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Park Y, Song B, Cha J, An S. Microbiome signature of different stages of hypoxia event in Wonmun Bay. MARINE ENVIRONMENTAL RESEARCH 2024; 202:106673. [PMID: 39216437 DOI: 10.1016/j.marenvres.2024.106673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 06/24/2024] [Accepted: 08/08/2024] [Indexed: 09/04/2024]
Abstract
We investigated how microbial communities associated with different hypoxic stages respond to environmental changes across three water depths in Wonmun Bay, South Korea. Analysis of temperature, salinity, dissolved oxygen (DO), and nutrient concentrations revealed prominent seasonal shifts and strong stratification during summer hypoxia. Metabarcoding of prokaryotic 16 S rRNA genes and phototrophic eukaryotic chloroplasts along with quantitative PCR (qPCR) revealed variations in the abundance and composition of these communities. Chloroplast 16 S sequences in May were dominated by land plants (93% of Embryophyta), contrasting with the diverse phytoplankton taxa detected in other months. The water communities in May also had higher total microbial abundance than other months but significantly lower alpha diversity. These results suggest a major influence of freshwater discharge on water communities, pre-conditioning for hypoxia events by promoting organic matter decomposition coupled with DO consumption in bottom water. Subsequently, distinct microbial communities were observed across depths during hypoxia in June and July, while less variability was detected among different depths in September and later months when hypoxia events disappeared. Principal Coordinate analysis (PCoA) demonstrated the distinct patterns of microbial communities in May, June, and July from other months. Both sulfur-oxidizing and sulfate-reducing bacteria (SRB) were prevalent in June while the increase of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) was observed in mid and bottom water in July. This data suggests the intricate interaction between sulfur and nitrogen-cycling microbes during the hypoxia events in Wonmun Bay. In conclusion, this study provides valuable insights into the microbial community responses to the varying environmental conditions at different stages of hypoxia events in eutrophic coastal ecosystems.
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Affiliation(s)
- Yunjung Park
- Research Institute for Basic Sciences, College of Natural Sciences, Pusan National University, Busan, 46241, Republic of Korea
| | - Bongkeun Song
- Virginia Institute of Marine Science, College of William and Mary, Gloucester Point, VA, 23062, United States
| | - Jaeho Cha
- Department of Microbiology, College of Natural Sciences, Pusan National University, Busan, 46241, Republic of Korea
| | - Soonmo An
- Department of Oceanography and Marine Research Institute, Pusan National University, Busan, 46241, Republic of Korea.
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2
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Bandekar M, More KD, Seleyi SC, Ramaiah N, Kekäläinen J, Akkanen J. Comparative analysis of microbiome inhabiting oxygenated and deoxygenated habitats using V3 and V6 metabarcoding of 16S rRNA gene. MARINE ENVIRONMENTAL RESEARCH 2024; 199:106615. [PMID: 38941665 DOI: 10.1016/j.marenvres.2024.106615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 06/04/2024] [Accepted: 06/17/2024] [Indexed: 06/30/2024]
Abstract
We examine how oxygen levels and the choice of 16S ribosomal RNA (rRNA) tags impact marine bacterial communities using Next-Generation amplicon sequencing. Analyzing V3 and V6 regions, we assess microbial composition in both Oxygen minimum zones (OMZ) and non-OMZ (NOMZ) areas in the Arabian Sea (AS) and the Central Indian Ocean basin (CIOB) respectively. Operational taxonomic units (OTUs) at 97% similarity showed slightly higher richness and diversity with V6 compared to V3. Vertical diversity patterns were consistent across both regions. NOMZ showed greater richness and diversity than OMZ. AS and CIOB exhibited significant differences in bacterial community, diversity, and relative abundance at the order and family levels. Alteromonadaceae dominated the OMZ, while Pelagibacteraceae dominated the NOMZ. Synechococcaceae were found exclusively at 250 m in OMZ. Bacteria putatively involved in nitrification, denitrification, and sulfurylation were detected at both sites. Dissolved oxygen significantly influenced microbial diversity at both sites, while seasonal environmental parameters affected diversity consistently, with no observed temporal variation.
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Affiliation(s)
- Mandar Bandekar
- Department of Environmental and Biological Sciences, University of Eastern Finland, Joensuu, Kuopio, Finland; Biological Oceanography Division, CSIR-National Institute of Oceanography, Dona Paula, Goa, 403004, India.
| | - Kuldeep D More
- Business Development Group, CSIR-National Institute of Oceanography, Dona Paula, Goa, 403004, India
| | - Seyieleno C Seleyi
- Marine Biotechnology Division, National Institute of Ocean Technology, Ministry of Earth Sciences, Chennai, India
| | - Nagappa Ramaiah
- Biological Oceanography Division, CSIR-National Institute of Oceanography, Dona Paula, Goa, 403004, India
| | - Jukka Kekäläinen
- Department of Environmental and Biological Sciences, University of Eastern Finland, Joensuu, Kuopio, Finland
| | - Jarkko Akkanen
- Department of Environmental and Biological Sciences, University of Eastern Finland, Joensuu, Kuopio, Finland
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3
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Crump BC, Bowen JL. The Microbial Ecology of Estuarine Ecosystems. ANNUAL REVIEW OF MARINE SCIENCE 2024; 16:335-360. [PMID: 37418833 DOI: 10.1146/annurev-marine-022123-101845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/09/2023]
Abstract
Human civilization relies on estuaries, and many estuarine ecosystem services are provided by microbial communities. These services include high rates of primary production that nourish harvests of commercially valuable species through fisheries and aquaculture, the transformation of terrestrial and anthropogenic materials to help ensure the water quality necessary to support recreation and tourism, and mutualisms that maintain blue carbon accumulation and storage. Research on the ecology that underlies microbial ecosystem services in estuaries has expanded greatly across a range of estuarine environments, including water, sediment, biofilms, biological reefs, and stands of seagrasses, marshes, and mangroves. Moreover, the application of new molecular tools has improved our understanding of the diversity and genomic functions of estuarine microbes. This review synthesizes recent research on microbial habitats in estuaries and the contributions of microbes to estuarine food webs, elemental cycling, and interactions with plants and animals, and highlights novel insights provided by recent advances in genomics.
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Affiliation(s)
- Byron C Crump
- College of Earth, Ocean, and Atmospheric Sciences, Oregon State University, Corvallis, Oregon, USA;
| | - Jennifer L Bowen
- Marine Science Center, Department of Marine and Environmental Sciences, Northeastern University, Nahant, Massachusetts, USA;
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4
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Cram JA, Hollins A, McCarty AJ, Martinez G, Cui M, Gomes ML, Fuchsman CA. Microbial diversity and abundance vary along salinity, oxygen, and particle size gradients in the Chesapeake Bay. Environ Microbiol 2024; 26:e16557. [PMID: 38173306 DOI: 10.1111/1462-2920.16557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 11/27/2023] [Indexed: 01/05/2024]
Abstract
Marine snow and other particles are abundant in estuaries, where they drive biogeochemical transformations and elemental transport. Particles range in size, thereby providing a corresponding gradient of habitats for marine microorganisms. We used standard normalized amplicon sequencing, verified with microscopy, to characterize taxon-specific microbial abundances, (cells per litre of water and per milligrams of particles), across six particle size classes, ranging from 0.2 to 500 μm, along the main stem of the Chesapeake Bay estuary. Microbial communities varied in salinity, oxygen concentrations, and particle size. Many taxonomic groups were most densely packed on large particles (in cells/mg particles), yet were primarily associated with the smallest particle size class, because small particles made up a substantially larger portion of total particle mass. However, organisms potentially involved in methanotrophy, nitrite oxidation, and sulphate reduction were found primarily on intermediately sized (5-180 μm) particles, where species richness was also highest. All abundant ostensibly free-living organisms, including SAR11 and Synecococcus, appeared on particles, albeit at lower abundance than in the free-living fraction, suggesting that aggregation processes may incorporate them into particles. Our approach opens the door to a more quantitative understanding of the microscale and macroscale biogeography of marine microorganisms.
