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Kuwata K, Sato-Takabe Y, Nakai R, Sugimura Y, Tazato N, Kunihiro T, Morohoshi S, Iwataki M, Hamasaki K, Shiozaki T. Novel aerobic anoxygenic phototrophic bacterium Jannaschia pagri sp. nov., isolated from seawater around a fish farm. Antonie Van Leeuwenhoek 2024; 117:70. [PMID: 38658407 DOI: 10.1007/s10482-024-01971-z] [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: 12/13/2023] [Accepted: 04/18/2024] [Indexed: 04/26/2024]
Abstract
The genus Jannaschia is one of the representatives of aerobic anoxygenic phototrophic (AAP) bacteria, which is a strictly aerobic bacterium, producing a photosynthetic pigment bacteriochlorophyll (BChl) a. However, a part of the genus Jannaschia members have not been confirmed the photosynthetic ability. The partly presence of the ability in the genus Jannaschia could suggest the complexity of evolutionary history for anoxygenic photosynthesis in the genus, which is expected as gene loss and/or horizontal gene transfer. Here a novel AAP bacterium designated as strain AI_62T (= DSM 115720 T = NBRC 115938 T), was isolated from coastal seawater around a fish farm in the Uwa Sea, Japan. Its closest relatives were identified as Jannaschia seohaensis SMK-146 T (95.6% identity) and J. formosa 12N15T (94.6% identity), which have been reported to produce BChl a. The genomic characteristic of strain AI_62T clearly showed the possession of the anoxygenic photosynthesis related gene sets. This could be a useful model organism to approach the evolutionary mystery of anoxygenic photosynthesis in the genus Jannaschia. Based on a comprehensive consideration of both phylogenetic and phenotypic characteristics, we propose the classification of a novel species within the genus Jannaschia, designated as Jannaschia pagri sp. nov. The type strain for this newly proposed species is AI_62T (= DSM 115720 T = NBRC 115938 T).
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Affiliation(s)
- Koyo Kuwata
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Bunkyo-Ku, Tokyo, 113-8657, Japan
| | - Yuki Sato-Takabe
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwanoha 5-1-5, Kashiwa, Chiba, 277-8564, Japan.
- School of Economics, Senshu University, 2-1-1 Higashi-Mita, Tama-Ku, Kawasaki-Shi, Kanagawa, 214-8580, Japan.
| | - Ryosuke Nakai
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2-17-2-1 Tsukisamu-Higashi, Toyohira-Ku, Sapporo, 062-8517, Japan
| | - Yuya Sugimura
- Technical Department, TechnoSuruga Laboratory Co., Ltd, 388-1 Nagasaki, Shimizu-Ku, Shizuoka, 424-0065, Japan
| | - Nozomi Tazato
- Technical Department, TechnoSuruga Laboratory Co., Ltd, 388-1 Nagasaki, Shimizu-Ku, Shizuoka, 424-0065, Japan
| | - Tadao Kunihiro
- Technical Department, TechnoSuruga Laboratory Co., Ltd, 388-1 Nagasaki, Shimizu-Ku, Shizuoka, 424-0065, Japan
| | - Sho Morohoshi
- Technical Department, TechnoSuruga Laboratory Co., Ltd, 388-1 Nagasaki, Shimizu-Ku, Shizuoka, 424-0065, Japan
| | - Mitsunori Iwataki
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Bunkyo-Ku, Tokyo, 113-8657, Japan
| | - Koji Hamasaki
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwanoha 5-1-5, Kashiwa, Chiba, 277-8564, Japan
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8564, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-Ku, Tokyo, 113-8657, Japan
| | - Takuhei Shiozaki
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwanoha 5-1-5, Kashiwa, Chiba, 277-8564, Japan
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2
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Muñoz-Marín MDC, López-Lozano A, Moreno-Cabezuelo JÁ, Díez J, García-Fernández JM. Mixotrophy in cyanobacteria. Curr Opin Microbiol 2024; 78:102432. [PMID: 38325247 DOI: 10.1016/j.mib.2024.102432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Revised: 12/22/2023] [Accepted: 01/10/2024] [Indexed: 02/09/2024]
Abstract
Cyanobacteria evolved the oxygenic photosynthesis to generate organic matter from CO2 and sunlight, and they were responsible for the production of oxygen in the Earth's atmosphere. This made them a model for photosynthetic organisms, since they are easier to study than higher plants. Early studies suggested that only a minority among cyanobacteria might assimilate organic compounds, being considered mostly autotrophic for decades. However, compelling evidence from marine and freshwater cyanobacteria, including toxic strains, in the laboratory and in the field, has been obtained in the last decades: by using physiological and omics approaches, mixotrophy has been found to be a more widespread feature than initially believed. Furthermore, dominant clades of marine cyanobacteria can take up organic compounds, and mixotrophy is critical for their survival in deep waters with very low light. Hence, mixotrophy seems to be an essential trait in the metabolism of most cyanobacteria, which can be exploited for biotechnological purposes.
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Affiliation(s)
- María Del Carmen Muñoz-Marín
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Universitario ceiA3, Universidad de Córdoba, Edificio Severo Ochoa, planta 1, ala Este, Campus de Rabanales, 14071 Córdoba, Spain
| | - Antonio López-Lozano
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Universitario ceiA3, Universidad de Córdoba, Edificio Severo Ochoa, planta 1, ala Este, Campus de Rabanales, 14071 Córdoba, Spain
| | - José Ángel Moreno-Cabezuelo
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Universitario ceiA3, Universidad de Córdoba, Edificio Severo Ochoa, planta 1, ala Este, Campus de Rabanales, 14071 Córdoba, Spain
| | - Jesús Díez
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Universitario ceiA3, Universidad de Córdoba, Edificio Severo Ochoa, planta 1, ala Este, Campus de Rabanales, 14071 Córdoba, Spain.
| | - José Manuel García-Fernández
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Universitario ceiA3, Universidad de Córdoba, Edificio Severo Ochoa, planta 1, ala Este, Campus de Rabanales, 14071 Córdoba, Spain.
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3
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The “Dark Side” of Picocyanobacteria: Life as We Do Not Know It (Yet). Microorganisms 2022; 10:microorganisms10030546. [PMID: 35336120 PMCID: PMC8955281 DOI: 10.3390/microorganisms10030546] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 02/22/2022] [Accepted: 02/28/2022] [Indexed: 12/12/2022] Open
Abstract
Picocyanobacteria of the genus Synechococcus (together with Cyanobium and Prochlorococcus) have captured the attention of microbial ecologists since their description in the 1970s. These pico-sized microorganisms are ubiquitous in aquatic environments and are known to be some of the most ancient and adaptable primary producers. Yet, it was only recently, and thanks to developments in molecular biology and in the understanding of gene sequences and genomes, that we could shed light on the depth of the connection between their evolution and the history of life on the planet. Here, we briefly review the current understanding of these small prokaryotic cells, from their physiological features to their role and dynamics in different aquatic environments, focussing particularly on the still poorly understood ability of picocyanobacteria to adapt to dark conditions. While the recent discovery of Synechococcus strains able to survive in the deep Black Sea highlights how adaptable picocyanobacteria can be, it also raises more questions—showing how much we still do not know about microbial life. Using available information from brackish Black Sea strains able to perform and survive in dark (anoxic) conditions, we illustrate how adaptation to narrow ecological niches interacts with gene evolution and metabolic capacity.
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Coelho LF, Madden J, Kaltenegger L, Zinder S, Philpot W, Esquível MG, Canário J, Costa R, Vincent WF, Martins Z. Color Catalogue of Life in Ice: Surface Biosignatures on Icy Worlds. ASTROBIOLOGY 2022; 22:313-321. [PMID: 34964651 DOI: 10.1089/ast.2021.0008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
With thousands of discovered planets orbiting other stars and new missions that will explore our solar system, the search for life in the universe has entered a new era. However, a reference database to enable our search for life on the surface of icy exoplanets and exomoons by using records from Earth's icy biota is missing. Therefore, we developed a spectra catalogue of life in ice to facilitate the search for extraterrestrial signs of life. We measured the reflection spectra of 80 microorganisms-with a wide range of pigments-isolated from ice and water. We show that carotenoid signatures are wide-ranged and intriguing signs of life. Our measurements allow for the identification of such surface life on icy extraterrestrial environments in preparation for observations with the upcoming ground- and space-based telescopes. Dried samples reveal even higher reflectance, which suggests that signatures of surface biota could be more intense on exoplanets and moons that are drier than Earth or on environments like Titan where potential life-forms may use a different solvent. Our spectra library covers the visible to near-infrared and is available online. It provides a guide for the search for surface life on icy worlds based on biota from Earth's icy environments.
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Affiliation(s)
- Lígia F Coelho
- Centro de Química Estrutural, Departamento de Engenharia Química, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal
- Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal
| | - Jack Madden
- Department of Astronomy, Cornell University, Ithaca, New York, USA
- Carl Sagan Institute, Ithaca, New York, USA
| | - Lisa Kaltenegger
- Department of Astronomy, Cornell University, Ithaca, New York, USA
- Carl Sagan Institute, Ithaca, New York, USA
| | - Stephen Zinder
- Carl Sagan Institute, Ithaca, New York, USA
- Department of Microbiology, Cornell University, Ithaca, New York, USA
| | - William Philpot
- Carl Sagan Institute, Ithaca, New York, USA
- School of Civil and Environmental Engineering, Cornell University, Ithaca, New York, USA
| | - M Glória Esquível
- Landscape, Environment, Agriculture and Food-LEAF Centre, Instituto Superior de Agronomia, Universidade de Lisboa, Lisboa, Portugal
| | - João Canário
- Centro de Química Estrutural, Departamento de Engenharia Química, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal
| | - Rodrigo Costa
- Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal
| | - Warwick F Vincent
- Centre for Northern Studies (CEN), Takuvik & Biology Department, Université Laval, Québec, Canada
| | - Zita Martins
- Centro de Química Estrutural, Departamento de Engenharia Química, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal
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5
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Dynamics of actively dividing prokaryotes in the western Mediterranean Sea. Sci Rep 2022; 12:2064. [PMID: 35136122 PMCID: PMC8825817 DOI: 10.1038/s41598-022-06120-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 01/25/2022] [Indexed: 11/29/2022] Open
Abstract
Microbial community metabolism and functionality play a key role modulating global biogeochemical processes. However, the metabolic activities and contribution of actively growing prokaryotes to ecosystem energy fluxes remain underexplored. Here we describe the temporal and spatial dynamics of active prokaryotes in the different water masses of the Mediterranean Sea using a combination of bromodeoxyuridine labelling and 16S rRNA gene Illumina sequencing. Bulk and actively dividing prokaryotic communities were drastically different and depth stratified. Alteromonadales were rare in bulk communities (contributing 0.1% on average) but dominated the actively dividing community throughout the overall water column (28% on average). Moreover, temporal variability of actively dividing Alteromonadales oligotypes was evinced. SAR86, Actinomarinales and Rhodobacterales contributed on average 3–3.4% each to the bulk and 11, 8.4 and 8.5% to the actively dividing communities in the epipelagic zone, respectively. SAR11 and Nitrosopumilales contributed less to the actively dividing than to the bulk communities during all the study period. Noticeably, the large contribution of these two taxa to the total prokaryotic communities (23% SAR11 and 26% Nitrosopumilales), especially in the meso- and bathypelagic zones, results in important contributions to actively dividing communities (11% SAR11 and 12% Nitrosopumilales). The intense temporal and spatial variability of actively dividing communities revealed in this study strengthen the view of a highly dynamic deep ocean. Our results suggest that some rare or low abundant phylotypes from surface layers down to the deep sea can disproportionally contribute to the activity of the prokaryotic communities, exhibiting a more dynamic response to environmental changes than other abundant phylotypes, emphasizing the role they might have in community metabolism and biogeochemical processes.
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6
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Gazulla CR, Auladell A, Ruiz-González C, Junger PC, Royo-Llonch M, Duarte CM, Gasol JM, Sánchez O, Ferrera I. Global diversity and distribution of aerobic anoxygenic phototrophs in the tropical and subtropical oceans. Environ Microbiol 2022; 24:2222-2238. [PMID: 35084095 DOI: 10.1111/1462-2920.15835] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 10/17/2021] [Accepted: 10/29/2021] [Indexed: 01/04/2023]
Abstract
The aerobic anoxygenic phototrophic (AAP) bacteria are common in most marine environments but their global diversity and biogeography remain poorly characterized. Here, we analyzed AAP communities across 113 globally-distributed surface ocean stations sampled during the Malaspina Expedition in the tropical and subtropical ocean. By means of amplicon sequencing of the pufM gene, a genetic marker for this functional group, we show that AAP communities along the surface ocean were mainly composed of members of the Halieaceae (Gammaproteobacteria), which were adapted to a large range of environmental conditions, and of different clades of the Alphaproteobacteria, which seemed to dominate under particular circumstances, such as in the oligotrophic gyres. AAP taxa were spatially structured within each of the studied oceans, with communities from adjacent stations sharing more taxonomic similarities. AAP communities were composed of a large pool of rare members and several habitat specialists. When compared to the surface ocean prokaryotic and picoeukaryotic communities, it appears that AAP communities display an idiosyncratic global biogeographical pattern, dominated by selection processes and less influenced by dispersal limitation. Our study contributes to the understanding of how AAP communities are distributed in the horizontal dimension and the mechanisms underlying their distribution across the global surface ocean.
