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Liu X, Jiang N, Wang X, Yan H, Guan L, Kong L, Chen J, Zhang H, Ma H. Weissella cibaria Relieves Gut Inflammation Caused by Escherichia coli through Inflammation Modulation and Gut Microbiota Regulation. Foods 2024; 13:1133. [PMID: 38611436 PMCID: PMC11011356 DOI: 10.3390/foods13071133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 03/29/2024] [Accepted: 04/02/2024] [Indexed: 04/14/2024] Open
Abstract
The emergence of multi-drug-resistant (MDR) pathogens has considerably challenged the development of new drugs. Probiotics that inhibit MDR pathogens offer advantages over chemical antibiotics and drugs due to their increased safety and fewer side effects. This study reported that Weissella cibaria P-8 isolated from pickles showed excellent antibacterial activity against intestinal pathogens, particularly the antibacterial activity against MDR Escherichia coli B2 was the highest. This study showed that the survival rates of W. cibaria P-8 at pH 2.0 and 0.3% bile salt concentration were 72% and 71.56%, respectively, and it still had antibacterial activity under pepsin, trypsin, protease K, and catalase hydrolysis. Moreover, W. cibaria P-8 inhibits the expression of inflammatory factors interleukin-1β, tumor necrosis factor-α, and interleukin-6, upregulates the interleukin-10 level, and increases total antioxidant capacity and superoxide dismutase enzyme activity in serum. W. cibaria P-8 also efficiently repairs intestinal damage caused by E. coli infection. The gut microbiota analysis demonstrated that W. cibaria P-8 colonizes the intestine and increases the abundance of some beneficial intestinal microorganisms, particularly Prevotella. In conclusion, W. cibaria P-8 alleviated MDR E. coli-induced intestinal inflammation by regulating inflammatory cytokine and enzyme activity and rebalancing the gut microbiota, which could provide the foundation for subsequent clinical analyses and probiotic product development.
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Affiliation(s)
- Xiaoyu Liu
- College of Life Science, Jilin Agricultural University, Xincheng Street No. 2888, Changchun 130118, China; (X.L.); (N.J.); (X.W.); (H.Y.); (L.G.)
- The Engineering Research Center of Bioreactor and Drug Development, Ministry of Education, Jilin Agricultural University, Xincheng Street No. 2888, Changchun 130118, China
| | - Nan Jiang
- College of Life Science, Jilin Agricultural University, Xincheng Street No. 2888, Changchun 130118, China; (X.L.); (N.J.); (X.W.); (H.Y.); (L.G.)
- The Engineering Research Center of Bioreactor and Drug Development, Ministry of Education, Jilin Agricultural University, Xincheng Street No. 2888, Changchun 130118, China
| | - Xinyue Wang
- College of Life Science, Jilin Agricultural University, Xincheng Street No. 2888, Changchun 130118, China; (X.L.); (N.J.); (X.W.); (H.Y.); (L.G.)
- The Engineering Research Center of Bioreactor and Drug Development, Ministry of Education, Jilin Agricultural University, Xincheng Street No. 2888, Changchun 130118, China
| | - Haowen Yan
- College of Life Science, Jilin Agricultural University, Xincheng Street No. 2888, Changchun 130118, China; (X.L.); (N.J.); (X.W.); (H.Y.); (L.G.)
- The Engineering Research Center of Bioreactor and Drug Development, Ministry of Education, Jilin Agricultural University, Xincheng Street No. 2888, Changchun 130118, China
| | - Lili Guan
- College of Life Science, Jilin Agricultural University, Xincheng Street No. 2888, Changchun 130118, China; (X.L.); (N.J.); (X.W.); (H.Y.); (L.G.)
- The Engineering Research Center of Bioreactor and Drug Development, Ministry of Education, Jilin Agricultural University, Xincheng Street No. 2888, Changchun 130118, China
| | - Lingcong Kong
- College of Veterinary Medicine, Jilin Agricultural University, Xincheng Street No. 2888, Changchun 130118, China (J.C.)
- The Key Laboratory of New Veterinary Drug Research, Development of Jilin Province, Jilin Agricultural University, Xincheng Street No. 2888, Changchun 130118, China
| | - Jingrui Chen
- College of Veterinary Medicine, Jilin Agricultural University, Xincheng Street No. 2888, Changchun 130118, China (J.C.)
| | - Haipeng Zhang
- College of Life Science, Jilin Agricultural University, Xincheng Street No. 2888, Changchun 130118, China; (X.L.); (N.J.); (X.W.); (H.Y.); (L.G.)
- The Engineering Research Center of Bioreactor and Drug Development, Ministry of Education, Jilin Agricultural University, Xincheng Street No. 2888, Changchun 130118, China
| | - Hongxia Ma
- College of Life Science, Jilin Agricultural University, Xincheng Street No. 2888, Changchun 130118, China; (X.L.); (N.J.); (X.W.); (H.Y.); (L.G.)
- The Engineering Research Center of Bioreactor and Drug Development, Ministry of Education, Jilin Agricultural University, Xincheng Street No. 2888, Changchun 130118, China
- College of Veterinary Medicine, Jilin Agricultural University, Xincheng Street No. 2888, Changchun 130118, China (J.C.)
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2
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Dithugoe CD, Bezuidt OKI, Cavan EL, Froneman WP, Thomalla SJ, Makhalanyane TP. Bacteria and Archaea Regulate Particulate Organic Matter Export in Suspended and Sinking Marine Particle Fractions. mSphere 2023:e0042022. [PMID: 37093039 DOI: 10.1128/msphere.00420-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2023] Open
Abstract
The biological carbon pump (BCP) in the Southern Ocean is driven by phytoplankton productivity and is a significant organic matter sink. However, the role of particle-attached (PA) and free-living (FL) prokaryotes (bacteria and archaea) and their diversity in influencing the efficiency of the BCP is still unclear. To investigate this, we analyzed the metagenomes linked to suspended and sinking marine particles from the Sub-Antarctic Southern Ocean Time Series (SOTS) by deploying a Marine Snow Catcher (MSC), obtaining suspended and sinking particulate material, determining organic carbon and nitrogen flux, and constructing metagenome-assembled genomes (MAGs). The suspended and sinking particle-pools were dominated by bacteria with the potential to degrade organic carbon. Bacterial communities associated with the sinking fraction had more genes related to the degradation of complex organic carbon than those in the suspended fraction. Archaea had the potential to drive nitrogen metabolism via nitrite and ammonia oxidation, altering organic nitrogen concentration. The data revealed several pathways for chemoautotrophy and the secretion of recalcitrant dissolved organic carbon (RDOC) from CO2, with bacteria and archaea potentially sequestering particulate organic matter (POM) via the production of RDOC. These findings provide insights into the diversity and function of prokaryotes in suspended and sinking particles and their role in organic carbon/nitrogen export in the Southern Ocean. IMPORTANCE The biological carbon pump is crucial for the export of particulate organic matter in the ocean. Recent studies on marine microbes have shown the profound influence of bacteria and archaea as regulators of particulate organic matter export. Yet, despite the importance of the Southern Ocean as a carbon sink, we lack comparable insights regarding microbial contributions. This study provides the first insights regarding prokaryotic contributions to particulate organic matter export in the Southern Ocean. We reveal evidence that prokaryotic communities in suspended and sinking particle fractions harbor widespread genomic potential for mediating particulate organic matter export. The results substantially enhance our understanding of the role played by microorganisms in regulating particulate organic matter export in suspended and sinking marine fractions in the Southern Ocean.
