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Bruhn CS, Lundholm N, Hansen PJ, Wohlrab S, John U. Transition from a mixotrophic/heterotrophic protist community during the dark winter to a photoautotrophic spring community in surface waters of Disko Bay, Greenland. Front Microbiol 2024; 15:1407888. [PMID: 38887716 PMCID: PMC11180815 DOI: 10.3389/fmicb.2024.1407888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Accepted: 05/17/2024] [Indexed: 06/20/2024] Open
Abstract
Unicellular eukaryotic plankton communities (protists) are the major basis of the marine food web. The spring bloom is especially important, because of its high biomass. However, it is poorly described how the protist community composition in Arctic surface waters develops from winter to spring. We show that mixotrophic and parasitic organisms are prominent in the dark winter period. The transition period toward the spring bloom event was characterized by a high relative abundance of mixotrophic dinoflagellates, while centric diatoms and the haptophyte Phaeocystis pouchetii dominated the successive phototrophic spring bloom event during the study. The data shows a continuous community shift from winter to spring, and not just a dormant spring community waiting for the right environmental conditions. The spring bloom initiation commenced while sea ice was still scattering and absorbing the sunlight, inhibiting its penetration into the water column. The initial increase in fluorescence was detected relatively deep in the water column at ~55 m depth at the halocline, at which the photosynthetic cells accumulated, while a thick layer of snow and sea ice was still obstructing sunlight penetration of the surface water. This suggests that water column stratification and a complex interplay of abiotic factors eventually promote the spring bloom initiation.
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Affiliation(s)
- Claudia Sabine Bruhn
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
- Helmholtz-Centre Potsdam, German Research Centre for Geosciences GFZ, Potsdam, Germany
| | - Nina Lundholm
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Per Juel Hansen
- Department of Biology, Marine Biological Station, University of Copenhagen, Helsingør, Denmark
| | - Sylke Wohlrab
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
- Helmholtz Institute for Functional Marine Biodiversity at the University of Oldenburg, Oldenburg, Germany
| | - Uwe John
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
- Helmholtz Institute for Functional Marine Biodiversity at the University of Oldenburg, Oldenburg, Germany
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2
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Xu D, Kong H, Yang EJ, Wang Y, Li X, Sun P, Jiao N, Lee Y, Jung J, Cho KH. Spatial dynamics of active microeukaryotes along a latitudinal gradient: Diversity, assembly process, and co-occurrence relationships. ENVIRONMENTAL RESEARCH 2022; 212:113234. [PMID: 35390306 DOI: 10.1016/j.envres.2022.113234] [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: 06/29/2021] [Revised: 03/24/2022] [Accepted: 03/28/2022] [Indexed: 06/14/2023]
Abstract
Recent global warming is profoundly and increasingly influencing the Arctic ecosystem. Understanding how microeukaryote communities respond to changes in the Arctic Ocean is crucial for understanding their roles in the biogeochemical cycles of nutrients and elements. Between July 22 and August 19, 2016, during cruise ARA07, seawater samples were collected along a latitudinal transect extending from the East Sea of Korea to the central Arctic Ocean. Environmental RNA was extracted and the V4 hypervariable regions of the reverse transcribed SSU rRNA were amplified. The sequences generated by high throughput sequencing were clustered into zero-radius OTUs (ZOTUs), and the taxonomic identities of each ZOTU were assigned using SINTAX against the PR2 database. Thus, the diversity, community composition, and co-occurrence networks of size fractionated microeukaryotes were revealed. The present study found: 1) the alpha diversity of pico- and nano-sized microeukaryotes showed a latitudinal diversity gradient; 2) three distinct communities were identified, i.e., the Leg-A, Leg-B surface, and Leg-B subsurface chlorophyll a maximum (SCM) groups; 3) distinct network structure and composition were found in the three groups; and 4) water temperature was identified as the primary factor driving both the alpha and beta diversities of microeukaryotes. This study conducted a comprehensive and systematic survey of active microeukaryotes along a latitudinal gradient, elucidated the diversity, community composition, co-occurrence relationships, and community assembly processes among major microeukaryote assemblages, and will help shed more light on our understanding of the responses of microeukaryote communities to the changing Arctic Ocean.
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Affiliation(s)
- Dapeng Xu
- State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China; Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China.
| | - Hejun Kong
- State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China; Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
| | - Eun-Jin Yang
- Division of Polar Ocean Science, Korea Polar Research Institute, Incheon, South Korea
| | - Ying Wang
- State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China; Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
| | - Xinran Li
- State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China; Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
| | - Ping Sun
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystem, College of the Environment and Ecology, Xiamen University, Xiamen, 361102, China; Fujian Provincial Key Laboratory for Coastal Ecology and Environmental Studies, Xiamen University, Xiamen 361102, China.
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China; Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
| | - Youngju Lee
- Division of Polar Ocean Science, Korea Polar Research Institute, Incheon, South Korea
| | - Jinyoung Jung
- Division of Polar Ocean Science, Korea Polar Research Institute, Incheon, South Korea
| | - Kyoung-Ho Cho
- Division of Polar Ocean Science, Korea Polar Research Institute, Incheon, South Korea
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3
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Freyria NJ, Joli N, Lovejoy C. A decadal perspective on north water microbial eukaryotes as Arctic Ocean sentinels. Sci Rep 2021; 11:8413. [PMID: 33863972 PMCID: PMC8052464 DOI: 10.1038/s41598-021-87906-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 04/06/2021] [Indexed: 11/09/2022] Open
Abstract
The North Water region, between Greenland and Ellesmere Island, with high populations of marine birds and mammals, is an Arctic icon. Due to climate related changes, seasonal patterns in water column primary production are changing but the implications for the planktonic microbial eukaryote communities that support the ecosystem are unknown. Here we report microbial community phenology in samples collected over 12 years (2005–2018) from July to October and analysed using high throughput 18S rRNA V4 amplicon sequencing. Community composition was tied to seasonality with summer communities more variable than distinct October communities. In summer, sentinel pan-Arctic species, including a diatom in the Chaetoceros socialis-gelidus complex and the picochlorophyte Micromonas polaris dominated phytoplankton and were summer specialists. In autumn, uncultured undescribed open water dinoflagellates were favored, and their ubiquity suggests they are sentinels of arctic autumn conditions. Despite the input of nutrients into surface waters, autumn chlorophyll concentrations remained low, refuting projected scenarios that longer ice-free seasons are synonymous with high autumn production and a diatom dominated bloom. Overall, the summer sentinel microbial taxa are persisting, and a subset oceanic dinoflagellate should be monitored for possible ecosystem shifts as later autumn ice formation becomes prevalent elsewhere.
