Agricultural Freshwater Pond Supports Diverse and Dynamic Bacterial and Viral Populations
Agricultural ponds have a great potential as a means of capture and storage of water for irrigation. However, pond topography (small size, shallow depth) leaves them susceptible to environmental, agricultural, and anthropogenic exposures that may influence microbial dynamics. Therefore, the aim of t...
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doaj-43db3e3c2e5b4eea8b2fa8aefcd8d4e22020-11-24T22:24:37ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2018-04-01910.3389/fmicb.2018.00792364892Agricultural Freshwater Pond Supports Diverse and Dynamic Bacterial and Viral PopulationsJessica Chopyk0Sarah Allard1Daniel J. Nasko2Anthony Bui3Emmanuel F. Mongodin4Amy R. Sapkota5Maryland Institute for Applied Environmental Health, University of Maryland School of Public Health, College Park, MD, United StatesMaryland Institute for Applied Environmental Health, University of Maryland School of Public Health, College Park, MD, United StatesCenter for Bioinformatics and Computational Biology, University of Maryland, College Park, College Park, MD, United StatesMaryland Institute for Applied Environmental Health, University of Maryland School of Public Health, College Park, MD, United StatesInstitute for Genome Sciences and Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, United StatesMaryland Institute for Applied Environmental Health, University of Maryland School of Public Health, College Park, MD, United StatesAgricultural ponds have a great potential as a means of capture and storage of water for irrigation. However, pond topography (small size, shallow depth) leaves them susceptible to environmental, agricultural, and anthropogenic exposures that may influence microbial dynamics. Therefore, the aim of this project was to characterize the bacterial and viral communities of pond water in the Mid-Atlantic United States with a focus on the late season (October–December), where decreasing temperature and nutrient levels can affect the composition of microbial communities. Ten liters of freshwater from an agricultural pond were sampled monthly, and filtered sequentially through 1 and 0.2 μm filter membranes. Total DNA was then extracted from each filter, and the bacterial communities were characterized using 16S rRNA gene sequencing. The remaining filtrate was chemically concentrated for viruses, DNA-extracted, and shotgun sequenced. Bacterial community profiling showed significant fluctuations over the sampling period, corresponding to changes in the condition of the pond freshwater (e.g., pH, nutrient load). In addition, there were significant differences in the alpha-diversity and core bacterial operational taxonomic units (OTUs) between water fractions filtered through different pore sizes. The viral fraction was dominated by tailed bacteriophage of the order Caudovirales, largely those of the Siphoviridae family. Moreover, while present, genes involved in virulence/antimicrobial resistance were not enriched within the viral fraction during the study period. Instead, the viral functional profile was dominated by phage associated proteins, as well as those related to nucleotide production. Overall, these data suggest that agricultural pond water harbors a diverse core of bacterial and bacteriophage species whose abundance and composition are influenced by environmental variables characteristic of pond topology and the late season.http://journal.frontiersin.org/article/10.3389/fmicb.2018.00792/fullviral metagenomics16S rRNAbacteriophagepolymerase Amicrobiotavirome |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Jessica Chopyk Sarah Allard Daniel J. Nasko Anthony Bui Emmanuel F. Mongodin Amy R. Sapkota |
spellingShingle |
Jessica Chopyk Sarah Allard Daniel J. Nasko Anthony Bui Emmanuel F. Mongodin Amy R. Sapkota Agricultural Freshwater Pond Supports Diverse and Dynamic Bacterial and Viral Populations Frontiers in Microbiology viral metagenomics 16S rRNA bacteriophage polymerase A microbiota virome |
author_facet |
Jessica Chopyk Sarah Allard Daniel J. Nasko Anthony Bui Emmanuel F. Mongodin Amy R. Sapkota |
author_sort |
Jessica Chopyk |
title |
Agricultural Freshwater Pond Supports Diverse and Dynamic Bacterial and Viral Populations |
title_short |
Agricultural Freshwater Pond Supports Diverse and Dynamic Bacterial and Viral Populations |
title_full |
Agricultural Freshwater Pond Supports Diverse and Dynamic Bacterial and Viral Populations |
title_fullStr |
Agricultural Freshwater Pond Supports Diverse and Dynamic Bacterial and Viral Populations |
title_full_unstemmed |
Agricultural Freshwater Pond Supports Diverse and Dynamic Bacterial and Viral Populations |
title_sort |
agricultural freshwater pond supports diverse and dynamic bacterial and viral populations |
publisher |
Frontiers Media S.A. |
series |
Frontiers in Microbiology |
issn |
1664-302X |
publishDate |
2018-04-01 |
description |
Agricultural ponds have a great potential as a means of capture and storage of water for irrigation. However, pond topography (small size, shallow depth) leaves them susceptible to environmental, agricultural, and anthropogenic exposures that may influence microbial dynamics. Therefore, the aim of this project was to characterize the bacterial and viral communities of pond water in the Mid-Atlantic United States with a focus on the late season (October–December), where decreasing temperature and nutrient levels can affect the composition of microbial communities. Ten liters of freshwater from an agricultural pond were sampled monthly, and filtered sequentially through 1 and 0.2 μm filter membranes. Total DNA was then extracted from each filter, and the bacterial communities were characterized using 16S rRNA gene sequencing. The remaining filtrate was chemically concentrated for viruses, DNA-extracted, and shotgun sequenced. Bacterial community profiling showed significant fluctuations over the sampling period, corresponding to changes in the condition of the pond freshwater (e.g., pH, nutrient load). In addition, there were significant differences in the alpha-diversity and core bacterial operational taxonomic units (OTUs) between water fractions filtered through different pore sizes. The viral fraction was dominated by tailed bacteriophage of the order Caudovirales, largely those of the Siphoviridae family. Moreover, while present, genes involved in virulence/antimicrobial resistance were not enriched within the viral fraction during the study period. Instead, the viral functional profile was dominated by phage associated proteins, as well as those related to nucleotide production. Overall, these data suggest that agricultural pond water harbors a diverse core of bacterial and bacteriophage species whose abundance and composition are influenced by environmental variables characteristic of pond topology and the late season. |
topic |
viral metagenomics 16S rRNA bacteriophage polymerase A microbiota virome |
url |
http://journal.frontiersin.org/article/10.3389/fmicb.2018.00792/full |
work_keys_str_mv |
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