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Affiliation(s)
- Choaro D Dithugoe
- Southern Ocean Carbon-Climate Observatory (SOCCO), Council of Scientific & Industrial Research (CSIR), Rosebank, Cape Town, South Africa
- SARChI Chair: Marine Ecosystems and Resources, Department of Entomology & Zoology, Rhodes University (RU), Makhanda, Eastern Cape, South Africa
- SARChI Chair: Marine Microbiomics, microbiome@UP, Department of Biochemistry, Genetics and Microbiology, University of Pretoria (UP), Hatfield, Pretoria, South Africa
| | - Oliver K I Bezuidt
- SARChI Chair: Marine Microbiomics, microbiome@UP, Department of Biochemistry, Genetics and Microbiology, University of Pretoria (UP), Hatfield, Pretoria, South Africa
| | - Emma L Cavan
- Imperial College London, Berks, Silwood Park, Berkshire, United Kingdom
| | - William P Froneman
- SARChI Chair: Marine Ecosystems and Resources, Department of Entomology & Zoology, Rhodes University (RU), Makhanda, Eastern Cape, South Africa
| | - Sandy J Thomalla
- Southern Ocean Carbon-Climate Observatory (SOCCO), Council of Scientific & Industrial Research (CSIR), Rosebank, Cape Town, South Africa
| | - Thulani P Makhalanyane
- SARChI Chair: Marine Microbiomics, microbiome@UP, Department of Biochemistry, Genetics and Microbiology, University of Pretoria (UP), Hatfield, Pretoria, South Africa
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3
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Castillo DJ, Dithugoe CD, Bezuidt OK, Makhalanyane TP. Microbial ecology of the Southern Ocean. FEMS Microbiol Ecol 2022; 98:6762916. [PMID: 36255374 DOI: 10.1093/femsec/fiac123] [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: 02/09/2022] [Revised: 09/23/2022] [Accepted: 10/14/2022] [Indexed: 01/21/2023] Open
Abstract
The Southern Ocean (SO) distributes climate signals and nutrients worldwide, playing a pivotal role in global carbon sequestration. Microbial communities are essential mediators of primary productivity and carbon sequestration, yet we lack a comprehensive understanding of microbial diversity and functionality in the SO. Here, we examine contemporary studies in this unique polar system, focusing on prokaryotic communities and their relationships with other trophic levels (i.e. phytoplankton and viruses). Strong seasonal variations and the characteristic features of this ocean are directly linked to community composition and ecosystem functions. Specifically, we discuss characteristics of SO microbial communities and emphasise differences from the Arctic Ocean microbiome. We highlight the importance of abundant bacteria in recycling photosynthetically derived organic matter. These heterotrophs appear to control carbon flux to higher trophic levels when light and iron availability favour primary production in spring and summer. Conversely, during winter, evidence suggests that chemolithoautotrophs contribute to prokaryotic production in Antarctic waters. We conclude by reviewing the effects of climate change on marine microbiota in the SO.
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Affiliation(s)
- Diego J Castillo
- Department of Biochemistry, Genetics and Microbiology, Microbiome Research Group, University of Pretoria, Pretoria 0028, South Africa.,Department of Science and Innovation/South African Research Chair in Marine Microbiomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0028, South Africa
| | - Choaro D Dithugoe
- Department of Biochemistry, Genetics and Microbiology, Microbiome Research Group, University of Pretoria, Pretoria 0028, South Africa.,Department of Science and Innovation/South African Research Chair in Marine Microbiomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0028, South Africa
| | - Oliver K Bezuidt
- Department of Biochemistry, Genetics and Microbiology, Microbiome Research Group, University of Pretoria, Pretoria 0028, South Africa.,Department of Science and Innovation/South African Research Chair in Marine Microbiomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0028, South Africa
| | - Thulani P Makhalanyane
- Department of Biochemistry, Genetics and Microbiology, Microbiome Research Group, University of Pretoria, Pretoria 0028, South Africa.,Department of Science and Innovation/South African Research Chair in Marine Microbiomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0028, South Africa
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Sow SLS, Brown MV, Clarke LJ, Bissett A, van de Kamp J, Trull TW, Raes EJ, Seymour JR, Bramucci AR, Ostrowski M, Boyd PW, Deagle BE, Pardo PC, Sloyan BM, Bodrossy L. Biogeography of Southern Ocean prokaryotes: a comparison of the Indian and Pacific sectors. Environ Microbiol 2022; 24:2449-2466. [PMID: 35049099 PMCID: PMC9303206 DOI: 10.1111/1462-2920.15906] [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: 10/24/2021] [Accepted: 01/13/2022] [Indexed: 11/27/2022]
Abstract
We investigated the Southern Ocean (SO) prokaryote community structure via zero‐radius operational taxonomic unit (zOTU) libraries generated from 16S rRNA gene sequencing of 223 full water column profiles. Samples reveal the prokaryote diversity trend between discrete water masses across multiple depths and latitudes in Indian (71–99°E, summer) and Pacific (170–174°W, autumn‐winter) sectors of the SO. At higher taxonomic levels (phylum‐family) we observed water masses to harbour distinct communities across both sectors, but observed sectorial variations at lower taxonomic levels (genus‐zOTU) and relative abundance shifts for key taxa such as Flavobacteria, SAR324/Marinimicrobia, Nitrosopumilus and Nitrosopelagicus at both epi‐ and bathy‐abyssopelagic water masses. Common surface bacteria were abundant in several deep‐water masses and vice‐versa suggesting connectivity between surface and deep‐water microbial assemblages. Bacteria from same‐sector Antarctic Bottom Water samples showed patchy, high beta‐diversity which did not correlate well with measured environmental parameters or geographical distance. Unconventional depth distribution patterns were observed for key archaeal groups: Crenarchaeota was found across all depths in the water column and persistent high relative abundances of common epipelagic archaeon Nitrosopelagicus was observed in deep‐water masses. Our findings reveal substantial regional variability of SO prokaryote assemblages that we argue should be considered in wide‐scale SO ecosystem microbial modelling.
