Abstract
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.
Highlights
Growing urbanization and climate variability have placed immense pressure on the finite supply of groundwater available for agricultural irrigation
The most abundant pond water phyla were Actinobacteria, Proteobacteria, and Bacteroidetes in all samples, their average relative abundance fluctuated over the time course and between filter pore sizes (Figure 1A and Supplementary Table S1, S2)
While ponds represent a potential source of irrigation water, provided adequate filtering and monitoring technologies are employed, it is important to keep in mind their role in the ecosphere. Their small size and shallow depth enables a complex community of aquatic plants and macroinvertebrate species, as well as an interacting community of microorganisms
Summary
Growing urbanization and climate variability have placed immense pressure on the finite supply of groundwater available for agricultural irrigation. Dynamic Microbial Populations in Freshwater Pond standard, ponds are generally defined as small (1 m2 to ∼50,000 m2), shallow, standing water bodies that can either permanently or temporarily collect freshwater (Biggs et al, 2005; De Meester et al, 2005; Céréghino et al, 2008). These small water bodies are known to house a rich tapestry of aquatic plant and macroinvertebrate species, even greater than that of other larger water bodies (e.g., lakes and rivers) (Biggs et al, 2005). Assessing the microbial diversity and interactions of these complex water bodies is a critical first step with regard to completing a comprehensive characterization of pond biodiversity, and evaluating the suitability of pond freshwater for agricultural applications, such as the irrigation of food crops
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