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Affiliation(s)
- Nastasia J Freyria
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Quebec, QC, Canada. .,Département de Biologie, Institut de Biologie Intégrative et des Systèmes, Université Laval, Quebec, QC, G1R1V6, Canada.
| | - Nathalie Joli
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Quebec, QC, Canada.,Institut de Biologie de L'École Normale Supérieure (IBENS), 75005, Paris, France
| | - Connie Lovejoy
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Quebec, QC, Canada. .,Département de Biologie, Institut de Biologie Intégrative et des Systèmes, Université Laval, Quebec, QC, G1R1V6, Canada.
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4
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Mars Brisbin M, Conover AE, Mitarai S. Influence of Regional Oceanography and Hydrothermal Activity on Protist Diversity and Community Structure in the Okinawa Trough. MICROBIAL ECOLOGY 2020; 80:746-761. [PMID: 32948905 DOI: 10.1007/s00248-020-01583-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 08/24/2020] [Indexed: 06/11/2023]
Abstract
Microbial eukaryotes (protists) contribute substantially to ecological functioning in marine ecosystems, but the relative importance of factors shaping protist diversity, such as environmental selection and dispersal, remains difficult to parse. Water masses of a back-arc basin with hydrothermal activity provide a unique opportunity for studying the effects of dispersal and environmental selection on protist communities. In this study, we used metabarcoding to characterize protist communities in the Okinawa Trough, a back-arc spreading basin containing at least twenty-five active hydrothermal vent fields. Water was sampled from four depths at fourteen stations spanning the length of the Okinawa Trough, including three sites influenced by nearby hydrothermal vent sites. While significant differences in community structure reflecting water depth were present, protist communities were mostly homogeneous horizontally. Protist communities in the bottom waters affected by hydrothermal activity were significantly different from communities in other bottom waters, suggesting that environmental factors can be especially important in shaping community composition under specific conditions. Amplicon sequence variants that were enriched in hydrothermally influenced bottom waters largely derived from cosmopolitan protists that were present, but rare, in other near-bottom samples, thus highlighting the importance of the rare biosphere.
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Affiliation(s)
- Margaret Mars Brisbin
- Marine Biophysics Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa, 904-0412, Japan.
| | - Asa E Conover
- Marine Biophysics Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa, 904-0412, Japan
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Satoshi Mitarai
- Marine Biophysics Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa, 904-0412, Japan
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5
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Photosynthetic Picoeukaryotes Diversity in the Underlying Ice Waters of the White Sea, Russia. DIVERSITY-BASEL 2020. [DOI: 10.3390/d12030093] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The White Sea is a unique basin combining features of temperate and arctic seas. The current state of its biocenoses can serve as a reference point in assessing the expected desalination of the ocean as a result of climate change. A metagenomic study of under-ice ice photosynthetic picoeukaryotes (PPEs) was undertaken by Illumina high-throughput sequencing of the 18S rDNA V4 region from probes collected in March 2013 and 2014. The PPE biomass in samples was 0.03–0.17 µg C·L−1 and their abundance varied from 10 cells·mL−1 to 140 cells·mL−1. There were representatives of 16 algae genera from seven classes and three supergroups, but Chlorophyta, especially Mamiellophyceae, dominated. The most represented genera were Micromonas and Mantoniella. For the first time, the predominance of Mantoniella (in four samples) and Bolidophyceae (in one sample) was observed in under-ice water. It can be assumed that a change in environmental conditions will lead to a considerable change in the structure of arctic PPE communities.
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6
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Nitrate Consumers in Arctic Marine Eukaryotic Communities: Comparative Diversities of 18S rRNA, 18S rRNA Genes, and Nitrate Reductase Genes. Appl Environ Microbiol 2019; 85:AEM.00247-19. [PMID: 31053582 DOI: 10.1128/aem.00247-19] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 04/27/2019] [Indexed: 11/20/2022] Open
Abstract
For photosynthetic microbial eukaryotes, the rate-limiting step in NO3 - assimilation is its reduction to nitrite (NO2 -), which is catalyzed by assimilatory nitrate reductase (NR). Oceanic productivity is primarily limited by available nitrogen and, although nitrate is the most abundant form of available nitrogen in oceanic waters, little is known about the identity of microbial eukaryotes that take up nitrate. This lack of knowledge is especially severe for ice-covered seas that are being profoundly affected by climate change. To address this, we examined the distribution and diversity of NR genes in the Arctic region by way of clone libraries and data mining of available metagenomes (total of 4.24 billion reads). We directly compared NR clone phylogenies with the V4 region of the 18S rRNA gene (DNA pool) and 18S rRNA (RNA pool) at two ice-influenced stations in the Canada Basin (Beaufort Sea). The communities from the two nucleic acid templates were similar at the level of major groups, and species identified by way of NR gene phylogeny and microscopy were a subset of the 18S results. Most NR genes from arctic clone libraries matched diatoms and chromist nanoflagellates, including novel clades, while the NR genes in arctic eukaryote metagenomes were dominated by chlorophyte NR, in keeping with the ubiquitous occurrence of Mamiellophyceae in the Arctic Ocean. Overall, these data suggest that a dynamic and mixed eukaryotic community utilizes nitrate across the Arctic region, and they show the potential utility of NR as a tool to identify ongoing changes in arctic photosynthetic communities.IMPORTANCE To better understand the diversity of primary producers in the Arctic Ocean, we targeted a nitrogen cycle gene, NR, which is required for phytoplankton to assimilate nitrate into organic forms of nitrogen macromolecules. We compared this to the more detailed taxonomy from ice-influenced stations using a general taxonomic gene (18S rRNA). NR genes were ubiquitous and could be classified as belonging to diatoms, dinoflagellates, other flagellates, chlorophytes, and unknown microbial eukaryotes, suggesting novel diversity of both species and metabolism in arctic phytoplankton.
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7
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Cunningham BR, Greenwold MJ, Lachenmyer EM, Heidenreich KM, Davis AC, Dudycha JL, Richardson TL. Light capture and pigment diversity in marine and freshwater cryptophytes. JOURNAL OF PHYCOLOGY 2019; 55:552-564. [PMID: 30468692 DOI: 10.1111/jpy.12816] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 10/22/2018] [Indexed: 06/09/2023]
Abstract
Phenotypic traits associated with light capture and phylogenetic relationships were characterized in 34 strains of diversely pigmented marine and freshwater cryptophytes. Nuclear SSU and partial LSU rDNA sequence data from 33 of these strains plus an additional 66 strains produced a concatenated rooted maximum likelihood tree that classified the strains into 7 distinct clades. Molecular and phenotypic data together support: (i) the reclassification of Cryptomonas irregularis NIES 698 to the genus Rhodomonas, (ii) revision of phycobiliprotein (PBP) diversity within the genus Hemiselmis to include cryptophyte phycocyanin (Cr-PC) 569, (iii) the inclusion of previously unidentified strain CCMP 2293 into the genus Falcomonas, even though it contains cryptophyte phycoerythrin 545 (Cr-PE 545), and (iv) the inclusion of previously unidentified strain CCMP 3175, which contains Cr-PE 545, in a clade with PC-containing Chroomonas species. A discriminant analysis-based model of group membership correctly predicted 70.6% of the clades using three traits: PBP concentration · cell-1 , the wavelength of PBP maximal absorption, and habitat. Non-PBP pigments (alloxanthin, chl-a, chl-c2 , α-carotene) did not contribute significantly to group classification, indicating the potential plasticity of these pigments and the evolutionary conservation of the PBPs. Pigment data showed evidence of trade-offs in investments in PBPs vs. chlorophylls (a +c2 ).
