Microscale evidence for a high decrease of soil bacterial density and diversity by cropping

Constancias, Florentin; Prévost-Bouré, Nicolas Chemidlin; Terrat, Sébastien; Aussems, Simon; Nowak, Virginie; Guillemin, Jean‐Philippe; Bonnotte, Aline; Biju‐Duval, Luc; Navel, Aline; Martins, Jean M.F.; Maron, Pierre‐Alain; Ranjard, Lionel

doi:10.1007/s13593-013-0204-3

Cited by 43 publications

(40 citation statements)

References 35 publications

(62 reference statements)

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“…Biotic homogenization is a common pattern of the above-ground community in conventional systems (Gabriel et al, 2006), and recently was reported for microbial communities as a response to long-term cultivation (Montecchia et al, 2015). When poor agricultural practices are applied, such as uniformly crop monocultures, fertilization and intensive use of agrochemicals, the chain-reaction of (bio)diversity loss reduce the ecological niches leading to a homogenization of the microbial community and their functional gene pool, altering the ecosystem functioning and reducing the ecosystem resilience (Olden et al, 2004; Constancias et al, 2014; Figuerola et al, 2015). We acknowledge that the plant species planted in conventional and organic systems between 2006 and 2013 were not the same.…”

Section: Discussionmentioning

confidence: 99%

Soil Microbiome Is More Heterogeneous in Organic Than in Conventional Farming System

et al. 2017

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Organic farming system and sustainable management of soil pathogens aim at reducing the use of agricultural chemicals in order to improve ecosystem health. Despite the essential role of microbial communities in agro-ecosystems, we still have limited understanding of the complex response of microbial diversity and composition to organic and conventional farming systems and to alternative methods for controlling plant pathogens. In this study we assessed the microbial community structure, diversity and richness using 16S rRNA gene next generation sequences and report that conventional and organic farming systems had major influence on soil microbial diversity and community composition while the effects of the soil health treatments (sustainable alternatives for chemical control) in both farming systems were of smaller magnitude. Organically managed system increased taxonomic and phylogenetic richness, diversity and heterogeneity of the soil microbiota when compared with conventional farming system. The composition of microbial communities, but not the diversity nor heterogeneity, were altered by soil health treatments. Soil health treatments exhibited an overrepresentation of specific microbial taxa which are known to be involved in soil suppressiveness to pathogens (plant-parasitic nematodes and soil-borne fungi). Our results provide a comprehensive survey on the response of microbial communities to different agricultural systems and to soil treatments for controlling plant pathogens and give novel insights to improve the sustainability of agro-ecosystems by means of beneficial microorganisms.

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Section: Discussionmentioning

confidence: 99%

Soil Microbiome Is More Heterogeneous in Organic Than in Conventional Farming System

et al. 2017

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“…In accordance with our results, previous studies that reported differences in the relative abundances of groups of bacteria with contrasting trophic lifestyles in different sized aggregates suggesting that these groups occupy different ecological niches (Davinic et al ., ; Constancias et al ., ; Trivedi et al ., ). Community analysis using MiSeq revealed that samples from different aggregate sized grouped separately; however clear groups among samples based on the management practices was only observed in mega‐ and macro‐aggregates.…”

Section: Discussionmentioning

confidence: 99%

“…Community analysis using MiSeq revealed that samples from different aggregate sized grouped separately; however clear groups among samples based on the management practices was only observed in mega‐ and macro‐aggregates. This observation is supported by earlier studies that that reported similar results for different soil types and land management practices (Mummey et al ., ; Davinic et al ., ; Constancias et al ., ; Trivedi et al ., ). These observations might be related to the processes of community assemblages resulting from the balance between the effects of management practices versus soil aggregate structure (Martiny et al ., ).…”

Section: Discussionmentioning

confidence: 99%

Soil aggregation and associated microbial communities modify the impact of agricultural management on carbon content

