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Ha AD, Moniruzzaman M, Aylward FO. Assessing the biogeography of marine giant viruses in four oceanic transects. ISME COMMUNICATIONS 2023; 3:43. [PMID: 37120676 PMCID: PMC10148842 DOI: 10.1038/s43705-023-00252-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 04/11/2023] [Accepted: 04/19/2023] [Indexed: 05/01/2023]
Abstract
Viruses of the phylum Nucleocytoviricota are ubiquitous in ocean waters and play important roles in shaping the dynamics of marine ecosystems. In this study, we leveraged the bioGEOTRACES metagenomic dataset collected across the Atlantic and Pacific Oceans to investigate the biogeography of these viruses in marine environments. We identified 330 viral genomes, including 212 in the order Imitervirales and 54 in the order Algavirales. We found that most viruses appeared to be prevalent in shallow waters (<150 m), and that viruses of the Mesomimiviridae (Imitervirales) and Prasinoviridae (Algavirales) are by far the most abundant and diverse groups in our survey. Five mesomimiviruses and one prasinovirus are particularly widespread in oligotrophic waters; annotation of these genomes revealed common stress response systems, photosynthesis-associated genes, and oxidative stress modulation genes that may be key to their broad distribution in the pelagic ocean. We identified a latitudinal pattern in viral diversity in one cruise that traversed the North and South Atlantic Ocean, with viral diversity peaking at high latitudes of the northern hemisphere. Community analyses revealed three distinct Nucleocytoviricota communities across latitudes, categorized by latitudinal distance towards the equator. Our results contribute to the understanding of the biogeography of these viruses in marine systems.
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Affiliation(s)
- Anh D Ha
- Department of Biological Sciences, Virginia Tech, 926 West Campus Drive, Blacksburg, VA, 24061, USA
| | - Mohammad Moniruzzaman
- Department of Marine Biology and Ecology, Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, 4600 Rickenbacker Causeway, Miami, FL, 33149, USA
| | - Frank O Aylward
- Department of Biological Sciences, Virginia Tech, 926 West Campus Drive, Blacksburg, VA, 24061, USA.
- Center for Emerging, Zoonotic, and Arthropod-Borne Infectious Disease, Virginia Tech, Blacksburg, VA, 24061, USA.
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Ha AD, Moniruzzaman M, Aylward FO. Assessing the biogeography of marine giant viruses in four oceanic transects. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.30.526306. [PMID: 36778472 PMCID: PMC9915497 DOI: 10.1101/2023.01.30.526306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Viruses of the phylum Nucleocytoviricota are ubiquitous in ocean waters and play important roles in shaping the dynamics of marine ecosystems. In this study, we leveraged the bioGEOTRACES metagenomic dataset collected across the Atlantic and Pacific Oceans to investigate the biogeography of these viruses in marine environments. We identified 330 viral genomes, including 212 in the order Imitervirales and 54 in the order Algavirales . We found that most viruses appeared to be prevalent in shallow waters (<150 meters), and that viruses of the Mesomimiviridae ( Imitervirales ) and Prasinoviridae ( Algavirales ) are by far the most abundant and diverse groups in our survey. Five mesomimiviruses and one prasinovirus are particularly widespread in oligotrophic waters; annotation of these genomes revealed common stress response systems, photosynthesis-associated genes, and oxidative stress modulation that may be key to their broad distribution in the pelagic ocean. We identified a latitudinal pattern in viral diversity in one cruise that traversed the North and South Atlantic Ocean, with viral diversity peaking at high latitudes of the northern hemisphere. Community analyses revealed three distinct Nucleocytoviricota communities across latitudes, categorized by latitudinal distance towards the equator. Our results contribute to the understanding of the biogeography of these viruses in marine systems.
