scholarly journals Microbiome of the Rhizosphere: from Structure to Functions

2021 ◽  
Author(s):  
Ning Ling ◽  
Tingting Wang ◽  
Yakov Kuzyakov
Keyword(s):  
Nitrogen Fixation ◽  
Microbial Ecology ◽  
16S Rdna ◽  
N Cycling ◽  
Microbial Interactions ◽  
Community Diversity ◽  
Organic Substances ◽  
Microbial Composition ◽  
Soil Function ◽  
Copiotrophic Bacteria

Abstract Microbial composition and functioning in the rhizosphere are among the most fascinating but hidden topics in microbial ecology. We generalized bacterial traits regarding community diversity, composition and functions using published 16s rDNA amplicon sequences of 584 pairs of bulk soils vs rhizosphere of crops. The lower bacterial diversity in the rhizosphere (-7% richness) compared to root-free soil reflects the excess of available organic substances near the root. The rhizosphere is enriched by Bacteroidetes, Proteobacteria and Cyanobacteria as well as other copiotrophic bacteria (r strategists). Complex but unstable bacterial networks in rhizosphere reflect tight microbial interactions and adaptations to fluctuating conditions common for r strategists. The dominant dormancy strategy in the rhizosphere is the toxin-antitoxin system, while sporulation is common in bulk soil. Function prediction analysis showed that the rhizosphere is strongly enriched (50–115%) in methanol oxidation, ureolysis, cellulolysis, chitinolysis and nitrogen fixation, but strongly depleted in functions related to N-cycling.

Application of 16S rDNA-DGGE to examine the microbial ecology associated with a social wasp Vespula germanica

2003 ◽  
Vol 12 (1) ◽  
pp. 85-91 ◽  
Author(s):  
A. F. Reeson ◽  
T. Jankovic ◽  
M. L. Kasper ◽  
S. Rogers ◽  
A. D. Austin
Keyword(s):  
Microbial Ecology ◽  
16S Rdna ◽  
Social Wasp ◽  
Vespula Germanica

Application of biochemical studies to improving nitrogen fixation

2001 ◽  
Vol 41 (3) ◽  
pp. 403 ◽  
Author(s):  
C. P. Vance ◽  
J. F. S. Lamb
Keyword(s):  
Nitrogen Fixation ◽  
Plant Breeding ◽  
Microbial Ecology ◽  
Carbon Metabolism ◽  
Multidisciplinary Approach ◽  
Symbiotic Nitrogen Fixation ◽  
Plant Biochemistry ◽  
Biochemical Studies ◽  
Plant Genes ◽  
Medicago Sativa L

Improvement of symbiotic nitrogen fixation requires a multidisciplinary approach with a comprehensive program ranging from microbial ecology to plant breeding and genomics. Achievement of symbiotic nitrogen fixation requires at least 100 genes from each partner interacting in a favorable environment. The more information that we obtain from applied and fundamental studies of Rhizobium–legume and Frankia–non-legume symbioses, the greater are our chances to extend nitrogen fixation to non-fixing species. Studies with alfalfa (Medicago sativa L.) aimed at improving symbiotic nitrogen fixation have resulted in significant advances in germplasm development, plant biochemistry, microbial ecology and the understanding of plant genes involved in nodule nitrogen and carbon metabolism. However, translation to field improvement of symbiotic nitrogen fixation has proven elusive.

scholarly journals An Overview of Bioinformatics Tools for DNA Meta-Barcoding Analysis of Microbial Communities of Bioaerosols: Digest for Microbiologists

Life ◽  
2020 ◽  
Vol 10 (9) ◽  
pp. 185
Author(s):  
Hamza Mbareche ◽  
Nathan Dumont-Leblond ◽  
Guillaume J. Bilodeau ◽  
Caroline Duchaine
Keyword(s):  
Microbial Communities ◽  
Microbial Ecology ◽  
Statistical Tests ◽  
Repeated Measurements ◽  
Microbial Composition ◽  
Alpha And Beta Diversity ◽  
Bioinformatic Tools ◽  
Bioinformatics Tools ◽  
Wide Range ◽  
Guided Tour

