Soil microbial communities in the face of changing farming practices: A case study in an agricultural landscape in France.
ABSTRACT: According to biogeography studies, the abundance and richness of soil microorganisms vary across multiple spatial scales according to soil properties and farming practices. However, soil microorganisms also exhibit poorly understood temporal variations. This study aimed at better understanding how soil microbial communities respond to changes in farming practices at a landscape scale over time. A regular grid of 269 sites was set up across a 1,200 ha farming landscape, and soil samples were characterized for their molecular microbial biomass and bacterial richness at two dates (2011 and 2016). A mapping approach highlighted that spatial microbial patterns were stable over time, while abundance and richness levels were modified. The drivers of these changes were investigated though a PLS-PM (partial least square path-modeling) approach. Soil properties were stable over time, but farming practices changed. Molecular microbial biomass was mainly driven by soil resources, whereas bacterial richness depended on both farming practices and ecological parameters. Previous-crop and management effects and a temporal dependence of the microbial community on the historical farming management were also highlighted.
Project description:Soil microorganisms are essential to agroecosystem functioning and services. Yet, we still lack information on which farming practices can effectively shape the soil microbial communities. The aim of this study was to identify the farming practices, which are most effective at positively or negatively modifying bacterial and fungal diversity while considering the soil environmental variation at a landscape scale. A long-term research study catchment (12 km2 ) representative of intensive mixed farming (livestock and crop) in Western Europe was investigated using a regular grid for soil sampling (n = 186). Farming systems on this landscape scale were described in terms of crop rotation, use of fertilizer, soil tillage, pesticides treatments, and liming. Molecular microbial biomass was estimated by soil DNA recovery. Bacterial and fungal communities were analyzed by 16S and 18S rRNA gene pyrosequencing. Microbial biomass was significantly stimulated by the presence of pasture during the crop rotation since temporary and permanent pastures, as compared to annual crops, increased the soil microbial biomass by +23% and +93% respectively. While soil properties (mainly pH) explained much of the variation in bacterial diversity, soil tillage seemed to be the most influential among the farming practices. A 2.4% increase in bacterial richness was observed along our gradient of soil tillage intensity. In contrast, farming practices were the predominant drivers of fungal diversity, which was mainly determined by the presence of pastures during the crop rotation. Compared to annual crops, temporary and permanent pastures increased soil fungal richness by +10% and +14.5%, respectively. Altogether, our landscape-scale investigation allows the identification of farming practices that can effectively shape the soil microbial abundance and diversity, with the goal to improve agricultural soil management and soil ecological integrity.
Project description:Understanding the response of biodiversity to organic farming is crucial to design more sustainable agriculture. While it is known that organic farming benefits biodiversity on average, large variability in the effects of this farming system exists. Moreover, it is not clear how different practices modulate the performance of organic farming for biodiversity conservation. In this study, we investigated how the abundance and taxonomic richness of multiple species groups responds to certified organic farming and conventional farming in vineyards. Our analyses revealed that farming practices at the field scale are more important drivers of community abundance than landscape context. Organic farming enhanced the abundances of springtails (+ 31.6%) and spiders (+ 84%), had detrimental effects on pollinator abundance (- 11.6%) and soil microbial biomass (- 9.1%), and did not affect the abundance of ground beetles, mites or microarthropods. Farming practices like tillage regime, insecticide use and soil copper content drove most of the detected effects of farming system on biodiversity. Our study revealed varying effects of organic farming on biodiversity and clearly indicates the need to consider farming practices to understand the effects of farming systems on farmland biodiversity.
