Long-term use of cover crops and no-till shift soil microbial community life strategies in agricultural soil

Schmidt, Radomir; Gravuer, Kelly; Bossange, Anne V.; Mitchell, Jeffrey P.; Scow, Kate M.

doi:10.1371/journal.pone.0192953

Cited by 191 publications

(131 citation statements)

References 76 publications

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“…However, meta-analyses of microbial communities to infer CSR strategies can be challenging due to the different factors related to experimental design and techniques employed across different studies, which could heavily affect the observations in comparison. Recent studies on soil-bacterial communities in cadmium-contaminated rhizospheres (Wood et al, 2018) and tillage-disturbed fields (Schmidt et al, 2018) also suggested the applicability of the CSR approach to soilmicrobial communities. To the best of our knowledge, the CSR framework has not yet been employed within a single study to changes in microbial communities upon disturbance in any microbiome other than soil.…”

Section: Introductionmentioning

confidence: 99%

Trait‐based life‐history strategies explain succession scenario for complex bacterial communities under varying disturbance

Santillan

Seshan

Constancias

et al. 2019

Environmental Microbiology

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Summary Trait‐based approaches are increasingly gaining importance in community ecology, as a way of finding general rules for the mechanisms driving changes in community structure and function under the influence of perturbations. Frameworks for life‐history strategies have been successfully applied to describe changes in plant and animal communities upon disturbance. To evaluate their applicability to complex bacterial communities, we operated replicated wastewater treatment bioreactors for 35 days and subjected them to eight different disturbance frequencies of a toxic pollutant (3‐chloroaniline), starting with a mixed inoculum from a full‐scale treatment plant. Relevant ecosystem functions were tracked and microbial communities assessed through metagenomics and 16S rRNA gene sequencing. Combining a series of ordination, statistical and network analysis methods, we associated different life‐history strategies with microbial communities across the disturbance range. These strategies were evaluated using tradeoffs in community function and genotypic potential, and changes in bacterial genus composition. We further compared our findings with other ecological studies and adopted a semi‐quantitative competitors, stress‐tolerants, ruderals (CSR) classification. The framework reduces complex data sets of microbial traits, functions and taxa into ecologically meaningful components to help understand the system response to disturbance and hence represents a promising tool for managing microbial communities.

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Section: Introductionmentioning

confidence: 99%

Trait‐based life‐history strategies explain succession scenario for complex bacterial communities under varying disturbance

Santillan

Seshan

Constancias

et al. 2019

Environmental Microbiology

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“…However, meta-analyses of microbial communities to infer CSR strategies can be challenging due to 83 the different factors related to experimental design and techniques employed across different studies, 84 which could heavily affect the observations in comparison. Recent studies on soil-bacterial 85 communities in cadmium-contaminated rhizospheres (Wood et al 2018) and tillage-disturbed fields 86 (Schmidt et al 2018) also suggested the applicability of the CSR approach to soil-microbial 87 communities. To our knowledge, the CSR framework has not yet been employed within a single study 88 to changes in microbial communities upon disturbance in any microbiome other than soil.…”

Section: Introduction 44mentioning

confidence: 99%

Trait-based life-history strategies explain succession scenario for complex bacterial communities under varying disturbance

Santillan

Seshan

Constancias

et al. 2019

Preprint

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Originality-Significance Statement 22This study establishes, for the first time, CSR life-history strategies in the context of bacterial 23 communities. This framework is explained using community aggregated traits in an environment other 24 than soil, also a first, using a combination of ordination methods, network analysis, and genotypic 25 information from shotgun metagenomics and 16S rRNA gene amplicon sequencing. 26 Summary 27Trait-based approaches are increasingly gaining importance in community ecology, as a way of finding 28 general rules for the mechanisms driving changes in community structure and function under the 29 influence of perturbations. Frameworks for life-history strategies have been successfully applied to 30 describe changes in plant and animal communities upon disturbance. To evaluate their applicability to 31 complex bacterial communities, we operated replicated wastewater treatment bioreactors for 35 days 32 and subjected them to eight different disturbance frequencies of a toxic pollutant (3-chloroaniline), 33 starting with a mixed inoculum from a full-scale treatment plant. Relevant ecosystem functions were 34 tracked and microbial communities assessed through metagenomics and 16S rRNA gene sequencing. 35Combining a series of ordination, statistical and network analysis methods, we associated different life-36 history strategies with microbial communities across the disturbance range. These strategies were 37 evaluated using tradeoffs in community function and genotypic potential, and changes in bacterial genus 38 composition. We further compared our findings with other ecological studies and adopted a semi-39 quantitative CSR (competitors, ruderals, stress-tolerants) classification. The framework reduces 40 complex datasets of microbial traits, functions, and taxa into ecologically meaningful components to 41 help understand the system response to disturbance, and hence represents a promising tool for managing 42 microbial communities. 43

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“…Indeed, soil bacterial and fungal communities are known to change in association with plant traits that reflect plant productivity, such as foliar C:N and leaf dry matter content (Sayer et al, 2017). Links between plant CSR strategies, root exudates and the rhizosphere microbiome are also suggested by models (Krause et al, 2014;Schmidt, Gravuer, Bossange, Mitchell, & Scow, 2018;Thijs, Sillen, Rineau, Weyens, & Vangronsveld, 2018). Thus, changes in plant strategies along the productivity/disturbance gradients underpinning the humped-back curve should impose effects on rhizosphere biological diversity.…”

Section: Introductionmentioning

confidence: 99%

Differential biodiversity responses between kingdoms (plants, fungi, bacteria and metazoa) along an Alpine succession gradient

et al. 2018

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Biological diversities of multiple kingdoms potentially respond in similar ways to environmental changes. However, studies either compare details of microbial diversity across general vegetation or land use classes or relate details of plant community diversity with the extent of microbially governed soil processes, via physiological profiling. Here, we test the hypothesis of shared responses of plant and rhizosphere bacterial, fungal and metazoan biodiversities (especially across-habitat β-diversity patterns) along a disturbance gradient encompassing grazed to abandoned Alpine pasture, on acid soil in the European Central Alps. Rhizosphere biological diversity was inferred from eDNA fractions specific to bacteria, fungi and metazoans from contrasting plant habitats indicative of different disturbance levels. We found that soil β-diversity patterns were weakly correlated with plant diversity measures and similarly ordinated along an evident edaphic (pH, C:N, assimilable P) and disturbance gradient but, contrary to our hypothesis, did not demonstrate the same diversity patterns. While plant communities were well separated along the disturbance gradient, correlating with fungal diversity, the majority of bacterial taxa were shared between disturbance levels (75% of bacteria were ubiquitous, cf. 29% plant species). Metazoa exhibited an intermediate response, with communities at the lowest levels of disturbance partially overlapping. Thus, plant and soil biological diversities were only loosely dependent and did not exhibit strictly linked environmental responses. This probably reflects the different spatial scales of organisms (and their habitats) and capacity to invest resources in persistent multicellular tissues, suggesting that vegetation responses to environmental change are unreliable indicators of below-ground biodiversity responses.

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Long-term use of cover crops and no-till shift soil microbial community life strategies in agricultural soil

Cited by 191 publications

References 76 publications

Trait‐based life‐history strategies explain succession scenario for complex bacterial communities under varying disturbance

Trait‐based life‐history strategies explain succession scenario for complex bacterial communities under varying disturbance

Trait-based life-history strategies explain succession scenario for complex bacterial communities under varying disturbance

Differential biodiversity responses between kingdoms (plants, fungi, bacteria and metazoa) along an Alpine succession gradient

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