High-throughput DNA sequencing (HTS) has changed our understanding of the microbial composition present in a wide range of environments. Applying HTS methods to air samples from different environments allows the identification and quantification (relative abundance) of the microorganisms present and gives a better understanding of human exposure to indoor and outdoor bioaerosols. To make full use of the avalanche of information made available by these sequences, repeated measurements must be taken, community composition described, error estimates made, correlations of microbiota with covariates (variables) must be examined, and increasingly sophisticated statistical tests must be conducted, all by using bioinformatics tools. Knowing which analysis to conduct and which tools to apply remains confusing for bioaerosol scientists, as a litany of tools and data resources are now available for characterizing microbial communities. The goal of this review paper is to offer a guided tour through the bioinformatics tools that are useful in studying the microbial ecology of bioaerosols. This work explains microbial ecology features like alpha and beta diversity, multivariate analyses, differential abundances, taxonomic analyses, visualization tools and statistical tests using bioinformatics tools for bioaerosol scientists new to the field. It illustrates and promotes the use of selected bioinformatic tools in the study of bioaerosols and serves as a good source for learning the “dos and don’ts” involved in conducting a precise microbial ecology study.

scholarly journals Regional biogeography of microbiota composition in the Chagas disease vector Rhodnius pallescens

2019 ◽  
Vol 12 (1) ◽  
Author(s):  
Troy J. Kieran ◽  
Kaylee M. H. Arnold ◽  
Jesse C. Thomas ◽  
Christina P. Varian ◽  
Azael Saldaña ◽  
...  
Keyword(s):  
Microbial Ecology ◽  
Chagas Disease ◽  
Management Strategies ◽  
Geographical Location ◽  
Protozoan Parasite ◽  
Illumina Miseq ◽  
Whole Body ◽  
Microbial Composition ◽  
Bacterial Phyla ◽  
Rhodnius Pallescens

Abstract Background Triatomine bugs are vectors of the protozoan parasite Trypanosoma cruzi, which causes Chagas disease. Rhodnius pallescens is a major vector of Chagas disease in Panama. Understanding the microbial ecology of disease vectors is important in the development of vector management strategies that target vector survival and fitness. In this study we examined the whole-body microbial composition of R. pallescens from three locations in Panama. Methods We collected 89 R. pallescens specimens using Noireau traps in Attalea butyracea palms. We then extracted total DNA from whole-bodies of specimens and amplified bacterial microbiota using 16S rRNA metabarcoding PCR. The 16S libraries were sequenced on an Illumina MiSeq and analyzed using QIIME2 software. Results We found Proteobacteria, Actinobacteria, Bacteroidetes and Firmicutes to be the most abundant bacterial phyla across all samples. Geographical location showed the largest difference in microbial composition with northern Veraguas Province having the most diversity and Panama Oeste Province localities being most similar to each other. Wolbachia was detected in high abundance (48–72%) at Panama Oeste area localities with a complete absence of detection in Veraguas Province. No significant differences in microbial composition were detected between triatomine age class, primary blood meal source, or T. cruzi infection status. Conclusions We found biogeographical regions differ in microbial composition among R. pallescens populations in Panama. While overall the microbiota has bacterial taxa consistent with previous studies in triatomine microbial ecology, locality differences are an important observation for future studies. Geographical heterogeneity in microbiomes of vectors is an important consideration for future developments that leverage microbiomes for disease control.

scholarly journals Dietary Supplementation With Creatine Pyruvate Alters Rumen Microbiota Protein Function in Heat-Stressed Beef Cattle

2021 ◽  
Vol 12 ◽  
Author(s):  
Yanjiao Li ◽  
Yitian Zang ◽  
Xianghui Zhao ◽  
Lin Liu ◽  
Qinghua Qiu ◽  
...  
Keyword(s):  
Heat Stress ◽  
Fatty Acid ◽  
Beef Cattle ◽  
16S Rdna ◽  
Rumen Fermentation ◽  
16S Rdna Sequencing ◽  
Microbial Protein ◽  
Microbial Composition ◽  
Citrate Cycle ◽  
Rdna Sequencing