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Affiliation(s)
- Anh D. Ha
- Department of Biological Sciences, Virginia Tech, Blacksburg VA, 24061
| | - Mohammad Moniruzzaman
- Rosenstiel School of Marine Atmospheric, and Earth Science, University of Miami, Coral Gables FL 33149
| | - Frank O. Aylward
- Department of Biological Sciences, Virginia Tech, Blacksburg VA, 24061
- Center for Emerging, Zoonotic, and Arthropod-Borne Infectious Disease, Virginia Tech, Blacksburg VA, 24061
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Raes EJ, Karsh K, Sow SLS, Ostrowski M, Brown MV, van de Kamp J, Franco-Santos RM, Bodrossy L, Waite AM. Metabolic pathways inferred from a bacterial marker gene illuminate ecological changes across South Pacific frontal boundaries. Nat Commun 2021; 12:2213. [PMID: 33850115 PMCID: PMC8044245 DOI: 10.1038/s41467-021-22409-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 03/09/2021] [Indexed: 02/01/2023] Open
Abstract
Global oceanographic monitoring initiatives originally measured abiotic essential ocean variables but are currently incorporating biological and metagenomic sampling programs. There is, however, a large knowledge gap on how to infer bacterial functions, the information sought by biogeochemists, ecologists, and modelers, from the bacterial taxonomic information (produced by bacterial marker gene surveys). Here, we provide a correlative understanding of how a bacterial marker gene (16S rRNA) can be used to infer latitudinal trends for metabolic pathways in global monitoring campaigns. From a transect spanning 7000 km in the South Pacific Ocean we infer ten metabolic pathways from 16S rRNA gene sequences and 11 corresponding metagenome samples, which relate to metabolic processes of primary productivity, temperature-regulated thermodynamic effects, coping strategies for nutrient limitation, energy metabolism, and organic matter degradation. This study demonstrates that low-cost, high-throughput bacterial marker gene data, can be used to infer shifts in the metabolic strategies at the community scale.
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Affiliation(s)
- Eric J Raes
- CSIRO Oceans and Atmosphere, Hobart, TAS, Australia.
- Ocean Frontier Institute and Department of Oceanography, Dalhousie University, Halifax, NS, Canada.
| | | | - Swan L S Sow
- CSIRO Oceans and Atmosphere, Hobart, TAS, Australia
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS, Australia
- NIOZ Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, Den Burg, The Netherlands
| | - Martin Ostrowski
- Climate Change Cluster, University of Technology Sydney, Sydney, NSW, Australia
| | - Mark V Brown
- School of Environmental and Life Sciences, The University of Newcastle, Callaghan, NSW, Australia
| | | | - Rita M Franco-Santos
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS, Australia
| | | | - Anya M Waite
- Ocean Frontier Institute and Department of Oceanography, Dalhousie University, Halifax, NS, Canada
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Semedo M, Lopes E, Baptista MS, Oller-Ruiz A, Gilabert J, Tomasino MP, Magalhães C. Depth Profile of Nitrifying Archaeal and Bacterial Communities in the Remote Oligotrophic Waters of the North Pacific. Front Microbiol 2021; 12:624071. [PMID: 33732221 PMCID: PMC7959781 DOI: 10.3389/fmicb.2021.624071] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 02/01/2021] [Indexed: 12/21/2022] Open
Abstract
Nitrification is a vital ecosystem function in the open ocean that regenerates inorganic nitrogen and promotes primary production. Recent studies have shown that the ecology and physiology of nitrifying organisms is more complex than previously postulated. The distribution of these organisms in the remote oligotrophic ocean and their interactions with the physicochemical environment are relatively understudied. In this work, we aimed to evaluate the depth profile of nitrifying archaea and bacteria in the Eastern North Pacific Subtropical Front, an area with limited biological surveys but with intense trophic transferences and physicochemical gradients. Furthermore, we investigated the dominant physicochemical and biological relationships within and between ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), and nitrite-oxidizing bacteria (NOB) as well as with the overall prokaryotic community. We used a 16S rRNA gene sequencing approach to identify and characterize the nitrifying groups within the first 500 m of the water column and to analyze their abiotic and biotic interactions. The water column was characterized mainly by two contrasting environments, warm O2-rich surface waters with low dissolved inorganic nitrogen (DIN) and a cold O2-deficient mesopelagic layer with high concentrations of nitrate (NO3–). Thaumarcheotal AOA and bacterial NOB were highly abundant below the deep chlorophyll maximum (DCM) and in the mesopelagic. In the mesopelagic, AOA and NOB represented up to 25 and 3% of the total prokaryotic community, respectively. Interestingly, the AOA community in the mesopelagic was dominated by unclassified genera that may constitute a novel group of AOA highly adapted to the conditions observed at those depths. Several of these unclassified amplicon sequence variants (ASVs) were positively correlated with NO3– concentrations and negatively correlated with temperature and O2, whereas known thaumarcheotal genera exhibited the opposite behavior. Additionally, we found a large network of positive interactions within and between putative nitrifying ASVs and other prokaryotic groups, including 13230 significant correlations and 23 sub-communities of AOA, AOB, NOB, irrespective of their taxonomic classification. This study provides new insights into our understanding of the roles that AOA may play in recycling inorganic nitrogen in the oligotrophic ocean, with potential consequences to primary production in these remote ecosystems.