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Affiliation(s)
- Jacob A Cram
- Horn Point Laboratory, University of Maryland Center for Environmental Science, Cambridge, Maryland, USA
| | - Ashley Hollins
- Horn Point Laboratory, University of Maryland Center for Environmental Science, Cambridge, Maryland, USA
| | - Alexandra J McCarty
- Horn Point Laboratory, University of Maryland Center for Environmental Science, Cambridge, Maryland, USA
- Marine Advisory Program, Virginia Institute of Marine Science, Gloucester, Virginia, USA
| | | | - Minming Cui
- Earth and Planetary Sciences, Johns Hopkins University, Baltimore, Maryland, USA
| | - Maya L Gomes
- Earth and Planetary Sciences, Johns Hopkins University, Baltimore, Maryland, USA
| | - Clara A Fuchsman
- Horn Point Laboratory, University of Maryland Center for Environmental Science, Cambridge, Maryland, USA
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Pu H, Yuan Y, Qin L, Liu X. pH Drives Differences in Bacterial Community β-Diversity in Hydrologically Connected Lake Sediments. Microorganisms 2023; 11:microorganisms11030676. [PMID: 36985249 PMCID: PMC10056738 DOI: 10.3390/microorganisms11030676] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 02/25/2023] [Accepted: 02/28/2023] [Indexed: 03/09/2023] Open
Abstract
As microorganisms are very sensitive to changes in the lake environment, a comprehensive and systematic understanding of the structure and diversity of lake sediment microbial communities can provide feedback on sediment status and lake ecosystem protection. Xiao Xingkai Lake (XXL) and Xingkai Lake (XL) are two neighboring lakes hydrologically connected by a gate and dam, with extensive agricultural practices and other human activities existing in the surrounding area. In view of this, we selected XXL and XL as the study area and divided the area into three regions (XXLR, XXLD, and XLD) according to different hydrological conditions. We investigated the physicochemical properties of surface sediments in different regions and the structure and diversity of bacterial communities using high-throughput sequencing. The results showed that various nutrients (nitrogen, phosphorus) and carbon (DOC, LOC, TC) were significantly enriched in the XXLD region. Proteobacteria, Firmicutes, and Bacteroidetes were the dominant bacterial phyla in the sediments, accounting for more than 60% of the entire community in all regions. Non-metric multidimensional scaling analysis and analysis of similarities confirmed that β-diversity varied among different regions. In addition, the assembly of bacterial communities was dominated by a heterogeneous selection in different regions, indicating the important influence of sediment environmental factors on the community. Among these sediment properties, the partial least squares path analysis revealed that pH was the best predictor variable driving differences in bacterial communities in different regions, with higher pH reducing beta diversity among communities. Overall, our study focused on the structure and diversity of bacterial communities in lake sediments of the Xingkai Lake basin and revealed that high pH causes the β-diversity of bacterial communities in the sediment to decrease. This provides a reference for further studies on sediment microorganisms in the Xingkai Lake basin in the future.
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Affiliation(s)
- Haiguang Pu
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
- University of Chinese Academy of Sciences, Beijing 101408, China
| | - Yuxiang Yuan
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
| | - Lei Qin
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
| | - Xiaohui Liu
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
- University of Chinese Academy of Sciences, Beijing 101408, China
- Correspondence:
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6
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Wang Y, Li X, Chi Y, Song W, Yan Q, Huang J. Changes of the Freshwater Microbial Community Structure and Assembly Processes during Different Sample Storage Conditions. Microorganisms 2022; 10:1176. [PMID: 35744694 PMCID: PMC9229623 DOI: 10.3390/microorganisms10061176] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Revised: 06/02/2022] [Accepted: 06/06/2022] [Indexed: 12/04/2022] Open
Abstract
A long-standing dilemma for microbial analyses is how to handle and store samples, as it is widely assumed that the microbial diversity and community patterns would be affected by sample storage conditions. However, it is quite challenging to maintain consistency in field sampling, especially for water sample collection and storage. To obtain a comprehensive understanding of how sample storage conditions impact microbial community analyses and the magnitude of the potential storage effects, freshwater samples were collected and stored in bottles with lid closed and without lid at room temperature for up to 6 days. We revealed the dynamics of prokaryotic and eukaryotic microbial communities under different storage conditions over time. The eukaryotic microbial communities changed at a faster rate than the prokaryotic microbial communities during storage. The alpha diversity of the eukaryotic microbial communities was not substantially influenced by container status or storage time for up to 12 h, but the beta diversity differed significantly between the control and all treatment samples. By contrast, no significant changes of either the alpha or beta diversity of the prokaryotic microbial communities were observed within 12 h of room-temperature storage, regardless of the container status. The potential interactions between microbial taxa were more complex when samples were stored in sealed bottles, and the deterministic processes played an increasingly important role in shaping the freshwater microbial communities with storage time. Our results suggest that water samples collected and stored without refrigeration for no more than 12 h may still be useful for downstream analyses of prokaryotic microbial communities. If the eukaryotic microbial communities are desired, storage of water samples should be limited to 3 h at room temperature.
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Affiliation(s)
- Yunfeng Wang
- Institute of Evolution & Marine Biodiversity, College of Fisheries, Ocean University of China, Qingdao 266003, China; (Y.W.); (Y.C.); (W.S.)
- Donghu Experimental Station of Lake Ecosystems, Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Xinghao Li
- Key Laboratory of Regional Development and Environmental Response, Hubei Engineering Research Center for Rural Drinking Water Security, Hubei University, Wuhan 430062, China;
| | - Yong Chi
- Institute of Evolution & Marine Biodiversity, College of Fisheries, Ocean University of China, Qingdao 266003, China; (Y.W.); (Y.C.); (W.S.)
- Donghu Experimental Station of Lake Ecosystems, Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Weibo Song
- Institute of Evolution & Marine Biodiversity, College of Fisheries, Ocean University of China, Qingdao 266003, China; (Y.W.); (Y.C.); (W.S.)
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Qingyun Yan
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China;
| | - Jie Huang
- Donghu Experimental Station of Lake Ecosystems, Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
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7
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Arora-Williams K, Holder C, Secor M, Ellis H, Xia M, Gnanadesikan A, Preheim SP. Abundant and persistent sulfur-oxidizing microbial populations are responsive to hypoxia in the Chesapeake Bay. Environ Microbiol 2022; 24:2315-2332. [PMID: 35304940 PMCID: PMC9310604 DOI: 10.1111/1462-2920.15976] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 03/07/2022] [Accepted: 03/12/2022] [Indexed: 01/04/2023]
Abstract
The number, size and severity of aquatic low‐oxygen dead zones are increasing worldwide. Microbial processes in low‐oxygen environments have important ecosystem‐level consequences, such as denitrification, greenhouse gas production and acidification. To identify key microbial processes occurring in low‐oxygen bottom waters of the Chesapeake Bay, we sequenced both 16S rRNA genes and shotgun metagenomic libraries to determine the identity, functional potential and spatiotemporal distribution of microbial populations in the water column. Unsupervised clustering algorithms grouped samples into three clusters using water chemistry or microbial communities, with extensive overlap of cluster composition between methods. Clusters were strongly differentiated by temperature, salinity and oxygen. Sulfur‐oxidizing microorganisms were found to be enriched in the low‐oxygen bottom water and predictive of hypoxic conditions. Metagenome‐assembled genomes demonstrate that some of these sulfur‐oxidizing populations are capable of partial denitrification and transcriptionally active in a prior study. These results suggest that microorganisms capable of oxidizing reduced sulfur compounds are a previously unidentified microbial indicator of low oxygen in the Chesapeake Bay and reveal ties between the sulfur, nitrogen and oxygen cycles that could be important to capture when predicting the ecosystem response to remediation efforts or climate change.
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Affiliation(s)
- Keith Arora-Williams
- Department of Environmental Health and Engineering, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA
| | - Christopher Holder
- Department of Earth and Planetary Sciences, 3400 N. Charles Street, Baltimore, MD 21218, USA
| | - Maeve Secor
- Department of Environmental Health and Engineering, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA
| | - Hugh Ellis
- Department of Environmental Health and Engineering, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA
| | - Meng Xia
- Department of Natural Sciences, University of Maryland Eastern Shore, Princess Anne, MD 21853, USA
| | - Anand Gnanadesikan
- Department of Earth and Planetary Sciences, 3400 N. Charles Street, Baltimore, MD 21218, USA
| | - Sarah P Preheim
- Department of Environmental Health and Engineering, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA
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Dynamics and Distribution of Marine Synechococcus Abundance and Genotypes during Seasonal Hypoxia in a Coastal Marine Ranch. JOURNAL OF MARINE SCIENCE AND ENGINEERING 2021. [DOI: 10.3390/jmse9050549] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Marine Synechococcus are an ecologically important picocyanobacterial group widely distributed in various oceanic environments. Little is known about the dynamics and distribution of Synechococcus abundance and genotypes during seasonal hypoxia in coastal zones. In this study, an investigation was conducted in a coastal marine ranch along two transects in Muping, Yantai, where hypoxic events (defined here as the dissolved oxygen concentration <3 mg L−1) occurred in the summer of 2015. The hypoxia occurred in the bottom waters from late July and persisted until late August. It was confined at nearshore stations of the two transects, one running across a coastal ranch and the other one outside. During this survey, cell abundance of Synechococcus was determined with flow cytometry, showing great variations ranging from 1 × 104 to 3.0 × 105 cells mL−1, and a bloom of Synechococcus occurred when stratification disappeared and hypoxia faded out outside the ranch. Regression analysis indicated that dissolved oxygen, pH, and inorganic nutrients were the most important abiotic factors in explaining the variation in Synechococcus cell abundance. Diverse genotypes (mostly belonged to the sub-clusters 5.1 and 5.2) were detected using clone library sequencing and terminal restriction fragment length polymorphism analysis of the 16S–23S rRNA internal transcribed spacer region. The richness of genotypes was significantly related to salinity, temperature, silicate, and pH, but not dissolved oxygen. Two environmental factors, temperature and salinity, collectively explained 17% of the variation in Synechococcus genotype assemblage. With the changes in population composition in diverse genotypes, the Synechococcus assemblages survived in the coastal hypoxia event and thrived when hypoxia faded out.