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Affiliation(s)
- Brady R Cunningham
- School of the Earth, Ocean & Environment, University of South Carolina, Columbia, South Carolina, 29208, USA
| | - Matthew J Greenwold
- Department of Biological Sciences, University of South Carolina, Columbia, South Carolina, 29208, USA
| | - Eric M Lachenmyer
- School of the Earth, Ocean & Environment, University of South Carolina, Columbia, South Carolina, 29208, USA
| | - Kristin M Heidenreich
- School of the Earth, Ocean & Environment, University of South Carolina, Columbia, South Carolina, 29208, USA
| | - Abigail C Davis
- School of the Earth, Ocean & Environment, University of South Carolina, Columbia, South Carolina, 29208, USA
| | - Jeffry L Dudycha
- Department of Biological Sciences, University of South Carolina, Columbia, South Carolina, 29208, USA
| | - Tammi L Richardson
- School of the Earth, Ocean & Environment, University of South Carolina, Columbia, South Carolina, 29208, USA
- Department of Biological Sciences, University of South Carolina, Columbia, South Carolina, 29208, USA
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8
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Hassett BT, Borrego EJ, Vonnahme TR, Rämä T, Kolomiets MV, Gradinger R. Arctic marine fungi: biomass, functional genes, and putative ecological roles. ISME JOURNAL 2019; 13:1484-1496. [PMID: 30745572 DOI: 10.1038/s41396-019-0368-1] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2018] [Revised: 01/06/2019] [Accepted: 01/22/2019] [Indexed: 01/07/2023]
Abstract
Recent molecular evidence suggests a global distribution of marine fungi; however, the ecological relevance and corresponding biological contributions of fungi to marine ecosystems remains largely unknown. We assessed fungal biomass from the open Arctic Ocean by applying novel biomass conversion factors from cultured isolates to environmental sterol and CARD-FISH data. We found an average of 16.54 nmol m-3 of ergosterol in sea ice and seawater, which corresponds to 1.74 mg C m-3 (444.56 mg C m-2 in seawater). Using Chytridiomycota-specific probes, we observed free-living and particulate-attached cells that averaged 34.07 µg C m-3 in sea ice and seawater (11.66 mg C m-2 in seawater). Summed CARD-FISH and ergosterol values approximate 1.77 mg C m-3 in sea ice and seawater (456.23 mg C m-2 in seawater), which is similar to biomass estimates of other marine taxa generally considered integral to marine food webs and ecosystem processes. Using the GeoChip microarray, we detected evidence for fungal viruses within the Partitiviridae in sediment, as well as fungal genes involved in the degradation of biomass and the assimilation of nitrate. To bridge our observations of fungi on particulate and the detection of degradative genes, we germinated fungal conidia in zooplankton fecal pellets and germinated fungal conidia after 8 months incubation in sterile seawater. Ultimately, these data suggest that fungi could be as important in oceanic ecosystems as they are in freshwater environments.
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Affiliation(s)
- B T Hassett
- UiT Norges arktiske universitet, BFE, NFH bygget, Framstredet 6, 9019, Tromsø, Norway.
| | - E J Borrego
- Texas A&M University, 435 Nagle Street, 2132 TAMU, College Station, TX, 77833, USA
| | - T R Vonnahme
- UiT Norges arktiske universitet, BFE, NFH bygget, Framstredet 6, 9019, Tromsø, Norway
| | - T Rämä
- UiT Norges arktiske universitet, BFE, NFH bygget, Framstredet 6, 9019, Tromsø, Norway
| | - M V Kolomiets
- Texas A&M University, 435 Nagle Street, 2132 TAMU, College Station, TX, 77833, USA
| | - R Gradinger
- UiT Norges arktiske universitet, BFE, NFH bygget, Framstredet 6, 9019, Tromsø, Norway
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Wang Y, Wang C, Jiang Y, Katz LA, Gao F, Yan Y. Further analyses of variation of ribosome DNA copy number and polymorphism in ciliates provide insights relevant to studies of both molecular ecology and phylogeny. SCIENCE CHINA-LIFE SCIENCES 2019; 62:203-214. [PMID: 30671886 DOI: 10.1007/s11427-018-9422-5] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 09/08/2018] [Accepted: 11/06/2018] [Indexed: 11/26/2022]
Abstract
Sequence-based approaches, such as analyses of ribosome DNA (rDNA) clone libraries and high-throughput amplicon sequencing, have been used extensively to infer evolutionary relationships and elucidate the biodiversity in microbial communities. However, recent studies demonstrate both rDNA copy number variation and intra-individual (intra-genomic) sequence variation in many organisms, which challenges the application of the rDNA-based surveys. In ciliates, an ecologically important clade of microbial eukaryotes, rDNA copy number and sequence variation are rarely studied. In the present study, we estimate the intraindividual small subunit rDNA (SSU rDNA) copy number and sequence variation in a wide range of taxa covering nine classes and 18 orders of the phylum Ciliophora. Our studies reveal that: (i) intra-individual sequence variation of SSU rDNA is ubiquitous in all groups of ciliates detected and the polymorphic level varies among taxa; (ii) there is a most common version of SSU rDNA sequence in each cell that is highly predominant and may represent the germline micronuclear template; (iii) compared with the most common version, other variant sequences differ in only 1-3 nucleotides, likely generated during macronuclear (somatic) amplification; (iv) the intra-cell sequence variation is unlikely to impact phylogenetic analyses; (v) the rDNA copy number in ciliates is highly variable, ranging from 103 to 106, with the highest record in Stentor roeselii. Overall, these analyses indicate the need for careful consideration of SSU rDNA variation in analyses of the role of ciliates in ecosystems.
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Affiliation(s)
- Yurui Wang
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
- Key Laboratory of Mariculture, Ocean University of China, Ministry of Education, Qingdao, 266003, China
| | - Chundi Wang
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
- Key Laboratory of Mariculture, Ocean University of China, Ministry of Education, Qingdao, 266003, China
| | - Yaohan Jiang
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
- Key Laboratory of Mariculture, Ocean University of China, Ministry of Education, Qingdao, 266003, China
| | - Laura A Katz
- Department of Biological Sciences, Smith College, Northampton, MA, 01063, USA
| | - Feng Gao
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China.