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Affiliation(s)
- Carlota R Gazulla
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, Catalunya, 08193, Spain.,Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, ICM-CSIC, Barcelona, Catalunya, 08003, Spain
| | - Adrià Auladell
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, ICM-CSIC, Barcelona, Catalunya, 08003, Spain
| | - Clara Ruiz-González
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, ICM-CSIC, Barcelona, Catalunya, 08003, Spain
| | - Pedro C Junger
- Department of Hydrobiology (DHB), Laboratory of Microbial Processes and Biodiversity (LMPB), Universidade Federal de São Carlos (UFSCar), São Carlos, SP, 13565-905, Brazil
| | - Marta Royo-Llonch
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, ICM-CSIC, Barcelona, Catalunya, 08003, Spain
| | - Carlos M Duarte
- Red Sea Research Center (RSRC) and Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Josep M Gasol
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, ICM-CSIC, Barcelona, Catalunya, 08003, Spain.,Centre for Marine Ecosystems Research, School of Sciences, Edith Cowan University, Joondalup, WA, Australia
| | - Olga Sánchez
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, Catalunya, 08193, Spain
| | - Isabel Ferrera
- Centro Oceanográfico de Málaga, Instituto Español de Oceanografía, IEO-CSIC, 29640 Fuengirola, Málaga, Spain
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7
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Viral Characteristics of the Warm Atlantic and Cold Arctic Water Masses in the Nordic Seas. Appl Environ Microbiol 2021; 87:e0116021. [PMID: 34469192 DOI: 10.1128/aem.01160-21] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Nordic Seas are the subarctic seas connecting the Arctic Ocean and North Atlantic Ocean with complex water masses, experiencing an abrupt climate change. Though knowledge of the marine virosphere has expanded rapidly, the diversity of viruses and their relationships with host cells and water masses in the Nordic Seas remain to be fully revealed. Here, we establish the Nordic Sea DNA virome (NSV) data set of 55,315 viral contigs including 1,478 unique viral populations from seven stations influenced by both the warm Atlantic and cold Arctic water masses. Caudovirales dominated in the seven NSVs, especially in the warm Atlantic waters. The major giant nucleocytoplasmic large DNA viruses (NCLDVs) contributed a significant proportion of the classified viral contigs in the NSVs (32.2%), especially in the cold Arctic waters (44.9%). The distribution patterns of Caudovirales and NCLDVs were a reflection of the community structure of their hosts in the corresponding water masses and currents. Latitude, pH, and flow speed were found to be key factors influencing the microbial communities and coinfluencing the variation of viral communities. Network analysis illustrated the tight coupling between the variation of viral communities and microbial communities in the Nordic Seas. This study suggests a probable linkage between viromes, host cells, and surface water masses from both the cool Arctic and warm Atlantic Oceans. IMPORTANCE This is a systematic study of Nordic Sea viromes using metagenomic analysis. The viral diversity, community structure, and their relationships with host cells and the complex water masses from both the cool Arctic and the warm Atlantic oceans were illustrated. The NCLDVs and Caudovirales are proposed as the viral characteristics of the cold Arctic and warm Atlantic waters, respectively. This study provides an important background for the viromes in the subarctic seas connecting the Arctic Ocean and North Atlantic Ocean and sheds light on their responses to abrupt climate change in the future.
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Coe A, Biller SJ, Thomas E, Boulias K, Bliem C, Arellano A, Dooley K, Rasmussen AN, LeGault K, O'Keefe TJ, Stover S, Greer EL, Chisholm SW. Coping with darkness: The adaptive response of marine picocyanobacteria to repeated light energy deprivation. LIMNOLOGY AND OCEANOGRAPHY 2021; 66:3300-3312. [PMID: 34690365 PMCID: PMC8518828 DOI: 10.1002/lno.11880] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 03/22/2021] [Accepted: 05/29/2021] [Indexed: 06/13/2023]
Abstract
The picocyanobacteria Prochlorococcus and Synechococcus are found throughout the ocean's euphotic zone, where the daily light:dark cycle drives their physiology. Periodic deep mixing events can, however, move cells below this region, depriving them of light for extended periods of time. Here, we demonstrate that members of these genera can adapt to tolerate repeated periods of light energy deprivation. Strains kept in the dark for 3 d and then returned to the light initially required 18-26 d to resume growth, but after multiple rounds of dark exposure they began to regrow after only 1-2 d. This dark-tolerant phenotype was stable and heritable; some cultures retained the trait for over 132 generations even when grown in a standard 13:11 light:dark cycle. We found no genetic differences between the dark-tolerant and parental strains of Prochlorococcus NATL2A, indicating that an epigenetic change is likely responsible for the adaptation. To begin to explore this possibility, we asked whether DNA methylation-one potential mechanism mediating epigenetic inheritance in bacteria-occurs in Prochlorococcus. LC-MS/MS analysis showed that while DNA methylations, including 6 mA and 5 mC, are found in some other Prochlorococcus strains, there were no methylations detected in either the parental or dark-tolerant NATL2A strains. These findings suggest that Prochlorococcus utilizes a yet-to-be-determined epigenetic mechanism to adapt to the stress of extended light energy deprivation, and highlights phenotypic heterogeneity as an additional dimension of Prochlorococcus diversity.
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Affiliation(s)
- Allison Coe
- Department of Civil and Environmental EngineeringMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
| | - Steven J. Biller
- Department of Biological SciencesWellesley CollegeWellesleyMassachusettsUSA
| | - Elaina Thomas
- Department of Civil and Environmental EngineeringMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
| | - Konstantinos Boulias
- Division of Newborn MedicineBoston Children's HospitalBostonMassachusettsUSA
- Department of PediatricsHarvard Medical SchoolBostonMassachusettsUSA
| | - Christina Bliem
- Department of Civil and Environmental EngineeringMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
| | - Aldo Arellano
- Department of Civil and Environmental EngineeringMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
| | - Keven Dooley
- Department of Civil and Environmental EngineeringMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
| | - Anna N. Rasmussen
- Department of Civil and Environmental EngineeringMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
| | - Kristen LeGault
- Department of Civil and Environmental EngineeringMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
| | - Tyler J. O'Keefe
- Department of Civil and Environmental EngineeringMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
| | - Sarah Stover
- Department of Civil and Environmental EngineeringMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
| | - Eric L. Greer
- Division of Newborn MedicineBoston Children's HospitalBostonMassachusettsUSA
- Department of PediatricsHarvard Medical SchoolBostonMassachusettsUSA
| | - Sallie W. Chisholm
- Department of Civil and Environmental EngineeringMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
- Department of BiologyMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
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Abstract
Microbial proton-pumping rhodopsins are considered the simplest strategy among phototrophs to conserve energy from light. Proteorhodopsins are the most studied rhodopsins thus far because of their ubiquitous presence in the ocean, except in Antarctica, where they remain understudied. We analyzed proteorhodopsin abundance and transcriptional activity in the Western Antarctic coastal seawaters. Combining quantitative PCR (qPCR) and metagenomics, the relative abundance of proteorhodopsin-bearing bacteria accounted on average for 17, 3.5, and 29.7% of the bacterial community in Chile Bay (South Shetland Islands) during 2014, 2016, and 2017 summer-autumn, respectively. The abundance of proteorhodopsin-bearing bacteria changed in relation to environmental conditions such as chlorophyll a and temperature. Alphaproteobacteria, Gammaproteobacteria, and Flavobacteriia were the main bacteria that transcribed the proteorhodopsin gene during day and night. Although green light-absorbing proteorhodopsin genes were more abundant than blue-absorbing ones, the latter were transcribed more intensely, resulting in >50% of the proteorhodopsin transcripts during the day and night. Flavobacteriia were the most abundant proteorhodopsin-bearing bacteria in the metagenomes; however, Alphaproteobacteria and Gammaproteobacteria were more represented in the metatranscriptomes, with qPCR quantification suggesting the dominance of the active SAR11 clade. Our results show that proteorhodopsin-bearing bacteria are prevalent in Antarctic coastal waters in late austral summer and early autumn, and their ecological relevance needs to be elucidated to better understand how sunlight energy is used in this marine ecosystem. IMPORTANCE Proteorhodopsin-bearing microorganisms in the Southern Ocean have been overlooked since their discovery in 2000. The present study identify taxonomy and quantify the relative abundance of proteorhodopsin-bearing bacteria and proteorhodopsin gene transcription in the West Antarctic Peninsula's coastal waters. This information is crucial to understand better how sunlight enters this marine environment through alternative ways unrelated to chlorophyll-based strategies. The relative abundance of proteorhodopsin-bearing bacteria seems to be related to environmental parameters (e.g., chlorophyll a, temperature) that change yearly at the coastal water of the West Antarctic Peninsula during the austral late summers and early autumns. Proteorhodopsin-bearing bacteria from Antarctic coastal waters are potentially able to exploit both the green and blue spectrum of sunlight and are a prevalent group during the summer in this polar environment.
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Belevich TA, Demidov АB, Makkaveev PN, Shchuka SA, Flint MV. Picophytoplankton distribution along Khatanga Bay-shelf-continental slope environment gradients in the western Laptev Sea. Heliyon 2021; 7:e06224. [PMID: 33665416 PMCID: PMC7905456 DOI: 10.1016/j.heliyon.2021.e06224] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Revised: 09/23/2020] [Accepted: 02/03/2021] [Indexed: 11/19/2022] Open
Abstract
The spatial variations of photosynthetic picoplankton abundance and biomass and the picoplankton's contribution to chlorophyll a concentration along the transect from Khatanga Bay to the continental slope in the western part of the Laptev Sea were studied in September 2017. Picoeukaryotes dominated in the picophytoplankton communities. Picophytoplankton in Khatanga Bay showed more variability than those over the Laptev shelf and continental slope: abundance and biomass were the highest in the southern part of the bay and markedly decreased with increasing salinity in its northern part. Picocyanobacteria were found over the shelf and slope at temperatures of +2.4 to -1.6°С and salinity from 22 to 34. Picophytoplankton contribution to total chlorophyll a on the shelf was higher than in Khatanga Bay. The study of picophytoplankton of Khatanga Bay and in the western Laptev Sea can serve as a baseline for future assessment of the Laptev Sea ecosystem response to interannual and climate changes.
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Affiliation(s)
- Tatiana A. Belevich
- Department of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
- Belozersky Institute for Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
- Corresponding author.
| | - Аndrey B. Demidov
- Shirshov Institute of Oceanology, Russian Academy of Science, Moscow, 117997, Russia
| | | | - Sergei A. Shchuka
- Shirshov Institute of Oceanology, Russian Academy of Science, Moscow, 117997, Russia
| | - Mikhail V. Flint
- Shirshov Institute of Oceanology, Russian Academy of Science, Moscow, 117997, Russia
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11
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Baker KD, Kellogg CTE, McClelland JW, Dunton KH, Crump BC. The Genomic Capabilities of Microbial Communities Track Seasonal Variation in Environmental Conditions of Arctic Lagoons. Front Microbiol 2021; 12:601901. [PMID: 33643234 PMCID: PMC7906997 DOI: 10.3389/fmicb.2021.601901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 01/04/2021] [Indexed: 11/30/2022] Open
Abstract
In contrast to temperate systems, Arctic lagoons that span the Alaska Beaufort Sea coast face extreme seasonality. Nine months of ice cover up to ∼1.7 m thick is followed by a spring thaw that introduces an enormous pulse of freshwater, nutrients, and organic matter into these lagoons over a relatively brief 2–3 week period. Prokaryotic communities link these subsidies to lagoon food webs through nutrient uptake, heterotrophic production, and other biogeochemical processes, but little is known about how the genomic capabilities of these communities respond to seasonal variability. Replicate water samples from two lagoons and one coastal site near Kaktovik, AK were collected in April (full ice cover), June (ice break up), and August (open water) to represent winter, spring, and summer, respectively. Samples were size fractionated to distinguish free-living and particle-attached microbial communities. Multivariate analysis of metagenomes indicated that seasonal variability in gene abundances was greater than variability between size fractions and sites, and that June differed significantly from the other months. Spring (June) gene abundances reflected the high input of watershed-sourced nutrients and organic matter via spring thaw, featuring indicator genes for denitrification possibly linked to greater organic carbon availability, and genes for processing phytoplankton-derived organic matter associated with spring blooms. Summer featured fewer indicator genes, but had increased abundances of anoxygenic photosynthesis genes, possibly associated with elevated light availability. Winter (April) gene abundances suggested low energy inputs and autotrophic bacterial metabolism, featuring indicator genes for chemoautotrophic carbon fixation, methane metabolism, and nitrification. Winter indicator genes for nitrification belonged to Thaumarchaeota and Nitrosomonadales, suggesting these organisms play an important role in oxidizing ammonium during the under-ice period. This study shows that high latitude estuarine microbial assemblages shift metabolic capabilities as they change phylogenetic composition between these extreme seasons, providing evidence that these communities may be resilient to large hydrological events in a rapidly changing Arctic.
