Cover crops in arable lands increase functional complementarity and redundancy of bacterial communities

Abstract

Reducing the deleterious effects of intensive tillage and fertilization on ecosystem integrity and human health is challenging for sustainable agriculture. The use of cover crops has been advocated as a suitable technique for this purpose, but scientific evidence to support this has been scarce. After four years and a complete rotation, including wheat, maize, and green pea as main crops in a ploughing system, we investigated the respective and combined effects of cover crops and nitrogen fertilization on soil chemical and biological properties using a controlled experiment combining soil chemical analyses, high‐throughput sequencing and community level physiological profiles. Cover crops impeded the soil carbon and nitrogen depletion induced by intensive tillage, not only in the topsoil but also within deeper soil horizons, where more specialized bacterial communities established. Cover crops induced a significant shift in soil bacterial community diversity and composition, which was associated with changes in soil chemical features and bacterial metabolic activities along the entire soil profile. Cover crops enhanced soil resilience to nitrogen fertilization by increasing functional redundancy and complementarity within soil bacterial communities and across soil horizons. Synthesis and applications. In the ploughing systems commonly used for intensive agriculture in Western Europe, the use of cover crops fosters a high functional diversity among soil bacteria and thus can help to achieve a more sustainable agriculture by reducing nitrogen fertilization while maintaining yields.

Microbial Shifts Following Five Years of Cover Cropping and Tillage Practices in Fertile Agroecosystems

“…These sensitive taxa may serve as useful indicators for probing the complex microbial behaviors, or even as bioindicators of soil health [26]. Studies on responsive taxa have thus far shown that CC and tillage primarily impose selection pressures on the soil microbes by changing the soil nutrient availability and quality [30,34,35]. Due to the novelty of metagenomics studies in agricultural research, field studies searching for indicator taxa within systems deploying cover cropping and tillage are still scarce.…”

“…Due to the novelty of metagenomics studies in agricultural research, field studies searching for indicator taxa within systems deploying cover cropping and tillage are still scarce. Prior studies either only identified responsive taxa in the samples from CC treatments that showed significant differences in ordination methods [30] or searched for microbes with specific genes, such as those related to residue decomposition [36]. No CC metagenomics study has sought indicator taxa at lower taxonomic ranks without any such constraining conditions.…”

“…New metagenomics research allows for a closer look into the soil microbial composition and function and the changes brought about by agricultural practices [ 25 , 26 , 27 ]. This usually involves using β-diversity measures to detect shifts in the microbial community structure between samples [ 28 ], interpreting the changes with further analyses targeting specific functional genes, such as amo A, involved in nitrification [ 29 ], and characterizing the compositional shifts that identify the responsive taxa [ 30 , 31 ]. So far, these responsive taxa have been identified at different scales, from phyla [ 32 ] to operational taxonomic units (OTUs) [ 30 ] or species [ 33 ] level.…”

“…This usually involves using β-diversity measures to detect shifts in the microbial community structure between samples [ 28 ], interpreting the changes with further analyses targeting specific functional genes, such as amo A, involved in nitrification [ 29 ], and characterizing the compositional shifts that identify the responsive taxa [ 30 , 31 ]. So far, these responsive taxa have been identified at different scales, from phyla [ 32 ] to operational taxonomic units (OTUs) [ 30 ] or species [ 33 ] level. These sensitive taxa may serve as useful indicators for probing the complex microbial behaviors, or even as bioindicators of soil health [ 26 ].…”

Low-disturbance Farming Regenerates Healthy Deep Soil towards Sustainable Agriculture

“…Microorganisms also respond quickly to changes in soil environment conditions, due to their high surface to volume ratio, which can provide an early signal in soil improvement or degradation, thus has been recommend as a key indicator of soil health(Nielsen et al ., 2002). However, the effect of tillage practices on soil microbial communities are complex and diverse(Helgason et al ., 2010; Sun et al ., 2018; Li et al ., 2020; Rincon-Florez et al ., 2020) and most studies by now mainly focused on farmland topsoil or soils within 1-m depth(Hartman et al ., 2018; Nevins et al ., 2018; Alahmad et al ., 2019), and soil below 1 meter, which contains more carbon than the topsoil(Jobbágy and Jackson, 2000) and belongs to Earth’s Critical zone, was often overlooked. However, microbes inhabiting in the deep soils (> 1 m) may substantially impact long-term carbon sequestration, mineral weathering and crop production(Eilers et al ., 2012; Sagova-Mareckova et al ., 2016; Pries et al ., 2017), and play important roles in bridging aboveground vegetation with parent soils and even acts as an essential buffer protecting underground water(Chorover et al ., 2007).…”