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Stephens D, Faghihi Z, Moniruzzaman M. Widespread occurrence and diverse origins of polintoviruses influence lineage-specific genome dynamics in stony corals. Virus Evol 2024; 10:veae039. [PMID: 38808038 PMCID: PMC11131425 DOI: 10.1093/ve/veae039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 04/29/2024] [Accepted: 05/12/2024] [Indexed: 05/30/2024] Open
Abstract
Stony corals (Order: Scleractinia) are central to vital marine habitats known as coral reefs. Numerous stressors in the Anthropocene are contributing to the ongoing decline in coral reef health and coverage. While viruses are established modulators of marine microbial dynamics, their interactions within the coral holobiont and impact on coral health and physiology remain unclear. To address this key knowledge gap, we investigated diverse stony coral genomes for 'endogenous' viruses. Our study uncovered a remarkable number of integrated viral elements recognized as 'Polintoviruses' (Class Polintoviricetes) in thirty Scleractinia genomes; with several species harboring hundreds to thousands of polintoviruses. We reveal massive paralogous expansion of polintoviruses in stony coral genomes, alongside the presence of integrated elements closely related to Polinton-like viruses (PLVs), a group of viruses that exist as free virions. These results suggest multiple integrations of polintoviruses and PLV-relatives, along with paralogous expansions, shaped stony coral genomes. Re-analysis of existing gene expression data reveals all polintovirus structural and non-structural hallmark genes are expressed, providing support for free virion production from polintoviruses. Our results, revealing a significant diversity of polintovirus across the Scleractinia order, open a new research avenue into polintovirus and their possible roles in disease, genomic plasticity, and environmental adaptation in this key group of organisms.
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Affiliation(s)
- Danae Stephens
- Department of Marine Biology and Ecology, The Rosenstiel School of Marine, Atmospheric and Earth Science, University of Miami, 4600 Rickenbacker Causeway, Miami, FL 33149-1031, USA
| | - Zahra Faghihi
- Department of Marine Biology and Ecology, The Rosenstiel School of Marine, Atmospheric and Earth Science, University of Miami, 4600 Rickenbacker Causeway, Miami, FL 33149-1031, USA
| | - Mohammad Moniruzzaman
- Department of Marine Biology and Ecology, The Rosenstiel School of Marine, Atmospheric and Earth Science, University of Miami, 4600 Rickenbacker Causeway, Miami, FL 33149-1031, USA
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Wang H, Liu K, He Z, Chen Y, Hu Z, Chen W, Leaw CP, Chen N. Extensive intragenomic variations of the 18S rDNA V4 region in the toxigenic diatom species Pseudo-nitzschia multistriata revealed through high-throughput sequencing. MARINE POLLUTION BULLETIN 2024; 201:116198. [PMID: 38428045 DOI: 10.1016/j.marpolbul.2024.116198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Revised: 02/21/2024] [Accepted: 02/21/2024] [Indexed: 03/03/2024]
Abstract
Metabarcoding analysis is an effective technique for monitoring the domoic acid-producing Pseudo-nitzschia species in marine environments, uncovering high-levels of molecular diversity. However, such efforts may result in the overinterpretation of Pseudo-nitzschia species diversity, as molecular diversity not only encompasses interspecies and intraspecies diversities but also exhibits extensive intragenomic variations (IGVs). In this study, we analyzed the V4 region of the 18S rDNA of 30 strains of Pseudo-nitzschia multistriata collected from the coasts of China. The results showed that each P. multistriata strain harbored about a hundred of unique 18S rDNA V4 sequence varieties, of which each represented by a unique amplicon sequence variant (ASV). This study demonstrated the extensive degree of IGVs in P. multistriata strains, suggesting that IGVs may also present in other Pseudo-nitzschia species and other phytoplankton species. Understanding the scope and levels of IGVs is crucial for accurately interpreting the results of metabarcoding analysis.
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Affiliation(s)
- Hui Wang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266200, China; College of Marine Science, University of Chinese Academy of Sciences, Beijing 100039, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Kuiyan Liu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266200, China; College of Marine Science, University of Chinese Academy of Sciences, Beijing 100039, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Ziyan He
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266200, China; College of Marine Science, University of Chinese Academy of Sciences, Beijing 100039, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Yang Chen
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266200, China; College of Marine Science, University of Chinese Academy of Sciences, Beijing 100039, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Zhangxi Hu
- Department of Aquaculture, College of Fisheries, Guangdong Ocean University, Zhanjiang, Guangdong 524088, China
| | - Weizhou Chen
- Institution of Marine Biology, Shantou University, Shantou, Guangdong 515063, China
| | - Chui Pin Leaw
- Bachok Marine Research Station, Institute of Ocean and Earth Sciences, University of Malaya, 16310 Bachok, Kelantan, Malaysia
| | - Nansheng Chen
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266200, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China; Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia, V5A 1S6, Canada.