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Affiliation(s)
- Swan L S Sow
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Tasmania, 7000, Australia.,Oceans and Atmosphere, Commonwealth Scientific and Industrial Research Organisation, Hobart, Tasmania, 7000, Australia
| | - Mark V Brown
- School of Environmental and Life Sciences, University of Newcastle, New South Wales, 2308, Australia
| | - Laurence J Clarke
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Tasmania, 7000, Australia.,Australian Antarctic Division, Channel Highway, Kingston, Tasmania, 7050, Australia
| | - Andrew Bissett
- Oceans and Atmosphere, Commonwealth Scientific and Industrial Research Organisation, Hobart, Tasmania, 7000, Australia
| | - Jodie van de Kamp
- Oceans and Atmosphere, Commonwealth Scientific and Industrial Research Organisation, Hobart, Tasmania, 7000, Australia
| | - Thomas W Trull
- Oceans and Atmosphere, Commonwealth Scientific and Industrial Research Organisation, Hobart, Tasmania, 7000, Australia
| | - Eric J Raes
- Oceans and Atmosphere, Commonwealth Scientific and Industrial Research Organisation, Hobart, Tasmania, 7000, Australia
| | - Justin R Seymour
- Climate Change Cluster, University of Technology Sydney, New South Wales, 2007, Australia
| | - Anna R Bramucci
- Climate Change Cluster, University of Technology Sydney, New South Wales, 2007, Australia
| | - Martin Ostrowski
- Climate Change Cluster, University of Technology Sydney, New South Wales, 2007, Australia
| | - Philip W Boyd
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Tasmania, 7000, Australia
| | - Bruce E Deagle
- Australian Antarctic Division, Channel Highway, Kingston, Tasmania, 7050, Australia.,National Collections & Marine Infrastructure, Commonwealth Scientific and Industrial Research Organisation, Hobart, Tasmania, 7000, Australia
| | - Paula C Pardo
- Oceans and Atmosphere, Commonwealth Scientific and Industrial Research Organisation, Hobart, Tasmania, 7000, Australia
| | - Bernadette M Sloyan
- Oceans and Atmosphere, Commonwealth Scientific and Industrial Research Organisation, Hobart, Tasmania, 7000, Australia
| | - Levente Bodrossy
- Oceans and Atmosphere, Commonwealth Scientific and Industrial Research Organisation, Hobart, Tasmania, 7000, Australia
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5
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Garber AI, Zehnpfennig JR, Sheik CS, Henson MW, Ramírez GA, Mahon AR, Halanych KM, Learman DR. Metagenomics of Antarctic Marine Sediment Reveals Potential for Diverse Chemolithoautotrophy. mSphere 2021; 6:e0077021. [PMID: 34817234 PMCID: PMC8612310 DOI: 10.1128/msphere.00770-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Accepted: 11/10/2021] [Indexed: 11/30/2022] Open
Abstract
The microbial biogeochemical processes occurring in marine sediment in Antarctica remain underexplored due to limited access. Further, these polar habitats are unique, as they are being exposed to significant changes in their climate. To explore how microbes drive biogeochemistry in these sediments, we performed a shotgun metagenomic survey of marine surficial sediment (0 to 3 cm of the seafloor) collected from 13 locations in western Antarctica and assembled 16 high-quality metagenome assembled genomes for focused interrogation of the lifestyles of some abundant lineages. We observe an abundance of genes from pathways for the utilization of reduced carbon, sulfur, and nitrogen sources. Although organotrophy is pervasive, nitrification and sulfide oxidation are the dominant lithotrophic pathways and likely fuel carbon fixation via the reverse tricarboxylic acid and Calvin cycles. Oxygen-dependent terminal oxidases are common, and genes for reduction of oxidized nitrogen are sporadically present in our samples. Our results suggest that the underlying benthic communities are well primed for the utilization of settling organic matter, which is consistent with findings from highly productive surface water. Despite the genetic potential for nitrate reduction, the net catabolic pathway in our samples remains aerobic respiration, likely coupled to the oxidation of sulfur and nitrogen imported from the highly productive Antarctic water column above. IMPORTANCE The impacts of climate change in polar regions, like Antarctica, have the potential to alter numerous ecosystems and biogeochemical cycles. Increasing temperature and freshwater runoff from melting ice can have profound impacts on the cycling of organic and inorganic nutrients between the pelagic and benthic ecosystems. Within the benthos, sediment microbial communities play a critical role in carbon mineralization and the cycles of essential nutrients like nitrogen and sulfur. Metagenomic data collected from sediment samples from the continental shelf of western Antarctica help to examine this unique system and document the metagenomic potential for lithotrophic metabolisms and the cycles of both nitrogen and sulfur, which support not only benthic microbes but also life in the pelagic zone.
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Affiliation(s)
- Arkadiy I. Garber
- Biodesign Center for Mechanisms for Evolution, Arizona State University, Tempe, Arizona, USA
| | | | - Cody S. Sheik
- Biology Department and Large Lakes Observatory, University of Minnesota Duluth, Duluth, Minnesota, USA
| | - Michael W. Henson
- Department of Biology, Central Michigan University, Mt. Pleasant, Michigan, USA
| | - Gustavo A. Ramírez
- College of Veterinary Medicine, Western University of Health Sciences, Pomona, California, USA
- Department of Marine Biology, Haifa University, Haifa, Israel
| | - Andrew R. Mahon
- Department of Biology, Central Michigan University, Mt. Pleasant, Michigan, USA
| | - Kenneth M. Halanych
- Center for Marine Science, University of North Carolina Wilmington, Wilmington, North Carolina, USA
| | - Deric R. Learman
- Department of Biology, Central Michigan University, Mt. Pleasant, Michigan, USA
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6
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Raes EJ, Karsh K, Sow SLS, Ostrowski M, Brown MV, van de Kamp J, Franco-Santos RM, Bodrossy L, Waite AM. Metabolic pathways inferred from a bacterial marker gene illuminate ecological changes across South Pacific frontal boundaries. Nat Commun 2021; 12:2213. [PMID: 33850115 PMCID: PMC8044245 DOI: 10.1038/s41467-021-22409-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 03/09/2021] [Indexed: 02/01/2023] Open
Abstract
Global oceanographic monitoring initiatives originally measured abiotic essential ocean variables but are currently incorporating biological and metagenomic sampling programs. There is, however, a large knowledge gap on how to infer bacterial functions, the information sought by biogeochemists, ecologists, and modelers, from the bacterial taxonomic information (produced by bacterial marker gene surveys). Here, we provide a correlative understanding of how a bacterial marker gene (16S rRNA) can be used to infer latitudinal trends for metabolic pathways in global monitoring campaigns. From a transect spanning 7000 km in the South Pacific Ocean we infer ten metabolic pathways from 16S rRNA gene sequences and 11 corresponding metagenome samples, which relate to metabolic processes of primary productivity, temperature-regulated thermodynamic effects, coping strategies for nutrient limitation, energy metabolism, and organic matter degradation. This study demonstrates that low-cost, high-throughput bacterial marker gene data, can be used to infer shifts in the metabolic strategies at the community scale.