- Key Laboratory of Mariculture, Ocean University of China, Ministry of Education, Qingdao, 266003, China.
| | - Ying Yan
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China.
- Key Laboratory of Mariculture, Ocean University of China, Ministry of Education, Qingdao, 266003, China.
- Department of Biological Sciences, Smith College, Northampton, MA, 01063, USA.
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10
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Wang F, Xie Y, Wu W, Sun P, Wang L, Huang B. Picoeukaryotic Diversity And Activity in the Northwestern Pacific Ocean Based on rDNA and rRNA High-Throughput Sequencing. Front Microbiol 2019; 9:3259. [PMID: 30687258 PMCID: PMC6333705 DOI: 10.3389/fmicb.2018.03259] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 12/14/2018] [Indexed: 01/12/2023] Open
Abstract
Picoeukaryotes play an important role in the biogenic element cycle and energy flow in oligotrophic ecosystems. However, their biodiversity and activity are poorly studied in open ocean systems, such as the northwestern Pacific Ocean, which is characterized by a complex hydrological setting. Here, we investigated the diversity and activity of picoeukaryotes in the northwestern Pacific Ocean using high-throughput sequencing targeting the V9 region of 18S rDNA and rRNA. Our results showed that the DNA picoeukaryotic communities were mainly represented by Mamiellophyceae, MAST, MALV-II, Spirotrichea, Prymnesiophyceae, and MALV-I (69.33% of the total DNA reads), and the RNA communities were dominated by Spirotrichea, Mamiellophyceae, MAST, Pelagophyceae, and MALV-II (67.46% of the total RNA reads). The number of operational taxonomic units (OTUs) was significantly affected by temperature and salinity, and was decreased with the increasing nutrient concentration both in the DNA and RNA surveys. Significant differences were observed in the community composition between DNA-based and RNA-based molecular approaches, and these differences were mainly attributed to Mamiellophyceae, Spirotrichea, and Pelagophyceae. The RNA: DNA ratio was used as a proxy for relative metabolic activity of the individual OTUs. We found that the relative metabolic activities of Mamiellophyceae, Spirotrichea, and Pelagophyceae species in the northwestern Pacific Ocean were highly affected by the nutrient concentration, i.e., the NO3 + NO2 and SiO3 concentration. Overall, our study shed light on picoeukaryotic diversity and distribution in the northwestern Pacific Ocean and revealed the correlation between the diversity, relative metabolic activities of marine picoeukaryotes, and the environmental factors.
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Affiliation(s)
- Feipeng Wang
- Fujian Provincial Key Laboratory of Coastal Ecology and Environmental Studies, State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
| | - Yuyuan Xie
- Fujian Provincial Key Laboratory of Coastal Ecology and Environmental Studies, State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
| | - Wenxue Wu
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, China
| | - Ping Sun
- Fujian Provincial Key Laboratory of Coastal Ecology and Environmental Studies, State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
| | - Lei Wang
- Third Institute of Oceanography, State Oceanic Administration, Xiamen, China
| | - Bangqin Huang
- Fujian Provincial Key Laboratory of Coastal Ecology and Environmental Studies, State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
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11
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Joli N, Gosselin M, Ardyna M, Babin M, Onda DF, Tremblay JÉ, Lovejoy C. Need for focus on microbial species following ice melt and changing freshwater regimes in a Janus Arctic Gateway. Sci Rep 2018; 8:9405. [PMID: 29925879 PMCID: PMC6010473 DOI: 10.1038/s41598-018-27705-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Accepted: 06/08/2018] [Indexed: 11/16/2022] Open
Abstract
Oceanic gateways are sensitive to climate driven processes. By connecting oceans, they have a global influence on marine biological production and biogeochemical cycles. The furthest north of these gateways is Nares Strait at the top of the North Water between Greenland and Ellesmere Island (Canada). This gateway is globally beneficial, first by supporting high local mammal and bird populations and second with the outflow of phosphate-rich Arctic waters fueling the North Atlantic spring bloom. Both sides of the North Water are hydrologically distinct with counter currents that make this Arctic portal a Janus gateway, after Janus, the Roman god of duality. We examined oceanographic properties and differences in phytoplankton and other protist communities from the eastern and western sides of the North Water (latitude 76.5°N) and found that species differed markedly due to salinity stratification regimes and local hydrography. Typical Arctic communities were associated with south flowing currents along the Canadian side, while potentially noxious Pseudo-nitzschia spp. were dominant on the Greenland side and associated with greater surface freshening from ice melt. This susceptibility of the Greenland side to Pseudo-nitzschia spp. blooms suggest that monitoring species responses to climate mediated changes is needed.
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Affiliation(s)
- Nathalie Joli
- Département de biologie, Québec Océan and Takuvik Joint International Laboratory (UMI 3376), Université Laval (Canada) - CNRS (France), Université Laval, Québec, QC, G1V 0A6, Canada. .,Institut de biologie intégrative et des systèmes (IBIS), Université Laval, Québec, QC, GIV 0A6, Canada.
