Background: 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.
Goal: 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.
Objectives: (i) survey the bacterial consortium utilizing different filter pore sizes (1 μm and 0.2 μm); (ii) characterize the diversity and abundance of the bacteriophage within the viral community; and (iii) compare the phylogeny of pond viromes across time using the phylogenetically relevant, and biologically meaningful, Pol I protein.
Approach: 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.
Results: Bacterial community profiling showed significant shifts over time, 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.
Importance to public health: Overall, these data suggest that farm pond water harbors a diverse core of interacting microbial species whose abundance is influenced by environmental variables and, therefore, may require water treatment technologies to assure its safety for use in irrigation.