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Affiliation(s)
- Eric J Raes
- CSIRO Oceans and Atmosphere, Hobart, TAS, Australia.
- Ocean Frontier Institute and Department of Oceanography, Dalhousie University, Halifax, NS, Canada.
| | | | - Swan L S Sow
- CSIRO Oceans and Atmosphere, Hobart, TAS, Australia
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS, Australia
- NIOZ Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, Den Burg, The Netherlands
| | - Martin Ostrowski
- Climate Change Cluster, University of Technology Sydney, Sydney, NSW, Australia
| | - Mark V Brown
- School of Environmental and Life Sciences, The University of Newcastle, Callaghan, NSW, Australia
| | | | - Rita M Franco-Santos
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS, Australia
| | | | - Anya M Waite
- Ocean Frontier Institute and Department of Oceanography, Dalhousie University, Halifax, NS, Canada
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7
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Evans C, Brandsma J, Meredith MP, Thomas DN, Venables HJ, Pond DW, Brussaard CPD. Shift from Carbon Flow through the Microbial Loop to the Viral Shunt in Coastal Antarctic Waters during Austral Summer. Microorganisms 2021; 9:460. [PMID: 33672195 PMCID: PMC7927135 DOI: 10.3390/microorganisms9020460] [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: 01/28/2021] [Revised: 02/17/2021] [Accepted: 02/18/2021] [Indexed: 11/30/2022] Open
Abstract
The relative flow of carbon through the viral shunt and the microbial loop is a pivotal factor controlling the contribution of secondary production to the food web and to rates of nutrient remineralization and respiration. The current study examines the significance of these processes in the coastal waters of the Antarctic during the productive austral summer months. Throughout the study a general trend towards lower bacterioplankton and heterotrophic nanoflagellate (HNF) abundances was observed, whereas virioplankton concentration increased. A corresponding decline of HNF grazing rates and shift towards viral production, indicative of viral infection, was measured. Carbon flow mediated by HNF grazing decreased by more than half from 5.7 µg C L-1 day-1 on average in December and January to 2.4 µg C L-1 day-1 in February. Conversely, carbon flow through the viral shunt increased substantially over the study from on average 0.9 µg C L-1 day-1 in December to 7.6 µg C L-1 day-1 in February. This study shows that functioning of the coastal Antarctic microbial community varied considerably over the productive summer months. In early summer, the system favors transfer of matter and energy to higher trophic levels via the microbial loop, however towards the end of summer carbon flow is redirected towards the viral shunt, causing a switch towards more recycling and therefore increased respiration and regeneration.
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Affiliation(s)
- Claire Evans
- Royal Netherlands Institute for Sea Research, P.O. Box 59, Den Burg, 1790 AB Texel, The Netherlands; (J.B.); (C.P.D.B.)
- Ocean BioGeosciences, National Oceanography Centre, Southampton, European Way, Southampton SO14 3ZH, UK
| | - Joost Brandsma
- Royal Netherlands Institute for Sea Research, P.O. Box 59, Den Burg, 1790 AB Texel, The Netherlands; (J.B.); (C.P.D.B.)
- Austere Environments Consortium for Enhanced Sepsis Outcomes, Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20814, USA
| | - Michael P. Meredith
- British Antarctic Survey, Natural Environmental Research Council, High Cross, Madingley Road, Cambridge CB3 0ET, UK; (M.P.M.); (H.J.V.); (D.W.P.)
| | - David N. Thomas
- Ecosystems & Environment, Faculty of Biological and Environmental Sciences, University of Helsinki, 00014 Helsinki, Finland;
| | - Hugh J. Venables
- British Antarctic Survey, Natural Environmental Research Council, High Cross, Madingley Road, Cambridge CB3 0ET, UK; (M.P.M.); (H.J.V.); (D.W.P.)
| | - David W. Pond
- British Antarctic Survey, Natural Environmental Research Council, High Cross, Madingley Road, Cambridge CB3 0ET, UK; (M.P.M.); (H.J.V.); (D.W.P.)
- Faculty of Natural Sciences, University of Stirling, Stirling FK9 4LA, UK
| | - Corina P. D. Brussaard
- Royal Netherlands Institute for Sea Research, P.O. Box 59, Den Burg, 1790 AB Texel, The Netherlands; (J.B.); (C.P.D.B.)
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8
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Alcamán-Arias ME, Fuentes-Alburquenque S, Vergara-Barros P, Cifuentes-Anticevic J, Verdugo J, Polz M, Farías L, Pedrós-Alió C, Díez B. Coastal Bacterial Community Response to Glacier Melting in the Western Antarctic Peninsula. Microorganisms 2021; 9:microorganisms9010088. [PMID: 33401391 PMCID: PMC7823458 DOI: 10.3390/microorganisms9010088] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 12/20/2020] [Accepted: 12/21/2020] [Indexed: 01/04/2023] Open
Abstract
Current warming in the Western Antarctic Peninsula (WAP) has multiple effects on the marine ecosystem, modifying the trophic web and the nutrient regime. In this study, the effect of decreased surface salinity on the marine microbial community as a consequence of freshening from nearby glaciers was investigated in Chile Bay, Greenwich Island, WAP. In the summer of 2016, samples were collected from glacier ice and transects along the bay for 16S rRNA gene sequencing, while in situ dilution experiments were conducted and analyzed using 16S rRNA gene sequencing and metatranscriptomic analysis. The results reveal that certain common seawater genera, such as Polaribacter, Pseudoalteromonas and HTCC2207, responded positively to decreased salinity in both the bay transect and experiments. The relative abundance of these bacteria slightly decreased, but their functional activity was maintained and increased the over time in the dilution experiments. However, while ice bacteria, such as Flavobacterium and Polaromonas, tolerated the increased salinity after mixing with seawater, their gene expression decreased considerably. We suggest that these bacterial taxa could be defined as sentinels of freshening events in the Antarctic coastal system. Furthermore, these results suggest that a significant portion of the microbial community is resilient and can adapt to disturbances, such as freshening due to the warming effect of climate change in Antarctica.
