insights into the significance of the rhizosphere microbiota for plant growth and sustainable agriculture. },
author = {R Alegria Terrazas and S Robertson-Albertyn and AM Corral and C Escudero-Martinez and R Kapadia and K Balbirnie-Cumming and J Morris and PE Hedley and M Barret and G Torres-Cortes and Eric Paterson and Elizabeth M. Baggs and James Abbott and Davide Bulgarelli},
doi = {10.1128/msystems.00934-22},
issn = {23795077},
issue = {6},
journal = {mSystems},
month = {12},
publisher = {American Society for Microbiology},
title = {Defining Composition and Function of the Rhizosphere Microbiota of Barley Genotypes Exposed to Growth-Limiting Nitrogen Supplies},
volume = {7},
year = {2022},
}
@article{Arnhold2023,
abstract = {The lower yield of wheat grown after wheat (second wheat) compared with the first wheat after a break crop is frequently attributed to fungal disease occurrence, but has also been found without visible disease infection; thus, other factors might be responsible for the lower yield of the second wheat. The aims of this study were to analyze the effects of growing wheat as first and second wheat after oilseed rape, as well as monoculture in a long-term field experiment over three years on (i) aboveground biomass formation, root development and nutrient acquisition during the growing season, (ii) take-all occurrence, and (iii) grain yield and yield components. Subsoil root length density of winter wheat was significantly higher after oilseed rape as pre-crop than after wheat, which was independent of take-all occurrence. Differences in wheat aboveground biomass occurred at early growth stages and were persistent until harvest. Grain yield loss correlated well with take-all disease severity in a wet year but yield differences among crop rotational positions occurred also in a dry year without visible fungal infection. Thus, an effect of the crop rotational position of wheat beyond take-all disease pressure can be assumed. Overall, wheat root length density might be the key to understand wheat biomass formation and grain yield in different crop rotational positions.},
author = {Jessica Arnhold and Dennis Grunwald and Andrea Braun-Kiewnick and Heinz Josef Koch},
doi = {10.3389/fpls.2023.1265994},
issn = {1664462X},
journal = {Frontiers in Plant Science},
keywords = {biomass,grain yield,nitrogen uptake,oilseed rape,root length density,take-all disease},
publisher = {Frontiers Media SA},
title = {Effect of crop rotational position and nitrogen supply on root development and yield formation of winter wheat},
volume = {14},
year = {2023},
}
@article{Arnhold2023,
abstract = {Yield decline in wheat grown after wheat is frequently attributed to fungal disease occurrence, but it is also found without visible disease infection. Thus it is hypothesized that other factors such as N supply or soil structural degradation may lead to wheat yield decline when grown after wheat. The aims of this study were to analyze if (i) the crop rotational position of winter wheat causes differences in soil structure at the beginning of the growing season and (ii) the soil structure is related to differences in wheat biomass formation by this date. Different soil structural properties under winter wheat as well as total aboveground biomass of wheat grown in different crop rotational positions (monoculture, first, second and third wheat after oilseed rape) were investigated in two long-term field experiments with contrasting soil texture. At both field sites, no significant effect of the crop rotational position in any of the analyzed soil structural parameters was found. Wheat biomass in spring was on average 54% higher for wheat grown after oilseed rape compared to second and third wheat after oilseed rape or monoculture. In conclusion, growth reduction of wheat cultivated after wheat was not linked to soil structure as measured in spring.},
author = {Jessica Arnhold and Dennis Grunwald and Henning Kage and Heinz-Josef Koch},
doi = {10.1139/cjss-2023-0030},
issn = {0008-4271},
issue = {4},
journal = {Canadian Journal of Soil Science},
month = {12},
pages = {642-649},
publisher = {Canadian Science Publishing},
title = {No differences in soil structure under winter wheat grown in different crop rotational positions},
volume = {103},
year = {2023},
}
@article{Azarbad2020,
abstract = {There is little understanding about how soil water stress history and host genotype influence the response of wheat-associated microbiome under short-term decreases in soil moisture. To address this, we investigated how plant breeding history (four wheat genotypes; two with recognized drought resistance and two without) and soil water stress history (same wheat field soil from Saskatchewan with contrasting long-term irrigation) independently or interactively influenced the response of the rhizosphere, root and leaf bacterial and fungal microbiota to short-term decreases in soil water content (SWC). We used amplicon sequencing (16S rRNA gene for bacteria and ITS region for fungi) to characterize the wheat microbiome. Fungal and bacterial communities responses to short-term decreases in SWC were mainly constrained by soil water stress history, with some smaller, but significant influence of plant genotype. One exception was the leaf-associated fungal communities, for which the largest constraint was genotype, resulting in a clear differentiation of the communities based on the genotype's sensitivity to water stress. Our results clearly indicate that soil legacy does not only affect the response to water stress of the microbes inhabiting the soil, but also of the microorganisms more closely associated with the plant tissues, and even of the plant itself.},
author = {Hamed Azarbad and Julien Tremblay and Charlotte Giard-Laliberté and Luke D. Bainard and Etienne Yergeau},
doi = {10.1093/FEMSEC/FIAA098},
issn = {15746941},
issue = {7},
journal = {FEMS Microbiology Ecology},
keywords = {16S,ITS,Microbiome,Stress history,Water stress,Wheat},
pmid = {32440671},
publisher = {Oxford University Press},
title = {Four decades of soil water stress history together with host genotype constrain the response of the wheat microbiome to soil moisture},
volume = {96},
year = {2020},
}
@article{Azarbad2022,
abstract = {In a field experiment, we evaluated the impact of 37 years of contrasting water stress history on the microbial response in various plant compartments at two distinct developmental stages when four wheat genotypes were exposed to contemporary water stress. Seeds were collected and sampled at the end of the experiment to characterize endophytic and epiphytic microbial communities. Amplicon sequencing data revealed that plant development stage and water stress history were the main factors shaping the microbiome of the major plant parts in response to contemporary water limitation. Our results indicate that seeds can become colonized by divergent microbial communities within a single generation based on the initial pool of microbes as determined by historical contingencies, which was modulated by the contemporary environmental conditions and the plant genotype. Such information is essential to incorporate microbial-based strategies into conventional plant breeding to enhance plant resistance to stress.},
author = {Hamed Azarbad and Luke D Bainard and Asmaâ Agoussar and Julien Tremblay and Etienne Yergeau},
doi = {10.1038/s43705-022-00151-2},
issue = {1},
journal = {ISME Communications},
month = {12},
publisher = {Oxford University Press (OUP)},
title = {The response of wheat and its microbiome to contemporary and historical water stress in a field experiment},
volume = {2},
year = {2022},
}
@article{,
abstract = {A soil column split-root experiment was designed to investigate the ability of apple replant disease (ARD)-causing agents to spread in soil. 'M26' apple rootstocks grew into a top layer of Control soil, followed by a barrier-free split-soil layer (Control soil/ARD soil). We observed a severely reduced root growth, concomitant with enhanced gene expression of phytoalexin biosynthetic genes and phytoalexin content in roots from ARD soil, indicating a pronounced local plant defense response. Amplicon sequencing (bacteria, archaea, fungi) revealed local shifts in diversity and composition of microorganisms in the rhizoplane of roots from ARD soil. An enrichment of operational taxonomic units affiliated to potential ARD fungal pathogens (Ilyonectria and Nectria sp.) and bacteria frequently associated with ARD (Streptomyces, Variovorax) was noted. In conclusion, our integrated study supports the idea of ARD being local and not spreading into surrounding soil, as only the roots in ARD soil were affected in terms of growth, phytoalexin biosynthetic gene expression, phytoalexin production and altered microbiome structure. This study further reinforces the microbiological nature of ARD, being likely triggered by a disturbed soil microbiome enriched with low mobility of the ARD-causing agents that induce a strong plant defense and rhizoplane microbiome dysbiosis, concurring with root damage.},
author = {Alicia Balbín-Suárez and Samuel Jacquiod and Annmarie Deetja Rohr and Benye Liu and Henryk Flachowsky and Traud Winkelmann and Ludger Beerhues and Joseph Nesme and Søren J. Sørensen and Doris Vetterlein and Kornelia Smalla},
doi = {10.1093/femsec/fiab031},
issn = {15746941},
issue = {4},
journal = {FEMS Microbiology Ecology},
keywords = {X-ray computed tomography,phytoalexins,root system architecture,soil microbiome,split-root experiment},
month = {4},
pmid = {33587112},
publisher = {Oxford University Press},
title = {Root exposure to apple replant disease soil triggers local defense response and rhizoplane microbiome dysbiosis},
volume = {97},
year = {2021},
}
@misc{Ball2005,
abstract = {Increasing concern about the need to provide high-quality food with minimum environmental impact has led to a new interest in crop rotations as a tool to maintain sustainable crop production. We review the role of rotations in the development and preservation of soil structure. After first introducing the types of rotations in current practice and their impact on yield, we assess how soil and crop management in rotations determines soil structure, and in turn how soil structure influences crop growth and yield. We also briefly consider how soil structure might contribute to other beneficial effects of rotations, namely nutrient cycling and disease suppression. Emphasis is given to the influence of crop choice and, where relevant, interaction with tillage system and avoidance of compaction in the improvement and maintenance of soil structure. Crop rotations profoundly modify the soil environment. The sequence of crops in rotation not only influences the removal of nutrients from a soil, but also the return of crop residues, the development and distribution of biopores and the dynamics of microbial communities. These processes contribute to the development of soil structure. We have identified areas where further research is needed to enable the potential benefits of rotations in the management of soil structure to be fully exploited. These include: improved quantitative linkages between soil structure and crop growth, the consequences to soil structure and nutrient cycling of crop residue incorporation, developing natural disease suppression, amelioration of subsoils by crop roots, the fate of carbon deposited by plant roots in soil and the fate of organic nitrogen in soil.},
author = {B. C. Ball and I. Bingham and R. M. Rees and C. A. Watson and A. Litterick},
doi = {10.4141/S04-078},
issn = {00084271},
issue = {5},
journal = {Canadian Journal of Soil Science},
keywords = {Compaction,Disease suppression,Microbial activity,Nutrient cycling,Organic farming,Soil structure},
pages = {557-577},
publisher = {Agricultural Institute of Canada},
title = {The role of crop rotations in determining soil structure and crop growth conditions},
volume = {85},
year = {2005},
}
@article{Bandara2020,
abstract = {Use of seed-applied fungicides has become commonplace in the United States soybean production systems. Although fungicides have the potential to protect seed/seedlings from critical early stage diseases such as damping-off and root/stem rots, results from previous studies are not consistent in terms of seed-applied fungicide's ability to mitigate yield losses. In the current study, the relationship between estimated soybean production losses due to seedling diseases and estimated seed-applied fungicide use was investigated using annual data from 28 soybean growing states in the U.S. over the period of 2006 to 2014. National, regional (northern and southern U.S.), state, and temporal scale trends were explored using mixed effects version of the regression analysis. Mixed modeling allowed computing generalized R2 values for conditional (R2GLMM(c); contains fixed and random effects) and marginal (R2GLMM(m); contains only fixed effects) models. Similar analyses were conducted to investigate how soybean production was related to fungicide use. National and regional scale modeling revealed that R2GLMM(c) values were significantly larger compared to R2GLMM(m) values, meaning fungicide use had limited utility in explaining the national/regional scale variation of yield loss and production. The state scale analysis revealed the usefulness of seedapplied fungicides to mitigate seedling diseases-associated soybean yield losses in Illinois, Indiana, North Carolina, and Ohio. Further, fungicide use positively influenced the soybean production and yield in Illinois and South Dakota. Taken together, use of seed-applied fungicide did not appear to be beneficial to many of the states. Our findings corroborate the observations made by a number of scientists through field scale seed-applied fungicide trials across the U.S and reiterate the importance of need base-use of seed-applied fungicides rather than being a routine practice in soybean production systems.},
author = {Ananda Y. Bandara and Dilooshi K. Weerasooriya and Shawn P. Conley and Tom W. Allen and Paul D. Esker},
doi = {10.1371/journal.pone.0244424},
issn = {19326203},
issue = {12 December},
journal = {PLoS ONE},
month = {12},
pmid = {33370391},
publisher = {Public Library of Science},
title = {Modeling the relationship between estimated fungicide use and disease-associated yield losses of soybean in the United States II: Seedapplied fungicides vs seedling diseases},
volume = {15},
year = {2020},
}
@article{Behr2023,
abstract = {The beneficial effect of microbial consortium application on plants is strongly affected by soil conditions, which are influenced by farming practices. The establishment of microbial inoculants in the rhizosphere is a prerequisite for successful plant-microorganism interactions. This study investigated whether a consortium of beneficial microorganisms establishes in the rhizosphere of a winter crop during the vegetation period, including the winter growing season. In addition, we aimed for a better understanding of its effect on plant performance under different farming practices. Winter rye plants grown in a long-time field trial under conventional or organic farming practices were inoculated after plant emergence in autumn with a microbial consortium containing Pseudomonas sp. (RU47), Bacillus atrophaeus (ABi03) and Trichoderma harzianum (OMG16). The density of the microbial inoculants in the rhizosphere and root-associated soil was quantified in autumn and the following spring. Furthermore, the influence of the consortium on plant performance and on the rhizosphere bacterial community assembly was investigated using a multidisciplinary approach. Selective plating showed a high colonization density of individual microorganisms of the consortium in the rhizosphere and root-associated soil of winter rye throughout its early growth cycle. 16S rRNA gene amplicon sequencing showed that the farming practice affected mainly the rhizosphere bacterial communities in autumn and spring. However, the microbial consortium inoculated altered also the bacterial community composition at each sampling time point, especially at the beginning of the new growing season in spring. Inoculation of winter rye with the microbial consortium significantly improved the plant nutrient status and performance especially under organic farming. In summary, the microbial consortium showed sufficient efficacy throughout vegetation dormancy when inoculated in autumn and contributed to better plant performance, indicating the potential of microbe-based solutions in organic farming where nutrient availability is limited.},