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Affiliation(s)
- Kristina D Baker
- Department of Microbiology, Oregon State University, Corvallis, OR, United States
| | | | - James W McClelland
- The University of Texas at Austin Marine Science Institute, Port Aransas, TX, United States
| | - Kenneth H Dunton
- The University of Texas at Austin Marine Science Institute, Port Aransas, TX, United States
| | - Byron C Crump
- College of Earth, Ocean, and Atmospheric Sciences, Oregon State University, Corvallis, OR, United States
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12
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Su Y, Yang Y, Zhu XY, Zhang XH, Yu M. Metagenomic Insights Into the Microbial Assemblage Capable of Quorum Sensing and Quorum Quenching in Particulate Organic Matter in the Yellow Sea. Front Microbiol 2021; 11:602010. [PMID: 33519743 PMCID: PMC7843935 DOI: 10.3389/fmicb.2020.602010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 12/03/2020] [Indexed: 11/23/2022] Open
Abstract
Quorum sensing (QS) is a density-dependent communicating mechanism that allows bacteria to regulate a wide range of biogeochemical important processes and could be inhibited by quorum quenching (QQ). Increasing researches have demonstrated that QS can affect the degradation of particulate organic matter (POM) in the photic zone. However, knowledge of the diversity and variation of microbial QS and QQ systems in sinking POM is scarce. Here, POM samples were collected from surface seawater (SW), bottom seawater (BW), and surficial sediment (SS) in the Yellow Sea of China. 16S rRNA gene amplicon and metagenome sequencing were performed to analyze the community structure of particle-associated microorganisms and distribution of QS genes [acylated homoserine lactone (AHL) synthesizing gene luxI and AHL sensing gene luxR] and QQ genes (genes encoding for AHL lactonase and acylase) in POM. Shifting community structures were observed at different sampling depths, with an increase of microbial abundance and diversity from SW to BW. Along with the variation of microbial communities, the abundances of luxI and luxR decreased slightly but were restored or even exceeded when POM arrived at SS. Comparatively, abundances of AHL lactonase and acylase remained constant during the transportation process from SW to BW but increased dramatically in SS. Correlation tests indicated that abundances of luxI and luxR were positively correlated with temperature, while those of AHL acylase were positively correlated with depth, SiO42–, PO43–, and NO3–, but negatively correlated with temperature and pH. According to phylogenetic analyses, the retrieved QS and QQ genes are more diverse and distinctive than ever experimentally identified. Besides, the vertical transmission of QS and QQ genes along with POM sinking was observed, which could be one of the key factors leading to the prevalence of QS and QQ genes in marine ecosystems. Overall, our results increase the current knowledge of QS and QQ metabolic pathways in marine environment and shed light on the intertwined interspecies relationships to better investigate their dynamics and ecological roles in POM cycling.
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Affiliation(s)
- Ying Su
- College of Marine Life Sciences, Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Yuanzhi Yang
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, United States
| | - Xiao-Yu Zhu
- College of Marine Life Sciences, Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Xiao-Hua Zhang
- College of Marine Life Sciences, Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
| | - Min Yu
- College of Marine Life Sciences, Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
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13
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Zhang H, Wang Y, Huang T, Liu K, Huang X, Ma B, Li N, Sekar R. Mixed-culture aerobic anoxygenic photosynthetic bacterial consortia reduce nitrate: Core species dynamics, co-interactions and assessment in raw water of reservoirs. BIORESOURCE TECHNOLOGY 2020; 315:123817. [PMID: 32683291 DOI: 10.1016/j.biortech.2020.123817] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Revised: 07/03/2020] [Accepted: 07/06/2020] [Indexed: 06/11/2023]
Abstract
Three consortia of mixed-culture Aerobic Anoxygenic Photosynthetic Bacteria (AAPB) with excellent aerobic denitrifying ability were isolated from drinking water source reservoirs. The results showed that the removal of dissolved organic carbon (DOC) and nitrate nitrogen (NO3--N) by mixed-culture AAPB were higher than 90% and 99%, respectively. The Illumina MiSeq sequencing of pufM gene revealed that the dominant genera and their relative abundance changed over the culture periods. Sphingomonas sanxanigenens was the most dominant species observed at 9 h, whereas at 48 h, the most abundant species was Rhodobacter blasticus. A network analysis demonstrated that the co-interactions among the different genera were complex and variable. Mixed-culture AAPB removed more than 30% of NO3--N and 25% of DOC from the source water and this study suggests that mixed-culture AAPB can be regarded as a latent denitrifying microbial inoculum in the reservoir raw water treatment.
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Affiliation(s)
- Haihan Zhang
- Shaanxi Key Laboratory of Environmental Engineering, Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, School of Municipal and Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China.
| | - Yan Wang
- Shaanxi Key Laboratory of Environmental Engineering, Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, School of Municipal and Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Tinglin Huang
- Shaanxi Key Laboratory of Environmental Engineering, Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, School of Municipal and Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Kaiwen Liu
- Shaanxi Key Laboratory of Environmental Engineering, Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, School of Municipal and Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Xin Huang
- Shaanxi Key Laboratory of Environmental Engineering, Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, School of Municipal and Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Ben Ma
- Shaanxi Key Laboratory of Environmental Engineering, Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, School of Municipal and Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Nan Li
- Shaanxi Key Laboratory of Environmental Engineering, Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, School of Municipal and Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Raju Sekar
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou 215123, China
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14
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Muramatsu S, Kanamuro M, Sato-Takabe Y, Hirose S, Muramatsu Y, Takaichi S, Hanada S. Roseobacter cerasinus sp. nov., isolated from a fish farm. Int J Syst Evol Microbiol 2020; 70:4920-4926. [PMID: 32730197 DOI: 10.1099/ijsem.0.004360] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An obligate aerobic and bacteriochlorophyll a-containing bacterium, designated strain AI77T, was isolated from a fish farm in Uwa Sea, Japan. Cells were Gram-stain-negative, coccoid- to oval-shaped, and showed no motility. Phylogenetic analysis based on the 16S rRNA gene sequences revealed that strain AI77T is a member of the genus Roseobacter and closely related to Roseobacter ponti MM-7T (97.8 %), Roseobacter denitrificans OCh 114T (97.3 %) and Roseobacter litoralis OCh 149T (97.3 %). The G+C content of strain AI77T was 61.0 mol%. The average amino acid identity values of the genome in strain AI77T with those in R. denitrificans OCh 114T and R. litoralis OCh 149T were 73.26 % (SD 16.46) and 72.63 % (SD 16.76), respectively. The digital DNA-DNA hybridization values of strain AI77T with the type strains R. denitrificans OCh 114T and R. litoralis OCh 149T were 18.70 and 18.50 %, respectively. The dominant fatty acids (>10 % of total fatty acids) of AI77T were summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c) and saturated fatty acid C16 : 0. The sole respiratory quinone was ubiquinone-10. The predominant polar lipids were phosphatidylcholine, phosphatidylglycerol and diphosphatidylglycerol. Based on the genetic and phenotypic data obtained herein, we conclude that strain AI77T represents a new species of the genus Roseobacter, for which we propose the name Roseobacter cerasinus sp. nov.; the type strain is AI77T (=DSM 110091T=NBRC 114115T).
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Affiliation(s)
- So Muramatsu
- Department of Biological Sciences, Tokyo Metropolitan University, 1-1 Minamiosawa, Hachioji, Tokyo, 192-0397, Japan
| | - Masataka Kanamuro
- Department of Biological Sciences, Tokyo Metropolitan University, 1-1 Minamiosawa, Hachioji, Tokyo, 192-0397, Japan
| | - Yuki Sato-Takabe
- Institute for Environmental Management Technology, National Institute of Advanced Industrial Science and Technology (AIST), Onogawa 16-1, Tsukuba, Ibaraki, 305-8569, Japan.,Department of Biological Sciences, Tokyo Metropolitan University, 1-1 Minamiosawa, Hachioji, Tokyo, 192-0397, Japan
| | - Setsuko Hirose
- Department of Biological Sciences, Tokyo Metropolitan University, 1-1 Minamiosawa, Hachioji, Tokyo, 192-0397, Japan
| | - Yuki Muramatsu
- NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation (NITE), 2-5-8, Kazusakamatari, Kisarazu, Chiba, 292-0818, Japan
| | - Shinichi Takaichi
- Department of Molecular Microbiology, Tokyo University of Agriculture, 1-1-1, Sakuragaoka, Setagaya-ku, Tokyo, 156-8502, Japan
| | - Satoshi Hanada
- Department of Biological Sciences, Tokyo Metropolitan University, 1-1 Minamiosawa, Hachioji, Tokyo, 192-0397, Japan
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15
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Szabó-Tugyi N, Vörös L, V-Balogh K, Botta-Dukát Z, Bernát G, Schmera D, Somogyi B. Aerobic anoxygenic phototrophs are highly abundant in hypertrophic and polyhumic waters. FEMS Microbiol Ecol 2020; 95:5530753. [PMID: 31291460 DOI: 10.1093/femsec/fiz104] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 07/08/2019] [Indexed: 01/20/2023] Open
Abstract
Aerobic anoxygenic phototrophs (AAPs) are a group of photoheterotrophic bacteria common in natural waters. Here, AAP abundance and contribution to total bacterial abundance and biomass were investigated to test whether the trophic status of a lake or content of coloured dissolved organic matter (CDOM) play a role in determining AAP distribution and abundance in shallow inland lakes, with special focus on hypertrophic and polyhumic waters. Twenty-six different shallow lakes in Hungary were monitored. AAP abundance and biomass were determined by epifluorescence microscopy. The lakes exhibit a broad range of CDOM (2-7000 mg Pt L-1) and phytoplankton biomass (2-1200 μg L-1 chlorophyll a concentration). Very high AAP abundance (up to 3 × 107 cells mL-1) was observed in polyhumic and hypertrophic shallow lakes. AAP abundance was influenced by phytoplankton biomass and CDOM content, and these effects were interrelated. As determined, 40 μg L-1 chlorophyll a and 52 mg Pt L-1 CDOM are threshold levels above which these effects have a synergistic relationship. Hence, the observed high AAP abundance in some soda pans is a consequence of combined hypertrophy and high CDOM content. AAP contribution was influenced by total suspended solids (TSS) content: the success of AAP cells could be explained by high TSS levels, which might be explained by the decrease of their selective grazing control.
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Affiliation(s)
- Nóra Szabó-Tugyi
- MTA Centre for Ecological Research, Balaton Limnological Institute
| | - Lajos Vörös
- MTA Centre for Ecological Research, Balaton Limnological Institute
| | - Katalin V-Balogh
- MTA Centre for Ecological Research, Balaton Limnological Institute
| | | | - Gábor Bernát
- MTA Centre for Ecological Research, Balaton Limnological Institute
| | - Dénes Schmera
- MTA Centre for Ecological Research, Balaton Limnological Institute
| | - Boglárka Somogyi
- MTA Centre for Ecological Research, Balaton Limnological Institute
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16
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Edwards A, Cameron KA, Cook JM, Debbonaire AR, Furness E, Hay MC, Rassner SM. Microbial genomics amidst the Arctic crisis. Microb Genom 2020; 6:e000375. [PMID: 32392124 PMCID: PMC7371112 DOI: 10.1099/mgen.0.000375] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 04/16/2020] [Indexed: 12/16/2022] Open
Abstract
The Arctic is warming - fast. Microbes in the Arctic play pivotal roles in feedbacks that magnify the impacts of Arctic change. Understanding the genome evolution, diversity and dynamics of Arctic microbes can provide insights relevant for both fundamental microbiology and interdisciplinary Arctic science. Within this synthesis, we highlight four key areas where genomic insights to the microbial dimensions of Arctic change are urgently required: the changing Arctic Ocean, greenhouse gas release from the thawing permafrost, 'biological darkening' of glacial surfaces, and human activities within the Arctic. Furthermore, we identify four principal challenges that provide opportunities for timely innovation in Arctic microbial genomics. These range from insufficient genomic data to develop unifying concepts or model organisms for Arctic microbiology to challenges in gaining authentic insights to the structure and function of low-biomass microbiota and integration of data on the causes and consequences of microbial feedbacks across scales. We contend that our insights to date on the genomics of Arctic microbes are limited in these key areas, and we identify priorities and new ways of working to help ensure microbial genomics is in the vanguard of the scientific response to the Arctic crisis.
