scholarly journals Analysis of soil microbial communities based on amplicon sequencing of marker genes

2017 ◽  
Vol 53 (5) ◽  
pp. 485-489 ◽  
Author(s):  
Anne Schöler ◽  
Samuel Jacquiod ◽  
Gisle Vestergaard ◽  
Stefanie Schulz ◽  
Michael Schloter
Keyword(s):  
Microbial Communities ◽  
Soil Microbial Communities ◽  
Amplicon Sequencing ◽  
Marker Genes ◽  
Soil Microbial

scholarly journals Consistent responses of soil microbial communities to elevated nutrient inputs in grasslands across the globe

2015 ◽  
Vol 112 (35) ◽  
pp. 10967-10972 ◽  
Author(s):  
Jonathan W. Leff ◽  
Stuart E. Jones ◽  
Suzanne M. Prober ◽  
Albert Barberán ◽  
Elizabeth T. Borer ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Bacterial Communities ◽  
Soil Microbial Communities ◽  
Metagenomic Data ◽  
Life History Strategies ◽  
Marker Genes ◽  
Nutrient Inputs ◽  
Soil Microbial ◽  
Nutrient Additions ◽  
Relative Abundances

Soil microorganisms are critical to ecosystem functioning and the maintenance of soil fertility. However, despite global increases in the inputs of nitrogen (N) and phosphorus (P) to ecosystems due to human activities, we lack a predictive understanding of how microbial communities respond to elevated nutrient inputs across environmental gradients. Here we used high-throughput sequencing of marker genes to elucidate the responses of soil fungal, archaeal, and bacterial communities using an N and P addition experiment replicated at 25 globally distributed grassland sites. We also sequenced metagenomes from a subset of the sites to determine how the functional attributes of bacterial communities change in response to elevated nutrients. Despite strong compositional differences across sites, microbial communities shifted in a consistent manner with N or P additions, and the magnitude of these shifts was related to the magnitude of plant community responses to nutrient inputs. Mycorrhizal fungi and methanogenic archaea decreased in relative abundance with nutrient additions, as did the relative abundances of oligotrophic bacterial taxa. The metagenomic data provided additional evidence for this shift in bacterial life history strategies because nutrient additions decreased the average genome sizes of the bacterial community members and elicited changes in the relative abundances of representative functional genes. Our results suggest that elevated N and P inputs lead to predictable shifts in the taxonomic and functional traits of soil microbial communities, including increases in the relative abundances of faster-growing, copiotrophic bacterial taxa, with these shifts likely to impact belowground ecosystems worldwide.

scholarly journals Changes in soil microbial communities at Jinsha earthen site are associated with earthen site degradation

2019 ◽  
Author(s):  
Jing Li ◽  
Xiaoyue Zhang ◽  
Lin Xiao ◽  
Ke Liu ◽  
Yue Li ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Soil Microbial Communities ◽  
Amplicon Sequencing ◽  
Biological Factor ◽  
Rrna Gene ◽  
Biological Factors ◽  
Soil Microbial ◽  
Relative Abundances ◽  
Bacteria And Fungi ◽  
Degree Of Degradation

Abstract Background: Jinsha earthen site in Chengdu, China, plays an important role in understanding the ancient culture and history of Shu civilization. The site is undergoing soil degradation due to physical, chemical and biological factors, while very little is known about the influence of biological factors on earthen sites. To investigate the biological factor, we analyzed microbial communities and physicochemical properties from samples with no obvious, mild, moderate and severe degradation, referred to as S1, S2, S3 and S4 sample groups, respectively.Results: Amplicon sequencing targeting the 16S rRNA gene and ITS for bacteria and fungi, respectively, revealed high bacterial and relatively low fungal diversity; the bacterial OTUs were assigned into 36 phyla and 617 genera and the fungal OTUs into 5 phyla and 205 genera. The relative abundances of Bacteroidetes, Proteobacteria and Firmicutes were higher and that of Actinobacteria lower with higher degree of degradation. In the genus level, the relative abundances of Bacteroides and Ralstonia were higher and that of Rubrobacter lower with higher degree of degradation. The distribution of the fungal genera in the four sample groups seemed more random than that of bacteria; however, the relative abundance of the yeast genus Candida was highest in the severely degraded sample group. For both bacteria and fungi, the differences in community composition were associated with differences in EC, moisture, pH, and the concentrations of NH 4 + , K + , Mg 2+ , Ca 2+ and SO 4 2- .Conclusion: Taken together, the microbial communities in soil with different degree of degradation were distinctly different at Jinsha earthen site, and degradation was accompanied with bigger changes in the bacterial than in the fungal community.

