Seasonal dynamics in taxonomy and function within bacterial and viral metagenomic assemblages recovered from a freshwater agricultural pond

Jessica Chopyk,Sarah Allard,Anthony Bui,Mihai Pop,Emmanuel F Mongodin,Daniel J Nasko,Amy R Sapkota

doi:10.1186/s40793-020-00365-8

Abstract

BackgroundPonds are important freshwater habitats that support both human and environmental activities. However, relative to their larger counterparts (e.g. rivers, lakes), ponds are understudied, especially with regard to their microbial communities. Our study aimed to fill this knowledge gap by using culture-independent, high-throughput sequencing to assess the dynamics, taxonomy, and functionality of bacterial and viral communities in a freshwater agricultural pond.ResultsWater samples (n = 14) were collected from a Mid-Atlantic agricultural pond between June 2017 and May 2018 and filtered sequentially through 1 and 0.2 μm filter membranes. Total DNA was then extracted from each filter, pooled, and subjected to 16S rRNA gene and shotgun sequencing on the Illumina HiSeq 2500 platform. Additionally, on eight occasions water filtrates were processed for viral metagenomes (viromes) using chemical concentration and then shotgun sequenced. A ubiquitous freshwater phylum, Proteobacteria was abundant at all sampling dates throughout the year. However, environmental characteristics appeared to drive the structure of the community. For instance, the abundance of Cyanobacteria (e.g. Nostoc) increased with rising water temperatures, while a storm event appeared to trigger an increase in overall bacterial diversity, as well as the relative abundance of Bacteroidetes. This event was also associated with an increase in the number of antibiotic resistance genes. The viral fractions were dominated by dsDNA of the order Caudovirales, namely Siphoviridae and Myovirdae.ConclusionsOverall, this study provides one of the largest datasets on pond water microbial ecology to date, revealing seasonal trends in the microbial taxonomic composition and functional potential.

Highlights

Ponds are important freshwater habitats that support both human and environmental activities
Through the use of shotgun metagenomics, that features of the bacterial community are strongly influenced by seasonal forces, including temperature, conductivity, precipitation, and turbidity
We noted that the abundance of Cyanobacteria (e.g. Nostoc spp), increased with rising ambient water temperature

Summary

Introduction

Ponds are important freshwater habitats that support both human and environmental activities. Ponds occupy a greater total area than lakes and are considered to be functionally and ecologically distinct, playing a major role in the global cycling of carbon and supporting a high level of macro- and micro- species diversity [1,2,3,4,5,6]. Along with those that are formed by natural processes, there are many ponds that are human constructed for a variety of recreational, industrial, agricultural, and aesthetic purposes [1, 7]. Outside of extreme environments (e.g. saline/hypersaline [10,11,12], thermokarsts [13]), and aquaculture facilities [14,15,16] ponds remain largely understudied [17], especially with regard to their microbial communities

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Conclusion