scholarly journals Soil Bacterial Community Diversity and Composition as Affected by Tillage Intensity Treatments in Corn-Soybean Production Systems

2021 ◽  
Vol 12 (1) ◽  
pp. 157-172
Author(s):  
Shankar G. Shanmugam ◽  
Normie W. Buehring ◽  
Jon D. Prevost ◽  
William L. Kingery
Keyword(s):  
Microbial Community ◽  
Bacterial Community ◽  
Community Composition ◽  
Production System ◽  
Soil Microbial Community ◽  
Production Systems ◽  
Bacterial Community Composition ◽  
Soybean Production ◽  
Soil Microbial ◽  
Soil Bacterial

Our understanding on the effects of tillage intensity on the soil microbial community structure and composition in crop production systems are limited. This study evaluated the soil microbial community composition and diversity under different tillage management systems in an effort to identify management practices that effectively support sustainable agriculture. We report results from a three-year study to determine the effects on changes in soil microbial diversity and composition from four tillage intensity treatments and two residue management treatments in a corn-soybean production system using Illumina high-throughput sequencing of 16S rRNA genes. Soil samples were collected from tillage treatments at locations in the Southern Coastal Plain (Verona, Mississippi, USA) and Southern Mississippi River Alluvium (Stoneville, Mississippi, USA) for soil analysis and bacterial community characterization. Our results indicated that different tillage intensity treatments differentially changed the relative abundances of bacterial phyla. The Mantel test of correlations indicated that differences among bacterial community composition were significantly influenced by tillage regime (rM = 0.39, p ≤ 0.0001). Simpson’s reciprocal diversity index indicated greater bacterial diversity with reduction in tillage intensity for each year and study location. For both study sites, differences in tillage intensity had significant influence on the abundance of Proteobacteria. The shift in the soil bacterial community composition under different tillage systems was strongly correlated to changes in labile carbon pool in the system and how it affected the microbial metabolism. This study indicates that soil management through tillage intensity regime had a profound influence on diversity and composition of soil bacterial communities in a corn-soybean production system.

Changes in soil microbial community structure and function following degradation in a temperate grassland

2020 ◽  
Author(s):  
Yang Yu ◽  
Lang Zheng ◽  
Yijun Zhou ◽  
Weiguo Sang ◽  
Jianing Zhao ◽  
...  
Keyword(s):  
Microbial Community ◽  
Bacterial Community ◽  
Relative Abundance ◽  
Fungal Community ◽  
Soil Microbial Community ◽  
Temperate Grassland ◽  
Grassland Degradation ◽  
Soil Microbial Community Structure ◽  
Soil Microbial ◽  
Soil Bacterial

Abstract Aims Grassland degradation represents a major challenge in grassland productivity. This process has dramatic impacts on energy flows and soil nutrient dynamics and therefore may directly or indirectly influence soil microbes residing in surface soils. Here we aim to (1) examine changes in soil microbial composition, diversity, and functionality in response to different levels of grassland degradation (i.e., non-degraded, moderately degraded and severely degraded) in a temperate grassland in Inner Mongolia, and (2) elucidate biotic and abiotic factors that are responsible to these changes. Methods The composition structure of soil microbial community was determined by high-throughput sequencing. The functionality of bacterial communities was examined using the tool of FAPROTAX while functional guilds of fungal communities was quantified using the FUNGuild Pipeline. Important Findings Grassland degradation significantly decreased soil bacterial diversity but had no effect on fungal diversity. Belowground biomass, soil organic carbon, and total nitrogen were positively related to changes in diversity of bacterial community. Grassland degradation significantly increased the relative abundance of Chloroflexi (from 2.48% to 8.40%), and decreased Firmicutes (from 3.62% to 1.08%) of bacterial community. Degradation also significantly increased the relative abundance of Glomeromycota (from 0.17% to 1.53%), and decreased Basidiomycota (from 19.30% to 4.83%) of fungal community. The relative abundance of pathogenic fungi (Didymella and Fusarium) decreased significantly in response to degradation. In addition, degradation had a significant impact on putative functionality of soil bacteria related to soil carbon and nitrogen cycling. Our results suggest that soil bacterial community was more sensitive than fungal community in response to degradation in this temperate grassland.

scholarly journals Molecular Biology-Based Analysis of the Interactive Effect of Nickel and Xanthates on Soil Bacterial Community Diversity and Structure

