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Chen N, Xu Q, Zhu J, Song H, He L, Liu S, Song X, Yuan Y, Chen Y, Cao X, Yu Z. Chromosome-scale genome assembly reveals insights into the evolution and ecology of the harmful algal bloom species Phaeocystis globosa Scherffel. iScience 2024; 27:110575. [PMID: 39193189 PMCID: PMC11347835 DOI: 10.1016/j.isci.2024.110575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 05/26/2024] [Accepted: 07/22/2024] [Indexed: 08/29/2024] Open
Abstract
The phytoplankton Phaeocystis globosa plays an important role in sulfur cycling and climate control, and can develop harmful algal blooms (HABs). Here we report a chromosome-scale reference genome assembly of P. globosa, which enable in-depth analysis of molecular underpinnings of important ecological characteristics. Comparative genomic analyses detected two-rounds of genome duplications that may have fueled evolutionary innovations. The genome duplication may have resulted in the formation of dual HiDP and LoDP dimethylsulphoniopropionate (DMSP) biosynthesis pathways in P. globosa. Selective gene family expansions may have strengthened biological pathways critical for colonial formation that is often associated with the development of algal blooms. The copy numbers of rhodopsin genes are variable in different strains, suggesting that rhodopsin genes may play a role in strain-specific adaptation to ecological factors. The successful reconstruction of the P. globosa genome sets up an excellent platform that facilitates in-depth research on bloom development and DMSP metabolism.
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Affiliation(s)
- 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, BC V5A 1S6, Canada
| | - Qing Xu
- 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
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Jianan Zhu
- 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
- College of Marine Science, University of Chinese Academy of Sciences, Beijing 10039, China
| | - Huiyin Song
- 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
| | - Liyan 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
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Shuya 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
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Xiuxian Song
- 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
- College of Marine Science, University of Chinese Academy of Sciences, Beijing 10039, China
| | - Yongquan Yuan
- 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
| | - 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
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
- College of Marine Science, University of Chinese Academy of Sciences, Beijing 10039, China
| | - Xihua Cao
- 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
| | - Zhiming Yu
- 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 10039, China
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2
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West NJ, Landa M, Obernosterer I. Differential association of key bacterial groups with diatoms and Phaeocystis spp. during spring blooms in the Southern Ocean. Microbiologyopen 2024; 13:e1428. [PMID: 39119822 PMCID: PMC11310772 DOI: 10.1002/mbo3.1428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 07/10/2024] [Accepted: 07/10/2024] [Indexed: 08/10/2024] Open
Abstract
Interactions between phytoplankton and heterotrophic bacteria significantly influence the cycling of organic carbon in the ocean, with many of these interactions occurring at the micrometer scale. We explored potential associations between specific phytoplankton and bacteria in two size fractions, 0.8-3 µm and larger than 3 µm, at three naturally iron-fertilized stations and one high nutrient low chlorophyll station in the Southern Ocean. The composition of phytoplankton and bacterial communities was determined by sequencing the rbcL gene and 16S rRNA gene from DNA and RNA extracts, which represent presence and potential activity, respectively. Diatoms, particularly Thalassiosira, contributed significantly to the DNA sequences in the larger size fractions, while haptophytes were dominant in the smaller size fraction. Correlation analysis between the most abundant phytoplankton and bacterial operational taxonomic units revealed strong correlations between Phaeocystis and picoeukaryotes with SAR11, SAR116, Magnetospira, and Planktomarina. In contrast, most Thalassiosira operational taxonomic units showed the highest correlations with Polaribacter, Sulfitobacteria, Erythrobacter, and Sphingobium, while Fragilariopsis, Haslea, and Thalassionema were correlated with OM60, Fluviicola, and Ulvibacter. Our in-situ observations suggest distinct associations between phytoplankton and bacterial taxa, which could play crucial roles in nutrient cycling in the Southern Ocean.
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Affiliation(s)
- Nyree J. West
- CNRS FR3724, Observatoire Océanologique de Banyuls (OOB)Sorbonne UniversitéBanyuls sur merFrance
| | - Marine Landa
- Laboratoire d'Océanographie Microbienne, LOMIC, CNRSSorbonne UniversitéBanyuls sur merFrance
| | - Ingrid Obernosterer
- Laboratoire d'Océanographie Microbienne, LOMIC, CNRSSorbonne UniversitéBanyuls sur merFrance
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Vanharanta M, Santoro M, Villena-Alemany C, Piiparinen J, Piwosz K, Grossart HP, Labrenz M, Spilling K. Microbial remineralization processes during postspring-bloom with excess phosphate available in the northern Baltic Sea. FEMS Microbiol Ecol 2024; 100:fiae103. [PMID: 39039015 DOI: 10.1093/femsec/fiae103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 06/10/2024] [Accepted: 07/19/2024] [Indexed: 07/24/2024] Open
Abstract
The phosphorus (P) concentration is increasing in parts of the Baltic Sea following the spring bloom. The fate of this excess P-pool is an open question, and here we investigate the role of microbial degradation processes in the excess P assimilation phase. During a 17-day-long mesocosm experiment in the southwest Finnish archipelago, we examined nitrogen, phosphorus, and carbon acquiring extracellular enzyme activities in three size fractions (<0.2, 0.2-3, and >3 µm), bacterial abundance, production, community composition, and its predicted metabolic functions. The mesocosms received carbon (C) and nitrogen (N) amendments individually and in combination (NC) to distinguish between heterotrophic and autotrophic processes. Alkaline phosphatase activity occurred mainly in the dissolved form and likely contributed to the excess phosphate conditions together with grazing. At the beginning of the experiment, peptidolytic and glycolytic enzymes were mostly produced by free-living bacteria. However, by the end of the experiment, the NC-treatment induced a shift in peptidolytic and glycolytic activities and degradation of phosphomonoesters toward the particle-associated fraction, likely as a consequence of higher substrate availability. This would potentially promote retention of nutrients in the surface as opposed to sedimentation, but direct sedimentation measurements are needed to verify this hypothesis.
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Affiliation(s)
- Mari Vanharanta
- Tvärminne Zoological Station, University of Helsinki, J. A. Palménin tie 260, 10900 Hanko, Finland
- Marine and Freshwater Solutions, Finnish Environment Institute, Latokartanonkaari 11, 00790 Helsinki, Finland
| | - Mariano Santoro
- Department of Biological Oceanography, Leibniz Institute for Baltic Sea Research Warnemünde - IOW, Seestrasse 15, 18119 Rostock, Germany
- Department of Plant Physiology, Institute for Biosciences, University of Rostock, Albert-Einstein-Str. 3, 18059 Rostock, Germany
| | - Cristian Villena-Alemany
- Laboratory of Anoxygenic Phototrophs, Institute of Microbiology, Czech Academy of Sciences, Novohradská 237 - Opatovický mlýn, 379 01 Třeboň, Czech Republic
| | - Jonna Piiparinen
- Marine and Freshwater Solutions, Finnish Environment Institute, Latokartanonkaari 11, 00790 Helsinki, Finland
| | - Kasia Piwosz
- Department of Fisheries Oceanography and Marine Ecology, National Marine Fisheries Research Institute, ul. Kołłątaja 1, 81-332 Gdynia, Poland
| | - Hans-Peter Grossart
- Department of Plankton and Microbial Ecology, Leibniz Institute for Freshwater Ecology and Inland Fisheries, Alte Fischerhütte 2, OT Neuglobsow, 16775 Stechlin, Germany
- Institute of Biology and Biochemistry, Potsdam University, Maulbeerallee 2, 14469 Potsdam, Germany
| | - Matthias Labrenz
- Department of Biological Oceanography, Leibniz Institute for Baltic Sea Research Warnemünde - IOW, Seestrasse 15, 18119 Rostock, Germany
| | - Kristian Spilling
- Marine and Freshwater Solutions, Finnish Environment Institute, Latokartanonkaari 11, 00790 Helsinki, Finland
- Centre for Coastal Research, University of Agder, Universitetsveien 25, 4604 Kristiansand, Norway
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Piontek J, Hassenrück C, Zäncker B, Jürgens K. Environmental control and metabolic strategies of organic-matter-responsive bacterioplankton in the Weddell Sea (Antarctica). Environ Microbiol 2024; 26:e16675. [PMID: 39022885 DOI: 10.1111/1462-2920.16675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Accepted: 06/29/2024] [Indexed: 07/20/2024]
Abstract
Heterotrophic microbial communities play a significant role in driving carbon fluxes in marine ecosystems. Despite their importance, these communities remain understudied in remote polar oceans, which are known for their substantial contribution to the biological drawdown of atmospheric carbon dioxide. Our research focused on understanding the environmental factors and genetic makeup of key bacterial players involved in carbon remineralization in the Weddell Sea, including its coastal polynyas. Our experiments demonstrated that the combination of labile organic matter supply and temperature increase synergistically boosted bacterial growth. This suggests that, besides low seawater temperature, carbon limitation also hinders heterotrophic bacterial activity. Through the analysis of metagenome-assembled genomes, we discovered distinct genomic adaptation strategies in Bacteroidia and Gammaproteobacteria, both of which respond to organic matter. Both natural phytoplankton blooms and experimental addition of organic matter favoured Bacteroidia, which possess a large number of gene copies and a wide range of functional membrane transporters, glycoside hydrolases, and aminopeptidases. In contrast, the genomes of organic-matter-responsive Gammaproteobacteria were characterized by high densities of transcriptional regulators and transporters. Our findings suggest that bacterioplankton in the Weddell Sea, which respond to organic matter, employ metabolic strategies similar to those of their counterparts in temperate oceans. These strategies enable efficient growth at extremely low seawater temperatures, provided that organic carbon limitation is alleviated.
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Dawson HM, Connors E, Erazo NG, Sacks JS, Mierzejewski V, Rundell SM, Carlson LT, Deming JW, Ingalls AE, Bowman JS, Young JN. Microbial metabolomic responses to changes in temperature and salinity along the western Antarctic Peninsula. THE ISME JOURNAL 2023; 17:2035-2046. [PMID: 37709939 PMCID: PMC10579395 DOI: 10.1038/s41396-023-01475-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 06/28/2023] [Accepted: 06/30/2023] [Indexed: 09/16/2023]
Abstract
Seasonal cycles within the marginal ice zones in polar regions include large shifts in temperature and salinity that strongly influence microbial abundance and physiology. However, the combined effects of concurrent temperature and salinity change on microbial community structure and biochemical composition during transitions between seawater and sea ice are not well understood. Coastal marine communities along the western Antarctic Peninsula were sampled and surface seawater was incubated at combinations of temperature and salinity mimicking the formation (cold, salty) and melting (warm, fresh) of sea ice to evaluate how these factors may shape community composition and particulate metabolite pools during seasonal transitions. Bacterial and algal community structures were tightly coupled to each other and distinct across sea-ice, seawater, and sea-ice-meltwater field samples, with unique metabolite profiles in each habitat. During short-term (approximately 10-day) incubations of seawater microbial communities under different temperature and salinity conditions, community compositions changed minimally while metabolite pools shifted greatly, strongly accumulating compatible solutes like proline and glycine betaine under cold and salty conditions. Lower salinities reduced total metabolite concentrations in particulate matter, which may indicate a release of metabolites into the labile dissolved organic matter pool. Low salinity also increased acylcarnitine concentrations in particulate matter, suggesting a potential for fatty acid degradation and reduced nutritional value at the base of the food web during freshening. Our findings have consequences for food web dynamics, microbial interactions, and carbon cycling as polar regions undergo rapid climate change.
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Affiliation(s)
- H M Dawson
- School of Oceanography, University of Washington, Seattle, WA, 98195, USA.
| | - E Connors
- Scripps Institution of Oceanography, UC San Diego, La Jolla, CA, 92037, USA
| | - N G Erazo
- Scripps Institution of Oceanography, UC San Diego, La Jolla, CA, 92037, USA
- Center for Marine Biodiversity and Conservation, UC San Diego, La Jolla, CA, 92037, USA
| | - J S Sacks
- School of Oceanography, University of Washington, Seattle, WA, 98195, USA
| | - V Mierzejewski
- School of Earth and Space Exploration, Arizona State University, Tempe, AZ, 85287, USA
| | - S M Rundell
- School of Oceanography, University of Washington, Seattle, WA, 98195, USA
| | - L T Carlson
- School of Oceanography, University of Washington, Seattle, WA, 98195, USA
| | - J W Deming
- School of Oceanography, University of Washington, Seattle, WA, 98195, USA
| | - A E Ingalls
- School of Oceanography, University of Washington, Seattle, WA, 98195, USA
| | - J S Bowman
- Scripps Institution of Oceanography, UC San Diego, La Jolla, CA, 92037, USA
- Center for Marine Biodiversity and Conservation, UC San Diego, La Jolla, CA, 92037, USA
- Center for Microbiome Innovation, UC San Diego, La Jolla, CA, 92037, USA
| | - J N Young
- School of Oceanography, University of Washington, Seattle, WA, 98195, USA.
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Puigcorbé V, Ruiz-González C, Masqué P, Gasol JM. Impact of particle flux on the vertical distribution and diversity of size-fractionated prokaryotic communities in two East Antarctic polynyas. Front Microbiol 2023; 14:1078469. [PMID: 36910225 PMCID: PMC9995690 DOI: 10.3389/fmicb.2023.1078469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 01/27/2023] [Indexed: 02/25/2023] Open
Abstract
Antarctic polynyas are highly productive open water areas surrounded by ice where extensive phytoplankton blooms occur, but little is known about how these surface blooms influence carbon fluxes and prokaryotic communities from deeper waters. By sequencing the 16S rRNA gene, we explored the vertical connectivity of the prokaryotic assemblages associated with particles of three different sizes in two polynyas with different surface productivity, and we linked it to the magnitude of the particle export fluxes measured using thorium-234 (234Th) as particle tracer. Between the sunlit and the mesopelagic layers (700 m depth), we observed compositional changes in the prokaryotic communities associated with the three size-fractions, which were mostly dominated by Flavobacteriia, Alphaproteobacteria, and Gammaproteobacteria. Interestingly, the vertical differences between bacterial communities attached to the largest particles decreased with increasing 234Th export fluxes, indicating a more intense downward transport of surface prokaryotes in the most productive polynya. This was accompanied by a higher proportion of surface prokaryotic taxa detected in deep particle-attached microbial communities in the station with the highest 234Th export flux. Our results support recent studies evidencing links between surface productivity and deep prokaryotic communities and provide the first evidence of sinking particles acting as vectors of microbial diversity to depth in Antarctic polynyas, highlighting the direct influence of particle export in shaping the prokaryotic communities of mesopelagic waters.
