scholarly journals Assessment of microbial communities in Nakivubo wetland and its catchment areas in Lake Victoria Basin, Uganda

2020 ◽  
Author(s):  
Bernard N. Kanoi ◽  
Maribet Gamboa ◽  
Doris Ngonzi ◽  
Thomas G. Egwang
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Microbial Diversity ◽  
Microbial Community Structure ◽  
Lake Victoria ◽  
Rrna Gene ◽  
Lake Victoria Basin ◽  
Structure Changes ◽  
Catchment Areas ◽  
Polluted Sites

AbstractMicrobial community structure changes are key in detecting and characterizing the impacts of anthropogenic activities on aquatic ecosystems. Here, we evaluated the effect of river pollution of industrial and urban sites on the microbial community composition and distribution in the Nakivubo wetland and its catchment areas in Lake Victoria basin, Uganda. Samples were collected from two industrial and one urban polluted sites and the microbial diversity was analyzed based on a 16S rRNA gene clone library. Differences in microbial diversity and community structure were observed at different sampling points. Bacteria associated with bioremediation were found in sites receiving industrial waste, while a low proportion of important human-pathogenic bacteria were seen in urban polluted sites. While Escherichia spp. was the most dominant genus of bacteria for all sites, three unique bacteria, Bacillus sp., Pseudomonas sp., Thermomonas sp., which have been reported to transform contaminants such as heavy metals and hydrocarbons (such as oils) by their metabolic pathways were also identified. Our results may serve as a basis for further studies assessing microbial community structure changes among polluted sites at Nakivubo Water Channel for management and monitoring. The diversity of natural microbial consortia could also be a rich bioprospecting resource for novel industrial enzymes, medicinal and bioactive compounds.

scholarly journals Burial depth of anode affected the bacterial community structure of sediment microbial fuel cells

2019 ◽  
Vol 25 (6) ◽  
pp. 871-877 ◽  
Author(s):  
Yi-cheng Wu ◽  
Hong-jie Wu ◽  
Hai-yan Fu ◽  
Zhineng Dai ◽  
Ze-jie Wang
Keyword(s):  
Fuel Cells ◽  
Community Structure ◽  
Microbial Community ◽  
Microbial Diversity ◽  
Microbial Community Structure ◽  
Contaminated Soils ◽  
Microbial Fuel Cells ◽  
Rrna Gene ◽  
Burial Depth ◽  
Operational Taxonomic Units

Sediment microbial fuel cells (SMFCs) are attractive devices to in situ power environmental monitoring sensors and bioremediate contaminated soils/sediments. Burial depth of the anode was verified to affect the performance of SMFCs. The present research evaluated the differences in microbial community structure of anodic biofilms located at different depth. It was demonstrated that both microbial diversity and community structure of anodic biofilms were influenced by the depth of anode location. Microbial diversity decreased with increased anodic depth. The number of the operational taxonomic units (OTUs) was determined as 1438 at the anode depth of 5 cm, which reduced to 1275 and 1005 at 10 cm and 15 cm, respectively. Cluster analysis revealed that microbial communities of 5 cm and 10 cm were clustered together, separated from the original sediment and 15 cm. Proteobacteria was the predominant phylum in all samples, followed by Bacteroidetes and Firmicutes. Beta-and Gamma-proteobacteria were the most abundant classes. A total of 23 OTUs showed high identity to 16S rRNA gene of exoelectrogens such as Geobacter and Pseudomonas. The present results provided insights into the effects of anode depth on the performance of SMFC from the perspectives of microbial community structure.

scholarly journals Analysis of the Microbial Community Structure in Coastal Sediment of an Ascidian Farm in South Korea through 16S rRNA Gene Amplicon Sequencing

2021 ◽  
Vol 10 (30) ◽  
Author(s):  
Ilwon Jeong ◽  
Jong-Oh Kim ◽  
Seokjin Yoon ◽  
Kyunghoi Kim
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Microbial Community Structure ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Content Type ◽  
Styela Clava ◽  
Structure Changes

Aquaculture places contamination pressure on the coastal environment. We investigated the microbial community structure changes in sediment in an ascidian Styela clava farm. Data profiling of the 16S rRNA gene amplicon sequence shows that the microbial diversity of sediment in the Styela clava farm is dominated by Proteobacteria phyla (relative abundance, 95.34 to 97.85%).