scholarly journals Soil microbial communities in diverse agroecosystems exposed to glyphosate

2018 ◽  
Author(s):  
Ryan M. Kepler ◽  
Dietrich J. Epp Schmidt ◽  
Stephanie A. Yarwood ◽  
Krishna N. Reddy ◽  
Stephen O. Duke ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Plant Pathogens ◽  
Foliar Application ◽  
Microbial Community Composition ◽  
Soil Microbial Communities ◽  
Farming Systems ◽  
Amplicon Sequencing ◽  
Farming System ◽  
Conventional Farming ◽  
Soil Microbial

AbstractIn spite of glyphosate’s wide use in agriculture, questions remain about effects of the herbicide on soil microbial communities. Conflicting scientific literature reports divergent results; from no observable effect of glyphosate to the enrichment of common agricultural pathogens such as Fusarium. We conducted a comprehensive field-based study to compare treatments that did and did not receive foliar application of glyphosate spray. The study included two field sites, Maryland and Mississippi; two crops, soybean and corn; four site years, 2013 and 2014; and a variety of organic and conventional farming systems. Using amplicon sequencing, the prokaryotic (16S rRNA) and fungal (ITS) communities were described along with chemical and physical properties of the soil. Sections of corn and soy roots were plated to screen for the presence of plant pathogens. Geography, farming system, and seasonal progression were significant factors determining composition of fungal and bacterial communities. Plots treated with or without glyphosate did not differ in overall microbial community composition after controlling for these factors. No differential effect of glyphosate treatment was found in the relative abundance of organisms such as Fusarium spp. or putative growth-promoting bacteria Pseudomonas spp.

scholarly journals Responses of soil microbial communities to a short-term application of seaweed fertilizer revealed by deep amplicon sequencing

2018 ◽  
Vol 125 ◽  
pp. 288-296 ◽  
Author(s):  
Mingpeng Wang ◽  
Lei Chen ◽  
Yuntao Li ◽  
Lin Chen ◽  
Zhengyi Liu ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Soil Microbial Communities ◽  
Amplicon Sequencing ◽  
Short Term ◽  
Soil Microbial

Alkaline soil pH affects bulk soil, rhizosphere and root endosphere microbiomes of plants growing in a Sandhills ecosystem

2021 ◽  
Vol 97 (4) ◽  
Author(s):  
Lucas Dantas Lopes ◽  
Jingjie Hao ◽  
Daniel P Schachtman
Keyword(s):  
Microbial Communities ◽  
Plant Species ◽  
Soil Ph ◽  
Soil Microbial Communities ◽  
Bulk Soil ◽  
Strong Impact ◽  
Alkaline Soil ◽  
Alkaline Soils ◽  
Soil Microbial ◽  
Soil Rhizosphere

ABSTRACT Soil pH is a major factor shaping bulk soil microbial communities. However, it is unclear whether the belowground microbial habitats shaped by plants (e.g. rhizosphere and root endosphere) are also affected by soil pH. We investigated this question by comparing the microbial communities associated with plants growing in neutral and strongly alkaline soils in the Sandhills, which is the largest sand dune complex in the northern hemisphere. Bulk soil, rhizosphere and root endosphere DNA were extracted from multiple plant species and analyzed using 16S rRNA amplicon sequencing. Results showed that rhizosphere, root endosphere and bulk soil microbiomes were different in the contrasting soil pH ranges. The strongest impact of plant species on the belowground microbiomes was in alkaline soils, suggesting a greater selective effect under alkali stress. Evaluation of soil chemical components showed that in addition to soil pH, cation exchange capacity also had a strong impact on shaping bulk soil microbial communities. This study extends our knowledge regarding the importance of pH to microbial ecology showing that root endosphere and rhizosphere microbial communities were also influenced by this soil component, and highlights the important role that plants play particularly in shaping the belowground microbiomes in alkaline soils.

LDPE microplastics affect soil microbial communities and nitrogen cycling

2021 ◽  
Vol 773 ◽  
pp. 145640
Author(s):  
Lili Rong ◽  
Longfei Zhao ◽  
Leicheng Zhao ◽  
Zhipeng Cheng ◽  
Yiming Yao ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Nitrogen Cycling ◽  
Soil Microbial Communities ◽  
Soil Microbial
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