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Affiliation(s)
- Viena Puigcorbé
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM-CSIC), Barcelona, Catalunya, Spain.,Centre for Marine Ecosystems Research, School of Science, Edith Cowan University, Joondalup, WA, Australia
| | - Clara Ruiz-González
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM-CSIC), Barcelona, Catalunya, Spain
| | - Pere Masqué
- Centre for Marine Ecosystems Research, School of Science, Edith Cowan University, Joondalup, WA, Australia.,International Atomic Energy Agency, City of Monaco, Monaco
| | - Josep M Gasol
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM-CSIC), Barcelona, Catalunya, Spain
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Jacquemot L, Vigneron A, Tremblay JÉ, Lovejoy C. Contrasting sea ice conditions shape microbial food webs in Hudson Bay (Canadian Arctic). ISME COMMUNICATIONS 2022; 2:104. [PMID: 37938285 PMCID: PMC9723562 DOI: 10.1038/s43705-022-00192-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 10/07/2022] [Accepted: 10/12/2022] [Indexed: 01/07/2023]
Abstract
The transition from ice-covered to open water is a recurring feature of the Arctic and sub-Arctic, but microbial diversity and cascading effects on the microbial food webs is poorly known. Here, we investigated microbial eukaryote, bacterial and archaeal communities in Hudson Bay (sub-Arctic, Canada) under sea-ice cover and open waters conditions. Co-occurrence networks revealed a <3 µm pico‒phytoplankton-based food web under the ice and a >3 µm nano‒microphytoplankton-based food web in the open waters. The ice-edge communities were characteristic of post-bloom conditions with high proportions of the picophytoplankton Micromonas and Bathycoccus. Nano‒ to micro‒phytoplankton and ice associated diatoms were detected throughout the water column, with the sympagic Melosira arctica exclusive to ice-covered central Hudson Bay and Thalassiosira in open northwestern Hudson Bay. Heterotrophic microbial eukaryotes and prokaryotes also differed by ice-state, suggesting a linkage between microbes at depth and surface phytoplankton bloom state. The findings suggest that a longer open water season may favor the establishment of a large phytoplankton-based food web at the subsurface chlorophyll maxima (SCM), increasing carbon export from pelagic diatoms to deeper waters and affect higher trophic levels in the deep Hudson Bay.
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Affiliation(s)
- Loïc Jacquemot
- Département de Biologie, Université Laval, Québec, QC, Canada.
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada.
| | - Adrien Vigneron
- Département de Biologie, Université Laval, Québec, QC, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
| | | | - Connie Lovejoy
- Département de Biologie, Université Laval, Québec, QC, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
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Roland HB, Whitehead C, Fleming LE, Berdalet E, Enevoldsen HO, Gribble MO. Knowledge Sharing to Reduce Toxin Exposure Risks from Harmful Algal Blooms: Global Networks and Political Barriers. Ethn Dis 2022; 32:285-292. [PMID: 36388868 PMCID: PMC9590605 DOI: 10.18865/ed.32.4.285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Harmful algal blooms (HABs) are a significant global environmental management challenge, especially with respect to microalgae that produce dangerous natural toxins. Examples of HAB toxin diseases with major global health impact include: ciguatera poisoning, paralytic shellfish poisoning (PSP), amnesic shellfish poisoning (ASP), diarrhetic shellfish poisoning (DSP), and neurotoxic (brevetoxin) shellfish poisoning (NSP). Such diseases affect communities globally and contribute to health inequalities within the United States and beyond. Sharing data and lessons learned about the factors determining bloom occurrence and associated exposure to contaminated seafood across locations can reduce public health risks. Knowledge sharing is particularly important as ongoing global environmental changes seem to alter the intensity, location, and timing of toxic HAB events, reducing the reliability of conventional guidance where toxin risks have been endemic and leading to emerging challenges in new settings. Political changes that disrupt membership in knowledge-sharing networks may impede efforts to share scientific expertise and best practices. In this commentary, we stress the importance of community and expert knowledge sharing for reducing HAB risks, both for vulnerable communities in the United States and globally. Considering the impacts of political changes, we note the indirect engagement sometimes required for continued participation in international coordination programs. As an example, we highlight how lessons learned from a Native-led toxin monitoring and testing program (the Southeast Alaska Tribal Ocean Research partnership) can inform programs in other settings. We also describe how international knowledge is mutually valuable for this program in Southeast Alaska.
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Affiliation(s)
- Hugh B. Roland
- Department of Epidemiology, School of Public Health, University of Alabama at Birmingham, Birmingham, AL
| | | | - Lora E. Fleming
- European Centre for Environment and Human Health, University of Exeter Medical School, Truro, Cornwall, United Kingdom
| | - Elisa Berdalet
- Marine Biology and Oceanography, Institute of Marine Sciences, Spanish National Research Council (ICM-CSIC), Barcelona, Spain
| | - Henrik Oksfeldt Enevoldsen
- Intergovernmental Oceanographic Commission Science and Communication Centre on Harmful Algae, IOC UNESCO, Copenhagen, Denmark
| | - Matthew O. Gribble
- Department of Epidemiology, School of Public Health, University of Alabama at Birmingham, Birmingham, AL
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9
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Mars Brisbin M, Mitarai S, Saito MA, Alexander H. Microbiomes of bloom-forming Phaeocystis algae are stable and consistently recruited, with both symbiotic and opportunistic modes. THE ISME JOURNAL 2022; 16:2255-2264. [PMID: 35764675 PMCID: PMC9381791 DOI: 10.1038/s41396-022-01263-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 05/11/2022] [Accepted: 05/31/2022] [Indexed: 05/29/2023]
Abstract
Phaeocystis is a cosmopolitan, bloom-forming phytoplankton genus that contributes significantly to global carbon and sulfur cycles. During blooms, Phaeocystis species produce large carbon-rich colonies, creating a unique interface for bacterial interactions. While bacteria are known to interact with phytoplankton-e.g., they promote growth by producing phytohormones and vitamins-such interactions have not been shown for Phaeocystis. Therefore, we investigated the composition and function of P. globosa microbiomes. Specifically, we tested whether microbiome compositions are consistent across individual colonies from four P. globosa strains, whether similar microbiomes are re-recruited after antibiotic treatment, and how microbiomes affect P. globosa growth under limiting conditions. Results illuminated a core colonial P. globosa microbiome-including bacteria from the orders Alteromonadales, Burkholderiales, and Rhizobiales-that was re-recruited after microbiome disruption. Consistent microbiome composition and recruitment is indicative that P. globosa microbiomes are stable-state systems undergoing deterministic community assembly and suggests there are specific, beneficial interactions between Phaeocystis and bacteria. Growth experiments with axenic and nonaxenic cultures demonstrated that microbiomes allowed continued growth when B-vitamins were withheld, but that microbiomes accelerated culture collapse when nitrogen was withheld. In sum, this study reveals symbiotic and opportunistic interactions between Phaeocystis colonies and microbiome bacteria that could influence large-scale phytoplankton bloom dynamics and biogeochemical cycles.
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Affiliation(s)
- Margaret Mars Brisbin
- Marine Biophysics Unit, Okinawa Institute of Science and Technology, Okinawa, Japan.
- Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA.
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA.
| | - Satoshi Mitarai
- Marine Biophysics Unit, Okinawa Institute of Science and Technology, Okinawa, Japan
| | - Mak A Saito
- Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Harriet Alexander
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA.
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O’Brien J, McParland EL, Bramucci AR, Ostrowski M, Siboni N, Ingleton T, Brown MV, Levine NM, Laverock B, Petrou K, Seymour J. The Microbiological Drivers of Temporally Dynamic Dimethylsulfoniopropionate Cycling Processes in Australian Coastal Shelf Waters. Front Microbiol 2022; 13:894026. [PMID: 35783424 PMCID: PMC9240709 DOI: 10.3389/fmicb.2022.894026] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 05/20/2022] [Indexed: 01/04/2023] Open
Abstract
The organic sulfur compounds dimethylsulfoniopropionate (DMSP) and dimethyl sulfoxide (DMSO) play major roles in the marine microbial food web and have substantial climatic importance as sources and sinks of dimethyl sulfide (DMS). Seasonal shifts in the abundance and diversity of the phytoplankton and bacteria that cycle DMSP are likely to impact marine DMS (O) (P) concentrations, but the dynamic nature of these microbial interactions is still poorly resolved. Here, we examined the relationships between microbial community dynamics with DMS (O) (P) concentrations during a 2-year oceanographic time series conducted on the east Australian coast. Heterogenous temporal patterns were apparent in chlorophyll a (chl a) and DMSP concentrations, but the relationship between these parameters varied over time, suggesting the phytoplankton and bacterial community composition were affecting the net DMSP concentrations through differential DMSP production and degradation. Significant increases in DMSP were regularly measured in spring blooms dominated by predicted high DMSP-producing lineages of phytoplankton (Heterocapsa, Prorocentrum, Alexandrium, and Micromonas), while spring blooms that were dominated by predicted low DMSP-producing phytoplankton (Thalassiosira) demonstrated negligible increases in DMSP concentrations. During elevated DMSP concentrations, a significant increase in the relative abundance of the key copiotrophic bacterial lineage Rhodobacterales was accompanied by a three-fold increase in the gene, encoding the first step of DMSP demethylation (dmdA). Significant temporal shifts in DMS concentrations were measured and were significantly correlated with both fractions (0.2-2 μm and >2 μm) of microbial DMSP lyase activity. Seasonal increases of the bacterial DMSP biosynthesis gene (dsyB) and the bacterial DMS oxidation gene (tmm) occurred during the spring-summer and coincided with peaks in DMSP and DMSO concentration, respectively. These findings, along with significant positive relationships between dsyB gene abundance and DMSP, and tmm gene abundance with DMSO, reinforce the significant role planktonic bacteria play in producing DMSP and DMSO in ocean surface waters. Our results highlight the highly dynamic nature and myriad of microbial interactions that govern sulfur cycling in coastal shelf waters and further underpin the importance of microbial ecology in mediating important marine biogeochemical processes.
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Affiliation(s)
- James O’Brien
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, Australia
- School of Life Sciences, University of Technology Sydney, Ultimo, NSW, Australia
| | - Erin L. McParland
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, United States
| | - Anna R. Bramucci
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, Australia
| | - Martin Ostrowski
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, Australia
| | - Nachshon Siboni
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, Australia
| | - Timothy Ingleton
- Water, Wetlands and Coastal Science, NSW Department of Planning, Industry and Environment, Lidcombe, NSW, Australia
| | - Mark V. Brown
- School of Environmental and Life Sciences, The University of Newcastle, Callaghan, NSW, Australia
| | - Naomi M. Levine
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, United States
| | - Bonnie Laverock
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, Australia
| | - Katherina Petrou
- School of Life Sciences, University of Technology Sydney, Ultimo, NSW, Australia
| | - Justin Seymour
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, Australia
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11
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Piontek J, Meeske C, Hassenrück C, Engel A, Jürgens K. Organic matter availability drives the spatial variation in the community composition and activity of Antarctic marine bacterioplankton. Environ Microbiol 2022; 24:4030-4048. [PMID: 35656758 DOI: 10.1111/1462-2920.16087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 05/27/2022] [Indexed: 11/30/2022]
Abstract
Carbon cycling by Antarctic microbial plankton is poorly understood but it plays a major role in CO2 sequestration in the Southern Ocean. We investigated the summer bacterioplankton community in the largely understudied Weddell Sea, applying Illumina amplicon sequencing, measurements of bacterial production and chemical analyses of organic matter. The results revealed that the patchy distribution of productive coastal polynyas and less productive, mostly ice-covered sites was the major driver of the spatial changes in the taxonomic composition and activity of bacterioplankton. Gradients in organic matter availability induced by phytoplankton blooms were reflected in the concentrations and composition of dissolved carbohydrates and proteins. Bacterial production at bloom stations was, on average, 2.7 times higher than at less productive sites. Abundant bloom-responsive lineages were predominately affiliated with ubiquitous marine taxa, including Polaribacter, Yoonia-Loktanella, Sulfitobacter, the SAR92 clade, and Ulvibacter, suggesting a widespread genetic potential for adaptation to sub-zero seawater temperatures. A co-occurrence network analysis showed that dominant taxa at stations with low phytoplankton productivity were highly connected, indicating beneficial interactions. Overall, our study demonstrates that heterotrophic bacterial communities along Weddell Sea ice shelves were primarily constrained by the availability of labile organic matter rather than low seawater temperature. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Judith Piontek
- Leibniz Institute for Baltic Sea Research Warnemünde, Germany
| | | | | | - Anja Engel
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Germany
| | - Klaus Jürgens
- Leibniz Institute for Baltic Sea Research Warnemünde, Germany
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12
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Gibson K, Song H, Chen N. Metabarcoding analysis of microbiome dynamics during a Phaeocystis globosa bloom in the Beibu Gulf, China. HARMFUL ALGAE 2022; 114:102217. [PMID: 35550291 DOI: 10.1016/j.hal.2022.102217] [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: 08/03/2021] [Revised: 02/21/2022] [Accepted: 02/26/2022] [Indexed: 06/15/2023]
Abstract
Phaeocystis globosa is an ecologically important haptophyte that can form harmful algal blooms (HABs). In this study, we used 16S rDNA V3-V4 amplicon sequencing data to explore the ecological mechanisms underlying a P. globosa bloom in the Beibu Gulf, China. Using field samples collected from three time points of a bloom, we observed a distinct succession in the bacteria, archaea and phytoplankton community composition throughout the bloom. We also observed temporal variation in response to the bloom at the nucleotide level, which supports a previously underappreciated amount of intragroup variation in the niches taken up by microbes during HABs. We developed a preliminary model for the development and progression of the P. globosa bloom using the spatial-temporal dynamics of P. globosa and the bacteria, archaea, phytoplankton and environmental variables. We also identified microbes with putative interactions with P. globosa during the bloom by identifying microbes correlated with P. globosa in interaction networks, identifying particle-associated microbes and exploring the P. globosa colony microbiome using sequences from whole P. globosa colonies collected during the bloom. This study revealed novel insight into the development of P. globosa HABs and many testable hypotheses that will guide future research on the mechanisms of P. globosa HABs.
