Microbial Community Composition in the Marine Sediments of Jeju Island: Next-Generation Sequencing Surveys

2016 ◽  
Vol 26 (5) ◽  
pp. 883-890 ◽  
Author(s):  
Heebok Choi ◽  
Hyeon-Woo Koh ◽  
Hongik Kim ◽  
Jong-Chan Chae ◽  
Soo-Je Park
Keyword(s):  
Microbial Community ◽  
Next Generation Sequencing ◽  
Community Composition ◽  
Marine Sediments ◽  
Microbial Community Composition ◽  
Jeju Island ◽  
Next Generation ◽  
Generation Sequencing

scholarly journals Solar Septic Tank: Next Generation Sequencing Reveals Effluent Microbial Community Composition as a Useful Index of System Performance

Water ◽  
2019 ◽  
Vol 11 (12) ◽  
pp. 2660 ◽  
Author(s):  
Stephanie Connelly ◽  
Tatchai Pussayanavin ◽  
Richard J. Randle-Boggis ◽  
Araya Wicheansan ◽  
Suparat Jampathong ◽  
...  
Keyword(s):  
Microbial Community ◽  
Next Generation Sequencing ◽  
Community Composition ◽  
Microbial Community Composition ◽  
Effluent Treatment ◽  
Septic Tank ◽  
Next Generation ◽  
Sampling System ◽  
Treatment Performance ◽  
Generation Sequencing

Septic tanks are widely deployed for off-grid sewage management but are typified by poor treatment performance, discharge of polluting effluents and the requirement for frequent de-sludging. The Solar Septic Tank (SST) is a novel septic tank design that uses passive heat from the sun to raise in-tank temperatures and improves solids degradation, resulting in a cleaner effluent. Treatment has been shown to exceed conventional systems, however, the underlying biology driving treatment in the system is poorly understood. We used next generation sequencing (Illumina Miseq (San Diego, CA, USA), V4 region 16S DNA) to monitor the microbiology in the sludge and effluent of two mature systems, a conventional septic tank and an SST, during four months of routine operation in Bangkok, Thailand, and evaluated the ecology against a suite of operating and performance data collected during the same time period. Significant differences were observed between the microbiome of the sludge and effluent in each system and the dominant taxa in each appeared persistent over time. Furthermore, variation in the microbial community composition in the system effluents correlated with effluent water quality and treatment performance parameters, including the removal of chemical and biochemical oxygen demand and the concentration of fecal and total coliforms in the effluent. Thus, we propose that a wide-scale survey of the biology underlying decentralised biotechnologies for sewage treatment such as the SST could be conducted by sampling system effluent rather than sampling sludge. This is advantageous as accessing sludge during sampling is both hazardous and potentially disruptive to the anaerobic methanogenic consortia underlying treatment in the systems.

scholarly journals Effects of Actinomycete Secondary Metabolites on Sediment Microbial Communities

2016 ◽  
Vol 83 (4) ◽  
Author(s):  
Nastassia V. Patin ◽  
Michelle Schorn ◽  
Kristen Aguinaldo ◽  
Tommie Lincecum ◽  
Bradley S. Moore ◽  
...  
Keyword(s):  
Microbial Community ◽  
Secondary Metabolites ◽  
Microbial Communities ◽  
Community Composition ◽  
Marine Sediments ◽  
Microbial Community Composition ◽  
Amplicon Sequencing ◽  
Next Generation ◽  
Content Type ◽  
Predatory Bacteria

ABSTRACT Marine sediments harbor complex microbial communities that remain poorly studied relative to other biomes such as seawater. Moreover, bacteria in these communities produce antibiotics and other bioactive secondary metabolites, yet little is known about how these compounds affect microbial community structure. In this study, we used next-generation amplicon sequencing to assess native microbial community composition in shallow tropical marine sediments. The results revealed complex communities comprised of largely uncultured taxa, with considerable spatial heterogeneity and known antibiotic producers comprising only a small fraction of the total diversity. Organic extracts from cultured strains of the sediment-dwelling actinomycete genus Salinispora were then used in mesocosm studies to address how secondary metabolites shape sediment community composition. We identified predatory bacteria and other taxa that were consistently reduced in the extract-treated mesocosms, suggesting that they may be the targets of allelopathic interactions. We tested related taxa for extract sensitivity and found general agreement with the culture-independent results. Conversely, several taxa were enriched in the extract-treated mesocosms, suggesting that some bacteria benefited from the interactions. The results provide evidence that bacterial secondary metabolites can have complex and significant effects on sediment microbial communities. IMPORTANCE Ocean sediments represent one of Earth's largest and most poorly studied biomes. These habitats are characterized by complex microbial communities where competition for space and nutrients can be intense. This study addressed the hypothesis that secondary metabolites produced by the sediment-inhabiting actinomycete Salinispora arenicola affect community composition and thus mediate interactions among competing microbes. Next-generation amplicon sequencing of mesocosm experiments revealed complex communities that shifted following exposure to S. arenicola extracts. The results reveal that certain predatory bacteria were consistently less abundant following exposure to extracts, suggesting that microbial metabolites mediate competitive interactions. Other taxa increased in relative abundance, suggesting a benefit from the extracts themselves or the resulting changes in the community. This study takes a first step toward assessing the impacts of bacterial metabolites on sediment microbial communities. The results provide insight into how low-abundance organisms may help structure microbial communities in ocean sediments.