| | - Michel Gosselin
- Institut des sciences de la mer de Rimouski, Université du Québec à Rimouski, 310 Allée des Ursulines, Rimouski, QC, G5L 3A1, Canada
| | - Mathieu Ardyna
- Sorbonne Universités, UPMC Paris 06, INSU-CNRS, Laboratoire d'Océanographie de Villefranche, 181 Chemin du Lazaret, 06230, Villefranche-sur-mer, France.,Department of Earth System Science, Stanford University, Stanford, CA, 94305, USA
| | - Marcel Babin
- Département de biologie, Québec Océan and Takuvik Joint International Laboratory (UMI 3376), Université Laval (Canada) - CNRS (France), Université Laval, Québec, QC, G1V 0A6, Canada
| | - Deo Florence Onda
- Département de biologie, Québec Océan and Takuvik Joint International Laboratory (UMI 3376), Université Laval (Canada) - CNRS (France), Université Laval, Québec, QC, G1V 0A6, Canada.,Institut de biologie intégrative et des systèmes (IBIS), Université Laval, Québec, QC, GIV 0A6, Canada
| | - Jean-Éric Tremblay
- Département de biologie, Québec Océan and Takuvik Joint International Laboratory (UMI 3376), Université Laval (Canada) - CNRS (France), Université Laval, Québec, QC, G1V 0A6, Canada
| | - Connie Lovejoy
- Département de biologie, Québec Océan and Takuvik Joint International Laboratory (UMI 3376), Université Laval (Canada) - CNRS (France), Université Laval, Québec, QC, G1V 0A6, Canada.,Institut de biologie intégrative et des systèmes (IBIS), Université Laval, Québec, QC, GIV 0A6, Canada
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12
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Wang Y, Guo X, Zheng P, Zou S, Li G, Gong J. Distinct seasonality of chytrid-dominated benthic fungal communities in the neritic oceans (Bohai Sea and North Yellow Sea). FUNGAL ECOL 2017. [DOI: 10.1016/j.funeco.2017.08.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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13
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Tucker SJ, McManus GB, Katz LA, Grattepanche JD. Distribution of Abundant and Active Planktonic Ciliates in Coastal and Slope Waters Off New England. Front Microbiol 2017; 8:2178. [PMID: 29250036 PMCID: PMC5715329 DOI: 10.3389/fmicb.2017.02178] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Accepted: 10/23/2017] [Indexed: 11/18/2022] Open
Abstract
Despite their important role of linking microbial and classic marine food webs, data on biogeographical patterns of microbial eukaryotic grazers are limited, and even fewer studies have used molecular tools to assess active (i.e., those expressing genes) community members. Marine ciliate diversity is believed to be greatest at the chlorophyll maximum, where there is an abundance of autotrophic prey, and is often assumed to decline with depth. Here, we assess the abundant (DNA) and active (RNA) marine ciliate communities throughout the water column at two stations off the New England coast (Northwest Atlantic)—a coastal station 43 km from shore (40 m depth) and a slope station 135 km off shore (1,000 m). We analyze ciliate communities using a DNA fingerprinting technique, Denaturing Gradient Gel Electrophoresis (DGGE), which captures patterns of abundant community members. We compare estimates of ciliate communities from SSU-rDNA (abundant) and SSU-rRNA (active) and find complex patterns throughout the water column, including many active lineages below the photic zone. Our analyses reveal (1) a number of widely-distributed taxa that are both abundant and active; (2) considerable heterogeneity in patterns of presence/absence of taxa in offshore samples taken 50 m apart throughout the water column; and (3) three distinct ciliate assemblages based on position from shore and depth. Analysis of active (RNA) taxa uncovers biodiversity hidden to traditional DNA-based approaches (e.g., clone library, rDNA amplicon studies).
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Affiliation(s)
- Sarah J Tucker
- Department of Biological Sciences, Smith College, Northampton, MA, United States
| | - George B McManus
- Department of Marine Sciences, University of Connecticut, Groton, CT, United States
| | - Laura A Katz
- Department of Biological Sciences, Smith College, Northampton, MA, United States.,Program in Organismic and Evolutionary Biology, University of Massachusetts, Amherst, MA, United States
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14
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Wang C, Zhang T, Wang Y, Katz LA, Gao F, Song W. Disentangling sources of variation in SSU rDNA sequences from single cell analyses of ciliates: impact of copy number variation and experimental error. Proc Biol Sci 2017; 284:20170425. [PMID: 28747472 PMCID: PMC5543213 DOI: 10.1098/rspb.2017.0425] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 06/19/2017] [Indexed: 12/25/2022] Open
Abstract
Small subunit ribosomal DNA (SSU rDNA) is widely used for phylogenetic inference, barcoding and other taxonomy-based analyses. Recent studies indicate that SSU rDNA of ciliates may have a high level of sequence variation within a single cell, which impacts the interpretation of rDNA-based surveys. However, sequence variation can come from a variety of sources including experimental errors, especially the mutations generated by DNA polymerase in PCR. In the present study, we explore the impact of four DNA polymerases on sequence variation and find that low-fidelity polymerases exaggerate the estimates of single-cell sequence variation. Therefore, using a polymerase with high fidelity is essential for surveys of sequence variation. Another source of variation results from errors during amplification of SSU rDNA within the polyploidy somatic macronuclei of ciliates. To investigate further the impact of SSU rDNA copy number variation, we use a high-fidelity polymerase to examine the intra-individual SSU rDNA polymorphism in ciliates with varying levels of macronuclear amplification: Halteria grandinella, Blepharisma americanum and Strombidium stylifer We estimate the rDNA copy numbers of these three species by single-cell quantitative PCR. The results indicate that: (i) sequence variation of SSU rDNA within a single cell is authentic in ciliates, but the level of intra-individual SSU rDNA polymorphism varies greatly among species; (ii) rDNA copy numbers vary greatly among species, even those within the same class; (iii) the average rDNA copy number of Halteria grandinella is about 567 893 (s.d. = 165 481), which is the highest record of rDNA copy number in ciliates to date; and (iv) based on our data and the records from previous studies, it is not always true in ciliates that rDNA copy numbers are positively correlated with cell or genome size.
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Affiliation(s)
- Chundi Wang
- Insititute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, People's Republic of China
| | - Tengteng Zhang
- Insititute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, People's Republic of China
| | - Yurui Wang
- Insititute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, People's Republic of China
| | - Laura A Katz
- Department of Biological Sciences, Smith College, Northampton, MA 01063, USA
| | - Feng Gao
- Insititute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, People's Republic of China
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Qingdao 266003, People's Republic of China
| | - Weibo Song
- Insititute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, People's Republic of China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, People's Republic of China
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15
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Meshram AR, Vader A, Kristiansen S, Gabrielsen TM. Microbial Eukaryotes in an Arctic Under-Ice Spring Bloom North of Svalbard. Front Microbiol 2017; 8:1099. [PMID: 28702000 PMCID: PMC5487457 DOI: 10.3389/fmicb.2017.01099] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 05/30/2017] [Indexed: 12/03/2022] Open
Abstract
Microbial eukaryotes can play prominent roles in the Arctic marine ecosystem, but their diversity and variability is not well known in the ice-covered ecosystems. We determined the community composition of microbial eukaryotes in an Arctic under-ice spring bloom north of Svalbard using metabarcoding of DNA and RNA from the hypervariable V4 region of 18S nrDNA. At the two stations studied, the photosynthetic biomass was dominated by protists >3 μm and was concentrated in the upper 70–80 m, above the thermocline and halocline. Hierarchical cluster analyses as well as ordination analyses showed a distinct clustering of the microbial eukaryote communities according to a combination of water mass and local environmental characteristics. While samples collected in the surface mixed layer differed distinctly between the two sites, the deeper communities collected in Atlantic Water were fairly similar despite being geographically distant. The differentiation of the microbial eukaryote communities of the upper mixed water was probably driven by local development and advection, while the lack of such differentiation in the communities of Atlantic Water reflects the homogenizing effect of water currents on microbial communities.
