Differences in Soil Bacterial Community Compositions in Paddy Fields under Organic and Conventional Farming Conditions.
Ontology highlight
ABSTRACT:
SUBMITTER: Suzuki K
PROVIDER: S-EPMC6440725 | biostudies-literature | 2019 Mar
REPOSITORIES: biostudies-literature
Publications
Differences in Soil Bacterial Community Compositions in Paddy Fields under Organic and Conventional Farming Conditions.
Suzuki Kazuki K Takemura Manami M Miki Takaaki T Nonaka Masanori M Harada Naoki N
Microbes and environments 20190213 1
Soil bacterial community compositions and temporal changes in organic paddy fields were elucidated using a 16S rRNA gene amplicon sequencing analysis with a high-throughput next generation sequencer. At transplanting, bacterial community compositions in organic and conventional paddy fields were mostly similar despite differences in field management. The bacterial community composition in organic fields differed from that under conventional management during the rice growth period, possibly as a ...[more]
Similar Datasets
Project description:Low-input agricultural systems aim at reducing the use of synthetic fertilizers and pesticides in order to improve sustainable production and ecosystem health. Despite the integral role of the soil microbiome in agricultural production, we still have a limited understanding of the complex response of microbial diversity to organic and conventional farming. Here we report on the structural response of the soil microbiome to more than two decades of different agricultural management in a long-term field experiment using a high-throughput pyrosequencing approach of bacterial and fungal ribosomal markers. Organic farming increased richness, decreased evenness, reduced dispersion and shifted the structure of the soil microbiota when compared with conventionally managed soils under exclusively mineral fertilization. This effect was largely attributed to the use and quality of organic fertilizers, as differences became smaller when conventionally managed soils under an integrated fertilization scheme were examined. The impact of the plant protection regime, characterized by moderate and targeted application of pesticides, was of subordinate importance. Systems not receiving manure harboured a dispersed and functionally versatile community characterized by presumably oligotrophic organisms adapted to nutrient-limited environments. Systems receiving organic fertilizer were characterized by specific microbial guilds known to be involved in degradation of complex organic compounds such as manure and compost. The throughput and resolution of the sequencing approach permitted to detect specific structural shifts at the level of individual microbial taxa that harbours a novel potential for managing the soil environment by means of promoting beneficial and suppressing detrimental organisms.
| S-EPMC4409162 | biostudies-literature
Project description:Water deficit tolerance is critical for plant fitness and survival, especially when successive drought events happen. Specific soil microorganisms are however able to improve plant tolerance to stresses, such as those displaying a 1-aminocyclopropane-1-carboxylate (ACC) deaminase activity. Microorganisms adapted to dry conditions can be selected by plants over time because of properties such as sporulation, substrate preference, or cell-wall thickness. However, the complexity and interconnection between abiotic factors, like drought or soil management, and biotic factors, like plant species identity, make it difficult to elucidate the general selection processes of such microorganisms. Using a pot experiment in which wheat and barley were grown on conventional and organic farming soils, we determined the effect of water deficit history on soil microorganisms by comparing single and successive events of water limitation. The analysis showed that water deficit strongly impacts the composition of both the total microbial community (16S rRNA genes) and one of ACC deaminase-positive (acdS +) microorganisms in the rhizosphere. In contrast, successive dry conditions moderately influence the abundance and diversity of both communities compared to a single dry event. We revealed interactive effects of the farming soil type and the water deficit conditioning treatment. Indeed, possibly due to better nutrient status, plants grown on soils from conventional farming showed higher growth and were able to select more adapted microbial taxa. Some of them are already known for their plant-beneficial properties like the Actinobacteria Streptomyces, but interestingly, some Proteobacteria were also enriched after a water deficit history under conventional farming. Our approach allowed us to identify key microbial taxa promoting drought adaptation of cereals, thus improving our understanding of drought effects on plant-microbe interactions.
| S-EPMC9234553 | biostudies-literature
Project description:Organic farming aims to reduce the effect on the ecosystem and enhance biodiversity in agricultural areas, but the long-term effectiveness of its application is unclear. Assessments have rarely included various taxonomic groups with different ecological and economic roles. In paddy fields with different numbers of years elapsed since the transition from conventional to organic farming, we investigated changes in the abundance of insect pests, generalist predators, and species of conservation concern. The abundance of various arthropods exhibited diverse trends with respect to years elapsed since the transition to organic farming. Larval lepidopterans, Tetragnatha spiders, and some planthoppers and stink bugs showed non-linear increases over time, eventually reaching saturation, such as the abundance increasing for several years and then becoming stable after 10 years. This pattern can be explained by the effects of residual pesticides, the lag time of soil mineralization, and dispersal limitation. A damselfly (Ischnura asiatica) did not show a particular trend over time, probably due to its rapid immigration from source habitats. Unexpectedly, both planthoppers and some leafhoppers exhibited gradual decreases over time. As their abundances were negatively related to the abundance of Tetragnatha spiders, increased predation by natural enemies might gradually decrease these insect populations. These results suggest that the consideration of time-dependent responses of organisms is essential for the evaluation of the costs and benefits of organic farming, and such evaluations could provide a basis for guidelines regarding the length of time for organic farming to restore biodiversity or the economic subsidy needed to compensate for pest damage.