Project description:Soil microorganisms play a crucial role in the biogeochemical cycling of nutrient elements and maintaining soil health. We aimed to investigate the response of bacteria communities to organic farming over different crops (rice, tea and vegetable) along the middle and lower reaches of the Yangtze River of China. Compared with conventional farming, organic farming significantly increased soil nutrients, soil enzyme activities, and bacterial richness and diversity. A Venn diagram and principal component analysis revealed that the soils with 3 different crops under organic farming have more number and percent of shared OTUs (operational taxonomic units), and shared a highly similar microbial community structure. Under organic farming, several predominant guilds and major bacterial lineages (Rhizobiales, Thiotrichaceae, Micromonosporaceae, Desulfurellaceae and Myxococcales) contributing to nutrient (C, N, S and P) cycling were enriched, whereas the relative abundances of acid and alkali resistant microorganisms (Acidobacteriaceae and Sporolactobacillaceae) were increased under conventional farming practices. Our results indicated that, for all three crops, organic farming have a more stable microflora and the uniformity of the bacterial community structure. Organic agriculture significantly increased the abundance of some nutrition-related bacteria, while reducing some of the abundance of acid and alkali resistant bacteria.
Project description:Despite the relevance of landscape, regarding the spatial patterning of microbial communities and the relative influence of environmental parameters versus human activities, few investigations have been conducted at this scale. Here, we used a systematic grid to characterize the distribution of soil microbial communities at 278 sites across a monitored agricultural landscape of 13 km². Molecular microbial biomass was estimated by soil DNA recovery and bacterial diversity by 16S rRNA gene pyrosequencing. Geostatistics provided the first maps of microbial community at this scale and revealed a heterogeneous but spatially structured distribution of microbial biomass and diversity with patches of several hundreds of meters. Variance partitioning revealed that both microbial abundance and bacterial diversity distribution were highly dependent of soil properties and land use (total variance explained ranged between 55% and 78%). Microbial biomass and bacterial richness distributions were mainly explained by soil pH and texture whereas bacterial evenness distribution was mainly related to land management. Bacterial diversity (richness, evenness, and Shannon index) was positively influenced by cropping intensity and especially by soil tillage, resulting in spots of low microbial diversity in soils under forest management. Spatial descriptors also explained a small but significant portion of the microbial distribution suggesting that landscape configuration also shapes microbial biomass and bacterial diversity.
Project description: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.
Project description:Population growth and climate change challenge our food and farming systems and provide arguments for an increased intensification of agriculture. A promising option is eco-functional intensification through organic farming, an approach based on using and enhancing internal natural resources and processes to secure and improve agricultural productivity, while minimizing negative environmental impacts. In this concept an active soil microbiota plays an important role for various soil based ecosystem services such as nutrient cycling, erosion control and pest and disease regulation. Several studies have reported a positive effect of organic farming on soil health and quality including microbial community traits. However, so far no systematic quantification of whether organic farming systems comprise larger and more active soil microbial communities compared to conventional farming systems was performed on a global scale. Therefore, we conducted a meta-analysis on current literature to quantify possible differences in key indicators for soil microbial abundance and activity in organic and conventional cropping systems. All together we integrated data from 56 mainly peer-reviewed papers into our analysis, including 149 pairwise comparisons originating from different climatic zones and experimental duration ranging from 3 to more than 100 years. Overall, we found that organic systems had 32% to 84% greater microbial biomass carbon, microbial biomass nitrogen, total phospholipid fatty-acids, and dehydrogenase, urease and protease activities than conventional systems. Exclusively the metabolic quotient as an indicator for stresses on microbial communities remained unaffected by the farming systems. Categorical subgroup analysis revealed that crop rotation, the inclusion of legumes in the crop rotation and organic inputs are important farming practices affecting soil microbial community size and activity. Furthermore, we show that differences in microbial size and activity between organic and conventional farming systems vary as a function of land use (arable, orchards, and grassland), plant life cycle (annual and perennial) and climatic zone. In summary, this study shows that overall organic farming enhances total microbial abundance and activity in agricultural soils on a global scale.
Project description: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.