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Affiliation(s)
- Miguel Semedo
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Matosinhos, Portugal
| | - Eva Lopes
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Matosinhos, Portugal
| | - Mafalda S Baptista
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Matosinhos, Portugal.,Faculty of Sciences, University of Porto, Porto, Portugal.,International Centre for Terrestrial Antarctic Research, University of Waikato, Hamilton, New Zealand
| | - Ainhoa Oller-Ruiz
- Department of Chemical & Environmental Engineering, Universidad Politécnica de Cartagena (UPCT), Cartagena, Spain
| | - Javier Gilabert
- Department of Chemical & Environmental Engineering, Universidad Politécnica de Cartagena (UPCT), Cartagena, Spain
| | - Maria Paola Tomasino
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Matosinhos, Portugal
| | - Catarina Magalhães
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Matosinhos, Portugal.,Faculty of Sciences, University of Porto, Porto, Portugal.,School of Science, Faculty of Science and Engineering, University of Waikato, Hamilton, New Zealand
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Annual phytoplankton dynamics in coastal waters from Fildes Bay, Western Antarctic Peninsula. Sci Rep 2021; 11:1368. [PMID: 33446791 PMCID: PMC7809266 DOI: 10.1038/s41598-020-80568-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 12/22/2020] [Indexed: 01/04/2023] Open
Abstract
Year-round reports of phytoplankton dynamics in the West Antarctic Peninsula are rare and mainly limited to microscopy and/or pigment-based studies. We analyzed the phytoplankton community from coastal waters of Fildes Bay in the West Antarctic Peninsula between January 2014 and 2015 using metabarcoding of the nuclear and plastidial 18/16S rRNA gene from both size-fractionated and flow cytometry sorted samples. Overall 14 classes of photosynthetic eukaryotes were present in our samples with the following dominating: Bacillariophyta (diatoms), Pelagophyceae and Dictyochophyceae for division Ochrophyta, Mamiellophyceae and Pyramimonadophyceae for division Chlorophyta, Haptophyta and Cryptophyta. Each metabarcoding approach yielded a different image of the phytoplankton community with for example Prymnesiophyceae more prevalent in plastidial metabarcodes and Mamiellophyceae in nuclear ones. Diatoms were dominant in the larger size fractions and during summer, while Prymnesiophyceae and Cryptophyceae were dominant in colder seasons. Pelagophyceae were particularly abundant towards the end of autumn (May). In addition of Micromonas polaris and Micromonas sp. clade B3, both previously reported in Arctic waters, we detected a new Micromonas 18S rRNA sequence signature, close to, but clearly distinct from M. polaris, which potentially represents a new clade specific of the Antarctic. These results highlight the need for complementary strategies as well as the importance of year-round monitoring for a comprehensive description of phytoplankton communities in Antarctic coastal waters.
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