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Affiliation(s)
- María Estrella Alcamán-Arias
- Department of Oceanography, Universidad de Concepcion, Concepcion 4030000, Chile; (M.E.A.-A.); (L.F.)
- Center for Climate and Resilience Research (CR)2, Santiago 8320000, Chile
- Escuela de Medicina, Universidad Espíritu Santo, Guayaquil 0901952, Ecuador
| | - Sebastián Fuentes-Alburquenque
- Centro de Investigación en Recursos Naturales y Sustentabilidad, Universidad Bernardo O’Higgins, Santiago 8370993, Chile;
- Facultad de Ingeniería, Ciencia y Tecnología, Universidad Bernardo O’Higgins, Santiago 8370993, Chile
| | - Pablo Vergara-Barros
- Department of Molecular Genetics and Microbiology, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile; (P.V.-B.); (J.C.-A.)
| | - Jerónimo Cifuentes-Anticevic
- Department of Molecular Genetics and Microbiology, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile; (P.V.-B.); (J.C.-A.)
| | - Josefa Verdugo
- Alfred-Wegener-Institute, Helmholtz-Centre for Polar and Marine Research, 27570 Bremerhaven, Germany;
| | - Martin Polz
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA;
| | - Laura Farías
- Department of Oceanography, Universidad de Concepcion, Concepcion 4030000, Chile; (M.E.A.-A.); (L.F.)
- Center for Climate and Resilience Research (CR)2, Santiago 8320000, Chile
| | - Carlos Pedrós-Alió
- Departamento de Biología de Sistemas, Centro Nacional de Biotecnología (CSIC), Darwin 3, 28049 Madrid, Spain;
| | - Beatriz Díez
- Center for Climate and Resilience Research (CR)2, Santiago 8320000, Chile
- Department of Molecular Genetics and Microbiology, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile; (P.V.-B.); (J.C.-A.)
- Correspondence:
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9
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Quero GM, Celussi M, Relitti F, Kovačević V, Del Negro P, Luna GM. Inorganic and Organic Carbon Uptake Processes and Their Connection to Microbial Diversity in Meso- and Bathypelagic Arctic Waters (Eastern Fram Strait). MICROBIAL ECOLOGY 2020; 79:823-839. [PMID: 31728602 DOI: 10.1007/s00248-019-01451-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 10/02/2019] [Indexed: 06/10/2023]
Abstract
The deep Arctic Ocean is increasingly vulnerable to climate change effects, yet our understanding of its microbial processes is limited. We collected samples from shelf waters, mesopelagic Atlantic Waters (AW) and bathypelagic Norwegian Sea Deep Waters (NSDW) in the eastern Fram Strait, along coast-to-offshore transects off Svalbard during boreal summer. We measured community respiration, heterotrophic carbon production (HCP), and dissolved inorganic carbon utilization (DICu) together with prokaryotic abundance, diversity, and metagenomic predictions. In deep samples, HCP was significantly faster in AW than in NSDW, while we observed no differences in DICu rates. Organic carbon uptake was higher than its inorganic counterpart, suggesting a major reliance of deep microbial Arctic communities on heterotrophic metabolism. Community structure and spatial distribution followed the hydrography of water masses. Distinct from other oceans, the most abundant OTU in our deep samples was represented by the archaeal MG-II. To address the potential biogeochemical role of each water mass-specific microbial community, as well as their link with the measured rates, PICRUSt-based predicted metagenomes were built. The results showed that pathways of auto- and heterotrophic carbon utilization differed between the deep water masses, although this was not reflected in measured DICu rates. Our findings provide new insights to understand microbial processes and diversity in the dark Arctic Ocean and to progress toward a better comprehension of the biogeochemical cycles and their trends in light of climate changes.
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Affiliation(s)
- Grazia Marina Quero
- Stazione Zoologica Anton Dohrn, Integrative Marine Ecology Department, Napoli, Italy
- Istituto per le Risorse Biologiche e le Biotecnologie Marine (CNR-IRBIM), Consiglio Nazionale delle Ricerche, Ancona, Italy
| | - Mauro Celussi
- Oceanography Division, Istituto Nazionale di Oceanografia e di Geofisica Sperimentale - OGS, Trieste, Italy.
| | - Federica Relitti
- Oceanography Division, Istituto Nazionale di Oceanografia e di Geofisica Sperimentale - OGS, Trieste, Italy
| | - Vedrana Kovačević
- Oceanography Division, Istituto Nazionale di Oceanografia e di Geofisica Sperimentale - OGS, Trieste, Italy
| | - Paola Del Negro
- Oceanography Division, Istituto Nazionale di Oceanografia e di Geofisica Sperimentale - OGS, Trieste, Italy
| | - Gian Marco Luna
- Istituto per le Risorse Biologiche e le Biotecnologie Marine (CNR-IRBIM), Consiglio Nazionale delle Ricerche, Ancona, Italy
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10
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Azzaro M, Packard TT, Monticelli LS, Maimone G, Rappazzo AC, Azzaro F, Grilli F, Crisafi E, La Ferla R. Microbial metabolic rates in the Ross Sea: the ABIOCLEAR Project. NATURE CONSERVATION 2019. [DOI: 10.3897/natureconservation.34.30631] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The Ross Sea is one of the most productive areas of the Southern Ocean and includes several functionally different marine ecosystems. With the aim of identifying signs and patterns of microbial response to current climate change, seawater microbial populations were sampled at different depths, from surface to the bottom, at two Ross Sea mooring areas southeast of Victoria Land in Antarctica. This oceanographic experiment, the XX Italian Antarctic Expedition, 2004-05, was carried out in the framework of the ABIOCLEAR project as part of LTER-Italy. Here, microbial biogeochemical rates of respiration, carbon dioxide production, total community heterotrophic energy production, prokaryotic heterotrophic activity, production (by3H-leucine uptake) and prokaryotic biomass (by image analysis) were determined throughout the water column. As ancillary parameters, chlorophylla, adenosine-triphosphate concentrations, temperature and salinity were measured and reported. Microbial metabolism was highly variable amongst stations and depths. In epi- and mesopelagic zones, respiratory rates varied between 52.4–437.0 and 6.3–271.5 nanol O2l-1h-1; prokaryotic heterotrophic production varied between 0.46–29.5 and 0.3–6.11 nanog C l-1h-1; and prokaryotic biomass varied between 0.8–24.5 and 1.1–9.0 µg C l-1, respectively. The average heterotrophic energy production ranged between 570 and 103 mJ l-1h-1in upper and deeper layers, respectively. In the epipelagic layer, the Prokaryotic Carbon Demand and Prokaryotic Growth Efficiency averaged 9 times higher and 2 times lower, respectively, than in the mesopelagic one. The distribution of plankton metabolism and organic matter degradation was mainly related to the different hydrological and trophic conditions. In comparison with previous research, the Ross Sea results, here, evidenced a relatively impoverished oligotrophic microbial community, throughout the water column.
