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 Distribution of Microbial Community Structure in Sediment from the Suyeong River and Bay of Busan, Republic of Korea, Determined by 16S rRNA Gene Amplicon Sequencing

2021 ◽  
Vol 10 (46) ◽  
Author(s):  
Ilwon Jeong ◽  
Junho Lee ◽  
Jong-Oh Kim ◽  
Seokjin Yoon ◽  
Kyunghoi Kim
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Sequence Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Microbial Community Structure ◽  
Amplicon Sequencing ◽  
Republic Of Korea ◽  
Rrna Gene ◽  
Sediment Samples

Here, we report a 16S rRNA gene amplicon sequence analysis presenting the microbial community in sediments from the Suyeong River and Suyeong Bay, Republic of Korea. The dominant phyla in all sediment samples were Proteobacteria (39.69 to 53.62%) and Bacteroidetes (29.78 to 33.89%).

scholarly journals Extent of the annual Gulf of Mexico hypoxic zone influences microbial community structure

2018 ◽  
Author(s):  
Lauren Gillies Campbell ◽  
J. Cameron Thrash ◽  
Nancy N. Rabalais ◽  
Olivia U. Mason
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Gulf Of Mexico ◽  
Dissolved Oxygen ◽  
Microbial Community Structure ◽  
Rrna Gene ◽  
Hypoxic Zone ◽  
Low Do

AbstractRich geochemical datasets generated over the past 30 years have provided fine-scale resolution on the northern Gulf of Mexico (nGOM) coastal hypoxic (≤ 2 mg of O2 L-1) zone. In contrast, little is known about microbial community structure and activity in the hypoxic zone despite the implication that microbial respiration is responsible for forming low dissolved oxygen (DO) conditioXSns. Here, we hypothesized that the extent of the hypoxic zone is a driver in determining microbial community structure, and in particular, the abundance of ammonia-oxidizing archaea (AOA). Samples collected across the shelf for two consecutive hypoxic seasons in July 2013 and 2014 were analyzed using 16S rRNA gene sequencing, oligotyping, microbial co-occurrence analysis and quantification of thaumarchaeal 16S rRNA and archaeal ammonia-monooxygenase (amoA) genes. In 2014 Thaumarchaeota were enriched and inversely correlated with DO while Cyanobacteria, Acidimicrobiia and Proteobacteria where more abundant in oxic samples compared to hypoxic. Oligotyping analysis of Nitrosopumilus 16S rRNA gene sequences revealed that one oligotype was significantly inversely correlated with dissolved oxygen (DO) in both years and that low DO concentrations, and the high Thaumarchaeota abundances, influenced microbial co-occurrence patterns. Taken together, the data demonstrated that the extent of hypoxic conditions could potentially influence patterns in microbial community structure, with two years of data revealing that the annual nGOM hypoxic zone is emerging as a low DO adapted AOA hotspot.

scholarly journals Nested PCR Biases in Interpreting Microbial Community Structure in 16S rRNA Gene Sequence Datasets

PLoS ONE ◽  
2015 ◽  
Vol 10 (7) ◽  
pp. e0132253 ◽  
Author(s):  
Guoqin Yu ◽  
Doug Fadrosh ◽  
James J. Goedert ◽  
Jacques Ravel ◽  
Alisa M. Goldstein
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Microbial Community Structure ◽  
Nested Pcr ◽  
Gene Sequence ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence

scholarly journals Interpretations of Environmental Microbial Community Studies Are Biased by the Selected 16S rRNA (Gene) Amplicon Sequencing Pipeline

2020 ◽  
Vol 11 ◽  
Author(s):  
Daniel Straub ◽  
Nia Blackwell ◽  
Adrian Langarica-Fuentes ◽  
Alexander Peltzer ◽  
Sven Nahnsen ◽  
...  
Keyword(s):  
Microbial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Community Studies

scholarly journals Analysis of the Gull Fecal Microbial Community Reveals the Dominance of Catellicoccus marimammalium in Relation to Culturable Enterococci

2013 ◽  
Vol 80 (2) ◽  
pp. 757-765 ◽  
Author(s):  
Amber M. Koskey ◽  
Jenny C. Fisher ◽  
Mary F. Traudt ◽  
Ryan J. Newton ◽  
Sandra L. McLellan
Keyword(s):  
Microbial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
16S Rrna Gene Sequencing ◽  
Illumina Miseq ◽  
Rrna Gene ◽  
Sequence Comparisons ◽  
Fecal Indicator ◽  
Fecal Samples ◽  
Content Type