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Liu K, Huang X, Ding X, Chen N. The high molecular diversity in Noctiluca scintillans is dominated by intra-genomic variations revealed by single cell high-throughput sequencing of 18S rDNA V4. HARMFUL ALGAE 2024; 132:102568. [PMID: 38331542 DOI: 10.1016/j.hal.2024.102568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 12/21/2023] [Accepted: 01/03/2024] [Indexed: 02/10/2024]
Abstract
The application of high-throughput sequencing (HTS) technologies has revolutionized research on phytoplankton biodiversity by generating an unprecedented amount of molecular data in marine ecosystem surveys. However, high-level of molecular diversity uncovered in HTS-based metabarcoding analyses may lead to overinterpretation of phytoplankton diversity due to excessive intra-genomic variations (IGVs). The aims in this study are to explore the nature of phytoplankton molecular diversity and to test the hypothesis. We carried out single-cell metabarcoding analysis of 18S rDNA V4 sequences obtained in single Noctiluca scintillans cells isolated from various sites in coastal waters of China. Results showed that each single N. scintillans cell harbored a high level of IGVs with about 100 amplicon sequence variants (ASVs). The large numbers of non-dominant ASVs identified in N. scintillans cells, which might correspond to the larger numbers of ASVs annotated as N. scintillans and showed similar temporal dynamics in metabarcoding analyses, could inflate the inter-species diversity or intra-species genetic diversity. In addition, there were large numbers of additional ASVs that were not annotated as N. scintillans. These non-N. scintillans ASVs might represent diverse preys for N. scintillans, consistent with previous reports that N. scintillans may act as chance predator of a broad-spectrum preys. This single-cell study has unambiguously demonstrated that the existence of high levels of IGVs in N. scintillans and most likely many other phytoplankton species, demonstrating that the majority of the molecular diversity revealed in metabarcoding analysis, which were generally interpreted as the sum of inter-species diversity and intra-species diversity, actually included high levels of IGVs and should be interpreted with caution.
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Affiliation(s)
- Kuiyan Liu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266200, China; College of Marine Science, University of Chinese Academy of Sciences, Beijing 100039, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Xianliang Huang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266200, China; College of Marine Science, University of Chinese Academy of Sciences, Beijing 100039, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Xiangxiang Ding
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266200, China; College of Marine Science, University of Chinese Academy of Sciences, Beijing 100039, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Nansheng Chen
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266200, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China; Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia, V5A 1S6, Canada.
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Terzin M, Laffy PW, Robbins S, Yeoh YK, Frade PR, Glasl B, Webster NS, Bourne DG. The road forward to incorporate seawater microbes in predictive reef monitoring. ENVIRONMENTAL MICROBIOME 2024; 19:5. [PMID: 38225668 PMCID: PMC10790441 DOI: 10.1186/s40793-023-00543-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 12/11/2023] [Indexed: 01/17/2024]
Abstract
Marine bacterioplankton underpin the health and function of coral reefs and respond in a rapid and sensitive manner to environmental changes that affect reef ecosystem stability. Numerous meta-omics surveys over recent years have documented persistent associations of opportunistic seawater microbial taxa, and their associated functions, with metrics of environmental stress and poor reef health (e.g. elevated temperature, nutrient loads and macroalgae cover). Through positive feedback mechanisms, disturbance-triggered heterotrophic activity of seawater microbes is hypothesised to drive keystone benthic organisms towards the limit of their resilience and translate into shifts in biogeochemical cycles which influence marine food webs, ultimately affecting entire reef ecosystems. However, despite nearly two decades of work in this space, a major limitation to using seawater microbes in reef monitoring is a lack of a unified and focused approach that would move beyond the indicator discovery phase and towards the development of rapid microbial indicator assays for (near) real-time reef management and decision-making. By reviewing the current state of knowledge, we provide a comprehensive framework (defined as five phases of research and innovation) to catalyse a shift from fundamental to applied research, allowing us to move from descriptive to predictive reef monitoring, and from reactive to proactive reef management.
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Affiliation(s)
- Marko Terzin
- Australian Institute of Marine Science, PMB no3 Townsville MC, Townsville, QLD, 4810, Australia.
- College of Science and Engineering, James Cook University, Townsville, QLD, 4811, Australia.