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Affiliation(s)
- Arwyn Edwards
- Interdisciplinary Centre for Environmental Microbiology, Institute of Biological, Environmental and Rural Sciences, Cledwyn Building, Aberystwyth University, Cymru SY23 3DD, UK
| | - Karen A. Cameron
- Interdisciplinary Centre for Environmental Microbiology, Institute of Biological, Environmental and Rural Sciences, Cledwyn Building, Aberystwyth University, Cymru SY23 3DD, UK
| | - Joseph M. Cook
- Interdisciplinary Centre for Environmental Microbiology, Institute of Biological, Environmental and Rural Sciences, Cledwyn Building, Aberystwyth University, Cymru SY23 3DD, UK
| | - Aliyah R. Debbonaire
- Interdisciplinary Centre for Environmental Microbiology, Institute of Biological, Environmental and Rural Sciences, Cledwyn Building, Aberystwyth University, Cymru SY23 3DD, UK
| | - Eleanor Furness
- Interdisciplinary Centre for Environmental Microbiology, Institute of Biological, Environmental and Rural Sciences, Cledwyn Building, Aberystwyth University, Cymru SY23 3DD, UK
| | - Melanie C. Hay
- Interdisciplinary Centre for Environmental Microbiology, Institute of Biological, Environmental and Rural Sciences, Cledwyn Building, Aberystwyth University, Cymru SY23 3DD, UK
| | - Sara M.E. Rassner
- Interdisciplinary Centre for Environmental Microbiology, Institute of Biological, Environmental and Rural Sciences, Cledwyn Building, Aberystwyth University, Cymru SY23 3DD, UK
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17
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Muñoz-Marín MC, Gómez-Baena G, López-Lozano A, Moreno-Cabezuelo JA, Díez J, García-Fernández JM. Mixotrophy in marine picocyanobacteria: use of organic compounds by Prochlorococcus and Synechococcus. THE ISME JOURNAL 2020; 14:1065-1073. [PMID: 32034281 PMCID: PMC7174365 DOI: 10.1038/s41396-020-0603-9] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 01/28/2020] [Accepted: 01/28/2020] [Indexed: 12/23/2022]
Abstract
Marine picocyanobacteria of the Prochlorococcus and Synechococcus genera have been longtime considered as autotrophic organisms. However, compelling evidence published over the last 15 years shows that these organisms can use different organic compounds containing key elements to survive in oligotrophic oceans, such as N (amino acids, amino sugars), S (dimethylsulfoniopropionate, DMSP), or P (ATP). Furthermore, marine picocyanobacteria can also take up glucose and use it as a source of carbon and energy, despite the fact that this compound is devoid of limiting elements and can also be synthesized by using standard metabolic pathways. This review will outline the main findings suggesting mixotrophy in the marine picocyanobacteria Prochlorococcus and Synechococcus, and its ecological relevance for these important primary producers.
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Affiliation(s)
- M C Muñoz-Marín
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario CeiA3, Edificio Severo Ochoa, planta 1, ala Este, Campus de Rabanales, Universidad de Córdoba, 14071, Córdoba, Spain
| | - G Gómez-Baena
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario CeiA3, Edificio Severo Ochoa, planta 1, ala Este, Campus de Rabanales, Universidad de Córdoba, 14071, Córdoba, Spain
| | - A López-Lozano
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario CeiA3, Edificio Severo Ochoa, planta 1, ala Este, Campus de Rabanales, Universidad de Córdoba, 14071, Córdoba, Spain
| | - J A Moreno-Cabezuelo
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario CeiA3, Edificio Severo Ochoa, planta 1, ala Este, Campus de Rabanales, Universidad de Córdoba, 14071, Córdoba, Spain
| | - J Díez
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario CeiA3, Edificio Severo Ochoa, planta 1, ala Este, Campus de Rabanales, Universidad de Córdoba, 14071, Córdoba, Spain
| | - J M García-Fernández
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario CeiA3, Edificio Severo Ochoa, planta 1, ala Este, Campus de Rabanales, Universidad de Córdoba, 14071, Córdoba, Spain.
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18
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Ruiz-González C, Garcia-Chaves MC, Ferrera I, Niño-García JP, Del Giorgio PA. Taxonomic differences shape the responses of freshwater aerobic anoxygenic phototrophic bacterial communities to light and predation. Mol Ecol 2020; 29:1267-1283. [PMID: 32147876 DOI: 10.1111/mec.15404] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 02/25/2020] [Accepted: 02/26/2020] [Indexed: 11/29/2022]
Abstract
Aerobic anoxygenic phototrophic (AAP) bacteria are a phylogenetically diverse and ubiquitous group of prokaryotes that use organic matter but can harvest light using bacteriochlorophyll a. Although the factors regulating AAP ecology have long been investigated through field surveys, the few available experimental studies have considered AAPs as a group, thus disregarding the potential differential responses between taxonomically distinct AAP assemblages. Here, we used sequencing of the pufM gene to describe the diversity of AAPs in 10 environmentally distinct temperate lakes, and to investigate the taxonomic responses of AAP communities in these lakes when subjected to similar experimental manipulations of light and predator removal. The studied communities were clearly dominated by Limnohabitans AAP but presented a clear taxonomic segregation between lakes presumably driven by local conditions, which was maintained after experimental manipulations. Predation reduction (but not light exposure) caused significant compositional shifts across most assemblages, but the magnitude of these changes could not be clearly related to changes in bulk AAP abundances or taxonomic richness of AAP assemblages during experiments. Only a few operational taxonomic units, which differed taxonomically between lakes, were found to respond positively during experimental treatments. Our results highlight that different freshwater AAP communities respond differently to similar control mechanisms, highlighting that in-depth knowledge on AAP diversity is essential to understand the ecology and potential role of these photoheterotrophs.
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Affiliation(s)
- Clara Ruiz-González
- Institut de Ciències del Mar (ICM-CSIC), Barcelona, Spain.,Groupe de Recherche Interuniversitaire en Limnologie et en Environnement Aquatique (GRIL), Département des Sciences Biologiques, Université du Québec à Montréal, Montréal, QC, Canada
| | - Maria Carolina Garcia-Chaves
- Groupe de Recherche Interuniversitaire en Limnologie et en Environnement Aquatique (GRIL), Département des Sciences Biologiques, Université du Québec à Montréal, Montréal, QC, Canada.,Escuela de Microbiología, Universidad de Antioquia, Medellín, Colombia
| | - Isabel Ferrera
- Institut de Ciències del Mar (ICM-CSIC), Barcelona, Spain.,Centro Oceanográfico de Málaga, Instituto Español de Oceanografía, Málaga, Spain
| | - Juan Pablo Niño-García
- Groupe de Recherche Interuniversitaire en Limnologie et en Environnement Aquatique (GRIL), Département des Sciences Biologiques, Université du Québec à Montréal, Montréal, QC, Canada.,Escuela de Microbiología, Universidad de Antioquia, Medellín, Colombia
| | - Paul A Del Giorgio
- Groupe de Recherche Interuniversitaire en Limnologie et en Environnement Aquatique (GRIL), Département des Sciences Biologiques, Université du Québec à Montréal, Montréal, QC, Canada
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19
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Al-Otaibi N, Huete-Stauffer TM, Calleja ML, Irigoien X, Morán XAG. Seasonal variability and vertical distribution of autotrophic and heterotrophic picoplankton in the Central Red Sea. PeerJ 2020; 8:e8612. [PMID: 32140305 PMCID: PMC7045887 DOI: 10.7717/peerj.8612] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 01/21/2020] [Indexed: 12/21/2022] Open
Abstract
The Red Sea is characterized by higher temperatures and salinities than other oligotrophic tropical regions. Here, we investigated the vertical and seasonal variations in the abundance and biomass of autotrophic and heterotrophic picoplankton. Using flow cytometry, we consistently observed five groups of autotrophs (Prochlorococcus, two populations of Synechococcus separated by their relative phycoerythrin fluorescence, low (LF-Syn) and high (HF-Syn), and two differently-sized groups of picoeukaryotes, small (Speuk) and large (Lpeuk)) and two groups of heterotrophic prokaryotes of low and high nucleic acid content (LNA and HNA, respectively). Samples were collected in 15 surveys conducted from 2015 to 2017 at a 700-m depth station in the central Red Sea. Surface temperature ranged from 24.6 to 32.6 °C with a constant value of 21.7 °C below 200 m. Integrated (0-100 m) chlorophyll a concentrations were low, with maximum values in fall (24.0 ± 2.7 mg m-2) and minima in spring and summer (16.1 ± 1.9 and 1.1 mg m-2, respectively). Picoplankton abundance was generally lower than in other tropical environments. Vertical distributions differed for each group, with Synechococcus and LNA prokaryotes more abundant at the surface while Prochlorococcus, picoeukaryotes and HNA prokaryotes peaked at the deep chlorophyll maximum, located between 40 and 76 m. Surface to 100 m depth-weighted abundances exhibited clear seasonal patterns for Prochlorococcus, with maxima in summer (7.83 × 104 cells mL-1, July 2015) and minima in winter (1.39 × 104 cells mL-1, January 2015). LF-Syn (0.32 - 2.70 × 104 cells mL-1 ), HF-Syn (1.11 - 3.20 × 104 cells mL-1) and Speuk (0.99 - 4.81 × 102 cells mL-1) showed an inverse pattern to Prochlorococcus, while Lpeuk (0.16 - 7.05 × 104 cells mL-1) peaked in fall. Synechococcus unexpectedly outnumbered Prochlorococcus in winter and at the end of fall. The seasonality of heterotrophic prokaryotes (2.29 - 4.21×105 cells mL-1 ) was less noticeable than autotrophic picoplankton. The contribution of HNA cells was generally low in the upper layers, ranging from 36% in late spring and early summer to ca. 50% in winter and fall. Autotrophs dominated integrated picoplankton biomass in the upper 100 m, with 1.4-fold higher values in summer than in winter (mean 387 and 272 mg C m-2, respectively). However, when the whole water column was considered, the biomass of heterotrophic prokaryotes exceeded that of autotrophic picoplankton with an average of 411 mg C m-2. Despite being located in tropical waters, our results show that the picoplankton community seasonal differences in the central Red Sea are not fundamentally different from higher latitude regions.
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Affiliation(s)
- Najwa Al-Otaibi
- Red Sea Research Center (RSRC), Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Tamara M Huete-Stauffer
- Red Sea Research Center (RSRC), Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Maria Ll Calleja
- Department of Climate Geochemistry, Max Planck Institute for Chemistry (MPIC), Mainz, Germany
| | - Xabier Irigoien
- AZTI - Marine Research, Pasaia, Spain.,Basque Foundation for Science, IKERBASQUE, Bilbao, Spain
| | - Xosé Anxelu G Morán
- Red Sea Research Center (RSRC), Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
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20
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Li Y, Tang BL, Ren XB, Dang YR, Sun LL, Zhang XY, Chen XL, Qin QL, Wang P. Complete genome sequence of Flavobacterium arcticum SM1502T, exhibiting adaption to the Arctic marine salty environment. Mar Genomics 2019. [DOI: 10.1016/j.margen.2019.03.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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21
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Filatova TS, Abramochkin DV, Shiels HA. Thermal acclimation and seasonal acclimatization: a comparative study of cardiac response to prolonged temperature change in shorthorn sculpin. ACTA ACUST UNITED AC 2019; 222:jeb.202242. [PMID: 31315933 DOI: 10.1242/jeb.202242] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 07/15/2019] [Indexed: 12/30/2022]
Abstract
Seasonal thermal remodelling (acclimatization) and laboratory thermal remodelling (acclimation) can induce different physiological changes in ectothermic animals. As global temperatures are changing at an increasing rate, there is urgency to understand the compensatory abilities of key organs such as the heart to adjust under natural conditions. Thus, the aim of the present study was to directly compare the acclimatization and acclimatory response within a single eurythermal fish species, the European shorthorn sculpin (Myoxocephalus scorpio). We used current- and voltage-clamp to measure ionic current densities in both isolated atrial and ventricular myocytes from three groups of fish: (1) summer-caught fish kept at 12°C ('summer-acclimated'); (2) summer-caught fish kept at 3°C ('cold acclimated'); and (3) fish caught in March ('winter-acclimatized'). At a common test temperature of 7.5°C, action potential (AP) was shortened by both winter acclimatization and cold acclimation compared with summer acclimation; however, winter acclimatization caused a greater shortening than did cold acclimation. Shortening of AP was achieved mostly by a significant increase in repolarizing current density (I Kr and I K1) following winter acclimatization, with cold acclimation having only minor effects. Compared with summer acclimation, the depolarizing L-type calcium current (I Ca) was larger following winter acclimatization, but again, there was no effect of cold acclimation on I Ca Interestingly, the other depolarizing current, I Na, was downregulated at low temperatures. Our further analysis shows that ionic current remodelling is primarily due to changes in ion channel density rather than current kinetics. In summary, acclimatization profoundly modified the electrical activity of the sculpin heart while acclimation to the same temperature for >1.5 months produced very limited remodelling effects.
