Bacterial community composition of anthropogenic biochar and Amazonian anthrosols assessed by 16S rRNA gene 454 pyrosequencing

2013 ◽  
Vol 104 (2) ◽  
pp. 233-242 ◽  
Author(s):  
Rodrigo Gouvêa Taketani ◽  
Amanda Barbosa Lima ◽  
Ederson da Conceição Jesus ◽  
Wenceslau Geraldes Teixeira ◽  
James M. Tiedje ◽  
...  
Keyword(s):  
Bacterial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Community Composition ◽  
454 Pyrosequencing ◽  
Bacterial Community Composition ◽  
Rrna Gene

Dynamics of the bacterial community in a channel catfish nursery pond with a cage–pond integration system

2018 ◽  
Vol 64 (12) ◽  
pp. 954-967 ◽  
Author(s):  
Liqiang Zhong ◽  
Daming Li ◽  
Minghua Wang ◽  
Xiaohui Chen ◽  
Wenji Bian ◽  
...  
Keyword(s):  
Bacterial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Community Composition ◽  
Channel Catfish ◽  
Bacterial Community Composition ◽  
Rrna Gene ◽  
Integration System ◽  
Nursery Pond ◽  
Site Variation

The changes in the bacterial community composition in a channel catfish nursery pond with a cage–pond integration system were investigated by sequencing of the 16S rRNA gene through Illumina MiSeq sequencing platforms. A total of 1 362 877 sequences and 1440 operational taxonomic units were obtained. Further analysis showed that the dominant phyla in the cage and pond groups were similar, including Actinobacteria, Cyanobacteria, Proteobacteria, and Bacteroidetes, although a significant difference was detected between them by ANOSIM (P < 0.05). Temporal changes and site variation were significantly related to the variation of the bacterial community. A comprehensive analysis of the diversity and evenness of the bacterial 16S rRNA gene, redundancy analysis (RDA), and partial Mantel test showed that the bacterial community composition in a cage–pond integration system was shaped more by temporal variation than by site variation. RDA also indicated that water temperature, total dissolved solids, and Secchi depth had the largest impact on bacterial populations.

scholarly journals High-Resolution Melt Analysis for Rapid Comparison of Bacterial Community Compositions

2014 ◽  
Vol 80 (12) ◽  
pp. 3568-3575 ◽  
Author(s):  
Mathis Hjort Hjelmsø ◽  
Lars Hestbjerg Hansen ◽  
Jacob Bælum ◽  
Louise Feld ◽  
William E. Holben ◽  
...  
Keyword(s):  
High Resolution ◽  
Bacterial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Community Composition ◽  
Bacterial Community Composition ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
High Resolution Melt ◽  
Hrm Analysis

ABSTRACTIn the study of bacterial community composition, 16S rRNA gene amplicon sequencing is today among the preferred methods of analysis. The cost of nucleotide sequence analysis, including requisite computational and bioinformatic steps, however, takes up a large part of many research budgets. High-resolution melt (HRM) analysis is the study of the melt behavior of specific PCR products. Here we describe a novel high-throughput approach in which we used HRM analysis targeting the 16S rRNA gene to rapidly screen multiple complex samples for differences in bacterial community composition. We hypothesized that HRM analysis of amplified 16S rRNA genes from a soil ecosystem could be used as a screening tool to identify changes in bacterial community structure. This hypothesis was tested using a soil microcosm setup exposed to a total of six treatments representing different combinations of pesticide and fertilization treatments. The HRM analysis identified a shift in the bacterial community composition in two of the treatments, both including the soil fumigant Basamid GR. These results were confirmed with both denaturing gradient gel electrophoresis (DGGE) analysis and 454-based 16S rRNA gene amplicon sequencing. HRM analysis was shown to be a fast, high-throughput technique that can serve as an effective alternative to gel-based screening methods to monitor microbial community composition.

Effects of geographic location and water quality on bacterial communities in full-scale biofilters across North America

2020 ◽  
Vol 96 (2) ◽  
Author(s):  
Ben Ma ◽  
Timothy M LaPara ◽  
Ashley N. Evans ◽  
Raymond M Hozalski
Keyword(s):  
Water Quality ◽  
North America ◽  
Bacterial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Community Composition ◽  
Bacterial Communities ◽  
Bacterial Community Composition ◽  
Geographic Location ◽  
Rrna Gene

