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.

scholarly journals Effect of Drought Stress and Developmental Stages on Microbial Community Structure and Diversity in Peanut Rhizosphere Soil

2019 ◽  
Vol 20 (9) ◽  
pp. 2265 ◽  
Author(s):  
Liangxiang Dai ◽  
Guanchu Zhang ◽  
Zipeng Yu ◽  
Hong Ding ◽  
Yang Xu ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Drought Tolerance ◽  
Microbial Communities ◽  
Microbial Community Structure ◽  
Defense Mechanism ◽  
Developmental Stages ◽  
Rrna Gene ◽  
Special Importance ◽  
Arachis Hypogaea L

Background: Peanut (Arachis hypogaea L.), an important oilseed and food legume, is widely cultivated in the semi-arid tropics. Drought is the major stress in this region which limits productivity. Microbial communities in the rhizosphere are of special importance to stress tolerance. However, relatively little is known about the relationship between drought and microbial communities in peanuts. Method: In this study, deep sequencing of the V3-V4 region of the 16S rRNA gene was performed to characterize the microbial community structure of drought-treated and untreated peanuts. Results: Taxonomic analysis showed that Actinobacteria, Proteobacteria, Saccharibacteria, Chloroflexi, Acidobacteria and Cyanobacteria were the dominant phyla in the peanut rhizosphere. Comparisons of microbial community structure of peanuts revealed that the relative abundance of Actinobacteria and Acidobacteria dramatically increased in the seedling and podding stages in drought-treated soil, while that of Cyanobacteria and Gemmatimonadetes increased in the flowering stage in drought-treated rhizospheres. Metagenomic profiling indicated that sequences related to metabolism, signaling transduction, defense mechanism and basic vital activity were enriched in the drought-treated rhizosphere, which may have implications for plant survival and drought tolerance. Conclusion: This microbial communities study will form the foundation for future improvement of drought tolerance of peanuts via modification of the soil microbes.

scholarly journals Water Quality and Microbial Community Changes in an Urban River after Micro-Nano Bubble Technology in Situ Treatment

Water ◽  
2019 ◽  
Vol 11 (1) ◽  
pp. 66 ◽  
Author(s):  
Yifei Wu ◽  
Hui Lin ◽  
Weizhao Yin ◽  
Sicheng Shao ◽  
Sihao Lv ◽  
...  
Keyword(s):  
Water Quality ◽  
Community Structure ◽  
Microbial Community ◽  
Microbial Community Structure ◽  
Oxygen Demand ◽  
Ammonia Nitrogen ◽  
Oxidation Reduction ◽  
Oxidation Reduction Potential ◽  
Dominant Bacteria

Currently, black-odor river has received great attention in China. In this study, the micro-nano bubble technology (MBT) was used to mitigate the water pollution rapidly and continuously by increasing the concentration of dissolved oxygen (DO) in water. During treatment, the concentration of DO increased from 0.60 mg/L to over 5.00 mg/L, and the oxidation reduction potential (ORP) also changed from a negative value to over 100.00 mV after only five days aeration. High throughput pyrosequencing technology was employed to identify the microbial community structure. At genus level, the dominant bacteria were anaerobic and nutrient-loving microbes (e.g., Arcobacter sp., Azonexus sp., and Citrobacter sp.) before, and the relative abundances of aerobic and functional microbes (e.g., Perlucidibaca sp., Pseudarcicella sp., Rhodoluna sp., and Sediminibacterium sp.) were increased after treatment. Meanwhile, the water quality was significantly improved with about 50% removal ratios of chemical oxygen demand (CODCr) and ammonia nitrogen (NH4+-N). Canonical correspondence analysis (CCA) results showed that microbial community structure shaped by COD, DO, NH4+-N, and TP, CCA1 and CCA2 explained 41.94% and 24.56% of total variances, respectively. Overall, the MBT could improve the water quality of urban black-odor river by raising the DO and activate the aerobic microbes.

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.

scholarly journals Analysis of enzyme activity and microbial community structure changes in the anaerobic digestion process of cattle manure at sub-mesophilic temperatures

2021 ◽  
Vol 10 (1) ◽  
pp. 644-657
Author(s):  
Xiaofei Zhen ◽  
Miao Luo ◽  
Haiying Dong ◽  
Lei Fang ◽  
Weiwei Wang ◽  
...  
Keyword(s):  
Enzyme Activity ◽  
Community Structure ◽  
Microbial Community ◽  
Anaerobic Digestion ◽  
Microbial Community Structure ◽  
Cattle Manure ◽  
Biogas Yield ◽  
Structure Changes ◽  
Dominant Bacteria ◽  
Experimental Group

Abstract To improve the biogas potential in anaerobic digestion of cattle manure in cold regions, we investigated, in this study, the potential of the anaerobic digestion of cattle manure through sequencing batch anaerobic digestion experiments at sub-mesophilic temperatures (15°C, 20°C, 25°C, and 37°C) for 50 days. Specifically, the changes in the biogas yield, pH, sCOD concentration, enzyme activity, and microbial community structure were examined. The maximum daily yield of biogas was 19.18 mL·gVS−1, which was recorded on day 6 at 37°C, and the final biogas accumulation yield at this temperature was 403.64 mL·gTS−1. The concentration of sCOD gradually increased as enzyme activity increased. The maximum activities of cellulase, hemicellulase, protease, and amylase were recorded in the 37°C experimental group. The decrease in temperature severely limited the activity of different types of enzymes, resulting in a decrease in the activity of microorganisms, which greatly influenced the methanogenic reaction. The dominant bacteria at the phylum level were Bacteroidetes and Proteobacteria, and the dominant methanogen at the genus level was Methanosaeta.

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