scholarly journals Bacterial abundance and community composition in green, brown and red water from intensive catfish (Clarias sp.) culture ponds in Yogyakarta, Indonesia

2021 ◽  
Vol 22 (9) ◽  
Author(s):  
Karunia Adetera Nungki Wijayanti ◽  
Indah Istiqomah ◽  
Murwantoko Murwantoko
Keyword(s):  
Next Generation Sequencing ◽  
Bacterial Community ◽  
16S Rrna ◽  
Community Composition ◽  
Water Samples ◽  
Bacterial Abundance ◽  
Rrna Gene ◽  
Next Generation ◽  
Aquaculture System ◽  
Generation Sequencing

Abstract. Wijayanti KAN, Istiqomah I, Murwantoko. 2021. Bacterial abundance and community composition in green, brown and red water from intensive Catfish (Clarias sp.) culture ponds in Yogyakarta, Indonesia. Biodiversitas 22: 3677-3684. Catfish (Clarias sp.) is an important aquaculture commodity in Indonesia and cultured in an intensive system. Microorganisms play an important role in maintaining water quality of aquaculture system. The objective of this study was to determine the bacterial abundance and community composition of green, brown and red water collected from intensive catfish culture ponds in Yogyakarta using next-generation sequencing method. The water samples were collected from intensive catfish culture ponds with different colors, namely green, brown and red ponds located in Yogyakarta. The DNA from water samples was extracted using DNA extraction kit and used as template for 16S rRNA amplification. The V3-V4 hypervariable regions of the 16S rRNA gene were amplified apply for next-generation sequencing technology. This study could explore effectively the bacterial community in water samples. The bacterial communities in this catfish culture water showed higher bacterial richness compared to the other aquaculture system. The diversity of the green, brown and red catfish culture water ponds was similar with the number OTUs of the green, brown and red water samples, which were 1269; 1387 and 1323 OTUs respectively. The 694 OTUs (34.42%) were common core microbiomes in all catfish culture ponds, the 212 OTUs (10.51%) are present on green and brown water ponds, the 182 OTUs (9.02%) were on green and red water ponds, and the 183 OTUs (9.07%) were present on green and brown water ponds. However, the composition of the bacterial community was different. The most dominant phylum in green and brown water ponds was Proteobacteria with relative abundance in green water and brown water 71.6% and 47.0% respectively, whereas, the most dominant phylum in red water was Firmicutes (29.5%). The dominance of Firmicutes phylum in red water ponds may be caused by application of probiotic bacteria, the high organic content, and low oxygen concentration.

scholarly journals Mercury contamination imposes structural shift on the microbial community of an agricultural soil

2019 ◽  
Vol 43 (1) ◽  
Author(s):  
Lateef Babatunde Salam ◽  
Halima Shomope ◽  
Zainab Ummi ◽  
Fatima Bukar
Keyword(s):  
Heavy Metals ◽  
Microbial Community ◽  
Next Generation Sequencing ◽  
Agricultural Soil ◽  
Mercury Contamination ◽  
Next Generation ◽  
Mercury Stress ◽  
Mercury Detoxification ◽  
Generation Sequencing ◽  
Detoxification Process