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9
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Wang W, Yi Y, Yang Y, Zhou Y, Jia W, Zhang S, Wang X, Yang Z. Response mechanisms of sediment microbial communities in different habitat types in a shallow lake. Ecosphere 2019. [DOI: 10.1002/ecs2.2948] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Wenjun Wang
- State Key Laboratory of Water Environment Simulation Beijing Normal University Beijing 100875 China
| | - Yujun Yi
- State Key Laboratory of Water Environment Simulation Beijing Normal University Beijing 100875 China
- School of Environment Ministry of Education Key Laboratory of Water and Sediment Science Beijing Normal University Beijing 100875 China
| | - Yufeng Yang
- State Key Laboratory of Water Environment Simulation Beijing Normal University Beijing 100875 China
| | - Yang Zhou
- State Key Laboratory of Water Environment Simulation Beijing Normal University Beijing 100875 China
| | - Wenfei Jia
- State Key Laboratory of Water Environment Simulation Beijing Normal University Beijing 100875 China
| | - Shanghong Zhang
- Renewable Energy School North China Electric Power University Beijing 102206 China
| | - Xuan Wang
- State Key Laboratory of Water Environment Simulation Beijing Normal University Beijing 100875 China
| | - Zhifeng Yang
- State Key Laboratory of Water Environment Simulation Beijing Normal University Beijing 100875 China
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Čanković M, Žučko J, Radić ID, Janeković I, Petrić I, Ciglenečki I, Collins G. Microbial diversity and long-term geochemical trends in the euxinic zone of a marine, meromictic lake. Syst Appl Microbiol 2019; 42:126016. [PMID: 31635887 DOI: 10.1016/j.syapm.2019.126016] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 08/30/2019] [Accepted: 09/07/2019] [Indexed: 01/04/2023]
Abstract
Hypoxic and anoxic niches of meromictic lakes are important sites for studying the microbial ecology of conditions resembling ancient Earth. The expansion and increasing global distribution of such environments also means that information about them serves to understand future phenomena. In this study, a long-term chemical dataset (1996-2015) was explored together with seasonal (in 2015) information on the diversity and abundance of bacterial and archaeal communities residing in the chemocline, monimolimnion and surface sediment of the marine meromictic Rogoznica Lake. The results of quantitative PCR assays, and high-throughput sequencing, targeting 16S rRNA genes and transcripts, revealed a clear vertical structure of the microbial community with Gammaproteobacteria (Halochromatium) and cyanobacteria (Synechococcus spp.) dominating the chemocline, Deltaproteobacteria and Bacteroidetes dominating the monimolimnion, and significantly more abundant archaeal populations in the surface sediment, most of which affiliated to Nanoarchaeota. Seasonal changes in the community structure and abundance were not pronounced. Diversity in Rogoznica Lake was found to be high, presumably as a consequence of stable environmental conditions accompanied by high dissolved carbon and nutrient concentrations. Long-term data indicated that Rogoznica Lake exhibited climate changes that could alter its physico-chemical features and, consequently, induce structural and physiological changes within its microbial community.
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Affiliation(s)
- Milan Čanković
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Bijenička cesta 54, 10 000 Zagreb, Croatia.
| | - Jurica Žučko
- Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10 000 Zagreb, Croatia
| | - Iris Dupčić Radić
- Institute for Marine and Coastal Research, University of Dubrovnik, Ul. kneza Damjana Jude 12, 20 000, Dubrovnik, Croatia
| | - Ivica Janeković
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Bijenička cesta 54, 10 000 Zagreb, Croatia
| | - Ines Petrić
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Bijenička cesta 54, 10 000 Zagreb, Croatia
| | - Irena Ciglenečki
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Bijenička cesta 54, 10 000 Zagreb, Croatia
| | - Gavin Collins
- Microbial Communities Laboratory, Microbiology, School of Natural Sciences, National University of Ireland Galway, University Road, Galway, H91 TK33, Ireland
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11
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Superville PJ, Ivanovsky A, Bhurtun P, Prygiel J, Billon G. Diel cycles of reduced manganese and their seasonal variability in the Marque River (northern France). THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 624:918-925. [PMID: 29275254 DOI: 10.1016/j.scitotenv.2017.12.189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 12/12/2017] [Accepted: 12/17/2017] [Indexed: 06/07/2023]
Abstract
Electrolabile reduced manganese (II) has been monitored by voltammetry during two periods of one month in summer 2014 and at the end of winter 2015 in a small river (the Marque River) located in northern France and going through a suburban area with agricultural activities. Diel variations, evolution within the one-month periods and seasonal differences have been observed. Taking into consideration the multiple physical, biological and chemical reactions regulating manganese speciation in aquatic systems, it has been demonstrated that manganese speciation is probably controlled by the competition of two antagonist reactions: the photoreduction of manganese oxides (in broad sense and represented thereafter by MnOx) and the biotic oxidation of Mn(II). Depending on the season, the biological activity in the river and the amount of luminosity reaching the MnOx, either the production of reduced labile Mn(II) or the precipitation of MnOx can become the dominant process. Other punctual events such as the drop of oxygen concentration due to large inputs of biodegradable organic matter and eutrophication phenomena, rainy events and high luminosity periods can also affect the behaviour of dissolved Mn(II) in the Marque River and so, of other contaminants.
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Affiliation(s)
- Pierre-Jean Superville
- LASIR CNRS UMR 8516, Université de Lille, Sciences et Technologies, 59655 Villeneuve d'Ascq Cedex, France.
| | - Anastasia Ivanovsky
- LASIR CNRS UMR 8516, Université de Lille, Sciences et Technologies, 59655 Villeneuve d'Ascq Cedex, France
| | - Pratima Bhurtun
- LASIR CNRS UMR 8516, Université de Lille, Sciences et Technologies, 59655 Villeneuve d'Ascq Cedex, France
| | - Jean Prygiel
- LASIR CNRS UMR 8516, Université de Lille, Sciences et Technologies, 59655 Villeneuve d'Ascq Cedex, France; Agence de l'Eau Artois-Picardie, 200 rue Marceline, 59500 Douai, France
| | - Gabriel Billon
- LASIR CNRS UMR 8516, Université de Lille, Sciences et Technologies, 59655 Villeneuve d'Ascq Cedex, France
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12
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Mori F, Umezawa Y, Kondo R, Wada M. Effects of bottom-water hypoxia on sediment bacterial community composition in a seasonally hypoxic enclosed bay (Omura Bay, West Kyushu, Japan). FEMS Microbiol Ecol 2018; 94:4951600. [DOI: 10.1093/femsec/fiy053] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 03/21/2018] [Indexed: 11/13/2022] Open
Affiliation(s)
- Fumiaki Mori
- Graduate School of Fisheries and Environmental Sciences, Nagasaki University, Bunkyo 1-14, Nagasaki, Nagasaki 852-8521, Japan
| | - Yu Umezawa
- Graduate School of Fisheries and Environmental Sciences, Nagasaki University, Bunkyo 1-14, Nagasaki, Nagasaki 852-8521, Japan
- Department of Environmental Science on Biosphere, Tokyo University of Agriculture and Technology, Tokyo 183-8509, Japan
| | - Ryuji Kondo
- Department of Marine Science and Technology, Fukui Prefectural University, Fukui 917-0003, Japan
| | - Minoru Wada
- Graduate School of Fisheries and Environmental Sciences, Nagasaki University, Bunkyo 1-14, Nagasaki, Nagasaki 852-8521, Japan
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13
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Pavloudi C, Kristoffersen JB, Oulas A, De Troch M, Arvanitidis C. Sediment microbial taxonomic and functional diversity in a natural salinity gradient challenge Remane's "species minimum" concept. PeerJ 2017; 5:e3687. [PMID: 29043106 PMCID: PMC5642246 DOI: 10.7717/peerj.3687] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 07/24/2017] [Indexed: 12/31/2022] Open
Abstract
Several models have been developed for the description of diversity in estuaries and other brackish habitats, with the most recognized being Remane’s Artenminimum (“species minimum”) concept. It was developed for the Baltic Sea, one of the world’s largest semi-enclosed brackish water body with a unique permanent salinity gradient, and it argues that taxonomic diversity of macrobenthic organisms is lowest within the horohalinicum (5 to 8 psu). The aim of the present study was to investigate the relationship between salinity and sediment microbial diversity at a freshwater-marine transect in Amvrakikos Gulf (Ionian Sea, Western Greece) and assess whether species composition and community function follow a generalized concept such as Remane’s. DNA was extracted from sediment samples from six stations along the aforementioned transect and sequenced for the 16S rRNA gene using high-throughput sequencing. The metabolic functions of the OTUs were predicted and the most abundant metabolic pathways were extracted. Key abiotic variables, i.e., salinity, temperature, chlorophyll-a and oxygen concentration etc., were measured and their relation with diversity and functional patterns was explored. Microbial communities were found to differ in the three habitats examined (river, lagoon and sea) with certain taxonomic groups being more abundant in the freshwater and less in the marine environment, and vice versa. Salinity was the environmental factor with the highest correlation to the microbial community pattern, while oxygen concentration was highly correlated to the metabolic functional pattern. The total number of OTUs showed a negative relationship with increasing salinity, thus the sediment microbial OTUs in this study area do not follow Remane’s concept.
