Microbial Community Composition of Mine Wastes in Cornwall and West Devon (UK)

2017 ◽  
Vol 262 ◽  
pp. 290-293
Author(s):  
Tomasa Sbaffi ◽  
Angus Buckling ◽  
Christopher G. Bryan
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Microbial Community Structure ◽  
Microbial Community Composition ◽  
Geochemical Data ◽  
Mine Wastes ◽  
Candidate Division ◽  
And Control ◽  
Controls Cluster ◽  
Total Diversity

Mine wastes and control soils from twelve sites around Cornwall and West Devon (UK) were analysed for microbial community structure, pH and readily extractible metals (an indication of mobility). About 70% of total diversity observed was constituted by six phyla (Acidobacteria, Chloroflexi, Planctomycetes, Proteobacteria, Verrucomicrobia, and candidate division AD3). Microbial community structure revealed patterns of distribution that mostly differed between waste samples and controls. Cluster analysis of the geochemical data (pH and readily extractible metals) indicated the presence of four groups; two groups of controls and two of samples defined by similar features. pH appeared to correlate with the portion of shared community.

scholarly journals Antibiotic resistome and microbial community structure during anaerobic co-digestion of food waste, paper and cardboard

2020 ◽  
Vol 96 (2) ◽  
Author(s):  
Kärt Kanger ◽  
Nigel G H Guilford ◽  
HyunWoo Lee ◽  
Camilla L Nesbø ◽  
Jaak Truu ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Solid State ◽  
Food Waste ◽  
Microbial Community Structure ◽  
Microbial Community Composition ◽  
Microbial Community Analysis ◽  
Waste Paper ◽  
Rrna Gene ◽  
Significant Shift

ABSTRACT Solid organic waste is a significant source of antibiotic resistance genes (ARGs) and effective treatment strategies are urgently required to limit the spread of antimicrobial resistance. Here, we studied ARG diversity and abundance as well as the relationship between antibiotic resistome and microbial community structure within a lab-scale solid-state anaerobic digester treating a mixture of food waste, paper and cardboard. A total of 10 samples from digester feed and digestion products were collected for microbial community analysis including small subunit rRNA gene sequencing, total community metagenome sequencing and high-throughput quantitative PCR. We observed a significant shift in microbial community composition and a reduction in ARG diversity and abundance after 6 weeks of digestion. ARGs were identified in all samples with multidrug resistance being the most abundant ARG type. Thirty-two per cent of ARGs detected in digester feed were located on plasmids indicating potential for horizontal gene transfer. Using metagenomic assembly and binning, we detected potential bacterial hosts of ARGs in digester feed, which included Erwinia, Bifidobacteriaceae, Lactococcus lactis and Lactobacillus. Our results indicate that the process of sequential solid-state anaerobic digestion of food waste, paper and cardboard tested herein provides a significant reduction in the relative abundance of ARGs per 16S rRNA gene.

scholarly journals Coupled changes in soil organic carbon fractions and microbial community composition in urban and suburban forests

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Xueying Zhang ◽  
Xiaomei Chen ◽  
Muying Liu ◽  
Zhanying Xu ◽  
Hui Wei
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Organic Carbon ◽  
Soil Organic Carbon ◽  
Community Composition ◽  
Microbial Community Structure ◽  
Soil Microorganisms ◽  
Microbial Community Composition ◽  
Soil C ◽  
Suburban Forests

Abstract Climate change and rapid urbanization have greatly impacted urban forest ecosystems and the carbon (C) cycle. To assess the effects of urbanization on forest soil C and soil microorganisms, six natural forests in a highly-urbanized region were selected as the research objects. Soil samples were collected to investigate the content and fractions of the soil organic carbon (SOC), as well as the soil microbial community composition. The results showed that the SOC content and fractions were substantially lower in the urban forests than in the suburban forests. Meanwhile, the total amount of phospholipid fatty acids (PLFAs) at suburban sites was twice more than that at urban sites, with shifts in microbial community structure. The potential differences in C inputs and nutrient limitation in urban forests may aggravate the low quantity and quality of SOC and consequently impact microbial community abundance and structure. Variation in microbial community structure was found to explain the loss of soil C pools by affecting the C inputs and promoting the decomposition of SOC. Therefore, the coupled changes in SOC and soil microorganisms induced by urbanization may adversely affect soil C sequestration in subtropical forests.