scholarly journals Stochastic Assembly Leads to Alternative Communities with Distinct Functions in a Bioreactor Microbial Community

mBio ◽  
2013 ◽  
Vol 4 (2) ◽  
Author(s):  
Jizhong Zhou ◽  
Wenzong Liu ◽  
Ye Deng ◽  
Yi-Huei Jiang ◽  
Kai Xue ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Microbial Diversity ◽  
Microbial Community Structure ◽  
Community Assembly ◽  
Ecosystem Functioning ◽  
Dominant Role ◽  
Microbial Biodiversity ◽  
Stochastic Assembly

ABSTRACTThe processes and mechanisms of community assembly and its relationships to community functioning are central issues in ecology. Both deterministic and stochastic factors play important roles in shaping community composition and structure, but the connection between community assembly and ecosystem functioning remains elusive, especially in microbial communities. Here, we used microbial electrolysis cell reactors as a model system to examine the roles of stochastic assembly in determining microbial community structure and functions. Under identical environmental conditions with the same source community, ecological drift (i.e., initial stochastic colonization) and subsequent biotic interactions created dramatically different communities with little overlap among 14 identical reactors, indicating that stochastic assembly played dominant roles in determining microbial community structure. Neutral community modeling analysis revealed that deterministic factors also played significant roles in shaping microbial community structure in these reactors. Most importantly, the newly formed communities differed substantially in community functions (e.g., H2production), which showed strong linkages to community structure. This study is the first to demonstrate that stochastic assembly plays a dominant role in determining not only community structure but also ecosystem functions. Elucidating the links among community assembly, biodiversity, and ecosystem functioning is critical to understanding ecosystem functioning, biodiversity preservation, and ecosystem management.IMPORTANCEMicroorganisms are the most diverse group of life known on earth. Although it is well documented that microbial natural biodiversity is extremely high, it is not clear why such high diversity is generated and maintained. Numerous studies have established the roles of niche-based deterministic factors (e.g., pH, temperature, and salt) in shaping microbial biodiversity, the importance of stochastic processes in generating microbial biodiversity is rarely appreciated. Moreover, while microorganisms mediate many ecosystem processes, the relationship between microbial diversity and ecosystem functioning remains largely elusive. Using a well-controlled laboratory system, this study provides empirical support for the dominant role of stochastic assembly in creating variations of microbial diversity and the first explicit evidence for the critical role of community assembly in influencing ecosystem functioning. The results presented in this study represent important contributions to the understanding of the mechanisms, especially stochastic processes, involved in shaping microbial biodiversity.

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 Natural Attenuation of Mn(II) in Metal Refinery Wastewater: Microbial Community Structure Analysis and Isolation of a New Mn(II)-Oxidizing Bacterium Pseudomonas sp. SK3

Water ◽  
2019 ◽  
Vol 11 (3) ◽  
pp. 507 ◽  
Author(s):  
Santisak Kitjanukit ◽  
Kyohei Takamatsu ◽  
Naoko Okibe
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Structure Analysis ◽  
Microbial Community Structure ◽  
Natural Attenuation ◽  
Rrna Gene ◽  
Pseudomonas Sp ◽  
Refinery Wastewater ◽  
Pipe Surface

Natural attenuation of Mn(II) was observed inside the metal refinery wastewater pipeline, accompanying dark brown-colored mineralization (mostly MnIVO2 with some MnIII2O3 and Fe2O3) on the inner pipe surface. The Mn-deposit hosted the bacterial community comprised of Hyphomicrobium sp. (22.1%), Magnetospirillum sp. (3.2%), Geobacter sp. (0.3%), Bacillus sp. (0.18%), Pseudomonas sp. (0.03%), and non-metal-metabolizing bacteria (74.2%). Culture enrichment of the Mn-deposit led to the isolation of a new heterotrophic Mn(II)-oxidizer Pseudomonas sp. SK3, with its closest relative Ps. resinovorans (with 98.4% 16S rRNA gene sequence identity), which was previously unknown as an Mn(II)-oxidizer. Oxidation of up to 100 mg/L Mn(II) was readily initiated and completed by isolate SK3, even in the presence of high contents of MgSO4 (a typical solute in metal refinery wastewaters). Additional Cu(II) facilitated Mn(II) oxidation by isolate SK3 (implying the involvement of multicopper oxidase enzyme), allowing a 2-fold greater Mn removal rate, compared to the well-studied Mn(II)-oxidizer Ps. putida MnB1. Poorly crystalline biogenic birnessite was formed by isolate SK3 via one-electron transfer oxidation, gradually raising the Mn AOS (average oxidation state) to 3.80 in 72 h. Together with its efficient in vitro Mn(II) oxidation behavior, a high Mn AOS level of 3.75 was observed with the pipeline Mn-deposit sample collected in situ. The overall results, including the microbial community structure analysis of the pipeline sample, suggest that the natural Mn(II) attenuation phenomenon was characterized by robust in situ activity of Mn(II) oxidizers (including strain SK3) for continuous generation of Mn(IV). This likely synergistically facilitated chemical Mn(II)/Mn(IV) synproportionation for effective Mn removal in the complex ecosystem established in this artificial pipeline structure. The potential utility of isolate SK3 is illustrated for further industrial application in metal refinery wastewater treatment processes.