| S-EPMC5764318 | biostudies-other
Project description:Intensive agriculture has increased global food production, but also impaired ecosystem services and soil biodiversity. Organic fertilization, essential to organic and integrated farming, can provide numerous benefits for soil quality but also compromise the environment by polluting soils and producing greenhouse gases through animal husbandry. The need for reduced stocking density is inevitably accompanied by lower FYM inputs, but little research is available on the impact of these effects on the soil microbiome. We collected soil samples from winter wheat plots of a 42-year-old long-term trial comparing different farming systems receiving farmyard manure at two intensities and measured soil quality parameters and microbial community diversity through DNA metabarcoding. High-input fertilization, corresponding to 1.4 livestock units (LU) improved the soil's nutritional status and increased soil microbial biomass and respiration when compared to low-input at 0.7 LU. Bacterial and fungal α-diversity was largely unaffected by fertilization intensity, whereas their community structure changed consistently, accompanied by an increase in the bacterial copiotroph-to-oligotroph ratio in high-input systems and by more copiotrophic indicator OTUs associated with high than low-input. This study shows that reduced nutrient availability under low-input selects oligotrophic microbes efficiently obtaining nutrients from various carbon sources; a potentially beneficial trait considering future agroecosystems.
| S-EPMC10236208 | biostudies-literature
Project description:It has been suggested that conversion to organic farming contributes to soil carbon sequestration, but until now a comprehensive quantitative assessment has been lacking. Therefore, datasets from 74 studies from pairwise comparisons of organic vs. nonorganic farming systems were subjected to metaanalysis to identify differences in soil organic carbon (SOC). We found significant differences and higher values for organically farmed soils of 0.18 ± 0.06% points (mean ± 95% confidence interval) for SOC concentrations, 3.50 ± 1.08 Mg C ha(-1) for stocks, and 0.45 ± 0.21 Mg C ha(-1) y(-1) for sequestration rates compared with nonorganic management. Metaregression did not deliver clear results on drivers, but differences in external C inputs and crop rotations seemed important. Restricting the analysis to zero net input organic systems and retaining only the datasets with highest data quality (measured soil bulk densities and external C and N inputs), the mean difference in SOC stocks between the farming systems was still significant (1.98 ± 1.50 Mg C ha(-1)), whereas the difference in sequestration rates became insignificant (0.07 ± 0.08 Mg C ha(-1) y(-1)). Analyzing zero net input systems for all data without this quality requirement revealed significant, positive differences in SOC concentrations and stocks (0.13 ± 0.09% points and 2.16 ± 1.65 Mg C ha(-1), respectively) and insignificant differences for sequestration rates (0.27 ± 0.37 Mg C ha(-1) y(-1)). The data mainly cover top soil and temperate zones, whereas only few data from tropical regions and subsoil horizons exist. Summarizing, this study shows that organic farming has the potential to accumulate soil carbon.
| S-EPMC3497757 | biostudies-literature
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.
| S-EPMC5209367 | biostudies-literature
Project description:This study examined fungal diversity and composition in conventional (CM) and desert farming (DE) systems in Oman. Fungal diversity in the rhizosphere of tomato was assessed using 454-pyrosequencing and culture-based techniques. Both techniques produced variable results in terms of fungal diversity, with 25% of the fungal classes shared between the two techniques. In addition, pyrosequencing recovered more taxa compared to direct plating. These findings could be attributed to the ability of pyrosequencing to recover taxa that cannot grow or are slow growing on culture media. Both techniques showed that fungal diversity in the conventional farm was comparable to that in the desert farm. However, the composition of fungal classes and taxa in the two farming systems were different. Pyrosequencing revealed that Microsporidetes and Dothideomycetes are the two most common fungal classes in CM and DE, respectively. However, the culture-based technique revealed that Eurotiomycetes was the most abundant class in both farming systems and some classes, such as Microsporidetes, were not detected by the culture-based technique. Although some plant pathogens (e.g., Pythium or Fusarium) were detected in the rhizosphere of tomato, the majority of fungal species in the rhizosphere of tomato were saprophytes. Our study shows that the cultivation system may have an impact on fungal diversity. The factors which affected fungal diversity in both farms are discussed.