2019 ◽  
Vol 11 (14) ◽  
pp. 3888
Author(s):  
Prudence Bararunyeretse ◽  
Yan Zhang ◽  
Hongbing Ji
Keyword(s):  
Microbial Community ◽  
Molecular Biology ◽  
Bacterial Community ◽  
Soil Microbial Community ◽  
Bacterial Species ◽  
Interactive Effect ◽  
Soil Bacterial Community ◽  
Community Diversity ◽  
Soil Microbial ◽  
Soil Bacterial

Metals and mineral flotation collector’s toxicity to the soil living system greatly compromise the sustainability of mining and ore processing. Their effects on the soil microbial community, the most active soil component, remain less understood and addressed particularly with regards to xanthates and their combination with metals. This study analyzed the interactive effects of Ni and xanthates, potassium ethyl xanthate and sodium isopropyl xanthate, on the soil bacterial community through an efficient molecular biology-based technique, the Miseq (Illumina). Both soil microbial community diversity and structure were more affected by xanthates than by Ni. The five most dominant phyla, representing 96.31% of the whole bacterial community, comprised Proteobacteria (54.16%), Firmicutes (17.51%), Actinobacteria (15.59%), Acidobacteria (4.87%), and Chloroflexi (4.16%). Different soil treatments exhibited greater difference in the species abundance/dominance than in the species numbers. Proteobacteria was the most dominant in the presence of xanthates, individually or in mixtures with nickel, while Firmicutes exhibited its highest proportion in the Ni/xanthate-treated samples. The most abundant and proportionally different bacterial species between different treatments were presented. The most abundant bacterial strains identified should be explored more for their potential application in biomining and for the prediction and biologically-based treatment and remediation of Ni and xanthate-contaminated systems.

scholarly journals Soil Microbial Community Successional Patterns during Forest Ecosystem Restoration

2011 ◽  
Vol 77 (17) ◽  
pp. 6158-6164 ◽  
Author(s):  
Natasha C. Banning ◽  
Deirdre B. Gleeson ◽  
Andrew H. Grigg ◽  
Carl D. Grant ◽  
Gary L. Andersen ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Bacterial Community ◽  
Fungal Community ◽  
Soil Microbial Community ◽  
Ecosystem Restoration ◽  
Community Structures ◽  
Soil Microbial ◽  
Soil Bacterial ◽  
Edaphic Variables

ABSTRACTSoil microbial community characterization is increasingly being used to determine the responses of soils to stress and disturbances and to assess ecosystem sustainability. However, there is little experimental evidence to indicate that predictable patterns in microbial community structure or composition occur during secondary succession or ecosystem restoration. This study utilized a chronosequence of developing jarrah (Eucalyptus marginata) forest ecosystems, rehabilitated after bauxite mining (up to 18 years old), to examine changes in soil bacterial and fungal community structures (by automated ribosomal intergenic spacer analysis [ARISA]) and changes in specific soil bacterial phyla by 16S rRNA gene microarray analysis. This study demonstrated that mining in these ecosystems significantly altered soil bacterial and fungal community structures. The hypothesis that the soil microbial community structures would become more similar to those of the surrounding nonmined forest with rehabilitation age was broadly supported by shifts in the bacterial but not the fungal community. Microarray analysis enabled the identification of clear successional trends in the bacterial community at the phylum level and supported the finding of an increase in similarity to nonmined forest soil with rehabilitation age. Changes in soil microbial community structure were significantly related to the size of the microbial biomass as well as numerous edaphic variables (including pH and C, N, and P nutrient concentrations). These findings suggest that soil bacterial community dynamics follow a pattern in developing ecosystems that may be predictable and can be conceptualized as providing an integrated assessment of numerous edaphic variables.

scholarly journals The effects of soil depth on the structure of microbial communities in agricultural soils in Iowa, USA

2020 ◽  
Author(s):  
Jingjie Hao ◽  
Yen Ning Chai ◽  
Raziel A. Ordóñez ◽  
Emily E. Wright ◽  
Sotirios Archontoulis ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Bacterial Community ◽  
Microbial Communities ◽  
Community Composition ◽  
Microbial Community Structure ◽  
Soil Depth ◽  
Bacterial Community Composition ◽  
Soil Microbial Communities ◽  
Soil Microbial