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Affiliation(s)
- Kate Gibson
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia, V5A 1S6, Canada
| | - Huiyin Song
- 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 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Nansheng Chen
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia, V5A 1S6, Canada; 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 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China.
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13
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Xu S, Wang X, Liu J, Zhou F, Guo K, Chen S, Wang ZH, Wang Y. Bacteria Associated With Phaeocystis globosa and Their Influence on Colony Formation. Front Microbiol 2022; 13:826602. [PMID: 35250943 PMCID: PMC8891983 DOI: 10.3389/fmicb.2022.826602] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 01/04/2022] [Indexed: 11/13/2022] Open
Abstract
Phaeocystis globosa (P. globosa) is one of the dominant algae during harmful algal blooms (HABs) in coastal regions of Southern China. P. globosa exhibits complex heteromorphic life cycles that could switch between solitary cells and colonies. The ecological success of P. globosa has been attributed to its colony formation, although underlying mechanisms remain unknown. Here, we investigated different bacterial communities associated with P. globosa colonies and their influence on colony formation of two P. globosa strains isolated from coastal waters of Guangxi (GX) and Shantou (ST). Eight operational taxonomic units (OTUs) were observed in ST co-cultures and were identified as biomarkers based on Linear discriminant analysis Effect Size (LEfSe) analysis, while seven biomarkers were identified in P. globosa GX co-cultures. Bacterial communities associated with the P. globosa GX were more diverse than those of the ST strain. The most dominant phylum in the two co-cultures was Proteobacteria, within which Marinobacter was the most abundant genus in both GX and ST co-cultures. Bacteroidota were only observed in the GX co-cultures and Planctomycetota were only observed in the ST co-cultures. Co-culture experiments revealed that P. globosa colony formation was not influenced by low and medium cell densities of Marinobacter sp. GS7, but was inhibited by high cell densities of Marinobacter sp. GS7. Overall, these results indicated that the associated bacteria are selected by different P. globosa strains, which may affect the colony formation and development of P. globosa.
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Affiliation(s)
- Shuaishuai Xu
- College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Xiaodong Wang
- College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Jie Liu
- College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Fengli Zhou
- College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Kangli Guo
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Songze Chen
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Zhao-hui Wang
- College of Life Science and Technology, Jinan University, Guangzhou, China
- *Correspondence: Zhao-hui Wang,
| | - Yan Wang
- College of Life Science and Technology, Jinan University, Guangzhou, China
- Yan Wang,
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14
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O'Brien J, McParland EL, Bramucci AR, Siboni N, Ostrowski M, Kahlke T, Levine NM, Brown MV, van de Kamp J, Bodrossy L, Messer LF, Petrou K, Seymour JR. Biogeographical and seasonal dynamics of the marine Roseobacter community and ecological links to DMSP-producing phytoplankton. ISME COMMUNICATIONS 2022; 2:16. [PMID: 37938744 PMCID: PMC9723663 DOI: 10.1038/s43705-022-00099-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 01/26/2022] [Accepted: 01/28/2022] [Indexed: 11/09/2023]
Abstract
Ecological interactions between marine bacteria and phytoplankton play a pivotal role in governing the ocean's major biogeochemical cycles. Among these, members of the marine Roseobacter Group (MRG) can establish mutualistic relationships with phytoplankton that are, in part, maintained by exchanges of the organosulfur compound, dimethylsulfoniopropionate (DMSP). Yet most of what is known about these interactions has been derived from culture-based laboratory studies. To investigate temporal and spatial co-occurrence patterns between members of the MRG and DMSP-producing phytoplankton we analysed 16S and 18S rRNA gene amplicon sequence variants (ASVs) derived from 5 years of monthly samples from seven environmentally distinct Australian oceanographic time-series. The MRG and DMSP-producer communities often displayed contemporaneous seasonality, which was greater in subtropical and temperate environments compared to tropical environments. The relative abundance of both groups varied latitudinally, displaying a poleward increase, peaking (MRG at 33% of total bacteria, DMSP producers at 42% of eukaryotic phototrophs) during recurrent spring-summer phytoplankton blooms in the most temperate site (Maria Island, Tasmania). Network analysis identified 20,140 significant positive correlations between MRG ASVs and DMSP producers and revealed that MRGs exhibit significantly stronger correlations to high DMSP producers relative to other DMSP-degrading bacteria (Pelagibacter, SAR86 and Actinobacteria). By utilising the power of a continental network of oceanographic time-series, this study provides in situ confirmation of interactions found in laboratory studies and demonstrates that the ecological dynamics of an important group of marine bacteria are shaped by the production of an abundant and biogeochemically significant organosulfur compound.
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Affiliation(s)
- James O'Brien
- Climate Change Cluster, University of Technology Sydney, Broadway, NSW, Australia.
- School of Life Sciences, University of Technology Sydney, Broadway, NSW, Australia.
| | - Erin L McParland
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Anna R Bramucci
- Climate Change Cluster, University of Technology Sydney, Broadway, NSW, Australia
| | - Nachshon Siboni
- Climate Change Cluster, University of Technology Sydney, Broadway, NSW, Australia
| | - Martin Ostrowski
- Climate Change Cluster, University of Technology Sydney, Broadway, NSW, Australia
| | - Tim Kahlke
- Climate Change Cluster, University of Technology Sydney, Broadway, NSW, Australia
| | - Naomi M Levine
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Mark V Brown
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW, Australia
| | | | | | - Lauren F Messer
- Climate Change Cluster, University of Technology Sydney, Broadway, NSW, Australia
- Centre for Microbiome Research, School of Biomedical Sciences, Queensland University of Technology, Brisbane, QLD, Australia
| | - Katherina Petrou
- School of Life Sciences, University of Technology Sydney, Broadway, NSW, Australia
| | - Justin R Seymour
- Climate Change Cluster, University of Technology Sydney, Broadway, NSW, Australia.
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15
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Cordone A, D’Errico G, Magliulo M, Bolinesi F, Selci M, Basili M, de Marco R, Saggiomo M, Rivaro P, Giovannelli D, Mangoni O. Bacterioplankton Diversity and Distribution in Relation to Phytoplankton Community Structure in the Ross Sea Surface Waters. Front Microbiol 2022; 13:722900. [PMID: 35154048 PMCID: PMC8828583 DOI: 10.3389/fmicb.2022.722900] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 01/05/2022] [Indexed: 01/04/2023] Open
Abstract
Primary productivity in the Ross Sea region is characterized by intense phytoplankton blooms whose temporal and spatial distribution are driven by changes in environmental conditions as well as interactions with the bacterioplankton community. However, the number of studies reporting the simultaneous diversity of the phytoplankton and bacterioplankton in Antarctic waters are limited. Here, we report data on the bacterial diversity in relation to phytoplankton community structure in the surface waters of the Ross Sea during the Austral summer 2017. Our results show partially overlapping bacterioplankton communities between the stations located in the Terra Nova Bay (TNB) coastal waters and the Ross Sea Open Waters (RSOWs), with a dominance of members belonging to the bacterial phyla Bacteroidetes and Proteobacteria. In the TNB coastal area, microbial communities were characterized by a higher abundance of sequences related to heterotrophic bacterial genera such as Polaribacter spp., together with higher phytoplankton biomass and higher relative abundance of diatoms. On the contrary, the phytoplankton biomass in the RSOW were lower, with relatively higher contribution of haptophytes and a higher abundance of sequences related to oligotrophic and mixothrophic bacterial groups like the Oligotrophic Marine Gammaproteobacteria (OMG) group and SAR11. We show that the rate of diversity change between the two locations is influenced by both abiotic (salinity and the nitrogen to phosphorus ratio) and biotic (phytoplankton community structure) factors. Our data provide new insight into the coexistence of the bacterioplankton and phytoplankton in Antarctic waters, suggesting that specific rather than random interaction contribute to the organic matter cycling in the Southern Ocean.
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Affiliation(s)
- Angelina Cordone
- Department of Biology, University of Naples Federico II, Naples, Italy
| | - Giuseppe D’Errico
- Department of Life Sciences, DISVA, Polytechnic University of Marche, Ancona, Italy
| | - Maria Magliulo
- Department of Biology, University of Naples Federico II, Naples, Italy
| | - Francesco Bolinesi
- Department of Biology, University of Naples Federico II, Naples, Italy
- *Correspondence: Francesco Bolinesi,
| | - Matteo Selci
- Department of Biology, University of Naples Federico II, Naples, Italy
| | - Marco Basili
- National Research Council, Institute of Marine Biological Resources and Biotechnologies CNR-IRBIM, Ancona, Italy
| | - Rocco de Marco
- National Research Council, Institute of Marine Biological Resources and Biotechnologies CNR-IRBIM, Ancona, Italy
| | | | - Paola Rivaro
- Department of Chemistry and Industrial Chemistry, University of Genoa, Genoa, Italy
| | - Donato Giovannelli
- Department of Biology, University of Naples Federico II, Naples, Italy
- Department of Life Sciences, DISVA, Polytechnic University of Marche, Ancona, Italy
- National Research Council, Institute of Marine Biological Resources and Biotechnologies CNR-IRBIM, Ancona, Italy
- Department of Marine and Coastal Science, Rutgers University, New Brunswick, NJ, United States
- Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, MA, United States
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan
- Donato Giovannelli,
| | - Olga Mangoni
- Department of Biology, University of Naples Federico II, Naples, Italy
- Consorzio Nazionale Interuniversitario delle Scienze del Mare (CoNISMa), Rome, Italy
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16
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Zhu Z, Meng R, Smith WO, Doan-Nhu H, Nguyen-Ngoc L, Jiang X. Bacterial Composition Associated With Giant Colonies of the Harmful Algal Species Phaeocystis globosa. Front Microbiol 2021; 12:737484. [PMID: 34721335 PMCID: PMC8555426 DOI: 10.3389/fmicb.2021.737484] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 08/17/2021] [Indexed: 12/05/2022] Open
Abstract
The cosmopolitan algae Phaeocystis globosa forms harmful algal blooms frequently in a number of tropical and subtropical coastal regions in the past two decades. During the bloom, the giant colony, which is formed by P. globosa, is the dominant morphotype. However, the microenvironment and the microbial composition in the intracolonial fluid are poorly understood. Here, we used high-throughput 16S rRNA amplicon sequencing to examine the bacterial composition and predicted functions in intracolonial fluid. Compared with the bacterial consortia in ambient seawater, intracolonial fluids possessed the lower levels of microbial richness and diversity, implying selectivity of bacteria by the unique intracolonial microenvironment enclosed within the P. globosa polysaccharide envelope. The bacterial consortia in intracolonial fluid were dominated by Balneola (48.6% of total abundance) and Labrezia (28.5%). The bacteria and microbial function enriched in intracolonial fluid were involved in aromatic benzenoid compounds degradation, DMSP and DMS production and consumption, and antibacterial compounds synthesis. We suggest that the P. globosa colonial envelope allows for the formation of a specific microenvironment; thus, the unique microbial consortia inhabiting intracolonial fluid has close interaction with P. globosa cells, which may benefit colony development.
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Affiliation(s)
- Zhu Zhu
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, China
| | - Rui Meng
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, China
| | - Walker O Smith
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, China
| | - Hai Doan-Nhu
- Vietnam Academy of Science and Technology, Institute of Oceanography, Nha Trang, Vietnam
| | - Lam Nguyen-Ngoc
- Vietnam Academy of Science and Technology, Institute of Oceanography, Nha Trang, Vietnam
| | - Xinjun Jiang
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, China
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17
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Abirami B, Radhakrishnan M, Kumaran S, Wilson A. Impacts of global warming on marine microbial communities. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 791:147905. [PMID: 34126492 DOI: 10.1016/j.scitotenv.2021.147905] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 04/26/2021] [Accepted: 05/16/2021] [Indexed: 06/12/2023]
Abstract
Global warming in ocean ecosystems alters temperature, acidification, oxygen content, circulation, stratification, and nutrient inputs. Microorganisms play a dominant role in global biogeochemical cycles crucial for a planet's sustainability. Since microbial communities are highly dependent on the temperature factor, fluctuations in the same will lead to adverse effects on the microbial community organization. Throughout the Ocean, increase in evaporation rates causes the surface mixed layer to become shallower. This intensified stratification inhibits vertical transport of nutrient supplies. Such density driven processes will decrease oxygen solubility in surface waters leading to significant decrease of oxygen from future Ocean. Metabolism and diversity of microbes along with ocean biogeochemistry will be at great risk due to global warming and its related effects. As a response to the changes in temperature, alteration in the distribution of phytoplankta communities is observed all over the planet, creating changes in the primary production of the ocean causing massive impact on the biosphere. Marine microbial communities try to adapt to the changing ocean environmental conditions by responding with biogeographic range shifts, community structure modifications, and adaptive evolution. Persistence of this climate change on ocean ecosystems, in future, will pose serious threat to the metabolism and distribution of marine microbes leading to fluctuations in the biogeochemical cycles thereby affecting the overall ecosystem functioning. Genomics plays an important role in marine microbial research by providing tools to study the association between environment and organisms. The ecological and genomic perspectives of marine microbes are being investigated to design effective models to understand their physiology and evolution in a changing ocean. Mesocosm/microcosm experimental studies and field studies are in the need of the hour to evaluate the impact of climate shifts on microbial genesis.