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11
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Celussi M, Malfatti F, Ziveri P, Giani M, Del Negro P. Uptake-release dynamics of the inorganic and organic carbon pool mediated by planktonic prokaryotes in the deep Mediterranean Sea. Environ Microbiol 2016; 19:1163-1175. [PMID: 28026100 DOI: 10.1111/1462-2920.13641] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Revised: 11/25/2016] [Accepted: 12/03/2016] [Indexed: 11/28/2022]
Abstract
Understanding the ecosystem functioning in the dark portion of the ocean is a challenge that microbial ecologists are still facing. Due to the large volume, the global deep Ocean plays a central role in the regulation of climate, possibly buffering the rise of atmospheric carbon dioxide if processes of CO2 fixation compensate for respiration. We investigated the rates of several prokaryotic activities (dissolved and particulate primary production, heterotrophic carbon production and respiration) in meso- and bathypelagic waters of the Mediterranean Sea, covering all sub-basins. Chemosynthesis was the main process for C uptake. The rates of organic C (OC) excretion (or viral-induced cell lysis) inferred from the dissolved primary production measurements were noteworthy, being comparable to particulate primary production, and possibly contributing to the formation of non-sinking particulate organic matter. Inorganic C fixation rates were significantly higher than those reported for other deep-sea systems, probably as a consequence of the persistently higher temperature of dark Mediterranean waters or to phylogenetically diverse communities involved in the process. Primary production was negatively correlated with dissolved organic carbon concentration and showed an inverse pattern to heterotrophic carbon production, indicating a niche partitioning between heterotrophs and autotrophs. In sum, the deep Mediterranean Sea harbors active autotrophic communities able to fix inorganic carbon faster than the heterotrophic carbon production rates.
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Affiliation(s)
- Mauro Celussi
- OGS (Istituto Nazionale di Oceanografia e di Geofisica Sperimentale), Oceanography Division, via A. Piccard 54, Trieste, 34151, Italy
| | - Francesca Malfatti
- OGS (Istituto Nazionale di Oceanografia e di Geofisica Sperimentale), Oceanography Division, via A. Piccard 54, Trieste, 34151, Italy
| | - Patrizia Ziveri
- Institute of Environmental Science and Technology, Autonomous University of Barcelona (UAB), Bellaterra, 08193, Spain.,ICREA, Pg. Lluis Companys 23, Barcelona, 08010, Spain
| | - Michele Giani
- OGS (Istituto Nazionale di Oceanografia e di Geofisica Sperimentale), Oceanography Division, via A. Piccard 54, Trieste, 34151, Italy
| | - Paola Del Negro
- OGS (Istituto Nazionale di Oceanografia e di Geofisica Sperimentale), Oceanography Division, via A. Piccard 54, Trieste, 34151, Italy
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12
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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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Contribution of ammonia oxidation to chemoautotrophy in Antarctic coastal waters. ISME JOURNAL 2016; 10:2605-2619. [PMID: 27187795 PMCID: PMC5113851 DOI: 10.1038/ismej.2016.61] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Revised: 02/04/2016] [Accepted: 03/22/2016] [Indexed: 11/09/2022]
Abstract
There are few measurements of nitrification in polar regions, yet geochemical evidence suggests that it is significant, and chemoautotrophy supported by nitrification has been suggested as an important contribution to prokaryotic production during the polar winter. This study reports seasonal ammonia oxidation (AO) rates, gene and transcript abundance in continental shelf waters west of the Antarctic Peninsula, where Thaumarchaeota strongly dominate populations of ammonia-oxidizing organisms. Higher AO rates were observed in the late winter surface mixed layer compared with the same water mass sampled during summer (mean±s.e.: 62±16 versus 13±2.8 nm per day, t-test P<0.0005). AO rates in the circumpolar deep water did not differ between seasons (21±5.7 versus 24±6.6 nm per day; P=0.83), despite 5- to 20-fold greater Thaumarchaeota abundance during summer. AO rates correlated with concentrations of Archaea ammonia monooxygenase (amoA) genes during summer, but not with concentrations of Archaea amoA transcripts, or with ratios of Archaea amoA transcripts per gene, or with concentrations of Betaproteobacterial amoA genes or transcripts. The AO rates we report (<0.1–220 nm per day) are ~10-fold greater than reported previously for Antarctic waters and suggest that inclusion of Antarctic coastal waters in global estimates of oceanic nitrification could increase global rate estimates by ~9%. Chemoautotrophic carbon fixation supported by AO was 3–6% of annualized phytoplankton primary production and production of Thaumarchaeota biomass supported by AO could account for ~9% of the bacterioplankton production measured in winter. Growth rates of thaumarchaeote populations inferred from AO rates averaged 0.3 per day and ranged from 0.01 to 2.1 per day.
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14
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Landa M, Blain S, Christaki U, Monchy S, Obernosterer I. Shifts in bacterial community composition associated with increased carbon cycling in a mosaic of phytoplankton blooms. ISME JOURNAL 2015. [PMID: 26196334 DOI: 10.1038/ismej.2015.105] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Marine microbes have a pivotal role in the marine biogeochemical cycle of carbon, because they regulate the turnover of dissolved organic matter (DOM), one of the largest carbon reservoirs on Earth. Microbial communities and DOM are both highly diverse components of the ocean system, yet the role of microbial diversity for carbon processing remains thus far poorly understood. We report here results from an exploration of a mosaic of phytoplankton blooms induced by large-scale natural iron fertilization in the Southern Ocean. We show that in this unique ecosystem where concentrations of DOM are lowest in the global ocean, a patchwork of blooms is associated with diverse and distinct bacterial communities. By using on-board continuous cultures, we identify preferences in the degradation of DOM of different reactivity for taxa associated with contrasting blooms. We used the spatial and temporal variability provided by this natural laboratory to demonstrate that the magnitude of bacterial production is linked to the extent of compositional changes. Our results suggest that partitioning of the DOM resource could be a mechanism that structures bacterial communities with a positive feedback on carbon cycling. Our study, focused on bacterial carbon processing, highlights the potential role of diversity as a driving force for the cycling of biogeochemical elements.