ABSTRACT Spatial patterns of bacterial community composition often follow a distance–decay relationship in which community dissimilarity increases with geographic distance. Such a relationship has been commonly observed in natural environments, but less so in engineered environments. In this study, bacterial abundance and community composition in filter media samples (n = 57) from full-scale rapid biofilters at 14 water treatment facilities across North America were determined using quantitative polymerase chain reaction and Illumina HiSeq high-throughput sequencing targeting the 16S rRNA gene, respectively. Bacteria were abundant on the filter media (108.8±0.3 to 1010.7±0.2 16S rRNA gene copies/cm3 bed volume) and the bacterial communities were highly diverse (Shannon index: 5.3 ± 0.1 to 8.4 ± 0.0). Significant inter-filter variations in bacterial community composition were observed, with weighted UniFrac dissimilarity values following a weak but highly significant distance–decay relationship (z = 0.0057 ± 0.0006; P = 1.8 × 10−22). Approximately 50% of the variance in bacterial community composition was explained by the water quality parameters measured at the time of media sample collection (i.e. pH, temperature and dissolved organic carbon concentration). Overall, this study suggested that the microbiomes of biofilters are primarily shaped by geographic location and local water quality conditions but the influence of these factors on the microbiomes is tempered by filter design and operating conditions.

MiSeq HV4 16S rRNA gene analysis of bacterial community composition among the cave sediments of Indo-Burma biodiversity hotspot

2016 ◽  
Vol 23 (12) ◽  
pp. 12216-12226 ◽  
Author(s):  
Surajit De Mandal ◽  
Zothansanga ◽  
Amrita Kumari Panda ◽  
Satpal Singh Bisht ◽  
Nachimuthu Senthil Kumar
Keyword(s):  
Bacterial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Community Composition ◽  
Bacterial Community Composition ◽  
Biodiversity Hotspot ◽  
Gene Analysis ◽  
Rrna Gene ◽  
16S Rrna Gene Analysis ◽  
Cave Sediments

scholarly journals Bacterial community composition in the gut content of Lampetra japonica revealed by 16S rRNA gene pyrosequencing

PLoS ONE ◽  
2017 ◽  
Vol 12 (12) ◽  
pp. e0188919 ◽  
Author(s):  
Yu Zuo ◽  
Wenfang Xie ◽  
Yue Pang ◽  
Tiesong Li ◽  
Qingwei Li ◽  
...  
Keyword(s):  
Bacterial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Community Composition ◽  
Bacterial Community Composition ◽  
Rrna Gene ◽  
Gut Content ◽  
Lampetra Japonica ◽  
16S Rrna Gene Pyrosequencing

183 Effects of Protein Supplementation on the Gut Bacterial Community Composition of Hybrid Striped Bass, Morone Chrysops X M. Saxatilis

2021 ◽  
Vol 99 (Supplement_1) ◽  
pp. 88-89
Author(s):  
Emily Fowler ◽  
Benoit St-Pierre ◽  
Prakash Poudel ◽  
Brandon White ◽  
Michael Brown
Keyword(s):  
Bacterial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Striped Bass ◽  
Bacterial Community Composition ◽  
Protein Supplementation ◽  
Rrna Gene ◽  
Hybrid Striped Bass ◽  
Morone Chrysops ◽  
Protein Sources

Abstract Plant-based protein ingredients have become an attractive substitute for traditional animal sources in the aquaculture feed industry. However, inclusion in carnivorous fish diets is limited due to reduced digestibility, presence of anti-nutritional factors, and increased risk of digestive tract inflammation. To gain further insight on the adaptation of the fish digestive tract environment to plant-based protein sources, intestinal bacterial communities from Hybrid Striped Bass, Morone chrysops x M. saxatilis, fed diets supplemented with different protein sources were compared. Data were generated by Illumina MiSeq 2X300 sequencing of PCR generated amplicons targeting the V1–V3 regions of the 16S rRNA gene. A comparative analysis using the non-parametric Kruskal-Wallis test identified 17 highly represented species-level Operational Taxonomic Units (OTUs) that differed in abundance across dietary treatments (P &lt; 0.05). Notably, OTU SD_McMs-0001 was at its highest abundance in samples from individuals fed poultry-fishmeal (PFM; 47.61% ± 0.92%) and plant protein-based (PP; 43.13% ± 1.76%) diets, while it was found in much lower abundance in the non-supplemented control diet samples (B; 4.29% ± 0.92%). It was predicted to be a novel species of the family Peptostreptococcaceae based on its limited 16S rRNA gene sequence identity to its closest valid relative (Peptostreptococcus russellii, 91%). In contrast, three Proteobacteria-affiliated OTUs (SD_McMs-0002, SD_McMs-0003, and SD_McMs-0004) were most highly represented in B diet samples, with averages of 30.28%, 27.22%, and 13.54%, respectively. They were in much lower abundance in the PFM and PP samples, with averages ranging between 0.18% and 4.82%, respectively. Based on 16S rRNA sequence comparisons, they were predicted to be strains of Plesiomonas shigelloides (99%), Ralstonia pickettii (99%) and Sphingomonas elodea (99%), respectively. These results indicate that protein supplementation affects gut bacterial community composition of Hybrid Striped Bass, but that the type of protein used has minimal or no detectable impact.

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