Evaluating nanopore sequencing for microbial community characterization in catfish pond water

IF 2.3 3区 农林科学 Q2 FISHERIES
Caitlin E. Older, Bradley M. Richardson, Monica Wood, Geoffrey C. Waldbieser, Cynthia Ware, Matt J. Griffin, Brian D. Ott
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Abstract

In the United States, catfish are primarily farmed in earthen ponds, resulting in an aquatic environment influenced both by management practices and natural ecological processes. Profiling pond water microbiota can be useful for understanding what conditions may lead to microbial communities associated with production issues and could inform management practices. The aim of this study was to identify appropriate methods for bacterial community profiling of catfish pond water with nanopore sequencing of the 16S rRNA gene. To this end, two forward primers, two reverse primers, and three different polymerase chain reaction (PCR) cycle numbers were tested on a mock community consisting of aquaculture-relevant bacteria. The optimized protocol was applied to water samples obtained from three experimental catfish ponds sampled in May, June, August, and September 2020. Applying these methods to pond samples allowed for the identification of 1488 genera, primarily within four dominating phyla: Actinobacteriota, Bacteroidota, Cyanobacteria, and Firmicutes. High variation was observed between individual ponds and sampling timepoints; only 18 of the 1488 genera were found in relative abundances ≥1% in all ponds from at least one sampling point. Despite this variation, consistent results could be observed. Samples obtained from the month of September had the highest number of observed genera, and samples from June had the lowest. Overall, these data demonstrated individual ponds represent distinct microcosms composed of unique bacterial communities, although this pond effect was secondary to the influence of sampling month on pond community composition.

Abstract Image

纳米孔测序用于鲶鱼池塘水中微生物群落特征的评价
在美国,鲶鱼主要在土塘中养殖,其水生环境受到管理方法和自然生态过程的双重影响。剖析池塘水体微生物群落有助于了解哪些条件可能导致与生产问题相关的微生物群落,并为管理实践提供信息。本研究的目的是利用 16S rRNA 基因的纳米孔测序确定鲶鱼池塘水细菌群落分析的适当方法。为此,在由水产养殖相关细菌组成的模拟群落上测试了两种正向引物、两种反向引物和三种不同的聚合酶链反应(PCR)周期数。优化方案适用于 2020 年 5 月、6 月、8 月和 9 月从三个实验性鲶鱼池塘采集的水样。将这些方法应用于池塘样本可鉴定出 1488 个菌属,主要属于四个主要门类:放线菌门、类杆菌门、蓝藻门和固着菌门。各个池塘和采样时间点之间的差异很大;在 1488 个菌属中,只有 18 个菌属在至少一个采样点的所有池塘中的相对丰度≥1%。尽管存在这种差异,但仍可观察到一致的结果。在 9 月份采集的样本中,观察到的种属数量最多,而在 6 月份采集的样本中,观察到的种属数量最少。总体而言,这些数据表明,单个池塘代表了由独特细菌群落组成的独特微生态系统,尽管这种池塘效应次于取样月份对池塘群落组成的影响。
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来源期刊
CiteScore
5.90
自引率
7.10%
发文量
69
审稿时长
2 months
期刊介绍: The Journal of the World Aquaculture Society is an international scientific journal publishing original research on the culture of aquatic plants and animals including: Nutrition; Disease; Genetics and breeding; Physiology; Environmental quality; Culture systems engineering; Husbandry practices; Economics and marketing.
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