Spatial variation in microbial community structure, richness, and diversity in an alluvial aquifer

2012 ◽  
Vol 58 (9) ◽  
pp. 1135-1151 ◽  
Author(s):  
P.G. Medihala ◽  
J.R. Lawrence ◽  
G.D.W. Swerhone ◽  
D.R. Korber
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Spatial Variability ◽  
Microbial Communities ◽  
Microbial Community Structure ◽  
Gel Electrophoresis ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Microbial Community Composition ◽  
Alluvial Aquifer ◽  
Gradient Gel Electrophoresis

Relatively little is known regarding the spatial variability of microbial communities in aquifers where well fouling is an issue. In this study 2 water wells were installed in an alluvial aquifer located adjacent to the North Saskatchewan River and an associated piezometer network developed to facilitate the study of microbial community structure, richness, and diversity. Carbon utilization data analysis revealed reduced microbial activity in waters collected close to the wells. Functional PCR and quantitative PCR analysis indicated spatial variability in the potential for iron-, sulphate-, and nitrate-reducing activity at all locations in the aquifer. Denaturing gradient gel electrophoresis analysis of aquifer water samples using principal components analyses indicated that the microbial community composition was spatially variable, and denaturing gradient gel electrophoresis sequence analysis revealed that bacteria belonging to the genera Acidovorax , Rhodobacter , and Sulfuricurvum were common throughout the aquifer. Shannon’s richness (H′) and Pielou’s evenness (J′) indices revealed a varied microbial diversity (H′ = 1.488–2.274) and an even distribution of microbial communities within the aquifer (J′ = 0.811–0.917). Overall, these analyses revealed that the aquifer’s microbial community varied spatially in terms of composition, richness, and metabolic activity. Such information may facilitate the diagnosis, prevention, and management of fouling.

Analysis of Microbial Community Structure in an Ecological Remediation Process of the River Water

2013 ◽  
Vol 864-867 ◽  
pp. 339-342
Author(s):  
Ji Hua Wang ◽  
Jan Fei Guan ◽  
Di Cui ◽  
Ang Li ◽  
Xiang Liu ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Microbial Community Structure ◽  
Microbial Community Composition ◽  
Environmental Parameters ◽  
Molecular Data ◽  
Vital Role ◽  
Structure Changes ◽  
And Function ◽  
Ecological Remediation

In urban river ecosystem, microorganism plays a vital role in maintaining ecological balance. Microbial community structure changes triggered with the river remediation progress. However, the change process in different sites from ecological remediation river has not been explored deeply before. We used polymerase chain reaction-denaturing gradient gelelectrophoresis (PCR-DGGE) to examine bacterial diversity of ecological remediated river in Changzhou City, China, and with rarely and severely contaminated rivers which from the same regions as reference. Molecular data were related to environmental parameters through multivariate analysis to investigate the relationship between potential impact of water quality and microbial community structure. As the ecological remediated river, NH3-N and TP were the important environmental variables influencing microbial community composition. After remediation, the microbial community structure showed a good consistency in each site, the microbial diversity and function were greatly improved, too.

scholarly journals Honeybee microbiome is stabilized in the presence of propolis

2020 ◽  
Vol 16 (5) ◽  
pp. 20200003 ◽  
Author(s):  
Perot Saelao ◽  
Renata S. Borba ◽  
Vincent Ricigliano ◽  
Marla Spivak ◽  
Michael Simone-Finstrom
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Gut Microbiota ◽  
Significant Role ◽  
Microbial Community Structure ◽  
Microbial Community Composition ◽  
Taxonomic Diversity ◽  
Honeybee Colony ◽  
Gut Symbionts ◽  
Microbial Symbionts

Honeybees have developed many unique mechanisms to help ensure the proper maintenance of homeostasis within the hive. One method includes the collection of chemically complex plant resins combined with wax to form propolis, which is deposited throughout the hive. Propolis is believed to play a significant role in reducing disease load in the colony due to its antimicrobial and antiseptic properties. However, little is known about how propolis may interact with bee-associated microbial symbionts, and if propolis alters microbial community structure. In this study, we found that propolis appears to maintain a stable microbial community composition and reduce the overall taxonomic diversity of the honeybee microbiome. Several key members of the gut microbiota were significantly altered in the absence of propolis, suggesting that it may play an important role in maintaining favourable abundance and composition of gut symbionts. Overall, these findings suggest that propolis may help to maintain honeybee colony microbial health by limiting changes to the overall microbial community.

scholarly journals Microbial community structure analysis in Acer palmatum bark and isolation of novel bacteria IAD-21 of the candidate division FBP

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7876
Author(s):  
Kazuki Kobayashi ◽  
Hideki Aoyagi
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
16S Rdna ◽  
Microbial Community Structure ◽  
Phylogenetic Analyses ◽  
Tree Bark ◽  
Molecular Phylogenetic ◽  
Candidate Division ◽  
Promising Source ◽  
Uncultured Microorganisms