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Affiliation(s)
- Archana R Meshram
- Department of Arctic Biology, University Centre in SvalbardLongyearbyen, Norway.,Department of Biosciences, Centre for Ecological and Evolutionary Synthesis, University of OsloOslo, Norway
| | - Anna Vader
- Department of Arctic Biology, University Centre in SvalbardLongyearbyen, Norway
| | - Svein Kristiansen
- Faculty of Biosciences, Fisheries and Economics, UiT The Arctic University of NorwayTromso, Norway
| | - Tove M Gabrielsen
- Department of Arctic Biology, University Centre in SvalbardLongyearbyen, Norway
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16
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Joli N, Monier A, Logares R, Lovejoy C. Seasonal patterns in Arctic prasinophytes and inferred ecology of Bathycoccus unveiled in an Arctic winter metagenome. THE ISME JOURNAL 2017; 11:1372-1385. [PMID: 28267153 PMCID: PMC5437359 DOI: 10.1038/ismej.2017.7] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 12/04/2016] [Accepted: 01/09/2017] [Indexed: 11/09/2022]
Abstract
Prasinophytes occur in all oceans but rarely dominate phytoplankton populations. In contrast, a single ecotype of the prasinophyte Micromonas is frequently the most abundant photosynthetic taxon reported in the Arctic from summer through autumn. However, seasonal dynamics of prasinophytes outside of this period are little known. To address this, we analyzed high-throughput V4 18S rRNA amplicon data collected from November to July in the Amundsen Gulf Region, Beaufort Sea, Arctic. Surprisingly during polar sunset in November and December, we found a high proportion of reads from both DNA and RNA belonging to another prasinophyte, Bathycoccus. We then analyzed a metagenome from a December sample and the resulting Bathycoccus metagenome assembled genome (MAG) covered ~90% of the Bathycoccus Ban7 reference genome. In contrast, only ~20% of a reference Micromonas genome was found in the metagenome. Our phylogenetic analysis of marker genes placed the Arctic Bathycoccus in the B1 coastal clade. In addition, substitution rates of 129 coding DNA sequences were ~1.6% divergent between the Arctic MAG and coastal Chilean upwelling MAGs and 17.3% between it and a South East Atlantic open ocean MAG in the B2 Clade. The metagenomic analysis also revealed a winter viral community highly skewed toward viruses targeting Micromonas, with a much lower diversity of viruses targeting Bathycoccus. Overall a combination of Micromonas being relatively less able to maintain activity under dark winter conditions and viral suppression of Micromonas may have contributed to the success of Bathycoccus in the Amundsen Gulf during winter.
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Affiliation(s)
- Nathalie Joli
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes, Québec Océan, Université Laval, Québec City, QC, Canada
- Takuvik Joint International Laboratory, Centre National de la Recherche Scientifique (France, CNRS UMI 3376), Université Laval, Québec City, QC, Canada
| | - Adam Monier
- School of Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, UK
| | - Ramiro Logares
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (CSIC), Barcelona, Spain
| | - Connie Lovejoy
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes, Québec Océan, Université Laval, Québec City, QC, Canada
- Takuvik Joint International Laboratory, Centre National de la Recherche Scientifique (France, CNRS UMI 3376), Université Laval, Québec City, QC, Canada
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17
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Sørensen N, Daugbjerg N, Richardson K, Nørregaard RD, Espersen L, Møhl M, Nielsen TG. Succession of picophytoplankton during the spring bloom 2012 in Disko Bay (West Greenland)—an unexpectedly low abundance of green algae. Polar Biol 2017. [DOI: 10.1007/s00300-016-1952-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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18
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Comeau AM, Vincent WF, Bernier L, Lovejoy C. Novel chytrid lineages dominate fungal sequences in diverse marine and freshwater habitats. Sci Rep 2016; 6:30120. [PMID: 27444055 PMCID: PMC4957111 DOI: 10.1038/srep30120] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 06/29/2016] [Indexed: 11/08/2022] Open
Abstract
In aquatic environments, fungal communities remain little studied despite their taxonomic and functional diversity. To extend the ecological coverage of this group, we conducted an in-depth analysis of fungal sequences within our collection of 3.6 million V4 18S rRNA pyrosequences originating from 319 individual marine (including sea-ice) and freshwater samples from libraries generated within diverse projects studying Arctic and temperate biomes in the past decade. Among the ~1.7 million post-filtered reads of highest taxonomic and phylogenetic quality, 23,263 fungal sequences were identified. The overall mean proportion was 1.35%, but with large variability; for example, from 0.01 to 59% of total sequences for Arctic seawater samples. Almost all sample types were dominated by Chytridiomycota-like sequences, followed by moderate-to-minor contributions of Ascomycota, Cryptomycota and Basidiomycota. Species and/or strain richness was high, with many novel sequences and high niche separation. The affinity of the most common reads to phytoplankton parasites suggests that aquatic fungi deserve renewed attention for their role in algal succession and carbon cycling.
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Affiliation(s)
- André M. Comeau
- Institut de Biologie Intégrative et des Systèmes (IBIS) and Centre d’Étude de la Forêt (CEF), Université Laval, Québec, Canada
| | - Warwick F. Vincent
- Centre d’Études Nordiques (CEN), Takuvik Joint International Laboratory (CNRS UMI-3376) and Département de Biologie, Université Laval, Québec, Canada
| | - Louis Bernier
- Institut de Biologie Intégrative et des Systèmes (IBIS) and Centre d’Étude de la Forêt (CEF), Université Laval, Québec, Canada
| | - Connie Lovejoy
- Institut de Biologie Intégrative et des Systèmes (IBIS), Takuvik Joint International Laboratory (CNRS UMI-3376) and Département de Biologie, Université Laval, Québec, Canada
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19
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Hassett BT, Ducluzeau ALL, Collins RE, Gradinger R. Spatial distribution of aquatic marine fungi across the western Arctic and sub-arctic. Environ Microbiol 2016; 19:475-484. [DOI: 10.1111/1462-2920.13371] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Brandon T. Hassett
- University of Alaska Fairbanks, School of Fisheries and Ocean Sciences; PO Box 757220 Fairbanks AK 99775-7220 USA
| | - Anne-Lise L Ducluzeau
- University of Alaska Fairbanks, School of Fisheries and Ocean Sciences; PO Box 757220 Fairbanks AK 99775-7220 USA
| | - Roy E. Collins
- University of Alaska Fairbanks, School of Fisheries and Ocean Sciences; PO Box 757220 Fairbanks AK 99775-7220 USA
| | - Rolf Gradinger
- University of Alaska Fairbanks, School of Fisheries and Ocean Sciences; PO Box 757220 Fairbanks AK 99775-7220 USA
- Institute of Marine Research; PO Box 6404 N-9294 Tromsø Norway
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20
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Hassett BT, Gradinger R. Chytrids dominate arctic marine fungal communities. Environ Microbiol 2016; 18:2001-9. [DOI: 10.1111/1462-2920.13216] [Citation(s) in RCA: 102] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Revised: 12/29/2015] [Accepted: 12/31/2015] [Indexed: 11/28/2022]
Affiliation(s)
- B. T. Hassett
- University of Alaska Fairbanks; School of Fisheries and Ocean Sciences; PO Box 757220 Fairbanks AK 99775-7220 USA
| | - R. Gradinger
- University of Alaska Fairbanks; School of Fisheries and Ocean Sciences; PO Box 757220 Fairbanks AK 99775-7220 USA
- UiT, Norges Arktiske Universitet; Institutt for Arktisk og Marin Biologi; Naturfagbygget, Dramsveien 201 N-9037 Tromsø Norway
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21
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Nguyen D, Maranger R, Balagué V, Coll-Lladó M, Lovejoy C, Pedrós-Alió C. Winter diversity and expression of proteorhodopsin genes in a polar ocean. ISME JOURNAL 2015; 9:1835-45. [PMID: 25700336 DOI: 10.1038/ismej.2015.1] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2014] [Revised: 12/09/2014] [Accepted: 12/12/2014] [Indexed: 12/25/2022]
Abstract
Mixotrophy is a valuable functional trait used by microbes when environmental conditions vary broadly or resources are limited. In the sunlit waters of the ocean, photoheterotrophy, a form of mixotrophy, is often mediated by proteorhodopsin (PR), a seven helices transmembrane protein binding the retinal chromophore. Altogether, they allow bacteria to capture photic energy for sensory and proton gradient formation cell functions. The seasonal occurrence and diversity of the gene coding for PR in cold oligotrophic polar oceans is not known and PR expression has not yet been reported. Here we show that PR is widely distributed among bacterial taxa, and that PR expression decreased markedly during the winter months in the Arctic Ocean. Gammaproteobacteria-like PR sequences were always dominant. However, within the second most common affiliation, there was a transition from Flavobacteria-like PR in early winter to Alphaproteobacteria-like PR in late winter. The phylogenetic shifts followed carbon dynamics, where patterns in expression were consistent with community succession, as identified by DNA community fingerprinting. Although genes for PR were always present, the trend in decreasing transcripts from January to February suggested reduced functional utility of PR during winter. Under winter darkness, sustained expression suggests that PR may continue to be useful for non-ATP forming functions, such as environmental sensing or small solute transport. The persistence of PR expression in winter among some bacterial groups may offer a competitive advantage, where its multifunctionality enhances microbial survival under harsh polar conditions.