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Affiliation(s)
- Christina Pavloudi
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR), Heraklion, Crete, Greece.,Marine Biology Research Group, Department of Biology, Faculty of Sciences, Ghent University, Ghent, Belgium.,Microbial Ecophysiology Group, Faculty of Biology/Chemistry and MARUM, University of Bremen, Bremen, Germany
| | - Jon B Kristoffersen
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR), Heraklion, Crete, Greece
| | - Anastasis Oulas
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR), Heraklion, Crete, Greece.,Bioinformatics Group, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Marleen De Troch
- Marine Biology Research Group, Department of Biology, Faculty of Sciences, Ghent University, Ghent, Belgium
| | - Christos Arvanitidis
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR), Heraklion, Crete, Greece
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14
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Weinke AD, Biddanda BA. From Bacteria to Fish: Ecological Consequences of Seasonal Hypoxia in a Great Lakes Estuary. Ecosystems 2017. [DOI: 10.1007/s10021-017-0160-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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15
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Thiele S, Richter M, Balestra C, Glöckner FO, Casotti R. Taxonomic and functional diversity of a coastal planktonic bacterial community in a river-influenced marine area. Mar Genomics 2017; 32:61-69. [DOI: 10.1016/j.margen.2016.12.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Revised: 12/22/2016] [Accepted: 12/28/2016] [Indexed: 01/19/2023]
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16
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Liu S, Wawrik B, Liu Z. Different Bacterial Communities Involved in Peptide Decomposition between Normoxic and Hypoxic Coastal Waters. Front Microbiol 2017; 8:353. [PMID: 28326069 PMCID: PMC5339267 DOI: 10.3389/fmicb.2017.00353] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Accepted: 02/20/2017] [Indexed: 11/13/2022] Open
Abstract
Proteins and peptides are key components of the labile dissolved organic matter pool in marine environments. Knowing which types of bacteria metabolize peptides can inform the factors that govern peptide decomposition and further carbon and nitrogen remineralization in marine environments. A 13C-labeled tetrapeptide, alanine-valine-phenylalanine-alanine (AVFA), was added to both surface (normoxic) and bottom (hypoxic) seawater from a coastal station in the northern Gulf of Mexico for a 2-day incubation experiment, and bacteria that incorporated the peptide were identified using DNA stable isotope probing (SIP). The decomposition rate of AVFA in the bottom hypoxic seawater (0.018–0.035 μM h-1) was twice as fast as that in the surface normoxic seawater (0.011–0.017 μM h-1). SIP experiments indicated that incorporation of 13C was highest among the Flavobacteria, Sphingobacteria, Alphaproteobacteria, Acidimicrobiia, Verrucomicrobiae, Cyanobacteria, and Actinobacteria in surface waters. In contrast, highest 13C-enrichment was mainly observed in several Alphaproteobacteria (Thalassococcus, Rhodobacteraceae, Ruegeria) and Gammaproteobacteria genera (Colwellia, Balneatrix, Thalassomonas) in the bottom water. These data suggest that a more diverse group of both oligotrophic and copiotrophic bacteria may be involved in metabolizing labile organic matter such as peptides in normoxic coastal waters, and several copiotrophic genera belonging to Alphaproteobacteria and Gammaproteobacteria and known to be widely distributed may contribute to faster peptide decomposition in the hypoxic waters.
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Affiliation(s)
- Shuting Liu
- Marine Science Institute, The University of Texas at Austin, Port Aransas TX, USA
| | - Boris Wawrik
- Department of Microbiology and Plant Biology, The University of Oklahoma, Norman OK, USA
| | - Zhanfei Liu
- Marine Science Institute, The University of Texas at Austin, Port Aransas TX, USA
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17
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Aylagas E, Borja Á, Tangherlini M, Dell'Anno A, Corinaldesi C, Michell CT, Irigoien X, Danovaro R, Rodríguez-Ezpeleta N. A bacterial community-based index to assess the ecological status of estuarine and coastal environments. MARINE POLLUTION BULLETIN 2017; 114:679-688. [PMID: 27784536 DOI: 10.1016/j.marpolbul.2016.10.050] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Revised: 10/18/2016] [Accepted: 10/18/2016] [Indexed: 05/27/2023]
Abstract
Biotic indices for monitoring marine ecosystems are mostly based on the analysis of benthic macroinvertebrate communities. Due to their high sensitivity to pollution and fast response to environmental changes, bacterial assemblages could complement the information provided by benthic metazoan communities as indicators of human-induced impacts, but so far, this biological component has not been well explored for this purpose. Here we performed 16S rRNA gene amplicon sequencing to analyze the bacterial assemblage composition of 51 estuarine and coastal stations characterized by different environmental conditions and human-derived pressures. Using the relative abundance of putative indicator bacterial taxa, we developed a biotic index that is significantly correlated with a sediment quality index calculated on the basis of organic and inorganic compound concentrations. This new index based on bacterial assemblage composition can be a sensitive tool for providing a fast environmental assessment and allow a more comprehensive integrative ecosystem approach for environmental management.
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Affiliation(s)
- Eva Aylagas
- AZTI - Marine Research, Herrera Kaia, Portualdea z/g - 20110 Pasaia, Gipuzkoa, Spain.
| | - Ángel Borja
- AZTI - Marine Research, Herrera Kaia, Portualdea z/g - 20110 Pasaia, Gipuzkoa, Spain.
| | - Michael Tangherlini
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Antonio Dell'Anno
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Cinzia Corinaldesi
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Craig T Michell
- Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Xabier Irigoien
- AZTI - Marine Research, Herrera Kaia, Portualdea z/g - 20110 Pasaia, Gipuzkoa, Spain; Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia; IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
| | - Roberto Danovaro
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
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18
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Frindte K, Allgaier M, Grossart HP, Eckert W. Redox stability regulates community structure of active microbes at the sediment-water interface. ENVIRONMENTAL MICROBIOLOGY REPORTS 2016; 8:798-804. [PMID: 27402503 DOI: 10.1111/1758-2229.12441] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Revised: 12/02/2015] [Indexed: 06/06/2023]
Abstract
Changes in redox conditions occur in a wide range of microbial habitats, in particular at the sediment-water interface (SWI) of aquatic systems. A mesocosm study using intact sediment cores from Lake Stechlin (Germany) was performed to investigate the impact of redox changes on microbial communities at the SWI. The SWI was exposed to permanent oxic (OX) or anoxic (ANOX) or to variable (VR) redox conditions, and for molecular analysis sediment samples were taken at the start and after seven days of the treatment. We performed 16S rRNA amplicon sequencing to identify redox-specific changes in the composition of metabolically active microbes. Generally, the community of active microbes in the VR cores was similar to in the OX cores, but differed significantly from the ANOX cores. Interestingly, VR conditions resulted in a high fraction of a Crenothrix-like microorganism increasing in read abundance from 4 to 5% initially, up to 69% over the experimental period. This implies that periodic redox fluctuations select for specific bacteria in environments such as seiches-affected sediments of stratified lakes. In Lake Stechlin sediment cores, these redox fluctuations lead to increased activities of specific microorganisms and high organic matter turnover rates with profound implications for aquatic organic matter cycling.