- AIMS@JCU, James Cook University, Townsville, QLD, 4811, Australia.
| | - Patrick W Laffy
- Australian Institute of Marine Science, PMB no3 Townsville MC, Townsville, QLD, 4810, Australia
- AIMS@JCU, James Cook University, Townsville, QLD, 4811, Australia
| | - Steven Robbins
- Australian Centre for Ecogenomics, University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Yun Kit Yeoh
- Australian Institute of Marine Science, PMB no3 Townsville MC, Townsville, QLD, 4810, Australia
- AIMS@JCU, James Cook University, Townsville, QLD, 4811, Australia
| | - Pedro R Frade
- Natural History Museum Vienna, 1010, Vienna, Austria
| | - Bettina Glasl
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, 1030, Vienna, Austria
| | - Nicole S Webster
- Australian Institute of Marine Science, PMB no3 Townsville MC, Townsville, QLD, 4810, Australia
- Australian Centre for Ecogenomics, University of Queensland, St. Lucia, QLD, 4072, Australia
- Australian Antarctic Program, Department of Climate Change, Energy, the Environment and Water, Kingston, TAS, 7050, Australia
| | - David G Bourne
- Australian Institute of Marine Science, PMB no3 Townsville MC, Townsville, QLD, 4810, Australia.
- College of Science and Engineering, James Cook University, Townsville, QLD, 4811, Australia.
- AIMS@JCU, James Cook University, Townsville, QLD, 4811, Australia.
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Alexander H, Hu SK, Krinos AI, Pachiadaki M, Tully BJ, Neely CJ, Reiter T. Eukaryotic genomes from a global metagenomic data set illuminate trophic modes and biogeography of ocean plankton. mBio 2023; 14:e0167623. [PMID: 37947402 PMCID: PMC10746220 DOI: 10.1128/mbio.01676-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 09/27/2023] [Indexed: 11/12/2023] Open
Abstract
Metagenomics is a powerful method for interpreting the ecological roles and physiological capabilities of mixed microbial communities. Yet, many tools for processing metagenomic data are neither designed to consider eukaryotes nor are they built for an increasing amount of sequence data. EukHeist is an automated pipeline to retrieve eukaryotic and prokaryotic metagenome-assembled genomes (MAGs) from large-scale metagenomic sequence data sets. We developed the EukHeist workflow to specifically process large amounts of both metagenomic and/or metatranscriptomic sequence data in an automated and reproducible fashion. Here, we applied EukHeist to the large-size fraction data (0.8-2,000 µm) from Tara Oceans to recover both eukaryotic and prokaryotic MAGs, which we refer to as TOPAZ (Tara Oceans Particle-Associated MAGs). The TOPAZ MAGs consisted of >900 environmentally relevant eukaryotic MAGs and >4,000 bacterial and archaeal MAGs. The bacterial and archaeal TOPAZ MAGs expand upon the phylogenetic diversity of likely particle- and host-associated taxa. We use these MAGs to demonstrate an approach to infer the putative trophic mode of the recovered eukaryotic MAGs. We also identify ecological cohorts of co-occurring MAGs, which are driven by specific environmental factors and putative host-microbe associations. These data together add to a number of growing resources of environmentally relevant eukaryotic genomic information. Complementary and expanded databases of MAGs, such as those provided through scalable pipelines like EukHeist, stand to advance our understanding of eukaryotic diversity through increased coverage of genomic representatives across the tree of life.IMPORTANCESingle-celled eukaryotes play ecologically significant roles in the marine environment, yet fundamental questions about their biodiversity, ecological function, and interactions remain. Environmental sequencing enables researchers to document naturally occurring protistan communities, without culturing bias, yet metagenomic and metatranscriptomic sequencing approaches cannot separate individual species from communities. To more completely capture the genomic content of mixed protistan populations, we can create bins of sequences that represent the same organism (metagenome-assembled genomes [MAGs]). We developed the EukHeist pipeline, which automates the binning of population-level eukaryotic and prokaryotic genomes from metagenomic reads. We show exciting insight into what protistan communities are present and their trophic roles in the ocean. Scalable computational tools, like EukHeist, may accelerate the identification of meaningful genetic signatures from large data sets and complement researchers' efforts to leverage MAG databases for addressing ecological questions, resolving evolutionary relationships, and discovering potentially novel biodiversity.
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Affiliation(s)
- Harriet Alexander
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
| | - Sarah K. Hu
- Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
| | - Arianna I. Krinos
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
- MIT-WHOI Joint Program in Oceanography/Applied Ocean Science and Engineering, Cambridge and Woods Hole, Massachusetts, USA
| | - Maria Pachiadaki
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
| | - Benjamin J. Tully
- Department of Biological Sciences, University of Southern California, Los Angeles, California, USA
| | - Christopher J. Neely
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, California, USA
| | - Taylor Reiter
- Population Health and Reproduction, University of California, Davis, Davis, California, USA
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