Project description:Drought and agricultural management influence soil microorganisms with unknown consequences for the functioning of agroecosystems. We simulated drought periods in organic (biodynamic) and conventional wheat fields and monitored effects on soil water content, microorganisms and crops. Above the wilting point, water content and microbial respiration were higher under biodynamic than conventional farming. Highest bacterial and fungal abundances were found in biodynamically managed soils, and distinct microbial communities characterised the farming systems. Most biological soil quality parameters and crop yields were only marginally affected by the experimental drought, except for arbuscular mycorrhizal fungi (AMF), which increased in abundance under the experimental drought in both farming systems. AMF were further strongly promoted by biodynamic farming resulting in almost three times higher AMF abundance under experimental drought in the biodynamic compared with the conventional farming system. Our data suggest an improved water storage capacity under biodynamic farming and confirms positive effects of biodynamic farming on biological soil quality. The interactive effects of the farming system and drought may further be investigated under more substantial droughts. Given the importance of AMF for the plant's water supply, more in-depth studies on AMF may help to clarify their role for yields under conditions predicted by future climate scenarios.
Project description:The importance of soil microbial flora in agro-ecosystems is well known, but there is limited understanding of the effects of long-term fertilization on soil microbial community succession in different farming management practices. Here, we report the responses of soil microbial community structure, abundance and activity to chemical (CF) and organic fertilization (OF) treatments in a sandy agricultural system of wheat-maize rotation over a 17-year period. Illumina MiSeq sequencing showed that the microbial community diversity and richness showed no significant changes in bacteria but decreased in fungi under both CF and OF treatments. The dominant species showing significant differences between fertilization regimes were Actinobacteria, Acidobacteria and Ascomycota at the phylum level, as well as some unclassified genera of other phyla at the genus level. As expected, soil organic matter content, nutrient element concentrations and bacterial abundance were enhanced by both types of fertilization, especially in OF, but fungal abundance was inhibited by OF. Redundancy analysis revealed that soil enzyme activities were closely related to both bacterial and fungal communities, and the soil nutrient, texture and pH value together determined the community structures. Bacterial abundance might be the primary driver of crop yield, and soil enzyme activities may reflect crop yield. Our results suggest a relatively permanent response of soil microbial communities to the long-term fertilization regimes in a reclaimed sandy agro-ecosystem from a mobile dune, and indicate that the appropriate dosage of chemical fertilizers is beneficial to sandy soil sustainability.
Project description:Soil rhizosphere microorganisms play crucial roles in promoting plant nutrient absorption and maintaining soil health. However, the effects of different phosphorus (P) managements on soil microbial communities in a slope farming system are poorly understood. Here, rhizosphere microbial communities under two P fertilization levels-conventional (125 kg P<sub>2</sub>O<sub>5</sub> ha<sup>-1</sup>, P125) and optimal (90 kg P<sub>2</sub>O<sub>5</sub> ha<sup>-1</sup>, P90)-were compared at four growth stages of maize in a typical sloped farming system. The richness and diversity of rhizosphere bacterial communities showed significant dynamic changes throughout the growth period of maize, while different results were observed in fungal communities. However, both the P fertilization levels and the growth stages influenced the structure and composition of the maize rhizosphere microbiota. Notably, compared to P125, <i>Pseudomonas</i>, <i>Conexibacter</i>, <i>Mycobacterium</i>, <i>Acidothermus</i>, Glomeromycota, and <i>Talaromyces</i> were significantly enriched in the different growth stages of maize under P90, while the relative abundance of <i>Fusarium</i> was significantly decreased during maize harvest. Soil total nitrogen (TN) and pH are the first environmental drivers of change in bacterial and fungal community structures, respectively. The abundance of Gemmatimonadota, Proteobacteria, and Cyanobacteria showed significant correlations with soil TN, while that of Basidiomycota and Mortierellomycota was significantly related to pH. Additionally, P90 strengthened the connection between bacteria, but reduced the links between fungi at the genus level. Our work helps in understanding the role of P fertilization levels in shaping the rhizosphere microbiota and may manipulate beneficial microorganisms for better P use efficiency.