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Affiliation(s)
- Katharina Frindte
- Institute of Crop Science and Resource Conservation, Molecular Biology of the Rhizosphere, Bonn University, Nussallee 13, Bonn, 53115, Germany
| | - Martin Allgaier
- Berlin Center for Genomics in Biodiversity Research (BeGenDiv), Königin-Luise-Straße 6-8, Berlin, 14195, Germany
| | - Hans-Peter Grossart
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Alte Fischerhuette 2, Stechlin, 16775, Germany
- Institute of Biochemistry and Biology, Potsdam University, Am Neuen Palais 10, Potsdam, 14469, Germany
| | - Werner Eckert
- The Yigal Allon Kinneret Limnological Laboratory, Israel Oceanographic and Limnological Research, Migdal, 14950, Israel
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19
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Field EK, Kato S, Findlay AJ, MacDonald DJ, Chiu BK, Luther GW, Chan CS. Planktonic marine iron oxidizers drive iron mineralization under low-oxygen conditions. GEOBIOLOGY 2016; 14:499-508. [PMID: 27384464 DOI: 10.1111/gbi.12189] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 04/25/2016] [Indexed: 06/06/2023]
Abstract
Observations of modern microbes have led to several hypotheses on how microbes precipitated the extensive iron formations in the geologic record, but we have yet to resolve the exact microbial contributions. An initial hypothesis was that cyanobacteria produced oxygen which oxidized iron abiotically; however, in modern environments such as microbial mats, where Fe(II) and O2 coexist, we commonly find microaerophilic chemolithotrophic iron-oxidizing bacteria producing Fe(III) oxyhydroxides. This suggests that such iron oxidizers could have inhabited niches in ancient coastal oceans where Fe(II) and O2 coexisted, and therefore contributed to banded iron formations (BIFs) and other ferruginous deposits. However, there is currently little evidence for planktonic marine iron oxidizers in modern analogs. Here, we demonstrate successful cultivation of planktonic microaerophilic iron-oxidizing Zetaproteobacteria from the Chesapeake Bay during seasonal stratification. Iron oxidizers were associated with low oxygen concentrations and active iron redox cycling in the oxic-anoxic transition zone (<3 μm O2 , <0.2 μm H2 S). While cyanobacteria were also detected in this transition zone, oxygen concentrations were too low to support significant rates of abiotic iron oxidation. Cyanobacteria may be providing oxygen for microaerophilic iron oxidation through a symbiotic relationship; at high Fe(II) levels, cyanobacteria would gain protection against Fe(II) toxicity. A Zetaproteobacteria isolate from this site oxidized iron at rates sufficient to account for deposition of geologic iron formations. In sum, our results suggest that once oxygenic photosynthesis evolved, microaerophilic chemolithotrophic iron oxidizers were likely important drivers of iron mineralization in ancient oceans.
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Affiliation(s)
- E K Field
- Department of Geological Sciences, University of Delaware, Newark, DE, USA
| | - S Kato
- Department of Geological Sciences, University of Delaware, Newark, DE, USA
| | - A J Findlay
- School of Marine Science and Policy, University of Delaware, Newark, Lewes, DE, USA
| | - D J MacDonald
- School of Marine Science and Policy, University of Delaware, Newark, Lewes, DE, USA
| | - B K Chiu
- Department of Geological Sciences, University of Delaware, Newark, DE, USA
| | - G W Luther
- School of Marine Science and Policy, University of Delaware, Newark, Lewes, DE, USA
| | - C S Chan
- Department of Geological Sciences, University of Delaware, Newark, DE, USA
- School of Marine Science and Policy, University of Delaware, Newark, Lewes, DE, USA
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20
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Obi CC, Adebusoye SA, Ugoji EO, Ilori MO, Amund OO, Hickey WJ. Microbial Communities in Sediments of Lagos Lagoon, Nigeria: Elucidation of Community Structure and Potential Impacts of Contamination by Municipal and Industrial Wastes. Front Microbiol 2016; 7:1213. [PMID: 27547200 PMCID: PMC4974257 DOI: 10.3389/fmicb.2016.01213] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 07/21/2016] [Indexed: 01/13/2023] Open
Abstract
Estuarine sediments are significant repositories of anthropogenic contaminants, and thus knowledge of the impacts of pollution upon microbial communities in these environments is important to understand potential effects on estuaries as a whole. The Lagos lagoon (Nigeria) is one of Africa’s largest estuarine ecosystems, and is impacted by hydrocarbon pollutants and other industrial and municipal wastes. The goal of this study was to elucidate microbial community structure in Lagos lagoon sediments to identify groups that may be adversely affected by pollution, and those that may serve as degraders of environmental contaminants, especially polycyclic aromatic hydrocarbons (PAHs). Sediment samples were collected from sites that ranged in types and levels of anthropogenic impacts. The sediments were characterized for a range of physicochemical properties, and microbial community structure was determined by Illumina sequencing of the 16S rRNA genes. Microbial diversity (species richness and evenness) in the Apapa and Eledu sediments was reduced compared to that of the Ofin site, and communities of both of the former two were dominated by a single operational taxonomic unit (OTU) assigned to the family Helicobacteraceae (Epsilonproteobacteria). In the Ofin community, Epsilonproteobacteria were minor constituents, while the major groups were Cyanobacteria, Bacteroidetes, and Firmicutes, which were all minor in the Apapa and Eledu sediments. Sediment oxygen demand (SOD), a broad indicator of contamination, was identified by multivariate analyses as strongly correlated with variation in alpha diversity. Environmental variables that explained beta diversity patterns included SOD, as well as levels of naphthalene, acenaphthylene, cobalt, cadmium, total organic matter, or nitrate. Of 582 OTU identified, abundance of 167 was significantly correlated (false discovery rate q≤ 0.05) to environmental variables. The largest group of OTU correlated with PAH levels were PAH/hydrocarbon-degrading genera of the Oceanospirillales order (Gammaproteobacteria), which were most abundant in the hydrocarbon-contaminated Apapa sediment. Similar Oceanospirillales taxa are responsive to marine oil spills and thus may present a unifying theme in marine microbiology as bacteria adapted for degradation of high hydrocarbon loads, and may represent a potential means for intrinsic remediation in the case of the Lagos lagoon sediments.
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Affiliation(s)
- Chioma C Obi
- Department of Microbiology, University of LagosLagos, Nigeria; O.N. Allen Laboratory for Soil Microbiology, Department of Soil Science, University of Wisconsin-Madison, MadisonWI, USA
| | | | - Esther O Ugoji
- Department of Microbiology, University of Lagos Lagos, Nigeria
| | - Mathew O Ilori
- Department of Microbiology, University of Lagos Lagos, Nigeria
| | | | - William J Hickey
- O.N. Allen Laboratory for Soil Microbiology, Department of Soil Science, University of Wisconsin-Madison, Madison WI, USA
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21
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Laas P, Šatova E, Lips I, Lips U, Simm J, Kisand V, Metsis M. Near-Bottom Hypoxia Impacts Dynamics of Bacterioplankton Assemblage throughout Water Column of the Gulf of Finland (Baltic Sea). PLoS One 2016; 11:e0156147. [PMID: 27213812 PMCID: PMC4877108 DOI: 10.1371/journal.pone.0156147] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Accepted: 05/10/2016] [Indexed: 11/19/2022] Open
Abstract
Over the past century the spread of hypoxia in the Baltic Sea has been drastic, reaching its ‘arm’ into the easternmost sub-basin, the Gulf of Finland. The hydrographic and climatological properties of the gulf offer a broad suite of discrete niches for microbial communities. The current study explores spatiotemporal dynamics of bacterioplankton community in the Gulf of Finland using massively parallel sequencing of 16S rRNA fragments obtained by amplifying community DNA from spring to autumn period. The presence of redoxcline and drastic seasonal changes make spatiotemporal dynamics of bacterioplankton community composition (BCC) and abundances in such estuary remarkably complex. To the best of our knowledge, this is the first study that analyses spatiotemporal dynamics of BCC in relation to phytoplankton bloom throughout the water column (and redoxcline), not only at the surface layer. We conclude that capability to survive (or benefit from) shifts between oxic and hypoxic conditions is vital adaptation for bacteria to thrive in such environments. Our results contribute to the understanding of emerging patterns in BCCs that occupy hydrographically similar estuaries dispersed all over the world, and we suggest the presence of a global redox- and salinity-driven metacommunity. These results have important implications for understanding long-term ecological and biogeochemical impacts of hypoxia expansion in the Baltic Sea (and similar ecosystems), as well as global biogeography of bacteria specialized inhabiting similar ecosystems.