Background The potential of unidentified microorganisms for academic and other applications is limitless. Plants have diverse microbial communities associated with their biomes. However, few studies have focused on the microbial community structure relevant to tree bark. Methods In this report, the microbial community structure of bark from the broad-leaved tree Acer palmatum was analyzed. Both a culture-independent approach using polymerase chain reaction (PCR) amplification and next generation sequencing, and bacterial isolation and sequence-based identification methods were used to explore the bark sample as a source of previously uncultured microorganisms. Molecular phylogenetic analyses based on PCR-amplified 16S rDNA sequences were performed. Results At the phylum level, Proteobacteria and Bacteroidetes were relatively abundant in the A. palmatum bark. In addition, microorganisms from the phyla Acidobacteria, Gemmatimonadetes, Verrucomicrobia, Armatimonadetes, and candidate division FBP, which contain many uncultured microbial species, existed in the A. palmatum bark. Of the 30 genera present at relatively high abundance in the bark, some genera belonging to the phyla mentioned were detected. A total of 70 isolates could be isolated and cultured using the low-nutrient agar media DR2A and PE03. Strains belonging to the phylum Actinobacteria were isolated most frequently. In addition, the newly identified bacterial strain IAP-33, presumed to belong to Acidobacteria, was isolated on PE03 medium. Of the isolated bacteria, 44 strains demonstrated less than 97% 16S rDNA sequence-similarity with type strains. Molecular phylogenetic analysis of IAD-21 showed the lowest similarity (79%), and analyses suggested it belongs to candidate division FBP. Culture of the strain IAD-21 was deposited in Japan Collection of Microorganisms (JCM) and Deutsche Sammlung von Mikroorganismen und Zellkulturen (DSMZ) as JCM 32665 and DSM 108248, respectively. Discussion Our results suggest that a variety of uncultured microorganisms exist in A. palmatum bark. Microorganisms acquirable from the bark may prove valuable for academic pursuits, such as studying microbial ecology, and the bark might be a promising source of uncultured bacterial isolates.

scholarly journals Mercury Methylating Microbial Community Structure in Boreal Wetlands Explained by Local Physicochemical Conditions

2021 ◽  
Vol 8 ◽  
Author(s):  
Jingying Xu ◽  
Van Liem-Nguyen ◽  
Moritz Buck ◽  
Stefan Bertilsson ◽  
Erik Björn ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Microbial Community Structure ◽  
Current Knowledge ◽  
Microbial Community Composition ◽  
Amplicon Sequencing ◽  
Nutrient Concentrations ◽  
Molecular Barcoding ◽  
Physicochemical Conditions ◽  
Wide Range

The potent neurotoxin methylmercury (MeHg) is a major concern due to its negative effects on wildlife and human health. Boreal wetlands play a crucial role in Hg cycling on a global scale, and therefore, it is crucial to understand the biogeochemical processes involved in MeHg formation in this landscape element. By combining high-throughput hgcA amplicon sequencing with molecular barcoding, we reveal diverse clades of potential HgII methylators in a wide range of wetland soils. Among Bacteria, Desulfuromonadota (14% of total reads), Desulfurobacterota_A, and Desulfurobacterota (up to 6% of total reads), previously classified as Deltaproteobacteria, were important members of the hgcA+ microbial community in the studied wetlands. We also identified Actinobacteriota (9.4% of total reads), Bacteroidota (2% of total reads), and Firmicutes (1.2% of total reads) as members of the hgcA+ microbial community. Within Archaea, Methanosarcinales represented up to 2.5% of the total reads. However, up to half of the hgcA+ community could not be resolved beyond domain Bacteria. Our survey also shows that local physicochemical conditions, such as pH, nutrient concentrations, water content, and prevailing redox states, are important for shaping the hgcA+ microbial community structure across the four studied wetlands. Furthermore, we observed a significant correlation between HgII methylation rate constants and the structure of the hgcA+ microbial community. Our findings expand the current knowledge on the hgcA+ microbial community composition in wetlands and the physicochemical factors underpinning spatial heterogeneity in such communities.

scholarly journals Early Effect of Pine Biochar on Peach-Tree Planting on Microbial Community Composition and Enzymatic Activity

2021 ◽  
Vol 11 (4) ◽  
pp. 1473
Author(s):  
Juan Pablo Frene ◽  
Mattie Frazier ◽  
Shuang Liu ◽  
Bernadette Clark ◽  
Michael Parker ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Microbial Community Structure ◽  
Prunus Persica ◽  
Microbial Community Composition ◽  
Sandy Soils ◽  
Tree Planting ◽  
Dynamic Surface ◽  
Early Effect ◽  
Structure And Functions

Biochar offers several benefits as a soil amendment, including increased soil fertility, carbon sequestration, and water-holding capacity in nutrient-poor soils. In this study, soil samples with and without biochar additives were collected for two consecutive years from an experimental field plot to examine its effect on the microbial community structure and functions in sandy soils under peach-trees (Prunus persica). The four treatments evaluated consisted of two different rates of biochar incorporated into the soil (5%, and 10%, v/v), one “dynamic” surface application of biochar, and a 0% biochar control. Fatty acid methyl ester (FAME) analysis was used to assess the microbial community structure, and enzyme activities involved in C, N, P, and S nutrient cycling were used as a means of assessing soil functionality. Total FAME and bacterial indicators increased by 18% and 12%, respectively, in the 10% incorporated and 5% surface applied treatments. Biochar applications increased β-glucosaminidase and arylsulfatase activities, 5–30% and 12–46%, respectively. β-glucosidase and acid phosphatase activities decreased by approximately 18–35% and 5–22% in the 0–15 cm soils. The overall results suggest that biochar’s addition to the sandy soils stimulated microbial activity, contributing to the increased mean weight diameter (MWD), C sequestration, and consequential soil health. The changes in microbial community structure and functions may be useful predictors of modifications in soil organic matter (SOM) dynamics due to the long-term application of pine biochar in these systems.

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