author = {Jan Helge Behr and Ioannis D. Kampouris and Doreen Babin and Loreen Sommermann and Davide Francioli and Theresa Kuhl-Nagel and Soumitra Paul Chowdhury and Joerg Geistlinger and Kornelia Smalla and Günter Neumann and Rita Grosch},
doi = {10.3389/fpls.2023.1232288},
issn = {1664462X},
journal = {Frontiers in Plant Science},
keywords = {16S rRNA gene amplicon sequencing,Bacillus,Pseudomonas,Trichoderma,conventional farming,organic farming},
publisher = {Frontiers Media SA},
title = {Beneficial microbial consortium improves winter rye performance by modulating bacterial communities in the rhizosphere and enhancing plant nutrient acquisition},
volume = {14},
year = {2023},
}
@misc{Berg2022,
abstract = {Background: One promise of the recently presented microbiome definition suggested that, in combination with unifying concepts and standards, microbiome research could be important for solving new challenges associated with anthropogenic-driven changes in various microbiota. With this commentary we want to further elaborate this suggestion, because we noticed specific signatures in microbiota affected by the Anthropocene. Results: Here, we discuss this based on a review of available literature and our own research targeting exemplarily the plant microbiome. It is not only crucial for plants themselves but also linked to planetary health. We suggest that different human activities are commonly linked to a shift of diversity and evenness of the plant microbiota, which is also characterized by a decrease of host specificity, and an increase of r-strategic microbes, pathogens, and hypermutators. The resistome, anchored in the microbiome, follows this shift by an increase of specific antimicrobial resistance (AMR) mechanisms as well as an increase of plasmid-associated resistance genes. This typical microbiome signature of the Anthropocene is often associated with dysbiosis and loss of resilience, and leads to frequent pathogen outbreaks. Although several of these observations are already confirmed by meta-studies, this issue requires more attention in upcoming microbiome studies. Conclusions: Our commentary aims to inspire holistic studies for the development of solutions to restore and save microbial diversity for ecosystem functioning as well as the closely connected planetary health. [MediaObject not available: see fulltext.]},
author = {Gabriele Berg and Tomislav Cernava},
doi = {10.1186/s40168-021-01224-5},
issn = {20492618},
issue = {1},
journal = {Microbiome},
month = {12},
pmid = {35346369},
publisher = {BioMed Central Ltd},
title = {The plant microbiota signature of the Anthropocene as a challenge for microbiome research},
volume = {10},
year = {2022},
}
@article{Berg2001,
abstract = {Aims: A screening approach was developed to assess the potential of rhizobacterial strains to control Verticillium wilt caused by Verticillium dahliae Kleb. Methods and Results: Sixty randomly chosen antagonistic bacterial strains originally isolated from rhizosphere of three different host plants of V. dahliae - strawberry, potato and oilseed rape - were evaluated for biocontrol and plant growth promotion by analysing in vitro antagonism towards V. dahliae and other plant pathogenic fungi, production of fungal cell wall-degrading enzymes and plant growth-promoting effects on strawberry seedlings. To test the plant growth-promoting effect, a microplate assay with strawberry seedlings was developed. Although the rhizobacterial strains were isolated from different plants they showed effects on the growth of strawberry seedlings. According to the in vitro biocontrol and plant growth-promoting activity, the three best candidates Pseudomonas putida B E2 (strawberry rhizosphere), Ps. chlororaphis K15 (potato rhizosphere) and Serratia plymuthica R12 (oilseed rape rhizosphere) were selected for greenhouse experiments to verify the in vitro screening results. Under greenhouse conditions the isolates selected according to this strategy were as effective, or more effective than commercial biocontrol agents and may therefore possibly be valuable as antagonists of V. dahliae. Conclusions: In this study, the screening strategy resulted in a selection of three interesting biocontrol candidates against Verticillium: Ps. putida B E2 (strawberry rhizosphere), Ps. chlororaphis K15 (potato rhizosphere) and Ser. plymuthica R12 (oilseed rape rhizosphere). Significance and Impact of the Study: A new combination of in vitro screening methods including a microplate assay with strawberry seedlings to test the plant growth promoting effect which allow to more efficiently select potential biological control agents was developed successfully.},
author = {G. Berg and A. Fritze and N. Roskot and K. Smalla},
doi = {10.1046/j.1365-2672.2001.01462.x},
issn = {13645072},
issue = {6},
journal = {Journal of Applied Microbiology},
pages = {963-971},
pmid = {11851803},
publisher = {Blackwell Publishing Ltd.},
title = {Evaluation of potential biocontrol rhizobacteria from different host plants of Verticillium dahliae Kleb},
volume = {91},
year = {2001},
}
@misc{Berg2021,
abstract = {Plant-associated microorganisms are involved in important functions related to growth, performance and health of their hosts. Understanding their modes of action is important for the design of promising microbial inoculants for sustainable agriculture. Plant-associated microorganisms are able to interact with their hosts and often exert specific functions toward potential pathogens; the underlying in vitro interactions are well studied. In contrast, in situ effects of inoculants, and especially their impact on the plant indigenous microbiome was mostly neglected so far. Recently, microbiome research has revolutionized our understanding of plants as coevolved holobionts but also of indigenous microbiome-inoculant interactions. Here we disentangle the effects of microbial inoculants on the indigenous plant microbiome and point out the following types of plant microbiome modulations: (i) transient microbiome shifts, (ii) stabilization or increase of microbial diversity, (iii) stabilization or increase of plant microbiome evenness, (iv) restoration of a dysbiosis/compensation or reduction of a pathogen-induced shift, (v) targeted shifts toward plant beneficial members of the indigenous microbiota, and (vi) suppression of potential pathogens. Therefore, we suggest microbiome modulations as novel and efficient mode of action for microbial inoculants that can also be mediated via the plant.},
author = {Gabriele Berg and Peter Kusstatscher and Ahmed Abdelfattah and Tomislav Cernava and Kornelia Smalla},
doi = {10.3389/fmicb.2021.650610},
issn = {1664302X},
journal = {Frontiers in Microbiology},
keywords = {healthy plant microbiome,holobiont,microbial diversity,microbiome shift,mode of action},
month = {4},
publisher = {Frontiers Media S.A.},
title = {Microbiome Modulation—Toward a Better Understanding of Plant Microbiome Response to Microbial Inoculants},
volume = {12},
year = {2021},
}
@article{Bithell2012,
abstract = {The lack of accurate detection of Gaeumannomyces graminis var. tritici inoculum in soil has hampered efforts to predict the risk of severe take-all for wheat growers. The current study used a molecular method to quantify soil G. graminis var. tritici concentrations in commercial wheat fields in New Zealand and to compare them with the proportion of crops surpassing the thresholds for visible and moderate to severe take-all over three growing seasons. The study evaluated a soil G. graminis var. tritici DNA-based take-all prediction system developed in Australia, with four take-all risk categories. These categories were found to be useful for predicting disease severity in second wheat but did not clearly separate risk between fields in medium- and high-risk categories. A sigmoidal relationship was identified between inoculum concentration and the proportion of fields exceeding the two disease thresholds. A logistic response curve was used to further examine this relationship and evaluate the boundaries between take-all risk categories. G. graminis var. tritici boundaries between medium- and high-risk categories were clustered near or within the upper plateau of the relationship. Alternative G. graminis var. tritici boundaries for a three-category system were identified that provided better separation of take-all risk between categories. This information could improve prediction of the risk of severe take-all. © 2012 The American Phytopathological Society.},
author = {Sean L. Bithell and Alan Mckay and Ruth C. Butler and Herdina and Kathy Ophel-Keller and Diana Hartley and Matthew G. Cromey},
doi = {10.1094/PDIS-05-11-0445},
issn = {01912917},
issue = {3},
journal = {Plant Disease},
month = {3},
pages = {443-451},
title = {Predicting take-all severity in second-year wheat using soil DNA concentrations of gaeumannomyces graminis var. tritici determined with qPCR},
volume = {96},
year = {2012},
}
@article{Brettin2015,
abstract = {The RAST (Rapid Annotation using Subsystem Technology) annotation engine was built in 2008 to annotate bacterial and archaeal genomes. It works by offering a standard software pipeline for identifying genomic features (i.e., protein-encoding genes and RNA) and annotating their functions. Recently, in order to make RAST a more useful research tool and to keep pace with advancements in bioinformatics, it has become desirable to build a version of RAST that is both customizable and extensible. In this paper, we describe the RAST tool kit (RASTtk), a modular version of RAST that enables researchers to build custom annotation pipelines. RASTtk offers a choice of software for identifying and annotating genomic features as well as the ability to add custom features to an annotation job. RASTtk also accommodates the batch submission of genomes and the ability to customize annotation protocols for batch submissions. This is the first major software restructuring of RAST since its inception.},
author = {Thomas Brettin and James J. Davis and Terry Disz and Robert A. Edwards and Svetlana Gerdes and Gary J. Olsen and Robert Olson and Ross Overbeek and Bruce Parrello and Gordon D. Pusch and Maulik Shukla and James A. Thomason and Rick Stevens and Veronika Vonstein and Alice R. Wattam and Fangfang Xia},
doi = {10.1038/srep08365},
issn = {20452322},
journal = {Scientific Reports},
month = {2},
pmid = {25666585},
publisher = {Nature Publishing Group},
title = {RASTtk: A modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes},
volume = {5},
year = {2015},
}
@article{Callahan2015,
author = {Benjamin J Callahan and Paul J Mcmurdie and Michael J Rosen and Andrew W Han and Amy Jo Johnson and Susan P Holmes},
doi = {10.1101/024034},
title = {DADA2: High resolution sample inference from amplicon data},
url = {https://doi.org/10.1101/024034},
year = {2015},
}
@article{Caporaso2011,
abstract = {The ongoing revolution in high-throughput sequencing continues to democratize the ability of small groups of investigators to map the microbial component of the biosphere. In particular, the coevolution of new sequencing platforms and new software tools allows data acquisition and analysis on an unprecedented scale. Here we report the next stage in this coevolutionary arms race, using the Illumina GAIIx platform to sequence a diverse array of 25 environmental samples and three known "mock communities" at a depth averaging 3.1 million reads per sample. We demonstrate excellent consistency in taxonomic recovery and recapture diversity patterns that were previously reported on the basis of meta-analysis of many studies from the literature (notably, the saline/nonsaline split in environmental samples and the split between host-associated and free-living communities). We also demonstrate that 2,000 Illumina single-end reads are sufficient to recapture the same relationships among samples that we observe with the full dataset. The results thus open up the possibility of conducting large-scale studies analyzing thousands of samples simultaneously to survey microbial communities at an unprecedented spatial and temporal resolution.},
author = {J. Gregory Caporaso and Christian L. Lauber and William A. Walters and Donna Berg-Lyons and Catherine A. Lozupone and Peter J. Turnbaugh and Noah Fierer and Rob Knight},
doi = {10.1073/pnas.1000080107},
issn = {10916490},
issue = {SUPPL. 1},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
keywords = {Human microbiome,Microbial community analysis,Microbial ecology,Next-generation sequencing},
month = {3},
pages = {4516-4522},
pmid = {20534432},
publisher = {National Academy of Sciences},
title = {Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample},
volume = {108},
year = {2011},
}
@article{Chaparro2012,
abstract = {A variety of soil factors are known to increase nutrient availability and plant productivity. The most influ- ential might be the organisms comprising the soil microbial community of the rhizosphere, which is the soil surrounding the roots of plants where complex interactions occur be- tween the roots, soil, and microorganisms. Root exudates act as substrates and signaling molecules for microbes creating a complex and interwoven relationship between plants and the microbiome. While individual microorganisms such as endophytes, symbionts, pathogens, and plant growth pro- moting rhizobacteria are increasingly featured in the litera- ture, the larger community of soil microorganisms, or soil microbiome, may have more far-reaching effects. Each mi- croorganism functions in coordination with the overall soil microbiome to influence plant health and crop productivity. Increasing evidence indicates that plants can shape the soil microbiome through the secretion of root exudates. The molecular communication fluctuates according to the plant development stage, proximity to neighboring species, man- agement techniques, and many other factors. This review seeks to summarize the current knowledge on this topic},
author = {Jacqueline M. Chaparro and Amy M. Sheflin and Daniel K. Manter and Jorge M. Vivanco},
doi = {10.1007/s00374-012-0691-4},
isbn = {0178-2762},
issn = {0178-2762},
issue = {5},
journal = {Biology and Fertility of Soils},
keywords = {Microbiome,Plant growth promoting rhizobacteria (PGPRs),Root exudates},
month = {7},
pages = {489-499},
title = {Manipulating the soil microbiome to increase soil health and plant fertility},
volume = {48},
url = {http://link.springer.com/10.1007/s00374-012-0691-4},
year = {2012},
}
@article{Chen2019,
abstract = {Background: Plant roots assemble microbial communities both inside the roots and in the rhizosphere, and these root-associated microbiomes play pivotal roles in plant nutrition and productivity. Although it is known that increased synthetic fertilizer input in Chinese farmlands over the past 50 years has resulted in not only increased yields but also environmental problems, we lack a comprehensive understanding of how crops under elevated nutrient input shape root-associated microbial communities, especially through adjusting the quantities and compositions of root metabolites and exudates. Methods: The compositions of bacterial and fungal communities from the roots and rhizosphere of wheat (Triticum aestivum L.) under four levels of long-term inorganic nitrogen (N) fertilization were characterized at the tillering, jointing and ripening stages. The root-released organic carbon (ROC), organic acids in the root exudates and soil organic carbon (SOC) and soil active carbon (SAC) in the rhizosphere were quantified. Results: ROC levels varied dramatically across wheat growth stages and correlated more with the bacterial community than with the fungal community. Rhizosphere SOC and SAC levels were elevated by long-term N fertilization but varied only slightly across growth stages. Variation in the microbial community structure across plant growth stages showed a decreasing trend with N fertilization level in the rhizosphere. In addition, more bacterial and fungal genera were significantly correlated in the jointing and ripening stages than in the tillering stage in the root samples. A number of bacterial genera that shifted in response to N fertilization, including Arthrobacter, Bacillus and Devosia, correlated significantly with acetic acid, oxalic acid, succinic acid and tartaric acid levels. Conclusions: Our results indicate that both plant growth status and N input drive changes in the microbial community structure in the root zone of wheat. Plant growth stage demostrated a stronger influence on bacterial than on fungal community composition. A number of bacterial genera that have been described as plant growth-promoting rhizobacteria (PGPR) responded positively to N fertilization, and their abundance correlated significantly with the organic acid level, suggesting that the secretion of organic acids may be a strategy developed by plants to recruit beneficial microbes in the root zone to cope with high N input. These results provide novel insight into the associations among increased N input, altered carbon availability, and shifts in microbial communities in the plant roots and rhizosphere of intensive agricultural ecosystems.},