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Affiliation(s)
- Baskaran Abirami
- Centre for Drug Discovery and Development, Sathyabama Institute of Science and Technology, Chennai 600 119, Tamil Nadu, India
| | - Manikkam Radhakrishnan
- Centre for Drug Discovery and Development, Sathyabama Institute of Science and Technology, Chennai 600 119, Tamil Nadu, India
| | - Subramanian Kumaran
- Centre for Drug Discovery and Development, Sathyabama Institute of Science and Technology, Chennai 600 119, Tamil Nadu, India
| | - Aruni Wilson
- Sathyabama Institute of Science and Technology, Chennai 600119, Tamil Nadu, India; School of Medicine, Loma Linda University, CA, USA; Musculoskeletal Disease Research Laboratory, US Department of Veteran Affairs, Loma Linda, CA, USA.
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18
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A novel random forest approach to revealing interactions and controls on chlorophyll concentration and bacterial communities during coastal phytoplankton blooms. Sci Rep 2021; 11:19944. [PMID: 34620921 PMCID: PMC8497483 DOI: 10.1038/s41598-021-98110-9] [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: 12/15/2020] [Accepted: 08/24/2021] [Indexed: 11/12/2022] Open
Abstract
Increasing occurrence of harmful algal blooms across the land–water interface poses significant risks to coastal ecosystem structure and human health. Defining significant drivers and their interactive impacts on blooms allows for more effective analysis and identification of specific conditions supporting phytoplankton growth. A novel iterative Random Forests (iRF) machine-learning model was developed and applied to two example cases along the California coast to identify key stable interactions: (1) phytoplankton abundance in response to various drivers due to coastal conditions and land-sea nutrient fluxes, (2) microbial community structure during algal blooms. In Example 1, watershed derived nutrients were identified as the least significant interacting variable associated with Monterey Bay phytoplankton abundance. In Example 2, through iRF analysis of field-based 16S OTU bacterial community and algae datasets, we independently found stable interactions of prokaryote abundance patterns associated with phytoplankton abundance that have been previously identified in laboratory-based studies. Our study represents the first iRF application to marine algal blooms that helps to identify ocean, microbial, and terrestrial conditions that are considered dominant causal factors on bloom dynamics.
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19
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Alarcón-Schumacher T, Guajardo-Leiva S, Martinez-Garcia M, Díez B. Ecogenomics and Adaptation Strategies of Southern Ocean Viral Communities. mSystems 2021; 6:e0039621. [PMID: 34374561 PMCID: PMC8407431 DOI: 10.1128/msystems.00396-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 07/21/2021] [Indexed: 11/20/2022] Open
Abstract
The Southern Ocean (SO) represents up to one-fifth of the total carbon drawdown worldwide. Intense selective pressures (low temperature, high UV radiation, and strong seasonality) and physical isolation characterize the SO, serving as a "natural" laboratory for the study of ecogenomics and unique adaptations of endemic viral populations. Here, we report 2,416 novel viral genomes from the SO, obtained from newly sequenced viral metagenomes in combination with mining of publicly available data sets, which represents a 25% increase in the SO viral genomes reported to date. They comprised 567 viral clusters (defined as approximately genus-level groups), with 186 genera endemic to the SO, demonstrating that the SO viral community is predominantly constituted by a large pool of genetically divergent viral species from widespread viral families. The predicted proteome from SO viruses revealed that several protein clusters related to cold-shock-event responses and quorum-sensing mechanisms involved in the lysogenic-lytic cycle shift decision were under positive selection, which is ultimately important for fine adaptation of viral populations in response to the strong selective pressures of the SO. Finally, changes in the hydrophobicity patterns and amino acid frequencies suggested marked temperature-driven genetic selection of the SO viral proteome. Our data provide valuable insights into how viruses adapt and remain successful in this extreme polar marine environment. IMPORTANCE Viruses are the most abundant biologic entities in marine systems and strongly influence the microbial community composition and diversity. However, little is known about viral communities' adaptation and diversification in the ocean. In this work, we take advantage of the geographical isolation and the intense selective pressures of the SO, to which viruses are exposed, to identify potential viral adaptations due to positive environmental selection and dispersal limitation. To that end, we recovered more than two thousand novel viral genomes, revealing a high degree of divergence in these SO endemic communities. Furthermore, we describe remarkable viral adaptations in amino acid frequencies and accessory proteins related to cold shock response and quorum sensing that allow them to thrive at lower temperatures. Consequently, our work greatly expands the understanding of the diversification of the viral communities of the SO and their particular adaptations to low temperatures.
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Affiliation(s)
- Tomás Alarcón-Schumacher
- Department of Molecular Genetics and Microbiology, Pontificia Universidad Católica de Chile, Santiago, Chile
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Sergio Guajardo-Leiva
- Department of Molecular Genetics and Microbiology, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Manuel Martinez-Garcia
- Department of Physiology, Genetics, and Microbiology, University of Alicante, Carretera San Vicente del Raspeig, San Vicente del Raspeig, Alicante, Spain
| | - Beatriz Díez
- Department of Molecular Genetics and Microbiology, Pontificia Universidad Católica de Chile, Santiago, Chile
- Center for Climate and Resilience Research (CR) 2, Santiago, Chile
- Center for Genome Regulation (CGR), Santiago, Chile
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20
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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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Physiological and Molecular Responses to Main Environmental Stressors of Microalgae and Bacteria in Polar Marine Environments. Microorganisms 2020; 8:microorganisms8121957. [PMID: 33317109 PMCID: PMC7764121 DOI: 10.3390/microorganisms8121957] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 11/27/2020] [Accepted: 11/28/2020] [Indexed: 12/18/2022] Open
Abstract
The Arctic and Antarctic regions constitute 14% of the total biosphere. Although they differ in their physiographic characteristics, both are strongly affected by snow and ice cover changes, extreme photoperiods and low temperatures, and are still largely unexplored compared to more accessible sites. This review focuses on microalgae and bacteria from polar marine environments and, in particular, on their physiological and molecular responses to harsh environmental conditions. The data reported in this manuscript show that exposure to cold, increase in CO2 concentration and salinity, high/low light, and/or combination of stressors induce variations in species abundance and distribution for both polar bacteria and microalgae, as well as changes in growth rate and increase in cryoprotective compounds. The use of -omics techniques also allowed to identify specific gene losses and gains which could have contributed to polar environmental adaptation, and metabolic shifts, especially related to lipid metabolism and defence systems, such as the up-regulation of ice binding proteins, chaperones and antioxidant enzymes. However, this review also provides evidence that -omics resources for polar species are still few and several sequences still have unknown functions, highlighting the need to further explore polar environments, the biology and ecology of the inhabiting bacteria and microalgae, and their interactions.
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22
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Microbial Diversity and Phage-Host Interactions in the Georgian Coastal Area of the Black Sea Revealed by Whole Genome Metagenomic Sequencing. Mar Drugs 2020; 18:md18110558. [PMID: 33202695 PMCID: PMC7697616 DOI: 10.3390/md18110558] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 10/29/2020] [Accepted: 10/30/2020] [Indexed: 01/18/2023] Open
Abstract
Viruses have the greatest abundance and highest genetic diversity in marine ecosystems. The interactions between viruses and their hosts is one of the hot spots of marine ecology. Besides their important role in various ecosystems, viruses, especially bacteriophages and their gene pool, are of enormous interest for the development of new gene products with high innovation value. Various studies have been conducted in diverse ecosystems to understand microbial diversity and phage-host interactions; however, the Black Sea, especially the Eastern coastal area, remains among the least studied ecosystems in this regard. This study was aimed at to fill this gap by analyzing microbial diversity and bacteriophage-host interactions in the waters of Eastern Black Sea using a metagenomic approach. To this end, prokaryotic and viral metagenomic DNA from two sampling sites, Poti and Gonio, were sequenced on the Illumina Miseq platform and taxonomic and functional profiles of the metagenomes were obtained using various bioinformatics tools. Our metagenomics analyses allowed us to identify the microbial communities, with Proteobacteria, Cyanobacteria, Actinibacteria, and Firmicutes found to be the most dominant bacterial phyla and Synechococcus and Candidatus Pelagibacter phages found to be the most dominant viral groups in the Black Sea. As minor groups, putative phages specific to human pathogens were identified in the metagenomes. We also characterized interactions between the phages and prokaryotic communities by determining clustered regularly interspaced short palindromic repeats (CRISPR), prophage-like sequences, and integrase/excisionase sequences in the metagenomes, along with identification of putative horizontally transferred genes in the viral contigs. In addition, in the viral contig sequences related to peptidoglycan lytic activity were identified as well. This is the first study on phage and prokaryote diversity and their interactions in the Eastern coastal area of the Black Sea using a metagenomic approach.
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23
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Sow SLS, Trull TW, Bodrossy L. Oceanographic Fronts Shape Phaeocystis Assemblages: A High-Resolution 18S rRNA Gene Survey From the Ice-Edge to the Equator of the South Pacific. Front Microbiol 2020; 11:1847. [PMID: 32849444 PMCID: PMC7424020 DOI: 10.3389/fmicb.2020.01847] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 07/15/2020] [Indexed: 01/01/2023] Open
Abstract
The cosmopolitan haptophyte Phaeocystis is recognized as a key contributor to marine biogeochemical cycling and important primary producer within polar marine environments. Yet, little is known about its solitary, non-colonial cell stages or its distribution during the colder, low-productivity seasons. We examined the biogeography of Phaeocystis along a high-resolution (0.5-degree latitudinal interval) transect from the Antarctic ice-edge to the equator of the South Pacific, in the austral autumn-winter. Using high-throughput 18S rRNA gene sequences with single nucleotide variable (zero-radius) operational taxonomic units (zOTUs) allowed us to explore the possibility of strain-level variation. From water samples within the upper water column, we show the presence of an abundant Phaeocystis assemblage that persisted during the colder months, contributing up to 9% of the microbial eukaryote community at high latitudes. The biogeography of Phaeocystis was strongly shaped by oceanographic boundaries, most prominently the polar and subantarctic fronts. Marked changes in dominant Phaeocystis antarctica zOTUs between different frontal zones support the concept that ecotypes may exist within the Phaeocystis assemblage. Our findings also show that the Phaeocystis assemblage did not abide by the classical latitudinal diversity gradient of increasing richness from the poles to the tropics; richness peaked at 30°S and declined to a minimum at 5°S. Another surprise was that P. globosa and P. cordata, previously thought to be restricted to the northern hemisphere, were detected at moderate abundances within the Southern Ocean. Our results emphasize the importance of oceanographic processes in shaping the biogeography of Phaeocystis and highlights the importance of genomics-based exploration of Phaeocystis, which have found the assemblage to be more complex than previously understood. The high winter relative abundance of the Phaeocystis assemblage suggests it could be involved in more complex ecological interactions during the less productive seasons, which should be considered in future studies to better understand the ecological role and strategies of this keystone species.
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Affiliation(s)
- Swan L S Sow
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS, Australia.,Oceans and Atmosphere, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Hobart, TAS, Australia
| | - Thomas W Trull
- Oceans and Atmosphere, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Hobart, TAS, Australia
| | - Levente Bodrossy
- Oceans and Atmosphere, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Hobart, TAS, Australia
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24
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Li N, Zhao H, Jiang G, Xu Q, Tang J, Li X, Wen J, Liu H, Tang C, Dong K, Kang Z. Phylogenetic Responses of Marine Free-Living Bacterial Community to Phaeocystis globosa Bloom in Beibu Gulf, China. Front Microbiol 2020; 11:1624. [PMID: 32765460 PMCID: PMC7378386 DOI: 10.3389/fmicb.2020.01624] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 06/22/2020] [Indexed: 12/21/2022] Open
Abstract
Phaeocystis globosa blooms are recognized as playing an essential role in shaping the structure of the marine community and its functions in marine ecosystems. In this study, we observed variation in the alpha diversity and composition of marine free-living bacteria during P. globosa blooms and identified key microbial community assembly patterns during the blooms. The results showed that the Shannon index was higher before the blooming of P. globosa in the subtropical bay. Marinobacterium (γ-proteobacteria), Erythrobacter (α-proteobacteria), and Persicobacter (Cytophagales) were defined as the most important genera, and they were more correlated with environmental factors at the terminal stage of P. globosa blooms. Furthermore, different community assembly processes were observed. Both the mean nearest relatedness index (NRI) and nearest taxon index (NTI) revealed the dominance of deterministic factors in the non-blooming and blooming periods of P. globosa, while the bacterial communities in marine waters after the blooms tended to be controlled by stochastic factors. Our findings revealed that the assembly of the bacterial community in marine P. globosa blooms is a complex process with mixture effects of marine microbiomes and environmental parameters.