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Affiliation(s)
- Tatiana S Filatova
- Department of Human and Animal Physiology, Lomonosov Moscow State University, Leninskiye gory, 1, 12, Moscow, Russia 119234 .,Department of Physiology, Russian National Research Medical University, Ostrovityanova str., 1, Moscow, Russia 117997
| | - Denis V Abramochkin
- Department of Human and Animal Physiology, Lomonosov Moscow State University, Leninskiye gory, 1, 12, Moscow, Russia 119234.,Department of Physiology, Russian National Research Medical University, Ostrovityanova str., 1, Moscow, Russia 117997.,Ural Federal University, Mira 19, Ekaterinburg, Russia 620002
| | - Holly A Shiels
- Faculty of Life Sciences, Core Technology Facility, 46 Grafton Street, University of Manchester, Manchester M13 9NT, UK
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22
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Long-term seasonal and interannual variability of marine aerobic anoxygenic photoheterotrophic bacteria. ISME JOURNAL 2019; 13:1975-1987. [PMID: 30914777 DOI: 10.1038/s41396-019-0401-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 02/21/2019] [Accepted: 03/06/2019] [Indexed: 01/22/2023]
Abstract
We studied the long-term temporal dynamics of the aerobic anoxygenic phototrophic (AAP) bacteria, a relevant functional group in the coastal marine microbial food web, using high-throughput sequencing of the pufM gene coupled with multivariate, time series and co-occurrence analyses at the Blanes Bay Microbial Observatory (NW Mediterranean). Additionally, using metagenomics, we tested whether the used primers captured accurately the seasonality of the most relevant AAP groups. Phylogroup K (Gammaproteobacteria) was the greatest contributor to community structure over all seasons, with phylogroups E and G (Alphaproteobacteria) being prevalent in spring. Diversity indices showed a clear seasonal trend, with maximum values in winter, which was inverse to that of AAP abundance. Multivariate analyses revealed sample clustering by season, with a relevant proportion of the variance explained by day length, temperature, salinity, phototrophic nanoflagellate abundance, chlorophyll a, and silicate concentration. Time series analysis showed robust rhythmic patterns of co-occurrence, but distinct seasonal behaviors within the same phylogroup, and even within different amplicon sequence variants (ASVs) conforming the same operational taxonomic unit (OTU). Altogether, our results picture the AAP assemblage as highly seasonal and recurrent but containing ecotypes showing distinctive temporal niche partitioning, rather than being a cohesive functional group.
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23
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The mesopelagic anoxic Black Sea as an unexpected habitat for Synechococcus challenges our understanding of global "deep red fluorescence". ISME JOURNAL 2019; 13:1676-1687. [PMID: 30820035 PMCID: PMC6776005 DOI: 10.1038/s41396-019-0378-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 01/28/2019] [Accepted: 01/31/2019] [Indexed: 11/23/2022]
Abstract
The Black Sea is the largest meromictic sea with a reservoir of anoxic water extending from 100 to 1000 m depth. These deeper layers are characterised by a poorly understood fluorescence signal called “deep red fluorescence”, a chlorophyll a- (Chl a) like signal found in deep dark oceanic waters. In two cruises, we repeatedly found up to 103 cells ml−1 of picocyanobacteria at 750 m depth in these waters and isolated two phycoerythrin-rich Synechococcus sp. strains (BS55D and BS56D). Tests on BS56D revealed its high adaptability, involving the accumulation of Chl a in anoxic/dark conditions and its capacity to photosynthesise when re-exposed to light. Whole-genome sequencing of the two strains showed the presence of genes that confirms the putative ability of our strains to survive in harsh mesopelagic environments. This discovery provides new evidence to support early speculations associating the “deep red fluorescence” signal to viable picocyanobacteria populations in the deep oxygen-depleted oceans, suggesting a reconsideration of the ecological role of a viable stock of Synechococcus in dark deep waters.
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24
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Fernández-Gómez B, Díez B, Polz MF, Arroyo JI, Alfaro FD, Marchandon G, Sanhueza C, Farías L, Trefault N, Marquet PA, Molina-Montenegro MA, Sylvander P, Snoeijs-Leijonmalm P. Bacterial community structure in a sympagic habitat expanding with global warming: brackish ice brine at 85-90 °N. THE ISME JOURNAL 2019; 13:316-333. [PMID: 30228379 PMCID: PMC6331608 DOI: 10.1038/s41396-018-0268-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 06/11/2018] [Accepted: 07/24/2018] [Indexed: 01/13/2023]
Abstract
Larger volumes of sea ice have been thawing in the Central Arctic Ocean (CAO) during the last decades than during the past 800,000 years. Brackish brine (fed by meltwater inside the ice) is an expanding sympagic habitat in summer all over the CAO. We report for the first time the structure of bacterial communities in this brine. They are composed of psychrophilic extremophiles, many of them related to phylotypes known from Arctic and Antarctic regions. Community structure displayed strong habitat segregation between brackish ice brine (IB; salinity 2.4-9.6) and immediate sub-ice seawater (SW; salinity 33.3-34.9), expressed at all taxonomic levels (class to genus), by dominant phylotypes as well as by the rare biosphere, and with specialists dominating IB and generalists SW. The dominant phylotypes in IB were related to Candidatus Aquiluna and Flavobacterium, those in SW to Balneatrix and ZD0405, and those shared between the habitats to Halomonas, Polaribacter and Shewanella. A meta-analysis for the oligotrophic CAO showed a pattern with Flavobacteriia dominating in melt ponds, Flavobacteriia and Gammaproteobacteria in solid ice cores, Flavobacteriia, Gamma- and Betaproteobacteria, and Actinobacteria in brine, and Alphaproteobacteria in SW. Based on our results, we expect that the roles of Actinobacteria and Betaproteobacteria in the CAO will increase with global warming owing to the increased production of meltwater in summer. IB contained three times more phylotypes than SW and may act as an insurance reservoir for bacterial diversity that can act as a recruitment base when environmental conditions change.
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Affiliation(s)
- Beatriz Fernández-Gómez
- Department of Molecular Genetics and Microbiology, Pontifical University Catholic of Chile, Santiago, Chile
- INTA-Universidad de Chile, Santiago, Chile
| | - Beatriz Díez
- Department of Molecular Genetics and Microbiology, Pontifical University Catholic of Chile, Santiago, Chile.
- Center for Climate and Resilience Research, Concepción, Chile.
| | - Martin F Polz
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, USA
| | - José Ignacio Arroyo
- Department of Ecology, Pontifical University Catholic of Chile, Santiago, Chile
| | - Fernando D Alfaro
- GEMA Center for Genomics, Ecology & Environment, Universidad Mayor, Santiago, Chile
- Instituto de Ciencias Biológicas, Universidad de Talca, Talca, Chile
| | - Germán Marchandon
- Department of Molecular Genetics and Microbiology, Pontifical University Catholic of Chile, Santiago, Chile
| | - Cynthia Sanhueza
- Department of Molecular Genetics and Microbiology, Pontifical University Catholic of Chile, Santiago, Chile
| | - Laura Farías
- Center for Climate and Resilience Research, Concepción, Chile
- Department of Oceanography, Universidad de Concepción, Concepción, Chile
| | - Nicole Trefault
- GEMA Center for Genomics, Ecology & Environment, Universidad Mayor, Santiago, Chile
| | - Pablo A Marquet
- Department of Ecology, Pontifical University Catholic of Chile, Santiago, Chile
- Instituto de Ecología y Biodiversidad, Universidad de Chile, Santiago, Chile
| | - Marco A Molina-Montenegro
- Instituto de Ciencias Biológicas, Universidad de Talca, Talca, Chile
- Centro de Estudios Avanzados en Zonas Áridas, Universidad Católica del Norte, Coquimbo, Chile
| | - Peter Sylvander
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
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25
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Sandaa RA, E Storesund J, Olesin E, Lund Paulsen M, Larsen A, Bratbak G, Ray JL. Seasonality Drives Microbial Community Structure, Shaping both Eukaryotic and Prokaryotic Host⁻Viral Relationships in an Arctic Marine Ecosystem. Viruses 2018; 10:v10120715. [PMID: 30558156 PMCID: PMC6315344 DOI: 10.3390/v10120715] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 11/30/2018] [Accepted: 12/08/2018] [Indexed: 12/21/2022] Open
Abstract
The Arctic marine environment experiences dramatic seasonal changes in light and nutrient availability. To investigate the influence of seasonality on Arctic marine virus communities, five research cruises to the west and north of Svalbard were conducted across one calendar year, collecting water from the surface to 1000 m in depth. We employed metabarcoding analysis of major capsid protein g23 and mcp genes in order to investigate T4-like myoviruses and large dsDNA viruses infecting prokaryotic and eukaryotic picophytoplankton, respectively. Microbial abundances were assessed using flow cytometry. Metabarcoding results demonstrated that seasonality was the key mediator shaping virus communities, whereas depth exerted a diversifying effect within seasonal virus assemblages. Viral diversity and virus-to-prokaryote ratios (VPRs) dropped sharply at the commencement of the spring bloom but increased across the season, ultimately achieving the highest levels during the winter season. These findings suggest that viral lysis may be an important process during the polar winter, when productivity is low. Furthermore, winter viral communities consisted of Operational Taxonomic Units (OTUs) distinct from those present during the spring-summer season. Our data provided a first insight into the diversity of viruses in a hitherto undescribed marine habitat characterized by extremes in light and productivity.
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Affiliation(s)
- Ruth-Anne Sandaa
- Department of Biosciences, University of Bergen, N-5020 Bergen, Norway.
| | - Julia E Storesund
- Department of Biosciences, University of Bergen, N-5020 Bergen, Norway.
| | - Emily Olesin
- Department of Biosciences, University of Bergen, N-5020 Bergen, Norway.
| | | | - Aud Larsen
- Department of Biosciences, University of Bergen, N-5020 Bergen, Norway.
- NORCE Norwegian Research Centre AS, Uni Research Environment, N-5020 Bergen, Norway.
| | - Gunnar Bratbak
- Department of Biosciences, University of Bergen, N-5020 Bergen, Norway.
| | - Jessica Louise Ray
- Department of Biosciences, University of Bergen, N-5020 Bergen, Norway.
- NORCE Norwegian Research Centre AS, Uni Research Environment, N-5020 Bergen, Norway.
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26
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Thiele S, Basse A, Becker JW, Lipski A, Iversen MH, Mollenhauer G. Microbial communities in the nepheloid layers and hypoxic zones of the Canary Current upwelling system. Microbiologyopen 2018; 8:e00705. [PMID: 30311417 PMCID: PMC6528590 DOI: 10.1002/mbo3.705] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2018] [Revised: 07/04/2018] [Accepted: 07/06/2018] [Indexed: 11/24/2022] Open
Abstract
Eastern boundary upwelling systems (EBUSs) are among the most productive marine environments in the world. The Canary Current upwelling system off the coast of Mauritania and Morocco is the second most productive of the four EBUS, where nutrient‐rich waters fuel perennial phytoplankton blooms, evident by high chlorophyll a concentrations off Cape Blanc, Mauritania. High primary production leads to eutrophic waters in the surface layers, whereas sinking phytoplankton debris and horizontally dispersed particles form nepheloid layers (NLs) and hypoxic waters at depth. We used Catalyzed Reporter Deposition Fluorescence In Situ Hybridization (CARD‐FISH) in combination with fatty acid (measured as methyl ester; FAME) profiles to investigate the bacterial and archaeal community composition along transects from neritic to pelagic waters within the “giant Cape Blanc filament” in two consecutive years (2010 and 2011), and to evaluate the usage of FAME data for microbial community studies. We also report the first fatty acid profile of Pelagibacterales strain HTCC7211 which was used as a reference profile for the SAR11 clade. Unexpectedly, the reference profile contained low concentrations of long chain fatty acids 18:1 cis11, 18:1 cis11 11methyl, and 19:0 cyclo11–12 fatty acids, the main compounds in other Alphaproteobacteria. Members of the free‐living SAR11 clade were found at increased relative abundance in the hypoxic waters in both years. In contrast, the depth profiles of Gammaproteobacteria (including Alteromonas and Pseudoalteromonas), Bacteroidetes, Roseobacter, and Synechococcus showed high abundances of these groups in layers where particle abundance was high, suggesting that particle attachment or association is an important mechanisms of dispersal for these groups. Collectively, our results highlight the influence of NLs, horizontal particle transport, and low oxygen on the structure and dispersal of microbial communities in upwelling systems.
