Cover crops in arable lands increase functional complementarity and redundancy of bacterial communities (original) (raw)
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Functional response of soil microbial communities to tillage, cover crops and nitrogen fertilization
Applied Soil Ecology, 2016
Agricultural practices such as tillage, cover crops, and nitrogen (N) fertilization affect physico-chemical and biological soil parameters. However, these factors were often studied separately and their combined effects remain unclear, especially with respect to soil microbial functional diversity and carbon (C) and N content. Thereafter, we aim to assess the links between cropping systems and functional response of microbial communities by using a large range of soil chemical and biological measurements. A 5-yr field experiment was conducted in Northern France using a combination of three factors: i) no-till (NT) vs. conventional tillage (CT); ii) with or without winter cover crops (bare fallow; cover crops with a low prevalence of legumes; cover crop with a high prevalence of legumes); and iii) with or without N fertilization. C and N inputs from cover crops and crop residues, C and N content, enzyme activities, and microbial functional diversity in the topsoil (0-10 cm) were measured over an industrial crop rotation: wheat, pea, corn, wheat, flax. No-till combined with any of the cover crops was characterized by increased total soil organic C and N contents by more than 20% between 2010 and 2015. Dehydrogenase and urease activities were significantly greatest under NT, irrespective of the presence of cover crops. Cover crops without N fertilization under no-till led to higher microbial functional activity (faster carbohydrate and phenolic compound degradation) and diversity. Bare fallow had lower soil microbial functional diversity and C and N contents compared with soil under NT and cover crops. On the other hand, NT associated with cover crops allowed to maintain the soil in both C and N, and to promote microbial activities without N fertilization. In conclusion, winter cover crops and/or NT are sustainable agricultural practices resulting in a greater soil quality index. These results demonstrate that NT and use of standard cover crops or cover crops with legumes for 5 years under a low biomass return in industrial crop production have a positive effect on: i) upper soil C content and microbial enzymes, irrespective of N fertilization regime; ii) soil microbial functional diversity in the absence of N fertilization. 2016 Elsevier B.V. All rights reserved.
Frontiers in Microbiology, 2019
Cover cropping plays a key role in the maintenance of arable soil health and the enhancement of agroecosystem services. However, our understanding of how cover crop management impacts soil microbial communities and how these interactions might affect soil nutrient cycling is still limited. Here, we studied the impact of four cover crop mixtures varying in species richness and functional diversity, three cover crop termination strategies (i.e., frost, rolling, and glyphosate) and two levels of irrigation at the cover crop sowing on soil nitrogen and carbon dynamics, soil microbial diversity, and structure as well as the abundance of total bacteria, archaea, and N-cycling microbial guilds. We found that total nitrogen and soil organic carbon were higher when cover crops were killed by frost compared to rolling and glyphosate termination treatments, while cover crop biomass was positively correlated to soil carbon and C:N ratio. Modifications of soil properties due to cover crop management rather than the composition of cover crop mixtures were related to changes in the abundance of ammonia oxidizers and denitrifiers, while there was no effect on the total bacterial abundance. Unraveling the underlying processes by which cover crop management shapes soil physico-chemical properties and bacterial communities is of importance to help selecting optimized agricultural practices for sustainable farming systems.
Spanish Journal of Agricultural Research, 2016
Agricultural systems where monoculture prevails are characterized by fertility losses and reduced contribution to ecosystem services. Including cover crops (CC) as part of an agricultural system is a promising choice in sustainable intensification of those demanding systems. We evaluated soil microbial functionality in cash crops in response to the inclusion of CC by analyzing soil microbial functions at two different periods of the agricultural year (cash crop harvest and CC desiccation) during 2013 and 2014. Three plant species were used as CC: oat (Avena sativa L.), vetch (Vicia sativa L.) and radish (Raphanus sativus L.) which were sown in two different mixtures of species: oat and radish mix (CC1) and oat, radish and vetch mix (CC2), with soybean monoculture and soybean/corn being the cash crops. The study of community level physiological profiles showed statistical differences in respiration of specific C sources indicating an improvement of catabolic diversity in CC treatment...
