Bacterial indicator taxa in soils under different long-term agricultural management

Jiménez‐Bueno, Norma G.; Valenzuela‐Encinas, César; Marsch, Rodolfo; Ortiz‐Gutiérrez, Daniel; Verhulst, Nele; Govaerts, Bram; Dendooven, Luc; Navarro‐Noya, Yendi E.

doi:10.1111/jam.13072

Cited by 57 publications

(32 citation statements)

References 61 publications

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“…In agreement with the first hypothesis of our study, the tillage regime was a significant driver of microbial β-diversity ( Figure 1A and Tables 2 , 3 ), which is consistent with the recent literature using high-resolution techniques (Quadros et al, 2012; Navarro-Noya et al, 2013; Carbonetto et al, 2014; Sengupta and Dick, 2015; Degrune et al, 2016; Jiménez-Bueno et al, 2016). However, the direction of change of some microbial groups was not consistent with the other studies.…”

Section: Discussionsupporting

confidence: 93%

“…Several studies have reported effects of soil tillage and/or crop residue management on soil microbial community structures (Quadros et al, 2012; Navarro-Noya et al, 2013; Carbonetto et al, 2014; Sengupta and Dick, 2015; Degrune et al, 2016; Jiménez-Bueno et al, 2016). For example, the diversity of arbuscular mycorrhizal fungi (AMF), a group of fungi supporting the host plant with enhanced nutrient acquisition and increased resistance against drought and root pathogens (Van Der Heijden et al, 1998), has shown to be increased under reduced tillage (Säle et al, 2015).…”

Section: Introductionmentioning

confidence: 99%

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Temporal Dynamics of Soil Microbial Communities below the Seedbed under Two Contrasting Tillage Regimes

et al. 2017

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Agricultural productivity relies on a wide range of ecosystem services provided by the soil biota. Plowing is a fundamental component of conventional farming, but longterm detrimental effects such as soil erosion and loss of soil organic matter have been recognized. Moving towards more sustainable management practices such as reduced tillage or crop residue retention can reduce these detrimental effects, but will also influence structure and function of the soil microbiota with direct consequences for the associated ecosystem services. Although there is increasing evidence that different tillage regimes alter the soil microbiome, we have a limited understanding of the temporal dynamics of these effects. Here, we used high-throughput sequencing of bacterial and fungal ribosomal markers to explore changes in soil microbial community structure under two contrasting tillage regimes (conventional and reduced tillage) either with or without crop residue retention. Soil samples were collected over the growing season of two crops (Vicia faba and Triticum aestivum) below the seedbed (15-20 cm). Tillage, crop and growing stage were significant determinants of microbial community structure, but the impact of tillage showed only moderate temporal dependency. Whereas the tillage effect on soil bacteria showed some temporal dependency and became less strong at later growing stages, the tillage effect on soil fungi was more consistent over time. Crop residue retention had only a minor influence on the community. Six years after the conversion from conventional to reduced tillage, soil moisture contents and nutrient levels were significantly lower under reduced than under conventional tillage. These changes in edaphic properties were related to specific shifts in microbial community structure. Notably, bacterial groups featuring copiotrophic lifestyles or potentially carrying the ability to degrade more recalcitrant compounds were favored under conventional tillage, whereas taxa featuring more oligotrophic lifestyles were more abundant under reduced tillage. Our study found that, under the specific edaphic and climatic context of central Belgium, different tillage regimes created different ecological niches that select for different microbial lifestyles with potential consequences for the ecosystem services provided to the plants and their environment.

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Section: Discussionsupporting

confidence: 93%

Section: Introductionmentioning

confidence: 99%

Temporal Dynamics of Soil Microbial Communities below the Seedbed under Two Contrasting Tillage Regimes

et al. 2017

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“…These investigations have identified that microbial attributes could reflect ecosystem processes such as crop productivity [3], the regulation of decomposition [4], nutrient cycling [5] and protection against soil-borne pathogens [6]. Several studies have shown that agricultural Sustainability 2018, 10, 3825 2 of 16 practices have significant influences on soil microbial communities and composition, including the tillage regime [7], fertilization [8], monoculture [9], crop residue management [10] and plant protection schemes [11]. Hence, the soil microbial community could be shifted to a positive organization for plant production and ecosystem sustainability by suitable agricultural practices [4].…”

Section: Introductionmentioning

confidence: 99%

“…Furthermore, high microbial diversity has been linked to high functional diversity in soil [5], which may cause the important ecological processes mentioned above. In addition, most researchers studied the microbial community under different agricultural management practices with field crops such as rice [3,21] and wheat [10], whereas little research has focused on vegetable cultivations [22]. Specifically, we still have a limited understanding of the long-term effects of organic and conventional management on soil microbial communities under open-field and protected conditions.…”