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Affiliation(s)
- Nan Li
- Key Laboratory of Environment Change and Resources Use in Beibu Gulf, Ministry of Education, Nanning Normal University, Nanning, China
| | - Huaxian Zhao
- Key Laboratory of Environment Change and Resources Use in Beibu Gulf, Ministry of Education, Nanning Normal University, Nanning, China
| | - Gonglingxia Jiang
- Key Laboratory of Environment Change and Resources Use in Beibu Gulf, Ministry of Education, Nanning Normal University, Nanning, China
| | - Qiangsheng Xu
- Key Laboratory of Environment Change and Resources Use in Beibu Gulf, Ministry of Education, Nanning Normal University, Nanning, China
| | - Jinli Tang
- Key Laboratory of Environment Change and Resources Use in Beibu Gulf, Ministry of Education, Nanning Normal University, Nanning, China
| | - Xiaoli Li
- Key Laboratory of Environment Change and Resources Use in Beibu Gulf, Ministry of Education, Nanning Normal University, Nanning, China
| | - Jiemei Wen
- Key Laboratory of Environment Change and Resources Use in Beibu Gulf, Ministry of Education, Nanning Normal University, Nanning, China
| | - Huimin Liu
- Key Laboratory of Environment Change and Resources Use in Beibu Gulf, Ministry of Education, Nanning Normal University, Nanning, China
| | - Chaowu Tang
- Key Laboratory of Environment Change and Resources Use in Beibu Gulf, Ministry of Education, Nanning Normal University, Nanning, China
| | - Ke Dong
- Department of Biological Sciences, Kyonggi University, Suwon-si, South Korea
| | - Zhenjun Kang
- Guangxi Key Laboratory of Marine Disaster in the Beibu Gulf, Beibu Gulf University, Qinzhou, China
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25
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Knapik K, Bagi A, Krolicka A, Baussant T. Metatranscriptomic Analysis of Oil-Exposed Seawater Bacterial Communities Archived by an Environmental Sample Processor (ESP). Microorganisms 2020; 8:E744. [PMID: 32429288 PMCID: PMC7284936 DOI: 10.3390/microorganisms8050744] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 05/12/2020] [Accepted: 05/14/2020] [Indexed: 11/17/2022] Open
Abstract
The use of natural marine bacteria as "oil sensors" for the detection of pollution events can be suggested as a novel way of monitoring oil occurrence at sea. Nucleic acid-based devices generically called genosensors are emerging as potentially promising tools for in situ detection of specific microbial marker genes suited for that purpose. Functional marker genes are particularly interesting as targets for oil-related genosensing but their identification remains a challenge. Here, seawater samples, collected in tanks with oil addition mimicking a realistic oil spill scenario, were filtered and archived by the Environmental Sample Processor (ESP), a fully robotized genosensor, and the samples were then used for post-retrieval metatranscriptomic analysis. After extraction, RNA from ESP-archived samples at start, Day 4 and Day 7 of the experiment was used for sequencing. Metatranscriptomics revealed that several KEGG pathways were significantly enriched in samples exposed to oil. However, these pathways were highly expressed also in the non-oil-exposed water samples, most likely as a result of the release of natural organic matter from decaying phytoplankton. Temporary peaks of aliphatic alcohol and aldehyde dehydrogenases and monoaromatic ring-degrading enzymes (e.g., ben, box, and dmp clusters) were observed on Day 4 in both control and oil-exposed and non-exposed tanks. Few alkane 1-monooxygenase genes were upregulated on oil, mostly transcribed by families Porticoccaceae and Rhodobacteraceae, together with aromatic ring-hydroxylating dioxygenases, mostly transcribed by Rhodobacteraceae. Few transcripts from obligate hydrocarbonoclastic genera of Alcanivorax, Oleispira and Cycloclasticus were significantly enriched in the oil-treated exposed tank in comparison to control the non-exposed tank, and these were mostly transporters and genes involved in nitrogen and phosphorous acquisition. This study highlights the importance of seasonality, i.e., phytoplankton occurrence and senescence leading to organic compound release which can be used preferentially by bacteria over oil compounds, delaying the latter process. As a result, such seasonal effect can reduce the sensitivity of genosensing tools employing bacterial functional genes to sense oil. A better understanding of the use of natural organic matter by bacteria involved in oil-biodegradation is needed to develop an array of functional markers enabling the rapid and specific in situ detection of anthropogenic pollution.
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Affiliation(s)
| | | | | | - Thierry Baussant
- NORCE Environment, NORCE Norwegian Research Centre AS, 4070 Randaberg, Norway; (K.K.); (A.B.); (A.K.)
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26
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Bowman JP. Out From the Shadows - Resolution of the Taxonomy of the Family Cryomorphaceae. Front Microbiol 2020; 11:795. [PMID: 32431677 PMCID: PMC7214798 DOI: 10.3389/fmicb.2020.00795] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 04/03/2020] [Indexed: 12/18/2022] Open
Abstract
The family Cryomorphaceae for many years has been a poorly defined taxonomic group within the order Flavobacteriales, phylum Bacteroidetes. Members of the Cryomorphaceae, apparently consisting of multiple-family level clades, have been mostly but not exclusively detected in saline ecosystems. The problems with the taxonomy of this group have stemmed from inadequate resolution of taxonomic groups using 16S rRNA gene sequences, sparse numbers of cultivated taxa, and limited phenotypic distinctiveness. The Genome Tiaxonomc Database (GTDB), which is based on normalized taxonomic ranks includes Cryomorphaceae as containing the genera Owenweeksia and Schleiferia. This is at odds with the official taxonomy that places these genera in the family Schleiferiaceae. The other Cryomorphaceae affiliated species have even more uncertain taxonomic positions including Cryomorpha ignava. To clarify the taxonomy of Cryomorphaceae, genomes were generated for all type strains of the family Cryomorphaceae lacking such data. The GTDB-toolkit (GTDB-tk) was used to place taxa in the GTDB, which revealed novelty at the family level for some of these type strains. 16S rRNA gene sequences and concatenated protein sequences were used to further evaluate the taxonomy of the order Flavobacteriales. From the data, the GTDB enabled successful clarification of the taxonomy of the family Cryomorphaceae. A number of placeholder families were given Latinized names. It is proposed that the family Cryomorphaceae is emended to include only the species Cryomorpha ignava. The family Schleiferiaceae is emended to account for the expansion of its membership. Luteibaculum oceani represents a new family designated Luteibaculaceae fam. nov. Vicingus serpentipes is the representative of Vicingaceae fam. nov. while Salibacter halophilus represents Salibacteraceae fam. nov.
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Affiliation(s)
- John P Bowman
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, TAS, Australia
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27
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Hou F, Zhang H, Xie W, Zhou X, Zhu X, Zhang D. Co-occurrence patterns and assembly processes of microeukaryotic communities in an early-spring diatom bloom. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 711:134624. [PMID: 31818596 DOI: 10.1016/j.scitotenv.2019.134624] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 09/21/2019] [Accepted: 09/22/2019] [Indexed: 06/10/2023]
Abstract
The interaction and assembly processes of microeukaryotic community compositions (MECs) are rarely elucidated in environment with strong disturbance such as harmful algal blooms. To fill this gap, we analyzed changes of MECs induced by a diatom bloom using 18S rRNA gene amplicon sequencing. The MECs were mainly dominated by Cercozoa (average relative abundance, 49.2%), Diatom (25.5%) and Dinoflagellata (15.6%). MECs changed significantly (ANOSIM P < 0.01) in four-bloom stages. Environmental factors including pH, DO, nitrate and phosphate, together with bacterial communities could significantly influence the variation of MECs. Co-occurrence network analysis revealed a complex interaction between microeukaryotic and bacterial communities. Most OTUs in modules of the co-occurrence network were specific to one particular bloom stage. Phylogenetic based β-nearest taxon distance analyses revealed that stochastic processes mainly dominated microeukaryotic community assembly in the initial and after-bloom stage. However, microeukaryotic community assembly in middle and late stage of the bloom were driven by deterministic processes. In conclusion, both stochastic and deterministic processes play important roles in distinct bloom stages. These findings may expand current understandings of assembly mechanisms and microbial interactions underlying microeukaryotic dynamics in eutrophic aquatic ecosystems where harmful algal blooms occurred frequently.
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Affiliation(s)
- Fanrong Hou
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, China; School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Huajun Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, China; School of Marine Sciences, Ningbo University, Ningbo, 315211, China.
| | - Weijuan Xie
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, China; School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Xiaoyan Zhou
- Environmental Monitoring Center of Ningbo, Ningbo, 315010, China
| | - Xiangyu Zhu
- Environmental Monitoring Center of Ningbo, Ningbo, 315010, China
| | - Demin Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, China; School of Marine Sciences, Ningbo University, Ningbo, 315211, China; Collaborative Innovation Center for Zhejiang Marine High-efficiency and Healthy Aquaculture, Ningbo, 315211, China.
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28
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Alcamán-Arias ME, Farías L, Verdugo J, Alarcón-Schumacher T, Díez B. Microbial activity during a coastal phytoplankton bloom on the Western Antarctic Peninsula in late summer. FEMS Microbiol Lett 2019; 365:4961137. [PMID: 29788084 DOI: 10.1093/femsle/fny090] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 04/03/2018] [Indexed: 12/19/2022] Open
Abstract
Phytoplankton biomass during the austral summer is influenced by freezing and melting cycles as well as oceanographic processes that enable nutrient redistribution in the West Antarctic Peninsula (WAP). Microbial functional capabilities, metagenomic and metatranscriptomic activities as well as inorganic 13C- and 15N-assimilation rates were studied in the surface waters of Chile Bay during two contrasting summer periods in 2014. Concentrations of Chlorophyll a (Chla) varied from 0.3 mg m-3 in February to a maximum of 2.5 mg m-3 in March, together with a decrease in nutrients; however, nutrients were never depleted. The microbial community composition remained similar throughout both sampling periods; however, microbial abundance and activity changed with Chla levels. An increased biomass of Bacillariophyta, Haptophyceae and Cryptophyceae was observed along with night-grazing activity of Dinophyceae and ciliates (Alveolates). During high Chla conditions, HCO3- uptake rates during daytime incubations increased 5-fold (>2516 nmol C L-1 d-1), and increased photosynthetic transcript numbers that were mainly associated with cryptophytes; meanwhile night time NO3- (>706 nmol N L-1 d-1) and NH4+ (41.7 nmol N L-1 d-1) uptake rates were 2- and 3-fold higher, respectively, due to activity from Alpha-/Gammaproteobacteria and Bacteroidetes (Flavobacteriia). Due to a projected acceleration in climate change in the WAP, this information is valuable for predicting the composition and functional changes in Antarctic microbial communities.
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Affiliation(s)
- María E Alcamán-Arias
- Department of Oceanography, Universidad de Concepción, 4070386 Concepción, Chile.,Department of Molecular Genetics and Microbiology, Pontificia Universidad Católica de Chile, 6513677 Santiago, Chile.,Center for Climate and Resilience Research (CR) 2, Universidad de Chile, 8370448 Santiago, Chile
| | - Laura Farías
- Department of Oceanography, Universidad de Concepción, 4070386 Concepción, Chile.,Center for Climate and Resilience Research (CR) 2, Universidad de Chile, 8370448 Santiago, Chile
| | - Josefa Verdugo
- Alfred-Wegener-Institute Helmholtz-Centre for Polar and Marine Research, 27570 Bremerhaven, Germany
| | - Tomás Alarcón-Schumacher
- Department of Molecular Genetics and Microbiology, Pontificia Universidad Católica de Chile, 6513677 Santiago, Chile
| | - Beatriz Díez
- Department of Molecular Genetics and Microbiology, Pontificia Universidad Católica de Chile, 6513677 Santiago, Chile.,Center for Climate and Resilience Research (CR) 2, Universidad de Chile, 8370448 Santiago, Chile
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29
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de Sousa AGG, Tomasino MP, Duarte P, Fernández-Méndez M, Assmy P, Ribeiro H, Surkont J, Leite RB, Pereira-Leal JB, Torgo L, Magalhães C. Diversity and Composition of Pelagic Prokaryotic and Protist Communities in a Thin Arctic Sea-Ice Regime. MICROBIAL ECOLOGY 2019; 78:388-408. [PMID: 30623212 DOI: 10.1007/s00248-018-01314-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 12/25/2018] [Indexed: 06/09/2023]
Abstract
One of the most prominent manifestations of climate change is the changing Arctic sea-ice regime with a reduction in the summer sea-ice extent and a shift from thicker, perennial multiyear ice towards thinner, first-year ice. These changes in the physical environment are likely to impact microbial communities, a key component of Arctic marine food webs and biogeochemical cycles. During the Norwegian young sea ICE expedition (N-ICE2015) north of Svalbard, seawater samples were collected at the surface (5 m), subsurface (20 or 50 m), and mesopelagic (250 m) depths on 9 March, 27 April, and 16 June 2015. In addition, several physical and biogeochemical data were recorded to contextualize the collected microbial communities. Through the massively parallel sequencing of the small subunit ribosomal RNA amplicon and metagenomic data, this work allows studying the Arctic's microbial community structure during the late winter to early summer transition. Results showed that, at compositional level, Alpha- (30.7%) and Gammaproteobacteria (28.6%) are the most frequent taxa across the prokaryotic N-ICE2015 collection, and also the most phylogenetically diverse. Winter to early summer trends were quite evident since there was a high relative abundance of thaumarchaeotes in the under-ice water column in late winter while this group was nearly absent during early summer. Moreover, the emergence of Flavobacteria and the SAR92 clade in early summer might be associated with the degradation of a spring bloom of Phaeocystis. High relative abundance of hydrocarbonoclastic bacteria, particularly Alcanivorax (54.3%) and Marinobacter (6.3%), was also found. Richness showed different patterns along the depth gradient for prokaryotic (highest at mesopelagic depth) and protistan communities (higher at subsurface depths). The microbial N-ICE2015 collection analyzed in the present study provides comprehensive new knowledge about the pelagic microbiota below drifting Arctic sea-ice. The higher microbial diversity found in late winter/early spring communities reinforces the need to continue with further studies to properly characterize the winter microbial communities under the pack-ice.
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Affiliation(s)
- António Gaspar G de Sousa
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208, Porto, Portugal.
