Spatial and Species Variations of Bacterial Community Structure and Putative Function in Seagrass Rhizosphere Sediment

Seagrasses are an important part of the coral reef ecosystem, and their rhizosphere microbes are of great ecological importance. However, variations in diversity, composition, and potential functions of bacterial communities in the seagrass rhizosphere of coral reef ecosystems remain unclear. This study employed the high-throughput sequencing based on 16S rDNA gene sequences and functional annotation of prokaryotic taxa (FAPROTAX) analysis to investigate these variations based on seagrass species and sampling locations, respectively. Results demonstrated that the seagrass rhizosphere microbial community was mainly dominated by phylum Proteobacteria (33.47%), Bacteroidetes (23.33%), and Planctomycetes (12.47%), while functional groups were mainly composed of sulfate respiration (14.09%), respiration of sulfur compounds (14.24%), aerobic chemoheterotrophy (20.87%), and chemoheterotrophy (26.85%). Significant differences were evident in alpha diversity, taxonomical composition and putative functional groups based on seagrass species and sampling locations. Moreover, the core microbial community of all investigated samples was identified, accounting for 63.22% of all obtained sequences. Network analysis indicated that most microbes had a positive correlation (82.41%), and two module hubs (phylum Proteobacteria) were investigated. Furthermore, a significant positive correlation was found between the OTUs numbers obtained and the functional groups assigned for seagrass rhizosphere microbial communities (p < 0.01). Our result would facilitate future investigation of the function of seagrass rhizosphere microbes.

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Response and Dynamic Change of Microbial Community during Bioremediation of Uranium Tailings by Bacillus sp.

Minerals ◽

10.3390/min11090967 ◽

2021 ◽

Vol 11 (9) ◽

pp. 967

Author(s):

Chuiyun Tang ◽

Juan Zhong ◽

Ying Lv ◽

Xingyu Liu ◽

Yongbin Li ◽

...

Keyword(s):

Microbial Community ◽

Treatment Group ◽

High Throughput Sequencing ◽

Dynamic Change ◽

Alpha Diversity ◽

Control Group ◽

Bacillus Sp ◽

Remediation Strategies ◽

Abundance And Diversity ◽

Uranium Tailings

Bacillus sp. is widely used in the remediation of uranium-contaminated sites. However, little is known about the competitive process of microbial community in the environment during bioremediation. The bioremediation of uranium tailings using Bacillus sp. was explored, and the bacterial community was analyzed by high-throughput sequencing at different stages of remediation. Bacillus sp. reduced the leaching of uranium from uranium tailings. The lowest uranium concentration was 17.25 μg/L. Alpha diversity revealed that the abundance and diversity of microorganisms increased with the extension of the culture time. The microbial abundance and diversity were higher in the treatment group than in the control group. The dominant species at the phyla level were Firmicutes and Proteobacteria in the uranium tailings environment, whereas the phylum of Proteobacteria was significantly increased in the treatment group. Based on the genus level, the proportions of Arthrobacter, Rhodococcus and Paenarthrobacter decreased significantly, whereas those of Clostridium sp., Bacillus and Pseudomonas increased dramatically. Hence, the remediation of uranium contamination in the environment was due to the functional microorganisms, which gradually became the dominant strain in the treatment, such as Desulfotomaculum, Desulfosporporosinus, Anaerocolumna, Ruminiclostridium and Burkholderia. These findings provided a promising outlook of the potential for remediation strategies of soil contaminated by uranium. The dynamic characteristics of the microbial community are likely to provide a foundation for the bioremediation process in practice.

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Activated sludge microbial community responses to single-walled carbon nanotubes: community structure does matter

Water Science & Technology ◽

10.2166/wst.2015.095 ◽

2015 ◽

Vol 71 (8) ◽

pp. 1235-1240 ◽

Cited By ~ 6

Author(s):

Qiao Ma ◽

Yuanyuan Qu ◽

Wenli Shen ◽

Jingwei Wang ◽

Zhaojing Zhang ◽

...