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Affiliation(s)
- Dan Nguyen
- Groupe de Recherche Interuniversitaire en Limnologie et en Environnement Aquatique (GRIL), Département de sciences biologiques, Université de Montréal, Montréal, Québec, Canada
| | - Roxane Maranger
- Groupe de Recherche Interuniversitaire en Limnologie et en Environnement Aquatique (GRIL), Département de sciences biologiques, Université de Montréal, Montréal, Québec, Canada
| | - Vanessa Balagué
- Institut de Ciències del Mar, CSIC, Passeig Marítim de la Barceloneta, Barcelona, Spain
| | - Montserrat Coll-Lladó
- Institut de Ciències del Mar, CSIC, Passeig Marítim de la Barceloneta, Barcelona, Spain
| | - Connie Lovejoy
- Département de biologie, Québec-Océan, Institut de biologie intégrative et des systèmes (IBIS), Université Laval, Pavillon Charles-Eugène-Marchand, Québec, Québec, Canada
| | - Carlos Pedrós-Alió
- Institut de Ciències del Mar, CSIC, Passeig Marítim de la Barceloneta, Barcelona, Spain
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22
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Biogeography of heterotrophic flagellate populations indicates the presence of generalist and specialist taxa in the Arctic Ocean. Appl Environ Microbiol 2015; 81:2137-48. [PMID: 25595764 DOI: 10.1128/aem.02737-14] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Heterotrophic marine flagellates (HF) are ubiquitous in the world's oceans and represented in nearly all branches of the domain Eukaryota. However, the factors determining distributions of major taxonomic groups are poorly known. The Arctic Ocean is a good model environment for examining the distribution of functionally similar but phylogenetically diverse HF because the physical oceanography and annual ice cycles result in distinct environments that could select for microbial communities or favor specific taxa. We reanalyzed new and previously published high-throughput sequencing data from multiple studies in the Arctic Ocean to identify broad patterns in the distribution of individual taxa. HF accounted for fewer than 2% to over one-half of the reads from the water column and for up to 60% of reads from ice, which was dominated by Cryothecomonas. In the water column, many HF phylotypes belonging to Telonemia and Picozoa, uncultured marine stramenopiles (MAST), and choanoflagellates were geographically widely distributed. However, for two groups in particular, Telonemia and Cryothecomonas, some species level taxa showed more restricted distributions. For example, several phylotypes of Telonemia favored open waters with lower nutrients such as the Canada Basin and offshore of the Mackenzie Shelf. In summary, we found that while some Arctic HF were successful over a range of conditions, others could be specialists that occur under particular conditions. We conclude that tracking species level diversity in HF not only is feasible but also provides a potential tool for understanding the responses of marine microbial ecosystems to rapidly changing ice regimes.
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23
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Archaeal amoA and ureC genes and their transcriptional activity in the Arctic Ocean. Sci Rep 2014; 4:4661. [PMID: 24722490 PMCID: PMC3983602 DOI: 10.1038/srep04661] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Accepted: 03/26/2014] [Indexed: 12/01/2022] Open
Abstract
Thaumarchaeota and the gene encoding for a subunit of ammonia monooxygenase (amoA) are ubiquitous in Polar Seas, and some Thaumarchaeota also have a gene coding for ureC, diagnostic for urease. Using quantitative PCR we investigated the occurrence of genes and transcripts of ureC and amoA in Arctic samples from winter, spring and summer. AmoA genes, ureC genes and amoA transcripts were always present, but ureC transcripts were rarely detected. Over a 48 h light manipulation experiment amoA transcripts persisted under light and dark conditions, but not ureC transcripts. In addition, maxima for amoA transcript were nearer the surface compared to amoA genes. Clone libraries using DNA template recovered shallow and deep amoA clades but only the shallow clade was recovered from cDNA (from RNA). These results imply environmental control of amoA expression with direct or indirect light effects, and rare ureC expression despite its widespread occurrence in the Arctic Ocean.