- Department of Biology, Faculty of Sciences, University of Porto, Rua Campo Alegre s/n, 4169-007, Porto, Portugal.
| | - Maria Paola Tomasino
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208, Porto, Portugal
| | - Pedro Duarte
- Norwegian Polar Institute, Fram Centre, N-9296, Tromsø, Norway
| | | | - Philipp Assmy
- Norwegian Polar Institute, Fram Centre, N-9296, Tromsø, Norway
| | - Hugo Ribeiro
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208, Porto, Portugal
| | - Jaroslaw Surkont
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande, 6, 2780-156, Oeiras, Portugal
| | - Ricardo B Leite
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande, 6, 2780-156, Oeiras, Portugal
| | - José B Pereira-Leal
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande, 6, 2780-156, Oeiras, Portugal
| | - Luís Torgo
- LIAAD - Laboratory of Artificial Intelligence and Decision Support, INESC Tec, Porto, Portugal
- Faculty of Computer Science, Dalhousie University, Halifax, Canada, USA
| | - Catarina Magalhães
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208, Porto, Portugal
- Department of Biology, Faculty of Sciences, University of Porto, Rua Campo Alegre s/n, 4169-007, Porto, Portugal
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30
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Alarcón-Schumacher T, Guajardo-Leiva S, Antón J, Díez B. Elucidating Viral Communities During a Phytoplankton Bloom on the West Antarctic Peninsula. Front Microbiol 2019; 10:1014. [PMID: 31139164 PMCID: PMC6527751 DOI: 10.3389/fmicb.2019.01014] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 04/24/2019] [Indexed: 01/16/2023] Open
Abstract
In Antarctic coastal waters where nutrient limitations are low, viruses are expected to play a major role in the regulation of bloom events. Despite this, research in viral identification and dynamics is scarce, with limited information available for the Southern Ocean (SO). This study presents an integrative-omics approach, comparing variation in the viral and microbial active communities on two contrasting sample conditions from a diatom-dominated phytoplankton bloom occurring in Chile Bay in the West Antarctic Peninsula (WAP) in the summer of 2014. The known viral community, initially dominated by Myoviridae family (∼82% of the total assigned reads), changed to become dominated by Phycodnaviridae (∼90%), while viral activity was predominantly driven by dsDNA members of the Phycodnaviridae (∼50%) and diatom infecting ssRNA viruses (∼38%), becoming more significant as chlorophyll a increased. A genomic and phylogenetic characterization allowed the identification of a new viral lineage within the Myoviridae family. This new lineage of viruses infects Pseudoalteromonas and was dominant in the phage community. In addition, a new Phycodnavirus (PaV) was described, which is predicted to infect Phaeocystis antarctica, the main blooming haptophyte in the SO. This work was able to identify the changes in the main viral players during a bloom development and suggests that the changes observed in the virioplankton could be used as a model to understand the development and decay of blooms that occur throughout the WAP.
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Affiliation(s)
- Tomás Alarcón-Schumacher
- Department of Molecular Genetics and Microbiology, Pontificia Universidad Católica de Chile, Santiago, Chile.,Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Sergio Guajardo-Leiva
- Department of Molecular Genetics and Microbiology, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Josefa Antón
- Department of Physiology, Genetics, and Microbiology, University of Alicante, Alicante, Spain
| | - Beatriz Díez
- Department of Molecular Genetics and Microbiology, Pontificia Universidad Católica de Chile, Santiago, Chile.,Center for Climate and Resilience Research (CR2), University of Chile, Santiago, Chile
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Liu Y, Debeljak P, Rembauville M, Blain S, Obernosterer I. Diatoms shape the biogeography of heterotrophic prokaryotes in early spring in the Southern Ocean. Environ Microbiol 2019; 21:1452-1465. [DOI: 10.1111/1462-2920.14579] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 02/21/2019] [Accepted: 03/03/2019] [Indexed: 11/30/2022]
Affiliation(s)
- Yan Liu
- Sorbonne Université, CNRSLaboratoire d'Océanographie Microbienne (LOMIC), 66650 Banyuls‐sur‐Mer France
| | - Pavla Debeljak
- Sorbonne Université, CNRSLaboratoire d'Océanographie Microbienne (LOMIC), 66650 Banyuls‐sur‐Mer France
- Department of Limnology and Bio‐OceanographyUniversity of Vienna, 1090 Vienna Austria
| | - Mathieu Rembauville
- Sorbonne Université, CNRSLaboratoire d'Océanographie Microbienne (LOMIC), 66650 Banyuls‐sur‐Mer France
| | - Stéphane Blain
- Sorbonne Université, CNRSLaboratoire d'Océanographie Microbienne (LOMIC), 66650 Banyuls‐sur‐Mer France
| | - Ingrid Obernosterer
- Sorbonne Université, CNRSLaboratoire d'Océanographie Microbienne (LOMIC), 66650 Banyuls‐sur‐Mer France
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32
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Towards Quantitative Microbiome Community Profiling Using Internal Standards. Appl Environ Microbiol 2019; 85:AEM.02634-18. [PMID: 30552195 DOI: 10.1128/aem.02634-18] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 12/10/2018] [Indexed: 12/16/2022] Open
Abstract
An inherent issue in high-throughput rRNA gene tag sequencing microbiome surveys is that they provide compositional data in relative abundances. This often leads to spurious correlations, making the interpretation of relationships to biogeochemical rates challenging. To overcome this issue, we quantitatively estimated the abundance of microorganisms by spiking in known amounts of internal DNA standards. Using a 3-year sample set of diverse microbial communities from the Western Antarctica Peninsula, we demonstrated that the internal standard method yielded community profiles and taxon cooccurrence patterns substantially different from those derived using relative abundances. We found that the method provided results consistent with the traditional CHEMTAX analysis of pigments and total bacterial counts by flow cytometry. Using the internal standard method, we also showed that chloroplast 16S rRNA gene data in microbial surveys can be used to estimate abundances of certain eukaryotic phototrophs such as cryptophytes and diatoms. In Phaeocystis, scatter in the 16S/18S rRNA gene ratio may be explained by physiological adaptation to environmental conditions. We conclude that the internal standard method, when applied to rRNA gene microbial community profiling, is quantitative and that its application will substantially improve our understanding of microbial ecosystems.IMPORTANCE High-throughput-sequencing-based marine microbiome profiling is rapidly expanding and changing how we study the oceans. Although powerful, the technique is not fully quantitative; it provides taxon counts only in relative abundances. In order to address this issue, we present a method to quantitatively estimate microbial abundances per unit volume of seawater filtered by spiking known amounts of internal DNA standards into each sample. We validated this method by comparing the calculated abundances to other independent estimates, including chemical markers (pigments) and total bacterial cell counts by flow cytometry. The internal standard approach allows us to quantitatively estimate and compare marine microbial community profiles, with important implications for linking environmental microbiomes to quantitative processes such as metabolic and biogeochemical rates.
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Kim SJ, Kim JG, Lee SH, Park SJ, Gwak JH, Jung MY, Chung WH, Yang EJ, Park J, Jung J, Hahn Y, Cho JC, Madsen EL, Rodriguez-Valera F, Hyun JH, Rhee SK. Genomic and metatranscriptomic analyses of carbon remineralization in an Antarctic polynya. MICROBIOME 2019; 7:29. [PMID: 30786927 PMCID: PMC6383258 DOI: 10.1186/s40168-019-0643-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 02/01/2019] [Indexed: 06/09/2023]
Abstract
BACKGROUND Polynyas in the Southern Ocean are regions of intense primary production, mainly by Phaeocystis antarctica. Carbon fixed by phytoplankton in the water column is transferred to higher trophic levels, and finally, to the deep ocean. However, in the Amundsen Sea, most of this organic carbon does not reach the sediment but is degraded in the water column due to high bacterial heterotrophic activity. RESULTS We reconstructed 12 key bacterial genomes from different phases of bloom and analyzed the expression of genes involved in organic carbon remineralization. A high correlation of gene expression between the peak and decline phases was observed in an individual genome bin-based pairwise comparison of gene expression. Polaribacter belonging to Bacteroidetes was found to be dominant in the peak phase, and its transcriptional activity was high (48.9% of the total mRNA reads). Two dominant Polaribacter bins had the potential to utilize major polymers in P. antarctica, chrysolaminarin and xylan, with a distinct set of glycosyl hydrolases. In the decline phase, Gammaproteobacteria (Ant4D3, SUP05, and SAR92), with the potential to utilize low molecular weight-dissolved organic matter (LMW-DOM) including compatible solutes, was increased. The versatility of Gammaproteobacteria may contribute to their abundance in organic carbon-rich polynya waters, while the SAR11 clade was found to be predominant in the sea ice-covered oligotrophic ocean. SAR92 clade showed transcriptional activity for utilization of both polysaccharides and LMW-DOM; this may account for their abundance both in the peak and decline phases. Ant4D3 clade was dominant in all phases of the polynya bloom, implicating the crucial roles of this clade in LMW-DOM remineralization in the Antarctic polynyas. CONCLUSIONS Genomic reconstruction and in situ gene expression analyses revealed the unique metabolic potential of dominant bacteria of the Antarctic polynya at a finer taxonomic level. The information can be used to predict temporal community succession linked to the availability of substrates derived from the P. antarctica bloom. Global warming has resulted in compositional changes in phytoplankton from P. antarctica to diatoms, and thus, repeated parallel studies in various polynyas are required to predict global warming-related changes in carbon remineralization.
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Affiliation(s)
- So-Jeong Kim
- Geologic Environment Research Division, Korea Institute of Geoscience and Mineral Resources, Daejeon, 34132, Republic of Korea
| | - Jong-Geol Kim
- Department of Microbiology, Chungbuk National University, Cheongju, 28644, Republic of Korea
| | - Sang-Hoon Lee
- Division of Polar Ocean Environment, Korea Polar Research Institute, Incheon, 21990, Republic of Korea
| | - Soo-Je Park
- Department of Biology, Jeju National University, Jeju, 63243, Republic of Korea
| | - Joo-Han Gwak
- Department of Microbiology, Chungbuk National University, Cheongju, 28644, Republic of Korea
| | - Man-Young Jung
- Department of Microbial Ecology, University of Vienna, 1090, Vienna, Austria
| | - Won-Hyung Chung
- Research Group of Gut Microbiome, Korea Food Research Institute, Sungnam, 13539, Republic of Korea
| | - Eun-Jin Yang
- Division of Polar Ocean Environment, Korea Polar Research Institute, Incheon, 21990, Republic of Korea
| | - Jisoo Park
- Division of Polar Ocean Environment, Korea Polar Research Institute, Incheon, 21990, Republic of Korea
| | - Jinyoung Jung
- Division of Polar Ocean Environment, Korea Polar Research Institute, Incheon, 21990, Republic of Korea
| | - Yoonsoo Hahn
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Jang-Cheon Cho
- Department of Biological Sciences, Inha University, Incheon, 22212, Republic of Korea
| | - Eugene L Madsen
- Department of Microbiology, Cornell University, Ithaca, NY, 14853-8101, USA
| | - Francisco Rodriguez-Valera
- Evolutionary Genomics Group, División de Microbiología, Universidad Miguel Hernández, Apartado 18, San Juan de Alicante, 03550, Alicante, Spain
| | - Jung-Ho Hyun
- Department of Marine Science and Convergence Engineering, Hanyang University ERICA Campus, Ansan, 15588, Republic of Korea
| | - Sung-Keun Rhee
- Department of Microbiology, Chungbuk National University, Cheongju, 28644, Republic of Korea.
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Fuentes S, Arroyo JI, Rodríguez-Marconi S, Masotti I, Alarcón-Schumacher T, Polz MF, Trefault N, De la Iglesia R, Díez B. Summer phyto- and bacterioplankton communities during low and high productivity scenarios in the Western Antarctic Peninsula. Polar Biol 2018. [DOI: 10.1007/s00300-018-2411-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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35
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Landa M, Blain S, Harmand J, Monchy S, Rapaport A, Obernosterer I. Major changes in the composition of a Southern Ocean bacterial community in response to diatom-derived dissolved organic matter. FEMS Microbiol Ecol 2018; 94:4935155. [DOI: 10.1093/femsec/fiy034] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 03/13/2018] [Indexed: 02/05/2023] Open
Affiliation(s)
- Marine Landa
- CNRS, Sorbonne Universités, UPMC Univ Paris 06, Laboratoire d'Océanographie Microbienne (LOMIC), Observatoire Océanologique, F-66650, Banyuls/mer, France
| | - Stéphane Blain
- CNRS, Sorbonne Universités, UPMC Univ Paris 06, Laboratoire d'Océanographie Microbienne (LOMIC), Observatoire Océanologique, F-66650, Banyuls/mer, France
| | | | - Sébastien Monchy
- Univ. Littoral Côte d'Opale, CNRS, Univ. Lille, UMR 8187, LOG, Laboratoire d'Océanologie et de Géosciences, F 59 000 Lille, France
| | - Alain Rapaport
- MISTEA, Univ. Montpellier, INRA, Montpellier SupAgro, 2, pl. Viala 34060 Montpellier, France
| | - Ingrid Obernosterer
- CNRS, Sorbonne Universités, UPMC Univ Paris 06, Laboratoire d'Océanographie Microbienne (LOMIC), Observatoire Océanologique, F-66650, Banyuls/mer, France
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36
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Luria CM, Amaral-Zettler LA, Ducklow HW, Repeta DJ, Rhyne AL, Rich JJ. Seasonal Shifts in Bacterial Community Responses to Phytoplankton-Derived Dissolved Organic Matter in the Western Antarctic Peninsula. Front Microbiol 2017; 8:2117. [PMID: 29163409 PMCID: PMC5675858 DOI: 10.3389/fmicb.2017.02117] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Accepted: 10/17/2017] [Indexed: 11/13/2022] Open
Abstract
Bacterial consumption of dissolved organic matter (DOM) drives much of the movement of carbon through the oceanic food web and the global carbon cycle. Understanding complex interactions between bacteria and marine DOM remains an important challenge. We tested the hypothesis that bacterial growth and community succession would respond differently to DOM additions due to seasonal changes in phytoplankton abundance in the environment. Four mesocosm experiments were conducted that spanned the spring transitional period (August-December 2013) in surface waters of the Western Antarctic Peninsula (WAP). Each mesocosm consisted of nearshore surface seawater (50 L) incubated in the laboratory for 10 days. The addition of DOM, in the form of cell-free exudates extracted from Thalassiosira weissflogii diatom cultures led to changes in bacterial abundance, production, and community composition. The timing of each mesocosm experiment (i.e., late winter vs. late spring) influenced the magnitude and direction of bacterial changes. For example, the same DOM treatment applied at different times during the season resulted in different levels of bacterial production and different bacterial community composition. There was a mid-season shift from Collwelliaceae to Polaribacter having the greatest relative abundance after incubation. This shift corresponded to a modest but significant increase in the initial relative abundance of Polaribacter in the nearshore seawater used to set up experiments. This finding supports a new hypothesis that starting community composition, through priority effects, influenced the trajectory of community succession in response to DOM addition. As strong inter-annual variability and long-term climate change may shift the timing of WAP phytoplankton blooms, and the corresponding production of DOM exudates, this study suggests a mechanism by which different seasonal successional patterns in bacterial communities could occur.