AbstractThe determination of how microbial community structure changes within the soil profile, will be beneficial to understanding the long-term health of agricultural soil ecosystems and will provide a first step towards elucidating how deep soil microbial communities contribute to carbon sequestration. This study aimed to investigate the differences in the microbial community abundance, composition and diversity throughout from the surface layers down to deep soils in corn and soybean fields in Iowa, USA. We used 16S rRNA amplicon sequencing of soil samples to characterize the change in microbial community structure. Our results revealed decreased richness and diversity in bacterial community structure with increasing soil depth. We also observed distinct distribution patterns of bacterial community composition along soil profiles. Soil and root data at different depths enabled us to demonstrate that the soil organic matter, soil bulk density and plant water availability were all significant factors in explaining the variation in soil microbial community composition. Our findings provide valuable insights in the changes in microbial community structure to depths of 180 cm in one of the most productive agricultural regions in the world. This knowledge will be important for future management and productivity of agroecosystems in the face of increasing demand for food and climate change.

scholarly journals Short-term effects of cover grass intensity on soil microbial communities in an apple orchard

2020 ◽  
Author(s):  
Pan Wan ◽  
Anzhi Wei
Keyword(s):  
Microbial Community ◽  
Bacterial Community ◽  
Community Composition ◽  
Soil Microbial Community ◽  
Soil Microbial Communities ◽  
Apple Orchard ◽  
Community Diversity ◽  
Moderate Intensity ◽  
Microbial Community Diversity ◽  
Soil Microbial

Soil microbiota play an important and diverse roles in horticultural crop nutrition or productivity. However, the soil microbial community composition and the relationships within the taxa in the microbial community populations after cover grass treatments in apple orchards are not well understood. We analysed the microbial community diversity, composition and microbial network of an apple orchard after covering with native wild grasses at different intensities for 2 years in the Loess Plateau, China. The cover grass intensities were 0%, 20%, 40%, 60% and 80%. Soil microbial community diversity was not obviously change by cover grass in the apple orchard. Cover grass altered the microbial bacterial community compositions, their changes exhibited significant differences at the phylum level that were caused by the Proteobacteria, Bacteroidetes, Chloroflexi, Gemmatimonadetes, Nitrospirae. However, low-intensity (20%) and moderate-intensity (40%) treatments were the only cover grass intensities that altered the soil fungal community composition; but their changes did not exhibit significant differences at the phylum level. The positive links among the bacterial taxa decreased with the increasing cover intensity, primarily among Proteobacteria, Acidobacteria, Actinobacteria, Chloroflexi and Gemmatimonadetes. Although cover grass increased the positive links between fungal taxa, these taxa were reduced with the increasing cover intensity. Here we demonstrate that cover grass changed the soil microbial community, and the changes may be attributed to the given phyla in the bacterial community; furthermore, the antagonistic effect between the soil bacterial and fungal communities was significantly increased by higher coverage than by lower coverage.

scholarly journals Dynamics of microbial community composition and soil organic carbon mineralization in soil following addition of pyrogenic and fresh organic matter

2015 ◽  
Author(s):  
Thea Whitman ◽  
Charles Pepe-Ranney ◽  
Akio Enders ◽  
Chantal Koechli ◽  
Ashley Campbell ◽  
...  
Keyword(s):  
Organic Matter ◽  
Microbial Community ◽  
Bacterial Community ◽  
Corn Stover ◽  
Community Composition ◽  
Bacterial Community Composition ◽  
Soil Microbial Communities ◽  
Co2 Fluxes ◽  
Soil Microbial ◽  
Fresh Organic Matter

Pyrogenic organic matter (PyOM) additions to soils can have large impacts on soil organic C (SOC) cycling. Because the soil microbial community drives SOC fluxes, understanding how PyOM additions affect soil microbes is essential to understanding how PyOM affects SOC. We studied SOC dynamics and surveyed soil microbial communities after OM additions in a field experiment. We produced and applied either 350°C corn stover PyOM or an equivalent amount of dried corn stover to a Typic Fragiudept soil. Stover increased SOC-derived and total CO2 fluxes (up to 6x), and caused rapid and persistent changes in bacterial community composition over 82 days. In contrast, PyOM only temporarily increased total soil CO2 fluxes (up to 2x) and caused fewer changes in bacterial community composition. 70% of the OTUs that increased in response to PyOM additions also responded to stover additions. These OTUs likely thrive on easily-mineralizable C that is found both in stover and, to a lesser extent, in PyOM. In contrast, we also identified unique PyOM-responders, which may respond to substrates such as polyaromatic C. In particular, members of Gemmatimonadetes tended to increase in relative abundance in response to PyOM but not to fresh organic matter. We identify taxa to target for future investigations of the mechanistic underpinnings of ecological phenomena associated with PyOM additions to soil.