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Affiliation(s)
- Peeter Laas
- Marine Systems Institute at Tallinn University of Technology, Akadeemia Rd. 15A, 12618, Tallinn, Estonia
- * E-mail:
| | - Elina Šatova
- Department of Gene Technology, Tallinn University of Technology, Akadeemia tee 15, 12618, Tallinn, Estonia
| | - Inga Lips
- Marine Systems Institute at Tallinn University of Technology, Akadeemia Rd. 15A, 12618, Tallinn, Estonia
| | - Urmas Lips
- Marine Systems Institute at Tallinn University of Technology, Akadeemia Rd. 15A, 12618, Tallinn, Estonia
| | - Jaak Simm
- Department of Gene Technology, Tallinn University of Technology, Akadeemia tee 15, 12618, Tallinn, Estonia
| | - Veljo Kisand
- Institute of Technology at University of Tartu, Nooruse 1, 50411, Tartu, Estonia
| | - Madis Metsis
- Institute of Mathematics and Natural Sciences, Tallinn University, Narva Rd. 25, 10120, Tallinn, Estonia
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22
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Jeffries TC, Schmitz Fontes ML, Harrison DP, Van-Dongen-Vogels V, Eyre BD, Ralph PJ, Seymour JR. Bacterioplankton Dynamics within a Large Anthropogenically Impacted Urban Estuary. Front Microbiol 2016; 6:1438. [PMID: 26858690 PMCID: PMC4726783 DOI: 10.3389/fmicb.2015.01438] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 12/02/2015] [Indexed: 02/01/2023] Open
Abstract
The abundant and diverse microorganisms that inhabit aquatic systems are both determinants and indicators of aquatic health, providing essential ecosystem services such as nutrient cycling but also causing harmful blooms and disease in impacted habitats. Estuaries are among the most urbanized coastal ecosystems and as a consequence experience substantial environmental pressures, providing ideal systems to study the influence of anthropogenic inputs on microbial ecology. Here we use the highly urbanized Sydney Harbor, Australia, as a model system to investigate shifts in microbial community composition and function along natural and anthopogenic physicochemical gradients, driven by stormwater inflows, tidal flushing and the input of contaminants and both naturally and anthropogenically derived nutrients. Using a combination of amplicon sequencing of the 16S rRNA gene and shotgun metagenomics, we observed strong patterns in microbial biogeography across the estuary during two periods: one of high and another of low rainfall. These patterns were driven by shifts in nutrient concentration and dissolved oxygen leading to a partitioning of microbial community composition in different areas of the harbor with different nutrient regimes. Patterns in bacterial composition were related to shifts in the abundance of Rhodobacteraceae, Flavobacteriaceae, Microbacteriaceae, Halomonadaceae, Acidomicrobiales, and Synechococcus, coupled to an enrichment of total microbial metabolic pathways including phosphorus and nitrogen metabolism, sulfate reduction, virulence, and the degradation of hydrocarbons. Additionally, community beta-diversity was partitioned between the two sampling periods. This potentially reflected the influence of shifting allochtonous nutrient inputs on microbial communities and highlighted the temporally dynamic nature of the system. Combined, our results provide insights into the simultaneous influence of natural and anthropogenic drivers on the structure and function of microbial communities within a highly urbanized aquatic ecosystem.
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Affiliation(s)
- Thomas C. Jeffries
- Plant Functional Biology and Climate Change Cluster, University of Technology SydneySydney, NSW, Australia
- Hawkesbury Institute for the Environment, Western Sydney UniversityPenrith, NSW, Australia
| | - Maria L. Schmitz Fontes
- Plant Functional Biology and Climate Change Cluster, University of Technology SydneySydney, NSW, Australia
| | - Daniel P. Harrison
- School of Geosciences, University of Sydney Institute of Marine Science, The University of SydneySydney, NSW, Australia
- Sydney Institute of Marine ScienceMosman, NSW, Australia
| | - Virginie Van-Dongen-Vogels
- Plant Functional Biology and Climate Change Cluster, University of Technology SydneySydney, NSW, Australia
| | - Bradley D. Eyre
- Centre for Coastal Management, Southern Cross UniversityLismore, NSW, Australia
| | - Peter J. Ralph
- Plant Functional Biology and Climate Change Cluster, University of Technology SydneySydney, NSW, Australia
| | - Justin R. Seymour
- Plant Functional Biology and Climate Change Cluster, University of Technology SydneySydney, NSW, Australia
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23
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Frindte K, Allgaier M, Grossart HP, Eckert W. Microbial Response to Experimentally Controlled Redox Transitions at the Sediment Water Interface. PLoS One 2015; 10:e0143428. [PMID: 26599000 PMCID: PMC4657962 DOI: 10.1371/journal.pone.0143428] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 11/04/2015] [Indexed: 11/29/2022] Open
Abstract
The sediment–water interface of freshwater lakes is characterized by sharp chemical gradients, shaped by the interplay between physical, chemical and microbial processes. As dissolved oxygen is depleted in the uppermost sediment, the availability of alternative electron acceptors, e.g. nitrate and sulfate, becomes the limiting factor. We performed a time series experiment in a mesocosm to simulate the transition from aerobic to anaerobic conditions at the sediment–water interface. Our goal was to identify changes in the microbial activity due to redox transitions induced by successive depletion of available electron acceptors. Monitoring critical hydrochemical parameters in the overlying water in conjunction with a new sampling strategy for sediment bacteria enabled us to correlate redox changes in the water to shifts in the active microbial community and the expression of functional genes representing specific redox-dependent microbial processes. Our results show that during several transitions from oxic-heterotrophic condition to sulfate-reducing condition, nitrate-availability and the on-set of sulfate reduction strongly affected the corresponding functional gene expression. There was evidence of anaerobic methane oxidation with NOx. DGGE analysis revealed redox-related changes in microbial activity and expression of functional genes involved in sulfate and nitrite reduction, whereas methanogenesis and methanotrophy showed only minor changes during redox transitions. The combination of high-frequency chemical measurements and molecular methods provide new insights into the temporal dynamics of the interplay between microbial activity and specific redox transitions at the sediment–water interface.
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Affiliation(s)
- Katharina Frindte
- Department of Soil Science, Institute for Crop Science and Resource Conservation (INRES), University of Bonn, Nußallee 13, Bonn, Germany
| | - Martin Allgaier
- Berlin Center for Genomics in Biodiversity Research (BeGenDiv), Königin-Luise-Straße 6-8, Berlin, Germany
| | - Hans-Peter Grossart
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Alte Fischerhütte 2, Stechlin, Germany
- Institute of Biochemistry and Biology, University of Potsdam, Am Neuen Palais 10, Potsdam, Germany
| | - Werner Eckert
- Israel Oceanographic and Limnological Research, The Yigal Allon Kinneret Limnological Laboratory, Migdal, Israel
- * E-mail:
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Light-dependent sulfide oxidation in the anoxic zone of the Chesapeake Bay can be explained by small populations of phototrophic bacteria. Appl Environ Microbiol 2015; 81:7560-9. [PMID: 26296727 DOI: 10.1128/aem.02062-15] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Accepted: 08/17/2015] [Indexed: 11/20/2022] Open
Abstract
Microbial sulfide oxidation in aquatic environments is an important ecosystem process, as sulfide is potently toxic to aerobic organisms. Sulfide oxidation in anoxic waters can prevent the efflux of sulfide to aerobic water masses, thus mitigating toxicity. The contribution of phototrophic sulfide-oxidizing bacteria to anaerobic sulfide oxidation in the Chesapeake Bay and the redox chemistry of the stratified water column were investigated in the summers of 2011 to 2014. In 2011 and 2013, phototrophic sulfide-oxidizing bacteria closely related to Prosthecochloris species of the phylum Chlorobi were cultivated from waters sampled at and below the oxic-anoxic interface, where measured light penetration was sufficient to support populations of low-light-adapted photosynthetic bacteria. In 2012, 2013, and 2014, light-dependent sulfide loss was observed in freshly collected water column samples. In these samples, extremely low light levels caused 2- to 10-fold increases in the sulfide uptake rate over the sulfide uptake rate under dark conditions. An enrichment, CB11, dominated by Prosthecochloris species, oxidized sulfide with a Ks value of 11 μM and a Vmax value of 51 μM min(-1) (mg protein(-1)). Using these kinetic values with in situ sulfide concentrations and light fluxes, we calculated that a small population of Chlorobi similar to those in enrichment CB11 can account for the observed anaerobic light-dependent sulfide consumption activity in natural water samples. We conclude that Chlorobi play a far larger role in the Chesapeake Bay than currently appreciated. This result has potential implications for coastal anoxic waters and expanding oxygen-minimum zones as they begin to impinge on the photic zone.
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25
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Laas P, Simm J, Lips I, Lips U, Kisand V, Metsis M. Redox-specialized bacterioplankton metacommunity in a temperate estuary. PLoS One 2015; 10:e0122304. [PMID: 25860812 PMCID: PMC4393233 DOI: 10.1371/journal.pone.0122304] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Accepted: 02/19/2015] [Indexed: 11/30/2022] Open
Abstract
This study explored the spatiotemporal dynamics of the bacterioplankton community composition in the Gulf of Finland (easternmost sub-basin of the Baltic Sea) based on phylogenetic analysis of 16S rDNA sequences acquired from community samples via pyrosequencing. Investigations of bacterioplankton in hydrographically complex systems provide good insight into the strategies by which microbes deal with spatiotemporal hydrographic gradients, as demonstrated by our research. Many ribotypes were closely affiliated with sequences isolated from environments with similar steep physiochemical gradients and/or seasonal changes, including seasonally anoxic estuaries. Hence, one of the main conclusions of this study is that marine ecosystems where oxygen and salinity gradients co-occur can be considered a habitat for a cosmopolitan metacommunity consisting of specialized groups occupying niches universal to such environments throughout the world. These niches revolve around functional capabilities to utilize different electron receptors and donors (including trace metal and single carbon compounds). On the other hand, temporal shifts in the bacterioplankton community composition at the surface layer were mainly connected to the seasonal succession of phytoplankton and the inflow of freshwater species. We also conclude that many relatively abundant populations are indigenous and well-established in the area.