| S-EPMC5539375 | biostudies-literature
Project description:In Central Europe, summer droughts are increasing in frequency which threatens production and biodiversity in agroecosystems. The potential of different farming systems to mitigate detrimental drought effects on soil animals is largely unknown. We investigated the effects of simulated drought on the abundance and community composition of soil microarthropods (Collembola and Oribatida and Meso-, Pro-, and Astigmata) in winter wheat fields under long-term conventional and organic farming in the DOK trial, Switzerland. We simulated drought by excluding 65% of the ambient precipitation during the wheat-growing season from March to June 2017. The abundance of Collembola and Oribatida declined more consistently in conventionally managed fields compared to organically managed fields under simulated drought. The abundance of Collembola as well as Meso-, Pro- and Astigmata, but not the abundance of Oribatida, increased in deeper soil layers due to simulated drought, suggesting vertical migration as a drought avoidance strategy. The species composition of Oribatida communities, but not of Collembola communities, differed significantly between drought treatments and between farming systems. Soil carbon content was a major factor structuring Oribatida communities. Our results suggest that organic farming buffers negative effects of drought on soil microarthropods, presumably due to higher soil carbon content and associated higher soil moisture and improved soil structure. This potential of organic farming systems to mitigate consequences of future droughts on soil biodiversity is promising and needs further exploration across larger climatic and spatial scales and should be extended to other groups of soil biota.
| S-EPMC8328414 | biostudies-literature
Project description:Agricultural practices affect the bacterial community structure, but how they determine the response of the bacterial community to drought, is still largely unknown. Conventional cultivated soil, i.e., inorganic fertilization, tillage, crop residue removal and maize (Zea mays L.) monoculture, and traditional organic farmed soil "milpa," i.e., minimum tillage, rotation of maize, pumpkin (Cucurbita sp.) and beans (Phaseolus vulgaris L.) and organic fertilization were sampled. Both soils from the central highlands of Mexico were characterized and incubated aerobically at 5% field capacity (5%FC) and 100% field capacity (FC) for 45 days, while the C and N mineralization, enzyme activity and the bacterial community structure were monitored. After applying the different agricultural practices 3 years, the organic C content was 1.8-times larger in the milpa than in the conventional cultivated soil, the microbial biomass C 1.3-times, and C and N mineralization 2.0-times (mean for soil incubated at 5%FC and FC). The dehydrogenase, activity was significantly higher in the conventional cultivated soil than in the milpa soil when incubated at 5%FC, but not when incubated at FC. The relative abundance of Gemmatimonadetes was larger in the conventional cultivated soil than in the milpa soil in soil both at 5%FC and FC, while that of Bacteroidetes showed an opposite trend. The relative abundance of other groups, such as Nitrospirae and Proteobacteria, was affected by cultivation technique, but controlled by soil water content. The relative abundance of other groups, e.g., FBP, Gemmatimonadetes and Proteobacteria, was affected by water content, but the effect depended on agricultural practice. For soil incubated at FC, the xenobiotics biodegradation and metabolism related functions were higher in the milpa soil than in the conventional cultivated soil, and carbohydrate metabolism showed an opposite trend. It was found that agricultural practices and soil water content had a strong effect on soil characteristics, C and N mineralization, enzyme activity, and the bacterial community structure and its functionality. Decreases or increases in the relative abundance of bacterial groups when the soil water content decreased, i.e., from FC to 5%FC, was defined often by the cultivation technique, and the larger organic matter content in the milpa soil did not prevent large changes in the bacterial community structure when the soil was dried.
| S-EPMC6246654 | biostudies-literature
Project description:Straw return (SR) and rice water-saving irrigation (WSI) affect the greenhouse gas emission of paddy fields. However, studies on CO2 exchange between paddy fields and the atmosphere with joint regulation of SR and WSI are few. We conducted a two-year field experiment to investigate the effects of SR on soil respiration and net ecosystem exchange of CO2 (NEE) in paddy fields under controlled irrigation (CI), which is a typical WSI technique. The rice yields, irrigation water use efficiency, seasonal variations in soil respiration, NEE, and soil organic carbon content were measured. Compared with the control (flooding irrigation and traditional chemical fertilizer), a significant increase in rice yield and irrigation water use efficiency in the paddy fields under CI and SR joint management (CS) was observed. CS increased the soil respiration rate during most of the rice growth stage and increased the net CO2 absorption rate before approximately 80 days after transplanting; afterward, the pattern reversed. Total CO2 emissions through soil respiration in CS paddy fields increased by 43.7% and 182% compared with the control in 2014 and 2015, respectively. However, CS also caused an increase in the total net CO2 absorption by 18.1% and 30.1% in these two years, respectively. The acceleration in the consumption and decomposition of soil organic carbon induced by frequent alternate wet-dry cycles of the CI paddy fields increased the soil respiration and decreased the net CO2 absorption. SR promoted soil respiration but also improved rice growth, increasing the net CO2 absorption. The soil organic carbon content of the CS paddy fields after harvesting increased by 23.2% compared with that before transplanting. The present study concluded that joint regulation of WSI and SR is an effective measure for maintaining yield, increasing irrigation water use efficiency, mitigating CO2 emission, and promoting paddy soil fertility.
| S-EPMC6191090 | biostudies-literature