scholarly journals Metagenomic and metatranscriptomic analysis of the microbial community structure and metabolic potential of fermented soybean in Yunnan Province

2020 ◽  
Vol 40 (1) ◽  
pp. 18-25
Author(s):  
Xiao-Feng LIU ◽  
Chen-Jian LIU ◽  
Xue-Qin ZENG ◽  
Hai-Yan ZHANG ◽  
Yi-Yong LUO ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Microbial Community Structure ◽  
Yunnan Province ◽  
Metabolic Potential ◽  
Fermented Soybean

scholarly journals Linking soil biology and chemistry using bacterial isolate exometabolite profiles

2017 ◽  
Author(s):  
Tami L. Swenson ◽  
Ulas Karaoz ◽  
Joel M. Swenson ◽  
Benjamin P. Bowen ◽  
Trent Northen
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Microbial Community Structure ◽  
Developmental Stages ◽  
Environmental Chemistry ◽  
Biological Soil Crust ◽  
Niche Partitioning ◽  
Soil Biology ◽  
Metabolic Potential ◽  
Dominant Bacteria

ABSTRACTSequencing provides a window into microbial community structure and metabolic potential; however, linking these data to exogenous metabolites that microorganisms process and produce (the exometabolome) remains challenging. Previously, we observed strong exometabolite niche partitioning among bacterial isolates from biological soil crust (biocrust). Here we examine native biocrust to determine if these patterns are reproduced in the environment. Overall, most soil metabolites displayed the expected relationship (positive or negative correlation) with four dominant bacteria following a wetting event and across biocrust developmental stages. For metabolites that were previously found to be consumed by an isolate, 78% were negatively correlated with the abundance ofin situisolate phylotypes whereas for released metabolites, 73% were positively correlated. Our results demonstrate that metabolite profiling, sequencing and exometabolomics can be successfully integrated to functionally link metagenomes and microbial community structure with environmental chemistry.

Microbial Community Structure and Metabolic Potential of the Hyporheic Zone of a Large Mid-Stream Channel Bar

2019 ◽  
Vol 36 (9) ◽  
pp. 765-776 ◽  
Author(s):  
Joshua D. Sackett ◽  
Christopher L. Shope ◽  
James C. Bruckner ◽  
Journét Wallace ◽  
Clay A. Cooper ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Microbial Community Structure ◽  
Hyporheic Zone ◽  
Stream Channel ◽  
Metabolic Potential ◽  
Channel Bar

scholarly journals Microbial Community Dynamics during Biodegradation of Crude Oil and Its Response to Biostimulation in Svalbard Seawater at Low Temperature

2021 ◽  
Vol 9 (12) ◽  
pp. 2425
Author(s):  
Hiie Nõlvak ◽  
Nga Phuong Dang ◽  
Marika Truu ◽  
Angela Peeb ◽  
Kertu Tiirik ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Crude Oil ◽  
Microbial Community Structure ◽  
Community Dynamics ◽  
Oil Spills ◽  
Hydrocarbon Degradation ◽  
Taxonomic Assignment ◽  
Metabolic Potential ◽  
Microbial Community Dynamics

The development of oil exploration activities and an increase in shipping in Arctic areas have increased the risk of oil spills in this cold marine environment. The objective of this experimental study was to assess the effect of biostimulation on microbial community abundance, structure, dynamics, and metabolic potential for oil hydrocarbon degradation in oil-contaminated Arctic seawater. The combination of amplicon-based and shotgun sequencing, together with the integration of genome-resolved metagenomics and omics data, was applied to assess microbial community structure and metabolic properties in naphthenic crude oil-amended microcosms. The comparison of estimates for oil-degrading microbial taxa obtained with different sequencing and taxonomic assignment methods showed substantial discrepancies between applied methods. Consequently, the data acquired with different methods was integrated for the analysis of microbial community structure, and amended with quantitative PCR, producing a more objective description of microbial community dynamics and evaluation of the effect of biostimulation on particular microbial taxa. Implementing biostimulation of the seawater microbial community with the addition of nutrients resulted in substantially elevated prokaryotic community abundance (103-fold), a distinctly different bacterial community structure from that in the initial seawater, 1.3-fold elevation in the normalized abundance of hydrocarbon degradation genes, and 12% enhancement of crude oil biodegradation. The bacterial communities in biostimulated microcosms after four months of incubation were dominated by Gammaproteobacterial genera Pseudomonas, Marinomonas, and Oleispira, which were succeeded by Cycloclasticus and Paraperlucidibaca after eight months of incubation. The majority of 195 compiled good-quality metagenome-assembled genomes (MAGs) exhibited diverse hydrocarbon degradation gene profiles. The results reveal that biostimulation with nutrients promotes naphthenic oil degradation in Arctic seawater, but this strategy alone might not be sufficient to effectively achieve bioremediation goals within a reasonable timeframe.

The First Use of Biofilm Microbial Community Structure as an Indicator of Impact of Two Dams on the Elwha River (Washington)

2009 ◽  
Vol 27 (4) ◽  
pp. 385-387
Author(s):  
W. D. Eaton ◽  
B. Wilmot ◽  
E. Epler ◽  
S. Mangiamelli ◽  
D. Barry
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Microbial Community Structure ◽  
Elwha River
Sign in / Sign up

Export Citation Format

Share Document