Abstract Background The purpose of this study is to use shotgun next-generation sequencing to unravel the microbial community structure of an agricultural soil, decipher the effects of mercury contamination on the structure of the microbial community and the soil physicochemistry and heavy metals content. Results The soil physicochemistry after mercury contamination revealed a shift in soil pH from neutral (6.99 ± 0.001) to acidic (5.96 ± 0.25), a decline in moisture content to < 4 %, and a significant decrease in the concentrations of all the macronutrients and the total organic matter. Significant decrease in all the heavy metals detected in the agricultural soil was also observed in mercury inundated SL3 microcosm. Structural analysis of the metagenomes of SL1 (agricultural soil) and SL3 (mercury-contaminated agricultural soil) using Illumina shotgun next-generation sequencing revealed the loss due to mercury contamination of 54.75 % of the microbial community consisting of an archaeal domain, 11 phyla, 12 classes, 24 orders, 36 families, 59 genera, and 86 species. The dominant phylum, class, genus, and species in SL1 metagenome are Proteobacteria, Bacilli, Staphylococcus, and Sphingobacterium sp. 21; while in SL3 metagenome, Proteobacteria, Alphaproteobacteria, Singulisphaera, and Singulisphaera acidiphila were preponderant. Mercury contamination resulted in a massive upscale in the population of members of the phylum Planctomycetes and the genera Singulisphaera, Brevundimonas, Sanguibacter, Exiguobacterium, Desulfobacca, and Proteus in SL3 metagenome while it causes massive decline in the population of genera Staphylococcus and Brachybacterium. Conclusions This study revealed that mercury contamination of the agricultural soil imposed selective pressure on the members of the microbial community, which negatively impact on their population, alter soil physicochemistry, and enriched sizable numbers of members of the community that are well adapted to mercury stress. It also reveals members of microbial community hitherto not reported to be important in mercury detoxification process.

scholarly journals Nanoliter-scale next-generation sequencing library-mediated high-throughput 16S rRNA microbial community profiling

BioTechniques ◽  
2020 ◽  
Vol 68 (4) ◽  
pp. 204-210
Author(s):  
Hui Zhang ◽  
Xiangdan Yu ◽  
Zhe Zhang ◽  
Zhenhua Liu ◽  
Cong Tang ◽  
...  
Keyword(s):  
Microbial Community ◽  
Next Generation Sequencing ◽  
Large Scale ◽  
Amplicon Sequencing ◽  
Next Generation ◽  
Library Construction ◽  
Microbial Community Profiling ◽  
Community Profiling ◽  
Sequencing Library ◽  
Generation Sequencing

An ultra-high-throughput workflow for next-generation sequencing library construction at nanoliter scale for amplicon sequencing, termed Smartchip Nanowell Platform for Target Enrichment, was established using a nanodispenser system and a nanoliter-scale PCR chip. To demonstrate its cost and time advantages over conventional methods for library construction, quality control and pooling for large-scale samples, target amplicon sequencing of the 16S ribosomal RNA gene V3-V4 region widely used for microbial community profiling was chosen for comparison. The finding of no significant difference in microbial community profiling between the two methods strongly supports the conclusion that Smartchip Nanowell Platform for Target Enrichment is a cost-effective method for next-generation sequencing library construction for large-scale samples to conduct amplicon sequencing-based applications.

Developmental Dynamic Analysis of the Excreted Microbiome of Chickens Using Next-Generation Sequencing

2015 ◽  
Vol 25 (4) ◽  
pp. 262-268 ◽  
Author(s):  
Sooyeon Lim ◽  
SooHyun Cho ◽  
Kelsey Caetano-Anolles ◽  
Seok Geun Jeong ◽  
Mi Hwa Oh ◽  
...  
Keyword(s):  
Microbial Community ◽  
Next Generation Sequencing ◽  
Broiler Chickens ◽  
Sequence Similarity ◽  
Population Analysis ◽  
Growth Period ◽  
Human Consumption ◽  
Next Generation ◽  
Genus Level ◽  
Generation Sequencing

Poultry contamination can be largely attributed to the presence of chicken feces during the production process. Fecal contamination is often found in raw chicken products sold for human consumption. Quantitative analysis of the fecal microbial community of chickens using next-generation sequencing techniques is the focus of this study. Fecal samples were collected from 30 broiler chickens at two time points: days 1 and 35 of development. 454 pyrosequencing was conducted on 16S rRNA extracted from each sample, and microbial population dynamics were investigated using various automated bioinformatics pipelines. Diversity of the microbial community at the genus level increased during the 5-week growth period. Despite this growth, only a few dominant bacteria groups (over 80%) were identified in each fecal sample, with most groups being unique and only a few were shared between samples. Population analysis at the genus level showed that microbial diversity increased with chicken growth and development. Classification and phylogenetic analysis of highly represented microbes (over 1%) clearly showed high levels of sequence similarity between groups such as Firmicutes and Proteobacteria. These results suggest that the chicken fecal excreted microbiome is a dynamic system with a differentiated population structure that harbors a highly restricted number of higher taxa.

Microbial community analysis of anaerobic granules in phenol-degrading UASB by next generation sequencing

2016 ◽  
Vol 112 ◽  
pp. 241-248 ◽  
Author(s):  
Jeong-Geol Na ◽  
Mo-Kwon Lee ◽  
Yeo-Myeong Yun ◽  
Chungman Moon ◽  
Mi-Sun Kim ◽  
...  
Keyword(s):  
Microbial Community ◽  
Next Generation Sequencing ◽  
Community Analysis ◽  
Microbial Community Analysis ◽  
Next Generation ◽  
Generation Sequencing
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