author = {Shuaimin Chen and Tatoba R. Waghmode and Ruibo Sun and Eiko E. Kuramae and Chunsheng Hu and Binbin Liu},
doi = {10.1186/s40168-019-0750-2},
issn = {20492618},
issue = {1},
journal = {Microbiome},
keywords = {Nitrogen fertilization,Organic acid,Plant growth stage,Root exudate,Root-associated microbiomes},
month = {10},
pmid = {31640813},
publisher = {BioMed Central Ltd.},
title = {Root-associated microbiomes of wheat under the combined effect of plant development and nitrogen fertilization},
volume = {7},
year = {2019},
}
@misc{Chernin1995,
abstract = {Three Enterobacter agglomerans strains which produce and excrete proteins with chitinolytic activity were found while screening soil-borne bacteria antagonistic to fungal plant pathogens. The chitinolytic activity was induced when the strains were grown in the presence of colloidal chitin as the sole carbon source. It was quantitated by using assays with chromogenic p-nitrophenyl analogs of disaccharide, trisaccharide, and tetrasaccharide derivatives of N-acetylglucosamine. A set of three fluorescent substrates with a 4-methylum-belliferyl group linked by-1,4 linkage to N-acetylglucosamine mono-or oligosaccharides were used to identify the chitinolytic activities of proteins which had been renatured following their separation by electrophoresis. This study provides the most complete evidence for the presence of a complex of chitinolytic enzymes in Enterobacter strains. Four enzymes were detected: two N-acetyl-D-glucosaminidases of 89 and 67 kDa, an endochitinase with an apparent molecular mass of 59 kDa, and a chitobiosidase of 50 kDa. The biocontrol ability of the chitinolytic strains was demonstrated under greenhouse conditions. The bacteria decreased the incidence of disease caused by Rhizoctonia solani in cotton by 64 to 86%. Two Tn5 mutants of one of the isolates, which were deficient in chitinolytic activity, were unable to protect plants against the disease. Various strains of Enterobacter spp. have been described as being effective biological control agents antagonistic to many fungal phytopathogens. Several isolates of Enterobacter cloacae are known to be biocontrol agents for different rots and preemergence damping-off of pea, beet, cotton, and cucumber plants incited by Pythium spp., as well as of Fusarium wilt of cucumber and some other plant diseases caused by fungal pathogens (7, 22, 35). Enterobacter aerogenes B8 significantly reduced infections of apple crown and root rot caused by Phytophtora cactorum (38). Some strains of Enterobacter agglo-merans were shown to be efficient in the control of plant diseases caused by different bacterial and fungal pathogens (10, 22, 27). Various traits expressed synchronously or in a controlled sequence are considered responsible for the action of these strains as biological control agents (24). The ability to produce an antibiotic-like substance was found in strain E. aerogenes B8 (39). Strains of E. cloacae and E. agglomerans were found to produce hydroxamate siderophores (2, 16) and different volatile and nonvolatile antifungal metabolites (11, 37). Competition for nutrients and rhizosphere colonization ability were considered possible mechanisms of antifungal activity in E. cloacae (40) and E. agglomerans (10), respectively. Although some strains of Enterobacter spp. suppress many fungal plant pathogens, data pertaining to the chitinolytic activity of these bacteria are still restricted to only one strain of E. cloacae, and these data are rather inconsistent (17, 29). It is well known, however, that chitin, an insoluble linear polymer of N-acetylglucosamine (GlcNAc) in a-1,4 linkage, is a major structural component of most fungal cell walls, and that many species of bacteria, streptomycetes, actinomycetes, fungi, and plants produce chitinolytic enzymes (21, 32). Bacteria from the genera Aeromonas (12) and Serratia (26) and fungi from the genera Gliocladium (4) and Trichoderma (5), all of which produce chitinolytic enzymes, have been shown to be potential agents for the biological control of plant diseases caused by various phytopathogenic fungi. Evidence that these enzymes are responsible for that effect has been presented (18, 33). Attachment to fungal hyphae was considered an important mechanism in the biocontrol activity of E. cloacae strains against Pythium ultimum (23), and the stimulation of this binding by chitinolytic enzymes from Trichoderma harzianum was demonstrated (17). In the present work, we found that three soil-borne strains of E. agglomerans, which are antagonists of many phytopatho-genic fungi, possess strong chitinolytic activity. The strains were isolated in the course of a screening program for rhizo-spheric bacteria exhibiting a broad range of antagonism toward microbial phytopathogens (3). These strains were found to produce and excrete a complex of chitinolytic enzymes, which were resolved and partially characterized. The role of the chiti-nolytic enzymes in suppressing fungal phytopathogens was studied by using Rhizoctonia solani in cotton as a model, comparing natural isolates with mutants deficient in chitinolytic activity. MATERIALS AND METHODS Cultures and growth media. The three strains of bacteria used in this work (IC960, IC993, and IC1270) were independently isolated from the rhizosphere of different grape bushes in vineyards in the Samarkand region (Republic of Uzbekistan). The isolates were identified as Enterobacter (Pantoea) agglomerans by microbiological and biochemical tests and by gas chromatographic analysis of the whole-cell fatty acid methyl esters. The identification was performed independently in the Bacterial Division of the All-Russia Collection of Microorganisms (Puschino, Moscow Region, Russia) and in the Department of Plant Pathology , Auburn University. The strains were found to produce as yet unidentified antibiotic-like substances and to exhibit proteolytic activity (our unpublished observation). Escherichia coli S17-1 [pro thi hsdR hsdM recA (RP4-2 Tc::Mu-Km::Tn7) inserted into the chromosome, Sm r Rif s ] carrying the pSUP2021 plasmid [Ap r Cm r Tc r Km r (Tn5) ColE1 replicon tra mob ], a suicide vector suitable for the introduction of transposon Tn5 into most gram-negative bacteria (34), was used for transposon mutagenesis. Phytopathogenic fungi were from our and from the Moscow University (Russia) collections. Plasmid pMNU4, which is a derivative of plasmid pUC18 carrying the Tn5 insertion in a},
author = {Leonid Chernin and Zafar Ismailov and Shoshan Haran and Ilan Chet},
isbn = {9728481128},
issue = {5},
journal = {APPLIED AND ENVIRONMENTAL MICROBIOLOGY},
pages = {1720-1726},
title = {Chitinolytic Enterobacter agglomerans Antagonistic to Fungal Plant Pathogens},
volume = {61},
year = {1995},
}
@article{Chng2015,
abstract = {Background and aims: Take-all, caused by the soilborne pathogen Gaeumannomyces graminis var. tritici, (Ggt), is an important root disease of wheat. Continuous wheat cropping has been shown to induce take-all decline (TAD). This research investigated the mechanisms of TAD in 13 New Zealand soils in two experiments and identified the associated microorganisms using denaturing gradient gel electrophoresis (DGGE). Methods: In Experiment 1, a sterile sand/maize-meal mixture inoculated or not inoculated with Ggt, was added at 4 % (w/w) to sterilised and non-sterilised soils to determine their ability to suppress take-all, and to help identify the nature of suppression. Experiment 2 investigated the transferability of suppressive properties in five of the soils from Experiment 1. The microbial communities of these five soils were analysed using PCR-DGGE. Results: Ten of the soils were able to suppress take-all but the suppression was biological in nature in only four of these soils. The suppressive properties of two of the soils were transferred to a γ-irradiated base soil amended with Ggt, indicating that suppression could be specific in nature (i.e., attributed to a specific microorganism or group of microorganisms). The suppressive properties in one soil were not transferrable, suggesting a general form of suppression, most probably because the conditions in the soil were suitable for other microorganisms to compete with Ggt. DGGE analyses of the microbial communities for five of the soils showed similar banding patterns for those with similar forms of suppression (specific, general and non-suppressive) and identified the potential microorganisms that distinguished them. Conclusion: These distinguishing microorganisms are likely to independently or interactively have a function in suppressing take-all.},
author = {Soonie Chng and Matthew G. Cromey and Sarah L. Dodd and Alison Stewart and Ruth C. Butler and Marlene V. Jaspers},
doi = {10.1007/s11104-015-2620-4},
issn = {15735036},
issue = {1-2},
journal = {Plant and Soil},
keywords = {DGGE,Gaeumannomyces graminis var. tritici,Ggt,Inoculum DNA,Microbial communities},
month = {12},
pages = {239-259},
publisher = {Springer International Publishing},
title = {Take-all decline in New Zealand wheat soils and the microorganisms associated with the potential mechanisms of disease suppression},
volume = {397},
year = {2015},
}
@article{Cole2014,
author = {James R Cole and Qiong Wang and Jordan A Fish and Benli Chai and Donna M. McGarrell and Yanni Sun and C Titus Brown and Andrea Porras-Alfaro and Cheryl R Kuske and James M Tiedje},
doi = {10.1093/nar/gkt1244},
issn = {0305-1048},
issue = {D1},
journal = {Nucleic Acids Research},
month = {1},
pages = {D633-D642},
title = {Ribosomal Database Project: data and tools for high throughput rRNA analysis},
volume = {42},
url = {http://nar.oxfordjournals.org/lookup/doi/10.1093/nar/gkt1244},
year = {2014},
}
@misc{Compant2021,
abstract = {The plant endosphere is colonized by complex microbial communities and microorganisms, which colonize the plant interior at least part of their lifetime and are termed endophytes. Their functions range from mutualism to pathogenicity. All plant organs and tissues are generally colonized by bacterial endophytes and their diversity and composition depend on the plant, the plant organ and its physiological conditions, the plant growth stage as well as on the environment. Plant-associated microorganisms, and in particular endophytes, have lately received high attention, because of the increasing awareness of the importance of host-associated microbiota for the functioning and performance of their host. Some endophyte functions are known from mostly lab assays, genome prediction and few metagenome analyses; however, we have limited understanding on in planta activities, particularly considering the diversity of micro-environments and the dynamics of conditions. In our review, we present recent findings on endosphere environments, their physiological conditions and endophyte colonization. Furthermore, we discuss microbial functions, the interaction between endophytes and plants as well as methodological limitations of endophyte research. We also provide an outlook on needs of future research to improve our understanding on the role of microbiota colonizing the endosphere on plant traits and ecosystem functioning.},
author = {Stéphane Compant and Marine C. Cambon and Corinne Vacher and Birgit Mitter and Abdul Samad and Angela Sessitsch},
doi = {10.1111/1462-2920.15240},
issn = {14622920},
issue = {4},
journal = {Environmental Microbiology},
month = {4},
pages = {1812-1829},
pmid = {32955144},
publisher = {Blackwell Publishing Ltd},
title = {The plant endosphere world – bacterial life within plants},
volume = {23},
year = {2021},
}
@misc{Cook2003,
abstract = {Take-all, caused by the soilborne fungus Gaeumannomyces graminis var. tritici, is arguably the most-studied root disease of any crop, yet remains the most important root disease of wheat worldwide. S. D. Garrett launched the study of root diseases and soilborne pathogens as an independent field of science starting in the middle of the 20th century, inspired by and based in large part on his research on take-all during the first half of the 20th century. Because there has been neither a source of host plant resistance nor an effective and economical fungicide for use against this disease, the focus for nearly a century has been on cultural and biological controls. In spite of the intensive and extensive works towards these controls, with mostly site-or soil-specific success, the only broadly and consistently effective controls require either crop rotation (break crops), or the converse, wheat monoculture to induce take-all decline. Take-all decline has become the model system for research on biological control of plant pathogens in the rhizosphere and provided the first proof to the scientific world after decades of debate that antibiotics are both produced in soils and play a role in the ecology of soil microorganisms. On the other hand, even the best yields following take-all decline are rarely equal to those achieved with crop rotation. Because of this, the continuing trends globally to shorten rather than lengthen the rotations in wheat-based cropping systems, and the growing use of direct-seed (no-till) trashy systems to reduce costs and protect soil and water resources, new methods to control take-all are needed more than ever. With high resolution maps of the genomes of cereals and other grasses now available, including a complete sequence of the rice genome, and the interesting differences as well as striking similarities among the genomes of cereals and related grasses, gene transfer to wheat from oats, rice, maize and other grass species resistant to G. graminis var. tritici should be pursued. © 2003 Elsevier Science Ltd. All rights reserved.},
author = {R. James Cook},
doi = {10.1016/S0885-5765(03)00042-0},
issn = {08855765},
issue = {2},
journal = {Physiological and Molecular Plant Pathology},
keywords = {Biological control,Crop rotation,Direct seeding,Gaeumannomyces graminis var. tritici,Root diseases,Soilborne plant pathogens,Take-all decline},
month = {2},
pages = {73-86},
publisher = {Academic Press},
title = {Take-all of wheat},
volume = {62},
year = {2003},
}
@article{Darriaut2023,
abstract = {Grapevine decline affects viticulture worldwide. It is caused by a wide range of individual and combined biotic and abiotic factors. Some declines remain unexplained because they are not associated with known pathological symptoms or mineral dysregulation. Vineyard microbiological quality is an important area of study, since grapevine-associated microbiome primarily originates in vineyard soils and determines host health and development. To understand the decrease of growth and yield, and the high mortality of plants in vineyards affected by these declines, a multisite study investigated soil microbial communities. Spatial (terroir: two distinct geographical locations) and temporal (season: autumn and spring) dimensions were added to the inter-row soil status factor (S for areas with symptomatic vines and AS for those with asymptomatic vines). The microbiomes of AS and S soils were analyzed using high-throughput sequencing based on the bacterial 16S rRNA gene, the fungal ITS1 region (Internal Transcribed Spacer), or the fungal 18S rRNA gene for Glomeromycota family. Geographical location was the strongest driver of bacterial and fungal microbial communities, while the seasonal factor primarily influenced bacterial community. Based on metabarcoding analysis, symptomatic soils presented enriched bacterial taxa that can be potentially beneficial for grapevine growth. In addition, fungal diversity and richness, including Glomeromycota division, were greater in symptomatic soils. Fungal genera associated with grapevine diseases were detected across all conditions, with higher abundances in symptomatic soils. These findings reveal that vineyard soils affected by unexplained decline are a potential source of both fungal pathogens and beneficial microorganisms.},
author = {Romain Darriaut and Joseph Tran and Guilherme Martins and Nathalie Ollat and Isabelle Masneuf-Pomarède and Virginie Lauvergeat},
