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Front. Microbiol. | doi: 10.3389/fmicb.2018.00792

Agricultural freshwater pond supports diverse and dynamic bacterial and viral populations

  • 1School of Public Health, University of Maryland, United States
  • 2Center for Bioinformatics and Computational Biology, University of Maryland, United States
  • 3University of Maryland, United States

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 μm 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.

Keywords: viral metagenomics, 16S rRNA, Bacteriophage, polymerase A, microbiota, virome

Received: 20 Feb 2018; Accepted: 09 Apr 2018.

Edited by:

George S. Bullerjahn, Bowling Green State University, United States

Reviewed by:

Hélène Montanié, University of La Rochelle, France
Pradeep Ram Angia Sriram, UMR6023 Laboratoire Microorganismes Génome Et Environnement (LMGE), France  

Copyright: © 2018 Chopyk, Allard, Nasko, Bui, Mongodin and Sapkota. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

* Correspondence: Dr. Amy R. Sapkota, School of Public Health, University of Maryland, College Park, United States, ars@umd.edu