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Affiliation(s)
- Stefan Thiele
- Max-Planck-Institute for Marine Microbiology, Bremen, Germany.,Friedrich Schiller University, Jena, Germany
| | - Andreas Basse
- Alfred Wegener Institute for Polar and Marine Research, Bremerhaven, Germany.,MARUM and University of Bremen, Bremen, Germany
| | - Jamie W Becker
- Department of Biology, Haverford College, Haverford, Pennsylvania
| | - Andre Lipski
- Department of Food Microbiology and Hygiene, Rheinische Friedrich-Wilhelms Universität Bonn, Bonn, Germany
| | - Morten H Iversen
- Alfred Wegener Institute for Polar and Marine Research, Bremerhaven, Germany.,MARUM and University of Bremen, Bremen, Germany
| | - Gesine Mollenhauer
- Alfred Wegener Institute for Polar and Marine Research, Bremerhaven, Germany.,MARUM and University of Bremen, Bremen, Germany
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27
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Sato-Takabe Y, Hamasaki K, Suzuki S. High temperature accelerates growth of aerobic anoxygenic phototrophic bacteria in seawater. Microbiologyopen 2018; 8:e00710. [PMID: 30054976 PMCID: PMC6528613 DOI: 10.1002/mbo3.710] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 07/07/2018] [Accepted: 07/09/2018] [Indexed: 11/22/2022] Open
Abstract
Temperature is an important controlling factor in the growth activity of all microorganisms. Aerobic anoxygenic phototrophic (AAP) bacteria actively grow in the ocean and are known as one of the main driving forces in organic matter cycling in surface seawater environments. Whether temperature change affects AAP bacteria activity from an ecological viewpoint remains an open question. To date, no known studies have reported the effect of temperature change on AAP bacteria growth in the ocean. We here show that the growth rate of AAP bacteria exceeded that of other bacterial types at high water temperatures in the absence of grazers. The slope of the regression line of the net growth rate of AAP bacteria as a function of water temperature was the same as that for non‐AAP bacteria at all temperatures (10, 20, and 30°C); however, when grazers were eliminated, it was 4.7 times higher than that of non‐AAP bacteria. This result suggests that AAP bacteria are more responsive to water temperature increases than other bacteria and that AAP bacteria might become more dominant than other bacteria under elevated water temperatures.
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Affiliation(s)
- Yuki Sato-Takabe
- Center for Marine Environmental Studies, Ehime University, Matsuyama, Ehime, Japan.,Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Japan
| | - Koji Hamasaki
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Japan
| | - Satoru Suzuki
- Center for Marine Environmental Studies, Ehime University, Matsuyama, Ehime, Japan
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28
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Biogeographic patterns of aerobic anoxygenic phototrophic bacteria reveal an ecological consistency of phylogenetic clades in different oceanic biomes. Sci Rep 2018. [PMID: 29515205 PMCID: PMC5841314 DOI: 10.1038/s41598-018-22413-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
In marine environments, aerobic anoxygenic phototrophic (AAP) bacterial assemblages vary in space and along environmental gradients but the factors shaping their diversity and distribution at different taxonomic levels remain poorly identified. Using sets of sequences encoding the M sub-unit of the photosynthetic apparatus from different oceanic regions, we prioritized the processes underlying AAP bacterial biogeographical patterns. The present analysis offers novel insights into the ecological distribution of marine AAP bacteria and highlights that physiological constraints play a key role in structuring AAP bacterial assemblages at a global scale. Salinity especially seems to favor lineage-specific adaptations. Moreover, by inferring the evolutionary history of habitat transitions, a substantial congruence between habitat and evolutionary relatedness was highlighted. The identification of ecological cohesive clades for AAP bacteria suggests that prediction of AAP bacterial assemblages is possible from marine habitat properties.
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29
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Piwosz K, Kaftan D, Dean J, Šetlík J, Koblížek M. Nonlinear effect of irradiance on photoheterotrophic activity and growth of the aerobic anoxygenic phototrophic bacteriumDinoroseobacter shibae. Environ Microbiol 2017; 20:724-733. [DOI: 10.1111/1462-2920.14003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2017] [Revised: 11/10/2017] [Accepted: 11/17/2017] [Indexed: 12/20/2022]
Affiliation(s)
- Kasia Piwosz
- Center Algatech; Institute of Microbiology CAS; Třeboň 37981 Czech Republic
| | - David Kaftan
- Center Algatech; Institute of Microbiology CAS; Třeboň 37981 Czech Republic
| | - Jason Dean
- Center Algatech; Institute of Microbiology CAS; Třeboň 37981 Czech Republic
| | - Jiří Šetlík
- Center Algatech; Institute of Microbiology CAS; Třeboň 37981 Czech Republic
| | - Michal Koblížek
- Center Algatech; Institute of Microbiology CAS; Třeboň 37981 Czech Republic
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30
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Callieri C. Synechococcus plasticity under environmental changes. FEMS Microbiol Lett 2017; 364:4582260. [DOI: 10.1093/femsle/fnx229] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 10/27/2017] [Indexed: 11/12/2022] Open
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31
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Liang Y, Zhang Y, Wang N, Luo T, Zhang Y, Rivkin RB. Estimating Primary Production of Picophytoplankton Using the Carbon-Based Ocean Productivity Model: A Preliminary Study. Front Microbiol 2017; 8:1926. [PMID: 29051755 PMCID: PMC5633608 DOI: 10.3389/fmicb.2017.01926] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 09/21/2017] [Indexed: 11/13/2022] Open
Abstract
Picophytoplankton are acknowledged to contribute significantly to primary production (PP) in the ocean while now the method to measure PP of picophytoplankton (PPPico) at large scales is not yet well established. Although the traditional 14C method and new technologies based on the use of stable isotopes (e.g., 13C) can be employed to accurately measure in situ PPPico, the time-consuming and labor-intensive shortage of these methods constrain their application in a survey on large spatiotemporal scales. To overcome this shortage, a modified carbon-based ocean productivity model (CbPM) is proposed for estimating the PPPico whose principle is based on the group-specific abundance, cellular carbon conversion factor (CCF), and temperature-derived growth rate of picophytoplankton. Comparative analysis showed that the estimated PPPico using CbPM method is significantly and positively related (r2 = 0.53, P < 0.001, n = 171) to the measured 14C uptake. This significant relationship suggests that CbPM has the potential to estimate the PPPico over large spatial and temporal scales. Currently this model application may be limited by the use of invariant cellular CCF and the relatively small data sets to validate the model which may introduce some uncertainties and biases. Model performance will be improved by the use of variable conversion factors and the larger data sets representing diverse growth conditions. Finally, we apply the CbPM-based model on the collected data during four cruises in the Bohai Sea in 2005. Model-estimated PPPico ranged from 0.1 to 11.9, 29.9 to 432.8, 5.5 to 214.9, and 2.4 to 65.8 mg C m-2 d-1 during March, June, September, and December, respectively. This study shed light on the estimation of global PPPico using carbon-based production model.
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Affiliation(s)
- Yantao Liang
- Research Center for Marine Biology and Carbon Sequestration, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China.,Institute of Marine Microbes and Ecospheres, State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
| | - Yongyu Zhang
- Research Center for Marine Biology and Carbon Sequestration, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Nannan Wang
- Institute of Marine Microbes and Ecospheres, State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
| | - Tingwei Luo
- Institute of Marine Microbes and Ecospheres, State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
| | - Yao Zhang
- Institute of Marine Microbes and Ecospheres, State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
| | - Richard B Rivkin
- Department of Ocean Sciences, Memorial University of Newfoundland, St. John's, NL, Canada
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32
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Jain A, Krishnan KP. Differences in free-living and particle-associated bacterial communities and their spatial variation in Kongsfjorden, Arctic. J Basic Microbiol 2017; 57:827-838. [DOI: 10.1002/jobm.201700216] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Revised: 06/16/2017] [Accepted: 07/07/2017] [Indexed: 11/06/2022]
Affiliation(s)
- Anand Jain
- Cryobiology Laboratory; National Centre for Antarctic and Ocean Research; Vasco-da-Gama, Goa India
| | - Kottekkatu P. Krishnan
- Cryobiology Laboratory; National Centre for Antarctic and Ocean Research; Vasco-da-Gama, Goa India
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33
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Marine Bacterioplankton Seasonal Succession Dynamics. Trends Microbiol 2017; 25:494-505. [DOI: 10.1016/j.tim.2016.12.013] [Citation(s) in RCA: 133] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Revised: 12/13/2016] [Accepted: 12/21/2016] [Indexed: 01/08/2023]
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34
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Stuart RK, Bundy R, Buck K, Ghassemain M, Barbeau K, Palenik B. Copper toxicity response influences mesotrophicSynechococcuscommunity structure. Environ Microbiol 2017; 19:756-769. [DOI: 10.1111/1462-2920.13630] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Revised: 11/17/2016] [Accepted: 11/19/2016] [Indexed: 11/28/2022]
Affiliation(s)
- Rhona K. Stuart
- Scripps Institution of Oceanography, University of California at San Diego; La Jolla CA USA
| | - Randelle Bundy
- University of California at San Diego; La Jolla 92093 CA USA
| | - Kristen Buck
- Scripps Institution of Oceanography, University of California at San Diego; La Jolla CA USA
| | | | - Kathy Barbeau
- Scripps Institution of Oceanography, University of California at San Diego; La Jolla CA USA
| | - Brian Palenik
- Scripps Institution of Oceanography, University of California at San Diego; La Jolla CA USA
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35
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Mohapatra RK, Parhi PK, Patra JK, Panda CR, Thatoi HN. Biodetoxification of Toxic Heavy Metals by Marine Metal Resistant Bacteria- A Novel Approach for Bioremediation of the Polluted Saline Environment. Microb Biotechnol 2017. [DOI: 10.1007/978-981-10-6847-8_15] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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36
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Tahon G, Tytgat B, Willems A. Diversity of Phototrophic Genes Suggests Multiple Bacteria May Be Able to Exploit Sunlight in Exposed Soils from the Sør Rondane Mountains, East Antarctica. Front Microbiol 2016; 7:2026. [PMID: 28066352 PMCID: PMC5165242 DOI: 10.3389/fmicb.2016.02026] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 12/02/2016] [Indexed: 01/10/2023] Open
Abstract
Microbial life in exposed terrestrial surface layers in continental Antarctica is faced with extreme environmental conditions, including scarcity of organic matter. Bacteria in these exposed settings can therefore be expected to use alternative energy sources such as solar energy, abundant during the austral summer. Using Illumina MiSeq sequencing, we assessed the diversity and abundance of four conserved protein encoding genes involved in different key steps of light-harvesting pathways dependent on (bacterio)chlorophyll (pufM, bchL/chlL, and bchX genes) and rhodopsins (actinorhodopsin genes), in exposed soils from the Sør Rondane Mountains, East Antarctica. Analysis of pufM genes, encoding a subunit of the type 2 photochemical reaction center found in anoxygenic phototrophic bacteria, revealed a broad diversity, dominated by Roseobacter- and Loktanella-like sequences. The bchL and chlL, involved in (bacterio)chlorophyll synthesis, on the other hand, showed a high relative abundance of either cyanobacterial or green algal trebouxiophyceael chlL reads, depending on the sample, while most bchX sequences belonged mostly to previously unidentified phylotypes. Rhodopsin-containing phototrophic bacteria could not be detected in the samples. Our results, while suggesting that Cyanobacteria and green algae are the main phototrophic groups, show that light-harvesting bacteria are nevertheless very diverse in microbial communities in Antarctic soils.
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Affiliation(s)
- Guillaume Tahon
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University Ghent, Belgium
| | - Bjorn Tytgat
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University Ghent, Belgium
| | - Anne Willems
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University Ghent, Belgium
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Sato-Takabe Y, Nakao H, Kataoka T, Yokokawa T, Hamasaki K, Ohta K, Suzuki S. Abundance of Common Aerobic Anoxygenic Phototrophic Bacteria in a Coastal Aquaculture Area. Front Microbiol 2016; 7:1996. [PMID: 28018324 PMCID: PMC5156720 DOI: 10.3389/fmicb.2016.01996] [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: 09/29/2016] [Accepted: 11/29/2016] [Indexed: 11/21/2022] Open
Abstract
Aerobic anoxygenic phototrophic bacteria (AAnPB) rely on not only heterotrophic but also phototrophic energy gain. AAnPB are known to have high abundance in oligotrophic waters and are the major portion of the bacterial carbon stock in the environment. In a yearlong study in an aquaculture area in the Uwa Sea, Japan, AAnPB, accounted for 4.7 to 24% of the total bacteria by count. Since the cell volume of AAnPB is 2.23 ± 0.674 times larger than the mean for total bacteria, AAnPB biomass is estimated to account for 10–53% of the total bacterial assemblage. By examining pufM gene sequence, a common phylogenetic AAnPB species was found in all sampling sites through the year. The common species and other season-specific species were phylogenetically close to unculturable clones recorded in the Sargasso Sea and Pacific Ocean. The present study suggests that the common species may be a cosmopolitan species with worldwide distribution that is abundant not only in the oligotrophic open ocean but also in eutrophic aquaculture areas.