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Affiliation(s)
- Catherine M. Luria
- Department of Ecology and Evolutionary Biology, Brown University, Providence, RI, United States
| | - Linda A. Amaral-Zettler
- Marine Biological Laboratory, Josephine Bay Paul Center, Woods Hole, MA, United States
- Department of Earth, Environmental and Planetary Sciences, Brown University, Providence, RI, United States
- NIOZ Royal Netherlands Institute for Sea Research, Utrecht University, Den Burg, Netherlands
| | - Hugh W. Ducklow
- Lamont-Doherty Earth Observatory, Columbia University, Palisades, NY, United States
| | - Daniel J. Repeta
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, United States
| | - Andrew L. Rhyne
- Department of Biology, Marine Biology, and Environmental Science, Roger Williams University, Bristol, RI, United States
| | - Jeremy J. Rich
- School of Marine Sciences, Darling Marine Center, University of Maine, Walpole, ME, United States
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37
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Karlsen C, Ottem KF, Brevik ØJ, Davey M, Sørum H, Winther-Larsen HC. The environmental and host-associated bacterial microbiota of Arctic seawater-farmed Atlantic salmon with ulcerative disorders. JOURNAL OF FISH DISEASES 2017; 40:1645-1663. [PMID: 28449237 DOI: 10.1111/jfd.12632] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 02/10/2017] [Accepted: 02/12/2017] [Indexed: 06/07/2023]
Abstract
The Norwegian aquaculture of Atlantic salmon (Salmo salar L.) is hampered by ulcerative disorders associated with bacterial infections. Chronic ulceration may provide microenvironments that disturb the normal microbial biodiversity of external surfaces. Studying the composition of microbial communities in skin ulcers will enhance our understanding of ulcer aetiology. To achieve this, we tested marine farmed Atlantic salmon and sampled the base and edge of ulcers at the end of winter (April) and end of summer (September), in addition to skin mucus of healthy individuals. In order to assess microbiota associated with the host and obtain insight into the environmental ecology, we also sampled sea water, the sediment layer underneath the farm facility and the distal intestine of Atlantic salmon. The skin microbiota of Atlantic salmon was different from that of the surrounding water. Residential Tenacibaculum and Arcobacter species persistently dominated the cutaneous skin and ulcer mucus surfaces of Atlantic salmon during both winter and summer periods. The intestinal microbiota was dominated by Mycoplasma with an increase in Aliivibrio and Alcaligenes abundance in the intestine of fish with ulcerative disorder at the end of winter. These findings suggest the presence of resilient microbes in the mucus surfaces of Atlantic salmon.
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Affiliation(s)
- C Karlsen
- Department of Food Safety and Infection Biology, Norwegian University of Life Sciences (NMBU), Oslo, Norway
- Laboratory for Microbial Dynamics (LaMDa), Department of Pharmaceutical Biosciences, Center of Integrative Microbial Evolution (CIME), School of Pharmacy, University of Oslo, Oslo, Norway
| | | | | | - M Davey
- Department of Biological Sciences, University of Oslo, Oslo, Norway
| | - H Sørum
- Department of Food Safety and Infection Biology, Norwegian University of Life Sciences (NMBU), Oslo, Norway
| | - H C Winther-Larsen
- Laboratory for Microbial Dynamics (LaMDa), Department of Pharmaceutical Biosciences, Center of Integrative Microbial Evolution (CIME), School of Pharmacy, University of Oslo, Oslo, Norway
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38
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Sipler RE, Kellogg CTE, Connelly TL, Roberts QN, Yager PL, Bronk DA. Microbial Community Response to Terrestrially Derived Dissolved Organic Matter in the Coastal Arctic. Front Microbiol 2017. [PMID: 28649233 PMCID: PMC5465303 DOI: 10.3389/fmicb.2017.01018] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Warming at nearly twice the global rate, higher than average air temperatures are the new ‘normal’ for Arctic ecosystems. This rise in temperature has triggered hydrological and geochemical changes that increasingly release carbon-rich water into the coastal ocean via increased riverine discharge, coastal erosion, and the thawing of the semi-permanent permafrost ubiquitous in the region. To determine the biogeochemical impacts of terrestrially derived dissolved organic matter (tDOM) on marine ecosystems we compared the nutrient stocks and bacterial communities present under ice-covered and ice-free conditions, assessed the lability of Arctic tDOM to coastal microbial communities from the Chukchi Sea, and identified bacterial taxa that respond to rapid increases in tDOM. Once thought to be predominantly refractory, we found that ∼7% of dissolved organic carbon and ∼38% of dissolved organic nitrogen from tDOM was bioavailable to receiving marine microbial communities on short 4 – 6 day time scales. The addition of tDOM shifted bacterial community structure toward more copiotrophic taxa and away from more oligotrophic taxa. Although no single order was found to respond universally (positively or negatively) to the tDOM addition, this study identified 20 indicator species as possible sentinels for increased tDOM. These data suggest the true ecological impact of tDOM will be widespread across many bacterial taxa and that shifts in coastal microbial community composition should be anticipated.
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Affiliation(s)
- Rachel E Sipler
- The Virginia Institute of Marine Science, College of William & Mary, Gloucester PointVA, United States
| | - Colleen T E Kellogg
- Department of Microbiology & Immunology, University of British Columbia, VancouverBC, Canada
| | - Tara L Connelly
- Department of Marine Sciences, University of Georgia, AthensGA, United States
| | - Quinn N Roberts
- The Virginia Institute of Marine Science, College of William & Mary, Gloucester PointVA, United States
| | - Patricia L Yager
- Department of Marine Sciences, University of Georgia, AthensGA, United States
| | - Deborah A Bronk
- The Virginia Institute of Marine Science, College of William & Mary, Gloucester PointVA, United States
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39
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Dinasquet J, Richert I, Logares R, Yager P, Bertilsson S, Riemann L. Mixing of water masses caused by a drifting iceberg affects bacterial activity, community composition and substrate utilization capability in the Southern Ocean. Environ Microbiol 2017; 19:2453-2467. [PMID: 28429510 DOI: 10.1111/1462-2920.13769] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 04/15/2017] [Indexed: 11/29/2022]
Abstract
The number of icebergs produced from ice-shelf disintegration has increased over the past decade in Antarctica. These drifting icebergs mix the water column, influence stratification and nutrient condition, and can affect local productivity and food web composition. Data on whether icebergs affect bacterioplankton function and composition are scarce, however. We assessed the influence of iceberg drift on bacterial community composition and on their ability to exploit carbon substrates during summer in the coastal Southern Ocean. An elevated bacterial production and a different community composition were observed in iceberg-influenced waters relative to the undisturbed water column nearby. These major differences were confirmed in short-term incubations with bromodeoxyuridine followed by CARD-FISH. Furthermore, one-week bottle incubations amended with inorganic nutrients and carbon substrates (a mix of substrates, glutamine, N-acetylglucosamine, or pyruvate) revealed contrasting capacity of bacterioplankton to utilize specific carbon substrates in the iceberg-influenced waters compared with the undisturbed site. Our study demonstrates that the hydrographical perturbations introduced by a drifting iceberg can affect activity, composition, and substrate utilization capability of marine bacterioplankton. Consequently, in a context of global warming, increased frequency of drifting icebergs in polar regions holds the potential to affect carbon and nutrient biogeochemistry at local and possibly regional scales.
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Affiliation(s)
- Julie Dinasquet
- Department of Natural Sciences, Linnaeus University, Kalmar, Sweden.,Marine Biological Section, University of Copenhagen, Helsingør, Denmark
| | - Inga Richert
- Department of Ecology and Genetics, Limnology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden.,Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, Microbial Ecosystem Services Group, Leipzig, Germany
| | | | - Patricia Yager
- Department of Marine Sciences, University of Georgia, Athens, GA, USA
| | - Stefan Bertilsson
- Department of Ecology and Genetics, Limnology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Lasse Riemann
- Marine Biological Section, University of Copenhagen, Helsingør, Denmark
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40
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Microbial communities of aquatic environments on Heard Island characterized by pyrotag sequencing and environmental data. Sci Rep 2017; 7:44480. [PMID: 28290555 PMCID: PMC5349573 DOI: 10.1038/srep44480] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Accepted: 02/09/2017] [Indexed: 12/23/2022] Open
Abstract
Heard Island in the Southern Ocean is a biological hotspot that is suffering the effects of climate change. Significant glacier retreat has generated proglacial lagoons, some of which are open to the ocean. We used pyrotag sequencing of SSU rRNA genes and environmental data to characterize microorganisms from two pools adjacent to animal breeding areas, two glacial lagoons and Atlas Cove (marine site). The more abundant taxa included Actinobacteria, Bacteroidetes and Proteobacteria, ciliates and picoflagellates (e.g. Micromonas), and relatively few Archaea. Seal Pool, which is rich in organic matter, was characterized by a heterotrophic degradative community, while the less eutrophic Atlas Pool had more eucaryotic primary producers. Brown Lagoon, with the lowest nutrient levels, had Eucarya and Bacteria predicted to be oligotrophs, possess small cell sizes, and have the ability to metabolize organic matter. The marine influence on Winston Lagoon was evident by its salinity and the abundance of marine-like Gammaproteobacteria, while also lacking typical marine eucaryotes indicating the system was still functioning as a distinct niche. This is the first microbiology study of Heard Island and revealed that communities are distinct at each location and heavily influenced by local environmental factors.
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41
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Berry MA, White JD, Davis TW, Jain S, Johengen TH, Dick GJ, Sarnelle O, Denef VJ. Are Oligotypes Meaningful Ecological and Phylogenetic Units? A Case Study of Microcystis in Freshwater Lakes. Front Microbiol 2017; 8:365. [PMID: 28337183 PMCID: PMC5341627 DOI: 10.3389/fmicb.2017.00365] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 02/21/2017] [Indexed: 11/13/2022] Open
Abstract
Oligotyping is a computational method used to increase the resolution of marker gene microbiome studies. Although oligotyping can distinguish highly similar sequence variants, the resulting units are not necessarily phylogenetically and ecologically informative due to limitations of the selected marker gene. In this perspective, we examine how oligotyping data is interpreted in recent literature, and we illustrate some of the method’s constraints with a case study of the harmful bloom-forming cyanobacterium Microcystis. We identified three Microcystis oligotypes from a western Lake Erie bacterial community 16S rRNA gene (V4 region) survey that had previously clustered into one OTU. We found the same three oligotypes and two additional sequence variants in 46 Microcystis cultures isolated from Michigan inland lakes spanning a trophic gradient. In Lake Erie, shifts in Microcystis oligotypes corresponded to spatial nutrient gradients and temporal transitions in bloom toxicity. In the cultures, Microcystis oligotypes showed preferential distributions for different trophic states, but genomic data revealed that the oligotypes identified in Lake Erie did not correspond to toxin gene presence. Thus, oligotypes could not be used for inferring toxic ecotypes. Most strikingly, Microcystis oligotypes were not monophyletic. Our study supports the utility of oligotyping for distinguishing sequence types along certain ecological features, while it stresses that 16S rRNA gene sequence types may not reflect ecologically or phylogenetically cohesive populations. Therefore, we recommend that studies employing oligotyping or related tools consider these caveats during data interpretation.
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Affiliation(s)
- Michelle A Berry
- Department of Ecology and Evolutionary Biology, University of Michigan Ann Arbor, MI, USA
| | - Jeffrey D White
- Department of Biology, Framingham State University Framingham, MA, USA
| | - Timothy W Davis
- NOAA Great Lakes Environmental Research Laboratory Ann Arbor, MI, USA
| | - Sunit Jain
- Department of Earth and Environmental Sciences, University of Michigan Ann Arbor, MI, USA
| | - Thomas H Johengen
- Cooperative Institute for Limnology and Ecosystems Research, University of Michigan Ann Arbor, MI, USA
| | - Gregory J Dick
- Department of Earth and Environmental Sciences, University of Michigan Ann Arbor, MI, USA
| | - Orlando Sarnelle
- Department of Fisheries and Wildlife, Michigan State University East Lansing, MI, USA
| | - Vincent J Denef
- Department of Ecology and Evolutionary Biology, University of Michigan Ann Arbor, MI, USA
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42
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Bacterial community segmentation facilitates the prediction of ecosystem function along the coast of the western Antarctic Peninsula. ISME JOURNAL 2017; 11:1460-1471. [PMID: 28106879 DOI: 10.1038/ismej.2016.204] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 10/27/2016] [Accepted: 11/16/2016] [Indexed: 11/09/2022]
Abstract
Bacterial community structure can be combined with observations of ecophysiological data to build predictive models of microbial ecosystem function. These models are useful for understanding how function might change in response to a changing environment. Here we use five spring-summer seasons of bacterial community structure and flow cytometry data from a productive coastal site along the western Antarctic Peninsula to construct models of bacterial production (BP), an ecosystem function that heterotrophic bacteria provide. Through a novel application of emergent self-organizing maps we identified eight recurrent modes in the structure of the bacterial community. A model that combined bacterial abundance, mode and the fraction of cells belonging to the high nucleic acid population (fHNA; R2=0.730, P<0.001) best described BP. Abrupt transitions between modes during the 2013-2014 spring-summer season corresponded to rapid shifts in fHNA. We conclude that parameterizing community structure data via segmentation can yield useful insights into microbial ecosystem function and ecosystem processes.