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Affiliation(s)
- Peeter Laas
- Marine Systems Institute at Tallinn University of Technology, Tallinn, Estonia
- * E-mail:
| | - Jaak Simm
- Department of Electrical Engineering (ESAT), STADIUS Center for Dynamical Systems, Signal Processing, and Data Analytics, KU Leuven, Leuven, Belgium
- iMinds Medical IT, Leuven, Belgium
- Department of Gene Technology, Tallinn University of Technology, Tallinn, Estonia
| | - Inga Lips
- Marine Systems Institute at Tallinn University of Technology, Tallinn, Estonia
| | - Urmas Lips
- Marine Systems Institute at Tallinn University of Technology, Tallinn, Estonia
| | - Veljo Kisand
- Institute of Technology at University of Tartu, Tartu, Estonia
| | - Madis Metsis
- Institute of Mathematics and Natural Sciences, Tallinn University, Tallinn, Estonia
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Liu J, Fu B, Yang H, Zhao M, He B, Zhang XH. Phylogenetic shifts of bacterioplankton community composition along the Pearl Estuary: the potential impact of hypoxia and nutrients. Front Microbiol 2015; 6:64. [PMID: 25713564 PMCID: PMC4322608 DOI: 10.3389/fmicb.2015.00064] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2014] [Accepted: 01/18/2015] [Indexed: 02/03/2023] Open
Abstract
The significance of salinity in shaping bacterial communities dwelling in estuarine areas has been well documented. However, the influences of other environmental factors such as dissolved oxygen and nutrients in determining distribution patterns of both individual taxa and bacterial communities inhabited local estuarine regions remain elusive. Here, bacterioplankton community structures of surface and bottom waters from eight sites along the Pearl Estuary were characterized with 16S rRNA gene pyrosequencing. The results showed significant differences of bacterioplankton community between freshwater and saltwater sites, and further between surface and bottom waters of saltwater sites. Synechococcus dominated the surface water of saltwater sites while Oceanospirillales, SAR11 and SAR406 were prevalent in the bottom water. Betaproteobacteria was abundant in freshwater sites, with no significant difference between water layers. Occurrence of phylogenetic shifts in taxa affiliated to the same clade was also detected. Dissolved oxygen explained most of the bacterial community variation in the redundancy analysis targeting only freshwater sites, whereas nutrients and salinity explained most of the variation across all samples in the Pearl Estuary. Methylophilales (mainly PE2 clade) was positively correlated to dissolved oxygen, whereas Rhodocyclales (mainly R.12up clade) was negatively correlated. Moreover, high nutrient inputs to the freshwater area of the Pearl Estuary have shifted the bacterial communities toward copiotrophic groups, such as Sphingomonadales. The present study demonstrated that the overall nutrients and freshwater hypoxia play important roles in determining bacterioplankton compositions and provided insights into the potential ecological roles of specific taxa in estuarine environments.
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Affiliation(s)
- Jiwen Liu
- College of Marine Life Sciences, Ocean University of China Qingdao, China
| | - Bingbing Fu
- College of Marine Life Sciences, Ocean University of China Qingdao, China
| | - Hongmei Yang
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China Qingdao, China
| | - Meixun Zhao
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China Qingdao, China
| | - Biyan He
- State Key Laboratory of Marine Environmental Science, Xiamen University Xiamen, China ; School of Bioengineering, Jimei University Xiamen, China
| | - Xiao-Hua Zhang
- College of Marine Life Sciences, Ocean University of China Qingdao, China
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Eggleston EM, Lee DY, Owens MS, Cornwell JC, Crump BC, Hewson I. Key respiratory genes elucidate bacterial community respiration in a seasonally anoxic estuary. Environ Microbiol 2015; 17:2306-18. [DOI: 10.1111/1462-2920.12690] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Accepted: 09/03/2014] [Indexed: 11/29/2022]
Affiliation(s)
| | - Dong Y. Lee
- Horn Point Laboratory; University of Maryland Center for Environmental Science; Cambridge MD USA
| | - Michael S. Owens
- Horn Point Laboratory; University of Maryland Center for Environmental Science; Cambridge MD USA
| | - Jeffrey C. Cornwell
- Horn Point Laboratory; University of Maryland Center for Environmental Science; Cambridge MD USA
| | - Byron C. Crump
- College of Earth, Ocean and Atmospheric Sciences; Oregon State University; Corvallis OR USA
| | - Ian Hewson
- Department of Microbiology; Cornell University; Ithaca NY USA
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Parsons RJ, Nelson CE, Carlson CA, Denman CC, Andersson AJ, Kledzik AL, Vergin KL, McNally SP, Treusch AH, Giovannoni SJ. Marine bacterioplankton community turnover within seasonally hypoxic waters of a subtropical sound: Devil's Hole, Bermuda. Environ Microbiol 2014; 17:3481-99. [DOI: 10.1111/1462-2920.12445] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Accepted: 02/23/2014] [Indexed: 12/22/2022]
Affiliation(s)
- Rachel J. Parsons
- Bermuda Institute for Ocean Science (BIOS); St. George's GE 01 Bermuda
| | - Craig E. Nelson
- Department of Ecology, Evolution and Marine Biology; Marine Science Institute; University of California; Santa Barbara CA USA
- Center for Microbial Oceanography: Research and Education; Department of Oceanography; University of Hawai‘i at Mānoa; Honolulu HI USA
| | - Craig A. Carlson
- Bermuda Institute for Ocean Science (BIOS); St. George's GE 01 Bermuda
- Department of Ecology, Evolution and Marine Biology; Marine Science Institute; University of California; Santa Barbara CA USA
| | - Carmen C. Denman
- Department of Microbiology; Oregon State University; Corvallis OR USA
- London School of Hygiene and Tropical Medicine; London UK
| | - Andreas J. Andersson
- Bermuda Institute for Ocean Science (BIOS); St. George's GE 01 Bermuda
- Scripps Institution of Oceanography; University of California San Diego; San Diego CA USA
| | - Andrew L. Kledzik
- Department of Marine and Environmental Systems; Florida Institute of Technology; Melbourne FL USA
| | - Kevin L. Vergin
- Department of Microbiology; Oregon State University; Corvallis OR USA
| | - Sean P. McNally
- Bermuda Institute for Ocean Science (BIOS); St. George's GE 01 Bermuda
- College of the Environment and Life Sciences; The University of Rhode Island; Kingston RI USA
| | - Alexander H. Treusch
- Department of Microbiology; Oregon State University; Corvallis OR USA
- Department of Biology; Nordic Centre for Earth Evolution; University of Southern Denmark; Odense Denmark
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Metatranscriptomic analyses of plankton communities inhabiting surface and subpycnocline waters of the Chesapeake Bay during oxic-anoxic-oxic transitions. Appl Environ Microbiol 2013; 80:328-38. [PMID: 24162577 DOI: 10.1128/aem.02680-13] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
We used metatranscriptomics to study the gene transcription patterns of microbial plankton (0.2 to 64 μm) at a mesohaline station in the Chesapeake Bay under transitions from oxic to anoxic waters in spring and from anoxic to oxic waters in autumn. Samples were collected from surface (i.e., above pycnocline) waters (3 m) and from waters beneath the pycnocline (16 to 22 m) in both 2010 and 2011. Metatranscriptome profiles based on function and potential phylogeny were different between 2010 and 2011 and strongly variable in 2011. This difference in variability corresponded with a highly variable ratio of eukaryotic to bacterial sequences (0.3 to 5.5), reflecting transient algal blooms in 2011 that were absent in 2010. The similarity between metatranscriptomes changed at a lower rate during the transition from oxic to anoxic waters than after the return to oxic conditions. Transcripts related to photosynthesis and low-affinity cytochrome oxidases were significantly higher in shallow than in deep waters, while in deep water genes involved in anaerobic metabolism, particularly sulfate reduction, succinyl coenzyme A (succinyl-CoA)-to-propionyl-CoA conversion, and menaquinone synthesis, were enriched relative to in shallow waters. Expected transitions in metabolism between oxic and anoxic deep waters were reflected in elevated levels of anaerobic respiratory reductases and utilization of propenediol and acetoin. The percentage of archaeal transcripts increased in both years in late summer (from 0.1 to 4.4% of all transcripts in 2010 and from 0.1 to 6.2% in 2011). Denitrification-related genes were expressed in a predicted pattern during the oxic-anoxic transition. Overall, our data suggest that Chesapeake Bay microbial assemblages express gene suites differently in shallow and deep waters and that differences in deep waters reflect variable redox states.