Keyword(s):

Carbon Nanotubes ◽

Microbial Community ◽

Activated Sludge ◽

High Throughput Sequencing ◽

Alpha Diversity ◽

Single Walled Carbon Nanotubes ◽

Community Structures ◽

Single Walled Carbon ◽

Microbial Responses ◽

Walled Carbon Nanotubes

The ecological effects of carbon nanotubes (CNTs) have been a worldwide research focus due to their extensive release and accumulation in environment. Activated sludge acting as an important gathering place will inevitably encounter and interact with CNTs, while the microbial responses have been rarely investigated. Herein, the activated sludges from six wastewater treatment plants were acclimated and treated with single-walled carbon nanotubes (SWCNTs) under identical conditions. Illumina high-throughput sequencing was applied to in-depth analyze microbial changes and results showed SWCNTs differently perturbed the alpha diversity of the six groups (one increase, two decrease, three no change). Furthermore, the microbial community structures were shifted, and specific bacterial performance in each group was different. Since the environmental and operational factors were identical in each group, it could be concluded that microbial responses to SWCNTs were highly depended on the original community structures.

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Microbial predictors of environmental perturbations in coral reef ecosystems

10.1101/524173 ◽

2019 ◽

Author(s):

Bettina Glasl ◽

David G. Bourne ◽

Pedro R. Frade ◽

Torsten Thomas ◽

Britta Schaffelke ◽

...

Keyword(s):

Coral Reef ◽

Microbial Community ◽

Microbial Communities ◽

Community Assembly ◽

Environmental Parameters ◽

Diagnostic Value ◽

Free Living ◽

Environmental Pressures ◽

Coral Reef Ecosystems ◽

Community Data

AbstractIncorporation of microbial community data into environmental monitoring programs could improve prediction and management of environmental pressures. Coral reefs have experienced dramatic declines due to cumulative impacts of local and global stressors. Here we assess the utility of free-living (i.e. seawater and sediment) and host-associated (i.e. corals, sponges and macroalgae) microbiomes for diagnosing environmental perturbation based on their habitat-specificity, environmental sensitivity and uniformity. We show that the seawater microbiome has the greatest diagnostic value, with environmental parameters explaining 56% of the observed compositional variation and temporal successions being dominated by uniform community assembly patterns. Host-associated microbiomes, in contrast, were five-times less affected by the environment and their community assembly patterns were generally less uniform. Further, seawater microbial community data provided an accurate prediction on the environmental state, highlighting the diagnostic value of microorganisms and illustrating how long-term coral reef monitoring initiatives could be enhanced by incorporating assessments of microbial communities in seawater.ImportanceThe recent success in disease diagnostics based on the human microbiome has highlighted the utility of this approach for model systems. However, despite improved prediction and management of environmental pressures from the inclusion of microbial community data in monitoring programs, this approach has not previously been applied to coral reef ecosystems. Coral reefs are facing unprecedented pressure on a local and global scale, and sensitive and rapid markers for ecosystem stress are urgently needed to underpin effective management and restoration strategies. In this study, we performed the first assessment of the diagnostic value of multiple free-living and host-associated reef microbiomes to infer the environmental state of coral reef ecosystems. Our results reveal that free-living microbial communities have a higher potential to infer environmental parameters than host-associated microbial communities due to their higher determinacy and environmental sensitivity. We therefore recommend timely integration of microbial sampling into current coral reef monitoring initiatives.

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Long-Term Effects of Perfluorooctanoic Acid (PFOA) and Perfluorooctane Sulfonic Acid (PFOS) on Soil Microbial Community

10.21203/rs.3.rs-190229/v1 ◽

2021 ◽

Author(s):

Wan Tao ◽

Rui Xu ◽

Hanzhi Lin ◽

Duanyi Huang ◽

Pingzhou Su ◽

...

Keyword(s):

Microbial Community ◽

Microbial Communities ◽

High Throughput Sequencing ◽

Gene Prediction ◽

Soil Microbial Communities ◽

Alpha Diversity ◽

Perfluorooctanoic Acid ◽

Long Term Effects ◽

Soil Microbial

Abstract The extensive application of perfluoroalkyl and polyfluoroalkyl substances (PFASs) causes their frequent detection in various environments. Nevertheless, the effects of PFASs exposure on environmental microorganisms still remain unknown. In current work, two typical PFASs, perfluorooctanoic acid (PFOA) and perfluorooctanesulfonic acid (PFOS), are selected to investigate their long-term effects on soil microbes. Microbial community structure and diversity were investigated by high-throughput sequencing and multiple statistical methods. Under 90-days of exposure, PFAS treatments increased the alpha-diversity of soil microbial communities with PFOS treatment, followed by PFOA treatment. The long-term exposure of PFASs substantially changed the compositions of soil microbial communities. The most abundant phylum Proteobacteria decreased from 82.9% (without amended PFASs) to 62.1% (with PFOA treatment) and 77.8% (with PFOS treatment). As a comparison, the relative abundance of Bacteroidetes, Chloroflexi, Acidobacteria, and Ignavibacteriae increased in the PFOA or PFOS groups. Comparative co-occurrence networks were constructed to investigate the biotic interactions in the two treatments. It was found that most taxonomy nodes in the PFOA and PFOS networks were associated with the genus Hydrogenophaga and Pseudoxanthomonas, respectively. The LEfSe analysis identified a set of core taxonomies (e.g., Azospirillum, Methyloversatilis, Ancylobacter, Hydrogenophaga, and Methylomonas) in the soil microbial communities and suggested their different preferences to PFAS exposures. Functional gene prediction suggested that the microbial metabolism processes, such as nucleotide transport and metabolism, cell motility, carbohydrate transport and metabolism, energy production and conversion, and secondary metabolites biosynthesis transport and catabolism, might be significantly inhibited under PFAS exposure, which may further affect soil ecological services.