doi = {10.1016/j.apsoil.2022.104767},
issn = {09291393},
journal = {Applied Soil Ecology},
keywords = {Bulk soil,Metabarcoding,Season,Taxa enrichment,Terroir,Vineyard},
month = {3},
publisher = {Elsevier B.V.},
title = {In grapevine decline, microbiomes are affected differently in symptomatic and asymptomatic soils},
volume = {183},
year = {2023},
}
@misc{,
abstract = {de Souza, J. T., Weller, D. M., and Raaijmakers, J. M. 2003. Frequency, diversity, and activity of 2,4-diacetylphloroglucinol-producing fluorescent Pseudomonas spp. in Dutch take-all decline soils. Phytopathology 93: 54-63.},
author = {Jorge T De Souza and David M Weller and Jos M Raaijmakers},
title = {Ecology and Population Biology Frequency, Diversity, and Activity of 2,4-Diacetylphloroglucinol-Producing Fluorescent Pseudomonas spp. in Dutch Take-all Decline Soils},
year = {2003},
}
@article{,
abstract = {Plants recruit beneficial microbial communities in the rhizosphere that are involved in a myriad of ecological services, such as improved soil quality, nutrient uptake, abiotic stress tolerance, and soil-borne disease suppression. Disease suppression caused by rhizosphere microbiomes has been important in managing soil-borne diseases in wheat. The low heritability of resistance in wheat to soil-borne diseases like Rhizoctonia root rot has made management of these diseases challenging, particularly in direct-seeded systems. Identification of wheat genotypes that recruit rhizosphere microbiomes that promote improved plant fitness and suppression of the pathogen could be an alternative approach to disease management through genetic improvement. Several growth chamber cycling experiments were conducted using six winter wheat genotypes (PI561725, PI561727, Eltan, Lewjain, Hill81, Madsen) to determine wheat genotypes that recruit suppressive microbiomes. At the end of the third cycle, suppression assays were done by inoculating R. solani into soils previously cultivated with specific wheat genotypes to test suppression of the pathogen by the microbiome. Microbiome composition was characterized by sequencing of 16S rDNA (V1-V3 region). Among the growth cycling lengths, 160-day growth cycles exhibited the most distinct rhizosphere microbiomes among the wheat genotypes. Suppression assays showed that rhizosphere microbiomes of different wheat genotypes resulted in significant differences in shoot length (value of p=0.018) and had an impact on the pathogenicity of R. solani, as observed in the reduced root disease scores (value of p=0.051). Furthermore, soils previously cultivated with the ALMT1 isogenic lines PI561725 and PI561727 exhibited better seedling vigor and reduced root disease. Microbiome analysis showed that Burkholderiales taxa, specifically Janthinobacterium, are differentially abundant in PI561727 and PI561725 cultivated soils and are associated with reduced root disease and better growth. This study demonstrates that specific wheat genotypes recruit different microbiomes in growth chamber conditions but the microbial community alterations were quite different from those previously observed in field plots, even though the same soils were used. Genotype selection or development appears to be a viable approach to controlling soil-borne diseases in a sustainable manner, and controlled environment assays can be used to see genetic differences but further work is needed to explain differences seen between growth chamber and field conditions.},
author = {Christine Jade Dilla-Ermita and Ricky W. Lewis and Tarah S. Sullivan and Scot H. Hulbert},
doi = {10.3389/fpls.2021.718264},
issn = {1664462X},
journal = {Frontiers in Plant Science},
keywords = {Rhizoctonia,genotype,microbiome,recruitment,rhizosphere,wheat},
month = {12},
publisher = {Frontiers Media S.A.},
title = {Wheat Genotype-Specific Recruitment of Rhizosphere Bacterial Microbiota Under Controlled Environments},
volume = {12},
year = {2021},
}
@article{Elvia2021,
abstract = {Beneficial bacteria associated with agricultural crops may potentially increase crop productivity and health. However, during various plant developmental processes, shifts in the diversity and function of bacterial communities often occur. This study investigated the diversity of bacterial communities associated with the rhizosphere, roots, and aboveground plant organs of wheat and canola at stem elongation, flowering, and ripening stages. The growth-chamber experiment consisted of wheat and canola grown in Orthic Brown Chernozem Calcic Kastanozem and Orthic Black Calcic Chernozem soils from agricultural fields in Saskatchewan, Canada. Rhizosphere bacterial communities of wheat and canola were mainly influenced by soil characteristics, whereas a specific root endophytic community was associated with each crop species. These results suggest that each crop may select distinct root bacterial endophytes from the rhizosphere. Bacteria associated with aboveground plant organs exhibited high variability among crop species and soils. The most abundant bacterial genera associated with the rhizosphere of the crops included Gemmatimonas, Solirubrobacter, and Nocardioides, as well as unclassified genera of families Commamonadaceae, Chitinophagaceae, and Sphingomonadaceae. Other genera (e.g., Stenotrophomonas, Streptomyces, and Variovorax) were predominant in wheat roots, whereas species of Lentzea and Pantoea were the most abundant root endophytes detected in canola. Bacterial communities associated with aboveground organs consisted mostly of species of Corynebacterium and Pseudomonas, and unclassified members of the family Enterobacteriacaeae. This study also revealed that plant growth stages can modulate the diversity of rhizosphere and endophytic bacteria. The influence of plant growth stages on the bacterial microbiome associated with wheat and canola was crop and organ specific.},
author = {Jorge Cordero Elvia and J. Renato De Freitas and James J. Germida},
doi = {10.1094/PBIOMES-10-20-0073-R},
issn = {24712906},
issue = {4},
journal = {Phytobiomes Journal},
keywords = {16S rRNA high-Throughput sequencing,Crop microbiome,Endophytic bacteria,Plant growth stages,Rhizosphere bacteria},
pages = {442-451},
publisher = {American Phytopathological Society},
title = {Bacterial microbiomes associated with the rhizosphere, root interior, and aboveground plant organs of wheat and canola at different growth stages},
volume = {5},
year = {2021},
}
@article{Felsenstein1985,
author = {Joseph Felsenstein},
doi = {10.1111/j.1558-5646.1985.tb00420.x},
issn = {0014-3820},
issue = {4},
journal = {Evolution},
month = {7},
pages = {783-791},
title = {CONFIDENCE LIMITS ON PHYLOGENIES: AN APPROACH USING THE BOOTSTRAP},
volume = {39},
url = {https://academic.oup.com/evolut/article/39/4/783/6872498},
year = {1985},
}
@article{,
abstract = {Introduction: Inoculation of plants with beneficial microorganisms may improve plant performance yet suffers from efficacy variability. A solution might be the combined application of different inoculants as consortium. The objective of the present study was to evaluate the effects of single or combined inoculation of Trichoderma harzianum, strain TGFG411, and a consortium of arbuscular mycorrhizal fungi (AMF) on plant growth, and native microbial communities (here bacteria/archaea, fungi and AMF) in root-associated soil (RAS) and rhizosphere (RH), that is, soil loosely or tightly attached to the roots, respectively. Materials and Methods: A greenhouse experiment was carried out with non-sterile agricultural soil and the model crop maize, which was single inoculated with either TGFG411 or AMF or received a combined inoculation of TGFG411 + AMF. Control plants received only water. Seven weeks after the second AMF inoculation, the plant growth promotion capacity of the inoculants was measured based on shoot and root parameters. Furthermore, RAS and RH microbiota (fungi including AMF, bacteria and archaea) were assessed via a combination of different cultivation-dependent, microscopic and DNA-based methods. Results: After 7 weeks of maize growth, both single and combined inoculation of AMF and TGFG411 enhanced shoot dry weight and led to a significant reduction in root biomass. The TGFG411 strain successfully established in the soil. However, no definite evidence for the establishment of the inoculated AMF was found. Single or combined inoculation of TGFG411 and AMF modified the composition of total bacterial in the RH, whereas modulated total fungal communities in the RAS. Conclusion: The combined inoculation did not result in a significant improvement of plant performance compared with single inoculation likely due to optimal nutrient supply. However, samples receiving the combined inoculation exhibited a distinct modulation of the native RAS/RH microbiota, which may influence the inoculant efficacy under less favourable conditions.},
author = {Gabriela Fernandez-Gnecco and Louis Gégu and Fernanda Covacevich and Veronica F. Consolo and Marie Lara Bouffaud and François Buscot and Kornelia Smalla and Doreen Babin},
doi = {10.1002/sae2.12091},
issn = {2767035X},
issue = {1},
journal = {Journal of Sustainable Agriculture and Environment},
keywords = {high-throughput sequencing,inoculants,plant growth promotion,soil microbes,sustainable agriculture},
month = {3},
publisher = {John Wiley and Sons Inc},
title = {Alone as effective as together: AMF and Trichoderma inoculation boost maize performance but differentially shape soil and rhizosphere microbiota},
volume = {3},
year = {2024},
}
@article{Gdanetz2017,
abstract = {Manipulating plant-associated microbes to reduce disease or improve crop yields requires a thorough understanding of interactions within the phytobiome. Plants were sampled from a wheat/maize/soybean crop rotation site that implements four different crop management strategies. We analyzed the fungal and bacterial communities of leaves, stems, and roots of wheat throughout the growing season using 16S and fungal internal transcribed spacer 2 rRNA gene amplicon sequencing. The most prevalent operational taxonomic units (OTUs) were shared across all samples, although levels of the low-abundance OTUs varied. Endophytes were isolated from plants, and tested for antagonistic activity toward the wheat pathogen Fusarium graminearum. Antagonistic strains were assessed for plant protective activity in seedling assays. Our results suggest that microbial communities were strongly affected by plant organ and plant age, and may be influenced by management strategy.},
author = {Kristi Gdanetz and Frances Trail},
doi = {10.1094/PBIOMES-05-17-0023-R},
issn = {24712906},
issue = {3},
journal = {Phytobiomes Journal},
pages = {158-168},
publisher = {American Phytopathological Society},
title = {The wheat microbiome under four management strategies, and potential for endophytes in disease protection},
volume = {1},
year = {2017},
}
@article{Gholizadeh2022,
abstract = {Background: Although coevolutionary signatures of host-microbe interactions are considered to engineer the healthy microbiome of humans, little is known about the changes in root-microbiome during plant evolution. To understand how the composition of the wheat and its ancestral species microbiome have changed over the evolutionary processes, we performed a 16S rRNA metagenomic analysis on rhizobacterial communities associated with a phylogenetic framework of four Triticum species T. urartu, T. turgidum, T. durum, and T. aestivum along with their ancestral species Aegilops speltoides, and Ae. tauschii during vegetative and reproductive stages. Results: In this study, we illustrated that the genome contents of wild species Aegilops speltoides and Ae. tauschii can be significant factors determining the composition of root-associated bacterial communities in domesticated bread wheat. Although it was found that domestication and modern breeding practices might have had a significant impact on microbiome-plant interactions especially at the reproductive stage, we observed an extensive and selective control by wheat genotypes on associated rhizobacterial communities at the same time. Our data also showed a strong genotypic variation within species of T. aestivum and Ae. tauschii, suggesting potential breeding targets for plants surveyed. Conclusions: This study performed with different genotypes of Triticum and Aegilops species is the first study showing that the genome contents of Ae. speltoides and Ae. tauschii along with domestication-related changes can be significant factors determining the composition of root-associated bacterial communities in bread wheat. It is also indirect evidence that shows a very extensive range of host traits and genes are probably involved in host-microbe interactions. Therefore, understanding the wheat root-associated microbiome needs to take into consideration of its polygenetic mosaic nature.},
author = {Somayeh Gholizadeh and Seyed Abolghasem Mohammadi and Ghasem Hosseini Salekdeh},
doi = {10.1186/s12866-022-02467-4},
issn = {14712180},
issue = {1},
journal = {BMC Microbiology},
keywords = {Breeding,Developmental stage,Differential abundance,Domestication,Genotype,Microbiome,Rhizosphere,Wheat species},
month = {12},
pmid = {35219318},
publisher = {BioMed Central Ltd},
title = {Changes in root microbiome during wheat evolution},
volume = {22},
year = {2022},
}
@article{Giongo2024,
abstract = { The plethora of microorganisms inhabiting the immediate vicinity of healthy root systems plays a pivotal role in facilitating optimal nutrient and water acquisition by plants. In this study, we investigated the soil microbial communities associated with wheat roots within distinct microhabitats, root-affected soil (RA), rhizosphere (RH), and rhizoplane (RP). These microhabitats were explored at five soil depths, and our investigation focused on wheat cultivated in a monoculture (WM) and wheat crop rotation (WR). Overall, there were significant differences in microbiota composition between WM and WR, although no difference in bacterial diversity was observed. Differentially abundant taxa between WM and WR were observed in all three microhabitats, emphasizing important insights on the localization of commonly associated bacteria to wheat roots. Comparing the microhabitats, RP exhibited the most dissimilar microbial composition between WM and WR. Taxa that were differentially abundant between WM and WR were observed in the three microhabitats. The high relative abundance of taxa belonging to the phylum Proteobacteria in the rhizoplane, such as Devosia , Pseudomonas , Shinella , and Sphingomonas , along with other genera, such as Pedobacter ( Bacteroidota ), Agromyces and Streptomyces ( Actinobacteriota ) highlight the recruitment of potentially beneficial bacterial taxa to the vicinity of the roots. Interestingly, these taxa were observed along the entire length of wheat roots, even at depths of up to 120 cm. The presence of specific taxa associated with wheat roots at all soil depths may be beneficial for coping with nutrient and water shortages, particularly under upcoming climate scenarios, where water may be a limiting factor for plant growth. This study provides valuable insights for designing management strategies to promote a diverse and healthy microbial community in wheat cropping systems, considering soil depth and microhabitats as key factors. Although, at this time, we cannot link specific bacterial taxa to yield reductions commonly observed in monocultural fields, we propose that some genera may enhance plant nutrient or water acquisition in rotation compared with monoculture. Advanced technologies, including functional analyses and culturomics, may further enhance our understanding of the ecological roles played by these microbes and their potential applications in sustainable agriculture. },
author = {Adriana Giongo and Jessica Arnhold and Dennis Grunwald and Kornelia Smalla and Andrea Braun-Kiewnick},
doi = {10.3389/frmbi.2024.1335791},
journal = {Frontiers in Microbiomes},
month = {2},
publisher = {Frontiers Media SA},
title = {Soil depths and microhabitats shape soil and root-associated bacterial and archaeal communities more than crop rotation in wheat},
volume = {3},
year = {2024},
}
@article{Gouy2010,
abstract = {We present SeaView version 4, a multiplatform program designed to facilitate multiple alignment and phylogenetic tree building from molecular sequence data through the use of a graphical user interface. SeaView version 4 combines all the functions of the widely used programs SeaView (in its previous versions) and Phylo-win, and expands them by adding network access to sequence databases, alignment with arbitrary algorithm, maximum-likelihood tree building with PhyML, and display, printing, and copy-to-clipboard of rooted or unrooted, binary or multifurcating phylogenetic trees. In relation to the wide present offer of tools and algorithms for phylogenetic analyses, SeaView is especially useful for teaching and for occasional users of such software. SeaView is freely available at http://pbil.univ-lyon1.fr/software/seaview.},
