Ponds 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. Water 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. Overall, 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.

中文翻译：

---

从淡水农业池塘中回收的细菌和病毒宏基因组组合的分类和功能的季节性动态


池塘是支持人类和环境活动的重要淡水栖息地。然而，相对于较大的池塘（例如河流、湖泊），池塘的研究还不够，特别是在微生物群落方面。我们的研究旨在通过使用独立于培养物的高通量测序来评估淡水农业池塘中细菌和病毒群落的动态、分类和功能来填补这一知识空白。水样 (n = 14) 于 2017 年 6 月至 2018 年 5 月期间从大西洋中部的一个农业池塘采集，并依次通过 1 和 0.2 μm 滤膜过滤。然后从每个过滤器中提取总 DNA，合并，并在 Illumina HiSeq 2500 平台上进行 16S rRNA 基因和鸟枪测序。此外，有八次使用化学浓缩对水滤液进行病毒宏基因组（病毒组）处理，然后进行鸟枪法测序。变形菌门是一种普遍存在的淡水门，在全年的所有采样日期都非常丰富。然而，环境特征似乎驱动了社区的结构。例如，蓝藻（例如发菜）的丰度随着水温的升高而增加，而风暴事件似乎引发了总体细菌多样性以及拟杆菌门的相对丰度的增加。这一事件还与抗生素抗性基因数量的增加有关。病毒部分以有尾病毒目（即Siphoviridae 和Myovirdae）的dsDNA 为主。总体而言，这项研究提供了迄今为止最大的池塘水微生物生态学数据集之一，揭示了微生物分类组成和功能潜力的季节性趋势。