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Tibetan wild asses (Equus Kiang) were superior to domestic donkeys (Equus Asinus) in terms of the composition and function of gut microbial community

10.21203/rs.2.14192/v1 ◽

2019 ◽

Author(s):

Hongjin Liu ◽

Xinquan Zhao ◽

Shixiao Xu ◽

Liang Zhao ◽

Linyong Hu ◽

...

Keyword(s):

Microbial Community ◽

Gut Microbiota ◽

Intestinal Microbiota ◽

Species Interactions ◽

High Throughput Sequencing ◽

Microbial Community Composition ◽

Alpha Diversity ◽

Significant Difference ◽

And Function ◽

Gut Microbial Community

Abstract Background: Tibetan wild asses are the only wild species of perissodactyls on the Qinghai-Tibetan Plateau, and appears on the International Union for Conversation of Nature (IUCN) 2012 Red List of threatened species. The gut microbiota has a great effect on the health and nutrition of the host, however, scant research is available on the characteristics of their intestinal microbiota. Therefor, understanding the gut microbita composition and function of TWAs can provide a theoretical for the situ conservation of wild animals in the future. Results: To characterize its composition and function, we analyzed the intestinal microbiota of wild asses and domestic donkeys by high-throughput sequencing of the 16s rDNA regions. No significant difference in alpha diversity was detected between these two groups. Beta diversity showed that the bacterial community structure of wild asses was acutely different from domestic donkeys. At the phylum level, the two dominant phyla of Bacteroidetes and Firmcutes in wild asses were significantly higher than that in domestic donkeys. At the genus level, Ruminococcaceae_NK4A214 , Phascolarctobacterium , Coprostanoligenes_group , Lachnospiraceae_XPB1014_group and Akkermansia in wild asses were significantly higher than domestic donkeys. Moreover, statistical comparisons showed that 40 different metabolic pathways exhibited significant differences . Among them, 29 pathways had richer concentrations in wild asses than domestic donkeys, mainly amino acid metabolism, carbohydrate metabolism, and energy metabolism. Of note, network analysis showed that wild asses harbored a relatively more complex bacterial network than domestic donkeys, possibly reflecting the specific niche adaption of gut bacterial communities through species interactions. Conclusions: Wild asses were superior to that of domestic in gut microbial community composition and function. For wild animal conservation, wild asses are more suitable to survive in wild than to be domesticated or captive. Key words: Tibetan wild asses, domestic donkeys, 16S ribosomal RNA gene, gut microbiota

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Comparative Analysis of Fecal Microbiota of Grazing Mongolian Cattle from Different Regions in Inner Mongolia, China

Animals ◽

10.3390/ani11071938 ◽

2021 ◽

Vol 11 (7) ◽

pp. 1938

Author(s):

Han Aricha ◽

Huasai Simujide ◽

Chunjie Wang ◽

Jian Zhang ◽

Wenting Lv ◽

...

Keyword(s):