author = {Manolo Gouy and Stéphane Guindon and Olivier Gascuel},
doi = {10.1093/molbev/msp259},
issn = {07374038},
issue = {2},
journal = {Molecular Biology and Evolution},
keywords = {Graphical user interface,Molecular phylogeny,Multiple sequence alignment,PhyML,SeaView},
month = {2},
pages = {221-224},
pmid = {19854763},
title = {Sea view version 4: A multiplatform graphical user interface for sequence alignment and phylogenetic tree building},
volume = {27},
year = {2010},
}
@misc{Hack1992,
abstract = {Die erweiterte BBCH-Skala zur einheitlichen Codierung der phänologischen Entwicklungsstadien mono-und dikotyler Pflanzen ist eine Gemeinschaftsarbeit der Biologischen Bun desanstalt für Land-und Forstwirtschaft (BBA), des Bundes sortenamtes (BSA) und des Industrieverbandes Agrar (IV A). Grundprinzipien für den allgemeinen Rahmen werden fest gelegt-und der Aufbau der Skala beschrieben. Der Aufbau der Skala als Dezimal-Skala, aufgeteilt in Makro-und Mikrosta dien, wurde bewußt in Anlehnung an die von ZADOKS et al. (1974) entwickelte Getreideskala gewählt, um größere Umstellungen dieser allgemein gebräuchlichen und seit lan gem bewährten Skala vermeiden zu können. Durch Einführung eines Mesostadiums kann der zweistel lige Code auf drei Stellen erweitert werden. Die Allgemeine BBCH-Skala stellt den verbindlichen Rah men dar, innerhalb dessen spezielle Skalen für wichtige mono und dikotyle Pflanzen erarbeitet und an gleicher Stelle in loser Folge veröffentlicht werden. Diese Allgemeine Skala kann immer dann Anwendung finden, wenn keine spezielle Skala vorliegt. Abstract The extcnded BBCH scale for thc uniform coding of phenologically identical growth stages of all mono-and dicotyledonous plants is presented. lt rcsults from the tcamwork betwcen Biologische Bundes anstalt für Land-und Forstwirtschaft (BBA). Bundessortenamt (BSA) and Industrieverband Agrar (!VA). Thc principles of the· general scale are explaincd. The decimal code (principal and sccondary growth stages) is based on the well-known code developed by ZADOKS et al. (1974) and avoids major changcs from this widely used phenological key. In some cases a three-digit code is offcred additionally. The dcfinitions and groupings employed for thc general BBCH scale allow its universal utilisation in all mono and dicotyledonous plants. The gcneral BBCH scale represents the frame for the compilation of spccific scales for the major plants which shall be published in the near future. This general scale can be uscd, when no specific crop and plant scale is available.},
author = {H Hack and H Bleiholder and L Buhr and U Meier and U Schnock-Fricke and E Weber and A Witzenberger Zusammenfassung},
issue = {12},
journal = {Nachrichtenbl. Deut. Pflanzenschutzd},
pages = {265-270},
title = {Einheitliche Codierung der phänologischen Entwicklungsstadien mono-und dikotyler Pflanzen.-Erweiterte BBCH-Skala, Allgemein-A uniform code for phenological growth stages of mono-and dicotyledonöus plants-Extended BBCH scale, general},
volume = {44},
year = {1992},
}
@misc{Heuer1997,
abstract = {A group-specific primer, F243 (positions 226 to 243, Escherichia coli numbering), was developed by comparison of sequences of genes encoding 16S rRNA (16S rDNA) for the detection of actinomycetes in the environment with PCR and temperature or denaturing gradient gel electrophoresis (TGGE or DGGE, respectively). The specificity of the forward primer in combination with different reverse ones was tested with genomic DNA from a variety of bacterial strains. Most actinomycetes investigated could be separated by TGGE and DGGE, with both techniques giving similar results. Two strategies were employed to study natural microbial communities. First, we used the selective amplification of actinomycete sequences (E. coli positions 226 to 528) for direct analysis of the products in denaturing gradients. Second, a nested PCR providing actinomycete-specific fragments (E. coli positions 226 to 1401) was used which served as template for a PCR when conserved primers were used. The products (E. coli positions 968 to 1401) of this indirect approach were then separated by use of gradient gels. Both approaches allowed detection of actinomycete communities in soil. The second strategy allowed the estimation of the relative abundance of actinomycetes within the bacterial community. Mixtures of PCR-derived 16S rDNA fragments were used as model communities consisting of five actinomycetes and five other bacterial species. Actinomycete products were obtained over a 100-fold dilution range of the actinomycete DNA in the model community by specific PCR; detection of the diluted actinomycete DNA was not possible when conserved primers were used. The methods tested for detection were applied to monitor actinomycete community changes in potato rhizosphere and to investigate actinomycete diversity in different soils.},
author = {Holger Heuer and Martin Krsek and Paul Baker and Kornelia Smalla and Elizabeth M H Wellington},
isbn = {00992240/97},
issue = {8},
journal = {APPLIED AND ENVIRONMENTAL MICROBIOLOGY},
pages = {3233-3241},
title = {Analysis of Actinomycete Communities by Specific Amplification of Genes Encoding 16S rRNA and Gel-Electrophoretic Separation in Denaturing Gradients},
volume = {63},
url = {https://journals.asm.org/journal/aem},
year = {1997},
}
@misc{Hohmann2020,
abstract = {The miCROPe 2019 symposium, which took place from 2 to 5 December 2019 in Vienna, Austria, has unified researchers and industry from around the world to discuss opportunities, challenges and needs of microbe-assisted crop production. There is broad consensus that microorganisms-with their abilities to alleviate biotic and abiotic stresses and to improve plant nutrition-offer countless opportunities to enhance plant productivity and to ameliorate agricultural sustainability. However, microbe-assisted cultivation approaches face challenges that need to be addressed before a breakthrough of such technologies can be expected. Following up on the miCROPe symposium and a linked satellite workshop on breeding for beneficial plant-microbe interactions, we carved out research priorities towards successful implementation of microbiome knowledge for modern agriculture. These include (i) to solve context dependency for microbial inoculation approaches and (ii) to identify the genetic determinants to allow breeding for beneficial plant-microbiome interactions. With the combination of emerging third generation sequencing technologies and new causal research approaches, we now stand at the crossroad of utilising microbe-assisted crop production as a reliable and sustainable agronomic practice.},
author = {Pierre Hohmann and Klaus Schlaeppi and Angela Sessitsch},
doi = {10.1093/femsec/fiaa177},
issn = {15746941},
issue = {10},
journal = {FEMS Microbiology Ecology},
keywords = {Biocontrol,GxExM,Microbial inoculation,Plant breeding,Plant genetics,Plant-microbiome interactions},
month = {10},
pmid = {32832989},
publisher = {Oxford University Press},
title = {MiCROPe 2019 - Emerging research priorities towards microbe-assisted crop production},
volume = {96},
year = {2020},
}
@book{,
abstract = {[3. ed.] Sul frontespizio: Update 2015},
author = {IUSS Working Group WRB},
isbn = {9789251083697},
publisher = {FAO},
title = {World reference base for soil resources 2014 : international soil classification system for naming soils and creating legends for soil maps},
year = {2014},
}
@article{Kaloterakis2024,
abstract = {Successive winter wheat (WW) rotations are associated with a substantial yield decline, and the underlying mechanisms remain elusive. An outdoor experiment was set up using sandy loam soil. WW was grown in rhizotrons, in soil after oilseed rape (KW1), after one season of WW (KW2), and after three successive seasons of WW (KW4). We applied zymography and harvested the plants at the stem elongation stage to observe changes in the activity of β-glucosidase (BGU) and leucine aminopeptidase (LAP), as well as using glucose (GLU) imaging to observe glucose release patterns in the rhizosphere of WW. Several biochemical and microbial properties of the bulk soil and the rhizosphere of the rotational positions were measured. KW2 and KW4 exhibited reduced plant biomass compared to KW1. There was a higher root length density and root mean diameter as well as a lower specific root length for KW1 compared to KW2 and KW4. KW1 soil had a lower mineral N concentration and microbial biomass carbon (C) and nitrogen (N) than KW2 and KW4, which translated to a lower plant C:N ratio. A greater rhizosphere extent of BGU and LAP across the soil profile was also visible for KW1 compared to KW2 and KW4 using zymography. Lower dissolved organic C and hotspot areas of GLU in the rhizosphere of successive WW might explain shifts in the microbial community composition, possibly leading to a dysbiosis with the soil microbes in the rhizosphere. Soil depth and rotational position explained most of the variance in the soil microbial communities. The relative abundance of Acidobacteriota, Gemmatimonadota, Nitrospirota, and Chloroflexi significantly varied among the rotational positions. Our results highlight the effect of WW rotational positions on soil and plant properties, as well as microbial community dynamics, and provide evidence for the pathways driving biomass decline in successively grown WW.},
author = {Nikolaos Kaloterakis and Mehdi Rashtbari and Bahar S. Razavi and Andrea Braun-Kiewnick and Adriana Giongo and Kornelia Smalla and Charlotte Kummer and Sirgit Kummer and Rüdiger Reichel and Nicolas Brüggemann},
doi = {10.1016/j.soilbio.2024.109343},
issn = {00380717},
journal = {Soil Biology and Biochemistry},
month = {4},
publisher = {Elsevier Ltd},
title = {Preceding crop legacy modulates the early growth of winter wheat by influencing root growth dynamics, rhizosphere processes, and microbial interactions},
volume = {191},
year = {2024},
}
@misc{Kavamura2021,
abstract = {Wheat is one of the world's most important crops, but its production relies heavily on agrochemical inputs which can be harmful to the environment when used excessively. It is well known that a multitude of microbes interact with eukaryotic organisms, including plants, and the sum of microbes and their functions associated with a given host is termed the microbiome. Plant-microbe interactions can be beneficial, neutral or harmful to the host plant. Over the last decade, with the development of next generation DNA sequencing technology, our understanding of the plant microbiome structure has dramatically increased. Considering that defining the wheat microbiome is key to leverage crop production in a sustainable way, here we describe how different factors drive microbiome assembly in wheat, including crop management, edaphic-environmental conditions and host selection. In addition, we highlight the benefits to take a multidisciplinary approach to define and explore the wheat core microbiome to generate solutions based on microbial (synthetic) communities or single inoculants. Advances in plant microbiome research will facilitate the development of microbial strategies to guarantee a sustainable intensification of crop production.},
author = {Vanessa N. Kavamura and Rodrigo Mendes and Adnane Bargaz and Tim H. Mauchline},
doi = {10.1016/j.csbj.2021.01.045},
issn = {20010370},
journal = {Computational and Structural Biotechnology Journal},
keywords = {Microbiome,Rhizosphere,Sustainable intensification,Wheat},
month = {1},
pages = {1200-1213},
publisher = {Elsevier B.V.},
title = {Defining the wheat microbiome: Towards microbiome-facilitated crop production},
volume = {19},
year = {2021},
}
@article{Keenan2015,
abstract = {The soil-borne ascomycete Gaeumannomyces graminis var. tritici causes take-all of wheat (Triticum aestivum). Between host crops, G. graminis var. tritici survives saprophytically on crop debris and by infecting susceptible grass weeds or cereal volunteers. Invasion of roots in the following wheat crop results in reduced grain yield and quality. Take-all is commonly assessed in the field by visual inspection. Molecular-based methods are also available to detect G. graminis var. tritici, including a quantitative PCR (qPCR) assay that indirectly measures the amount of pathogen DNA in environmental samples. The qPCR is used as part of a commercial tool (known as PreDicta B™) to predict the risks of take-all in wheat crops prior to planting, which are dependent on the amount of Gaeumannomyces inoculum in field soils. Unfortunately, the costs associated with the PreDicta B™ test can be prohibitive to its use. As a result, in this study, an alternative qPCR assay was developed to measure directly the DNA of G. graminis var. tritici. The assay was shown to detect DNA of G. graminis var. tritici in both symptomatic and non-symptomatic wheat roots, with an increase in the amount of DNA detected having a strong relationship with an increase in take-all symptoms.},
author = {S. Keenan and M. G. Cromey and S. A. Harrow and S. L. Bithell and R. C. Butler and S. S. Beard and A. R. Pitman},
doi = {10.1007/s13313-015-0379-y},
issn = {14486032},
issue = {6},
journal = {Australasian Plant Pathology},
keywords = {Cereals,DNA quantification,Fungal pathogen},
month = {11},
pages = {591-597},
publisher = {Kluwer Academic Publishers},
title = {Quantitative PCR to detect Gaeumannomyces graminis var. tritici in symptomatic and non-symptomatic wheat roots},
volume = {44},
year = {2015},
}
@article{Kirkegaard2014,
abstract = {The impacts of broadleaf crop, pasture or fallow breaks within cereal-based cropping systems are widely acknowledged, but most studies have focussed on the first cereal crop after the break. We report a series of four field experiments in a semi-arid cropping zone of Southern Australia in which the impacts of a range of Year 1 sequence options (crops, pasture and fallow) on Year 3 and 4 wheat crops were investigated. In three of the experiments, two phases of the same experiment were commenced in successive years, providing seven sequence phases. In three of the seven phases (at three of the four sites), the Year 1 treatments influenced the yield of Year 3 or Year 4 wheat crops by 0.6, 0.9 and 0.9tha-1, although different responses between phases of the same experiments at two sites provided clear evidence of significant seasonal interactions. Interactions of Year 1 sequence treatments with tillage, crop species/varieties and/or added P-fertiliser treatments in intervening years also occurred at some sites. The largest persistent yield impacts related to the preservation of differences in residual nitrogen (N), and in some cases water following Year 1 crops through subsequent dry seasons, which were frequent in most experimental phases. Higher residual N levels after legumes and canola could persist for 2-3 years and induce yield penalties due to "haying-off" when Year 3 or 4 wheat crops experienced dry spring conditions. Such effects were offset following Year 1 fallow due to increased residual water at depth. Increases in the cereal root diseases take-all (Gaeumannomyces tritici) and rhizoctonia (Rhizoctonia solani AG8) due to Year 1 wheat also persisted through dry seasons and reduced Year 3 wheat yield in some experiments. We found no evidence for a significant role for arbuscular mycorrhizal fungi in yield of Year 3 and 4 wheat crops. We demonstrate that large and significant yield impacts (>0.5tha-1), both positive and negative, can persist for 3-4 years in semi-arid environments as a result of water, N and disease inoculum legacies of Year 1 crop sequence choices. Prolonged dry periods help to preserve these legacies, so that persistent and unpredictable crop sequence effects will be a feature of cropping systems in semi-arid areas with variable climates. © 2014 .},
author = {John A. Kirkegaard and Megan H. Ryan},
doi = {10.1016/j.fcr.2014.05.005},
issn = {03784290},
issue = {1},
journal = {Field Crops Research},
keywords = {Arbuscular mycorrhizal fungi,Break crops,Crop rotation,Drought,Drying climate},
month = {8},
pages = {154-165},
publisher = {Elsevier},
title = {Magnitude and mechanisms of persistent crop sequence effects on wheat},
volume = {164},
year = {2014},
}