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Affiliation(s)
- Marine Landa
- CNRS, Sorbonne Universités, UPMC Univ Paris 06, Laboratoire d'Océanographie Microbienne (LOMIC), Observatoire Océanologique, Banyuls/mer, Paris, France
| | - Stéphane Blain
- CNRS, Sorbonne Universités, UPMC Univ Paris 06, Laboratoire d'Océanographie Microbienne (LOMIC), Observatoire Océanologique, Banyuls/mer, Paris, France
| | - Urania Christaki
- INSU-CNRS, UMR 8187 LOG, Laboratoire d'Océanologie et de Géosciences, Université du Littoral Côte d'Opale, ULCO, Wimereux, France
| | - Sébastien Monchy
- INSU-CNRS, UMR 8187 LOG, Laboratoire d'Océanologie et de Géosciences, Université du Littoral Côte d'Opale, ULCO, Wimereux, France
| | - Ingrid Obernosterer
- CNRS, Sorbonne Universités, UPMC Univ Paris 06, Laboratoire d'Océanographie Microbienne (LOMIC), Observatoire Océanologique, Banyuls/mer, Paris, France
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15
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Xing M, Li Z, Wang W, Sun M. Diversity of bacterioplankton in the surface seawaters of Drake Passage near the Chinese Antarctic station. FEMS Microbiol Lett 2015; 362:fnv106. [PMID: 26184094 DOI: 10.1093/femsle/fnv106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/26/2015] [Indexed: 11/12/2022] Open
Abstract
The determination of relative abundances and distribution of different bacterial groups is a critical step toward understanding the functions of various bacteria and its surrounding environment. Few studies focus on the taxonomic composition and functional diversity of microbial communities in Drake Passage. In this study, marine bacterioplankton communities from surface seawaters at five locations in Drake Passage were examined by 16S rRNA gene sequence analyses. The results indicated that psychrophilic bacteria were the most abundant group in Drake Passage, and mainly made up of Bacillus, Aeromonas, Psychrobacter, Pseudomonas and Halomonas. Diversity analysis showed that surface seawater communities had no significant correlation with latitudinal gradient. Additionally, a clear difference among five surface seawater communities was evident, with 1.8% OTUs (only two) belonged to Bacillus consistent across five locations and 71% OTUs (80) existed in only one location. However, the few cosmopolitans had the largest population sizes. Our results support the hypothesis that the dominant bacterial groups appear to be analogous between geographical sites, but significant differences may be detected among rare bacterial groups. The microbial diversity of surface seawaters would be liable to be affected by environmental factors.
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Affiliation(s)
- Mengxin Xing
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, PR China
| | - Zhao Li
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, PR China
| | - Wei Wang
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, PR China
| | - Mi Sun
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, PR China
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16
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Signori CN, Thomas F, Enrich-Prast A, Pollery RCG, Sievert SM. Microbial diversity and community structure across environmental gradients in Bransfield Strait, Western Antarctic Peninsula. Front Microbiol 2014; 5:647. [PMID: 25566198 PMCID: PMC4267279 DOI: 10.3389/fmicb.2014.00647] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Accepted: 11/07/2014] [Indexed: 12/04/2022] Open
Abstract
The Southern Ocean is currently subject to intense investigations, mainly related to its importance for global biogeochemical cycles and its alarming rate of warming in response to climate change. Microbes play an essential role in the functioning of this ecosystem and are the main drivers of the biogeochemical cycling of elements. Yet, the diversity and abundance of microorganisms in this system remain poorly studied, in particular with regards to changes along environmental gradients. Here, we used amplicon sequencing of 16S rRNA gene tags using primers covering both Bacteria and Archaea to assess the composition and diversity of the microbial communities from four sampling depths (surface, the maximum and minimum of the oxygen concentration, and near the seafloor) at 10 oceanographic stations located in Bransfield Strait [northwest of the Antarctic Peninsula (AP)] and near the sea ice edge (north of the AP). Samples collected near the seafloor and at the oxygen minimum exhibited a higher diversity than those from the surface and oxygen maximum for both bacterial and archaeal communities. The main taxonomic groups identified below 100 m were Thaumarchaeota, Euryarchaeota and Proteobacteria (Gamma-, Delta-, Beta-, and Alphaproteobacteria), whereas in the mixed layer above 100 m Bacteroidetes and Proteobacteria (mainly Alpha- and Gammaproteobacteria) were found to be dominant. A combination of environmental factors seems to influence the microbial community composition. Our results help to understand how the dynamic seascape of the Southern Ocean shapes the microbial community composition and set a baseline for upcoming studies to evaluate the response of this ecosystem to future changes.
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Affiliation(s)
- Camila N Signori
- Instituto de Microbiologia Professor Paulo de Góes, Universidade Federal do Rio de Janeiro Rio de Janeiro, Brazil ; Laboratório de Biogeoquímica, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Centro de Ciências da Saúde Rio de Janeiro, Brazil ; Biology Department, Woods Hole Oceanographic Institution Woods Hole, MA, USA
| | - François Thomas
- Biology Department, Woods Hole Oceanographic Institution Woods Hole, MA, USA
| | - Alex Enrich-Prast
- Instituto de Microbiologia Professor Paulo de Góes, Universidade Federal do Rio de Janeiro Rio de Janeiro, Brazil ; Laboratório de Biogeoquímica, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Centro de Ciências da Saúde Rio de Janeiro, Brazil ; Department of Environmental Change, Linköping University Linköping, Sweden
| | - Ricardo C G Pollery
- Laboratório de Biogeoquímica, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Centro de Ciências da Saúde Rio de Janeiro, Brazil
| | - Stefan M Sievert
- Biology Department, Woods Hole Oceanographic Institution Woods Hole, MA, USA
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17
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Wilkins D, Yau S, Williams TJ, Allen MA, Brown MV, DeMaere MZ, Lauro FM, Cavicchioli R. Key microbial drivers in Antarctic aquatic environments. FEMS Microbiol Rev 2013; 37:303-35. [DOI: 10.1111/1574-6976.12007] [Citation(s) in RCA: 129] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2012] [Revised: 08/11/2012] [Accepted: 10/01/2012] [Indexed: 11/27/2022] Open
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18
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Soil Nematodes and Their Prokaryotic Prey Along an Elevation Gradient in The Mojave Desert (Death Valley National Park, California, USA). DIVERSITY-BASEL 2012. [DOI: 10.3390/d4040363] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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19
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Abstract
Marine dissolved organic carbon (DOC) exhibits a spectrum of reactivity, from very fast turnover of the most bioavailable forms in the surface ocean to long-lived materials circulating within the ocean abyss. These disparate reactivities group DOC by fractions with distinctive functions in the cycling of carbon, ranging from support of the microbial loop to involvement in the biological pump to a hypothesized major source/sink of atmospheric CO(2) driving paleoclimate variability. Here, the major fractions constituting the global ocean's recalcitrant DOC pool are quantitatively and qualitatively characterized with reference to their roles in carbon biogeochemistry. A nomenclature for the fractions is proposed based on those roles.