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43
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Luria CM, Amaral-Zettler LA, Ducklow HW, Rich JJ. Seasonal Succession of Free-Living Bacterial Communities in Coastal Waters of the Western Antarctic Peninsula. Front Microbiol 2016; 7:1731. [PMID: 27857708 PMCID: PMC5093341 DOI: 10.3389/fmicb.2016.01731] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Accepted: 10/17/2016] [Indexed: 01/05/2023] Open
Abstract
The marine ecosystem along the Western Antarctic Peninsula undergoes a dramatic seasonal transition every spring, from almost total darkness to almost continuous sunlight, resulting in a cascade of environmental changes, including phytoplankton blooms that support a highly productive food web. Despite having important implications for the movement of energy and materials through this ecosystem, little is known about how these changes impact bacterial succession in this region. Using 16S rRNA gene amplicon sequencing, we measured changes in free-living bacterial community composition and richness during a 9-month period that spanned winter to the end of summer. Chlorophyll a concentrations were relatively low until summer when a major phytoplankton bloom occurred, followed 3 weeks later by a high peak in bacterial production. Richness in bacterial communities varied between ~1,200 and 1,800 observed operational taxonomic units (OTUs) before the major phytoplankton bloom (out of ~43,000 sequences per sample). During peak bacterial production, OTU richness decreased to ~700 OTUs. The significant decrease in OTU richness only lasted a few weeks, after which time OTU richness increased again as bacterial production declined toward pre-bloom levels. OTU richness was negatively correlated with bacterial production and chlorophyll a concentrations. Unlike the temporal pattern in OTU richness, community composition changed from winter to spring, prior to onset of the summer phytoplankton bloom. Community composition continued to change during the phytoplankton bloom, with increased relative abundance of several taxa associated with phytoplankton blooms, particularly Polaribacter. Bacterial community composition began to revert toward pre-bloom conditions as bacterial production declined. Overall, our findings clearly demonstrate the temporal relationship between phytoplankton blooms and seasonal succession in bacterial growth and community composition. Our study highlights the importance of high-resolution time series sampling, especially during the relatively under-sampled Antarctic winter and spring, which enabled us to discover seasonal changes in bacterial community composition that preceded the summertime phytoplankton bloom.
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Affiliation(s)
- Catherine M Luria
- Department of Ecology and Evolutionary Biology, Brown University, Providence RI, USA
| | - Linda A Amaral-Zettler
- The Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods HoleMA, USA; Department of Earth, Environmental and Planetary Sciences, Brown University, ProvidenceRI, USA
| | - Hugh W Ducklow
- Department of Earth and Environmental Sciences, Lamont-Doherty Earth Observatory of Columbia University, Palisades NY, USA
| | - Jeremy J Rich
- School of Marine Sciences and Darling Marine Center, University of Maine, Walpole ME, USA
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44
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Chilling out: the evolution and diversification of psychrophilic algae with a focus on Chlamydomonadales. Polar Biol 2016. [DOI: 10.1007/s00300-016-2045-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Abstract
The large diversity of marine microorganisms harboured by oceans plays an important role in planet sustainability by driving globally important biogeochemical cycles; all primary and most secondary production in the oceans is performed by microorganisms. The largest part of the planet is covered by cold environments; consequently, cold-adapted microorganisms have crucial functional roles in globally important environmental processes and biogeochemical cycles cold-adapted extremophiles are a remarkable model to shed light on the molecular basis of survival at low temperature. The indigenous populations of Antarctic and Arctic microorganisms are endowed with genetic and physiological traits that allow them to live and effectively compete at the temperatures prevailing in polar regions. Some genes, e.g. glycosyltransferases and glycosylsynthetases involved in the architecture of the cell wall, may have been acquired/retained during evolution of polar strains or lost in tropical strains. This present work focusses on temperature and its role in shaping microbial adaptations; however, in assessing the impacts of climate changes on microbial diversity and biogeochemical cycles in polar oceans, it should not be forgotten that physiological studies need to include the interaction of temperature with other abiotic and biotic factors.
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46
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Gionfriddo CM, Tate MT, Wick RR, Schultz MB, Zemla A, Thelen MP, Schofield R, Krabbenhoft DP, Holt KE, Moreau JW. Microbial mercury methylation in Antarctic sea ice. Nat Microbiol 2016; 1:16127. [PMID: 27670112 DOI: 10.1038/nmicrobiol.2016.127] [Citation(s) in RCA: 102] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 06/29/2016] [Indexed: 11/09/2022]
Abstract
Atmospheric deposition of mercury onto sea ice and circumpolar sea water provides mercury for microbial methylation, and contributes to the bioaccumulation of the potent neurotoxin methylmercury in the marine food web. Little is known about the abiotic and biotic controls on microbial mercury methylation in polar marine systems. However, mercury methylation is known to occur alongside photochemical and microbial mercury reduction and subsequent volatilization. Here, we combine mercury speciation measurements of total and methylated mercury with metagenomic analysis of whole-community microbial DNA from Antarctic snow, brine, sea ice and sea water to elucidate potential microbially mediated mercury methylation and volatilization pathways in polar marine environments. Our results identify the marine microaerophilic bacterium Nitrospina as a potential mercury methylator within sea ice. Anaerobic bacteria known to methylate mercury were notably absent from sea-ice metagenomes. We propose that Antarctic sea ice can harbour a microbial source of methylmercury in the Southern Ocean.
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Affiliation(s)
- Caitlin M Gionfriddo
- School of Earth Sciences, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Michael T Tate
- Wisconsin Water Science Center, US Geological Survey, Middleton, Wisconsin 53562, USA
| | - Ryan R Wick
- Centre for Systems Genomics, University of Melbourne, Victoria 3010, Australia.,Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Victoria 3010, Australia
| | - Mark B Schultz
- Centre for Systems Genomics, University of Melbourne, Victoria 3010, Australia.,Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Victoria 3010, Australia
| | - Adam Zemla
- Computation Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550 USA
| | - Michael P Thelen
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, USA
| | - Robyn Schofield
- School of Earth Sciences, University of Melbourne, Parkville, Victoria 3010, Australia
| | - David P Krabbenhoft
- Wisconsin Water Science Center, US Geological Survey, Middleton, Wisconsin 53562, USA
| | - Kathryn E Holt
- Centre for Systems Genomics, University of Melbourne, Victoria 3010, Australia.,Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Victoria 3010, Australia
| | - John W Moreau
- School of Earth Sciences, University of Melbourne, Parkville, Victoria 3010, Australia
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47
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Chandler JW, Lin Y, Gainer PJ, Post AF, Johnson ZI, Zinser ER. Variable but persistent coexistence of Prochlorococcus ecotypes along temperature gradients in the ocean's surface mixed layer. ENVIRONMENTAL MICROBIOLOGY REPORTS 2016; 8:272-284. [PMID: 26743532 DOI: 10.1111/1758-2229.12378] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2015] [Accepted: 12/31/2015] [Indexed: 06/05/2023]
Abstract
The vast majority of the phytoplankton communities in surface mixed layer of the oligotrophic ocean are numerically dominated by one of two ecotypes of Prochlorococcus, eMIT9312 or eMED4. In this study, we surveyed large latitudinal transects in the Atlantic and Pacific Ocean to determine if these ecotypes discretely partition the surface mixed layer niche, or if populations exist as a continuum along key environmental gradients, particularly temperature. Transitions of dominance occurred at approximately 19-21°C, with the eMED4 ecotype dominating the colder, and eMIT9312 ecotype dominating the warmer regions. Within these zones of regional dominance, however, the minority ecotype was not competed to extinction. Rather, a robust log-linear relationship between ecotype ratio and temperature characterized this stabilized coexistence: for every 2.5°C increase in temperature, the eMIT9312:eMED4 ratio increased by an order of magnitude. This relationship was observed in both quantitative polymerase chain reaction and in pyrosequencing assays. Water column stratification also contributed to the ecotype ratio along the basin-scale transects, but to a lesser extent. Finally, instances where the ratio of the eMED4 and eMIT9312 abundances did not correlate well with temperature were identified. Such occurrences are likely due to changes in water temperatures outpacing changes in community structure.
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Affiliation(s)
- Jeremy W Chandler
- Department of Microbiology, The University of Tennessee, M409 WLS, Knoxville, TN, 37966, USA
| | - Yajuan Lin
- Nicholas School of the Environment and Earth Sciences, Duke University, 135 Marine Lab Rd., Beaufort, NC, 28516, USA
| | - P Jackson Gainer
- Department of Microbiology, The University of Tennessee, M409 WLS, Knoxville, TN, 37966, USA
| | - Anton F Post
- Graduate School of Oceanography, The University of Rhode Island, 220 South Ferry Road, Narragansett, RI, 02882, USA
| | - Zackary I Johnson
- Nicholas School of the Environment and Earth Sciences, Duke University, 135 Marine Lab Rd., Beaufort, NC, 28516, USA
| | - Erik R Zinser
- Department of Microbiology, The University of Tennessee, M409 WLS, Knoxville, TN, 37966, USA
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48
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Voudanta E, Kormas KA, Monchy S, Delegrange A, Vincent D, Genitsaris S, Christaki U. Mussel biofiltration effects on attached bacteria and unicellular eukaryotes in fish-rearing seawater. PeerJ 2016; 4:e1829. [PMID: 27069786 PMCID: PMC4824906 DOI: 10.7717/peerj.1829] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 02/28/2016] [Indexed: 12/13/2022] Open
Abstract
Mussel biofiltration is a widely used approach for the mitigation of aquaculture water. In this study, we investigated the effect of mussel biofiltration on the communities of particle-associated bacteria and unicellular eukaryotes in a sea bass aquaculture in southern North Sea. We assessed the planktonic community changes before and after biofiltration based on the diversity of the 16S and 18S rRNA genes by using next generation sequencing technologies. Although there was no overall reduction in the operational taxonomic units (OTU) numbers between the control (no mussels) and the test (with mussels) tanks, a clear reduction in the relative abundance of the top three most dominant OTUs in every sampling time was observed, ranging between 2-28% and 16-82% for Bacteria and Eukarya, respectively. The bacterial community was dominated by OTUs related to phytoplankton blooms and/or high concentrations of detritus. Among the eukaryotes, several fungal and parasitic groups were found. Their relative abundance in most cases was also reduced from the control to the test tanks; a similar decreasing pattern was also observed for both major higher taxa and functional (trophic) groups. Overall, this study showed the effectiveness of mussel biofiltration on the decrease of microbiota abundance and diversity in seawater fueling fish farms.
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Affiliation(s)
- Eleni Voudanta
- Laboratoire d’Océanologie et Géosciences (LOG), UMR CNRS 8187, Université du Littoral Côte d’ Opale, Wimereux, France
| | - Konstantinos Ar Kormas
- Department of Ichthyology & Aquatic Environment, School of Agricultural Sciences, University of Thessaly, Volos, Greece
| | - Sebastién Monchy
- Laboratoire d’Océanologie et Géosciences (LOG), UMR CNRS 8187, Université du Littoral Côte d’ Opale, Wimereux, France
| | - Alice Delegrange
- Laboratoire d’Océanologie et Géosciences (LOG), UMR CNRS 8187, Université du Littoral Côte d’ Opale, Wimereux, France
| | - Dorothée Vincent
- Laboratoire d’Océanologie et Géosciences (LOG), UMR CNRS 8187, Université du Littoral Côte d’ Opale, Wimereux, France
| | - Savvas Genitsaris
- Laboratoire d’Océanologie et Géosciences (LOG), UMR CNRS 8187, Université du Littoral Côte d’ Opale, Wimereux, France
| | - Urania Christaki
- Laboratoire d’Océanologie et Géosciences (LOG), UMR CNRS 8187, Université du Littoral Côte d’ Opale, Wimereux, France
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49
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Delmont TO, Eren AM, Vineis JH, Post AF. Genome reconstructions indicate the partitioning of ecological functions inside a phytoplankton bloom in the Amundsen Sea, Antarctica. Front Microbiol 2015; 6:1090. [PMID: 26579075 PMCID: PMC4620155 DOI: 10.3389/fmicb.2015.01090] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Accepted: 09/22/2015] [Indexed: 11/30/2022] Open
Abstract
Antarctica polynyas support intense phytoplankton blooms, impacting their environment by a substantial depletion of inorganic carbon and nutrients. These blooms are dominated by the colony-forming haptophyte Phaeocystis antarctica and they are accompanied by a distinct bacterial population. Yet, the ecological role these bacteria may play in P. antarctica blooms awaits elucidation of their functional gene pool and of the geochemical activities they support. Here, we report on a metagenome (~160 million reads) analysis of the microbial community associated with a P. antarctica bloom event in the Amundsen Sea polynya (West Antarctica). Genomes of the most abundant Bacteroidetes and Proteobacteria populations have been reconstructed and a network analysis indicates a strong functional partitioning of these bacterial taxa. Three of them (SAR92, and members of the Oceanospirillaceae and Cryomorphaceae) are found in close association with P. antarctica colonies. Distinct features of their carbohydrate, nitrogen, sulfur and iron metabolisms may serve to support mutualistic relationships with P. antarctica. The SAR92 genome indicates a specialization in the degradation of fatty acids and dimethylsulfoniopropionate (compounds released by P. antarctica) into dimethyl sulfide, an aerosol precursor. The Oceanospirillaceae genome carries genes that may enhance algal physiology (cobalamin synthesis). Finally, the Cryomorphaceae genome is enriched in genes that function in cell or colony invasion. A novel pico-eukaryote, Micromonas related genome (19.6 Mb, ~94% completion) was also recovered. It contains the gene for an anti-freeze protein, which is lacking in Micromonas at lower latitudes. These draft genomes are representative for abundant microbial taxa across the Southern Ocean surface.
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Affiliation(s)
- Tom O. Delmont
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological LaboratoryWoods Hole, MA, USA
| | - A. Murat Eren
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological LaboratoryWoods Hole, MA, USA
| | - Joseph H. Vineis
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological LaboratoryWoods Hole, MA, USA
| | - Anton F. Post
- Coastal Resources Center, Graduate School of Oceanography, University of Rhode IslandNarragansett, RI, USA
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