Section: Introductionmentioning

confidence: 99%

Organic Farming Improves Soil Microbial Abundance and Diversity under Greenhouse Condition: A Case Study in Shanghai (Eastern China)

2018

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Agricultural practices have significant impacts on soil properties and microbial communities; however, little is known about their responses to open field and plastic tunnels under organic and conventional farming. We therefore investigated the responses of soil chemical variables and microbial communities to different agricultural management and cultivation types, including organic management in open field (OF), organic management in plastic tunnels (OP), conventional management in open field (CF) and conventional management in plastic tunnels (CP), by using a pyrosequencing approach of 16S rRNA gene amplicon. Both factors had significant influences on the soil properties and microbial communities. Organic farming increased the nutrient-related soil variables compared to conventional farming regardless of cultivation type, especially for the available N and P, which were increased by 137% and 711%, respectively, in OP compared to CP. Additionally, OP had the highest microbial abundance and diversity among treatments, whereas no difference was found between OF, CF and CP. Furthermore, OP possessed diverse differential bacteria which were mainly related to the organic material turnover (e.g., Roseiflexus, Planctomyces and Butyrivibrio) and plant growth promotion (e.g., Nostoc, Glycomyces and Bacillus). Redundancy analysis (RDA) showed that pH, electrical conductivity (EC), nutrient levels (e.g., available N and available P) and total Zn content were significantly correlated to the structure of the microbial community. Overall, our results showed that the long-term organic farming with high fertilizer input increased soil nutrient levels and microbial abundance and diversity under plastic-tunnel condition compared to other cultivation systems.

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“…The relative abundances of individual phyla in different samples were computed by R packages. The indicator analysis based on genera-specific to each soil depth was conducted using indicspecies package of R with 9999 permutations, and the P-values were corrected for multiple testing using qvalue package of R(14, 66). Functional profiles of the microbial community were predicted by Tax4fun (an open-source package in R)(67) and further statistical analysis was conducted by STAMP using Welch’s t-test(68).…”

Section: Methodsmentioning

confidence: 99%

Low-disturbance Farming Regenerates Healthy Deep Soil towards Sustainable Agriculture

Deng

Wang

Xie

et al. 2019

Preprint

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SummaryIntensive conventional farming has degraded farmland topsoil and seriously threaten food and environment security globally. Although low-disturbance practices have been widely adapted to restore soil health, whether this measure in a long run can potentially recover the critical deep soil to meet sustainable intensification of crop production are still unclear. Here we compared soil microbiome, physiochemical parameters along 3-m deep soil profiles, and crop yield in Northeast China subjected to ten years of farming practices at 3 levels of disturbance, including conventional tillage (CT), no-tillage without stover mulching (NTNS), and no-tillage with stover mulching (NTSM). We found that low-disturbance practices (NTNS and NTSM) promoted the ability of the deep soil to retain water and nitrogen, regenerated whole-soil microbial diversity and function, and significantly improved corn yield in the drought year. This study implies that the low-disturbance practices could dig deeper for agricultural resource and reduce energy consumption and greenhouse gas emissions, thus regenerating highly efficient, sustainable agriculture.Science for SocietyBy 2050, how to feed 10 billion people on limited land without destroying the environment has become a global challenge. Prior research has shown that low-disturbance farming enhances biodiversity and natural biological processes in farmland topsoil, which benefit crop production. However, whether long-term low-disturbance farming could regenerate deep-soil health to meet sustainable intensification of crop production remains unclear. We evaluate the impact of low-disturbance practices on 3-meter soil profile after 10-year manipulations and provide an underneath mechanism on how long-term low-disturbance farming regenerate deep healthy soil. We found that low-disturbance farming not only promoted soil nutrient and water holding capacities, restored microbial diversity, richness, and ecological function in the whole 3-m soil profile, but also improved crop production (especially during drought) and potentially reduced energy consumption and greenhouse gas emissions, thus promoting sustainable agriculture and ensuring food and environment security.Graphical Abstract

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Bacterial indicator taxa in soils under different long-term agricultural management

Abstract: In this study, we report that agricultural practice affected soil bacterial communities. We also identified distinctive taxa and related their distribution to changes in the soil environment resulting from different agricultural practices.

Cited by 57 publications

References 61 publications

Temporal Dynamics of Soil Microbial Communities below the Seedbed under Two Contrasting Tillage Regimes

Temporal Dynamics of Soil Microbial Communities below the Seedbed under Two Contrasting Tillage Regimes

Organic Farming Improves Soil Microbial Abundance and Diversity under Greenhouse Condition: A Case Study in Shanghai (Eastern China)

Low-disturbance Farming Regenerates Healthy Deep Soil towards Sustainable Agriculture

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