ABSTRACTGulls are prevalent in beach environments and can be a major source of fecal contamination. Gulls have been shown to harbor a high abundance of fecal indicator bacteria (FIB), such asEscherichia coliand enterococci, which can be readily detected as part of routine beach monitoring. Despite the ubiquitous presence of gull fecal material in beach environments, the associated microbial community is relatively poorly characterized. We generated comprehensive microbial community profiles of gull fecal samples using Roche 454 and Illumina MiSeq platforms to investigate the composition and variability of the gull fecal microbial community and to measure the proportion of FIB.EnterococcaceaeandEnterobacteriaceaewere the two most abundant families in our gull samples. Sequence comparisons between short-read data and nearly full-length 16S rRNA gene clones generated from the same samples revealedCatellicoccus marimammaliumas the most numerous taxon among all samples. The identification of bacteria from gull fecal pellets cultured on membrane-Enterococcusindoxyl-β-d-glucoside (mEI) plates showed that the dominant sequences recovered in our sequence libraries did not represent organisms culturable on mEI. Based on 16S rRNA gene sequencing of gull fecal isolates cultured on mEI plates, 98.8% were identified asEnterococcusspp., 1.2% were identified asStreptococcusspp., and none were identified asC. marimammalium. Illumina deep sequencing indicated that gull fecal samples harbor significantly higher proportions ofC. marimammalium16S rRNA gene sequences (>50-fold) relative to typical mEI culturableEnterococcusspp.C. marimammaliumtherefore can be confidently utilized as a genetic marker to identify gull fecal pollution in the beach environment.

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 Restructuring of the Aquatic Bacterial Community by Hydric Dynamics Associated with Superstorm Sandy

2016 ◽  
Vol 82 (12) ◽  
pp. 3525-3536 ◽  
Author(s):  
Nikea Ulrich ◽  
Abigail Rosenberger ◽  
Colin Brislawn ◽  
Justin Wright ◽  
Collin Kessler ◽  
...  
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
High Throughput ◽  
Bacterial Community Structure ◽  
High Throughput Sequencing ◽  
Storm Event ◽  
Rrna Gene ◽  
Content Type

ABSTRACTBacterial community composition and longitudinal fluctuations were monitored in a riverine system during and after Superstorm Sandy to better characterize inter- and intracommunity responses associated with the disturbance associated with a 100-year storm event. High-throughput sequencing of the 16S rRNA gene was used to assess microbial community structure within water samples from Muddy Creek Run, a second-order stream in Huntingdon, PA, at 12 different time points during the storm event (29 October to 3 November 2012) and under seasonally matched baseline conditions. High-throughput sequencing of the 16S rRNA gene was used to track changes in bacterial community structure and divergence during and after Superstorm Sandy. Bacterial community dynamics were correlated to measured physicochemical parameters and fecal indicator bacteria (FIB) concentrations. Bioinformatics analyses of 2.1 million 16S rRNA gene sequences revealed a significant increase in bacterial diversity in samples taken during peak discharge of the storm. Beta-diversity analyses revealed longitudinal shifts in the bacterial community structure. Successional changes were observed, in whichBetaproteobacteriaandGammaproteobacteriadecreased in 16S rRNA gene relative abundance, while the relative abundance of members of theFirmicutesincreased. Furthermore, 16S rRNA gene sequences matching pathogenic bacteria, including strains ofLegionella,Campylobacter,Arcobacter, andHelicobacter, as well as bacteria of fecal origin (e.g.,Bacteroides), exhibited an increase in abundance after peak discharge of the storm. This study revealed a significant restructuring of in-stream bacterial community structure associated with hydric dynamics of a storm event.IMPORTANCEIn order to better understand the microbial risks associated with freshwater environments during a storm event, a more comprehensive understanding of the variations in aquatic bacterial diversity is warranted. This study investigated the bacterial communities during and after Superstorm Sandy to provide fine time point resolution of dynamic changes in bacterial composition. This study adds to the current literature by revealing the variation in bacterial community structure during the course of a storm. This study employed high-throughput DNA sequencing, which generated a deep analysis of inter- and intracommunity responses during a significant storm event. This study has highlighted the utility of applying high-throughput sequencing for water quality monitoring purposes, as this approach enabled a more comprehensive investigation of the bacterial community structure. Altogether, these data suggest a drastic restructuring of the stream bacterial community during a storm event and highlight the potential of high-throughput sequencing approaches for assessing the microbiological quality of our environment.

Sign in / Sign up

Export Citation Format

Share Document