Creatine pyruvate (CrPyr) is a new multifunctional nutrient that can provide both pyruvate and creatine. It has been shown to relieve the heat stress of beef cattle by improving antioxidant activity and rumen microbial protein synthesis, but the mechanism of CrPyr influencing rumen fermentation remains unclear. This study aimed to combine 16S rDNA sequencing and metaproteomics technologies to investigate the microbial composition and function in rumen fluid samples taken from heat-stressed beef cattle treated with or without 60 g/day CrPyr. 16S rDNA sequencing revealed that there were no significant differences in the α-diversity indices between the two groups. By analyzing the level profiles of 700 distinct proteins, we found that the CrPyr administration increased the expression of enzymes involved in specific metabolic pathways including (i) fatty acid β-oxidation; (ii) interconversion from pyruvate to phosphoenolpyruvate, oxaloacetate, acetyl-CoA, and malate; (iii) glycolysis/gluconeogenesis and citrate cycle metabolism; and (iv) biosynthesis of amino acids. These results indicated that the increased generation of adenosine triphosphate during fatty acid β-oxidation or citrate cycle and the up-regulation synthesis of microbial protein in rumen of beef cattle treated with CrPyr may help decrease oxidative stress, regulate energy metabolism, and further improve the rumen fermentation characteristic under heat stress.

scholarly journals Dietary Supplementation With Creatine Pyruvate Alter Rumen Microbiota Protein Function in Heat-Stressed Beef Cattle

2020 ◽  
Author(s):  
Yanjiao Li ◽  
Xianghui Zhao ◽  
Lin Liu ◽  
Kang Mao ◽  
Mingren Qu ◽  
...  
Keyword(s):  
Heat Stress ◽  
Fatty Acid ◽  
Beef Cattle ◽  
16S Rdna ◽  
Rumen Fermentation ◽  
16S Rdna Sequencing ◽  
Microbial Protein ◽  
Microbial Composition ◽  
Citrate Cycle ◽  
Rdna Sequencing

Abstract Background: Creatine pyruvate (CrPyr) is a new multifunctional nutrient that can provide both pyruvate and creatine. It has been shown to relieve the heat stress of beef cattle by improving antioxidant activity and rumen microbial protein synthesis, but the mechanism of CrPyr influencing rumen fermentation remains unclear. This study aimed to combine 16S rDNA sequencing and metaproteomics technologies to investigate the microbial composition and function in rumen fluid samples taken from heat-stressed beef cattle treated with or without 60 g/d CrPyr. Results: 16S rDNA sequencing revealed that there was no significant differences in the α-diversity indices between the two groups. By analyzing the expression profiles of 700 distinct proteins, we found that CrPyr administration increased the fatty acid β-oxidation, promoted the interconversion from pyruvate to phosphoenolpyruvate, acetyl-CoA and malate, up-regulated gluconeogenesis and citrate cycle metabolism, and promoted the biosynthesis of amino acids. Conclusions: The increased generation of ATP during fatty acid β-oxidation or citrate cycle and the up-regulation synthesis of microbial protein in rumen of beef cattle treated with CrPyr, may help decreased oxidative stress, regulate energy metabolism, and further improve the rumen fermentation characteristic under heat stress.

scholarly journals Microbial network, phylogenetic diversity and community membership in the active layer across a permafrost thaw gradient

2017 ◽  
Author(s):  
Rhiannon Mondav ◽  
Carmody K McCalley ◽  
Suzanne B Hodgkins ◽  
Steve Frolking ◽  
Scott R Saleska ◽  
...  
Keyword(s):  
Active Layer ◽  
Radiative Forcing ◽  
Phylogenetic Diversity ◽  
Microbial Interactions ◽  
Climate Feedback ◽  
Microbial Composition ◽  
Permafrost Thaw ◽  
Microbial Network ◽  
Alpha Beta ◽  
Thawing Permafrost

SummaryBiogenic production and release of methane (CH4) from thawing permafrost has the potential to be a strong source of radiative forcing. We investigated changes in the active layer microbial community of three sites representative of distinct permafrost thaw stages at a palsa mire in northern Sweden. The palsa sites with intact permafrost, and low radiative forcing signature had a phylogenetically clustered community dominated byAcidobacteriaandProteobacteria.The bog with thawing permafrost and low radiative forcing signature was dominated by hydrogenotrophic methanogens andAcidobacteria, had lower alpha diversity, and midrange phylogenetic clustering, characteristic of ecosystem disturbance affecting habitat filtering, shifting from palsa-like to fen-like at the waterline. The fen had no underlying permafrost, and the highest alpha, beta and phylogenetic diversity, was dominated byProteobacteriaandEuryarchaeota,and was significantly enriched in methanogens. The mire microbial network was modular with module cores consisting of clusters ofAcidobacteria, Euryarchaeota,orXanthomonodales.Loss of underlying permafrost with associated hydrological shifts correlated to changes in microbial composition, alpha, beta, and phylogenetic diversity associated with a higher radiative forcing signature. These results support the complex role of microbial interactions in mediating carbon budget changes and climate feedback in response to climate forcing.