@article{Knudsen1999,
abstract = {Five sandy loam soils under organic, integrated and conventional management were chosen to investigate the effect of speci®c agricultural management practices on suppression of brown foot rot of cereals caused by Fusarium culmorum. The relationships between suppressiveness and C and N content of the soil microbial biomass and microbial activity were investigated. Fungistasis tests and plant bioassays were compared. Differences in suppressiveness were most marked in plant bioassays following seed inoculation with F. culmorum. When inoculum was applied to soil as conidia or mycelia, soil-suppressed transmission of the pathogen and disease development. This ®nding indicates that the competitive saprophytic ability of the isolate of F. culmorum is poor. The microbial biomass and activity of the soils under organic and integrated farming were high. However, high biomass and activity were not always correlated with high disease suppression. Speci®c organic amendments, such as mulching with straw and the practice of using lucerne as a break-crop in cereal cultivation may in¯uence inoculum potential of F. culmorum, disease outbreak and suppression. The possible signi®cance of soil abiotic factors on disease suppression is discussed. #},
author = {Inge M.B Knudsen and Kasia Debosz and John Hockenhull and Dan Funck Jensen and Susanne Elmholt},
doi = {10.1016/S0929-1393(98)00156-5},
issn = {09291393},
issue = {1},
journal = {Applied Soil Ecology},
keywords = {Biological control,Fungistasis,Fusarium culmorum,Plant bioassay,Suppressive soils,Sustainable agriculture},
month = {4},
pages = {61-72},
title = {Suppressiveness of organically and conventionally managed soils towards brown foot rot of barley},
volume = {12},
url = {https://linkinghub.elsevier.com/retrieve/pii/S0929139398001565},
year = {1999},
}
@article{Koch2018,
abstract = {In Europe, the framework for sugar beet (Beta vulgaris L.) production was subject to considerable changes and for the future it is expected that sugar beet cultivation might concentrate around the sugar factories for economic reasons. Based on data from a national sugar beet farmers’ survey and multi-year crop rotation trials, the effects of cropping interval (number of years in between two subsequent sugar beet crops) and of preceding crops on sugar yield were elucidated under current Central European management conditions. The dominating sugar beet cropping interval was ≥4 years in the farm survey with pronounced differences between regions. However, the cropping intervals 2, 3, and ≥4 years did not affect the sugar yield. Therefore, significant differences in sugar yield between regions were assumed to be caused by multiple interactions between year, site, and farmers’ skills. Throughout Germany, the dominating preceding crops in sugar beet cultivation were winter wheat (Triticum aestivum L.) and winter barley (Hordeum vulgare L.). In the field trials, the sugar yield was 5% higher after pea (Pisum sativum L.) compared to maize (Zea mays L.) as preceding crop, while differences between the preceding crops pea and winter wheat, and wheat and maize were not significant. Repeated measurements of canopy development and leaf color during the growing season revealed a higher N-availability after pea as preceding crop. However, decreased growth after maize was not completely compensated for by high N-fertilizer doses. Overall, the causes for the differences in sugar yield between the preceding crops remained open. The results do not support concerns about substantial yield losses in sugar beet production due to a reduction in the cropping interval from 3 to 2 years. Nevertheless, short rotations with maize and sugar beet might increase the risk of Rhizoctonia solani crown and root rot infestation. Leguminous crops such as pea offer the potential for higher sugar beet yield with lower N-fertilizer doses.},
author = {Heinz Josef Koch and Kerrin Trimpler and Anna Jacobs and Nicol Stockfisch},
doi = {10.3389/fpls.2018.00231},
issn = {1664462X},
journal = {Frontiers in Plant Science},
keywords = {Crop rotation,Cropping interval,Nitrogen,Preceding crop,Sugar yield},
month = {3},
publisher = {Frontiers Media S.A.},
title = {Crop rotational effects on yield formation in current sugar beet production – Results from a farm survey and field trials},
volume = {9},
year = {2018},
}
@article{Koo2010,
abstract = {Three hundred and seventy-four rhizobacteria were isolated from the rhizosphere soil (RS) or rhizoplane (RP) of Echinochloa crus-galli, Carex leiorhyncha, Commelina communis, Persicaria lapathifolia, Carex kobomugi, and Equisetum arvense, grown in contaminated soil with petroleum and heavy metals. The isolates were screened for plant growth-promoting trait (PGPT), including indole acetic acid (IAA) productivity, 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase activity, and siderophore(s) synthesis ability. IAA production was detected in 86 isolates (23.0%), ACC deaminase activity in 168 isolates (44.9%), and siderophore(s) synthesis in 213 isolates (57.0%). Among the rhizobacteria showing PGPT, 162 isolates had multiple traits showing more than two types of PGPT. The PGPT-possesing rhizobacteria were more abundant in the RP (82%) samples than the RS (75%). There was a negative correlation (-0.656, p<0.05) between the IAA producers and the ACC deaminase producers. Clustering analysis by principal component analysis showed that RP was the most important factor influencing the ecological distribution and physiological characterization of PGPT-possesing rhizobacteria.},
author = {Sun Koo and Hee Wook Ryu and Kyung-suk Cho},
doi = {10.4014/jmb.0907.07017},
issue = {3},
journal = {J. Microbiol. Biotechnol},
keywords = {1-aminocyclopropane-1-carboxylic acid (ACC) deaminase,Rhizobacteria,indole acetic acid (IAA),plant growth-promoting trait,siderophore(s)},
pages = {587-593},
title = {Plant Growth-Promoting Trait of Rhizobacteria Isolated from Soil Contaminated with Petroleum and Heavy Metals},
volume = {20},
year = {2010},
}
@misc{Kostka2012,
abstract = {We report the first genome sequences for six strains of Rhodanobacter species isolated from a variety of soil and subsurface environments. Three of these strains are capable of complete denitrification and three others are not. However, all six strains contain most of the genes required for the respiration of nitrate to gaseous nitrogen. The nondenitrifying members of the genus lack only the gene for nitrate reduction, the first step in the full denitrification pathway. The data suggest that the environmental role of bacteria from the genus Rhodanobacter should be reevaluated. © 2012, American Society for Microbiology.},
author = {Joel E. Kostka and Stefan J. Green and Lavanya Rishishwar and Om Prakash and Lee S. Katz and Leonardo Mariño-Ramírez and I. King Jordan and Christine Munk and Natalia Ivanova and Natalia Mikhailova and David B. Watson and Steven D. Brown and Anthony V. Palumbo and Scott C. Brooks},
doi = {10.1128/JB.00871-12},
issn = {00219193},
issue = {16},
journal = {Journal of Bacteriology},
month = {8},
pages = {4461-4462},
pmid = {22843592},
title = {Genome sequences for six Rhodanobacter strains, isolated from soils and the terrestrial subsurface, with variable denitrification capabilities},
volume = {194},
year = {2012},
}
@misc{,
abstract = {and aims to provide a comprehensive collection of tools and tutorials, with a particular focus on amplicon sequencing data. Getting started Overview (vignette) (https://bioconductor.org/packages/devel/bioc/vignettes/microbiome/inst/doc/vignette.html) Installation (Installation.html) Example data (Data.html) Data operations (Preprocessing.html) (subsetting, transformations etc.) Cleaning taxonomy table (cleaning_taxonomy_table.html) Microbiome analysis Alpha diversity (Alphadiversity.html) Beta diversity / Community heterogeneity (Betadiversity.html) Community composition (Composition.html) Core microbiota (Core.html) Shared core with venn diagram (core_venn.html) Dirichlet Multinomial Mixtures (DMM) for community typing (DMM.html) Dissimilarity-Overlap Analysis (DOC) (DOC.html) Landscapes (Landscaping.html) (population density analysis) Stability and tipping elements (Stability.html) 02.05.24, 12:35 Introduction to the microbiome R package},
author = {Leo Lahti and Sudarshan Shetty},
title = {Introduction to the microbiome R package},
url = {https://travis-ci.org/microbiome/microbiome https://gitter.im/microbiome/microbiome?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge https://codecov.io/github/microbiome/microbiome?branch=master http://joey711.github.io/phyloseq/import-data https://bioconductor.org/packages/devel/bioc/html/microbiome.html},
}
@misc{Lemanceau2017,
abstract = {The microbial community that is systematically associated with a given host plant is called the core microbiota. The definition of the core microbiota was so far based on its taxonomic composition, but we argue that it should also be based on its functions. This so-called functional core microbiota encompasses microbial vehicles carrying replicators (genes) with essential functions for holobiont (i.e., plant plus microbiota) fitness. It builds up from enhanced horizontal transfers of replicators as well as from ecological enrichment of their vehicles. The transmission pathways of this functional core microbiota vary over plant generations according to environmental constraints and its added value for holobiont fitness.},
author = {Philippe Lemanceau and Manuel Blouin and Daniel Muller and Yvan Moënne-Loccoz},
doi = {10.1016/j.tplants.2017.04.008},
issn = {13601385},
issue = {7},
journal = {Trends in Plant Science},
keywords = {agroecology,coevolution,core microbiota,holobiont,rhizosphere},
month = {7},
pages = {583-595},
pmid = {28549621},
publisher = {Elsevier Ltd},
title = {Let the Core Microbiota Be Functional},
volume = {22},
year = {2017},
}
@article{Letunic2021,
abstract = {The Interactive Tree Of Life (https://itol.embl.de) is an online tool for the display, manipulation and annotation of phylogenetic and other trees. It is freely available and open to everyone. iTOL version 5 introduces a completely new tree display engine, together with numerous new features. For example, a new dataset type has been added (MEME motifs), while annotation options have been expanded for several existing ones. Node metadata display options have been extended and now also support non-numerical categorical values, as well as multiple values per node. Direct manual annotation is now available, providing a set of basic drawing and labeling tools, allowing users to draw shapes, labels and other features by hand directly onto the trees. Support for tree and dataset scales has been extended, providing fine control over line and label styles. Unrooted tree displays can now use the equal-daylight algorithm, proving a much greater display clarity. The user account system has been streamlined and expanded with new navigation options and currently handles >1 million trees from >70 000 individual users.},
author = {Ivica Letunic and Peer Bork},
doi = {10.1093/nar/gkab301},
issn = {13624962},
issue = {W1},
journal = {Nucleic Acids Research},
month = {7},
pages = {W293-W296},
pmid = {33885785},
publisher = {Oxford University Press},
title = {Interactive tree of life (iTOL) v5: An online tool for phylogenetic tree display and annotation},
volume = {49},
year = {2021},
}
@article{Liu2023,
abstract = {Host plants and the microbiota living in the rhizosphere are interdependent, mutually reinforced and mutually beneficial but the assembly, functions and microbial interactions of the host-associated microbiota are still unclear. Herein, winter wheat was selected as a test plant to explore the assembly process of total bacteria from bulk soil (BS) and rhizosphere soil (RS), and phoD-harbouring bacteria in RS at a long-term (14 years) trial site. We also identified core microbes that are potentially relevant to soil carbon (C), nitrogen (N) and phosphorus (P) cycling genes and soil biogeochemical properties, and investigated the relationships between soil variables, functional genes and wheat productivity. The results showed that the microhabitat of the plant, rather than P fertilizer input, was the main factor affecting the microbial diversity, composition and co-occurrence networks. The BS bacterial community was driven by deterministic processes but the RS and phoD bacterial communities were dominated by stochastic processes. The influence of deterministic processes decreased with increasing soil nutrient content. A core microbial community consisted of 10 OTUs in different microhabitats and was significantly related to soil functional genes and properties. In the rhizosphere soil, significant correlations were found between soil variables, soil functional bacteria and genes, and crop productivity. Synthesis and applications. This study provides empirical evidence that the assembly process of the microbial community is governed by environmental factors in various soil environments and provides new perspectives on the sustainable improvement of crop productivity. Read the free Plain Language Summary for this article on the Journal blog.},
author = {Lei Liu and Ya Gao and Zhiyuan Gao and Li Zhu and Rong Yan and Wenjie Yang and Yu Yang and Jinshan Liu},
doi = {10.1111/1365-2435.14388},
issn = {13652435},
issue = {9},
journal = {Functional Ecology},
keywords = {bulk soil,community assembly,core microbiome,dryland wheat,phoD-harbouring bacteria,rhizosphere soil},
month = {9},
pages = {2325-2337},
publisher = {British Ecological Society},
title = {The core microbiota as a predictor of soil functional traits promotes soil nutrient cycling and wheat production in dryland farming},
volume = {37},
year = {2023},
}
@article{Love2014,
abstract = {In comparative high-throughput sequencing assays, a fundamental task is the analysis of count data, such as read counts per gene in RNA-seq, for evidence of systematic changes across experimental conditions. Small replicate numbers, discreteness, large dynamic range and the presence of outliers require a suitable statistical approach. We present DESeq2, a method for differential analysis of count data, using shrinkage estimation for dispersions and fold changes to improve stability and interpretability of estimates. This enables a more quantitative analysis focused on the strength rather than the mere presence of differential expression. The DESeq2 package is available at http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html.},
author = {Michael I. Love and Wolfgang Huber and Simon Anders},
doi = {10.1186/s13059-014-0550-8},
issn = {1474760X},
issue = {12},
journal = {Genome Biology},
month = {12},
pmid = {25516281},
publisher = {BioMed Central Ltd.},
title = {Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2},
volume = {15},
year = {2014},
}
@article{Lucas2018,
abstract = {Apple replant disease (ARD) is the phenomenon of soil decline occurring after repeated planting of apple trees at the same site. This study aimed to elucidate whether ARD is systemic, i.e. whether the contact of parts of the root system with ARD soil causes the whole plant to show poor shoot and root growth. A split-root experiment was conducted with seedlings of 'M26', offering the same plant for its root system the choice between the substrates ARD soil (+ARD), γ-sterilized ARD soil (-ARD) or soil from a grass parcel (Control) with the following combinations: +ARD/+ARD,-ARD/-ARD; +ARD/-ARD; +ARD/Control. Root growth was analysed throughout the 34-day growing period. Samples from bulk, rhizosphere and rhizoplane soil were collected separately for each compartment, and analysed by fingerprints of 16S rRNA gene or ITS fragments amplified from total community (TC) DNA. The response of the plant to +ARD was not systemic as root growth in-ARD compartment was always superior to root growth in +ARD soil. Crosswise 15N-labelling of the N-fertilizer applied to the split-root compartments showed that nitrate-N uptake efficiency was higher for roots in-ARD soil compared to those in +ARD. Bacterial and fungal community composition in the rhizoplane and rhizosphere of the same plants differed significantly between the compartments containing +ARD/-ARD or +ARD/Control. The strongest differences between the bacterial fingerprints were observed in the rhizoplane and rhizosphere. Bacterial genera with increased abundance in response to ARD were mainly Streptomyces but also Sphingobium, Novosphingobium, Rhizobium, Lysobacter and Variovorax. The strongest differences between the fungal fingerprints were observed in bulk soil. Our data showed that the response of the apple plant to ARD soil is local and not systemic.},