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Affiliation(s)
- Dennis A Hansell
- Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, FL, USA.
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20
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A metagenomic assessment of winter and summer bacterioplankton from Antarctica Peninsula coastal surface waters. ISME JOURNAL 2012; 6:1901-15. [PMID: 22534611 PMCID: PMC3446801 DOI: 10.1038/ismej.2012.31] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Antarctic surface oceans are well-studied during summer when irradiance levels are high, sea ice is melting and primary productivity is at a maximum. Coincident with this timing, the bacterioplankton respond with significant increases in secondary productivity. Little is known about bacterioplankton in winter when darkness and sea-ice cover inhibit photoautotrophic primary production. We report here an environmental genomic and small subunit ribosomal RNA (SSU rRNA) analysis of winter and summer Antarctic Peninsula coastal seawater bacterioplankton. Intense inter-seasonal differences were reflected through shifts in community composition and functional capacities encoded in winter and summer environmental genomes with significantly higher phylogenetic and functional diversity in winter. In general, inferred metabolisms of summer bacterioplankton were characterized by chemoheterotrophy, photoheterotrophy and aerobic anoxygenic photosynthesis while the winter community included the capacity for bacterial and archaeal chemolithoautotrophy. Chemolithoautotrophic pathways were dominant in winter and were similar to those recently reported in global ‘dark ocean' mesopelagic waters. If chemolithoautotrophy is widespread in the Southern Ocean in winter, this process may be a previously unaccounted carbon sink and may help account for the unexplained anomalies in surface inorganic nitrogen content.
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21
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Advances in understanding archaea-virus interactions in controlled and natural environments. Curr Opin Microbiol 2011; 14:497-503. [PMID: 21821465 DOI: 10.1016/j.mib.2011.07.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2011] [Revised: 06/10/2011] [Accepted: 07/05/2011] [Indexed: 11/21/2022]
Abstract
Our understanding of host-virus interactions in archaeal systems generally lags behind our knowledge of host-virus interactions in bacterial and eukaryotic systems. This is due to the limited number of archaeal host-virus systems available for study under laboratory conditions, as well as the absence of diseases known to be caused by archaea. However, in recent years there has been a rapid expansion of our understanding of archaeal host-virus interactions combining traditional genetic and biochemical approaches with 'omics' based approaches in both laboratory and natural environmental studies. We highlight here the emerging features of host-virus interactions in archaea with a particular emphasis on host-virus interactions gathered from the study of archaeal viruses from high temperature acidic thermal environments.
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22
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Shulse CN, Allen EE. Diversity and distribution of microbial long-chain fatty acid biosynthetic genes in the marine environment. Environ Microbiol 2010; 13:684-95. [PMID: 21105981 DOI: 10.1111/j.1462-2920.2010.02373.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Bacterial production of long-chain fatty acids via a polyketide synthase-related mechanism has thus far only been investigated in isolate-based studies. Here, the genetic capacity for production of long-chain fatty acids was investigated using a culture-independent approach. PCR primers targeting the keto-acyl synthase (KS) domain of the pfaA gene involved in omega-3 polyunsaturated fatty acid (PUFA) biosynthesis were used to construct clone libraries to investigate KS sequence diversity in disparate marine habitats. Of the 446 sequences recovered, 123 (27.6%) clustered with KS sequences involved in the synthesis of eicosapentaenoic acid (EPA, C20:5n-3), docosahexaenoic acid (DHA, C22:6n-3) and arachidonic acid (AA, C20:4n-6). The remaining 72.4% of clones formed environmental-only groups or grouped with the KS domains of pfaA homologues from organisms producing unidentified products. In total, 17 groups were recovered - four known and 13 newly identified. A query of metagenomic data sets revealed sequences related to EPA KS domains, as well as sequences related to four environmental-only groups discovered in the clone libraries. The phylogenetic affiliation and end product of these environmental-only KS clusters is unknown. These findings reveal a widespread capacity for long-chain fatty acid production in marine microorganisms, including biosynthetic pathways not yet characterized.
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Affiliation(s)
- Christine N Shulse
- Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
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23
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Jiao N, Herndl GJ, Hansell DA, Benner R, Kattner G, Wilhelm SW, Kirchman DL, Weinbauer MG, Luo T, Chen F, Azam F. Microbial production of recalcitrant dissolved organic matter: long-term carbon storage in the global ocean. Nat Rev Microbiol 2010; 8:593-9. [DOI: 10.1038/nrmicro2386] [Citation(s) in RCA: 939] [Impact Index Per Article: 67.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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25
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Abstract
We are becoming increasingly aware of the role played by archaea in the biogeochemical cycling of the elements. Metabolism of metals is linked to fundamental metabolic functions, including nitrogen fixation, energy production, and cellular processes based on oxidoreductions. Comparative genomic analyses have shown that genes for metabolism, resistance, and detoxification of metals are widespread throughout the archaeal domain. Archaea share with other organisms strategies allowing them to utilize essential metals and maintain metal ions within a physiological range, although comparative proteomics show, in a few cases, preferences for specific genetic traits related to metals. A more in-depth understanding of the physiology of acidophilic archaea might lead to the development of new strategies for the bioremediation of metal-polluted sites and other applications, such as biomining.
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Affiliation(s)
- Elisabetta Bini
- Department of Biochemistry and Microbiology, Rutgers-The State University of New Jersey, New Brunswick, NJ, USA.
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