scholarly journals Inhibition of Tumor Growth by Dietary Indole-3-Carbinol in a Prostate Cancer Xenograft Model May Be Associated with Disrupted Gut Microbial Interactions

Nutrients ◽  
2019 ◽  
Vol 11 (2) ◽  
pp. 467 ◽  
Author(s):  
Yanbei Wu ◽  
Robert Li ◽  
Haiqiu Huang ◽  
Arnetta Fletcher ◽  
Lu Yu ◽  
...  
Keyword(s):  
Prostate Cancer ◽  
Tumor Growth ◽  
Gut Microbiome ◽  
Species Interactions ◽  
Tumor Development ◽  
Xenograft Model ◽  
Microbial Interactions ◽  
Control Group ◽  
Rrna Gene ◽  
Microbial Composition

Accumulated evidence suggests that the cruciferous vegetables-derived compound indole-3-carbinol (I3C) may protect against prostate cancer, but the precise mechanisms underlying its action remain unclear. This study aimed to verify the hypothesis that the beneficial effect of dietary I3C may be due to its modulatory effect on the gut microbiome of mice. Athymic nude mice (5–7 weeks old, male, Balb c/c nu/nu) with established tumor xenografts were fed a basal diet (AIN-93) with or without 1 µmoles I3C/g for 9 weeks. The effects of dietary I3C on gut microbial composition and microbial species interactions were then examined by 16s rRNA gene-based sequencing and co-occurrence network analysis. I3C supplementation significantly inhibited tumor growth (p < 0.0001) and altered the structure of gut microbiome. The abundance of the phylum Deferribacteres, more specifically, Mucispirillum schaedleri, was significantly increased by dietary I3C. Additionally, I3C consumption also changed gut microbial co-occurrence patterns. One of the network modules in the control group, consisting of seven bacteria in family S-27, was positively correlated with tumor size (p < 0.009). Moreover, dietary I3C disrupted microbial interactions and altered this association between specific microbial network and tumor development. Our results unraveled complex relationships among I3C ingestion, gut microbiota, and prostate tumor development and may provide a novel insight into the mechanism for the chemopreventive effect of dietary I3C on prostate cancer.

scholarly journals Dietary resveratrol attenuated colitis and modulated gut microbiota in dextran sulfate sodium-treated mice

2020 ◽  
Vol 11 (1) ◽  
pp. 1063-1073 ◽  
Author(s):  
Fang Li ◽  
Yanhui Han ◽  
Xiaokun Cai ◽  
Min Gu ◽  
Jin Sun ◽  
...  
Keyword(s):  
Microbial Community ◽  
Gut Microbiota ◽  
Dextran Sulfate ◽  
Dextran Sulfate Sodium ◽  
Community Diversity ◽  
Microbial Composition ◽  
Microbial Community Diversity

Dietary resveratrol altered the microbial composition and restored microbial community diversity in colitic mice, which was associated with the suppression of colitis in the mice.

Microbial Community Analysis on Oxic-Settling-Anaerobic Process by Using PCR-DGGE Assay

2011 ◽  
Vol 255-260 ◽  
pp. 2934-2939 ◽  
Author(s):  
Jian Fang Wang ◽  
Qing Liang Zhao
Keyword(s):  
Microbial Community ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Community Analysis ◽  
Diversity Indices ◽  
Community Diversity ◽  
Microbial Community Analysis ◽  
Organic Loading Rate ◽  
Slight Variation ◽  
Biological Phosphorus Removal ◽  
Microbial Composition

In situ sludge reduction of the oxic-settling-anaerobic (OSA) process was investigated in this study and microbial community diversity in the system was analyzed by using a PCR-denaturing gradient gel electrophoresis (DGGE) approach. Comparing to the conventional activated sludge method, the production of excessive sludge in the OSA process was shown to be efficiently reduced by 44-50 % and the organic loading rate was observed to have a slight impact on sludge yield. As demonstrated by the slight variation of Shannon diversity indices (SDI), the dominant microbial composition remained stable in the OSA sludge with the increase ofNs. About 63% of clones represented by predominant bands in the DGGE pattern were affiliated with the subclass ofb-proteobacteria. A number of bacteria in the OSA process were phylogenetically related to uncultured bacteria isolated from enhanced biological phosphorus removal (EBPR) sludge.

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