Soil Biology and Biochemistry
Significant microbial community shifts due to no-till, cover crops and N-fertilization.Greater gram positive bacteria, mycorrhizae and actinomycetes under no-till.Vetch cover and N-fertilization decrease mycorrhizae abundance.Carbon, nitrogen and phosphorous cycling enzymes greater under no-till.Greater total carbon, nitrogen and yield under no-till with cover crop treatments.Conservation agriculture practices, such as reduced tillage, cover crops and fertilization, are often associated with greater microbial biomass and activity that are linked to improvements in soil quality. This study characterized the impact of long term (31 years) tillage (till and no-till), cover crops (Hairy vetch- Vicia villosa and winter wheat- Triticum aestivum, and a no cover control), and N-rates (0, 34, 67 and 101 kg N ha−1) on soil microbial community structure, activity and resultant soil quality calculated using the soil management assessment framework (SMAF) scoring index under continuous cotton (Gossypium hirsutum) production on a Lexington silt loam in West Tennessee.No-till treatments were characterized by a significantly greater (P < 0.05) abundance of Gram positive bacteria, actinomycetes and mycorrhizae fungi fatty acid methyl ester (FAME) biomarkers compared to till. Saprophytic fungal FAME biomarkers were significantly less abundant (P < 0.05) under no-till treatments resulting in a lower fungi to bacteria (F:B) ratio. Key enzymes associated with C, N & P cycling (β-glucosidase, β-glucosaminidase, and phosphodiesterase) had significantly higher rates under no-till relative to till, corresponding to significantly greater (P < 0.05) soil C and N, extractable nutrients (P, K and Ca) and yields. Mycorrhizae fungi biomarkers significantly decreased (P < 0.05) with increasing N-rate and was significantly less (P < 0.05) under the vetch cover crop compared to wheat and no cover. Treatments under vetch also had significantly higher β-glucosaminidase and basal microbial respiration rates compared to wheat and no cover.Consequently, the total organic carbon (TOC) and β-glucosidase SMAF quality scores were significantly greater under no-till compared to till and under the vetch compared to wheat and no cover treatments, resulting in a significantly greater overall soil quality index (SQI).Our results demonstrate that long-term no-till and use of cover crops under a low biomass monoculture crop production system like cotton results in significant shifts in the microbial community structure, activity, and conditions that favor C, N and P cycling compared to those under conventional tillage practices. These practices also led to increased yields and improved soil quality with no-till having 13% greater yields than till and treatments under vetch having 5% increase in soil quality compared to no cover and wheat.
Microorganisms, 2020
Metagenomics in agricultural research allows for searching for bioindicators of soil health to characterize changes caused by management practices. Cover cropping (CC) improves soil health by mitigating nutrient losses, yet the benefits depend on the tillage system used. Field studies searching for indicator taxa within these systems are scarce and narrow in their scope. Our goal was to identify bioindicators of soil health from microbes that were responsive to CC (three levels) and tillage (chisel tillage, no-till) treatments after five years under field conditions. We used rRNA gene-based analysis via Illumina HiSeq2500 technology with QIIME 2.0 processing to characterize the microbial communities. Our results indicated that CC and tillage differentially changed the relative abundances (RAs) of the copiotrophic and oligotrophic guilds. Corn–soybean rotations with legume–grass CC increased the RA of copiotrophic decomposers more than rotations with grass CC, whereas rotations with ...
Cover crops are used in agriculture to minimise soil erosion, prevent nutrient leaching and increase soil organic matter content. Cover crops can also be grown to stimulate the soil microbial community to improve soil biological conditions. Despite their widespread use, little is known about the impact of different cover crop species on the composition and activity of the soil microbiome. Here we investigate the effect of distinct cover crop species on the rhizosphere microbiome and to characterise both the resident (DNA-based) and the active (RNA-based) fractions of the bacterial, fungal, protist and metazoan communities in the cover crops rhizosphere. We conducted a field experiment using 70-litre bottomless containers in which we grew ten monocultures of commonly used cover crop species belonging to five plant families, and an unplanted control treatment (fallow). The total DNA and RNA were extracted from soil and the bacterial, fungal, protistan and metazoan communities were cha...