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Affiliation(s)
- Yuki Sato-Takabe
- Center for Marine Environmental Studies, Ehime University Matsuyama, Japan
| | - Hironori Nakao
- Center for Marine Environmental Studies, Ehime University Matsuyama, Japan
| | - Takafumi Kataoka
- Center for Marine Environmental Studies, Ehime University Matsuyama, Japan
| | - Taichi Yokokawa
- Center for Marine Environmental Studies, Ehime University Matsuyama, Japan
| | - Koji Hamasaki
- Atmosphere and Ocean Research Institute, The University of Tokyo Kashiwa, Japan
| | - Kohei Ohta
- South Ehime Fisheries Research Center, Ehime University Ainan, Japan
| | - Satoru Suzuki
- Center for Marine Environmental Studies, Ehime University Matsuyama, Japan
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Pitt FD, Millard A, Ostrowski M, Dervish S, Mazard S, Paulsen IT, Zubkov MV, Scanlan DJ. A Sample-to-Sequence Protocol for Genus Targeted Transcriptomic Profiling: Application to Marine Synechococcus. Front Microbiol 2016; 7:1592. [PMID: 27790194 PMCID: PMC5063861 DOI: 10.3389/fmicb.2016.01592] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 09/22/2016] [Indexed: 12/02/2022] Open
Abstract
Recent studies using whole community metagenomic and metatranscriptomic approaches are revealing important new insights into the functional potential and activity of natural marine microbial communities. Here, we complement these approaches by describing a complete ocean sample-to-sequence protocol, specifically designed to target a single bacterial genus for purposes of both DNA and RNA profiling using fluorescence activated cell sorting (FACS). The importance of defining and understanding the effects of a sampling protocol are critical if we are to gain meaningful data from environmental surveys. Rigorous pipeline trials with a cultured isolate, Synechococcus sp. BL107 demonstrate that water filtration has a well-defined but limited impact on the transcriptomic profile of this organism, whilst sample storage and multiple rounds of cell sorting have almost no effect on the resulting RNA sequence profile. Attractively, the means to replicate the sampling strategy is within the budget and expertise of most researchers.
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Affiliation(s)
- Frances D Pitt
- School of Life Sciences, University of Warwick Coventry, UK
| | - Andrew Millard
- Warwick Medical School, University of Warwick Coventry, UK
| | - Martin Ostrowski
- Department of Biochemistry and Biomolecular Science, Faculty of Science and Engineering, Macquarie University Sydney, NSW, Australia
| | - Suat Dervish
- Sydney Cytometry, Centenary Institute, University of Sydney Sydney, NSW, Australia
| | - Sophie Mazard
- Department of Biochemistry and Biomolecular Science, Faculty of Science and Engineering, Macquarie University Sydney, NSW, Australia
| | - Ian T Paulsen
- Department of Biochemistry and Biomolecular Science, Faculty of Science and Engineering, Macquarie University Sydney, NSW, Australia
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Boeuf D, Lami R, Cunnington E, Jeanthon C. Summer Abundance and Distribution of Proteorhodopsin Genes in the Western Arctic Ocean. Front Microbiol 2016; 7:1584. [PMID: 27790192 PMCID: PMC5061748 DOI: 10.3389/fmicb.2016.01584] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 09/21/2016] [Indexed: 11/13/2022] Open
Abstract
Proteorhodopsins (PR) are phylogenetically diverse and highly expressed proton pumps in marine bacterial communities. The phylogenetic diversity and in situ expression of the main PR groups in polar off-shore, coastal and estuarine waters is poorly known and their abundance has not yet been reported. Here, we show that PR gene sequences of the southern Beaufort Sea including MacKenzie shelf and estuary are mainly affiliated to Gammaproteobacteria, Alphaproteobacteria, and Bacteroidetes. Substantial overlap (78%) between DNA- and cDNA-based librairies indicated in situ PR transcription within a large fraction of PR-containing community. Sets of specific qPCR primers were designed to measure the absolute abundances of the major PR types. Spatial and depth profiles showed that PR-containing bacteria were abundant throughout the photic zone, comprising up to 45% of total bacteria. Although their abundance varied greatly with location and depth, Alphaproteobacteria predominated in the PR community in all water masses, with SAR11 as the major PR type. Low nutrient concentrations rather than light were the environmental drivers that best explained the abundance and distribution of arctic PR types. Together, our data suggests that PR-based phototrophy could be the major phototrophic prokaryotic process during the Arctic Ocean summer.
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Affiliation(s)
- Dominique Boeuf
- CNRS, Station Biologique, UMR 7144 Adaptation and Diversité en Milieu MarinRoscoff, France; Sorbonne Universités - UPMC Université Paris 06, Station Biologique, UMR 7144 Adaptation and Diversité en Milieu MarinRoscoff, France
| | - Raphaël Lami
- CNRS, USR 3579, Laboratoire de Biodiversité et Biotechnologies MicrobiennesBanyuls-sur-Mer, France; Sorbonne Universités - UPMC Université Paris 06, USR 3579, Observatoire OcéanologiqueBanyuls-sur-Mer, France
| | - Emelyne Cunnington
- CNRS, Station Biologique, UMR 7144 Adaptation and Diversité en Milieu MarinRoscoff, France; Sorbonne Universités - UPMC Université Paris 06, Station Biologique, UMR 7144 Adaptation and Diversité en Milieu MarinRoscoff, France
| | - Christian Jeanthon
- CNRS, Station Biologique, UMR 7144 Adaptation and Diversité en Milieu MarinRoscoff, France; Sorbonne Universités - UPMC Université Paris 06, Station Biologique, UMR 7144 Adaptation and Diversité en Milieu MarinRoscoff, France
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Marine Bacterial and Archaeal Ion-Pumping Rhodopsins: Genetic Diversity, Physiology, and Ecology. Microbiol Mol Biol Rev 2016; 80:929-54. [PMID: 27630250 DOI: 10.1128/mmbr.00003-16] [Citation(s) in RCA: 109] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The recognition of a new family of rhodopsins in marine planktonic bacteria, proton-pumping proteorhodopsin, expanded the known phylogenetic range, environmental distribution, and sequence diversity of retinylidene photoproteins. At the time of this discovery, microbial ion-pumping rhodopsins were known solely in haloarchaea inhabiting extreme hypersaline environments. Shortly thereafter, proteorhodopsins and other light-activated energy-generating rhodopsins were recognized to be widespread among marine bacteria. The ubiquity of marine rhodopsin photosystems now challenges prior understanding of the nature and contributions of "heterotrophic" bacteria to biogeochemical carbon cycling and energy fluxes. Subsequent investigations have focused on the biophysics and biochemistry of these novel microbial rhodopsins, their distribution across the tree of life, evolutionary trajectories, and functional expression in nature. Later discoveries included the identification of proteorhodopsin genes in all three domains of life, the spectral tuning of rhodopsin variants to wavelengths prevailing in the sea, variable light-activated ion-pumping specificities among bacterial rhodopsin variants, and the widespread lateral gene transfer of biosynthetic genes for bacterial rhodopsins and their associated photopigments. Heterologous expression experiments with marine rhodopsin genes (and associated retinal chromophore genes) provided early evidence that light energy harvested by rhodopsins could be harnessed to provide biochemical energy. Importantly, some studies with native marine bacteria show that rhodopsin-containing bacteria use light to enhance growth or promote survival during starvation. We infer from the distribution of rhodopsin genes in diverse genomic contexts that different marine bacteria probably use rhodopsins to support light-dependent fitness strategies somewhere between these two extremes.
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Bibiloni-Isaksson J, Seymour JR, Ingleton T, van de Kamp J, Bodrossy L, Brown MV. Spatial and temporal variability of aerobic anoxygenic photoheterotrophic bacteria along the east coast of Australia. Environ Microbiol 2016; 18:4485-4500. [PMID: 27376620 DOI: 10.1111/1462-2920.13436] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Accepted: 06/28/2016] [Indexed: 11/29/2022]
Abstract
Aerobic Anoxygenic Phototrophic Bacteria (AAnPB) are ecologically important microorganisms, widespread in oceanic photic zones. However, the key environmental drivers underpinning AAnPB abundance and diversity are still largely undefined. The temporal patterns in AAnPB dynamics at three oceanographic reference stations spanning at approximately 15° latitude along the Australian east coast were examined. AAnPB abundance was highly variable, with pufM gene copies ranging from 1.1 × 102 to 1.4 × 105 ml-1 and positively correlated with day length and solar radiation. pufM gene Miseq sequencing revealed that the majority of sequences were closely related to those obtained previously, suggesting that key AAnPB groups are widely distributed across similar environments globally. Temperature was a major structuring factor for AAnPB assemblages across large spatial scales, correlating positively with richness and Gammaproteobacteria (phylogroup K) abundance but negatively with Roseobacter-clade (phylogroup E) abundance, with temperatures between 16°C and 18°C identified as a potential transition zone between these groups. Network analysis revealed that discrete AAnPB populations exploit specific niches defined by varying temperature, light and nutrient conditions in the Tasman Sea system, with evidence for both niche sharing and partitioning amongst closely related operational taxonomic units.
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Affiliation(s)
- Jaime Bibiloni-Isaksson
- Plant Functional Biology and Climate Change Cluster, University of Technology Sydney, Sydney, Australia
| | - Justin R Seymour
- Plant Functional Biology and Climate Change Cluster, University of Technology Sydney, Sydney, Australia
| | - Tim Ingleton
- Department of Environment, Climate Change and Water, Waters and Coastal Science Section, Sydney South, NSW, 1232, Australia
| | - Jodie van de Kamp
- CSIRO Oceans and Atmosphere, Castray Esplanade, Hobart, TAS, 7000, Australia
| | - Levente Bodrossy
- CSIRO Oceans and Atmosphere, Castray Esplanade, Hobart, TAS, 7000, Australia
| | - Mark V Brown
- School of Biotechnology and Biomolecular Science, UNSW Australia, Sydney, 2052, Australia
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Cuadrat RRC, Ferrera I, Grossart HP, Dávila AMR. Picoplankton Bloom in Global South? A High Fraction of Aerobic Anoxygenic Phototrophic Bacteria in Metagenomes from a Coastal Bay (Arraial do Cabo--Brazil). OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2016; 20:76-87. [PMID: 26871866 PMCID: PMC4770915 DOI: 10.1089/omi.2015.0142] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Marine habitats harbor a great diversity of microorganism from the three domains of life, only a small fraction of which can be cultivated. Metagenomic approaches are increasingly popular for addressing microbial diversity without culture, serving as sensitive and relatively unbiased methods for identifying and cataloging the diversity of nucleic acid sequences derived from organisms in environmental samples. Aerobic anoxygenic phototrophic bacteria (AAP) play important roles in carbon and energy cycling in aquatic systems. In oceans, those bacteria are widely distributed; however, their abundance and importance are still poorly understood. The aim of this study was to estimate abundance and diversity of AAPs in metagenomes from an upwelling affected coastal bay in Arraial do Cabo, Brazil, using in silico screening for the anoxygenic photosynthesis core genes. Metagenomes from the Global Ocean Sample Expedition (GOS) were screened for comparative purposes. AAPs were highly abundant in the free-living bacterial fraction from Arraial do Cabo: 23.88% of total bacterial cells, compared with 15% in the GOS dataset. Of the ten most AAP abundant samples from GOS, eight were collected close to the Equator where solar irradiation is high year-round. We were able to assign most retrieved sequences to phylo-groups, with a particularly high abundance of Roseobacter in Arraial do Cabo samples. The high abundance of AAP in this tropical bay may be related to the upwelling phenomenon and subsequent picoplankton bloom. These results suggest a link between upwelling and light abundance and demonstrate AAP even in oligotrophic tropical and subtropical environments. Longitudinal studies in the Arraial do Cabo region are warranted to understand the dynamics of AAP at different locations and seasons, and the ecological role of these unique bacteria for biogeochemical and energy cycling in the ocean.
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Affiliation(s)
- Rafael R C Cuadrat
- 1 Computational and Systems Biology Laboratory, Oswaldo Cruz Institute , Fiocruz, Brazil .,2 Leibniz-Institute of Freshwater Ecology and Inland Fisheries , Berlin, Germany .,5 Berlin Center for Genomics in Biodiversity Research , Berlin, Germany
| | - Isabel Ferrera
- 2 Leibniz-Institute of Freshwater Ecology and Inland Fisheries , Berlin, Germany .,4 Institut de Ciències del Mar , CSIC, Barcelona, Spain
| | - Hans-Peter Grossart
- 2 Leibniz-Institute of Freshwater Ecology and Inland Fisheries , Berlin, Germany .,3 Potsdam University, Institute for Biochemistry and Biology , Potsdam, Germany
| | - Alberto M R Dávila
- 1 Computational and Systems Biology Laboratory, Oswaldo Cruz Institute , Fiocruz, Brazil
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Single-cell activity of freshwater aerobic anoxygenic phototrophic bacteria and their contribution to biomass production. ISME JOURNAL 2016; 10:1579-88. [PMID: 26771928 DOI: 10.1038/ismej.2015.242] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Revised: 11/18/2015] [Accepted: 11/20/2015] [Indexed: 11/08/2022]
Abstract
Aerobic anoxygenic phototrophic (AAP) bacteria are photoheterotrophs that despite their low abundances have been hypothesized to play an ecologically and biogeochemically important role in aquatic systems. Characterizing this role requires a better understanding of the in situ dynamics and activity of AAP bacteria. Here we provide the first assessment of the single-cell activity of freshwater AAP bacteria and their contribution to total bacterial production across lakes spanning a wide trophic gradient, and explore the role of light in regulating AAP activity. The proportion of cells that were active in leucine incorporation and the level of activity per cell were consistently higher for AAP than for bulk bacteria across lakes. As a result, AAP bacteria contributed disproportionately more to total bacterial production than to total bacterial abundance. Interestingly, although environmentally driven patterns in activity did not seem to differ largely between AAP and bulk bacteria, their response to light did, and exposure to light resulted in increases in the proportion of active AAP bacteria with no clear effect on their cell-specific activity. This suggests that light may play a role in the activation of AAP bacteria, enabling these photoheterotrophs to contribute more to the carbon cycle than suggested by their abundance.