author = {Maik Lucas and Alicia Balbín-Suárez and Kornelia Smalla and Doris Vetterlein},
doi = {10.1371/journal.pone.0204922},
issn = {19326203},
issue = {10},
journal = {PLoS ONE},
month = {10},
pmid = {30296282},
publisher = {Public Library of Science},
title = {Root growth, function and rhizosphere microbiome analyses show local rather than systemic effects in apple plant response to replant disease soil},
volume = {13},
year = {2018},
}
@article{Madeira2022,
abstract = {The EMBL-EBI search and sequence analysis tools frameworks provide integrated access to EMBL-EBI's data resources and core bioinformatics analytical tools. EBI Search (https://www.ebi.ac.uk/ebisearch) provides a full-text search engine across nearly 5 billion entries, while the Job Dispatcher tools framework (https://www.ebi.ac.uk/services) enables the scientific community to perform a diverse range of sequence analysis using popular bioinformatics applications. Both allow users to interact through user-friendly web applications, as well as via RESTful and SOAP-based APIs. Here, we describe recent improvements to these services and updates made to accommodate the increasing data requirements during the COVID-19 pandemic.},
author = {Fábio Madeira and Matt Pearce and Adrian R.N. Tivey and Prasad Basutkar and Joon Lee and Ossama Edbali and Nandana Madhusoodanan and Anton Kolesnikov and Rodrigo Lopez},
doi = {10.1093/nar/gkac240},
issn = {13624962},
issue = {W1},
journal = {Nucleic Acids Research},
month = {7},
pages = {W276-W279},
pmid = {35412617},
publisher = {Oxford University Press},
title = {Search and sequence analysis tools services from EMBL-EBI in 2022},
volume = {50},
year = {2022},
}
@article{Martiny2019,
abstract = {The paradigm that only 1% of microbes are culturable has had a profound impact on our understanding of microbial ecology and is still a major motivation for mostly using molecular tools to characterize microbial communities. However, this point is often expressed vaguely, suggesting that some scientists have different interpretations of the paradigm. In addition, there have been substantial advances in cultivation techniques suggesting that this paradigm may no longer be correct. To quantify bacterial culturability across six major biomes, I found that the median 16S rRNA similarity of bacteria to known cultured relatives was 97.3 ± 2.3% (s.d.). Furthermore, 52.0 ± 24% of sequences and 34.9 ± 23% of taxa (defined as >97% similar) had a closely related cultured relative. Thus, many cells and taxa across environments are culturable with known techniques, suggesting that the 1% paradigm is no longer correct.},
author = {Adam C. Martiny},
doi = {10.1038/s41396-019-0410-3},
issn = {17517370},
issue = {8},
journal = {ISME Journal},
month = {8},
pages = {2125-2128},
pmid = {30952994},
publisher = {Nature Publishing Group},
title = {High proportions of bacteria are culturable across major biomes},
volume = {13},
year = {2019},
}
@article{McMillan2018,
abstract = {Given the increasing demand for wheat which is forecast, cropping of wheat in short rotations will likely remain a common practice. However, in temperate wheat growing regions the soil-borne fungal pathogen Gaeumannomyces tritici becomes a major constraint on productivity. In cultivar rotation field experiments on the Rothamsted Farm (Hertfordshire, UK) we demonstrated a substantial reduction in take-all disease and grain yield increases of up to 2.4 tonnes/ha when a low take-all inoculum building wheat cultivar was grown in the first year of wheat cropping. Phenotyping of 71 modern elite wheat cultivars for the take-all inoculum build-up trait across six diverse trial sites identified a few cultivars which exhibited a consistent lowering of take-all inoculum build-up. However, there was also evidence of a significant interaction effect between trial site and cultivar when a pooled Residual Maximum Likelihood (REML) procedure was conducted. There was no evidence of an unusual rooting phenotype associated with take-all inoculum build-up in two independent field experiments and a sand column experiment. Together our results highlight the complex interactions between wheat genotype, environmental conditions and take-all inoculum build-up. Further work is required to determine the underlying genetic and mechanistic basis of this important phenomenon.},
author = {V. E. McMillan and G. Canning and J. Moughan and R. P. White and R. J. Gutteridge and K. E. Hammond-Kosack},
doi = {10.1038/s41598-018-25511-8},
issn = {20452322},
issue = {1},
journal = {Scientific Reports},
month = {12},
pmid = {29934522},
publisher = {Nature Publishing Group},
title = {Exploring the resilience of wheat crops grown in short rotations through minimising the build-up of an important soil-borne fungal pathogen},
volume = {8},
year = {2018},
}
@article{McMurdie2013,
author = {Paul J McMurdie and Susan Holmes},
doi = {10.1371/journal.pone.0061217},
journal = {PLoS ONE},
pages = {e61217},
title = {phyloseq : An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data},
volume = {8},
year = {2013},
}
@article{,
abstract = {Microbial taxonomy is increasingly influenced by genome-based computational methods. Yet such analyses can be complex and require expert knowledge. Here we introduce TYGS, the Type (Strain) Genome Server, a user-friendly high-throughput web server for genome-based prokaryote taxonomy, connected to a large, continuously growing database of genomic, taxonomic and nomenclatural information. It infers genome-scale phylogenies and state-of-the-art estimates for species and subspecies boundaries from user-defined and automatically determined closest type genome sequences. TYGS also provides comprehensive access to nomenclature, synonymy and associated taxonomic literature. Clinically important examples demonstrate how TYGS can yield new insights into microbial classification, such as evidence for a species-level separation of previously proposed subspecies of Salmonella enterica. TYGS is an integrated approach for the classification of microbes that unlocks novel scientific approaches to microbiologists worldwide and is particularly helpful for the rapidly expanding field of genome-based taxonomic descriptions of new genera, species or subspecies.},
author = {Jan P. Meier-Kolthoff and Markus Göker},
doi = {10.1038/s41467-019-10210-3},
issn = {20411723},
issue = {1},
journal = {Nature Communications},
month = {12},
pmid = {31097708},
publisher = {Nature Publishing Group},
title = {TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy},
volume = {10},
year = {2019},
}
@article{,
abstract = {Microbial systematics is heavily influenced by genome-based methods and challenged by an ever increasing number of taxon names and associated sequences in public data repositories. This poses a challenge for database systems, particularly since it is obviously advantageous if such data are based on a globally recognized approach to manage names, such as the International Code of Nomenclature of Prokaryotes. The amount of data can only be handled if accurate and reliable high-throughput platforms are available that are able to both comply with this demand and to keep track of all changes in an efficient and flexible way. The List of Prokaryotic names with Standing in Nomenclature (LPSN) is an expert-curated authoritative resource for prokaryotic nomenclature and is available at https://lpsn.dsmz.de. The Type (Strain) Genome Server (TYGS) is a high-throughput platform for accurate genome-based taxonomy and is available at https://tygs.dsmz.de. We here present important updates of these two previously introduced, heavily interconnected platforms for taxonomic nomenclature and classification, including new high-level facilities providing access to bioinformatic algorithms, a considerable expansion of the database content, and new ways to easily access the data.},
author = {Jan P. Meier-Kolthoff and Joaquim Sardà Carbasse and Rosa L. Peinado-Olarte and Markus Göker},
doi = {10.1093/nar/gkab902},
issn = {13624962},
issue = {D1},
journal = {Nucleic Acids Research},
month = {1},
pages = {D801-D807},
pmid = {34634793},
publisher = {Oxford University Press},
title = {TYGS and LPSN: A database tandem for fast and reliable genome-based classification and nomenclature of prokaryotes},
volume = {50},
year = {2022},
}
@article{,
abstract = {“Take-all” disease is the most important biotic factor affecting cereal productivity, causing 30–50% of crop losses. The causal agent is the ascomycete soil-borne pathogen Gaeumannomyces graminis var. tritici (Ggt). Current control measures are ineffective, because Ggt can remain saprophytic in soils for long periods. Therefore, the study of the microbiome residing in suppressive soils (SS) is a promising niche of Ggt biocontrol. Here, we evaluated the efficiency of Serratia sp., Bacillus sp., and Acinetobacter sp. isolated from SS against the incidence of Ggt on wheat. Our results demonstrated that plants inoculated with the bacterial consortium in both greenhouse and field conditions were highly efficient in Ggt biocontrol, more so than individual strains. The disease reduction was evidenced by higher biomass production, fewer copies of the Ggt genome with a concomitant curtailment of blackening of roots, a decrease of lipid peroxidation, and an increase of superoxide dismutase activity. The ability of the microbial consortium over that of single strains could be attributable to interspecies communication as a strategy to biocontrol; i.e., higher chitinase activity. In conclusion, bacterial consortia from SS are an important niche of Ggt biocontrol, serving as a model for other soil-borne pathogens.},
author = {Isabel Méndez and Ana Fallard and Isabel Soto and Gonzalo Tortella and María de la Luz Mora and Alex J. Valentine and Patricio Javier Barra and Paola Duran},
doi = {10.3390/agronomy11102008},
issn = {20734395},
issue = {10},
journal = {Agronomy},
keywords = {Biological control,Microbial consortium,Soil-borne pathogen,Specific suppression,Take-all disease,Triticum aestivum},
month = {10},
publisher = {MDPI},
title = {Efficient biocontrol of gaeumannomyces graminis var. Tritici in wheat: Using bacteria isolated from suppressive soils},
volume = {11},
year = {2021},
}
@misc{Mitter2021,
abstract = {Global population growth poses a threat to food security in an era of increased ecosystem degradation, climate change, soil erosion, and biodiversity loss. In this context, harnessing naturally-occurring processes such as those provided by soil and plant-associated microorganisms presents a promising strategy to reduce dependency on agrochemicals. Biofertilizers are living microbes that enhance plant nutrition by either by mobilizing or increasing nutrient availability in soils. Various microbial taxa including beneficial bacteria and fungi are currently used as biofertilizers, as they successfully colonize the rhizosphere, rhizoplane or root interior. Despite their great potential to improve soil fertility, biofertilizers have yet to replace conventional chemical fertilizers in commercial agriculture. In the last 10 years, multi-omics studies have made a significant step forward in understanding the drivers, roles, processes, and mechanisms in the plant microbiome. However, translating this knowledge on microbiome functions in order to capitalize on plant nutrition in agroecosystems still remains a challenge. Here, we address the key factors limiting successful field applications of biofertilizers and suggest potential solutions based on emerging strategies for product development. Finally, we discuss the importance of biosafety guidelines and propose new avenues of research for biofertilizer development.},
author = {Eduardo K. Mitter and Micaela Tosi and Dasiel Obregón and Kari E. Dunfield and James J. Germida},
doi = {10.3389/fsufs.2021.606815},
issn = {2571581X},
journal = {Frontiers in Sustainable Food Systems},
keywords = {bioformulation,bioprospecting,inoculation,microbiome,plant growth promotion,plant nutrition,soil health,sustainable agriculture},
month = {2},
publisher = {Frontiers Media S.A.},
title = {Rethinking Crop Nutrition in Times of Modern Microbiology: Innovative Biofertilizer Technologies},
volume = {5},
year = {2021},
}
@article{Nautiyal1999,
abstract = {A novel defined microbiological growth medium, National Botanical Research Institute's phosphate growth medium (NBRIP), which is more efficient than Pikovskaya medium (PVK), was developed for screening phosphate solubilizing microorganisms. In plate assay the efficiency of NBRIP was comparable to PVK; however, in broth assay NBRIP consistently demonstrated about 3-fold higher efficiency compared to PVK. The results indicated that the criterion for isolation of phosphate solubilizers based on the formation of visible halo/zone on agar plates is not a reliable technique, as many isolates which did not show any clear zone on agar plates solubilized insoluble inorganic phosphates in liquid medium. It may be concluded that soil microbes should be screened in NBRIP broth assay for the identification of the most efficient phosphate solubilizers.},
author = {C.Shekhar Nautiyal},
doi = {10.1111/j.1574-6968.1999.tb13383.x},
issn = {03781097},
issue = {1},
journal = {FEMS Microbiology Letters},
month = {1},
pages = {265-270},
pmid = {9919677},
publisher = {Oxford University Press (OUP)},
title = {An efficient microbiological growth medium for screening phosphate solubilizing microorganisms},
volume = {170},
year = {1999},
}
@article{Notredame2000,
abstract = {We describe a new method (T-Coffee) for multiple sequence alignment that provides a dramatic improvement in accuracy with a modest sacrifice in speed as compared to the most commonly used alternatives. The method is broadly based on the popular progressive approach to multiple alignment but avoids the most serious pitfalls caused by the greedy nature of this algorithm. With T-Coffee we pre-process a data set of all pair-wise alignments between the sequences. This provides us with a library of alignment information that can be used to guide the progressive alignment. Intermediate alignments are then based not only on the sequences to be aligned next but also on how all of the sequences align with each other. This alignment information can be derived from heterogeneous sources such as a mixture of alignment programs and/or structure superposition. Here, we illustrate the power of the approach by using a combination of local and global pair-wise alignments to generate the library. The resulting alignments are significantly more reliable, as determined by comparison with a set of 141 test cases, than any of the popular alternatives that we tried. The improvement, especially clear with the more difficult test cases, is always visible, regardless of the phylogenetic spread of the sequences in the tests. (C) 2000 Academic Press.},
author = {Cédric Notredame and Desmond G. Higgins and Jaap Heringa},
doi = {10.1006/jmbi.2000.4042},
issn = {00222836},
issue = {1},
journal = {Journal of Molecular Biology},
keywords = {Global alignment,Local alignment,Multiple sequence alignment,Pair-wise alignment,Progressive alignment},
month = {9},
pages = {205-217},
pmid = {10964570},
publisher = {Academic Press},
title = {T-coffee: A novel method for fast and accurate multiple sequence alignment},
volume = {302},
year = {2000},
}
@misc{Oksanen2022,
abstract = {Suggests parallel, tcltk, knitr, markdown Imports MASS, cluster, mgcv VignetteBuilder utils, knitr Description Ordination methods, diversity analysis and other functions for community and vegetation ecologists. License GPL-2},
author = {J Oksanen},
keywords = {1,Ben Bolker [aut],Daniel Borcard [aut],Eduard Szoecs [aut],F Guillaume Blanchet [aut],Gavin L Simpson [aut],Gustavo Carvalho [aut],Helene Wagner [aut],Heloisa Beatriz Antoniazi Evangelista [aut],M Henry H Stevens [aut],Matt Barbour [aut],Michael Bedward [aut],Michael Chirico [aut],Miquel De Caceres [aut],Peter R Minchin [aut],Peter Solymos [aut],Pierre Legendre [aut],RB O'Hara [aut],Roeland Kindt [aut],Sebastien Durand [aut],aut,cre]},
title = {Title Community Ecology Package},
year = {2022},
}
@article{Olson2023,
