Metagenomic Characterisation of the Viral Community of Lough Neagh, the Largest Freshwater Lake in Ireland

RESEARCH ARTICLE Metagenomic Characterisation of the Viral Community of Lough Neagh, the Largest Freshwater Lake in Ireland Timofey Skvortsov1, Colin de Leeuwe1, John P. Quinn1, John W. McGrath1, Christopher C. R. Allen1, Yvonne McElarney2, Catherine Watson2, Ksenia Arkhipova1, Rob Lavigne3, Leonid A. Kulakov1* 1 School of Biological Sciences, The Queen’s University of Belfast, Belfast, Northern Ireland, United Kingdom, 2 Agri-Food & Biosciences Institute, Belfast, Northern Ireland, United Kingdom, 3 Laboratory of Gene Technology, KU Leuven, Leuven, Belgium * Abstract OPEN ACCESS Citation: Skvortsov T, de Leeuwe C, Quinn JP, McGrath JW, Allen CCR, McElarney Y, et al. (2016) Metagenomic Characterisation of the Viral Community of Lough Neagh, the Largest Freshwater Lake in Ireland. PLoS ONE 11(2): e0150361. doi:10.1371/journal.pone.0150361 Editor: Bas E. Dutilh, Universiteit Utrecht, NETHERLANDS Received: September 2, 2015 Accepted: February 12, 2016 Published: February 29, 2016 Copyright: © 2016 Skvortsov et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Data Availability Statement: Unassembled unprocessed reads from Lough Neagh viral metagenome are available from NCBI SRA (http:// www.ncbi.nlm.nih.gov/sra) under the following accession numbers: STUDY: SRP062094; SAMPLE: SRS1024521; EXPERIMENT: SRX1134649; RUN: SRR2147000. Processed reads from Lough Neagh viral metagenome are available from MetaVir (http:// metavir-meb.univ-bpclermont.fr/) under the following accession numbers: 1. Unassembled reads: Project name: Lough Neagh – 4pW, MetaVir Project id: 4925; 2. Sequence reads from Lough Neagh viral Lough Neagh is the largest and the most economically important lake in Ireland. It is also one of the most nutrient rich amongst the world’s major lakes. In this study, 16S rRNA analysis of total metagenomic DNA from the water column of Lough Neagh has revealed a high proportion of Cyanobacteria and low levels of Actinobacteria, Acidobacteria, Chloroflexi, and Firmicutes. The planktonic virome of Lough Neagh has been sequenced and 2,298,791 2×300 bp Illumina reads analysed. Comparison with previously characterised lakes demonstrates that the Lough Neagh viral community has the highest level of sequence diversity. Only about 15% of reads had homologs in the RefSeq database and tailed bacteriophages (Caudovirales) were identified as a major grouping. Within the Caudovirales, the Podoviridae and Siphoviridae were the two most dominant families (34.3% and 32.8% of the reads with sequence homology to the RefSeq database), while ssDNA bacteriophages constituted less than 1% of the virome. Putative cyanophages were found to be abundant. 66,450 viral contigs were assembled with the largest one being 58,805 bp; its existence, and that of another 34,467 bp contig, in the water column was confirmed. Analysis of the contigs confirmed the high abundance of cyanophages in the water column. Introduction Lough Neagh is the largest freshwater lake in the British Isles. It is located in Northern Ireland about 30 km to the west of Belfast (54°370 06@N, 6°230 43@W) and has dimensions of 30 km by 15 km. With a mean depth of just 9 m, and a surface area of 392 km2, the relatively high mean wind speeds locally (>4.5 m sec -1) ensure that the 3.5 km3 of water it contains is completely mixed; oxygen saturation levels rarely drop below 60%. Lough Neagh serves as a main source of potable water in Northern Ireland, providing more than 40% of the region’s supply. Among its other uses, the lake contains Europe’s largest eel fishery, provides sand for the construction industry and offers many tourism and leisure activities. Full details of the lake and of its catchment can be found in [1]. PLOS ONE | DOI:10.1371/journal.pone.0150361 February 29, 2016 1 / 19 Metagenomic Analysis of the Virome of Lough Neagh metagenome assembled into contigs with IDBA-UD, Project name: Lough Neagh – 4pW contigs, MetaVir Project id: 5053. Unassembled reads from Lough Neagh viral metagenome processed by MG-RAST pipeline are available from MG-RAST webserver (http://metagenomics.anl.gov/metagenomics.cgi). MG-RAST ID: 4585272.3. Metagenome Name: Lough Neagh—4pW. Bacterial 16S rRNA sequences are available as Supporting Information file “S1 Datasets” accompanying the manuscript. Funding: The work was supported by Leverhulme Trust (https://www.leverhulme.ac.uk/); Grant RPG2013-040, received by LAK, JPQ, JWM, and CCRA. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The authors have declared that no competing interests exist. Lough Neagh also has a long history of cultural eutrophication; it receives discharges from several wastewater and sewage treatment plants and from diffuse agricultural sources across its catchment of 4,500 km2 with a population of 390,000 [2]. This has caused a shift from mesotrophic conditions at the start of the 20th century to its present status as one of the world’s most hypertrophic lakes–a situation that threatens to irreversibly change its ecosystem. For example, algal species richness has decreased over the last century, with a progressive increase in the dominance of cyanobacteria, most recently of non-diazotrophic species [2]. Although the ecology of Lough Neagh has been studied extensively during the last several decades, little is known about its total bacterial populations [3], whilst the viral community of Lough Neagh has never been studied, even though this is likely to make a major contribution to nutrient cycling in the lake. Bacteriophages represent the most numerous and important constituents of microbial communities and are likely to play an extremely important role in the cycling of nutrients [4, 5]. As a result, metagenomic analyses supported by next generation sequencing have been widely conducted in marine environments, but freshwater viromes have so far attracted much less attention. Among the first studies in this area was an investigation of viral communities in fish ponds [6], followed by the characterisation of RNA viromes from a freshwater lake [7] and the profiling of viral diversity in Lake Limnopolar (Byers Peninsula, Antarctica) [8]. Viral metagenomic studies have also been carried out on four freshwater ponds located in the Sahara Desert [9], on Feitsui freshwater reservoir in North Taiwan [10], and at two sites in the aquaculture facility of Kent SeaTech Corporation in California, USA [11]. The detailed study reported in [12] demonstrated the relatedness of viromes from two temperate but ecologically different French lakes, and their genetic distinctiveness from other aquatic communities. Among their findings was the demonstration of similarities in viromes from related environm (...truncated)