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44
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Colonization in the photic zone and subsequent changes during sinking determine bacterial community composition in marine snow. Appl Environ Microbiol 2016; 81:1463-71. [PMID: 25527538 DOI: 10.1128/aem.02570-14] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Due to sampling difficulties, little is known about microbial communities associated with sinking marine snow in the twilight zone. A drifting sediment trap was equipped with a viscous cryogel and deployed to collect intact marine snow from depths of 100 and 400 m off Cape Blanc (Mauritania). Marine snow aggregates were fixed and washed in situ to prevent changes in microbial community composition and to enable subsequent analysis using catalyzed reporter deposition fluorescence in situ hybridization (CARD-FISH). The attached microbial communities collected at 100 m were similar to the free-living community at the depth of the fluorescence maximum (20 m) but different from those at other depths (150, 400, 550, and 700 m). Therefore, the attached microbial community seemed to be “inherited” from that at the fluorescence maximum. The attached microbial community structure at 400 m differed from that of the attached community at 100 m and from that of any free-living community at the tested depths, except that collected near the sediment at 700 m. The differences between the particle-associated communities at 400 m and 100 m appeared to be due to internal changes in the attached microbial community rather than de novo colonization, detachment, or grazing during the sinking of marine snow. The new sampling method presented here will facilitate future investigations into the mechanisms that shape the bacterial community within sinking marine snow, leading to better understanding of the mechanisms which regulate biogeochemical cycling of settling organic matter.
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Tahon G, Tytgat B, Stragier P, Willems A. Analysis of cbbL, nifH, and pufLM in Soils from the Sør Rondane Mountains, Antarctica, Reveals a Large Diversity of Autotrophic and Phototrophic Bacteria. MICROBIAL ECOLOGY 2016; 71:131-149. [PMID: 26582318 DOI: 10.1007/s00248-015-0704-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Accepted: 11/02/2015] [Indexed: 06/05/2023]
Abstract
Cyanobacteria are generally thought to be responsible for primary production and nitrogen fixation in the microbial communities that dominate Antarctic ecosystems. Recent studies of bacterial communities in terrestrial Antarctica, however, have shown that Cyanobacteria are sometimes only scarcely present, suggesting that other bacteria presumably take over their role as primary producers and diazotrophs. The diversity of key genes in these processes was studied in surface samples from the Sør Rondane Mountains, Dronning Maud Land, using clone libraries of the large subunit of ribulose-1,5-biphosphate carboxylase/oxygenase (RuBisCO) genes (cbbL, cbbM) and dinitrogenase-reductase (nifH) genes. We recovered a large diversity of non-cyanobacterial cbbL type IC in addition to cyanobacterial type IB, suggesting that non-cyanobacterial autotrophs may contribute to primary production. The nifH diversity recovered was predominantly related to Cyanobacteria, particularly members of the Nostocales. We also investigated the occurrence of proteorhodopsin and anoxygenic phototrophy as mechanisms for non-Cyanobacteria to exploit solar energy. While proteorhodopsin genes were not detected, a large diversity of genes coding for the light and medium subunits of the type 2 phototrophic reaction center (pufLM) was observed, suggesting for the first time, that the aerobic photoheterotrophic lifestyle may be important in oligotrophic high-altitude ice-free terrestrial Antarctic habitats.
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Affiliation(s)
- Guillaume Tahon
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K.L. Ledeganckstraat 35, 9000, Ghent, Belgium
| | - Bjorn Tytgat
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K.L. Ledeganckstraat 35, 9000, Ghent, Belgium
| | - Pieter Stragier
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K.L. Ledeganckstraat 35, 9000, Ghent, Belgium
| | - Anne Willems
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K.L. Ledeganckstraat 35, 9000, Ghent, Belgium.
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Boeuf D, Audic S, Brillet-Guéguen L, Caron C, Jeanthon C. MicRhoDE: a curated database for the analysis of microbial rhodopsin diversity and evolution. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2015; 2015:bav080. [PMID: 26286928 PMCID: PMC4539915 DOI: 10.1093/database/bav080] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Accepted: 07/25/2015] [Indexed: 11/12/2022]
Abstract
Microbial rhodopsins are a diverse group of photoactive transmembrane proteins found in all three domains of life and in viruses. Today, microbial rhodopsin research is a flourishing research field in which new understandings of rhodopsin diversity, function and evolution are contributing to broader microbiological and molecular knowledge. Here, we describe MicRhoDE, a comprehensive, high-quality and freely accessible database that facilitates analysis of the diversity and evolution of microbial rhodopsins. Rhodopsin sequences isolated from a vast array of marine and terrestrial environments were manually collected and curated. To each rhodopsin sequence are associated related metadata, including predicted spectral tuning of the protein, putative activity and function, taxonomy for sequences that can be linked to a 16S rRNA gene, sampling date and location, and supporting literature. The database currently covers 7857 aligned sequences from more than 450 environmental samples or organisms. Based on a robust phylogenetic analysis, we introduce an operational classification system with multiple phylogenetic levels ranging from superclusters to species-level operational taxonomic units. An integrated pipeline for online sequence alignment and phylogenetic tree construction is also provided. With a user-friendly interface and integrated online bioinformatics tools, this unique resource should be highly valuable for upcoming studies of the biogeography, diversity, distribution and evolution of microbial rhodopsins. Database URL: http://micrhode.sb-roscoff.fr.
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Affiliation(s)
- Dominique Boeuf
- CNRS, UMR 7144, Marine Phototrophic Prokaryotes Team, Sorbonne Universités, UPMC Univ Paris 06, UMR 7144, Oceanic Plankton Group
| | - Stéphane Audic
- Sorbonne Universités, UPMC Univ Paris 06, UMR 7144, Oceanic Plankton Group, CNRS, UMR 7144, Team Evolution des Protistes et Ecosystèmes Pélagiques and
| | | | - Christophe Caron
- CNRS, UPMC, FR2424, ABiMS, Station Biologique de Roscoff, F-29680 Roscoff, France
| | - Christian Jeanthon
- CNRS, UMR 7144, Marine Phototrophic Prokaryotes Team, Sorbonne Universités, UPMC Univ Paris 06, UMR 7144, Oceanic Plankton Group,
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Koblížek M. Ecology of aerobic anoxygenic phototrophs in aquatic environments. FEMS Microbiol Rev 2015; 39:854-70. [DOI: 10.1093/femsre/fuv032] [Citation(s) in RCA: 131] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/05/2015] [Indexed: 11/13/2022] Open
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48
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Fauteux L, Cottrell MT, Kirchman DL, Borrego CM, Garcia-Chaves MC, del Giorgio PA. Patterns in Abundance, Cell Size and Pigment Content of Aerobic Anoxygenic Phototrophic Bacteria along Environmental Gradients in Northern Lakes. PLoS One 2015; 10:e0124035. [PMID: 25927833 PMCID: PMC4415779 DOI: 10.1371/journal.pone.0124035] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Accepted: 03/10/2015] [Indexed: 11/19/2022] Open
Abstract
There is now evidence that aerobic anoxygenic phototrophic (AAP) bacteria are widespread across aquatic systems, yet the factors that determine their abundance and activity are still not well understood, particularly in freshwaters. Here we describe the patterns in AAP abundance, cell size and pigment content across wide environmental gradients in 43 temperate and boreal lakes of Québec. AAP bacterial abundance varied from 1.51 to 5.49 x 105 cells mL-1, representing <1 to 37% of total bacterial abundance. AAP bacteria were present year-round, including the ice-cover period, but their abundance relative to total bacterial abundance was significantly lower in winter than in summer (2.6% and 7.7%, respectively). AAP bacterial cells were on average two-fold larger than the average bacterial cell size, thus AAP cells made a greater relative contribution to biomass than to abundance. Bacteriochlorophyll a (BChla) concentration varied widely across lakes, and was not related to AAP bacterial abundance, suggesting a large intrinsic variability in the cellular pigment content. Absolute and relative AAP bacterial abundance increased with dissolved organic carbon (DOC), whereas cell-specific BChla content was negatively related to chlorophyll a (Chla). As a result, both the contribution of AAP bacteria to total prokaryotic abundance, and the cell-specific BChla pigment content were positively correlated with the DOC:Chla ratio, both peaking in highly colored, low-chlorophyll lakes. Our results suggest that photoheterotrophy might represent a significant ecological advantage in highly colored, low-chlorophyll lakes, where DOC pool is chemically and structurally more complex.
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Affiliation(s)
- Lisa Fauteux
- Groupe de Recherche Interuniversitaire en Limnologie (GRIL), Département des sciences biologiques, Université du Québec à Montréal, CP 8888, Montréal, Québec, Canada
| | - Matthew T. Cottrell
- School of Marine Science and Policy, University of Delaware, 700 Pilottown Rd., Lewes, DE 19958, United States of America
| | - David L. Kirchman
- School of Marine Science and Policy, University of Delaware, 700 Pilottown Rd., Lewes, DE 19958, United States of America
| | - Carles M. Borrego
- Group of Molecular Microbial Ecology, Institute of Aquatic Ecology, University of Girona, Campus de Montilivi, E-17071, Girona, Spain
| | - Maria Carolina Garcia-Chaves
- Groupe de Recherche Interuniversitaire en Limnologie (GRIL), Département des sciences biologiques, Université du Québec à Montréal, CP 8888, Montréal, Québec, Canada
| | - Paul A. del Giorgio
- Groupe de Recherche Interuniversitaire en Limnologie (GRIL), Département des sciences biologiques, Université du Québec à Montréal, CP 8888, Montréal, Québec, Canada
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Zhang F, He J, Lin L, Jin H. Dominance of picophytoplankton in the newly open surface water of the central Arctic Ocean. Polar Biol 2015. [DOI: 10.1007/s00300-015-1662-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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50
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Nguyen D, Maranger R, Balagué V, Coll-Lladó M, Lovejoy C, Pedrós-Alió C. Winter diversity and expression of proteorhodopsin genes in a polar ocean. ISME JOURNAL 2015; 9:1835-45. [PMID: 25700336 DOI: 10.1038/ismej.2015.1] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2014] [Revised: 12/09/2014] [Accepted: 12/12/2014] [Indexed: 12/25/2022]
Abstract
Mixotrophy is a valuable functional trait used by microbes when environmental conditions vary broadly or resources are limited. In the sunlit waters of the ocean, photoheterotrophy, a form of mixotrophy, is often mediated by proteorhodopsin (PR), a seven helices transmembrane protein binding the retinal chromophore. Altogether, they allow bacteria to capture photic energy for sensory and proton gradient formation cell functions. The seasonal occurrence and diversity of the gene coding for PR in cold oligotrophic polar oceans is not known and PR expression has not yet been reported. Here we show that PR is widely distributed among bacterial taxa, and that PR expression decreased markedly during the winter months in the Arctic Ocean. Gammaproteobacteria-like PR sequences were always dominant. However, within the second most common affiliation, there was a transition from Flavobacteria-like PR in early winter to Alphaproteobacteria-like PR in late winter. The phylogenetic shifts followed carbon dynamics, where patterns in expression were consistent with community succession, as identified by DNA community fingerprinting. Although genes for PR were always present, the trend in decreasing transcripts from January to February suggested reduced functional utility of PR during winter. Under winter darkness, sustained expression suggests that PR may continue to be useful for non-ATP forming functions, such as environmental sensing or small solute transport. The persistence of PR expression in winter among some bacterial groups may offer a competitive advantage, where its multifunctionality enhances microbial survival under harsh polar conditions.
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Affiliation(s)
- Dan Nguyen
- Groupe de Recherche Interuniversitaire en Limnologie et en Environnement Aquatique (GRIL), Département de sciences biologiques, Université de Montréal, Montréal, Québec, Canada
| | - Roxane Maranger
- Groupe de Recherche Interuniversitaire en Limnologie et en Environnement Aquatique (GRIL), Département de sciences biologiques, Université de Montréal, Montréal, Québec, Canada
| | - Vanessa Balagué
- Institut de Ciències del Mar, CSIC, Passeig Marítim de la Barceloneta, Barcelona, Spain
| | - Montserrat Coll-Lladó
- Institut de Ciències del Mar, CSIC, Passeig Marítim de la Barceloneta, Barcelona, Spain
| | - Connie Lovejoy
- Département de biologie, Québec-Océan, Institut de biologie intégrative et des systèmes (IBIS), Université Laval, Pavillon Charles-Eugène-Marchand, Québec, Québec, Canada
| | - Carlos Pedrós-Alió
- Institut de Ciències del Mar, CSIC, Passeig Marítim de la Barceloneta, Barcelona, Spain
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