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24
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Charvet S, Vincent WF, Lovejoy C. Effects of light and prey availability on Arctic freshwater protist communities examined by high-throughput DNA and RNA sequencing. FEMS Microbiol Ecol 2014; 88:550-64. [DOI: 10.1111/1574-6941.12324] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Revised: 01/22/2014] [Accepted: 03/06/2014] [Indexed: 11/29/2022] Open
Affiliation(s)
- Sophie Charvet
- Département de Biologie; Université Laval; Québec QC Canada
- Québec-Océan and Institut de Biologie Intégrative et des Systèmes (IBIS); Québec QC Canada
- Centre d'études nordiques (CEN); Québec QC Canada
| | - Warwick F. Vincent
- Département de Biologie; Université Laval; Québec QC Canada
- Centre d'études nordiques (CEN); Québec QC Canada
| | - Connie Lovejoy
- Département de Biologie; Université Laval; Québec QC Canada
- Québec-Océan and Institut de Biologie Intégrative et des Systèmes (IBIS); Québec QC Canada
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25
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Holmes DE, Giloteaux L, Williams KH, Wrighton KC, Wilkins MJ, Thompson CA, Roper TJ, Long PE, Lovley DR. Enrichment of specific protozoan populations during in situ bioremediation of uranium-contaminated groundwater. THE ISME JOURNAL 2013; 7:1286-98. [PMID: 23446832 PMCID: PMC3695288 DOI: 10.1038/ismej.2013.20] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2012] [Revised: 01/07/2013] [Accepted: 01/10/2013] [Indexed: 11/09/2022]
Abstract
The importance of bacteria in the anaerobic bioremediation of groundwater polluted with organic and/or metal contaminants is well recognized and in some instances so well understood that modeling of the in situ metabolic activity of the relevant subsurface microorganisms in response to changes in subsurface geochemistry is feasible. However, a potentially significant factor influencing bacterial growth and activity in the subsurface that has not been adequately addressed is protozoan predation of the microorganisms responsible for bioremediation. In field experiments at a uranium-contaminated aquifer located in Rifle, CO, USA, acetate amendments initially promoted the growth of metal-reducing Geobacter species, followed by the growth of sulfate reducers, as observed previously. Analysis of 18S rRNA gene sequences revealed a broad diversity of sequences closely related to known bacteriovorous protozoa in the groundwater before the addition of acetate. The bloom of Geobacter species was accompanied by a specific enrichment of sequences most closely related to the ameboid flagellate, Breviata anathema, which at their peak accounted for over 80% of the sequences recovered. The abundance of Geobacter species declined following the rapid emergence of B. anathema. The subsequent growth of sulfate-reducing Peptococcaceae was accompanied by another specific enrichment of protozoa, but with sequences most similar to diplomonadid flagellates from the family Hexamitidae, which accounted for up to 100% of the sequences recovered during this phase of the bioremediation. These results suggest a prey-predator response with specific protozoa responding to increased availability of preferred prey bacteria. Thus, quantifying the influence of protozoan predation on the growth, activity and composition of the subsurface bacterial community is essential for predictive modeling of in situ uranium bioremediation strategies.
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Affiliation(s)
- Dawn E Holmes
- Department of Microbiology, Morrill Science Center IVN, University of Massachusetts Amherst, Amherst, MA 01003, USA.
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26
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Extremely High Copy Numbers and Polymorphisms of the rDNA Operon Estimated from Single Cell Analysis of Oligotrich and Peritrich Ciliates. Protist 2013; 164:369-79. [DOI: 10.1016/j.protis.2012.11.006] [Citation(s) in RCA: 179] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2012] [Revised: 10/31/2012] [Accepted: 11/30/2012] [Indexed: 11/13/2022]
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27
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Piwosz K, Wiktor JM, Niemi A, Tatarek A, Michel C. Mesoscale distribution and functional diversity of picoeukaryotes in the first-year sea ice of the Canadian Arctic. ISME JOURNAL 2013; 7:1461-71. [PMID: 23514779 DOI: 10.1038/ismej.2013.39] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2012] [Revised: 01/10/2013] [Accepted: 02/04/2013] [Indexed: 11/09/2022]
Abstract
Sea ice, a characteristic feature of polar waters, is home to diverse microbial communities. Sea-ice picoeukaryotes (unicellular eukaryotes with cell size <3 μm) have received little attention compared with diatoms that dominate the spring bloom in Arctic first-year sea ice. Here, we investigated the abundance of all picoeukaryotes, and of 11 groups (chlorophytes, cryptophytes, bolidophytes, haptophytes, Pavlovaphyceae, Phaeocystis spp., pedinellales, stramenopiles groups MAST-1, MAST-2 and MAST-6 and Syndiniales Group II) at 13 first-year sea-ice stations localized in Barrow Strait and in the vicinity of Cornwallis Island, Canadian Arctic Archipelago. We applied Catalyzed Reporter Deposition-Fluorescence In Situ Hybridization to identify selected groups at a single cell level. Pavlovaphyceae and stramenopiles from groups MAST-2 and MAST-6 were for the first time reported from sea ice. Total numbers of picoeukaryotes were significantly higher in the vicinity of Cornwallis Island than in Barrow Strait. Similar trend was observed for all the groups except for haptophytes. Chlorophytes and cryptophytes were the dominant plastidic, and MAST-2 most numerous aplastidic of all the groups investigated. Numbers of total picoeukaryotes, chlorophytes and MAST-2 stramenopiles were positively correlated with the thickness of snow cover. All studied algal and MAST groups fed on bacteria. Presence of picoeukaryotes from various trophic groups (mixotrophs, phagotrophic and parasitic heterotrophs) indicates the diverse ecological roles picoeukaryotes have in sea ice. Yet, >50% of total sea-ice picoeukaryote cells remained unidentified, highlighting the need for further study of functional and phylogenetic sea-ice diversity, to elucidate the risks posed by ongoing Arctic changes.
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Affiliation(s)
- Kasia Piwosz
- Department of Fisheries Oceanography and Marine Ecology, National Marine Fisheries Research Institute, Gdynia, Poland.
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Terrado R, Scarcella K, Thaler M, Vincent WF, Lovejoy C. Small phytoplankton in Arctic seas: vulnerability to climate change. ACTA ACUST UNITED AC 2013. [DOI: 10.1080/14888386.2012.704839] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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29
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Comparative analysis of eukaryotic marine microbial assemblages from 18S rRNA gene and gene transcript clone libraries by using different methods of extraction. Appl Environ Microbiol 2012; 78:3958-65. [PMID: 22447590 DOI: 10.1128/aem.06941-11] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Eukaryotic marine microbes play pivotal roles in biogeochemical nutrient cycling and ecosystem function, but studies that focus on the protistan biogeography and genetic diversity lag-behind studies of other microbes. 18S rRNA PCR amplification and clone library sequencing are commonly used to assess diversity that is culture independent. However, molecular methods are not without potential biases and artifacts. In this study, we compare the community composition of clone libraries generated from the same water sample collected at the San Pedro Ocean Time Series (SPOTs) station in the northwest Pacific Ocean. Community composition was assessed using different cell lysis methods (chemical and mechanical) and the extraction of different nucleic acids (DNA and RNA reverse transcribed to cDNA) to build Sanger ABI clone libraries. We describe specific biases for ecologically important phylogenetic groups resulting from differences in nucleic acid extraction methods that will inform future designs of eukaryotic diversity studies, regardless of the target sequencing platform planned.
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Deming JW, Fortier L. Introduction to the special issue on the biology of the circumpolar flaw lead (CFL) in the Amundsen Gulf of the Beaufort Sea (Arctic Ocean). Polar Biol 2011. [DOI: 10.1007/s00300-011-1125-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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