FEMS Microbiology Ecology
Conventional tillage and mineral fertilization (CTMF) jeopardize soil health in conventional vegetable production systems. Using a field experiment established in Uruguay in 2012, we aimed to compare the soil restoration potential of organic fertilization (compost and poultry manure) combined with conventional tillage and cover crop incorporated into the soil (CTOF) or with reduced tillage and the use of cover crop as mulch (RTOF). In 2017, table beet was cultivated under CTMF, CTOF and RTOF, and yields, soil aggregate composition and nutrients, as well as soil and table beet rhizosphere microbiota (here: bacteria and archaea) were evaluated. Microbiota was studied by high-throughput sequencing of 16S rRNA gene fragments amplified from total community DNA. RTOF exhibited higher soil aggregation, soil organic C, nutrient availability and microbial alpha-diversity than CTMF, and became more similar to an adjacent natural undisturbed site. The soil microbiota was strongly shaped by the...
Agriculture, Ecosystems & Environment, 2018
World population growth has led to a rise in resource demands imposed on agricultural systems, generating an increased global use of natural resources. However, agroecology proposes self-regulation in order to achieve a sustainable agricultural balance. Therefore, considering the rapid responses of microbial communities to small changes in soil use, the objective of this study was to assess the response of soil microbial communities to agroecological vs. conventional systems of extensive agriculture. Soil sampling was carried out in 2016 and 2017 with three different treatments using the sequence soybean/maize (Glycine max L./Zea mays L.) as the main crop: Agroecological (AE), conventional with cover crops (CC) and conventional without cover crops (control). Species used as cover crops were wheat (Triticum aestivum), vetch (Vicia sativa L.), oat (Avena sativa L.) and radish (Raphanus sativus L.). Agroecological treatment showed the lowest total nitrogen (0.18 mg N g −1) and organic carbon (1.99 mg C g −1) content of soil, and CC treatment showed the highest value of fluorescein diacetate hydrolysis, with values 63.2% and 12.1% higher than AE and the control, respectively. However, AE treatment also produced the highest F:B ratio (44.8) and the lowest metabolic quotient (1.14), which indicates an improvement in metabolic efficiency and soil quality. No significant differences were recorded in the abundance of fungal and bacterial communities between treatments. Our results suggest that agroecological management is characterised by fungal dominance in soil microbial communities and a higher microbial metabolic efficiency compared to conventional management. These results demonstrate more efficient use of carbon substrates in agroecological systems, which could counteract the negative effect of the lack of synthetic fertilisation and reduced-tillage in the long term. The findings demonstrate that sustainable agricultural tools with adequate management can be effectively used to preserve soil quality.
Microscale evidence for a high decrease of soil bacterial density and diversity by cropping
Agronomy for Sustainable Development, 2013
Soil microbes play major agricultural functions such as the transformation of soil organic matter into plant fertilizers. The effects of agricultural practices on soil microbes at the scale of plots, from meters to hectare, are well documented. However, the impact at soil microscale, from micrometers to millimeters, is much less known. Therefore, we studied bacterial community density and diversity at microscale in crop soil under grassland, tillage, and no tillage. We fractionated macroaggregates, from 2,000 to 250 μm and from 250 to 63 μm; microaggregates, from 63-20 μm and 20-2 μm; and clay particles, lower than 2 μm. We measured the bacterial density and diversity by real-time PCR and 454-pyrosequencing of 16S rRNA genes of soil DNA, respectively. Results show that bacterial density and diversity were heterogeneous among size aggregates. Tillage decreased bacterial density from 22 to 74 %, and diversity from 4 to 11 %, and changed taxonomic groups in micro-and macroaggregates. This change led to the homogenization of bacterial communities and is explained by a higher protection of microaggregates. As a consequence, microaggregates contained similar bacterial communities whatever the land management is, whereas strong differences were observed between communities inhabiting macroaggregates. These findings demonstrate that bacterial diversity in microaggregates was mainly controlled by historical contingency, whereas bacterial communities in macroaggregates are shaped by contemporary perturbations. Our findings thus revealed unprecedented insights of the effect of agriculture on soil microbes. Potential applications include using crop management options that preserve macroaggregate structure to promote soil heterogeneity and therefore microbial diversity.