Trivedi

Delgado‐Baquerizo

Jeffries

et al. 2017

Environmental Microbiology

188

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Soil carbon (C) stabilisation is known to depend in part on its distribution in structural aggregates, and upon soil microbial activity within the aggregates. However, the mechanisms and relative contributions of different microbial groups to C turnover in different aggregates under various management practices remain unclear. The aim of this study was to determine the role of soil aggregation and their associated microbial communities in driving the responses of soil organic matter (SOM) to multiple management practices. Our results demonstrate that higher amounts of C inputs coupled with greater soil aggregation in residue retention management practices has positive effects on soil C content. Our results provide evidence that different aggregate size classes support distinct microbial habitats which supports the colonisation of different microbial communities. Most importantly our results indicate that the effects of management practices on soil C is modulated by soil aggregate sizes and their associated microbial community and are more pronounced in macro-aggregate compared with micro-aggregate sizes. Based on our findings we recommend that differential response of management practices and microbial control on the C turnover in macro-aggregates and micro-aggregate should be explicitly considered when accounting for management impacts on soil C turnover.

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“…However, relationships between bacterial communities and critical variables associated with the nature and intensity of human land use are frequently overlooked or are studied in isolation. These include concentrations of the many heavy metals that accumulate and impact biological communities in urban settings (e.g., zinc, lead [15]) and rural settings (e.g., copper, chromium [16]), as well as core soil physical attributes, such as porosity, which can correlate negatively with stock density and can ultimately impact the production potential of agricultural land (17,18). The pairing of large-scale surveys of soil bacterial communities to data gathered through long-term soil monitoring programs (5,19,20) provides opportunities to uncover and quantify the strength of relationships between bacterial communities and a much wider range of soil physicochemical variables than had previously been achieved.…”

Section: Importancementioning

confidence: 99%

Bacteria as Emerging Indicators of Soil Condition

Hermans

Buckley

Case

et al. 2017

Appl Environ Microbiol

202

131

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Bacterial communities are important for the health and productivity of soil ecosystems and have great potential as novel indicators of environmental perturbations. To assess how they are affected by anthropogenic activity and to determine their ability to provide alternative metrics of environmental health, we sought to define which soil variables bacteria respond to across multiple soil types and land uses. We determined, through 16S rRNA gene amplicon sequencing, the composition of bacterial communities in soil samples from 110 natural or human-impacted sites, located up to 300 km apart. Overall, soil bacterial communities varied more in response to changing soil environments than in response to changes in climate or increasing geographic distance. We identified strong correlations between the relative abundances of members of Pirellulaceae and soil pH, members of Gaiellaceae and carbon-to-nitrogen ratios, members of Bradyrhizobium and the levels of Olsen P (a measure of plant available phosphorus), and members of Chitinophagaceae and aluminum concentrations. These relationships between specific soil attributes and individual soil taxa not only highlight ecological characteristics of these organisms but also demonstrate the ability of key bacterial taxonomic groups to reflect the impact of specific anthropogenic activities, even in comparisons of samples across large geographic areas and diverse soil types. Overall, we provide strong evidence that there is scope to use relative taxon abundances as biological indicators of soil condition. IMPORTANCEThe impact of land use change and management on soil microbial community composition remains poorly understood. Therefore, we explored the relationship between a wide range of soil factors and soil bacterial community composition. We included variables related to anthropogenic activity and collected samples across a large spatial scale to interrogate the complex relationships between various bacterial community attributes and soil condition. We provide evidence of strong relationships between individual taxa and specific soil attributes even across large spatial scales and soil and land use types. Collectively, we were able to demonstrate the largely untapped potential of microorganisms to indicate the condition of soil and thereby influence the way that we monitor the effects of anthropogenic activity on soil ecosystems into the future.

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Microscale evidence for a high decrease of soil bacterial density and diversity by cropping

Cited by 43 publications

References 35 publications

Soil Microbiome Is More Heterogeneous in Organic Than in Conventional Farming System

Soil Microbiome Is More Heterogeneous in Organic Than in Conventional Farming System

Soil aggregation and associated microbial communities modify the impact of agricultural management on carbon content

Bacteria as Emerging Indicators of Soil Condition

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