scholarly journals Groundcover Management Systems Influence Soil Microbial Community Composition in an Apple Orchard

HortScience ◽  
2004 ◽  
Vol 39 (4) ◽  
pp. 842C-842
Author(s):  
Shengrui Yao* ◽  
Ian A. Merwin ◽  
Janice E. Thies ◽  
George S. Abawi
Keyword(s):  
Microbial Community ◽  
Bacterial Community ◽  
Community Composition ◽  
Soil Microbial Community ◽  
Microbial Community Composition ◽  
Management Systems ◽  
Silty Clay ◽  
Soil Microbial ◽  
Surface Vegetation ◽  
Soil Microbial Community Composition

An apple (Malus domestica cv. Empire on M9/MM111 rootstock) orchard groundcover management systems (GMSs) study has been underway since 1992 in Ithaca, N.Y. Four GMS treatments are applied each year in 2-m wide tree-row strips: Pre-emergence herbicides (Pre-H: diuron + norflurazon + glyphosate); Post-emergence herbicide (Post-H: glyphosate); mowed-sod (Grass); and composted hardwood bark mulch (Mulch) treatment. The soil (silty clay loam) physical and chemical conditions have been monitored continuously. In May and Sept. 2003, we sampled topsoil beneath trees in each GMS and used PCR-DGGE combined with sequencing to characterize soil microbial community composition. Mulch had more culturable soil bacteria than the Pre-H treatment. Soil in Grass plots had the most culturable soil fungi. Soil microbial respiration rates were higher in Mulch than Grass and herbicide GMSs. Surface vegetation in the Grass and Post-H plots strongly influenced soil bacterial community composition. In Principal Component Analyses, Post-H and Grass treatments comprised one variance cluster, and Pre-H and Mulch treatments another. The soil fungal community was less diverse (fewer DGGE bands) than the bacterial community, and was less affected by GMS. Treatments with more surface vegetation (Post-H and Grass) also had more free-living and phytonematodes than Pre-H and Mulch. A total of 47 clones from 12 DGGE bands yielded 31 unique DNA sequences. Of these, 15 were novel sequences with no matches in the GenBank (NCBI) database. Another 10 (27 clones) could be matched with known fungal species at 96-100% identity. The primer pair used, ITS1F/ITS2, amplified a considerable number of Basidiomycetes and Ascomycetes, but there was no amplification for Zygomycetes and Oomycetes.

Impacts of invasive plant species on soil biodiversity: a case study of dog-strangling vine (Vincetoxicum rossicum) in a Canadian National Park

2018 ◽  
Vol 98 (4) ◽  
pp. 716-723 ◽  
Author(s):  
Laura N. Bugiel ◽  
Stuart W. Livingstone ◽  
Marney E. Isaac ◽  
Roberta R. Fulthorpe ◽  
Adam R. Martin
Keyword(s):  
Bacterial Community ◽  
Microbial Diversity ◽  
Community Composition ◽  
Invasive Plant ◽  
Bacterial Community Composition ◽  
Anthropogenic Disturbances ◽  
Soil Parameters ◽  
Invasive Plant Species ◽  
Vincetoxicum Rossicum ◽  
Soil Bacterial

Soil microbial diversity is expected to be altered by the establishment of invasive plant species, such as dog-strangling vine (DSV) [Vincetoxicum rossicum (Apocynaceae)]. However, in urban ecosystems where DSV invasion is high, there is little research evaluating the impacts of DSV and other anthropogenic disturbances on microbial diversity. Our study was based in Rouge National Urban Park, Canada, where we used terminal restriction fragment length polymorphism data to evaluate (i) if DSV has a detectable impact on soil bacterial community composition and (ii) if these impacts occur independently of other anthropogenic change or soil characteristics. Variation in soil bacterial communities was greatly reduced in DSV-invaded sites vs. less-invaded sites. The degree of DSV invasion independently explained 23.8% of variation in bacterial community composition: a value similar to the explanatory power of proximity to roadways (which explained 22.6% of the variation in community composition), and considerably greater than soil parameters (pH, moisture, carbon, and nitrogen concentrations) which explained only between 6.0% and 10.0% of variation in bacterial community composition. Our findings indicate that DSV influences soil bacterial community composition independent of other anthropogenic disturbances and soil parameters, with potential impacts on multiple facets of plant–soil interactions and plant invasion dynamics.

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