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.

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.

PSIX-6 Dietary crude protein modifies fecal microbial populations independent of feed efficiency status in dairy cows

2021 ◽  
Vol 99 (Supplement_3) ◽  
pp. 439-440
Author(s):  
Alvaro Morales ◽  
Leticia Campos ◽  
Jacquelyn Prestegaard ◽  
Kayla Alward ◽  
Connor Owens ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Microbial Community Structure ◽  
Feed Intake ◽  
Feed Efficiency ◽  
Crude Protein ◽  
High Energy ◽  
Repeated Measurements ◽  
Rrna Gene ◽  
Fecal Microbiome

Abstract Understanding the composition and structure of the fecal microbial community may provide insight into bacterial adaptation to dietary changes in cattle. The aim of this study was to determine relationships among the fecal microbiome, residual feed intake (RFI) and residual net energy intake (REI) with diets varying in crude protein (CP). Four Holstein lactating cows (806 ± 38 kg of BW) were randomly assigned to one of two treatments (LOW: 13.2% and BASE:16.6% CP) in a crossover design (2 periods of 18 d each). Cows were 260 ± 62 days in milk (DIM) and averaged 26.5 ± 12.0 kg milk yield (MY). Diets were formulated to meet animal needs. Individual feed intake measured by a Calan Gate system was used to calculate daily dry matter intake (DMI). BW, MY and milk components were also measured daily. A linear mixed model with repeated measurements over time was used to evaluate diet effect on DMI, MY, RFI and REI in SAS. Individual fecal samples were collected at the end of each period and extracted DNA was subject to 16S rRNA gene deep amplicon sequencing. Operational Taxonomic Units (OTU) were obtained using ≥97% similarity (SILVA database) and microbial community structure was assessed using alpha and beta diversity measures. No significant differences in phenotypic variables evaluated were observed between treatments or periods. We identified 927 concordant OTU among all cows, with 505 novel OTU identified in BASE cows and 403 in LOW cows. Microbial community structure was similar between treatments and feed efficiency measures. One OTU class, Erysipelotrichi, increased in abundance (P = 0.014) in BASE compared to LOW treatment. Findings reflect previous literature in which Erysipelotrichi was associated with high energy or high fat diets. Although no differences were observed in the phenotypic measurements between treatments, metagenomics analyses indicated differences in specific fecal microbial abundance.

scholarly journals Multistage A-O Activated Sludge Process for Paraformaldehyde Wastewater Treatment and Microbial Community Structure Analysis

2016 ◽  
Vol 2016 ◽  
pp. 1-7 ◽  
Author(s):  
Danyang Zheng ◽  
Yujiao Sun ◽  
Huijuan Li ◽  
Sidan Lu ◽  
Mingjun Shan ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Activated Sludge ◽  
Microbial Diversity ◽  
Microbial Community Structure ◽  
High Throughput Sequencing ◽  
Diversity Index ◽  
Public Health Issue ◽  
Activated Sludge Process ◽  
Degrading Bacteria

In recent years, the effect of formaldehyde on microorganisms and body had become a global public health issue. The multistage combination of anaerobic and aerobic process was adopted to treat paraformaldehyde wastewater. Microbial community structure in different reaction stages was analyzed through high-throughput sequencing. Results showed that multistage A-O activated sludge process positively influenced polyformaldehyde wastewater. The removal rates of formaldehyde were basically stable at more than 99% and those of COD were about 89%. Analysis of the microbial diversity index indicated that the microbial diversity of the reactor was high, and the treatment effect was good. Moreover, microbial community had certain similarity in the same system. Microbial communities in different units also showed typical representative characteristics affected by working conditions and influent concentrations. Proteobacteria, Firmicutes, and Bacteroidetes were the dominant fungal genera in the phylum level of community composition. As to family and genus levels, Peptostreptococcaceae was distributed at various stages and the dominant in this system. This bacterium also played an important role in organic matter removal, particularly decomposition of the acidified middle metabolites. In addition, Rhodobacteraceae and Rhodocyclaceae were the formaldehyde-degrading bacteria found in the reactor.

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