Community Structure ◽

Microbial Community ◽

Gut Microbiota ◽

Inner Mongolia ◽

Alpha Diversity ◽

Fecal Microbiota ◽

Composition Analysis ◽

Geographical Factors ◽

Rrna Sequencing ◽

Xilingol Grassland

Mongolian cattle from China have strong adaptability and disease resistance. We aimed to compare the gut microbiota community structure and diversity in grazing Mongolian cattle from different regions in Inner Mongolia and to elucidate the influence of geographical factors on the intestinal microbial community structure. We used high throughput 16S rRNA sequencing to analyze the fecal microbial community and diversity in samples from 60 grazing Mongolian cattle from Hulunbuir Grassland, Xilingol Grassland, and Alxa Desert. A total of 2,720,545 high-quality reads and sequences that were 1,117,505,301 bp long were obtained. Alpha diversity among the three groups showed that the gut microbial diversity in Mongolian cattle in the grasslands was significantly higher than that in the desert. The dominant phyla were Firmicutes and Bacteroidetes, whereas Verrucomicrobia presented the highest abundance in the gut of cattle in the Alxa Desert. The gut bacterial communities in cattle from the grasslands versus the Alxa Desert were distinctive, and those from the grasslands were closely clustered. Community composition analysis revealed significant differences in species diversity and richness. Overall, the composition of the gut microbiota in Mongolian cattle is affected by geographical factors. Gut microbiota may play important roles in the geographical adaptations of Mongolian cattle.

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Disentangling Responses of the Subsurface Microbiome to Wetland Status and Implications for Indicating Ecosystem Functions

Microorganisms ◽

10.3390/microorganisms9020211 ◽

2021 ◽

Vol 9 (2) ◽

pp. 211

Author(s):

Jie Gao ◽

Miao Liu ◽

Sixue Shi ◽

Ying Liu ◽

Yu Duan ◽

...

Keyword(s):

Microbial Community ◽

High Throughput Sequencing ◽

Carbon Fixation ◽

Microbial Community Composition ◽

Ecosystem Functions ◽

Microbial Composition ◽

Wetland Ecosystems ◽

Soil Microbial ◽

Geochemical Properties ◽

Microbial Groups

In this study, we analyzed microbial community composition and the functional capacities of degraded sites and restored/natural sites in two typical wetlands of Northeast China—the Phragmites marsh and the Carex marsh, respectively. The degradation of these wetlands, caused by grazing or land drainage for irrigation, alters microbial community components and functional structures, in addition to changing the aboveground vegetation and soil geochemical properties. Bacterial and fungal diversity at the degraded sites were significantly lower than those at restored/natural sites, indicating that soil microbial groups were sensitive to disturbances in wetland ecosystems. Further, a combined analysis using high-throughput sequencing and GeoChip arrays showed that the abundance of carbon fixation and degradation, and ~95% genes involved in nitrogen cycling were increased in abundance at grazed Phragmites sites, likely due to the stimulating impact of urine and dung deposition. In contrast, the abundance of genes involved in methane cycling was significantly increased in restored wetlands. Particularly, we found that microbial composition and activity gradually shifts according to the hierarchical marsh sites. Altogether, this study demonstrated that microbial communities as a whole could respond to wetland changes and revealed the functional potential of microbes in regulating biogeochemical cycles.

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Experimental infection with the hookworm, Necator americanus, is associated with stable gut microbial diversity in human volunteers with relapsing multiple sclerosis

BMC Biology ◽

10.1186/s12915-021-01003-6 ◽

2021 ◽

Vol 19 (1) ◽

Author(s):

Timothy P. Jenkins ◽

David I. Pritchard ◽

Radu Tanasescu ◽

Gary Telford ◽

Marina Papaiakovou ◽

...

Keyword(s):

Multiple Sclerosis ◽

Experimental Infection ◽

High Throughput Sequencing ◽

Alpha Diversity ◽

Placebo Treatment ◽

Sequencing Data ◽

Faecal Microbiota ◽

Microbial Composition ◽

Necator Americanus ◽

Human Volunteers

Abstract Background Helminth-associated changes in gut microbiota composition have been hypothesised to contribute to the immune-suppressive properties of parasitic worms. Multiple sclerosis is an immune-mediated autoimmune disease of the central nervous system whose pathophysiology has been linked to imbalances in gut microbial communities. Results In the present study, we investigated, for the first time, qualitative and quantitative changes in the faecal bacterial composition of human volunteers with remitting multiple sclerosis (RMS) prior to and following experimental infection with the human hookworm, Necator americanus (N+), and following anthelmintic treatment, and compared the findings with data obtained from a cohort of RMS patients subjected to placebo treatment (PBO). Bacterial 16S rRNA high-throughput sequencing data revealed significantly decreased alpha diversity in the faecal microbiota of PBO compared to N+ subjects over the course of the trial; additionally, we observed significant differences in the abundances of several bacterial taxa with putative immune-modulatory functions between study cohorts. Parabacteroides were significantly expanded in the faecal microbiota of N+ individuals for which no clinical and/or radiological relapses were recorded at the end of the trial. Conclusions Overall, our data lend support to the hypothesis of a contributory role of parasite-associated alterations in gut microbial composition to the immune-modulatory properties of hookworm parasites.

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