Microbial community structure of surface sediments from a tropical estuarine environment using next generation sequencing

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.

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

BioTechniques ◽

10.2144/btn-2019-0102 ◽

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.

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Assessment of Bioleaching Microbial Community Structure and Function Based on Next-Generation Sequencing Technologies

Minerals ◽

10.3390/min8120596 ◽

2018 ◽

Vol 8 (12) ◽

pp. 596 ◽

Cited By ~ 1

Author(s):

Shuang Zhou ◽

Min Gan ◽

Jianyu Zhu ◽

Xinxing Liu ◽

Guanzhou Qiu

Keyword(s):

Community Structure ◽

Next Generation Sequencing ◽

Microbial Ecology ◽

High Throughput ◽

High Throughput Sequencing ◽

Structure And Function ◽

Next Generation ◽

Sequencing Technologies ◽

And Function ◽

Generation Sequencing

It is widely known that bioleaching microorganisms have to cope with the complex extreme environment in which microbial ecology relating to community structure and function varies across environmental types. However, analyses of microbial ecology of bioleaching bacteria is still a challenge. To address this challenge, numerous technologies have been developed. In recent years, high-throughput sequencing technologies enabling comprehensive sequencing analysis of cellular RNA and DNA within the reach of most laboratories have been added to the toolbox of microbial ecology. The next-generation sequencing technology allowing processing DNA sequences can produce available draft genomic sequences of more bioleaching bacteria, which provides the opportunity to predict models of genetic and metabolic potential of bioleaching bacteria and ultimately deepens our understanding of bioleaching microorganism. High-throughput sequencing that focuses on targeted phylogenetic marker 16S rRNA has been effectively applied to characterize the community diversity in an ore leaching environment. RNA-seq, another application of high-throughput sequencing to profile RNA, can be for both mapping and quantifying transcriptome and has demonstrated a high efficiency in quantifying the changing expression level of each transcript under different conditions. It has been demonstrated as a powerful tool for dissecting the relationship between genotype and phenotype, leading to interpreting functional elements of the genome and revealing molecular mechanisms of adaption. This review aims to describe the high-throughput sequencing approach for bioleaching environmental microorganisms, particularly focusing on its application associated with challenges.

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

Journal of Molecular Microbiology and Biotechnology ◽

10.1159/000430865 ◽

2015 ◽

Vol 25 (4) ◽

pp. 262-268 ◽

Cited By ~ 6

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.

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