abstract = {The National Institute of Allergy and Infectious Diseases (NIAID) established the Bioinformatics Resource Center (BRC) program to assist researchers with analyzing the growing body of genome sequence and other omics-related data. In this report, we describe the merger of the PAThosystems Resource Integration Center (PATRIC), the Influenza Research Database (IRD) and the Virus Pathogen Database and Analysis Resource (ViPR) BRCs to form the Bacterial and Viral Bioinformatics Resource Center (BV-BRC) https://www.bv-brc.org/. The combined BV-BRC leverages the functionality of the bacterial and viral resources to provide a unified data model, enhanced web-based visualization and analysis tools, bioinformatics services, and a powerful suite of command line tools that benefit the bacterial and viral research communities.},
author = {Robert D. Olson and Rida Assaf and Thomas Brettin and Neal Conrad and Clark Cucinell and James J. Davis and Donald M. Dempsey and Allan Dickerman and Emily M. Dietrich and Ronald W. Kenyon and Mehmet Kuscuoglu and Elliot J. Lefkowitz and Jian Lu and Dustin Machi and Catherine Macken and Chunhong Mao and Anna Niewiadomska and Marcus Nguyen and Gary J. Olsen and Jamie C. Overbeek and Bruce Parrello and Victoria Parrello and Jacob S. Porter and Gordon D. Pusch and Maulik Shukla and Indresh Singh and Lucy Stewart and Gene Tan and Chris Thomas and Margo VanOeffelen and Veronika Vonstein and Zachary S. Wallace and Andrew S. Warren and Alice R. Wattam and Fangfang Xia and Hyunseung Yoo and Yun Zhang and Christian M. Zmasek and Richard H. Scheuermann and Rick L. Stevens},
doi = {10.1093/nar/gkac1003},
issn = {13624962},
issue = {1 D},
journal = {Nucleic Acids Research},
month = {1},
pages = {D678-D689},
pmid = {36350631},
publisher = {Oxford University Press},
title = {Introducing the Bacterial and Viral Bioinformatics Resource Center (BV-BRC): a resource combining PATRIC, IRD and ViPR},
volume = {51},
year = {2023},
}
@misc{,
abstract = {Take-all disease, caused by the fungal root pathogen Gaeumannomyces tritici, is considered to be the most important root disease of wheat worldwide. Here we review the advances in take-all research over the last 15 years, focusing on the identification of new sources of genetic resistance in wheat relatives and the role of the microbiome in disease development. We also highlight recent breakthroughs in the molecular interactions between G. tritici and wheat, including genome and transcriptome analyses. These new findings will aid the development of novel control strategies against take-all disease. In light of this growing understanding, the G. tritici–wheat interaction could provide a model study system for root-infecting fungal pathogens of cereals.},
author = {Javier Palma-Guerrero and Tania Chancellor and Jess Spong and Gail Canning and Jess Hammond and Vanessa E. McMillan and Kim E. Hammond-Kosack},
doi = {10.1016/j.tplants.2021.02.009},
issn = {13601385},
issue = {8},
journal = {Trends in Plant Science},
keywords = {Gaeumannomyces tritici,Magnaporthaceae,Triticum aestivum,genetic resistance,microbiome,molecular interactions},
month = {8},
pages = {836-848},
pmid = {33752966},
publisher = {Elsevier Ltd},
title = {Take-All Disease: New Insights into an Important Wheat Root Pathogen},
volume = {26},
year = {2021},
}
@article{Peralta2018,
abstract = {Microbiomes can aid in the protection of hosts from infection and disease, but the mechanisms underpinning these functions in complex environmental systems remain unresolved. Soils contain microbiomes that influence plant performance, including their susceptibility to disease. For example, some soil microorganisms produce antimicrobial compounds that suppress the growth of plant pathogens, which can provide benefits for sustainable agricultural management. Evidence shows that crop rotations increase soil fertility and tend to promote microbial diversity, and it has been hypothesized that crop rotations can enhance disease suppressive capacity, either through the influence of plant diversity impacting soil bacterial composition or through the increased abundance of disease suppressive microorganisms. In this study, we used a long-term field experiment to test the effects of crop diversity through time (i.e., rotations) on soil microbial diversity and disease suppressive capacity. We sampled soil from seven treatments along a crop diversity gradient (from monoculture to five crop species rotation) and a spring fallow (non-crop) treatment to examine crop diversity influence on soil microbiomes including bacteria that are capable of producing antifungal compounds. Crop diversity significantly influenced bacterial community composition, where the most diverse cropping systems with cover crops and fallow differed from bacterial communities in the 1–3 crop species diversity treatments. While soil bacterial diversity was about 4% lower in the most diverse crop rotation (corn–soybean–wheat + 2 cover crops) compared to monoculture corn, crop diversity increased disease suppressive functional group prnD gene abundance in the more diverse rotation by about 9% compared to monocultures. In addition, disease suppressive potential was significantly diminished in the (non-crop) fallow treatment compared to the most diverse crop rotation treatments. The composition of the microbial community could be more important than diversity to disease suppressive function in our study. Identifying patterns in microbial diversity and ecosystem function relationships can provide insight into microbiome management, which will require manipulating soil nutrients and resources mediated through plant diversity.},
author = {Ariane L. Peralta and Yanmei Sun and Marshall D. McDaniel and Jay T. Lennon},
doi = {10.1002/ecs2.2235},
issn = {21508925},
issue = {5},
journal = {Ecosphere},
keywords = {crop rotation,disease suppression,microbial diversity,structure–function relationships},
month = {5},
publisher = {Wiley-Blackwell},
title = {Crop rotational diversity increases disease suppressive capacity of soil microbiomes},
volume = {9},
year = {2018},
}
@article{Qi2020,
abstract = {Bacterial wilt (BW) disease causes huge economic loss. Heretofore there is no effective way to completely control BW. Here, cover crops (pea, rapeseed, and wheat) were used to restore declining soil properties and control BW. Cover crops can increase content of soil organic matter, alkali-hydrolyzable nitrogen and enzymatic activities, as well as suppress BW. Different kinds of cover crops are distinguished in recovering different soil properties. For instance, rapeseed can inhibit BW more effectively than wheat and pea, while wheat has the best effect on increasing soil organic matter, urease, and invertase. Nevertheless, pea improves catalase better than rapeseed and wheat. Moreover, relative abundance of plant-beneficial bacteria in cover crop treatments is higher than that in the control, with a negative correlation with disease index. For example, wheat has the best effect on improving the growth of plant-beneficial bacteria, followed by rapeseed. The bacteria involved in nitrogen cycling are enriched in pea treatments. However, the relative abundance of pathogen and denitrifying bacteria in cover crop treatments is lower than that in the control, with a positive correlation with disease index. The count of bacteria genes involved in nutrients cycling, antibiotics synthesis, and biodegradation of toxic compounds in cover crop treatments is higher than that in the control. Wheat includes more these genes than rapeseed and pea. Overall, cover crops can restore declining soil properties and suppress BW by increasing soil nutrients and beneficial bacteria as well as decreasing pathogen. Among all cover crops, wheat is considered as the optimal one.},
author = {Gaofu Qi and Shu Chen and Luxin Ke and Gaoqiang Ma and Xiuyun Zhao},
doi = {10.1016/j.micres.2020.126505},
issn = {09445013},
journal = {Microbiological Research},
keywords = {Bacterial wilt disease,Cover crops,Soil bacterial community,Soil properties},
month = {9},
pmid = {32516644},
publisher = {Elsevier GmbH},
title = {Cover crops restore declining soil properties and suppress bacterial wilt by regulating rhizosphere bacterial communities and improving soil nutrient contents},
volume = {238},
year = {2020},
}
@article{Quast2013,
author = {Christian Quast and Elmar Pruesse and Pelin Yilmaz and Jan Gerken and Timmy Schweer and Frank Oliver Glo and Pablo Yarza},
doi = {10.1093/nar/gks1219},
issue = {November 2012},
journal = {Nucleic Acids Research},
pages = {590-596},
title = {The SILVA ribosomal RNA gene database project: improved data processing and web-based tools},
volume = {41},
year = {2013},
}
@misc{,
author = {R Core team},
title = {R_Core_Team2021},
year = {2021},
}
@misc{Raaijmakers1997,
abstract = {The antibiotics phenazine-1-carboxylic acid (PCA) and 2,4-diacetylphloroglucinol (Phl) are major determinants of biological control of soilborne plant pathogens by various strains of fluorescent Pseudomonas spp. In this study, we described primers and probes that enable specific and efficient detection of a wide variety of fluorescent Pseudomonas strains that produce various phenazine antibiotics or Phl. PCR analysis and Southern hybridization demonstrated that specific genes within the biosynthetic loci for Phl and PCA are conserved among various Pseudomonas strains of worldwide origin. The frequency of Phl-and PCA-producing fluorescent pseudomonads was determined on roots of wheat grown in three soils suppressive to take-all disease of wheat and four soils conducive to take-all by colony hybridization followed by PCR. Phenazine-producing strains were not detected on roots from any of the soils. However, Phl-producing fluorescent pseudomonads were isolated from all three take-all-suppressive soils at densities ranging from approximately 5 10 5 to 2 10 6 CFU per g of root. In the complementary conducive soils, Phl-producing pseudomonads were not detected or were detected at densities at least 40-fold lower than those in the suppressive soils. We speculate that fluorescent Pseudomonas spp. that produce Phl play an important role in the natural suppressiveness of these soils to take-all disease of wheat.},
author = {Jos M Raaijmakers and David M Weller and Linda S Thomashow},
isbn = {00992240/97},
issue = {3},
journal = {APPLIED AND ENVIRONMENTAL MICROBIOLOGY},
pages = {881-887},
title = {Frequency of Antibiotic-Producing Pseudomonas spp. in Natural Environments},
volume = {63},
url = {https://journals.asm.org/journal/aem},
year = {1997},
}
@article{Robinson2016,
abstract = {Aims: To understand effects of tissue type, growth stage and soil fertilisers on bacterial endophyte communities of winter wheat (Triticum aestivum cv. Hereward). Methods: Endophytes were isolated from wheat grown under six fertiliser conditions in the long term Broadbalk Experiment at Rothamsted Research, UK. Samples were taken in May and July from root and leaf tissues. Results: Root and leaf communities differed in abundance and composition of endophytes. Endophytes were most abundant in roots and the Proteobacteria were most prevalent. In contrast, Firmicutes and Actinobacteria, the Gram positive phyla, were most prevalent in the leaves. Both fertiliser treatment and sample time influenced abundance and relative proportions of each phylum and genus in the endosphere. A higher density of endophytes was found in the Nil input treatment plants. Conclusions: Robust isolation techniques and stringent controls are critical for accurate recovery of endophytes. The plant tissue type, plant growth stage, and soil fertiliser treatment all contribute to the composition of the endophytic bacterial community in wheat. These results should help facilitate targeted development of endophytes for beneficial applications in agriculture.},
author = {Rebekah J. Robinson and Bart A. Fraaije and Ian M. Clark and Robert W. Jackson and Penny R. Hirsch and Tim H. Mauchline},
doi = {10.1007/s11104-015-2495-4},
issn = {15735036},
issue = {1-2},
journal = {Plant and Soil},
keywords = {Bacterial endophyte,Community structure,Culture dependent,Fertiliser,Nitrogen,RFLP},
month = {8},
pages = {381-396},
publisher = {Springer International Publishing},
title = {Endophytic bacterial community composition in wheat (Triticum aestivum) is determined by plant tissue type, developmental stage and soil nutrient availability},
volume = {405},
year = {2016},
}
@misc{Rolfe2019,
abstract = {Plants employ immunological and ecological strategies to resist biotic stress. Recent evidence suggests that plants adapt to biotic stress by changing their root exudation chemistry to assemble health-promoting microbiomes. This so-called ‘cry-for-help’ hypothesis provides a mechanistic explanation for previously characterized soil feedback responses to plant disease, such as the development of disease-suppressing soils upon successive cultivations of take all-infected wheat. Here, we divide the hypothesis into individual stages and evaluate the evidence for each component. We review how plant immune responses modify root exudation chemistry, as well as what impact this has on microbial activities, and the subsequent plant responses to these activities. Finally, we review the ecological relevance of the interaction, along with its translational potential for future crop protection strategies.},
author = {Stephen A. Rolfe and Joseph Griffiths and Jurriaan Ton},
doi = {10.1016/j.mib.2019.10.003},
issn = {18790364},
journal = {Current Opinion in Microbiology},
month = {6},
pages = {73-82},
pmid = {31731229},
publisher = {Elsevier Ltd},
title = {Crying out for help with root exudates: adaptive mechanisms by which stressed plants assemble health-promoting soil microbiomes},
volume = {49},
year = {2019},
}
@article{Rolli2022,
abstract = {Root endophytes establish beneficial interactions with plants, improving holobiont resilience and fitness, but how plant immunity accommodates beneficial microbes is poorly understood. The multi-stress tolerance-inducing endophyte Enterobacter sp. SA187 triggers a canonical immune response in Arabidopsis only at high bacterial dosage (>108 CFUs ml−1), suggesting that SA187 is able to evade or suppress the plant defence system at lower titres. Although SA187 flagellin epitopes are recognized by the FLS2 receptor, SA187-triggered salt tolerance functions independently of the FLS2 system. In contrast, overexpression of the chitin receptor components LYK4 and LYK5 compromised the beneficial effect of SA187 on Arabidopsis, while it was enhanced in lyk4 mutant plants. Transcriptome analysis revealed that the role of LYK4 is intertwined with a function in remodelling defence responses with growth and root developmental processes. LYK4 interferes with modification of plant ethylene homeostasis by Enterobacter SA187 to boost salt stress resistance. Collectively, these results contribute to unlock the crosstalk between components of the plant immune system and beneficial microbes and point to a new role for the Lys-motif receptor LYK4 in beneficial plant–microbe interaction.},
author = {Eleonora Rolli and Axel de Zélicourt and Hanin Alzubaidy and Michael Karampelias and Sabiha Parween and Naganand Rayapuram and Baoda Han and Katja Froehlich and Aala A. Abulfaraj and Hanna Alhoraibi and Kiruthiga Mariappan and Cristina Andrés-Barrao and Jean Colcombet and Heribert Hirt},
doi = {10.1111/1462-2920.15839},
issn = {14622920},
issue = {1},
journal = {Environmental Microbiology},
month = {1},
pages = {223-239},
pmid = {34951090},
publisher = {John Wiley and Sons Inc},
title = {The Lys-motif receptor LYK4 mediates Enterobacter sp. SA187 triggered salt tolerance in Arabidopsis thaliana},
volume = {24},
year = {2022},
}
@article{Saitou1987,
abstract = {A new method called the neighbor-joining method is proposed for reconstructing phylogenetic trees from evolutionary distance data. The principle of this method is to find pairs of operational taxonomic units (OTUs [ =neighbors]) that minimize the total branch length at each stage of clustering of OTUs starting with a starlike tree. The branch lengths as well as the topology of a parsimonious tree can quickly be obtained by using this method. Using computer simulation, we studied the efficiency of this method in obtaining the correct unrooted tree in comparison with that of five other tree-making methods: the unweighted pair group method of analysis , Far-r-is's method, Sattath and Tversky's method, Li's method, and Tateno et al.'s modified Fan-is method. The new, neighbor-joining method and Sattath and Tversky's method are shown to be generally better than the other methods.},
author = {Naruya Saitou and Masatoshi Nei},
journal = {Molecular Biology & Evolution},
pages = {406-425},
title = {The Neighbor-joining Method: A New Method for Reconstructing Phylogenetic Trees},
volume = {4},
url = {https://academic.oup.com/mbe/article/4/4/406/1029664},
year = {1987},