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.

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.

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

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.

scholarly journals Potential applications of next generation DNA sequencing of 16S rRNA gene amplicons in microbial water quality monitoring

2015 ◽  
Vol 72 (11) ◽  
pp. 1962-1972 ◽  
Author(s):  
J. Vierheilig ◽  
D. Savio ◽  
R. E. Ley ◽  
R. L. Mach ◽  
A. H. Farnleitner ◽  
...  
Keyword(s):  
Water Quality ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Sequencing ◽  
Bacterial Communities ◽  
Bacterial Community Composition ◽  
Detection Methods ◽  
Rrna Gene ◽  
Next Generation ◽  
Next Generation Dna Sequencing

The applicability of next generation DNA sequencing (NGS) methods for water quality assessment has so far not been broadly investigated. This study set out to evaluate the potential of an NGS-based approach in a complex catchment with importance for drinking water abstraction. In this multi-compartment investigation, total bacterial communities in water, faeces, soil, and sediment samples were investigated by 454 pyrosequencing of bacterial 16S rRNA gene amplicons to assess the capabilities of this NGS method for (i) the development and evaluation of environmental molecular diagnostics, (ii) direct screening of the bulk bacterial communities, and (iii) the detection of faecal pollution in water. Results indicate that NGS methods can highlight potential target populations for diagnostics and will prove useful for the evaluation of existing and the development of novel DNA-based detection methods in the field of water microbiology. The used approach allowed unveiling of dominant bacterial populations but failed to detect populations with low abundances such as faecal indicators in surface waters. In combination with metadata, NGS data will also allow the identification of drivers of bacterial community composition during water treatment and distribution, highlighting the power of this approach for monitoring of bacterial regrowth and contamination in technical systems.

scholarly journals Terrestrial Runoff Controls the Bacterial Community Composition of Biofilms along a Water Quality Gradient in the Great Barrier Reef

2012 ◽  
Vol 78 (21) ◽  
pp. 7786-7791 ◽  
Author(s):  
Verena Witt ◽  
Christian Wild ◽  
Sven Uthicke
Keyword(s):  
Water Quality ◽  
Bacterial Community ◽  
16S Rrna ◽  
Bacterial Communities ◽  
Bacterial Community Composition ◽  
Bacterial Biofilm ◽  
Rrna Gene ◽  
Barrier Reef ◽  
Terrestrial Runoff ◽  
Microbial Biofilms

ABSTRACT16S rRNA gene molecular analysis elucidated the spatiotemporal distribution of bacterial biofilm communities along a water quality gradient. Multivariate statistics indicated that terrestrial runoff, in particular dissolved organic carbon and chlorophyllaconcentrations, induced shifts of specific bacterial communities between locations and seasons, suggesting microbial biofilms could be suitable bioindicators for water quality.

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