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They NH, Ferreira LMH, Marins LF, Abreu PC. Stability of bacterial composition and activity in different salinity waters in the dynamic Patos Lagoon estuary: evidence from a lagrangian-like approach. MICROBIAL ECOLOGY 2013; 66:551-562. [PMID: 23812105 DOI: 10.1007/s00248-013-0259-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2012] [Accepted: 06/14/2013] [Indexed: 06/02/2023]
Abstract
We employed a Lagrangian-like sampling design to evaluate bacterial community composition (BCC--using temporal temperature gel gradient electrophoresis), community-level physiological profiles (CLPP--using the EcoPlate™ assay), and influencing factors in different salinity waters in the highly dynamic Patos Lagoon estuary (southern Brazil) and adjacent coastal zone. Samples were collected monthly by following limnetic-oligohaline (0-1), mesohaline (14-16), and polyhaline (28-31) waters for 1 year. The BCC was specific for each salinity range, whereas the CLPPs were similar for mesohaline and polyhaline waters, and both were different from the limnetic-oligohaline samples. The limnetic-oligohaline waters displayed an oxidation capacity for almost all organic substrates tested, whereas the mesohaline and polyhaline waters presented lower numbers of oxidized substrates, suggesting that potential activities of bacteria increased from the polyhaline to oligohaline waters. However, the polyhaline samples showed a higher utilization of some simple carbohydrates, amino acids, and polymers, indicating a shortage of inorganic nutrients (especially nitrogen) and organic substrates in coastal saltwater. The hypothesis of bacterial nitrogen limitation was corroborated by the higher Nuse index (an EcoPlate™-based nitrogen limitation indicator) in the polyhaline waters and the importance of NO(2)(-), NO(3)(-), low-molecular-weight substances, and the low-molecular-weight:high-molecular-weight substances ratio, indicated by the canonical correspondence analyses (CCAs). Our results demonstrate the important stability of microbial community composition and potential metabolic activity in the different water salinity ranges, which are independent of the region and time of the year of sample collection in the estuary. This is a quite unexpected result for a dynamic environment such as the Patos Lagoon estuary.
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Affiliation(s)
- Ng Haig They
- Post-graduation Program in Biological Oceanography, Institute of Oceanography, Federal University of Rio Grande (FURG), Av. Itália km 08, 96203-900, Rio Grande, RS, Brazil,
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Zdanowski MK, Żmuda-Baranowska MJ, Borsuk P, Świątecki A, Górniak D, Wolicka D, Jankowska KM, Grzesiak J. Culturable bacteria community development in postglacial soils of Ecology Glacier, King George Island, Antarctica. Polar Biol 2012. [DOI: 10.1007/s00300-012-1278-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Simister R, Taylor MW, Tsai P, Webster N. Sponge-microbe associations survive high nutrients and temperatures. PLoS One 2012; 7:e52220. [PMID: 23284943 PMCID: PMC3527390 DOI: 10.1371/journal.pone.0052220] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2012] [Accepted: 11/12/2012] [Indexed: 11/18/2022] Open
Abstract
Coral reefs are under considerable pressure from global stressors such as elevated sea surface temperature and ocean acidification, as well as local factors including eutrophication and poor water quality. Marine sponges are diverse, abundant and ecologically important components of coral reefs in both coastal and offshore environments. Due to their exceptionally high filtration rates, sponges also form a crucial coupling point between benthic and pelagic habitats. Sponges harbor extensive microbial communities, with many microbial phylotypes found exclusively in sponges and thought to contribute to the health and survival of their hosts. Manipulative experiments were undertaken to ascertain the impact of elevated nutrients and seawater temperature on health and microbial community dynamics in the Great Barrier Reef sponge Rhopaloeides odorabile. R. odorabile exposed to elevated nutrient levels including 10 µmol/L total nitrogen at 31°C appeared visually similar to those maintained under ambient seawater conditions after 7 days. The symbiotic microbial community, analyzed by 16S rRNA gene pyrotag sequencing, was highly conserved for the duration of the experiment at both phylum and operational taxonomic unit (OTU) (97% sequence similarity) levels with 19 bacterial phyla and 1743 OTUs identified across all samples. Additionally, elevated nutrients and temperatures did not alter the archaeal associations in R. odorabile, with sequencing of 16S rRNA gene libraries revealing similar Thaumarchaeota diversity and denaturing gradient gel electrophoresis (DGGE) revealing consistent amoA gene patterns, across all experimental treatments. A conserved eukaryotic community was also identified across all nutrient and temperature treatments by DGGE. The highly stable microbial associations indicate that R. odorabile symbionts are capable of withstanding short-term exposure to elevated nutrient concentrations and sub-lethal temperatures.
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Affiliation(s)
- Rachel Simister
- Centre for Microbial Innovation, The University of Auckland, Auckland, New Zealand
| | - Michael W. Taylor
- Centre for Microbial Innovation, The University of Auckland, Auckland, New Zealand
| | - Peter Tsai
- Bioinformatics Institute, School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Nicole Webster
- Australian Institute of Marine Science, Townsville Mail Centre, Qld 4810, Australia
- * E-mail:
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Fontes MLS, Abreu PC. A vigorous specialized microbial food web in the suboxic waters of a shallow subtropical coastal lagoon. MICROBIAL ECOLOGY 2012; 64:334-345. [PMID: 22450511 DOI: 10.1007/s00248-012-0040-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2011] [Accepted: 03/03/2012] [Indexed: 05/31/2023]
Abstract
To examine the extent of the microbial food web in suboxic waters of a shallow subtropical coastal lagoon, the density and biomass of bacteria and protozooplankton were quantified under different dissolved oxygen (DO) levels. In addition, bottom waters of a stratified site were compared with bottom waters of a homogeneous site under periods of high and low biological oxygen production/consumption in the lagoon. At the stratified site, microbial biomass decreased with oxygen decline, from oxia to suboxia, with a recovery of the initial total biomass after a 20-day period of persistent suboxia. A peak in density and biomass of purple sulfur bacteria (PSB) (90 μg C L(-1)) occurred in the suboxic waters 20 days prior to the peak in biomass of ciliates >50 μm (Loxophyllum sp. of 150 μm) (160 μg C L(-1)), demonstrating a top down biomass control. Ciliates >50 μm were positively correlated with PSB and bacteriochlorophyll a (photosynthetic pigment of PSB). Total protozoan biomass reached 430 μg C L(-1) in the suboxic waters of the stratified site, with ciliates >50 μm accounting for 90% of the total ciliate biomass and of 55 % of biomass of protozoa. At the homogeneous site, total protozoan biomass was only 66 μg C L(-1), where flagellates and ciliates <25 μm were the dominant microorganisms. Therefore, as light is available for primary producers in the bottom waters of shallow stratified coastal lagoons or estuaries, one can expect that high primary production of PSB may favor a specialized microbial food web composed by larger microorganisms, accessible to zooplankton that tolerate low DO levels.
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Affiliation(s)
- Maria Luiza S Fontes
- Institute of Oceanography, Federal University of Rio Grande, Av. Itália km 8, Campus Carreiros, Rio Grande, Rio Grande do Sul, Brazil.
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Rapid resonance Raman microspectroscopy to probe carbon dioxide fixation by single cells in microbial communities. ISME JOURNAL 2011; 6:875-85. [PMID: 22113377 DOI: 10.1038/ismej.2011.150] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Photosynthetic microorganisms play crucial roles in aquatic ecosystems and are the major primary producers in global marine ecosystems. The discovery of new bacteria and microalgae that play key roles in CO(2) fixation is hampered by the lack of methods to identify hitherto-unculturable microorganisms. To overcome this problem we studied single microbial cells using stable-isotope probing (SIP) together with resonance Raman (RR) microspectroscopy of carotenoids, the light-absorbing pigments present in most photosynthetic microorganisms. We show that fixation of (13)CO(2) into carotenoids produces a red shift in single-cell RR (SCRR) spectra and that this SCRR-SIP technique is sufficiently sensitive to detect as little as 10% of (13)C incorporation. Mass spectrometry (MS) analysis of labelled cellular proteins verifies that the red shift in carotenoid SCRR spectra acts as a reporter of the (13)C content of single cells. Millisecond Raman imaging of cells in mixed cultures and natural seawater samples was used to identify cells actively fixing CO(2), demonstrating that the SCRR-SIP is a noninvasive method for the rapid and quantitative detection of CO(2) fixation at the single cell level in a microbial community. The SCRR-SIP technique may provide a direct method for screening environmental samples, and could help to reveal the ecophysiology of hitherto-unculturable microorganisms, linking microbial species to their ecological function in the natural environment.
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Fortunato CS, Crump BC. Bacterioplankton community variation across river to ocean environmental gradients. MICROBIAL ECOLOGY 2011; 62:374-382. [PMID: 21286702 DOI: 10.1007/s00248-011-9805-z] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2010] [Accepted: 01/12/2011] [Indexed: 05/30/2023]
Abstract
Coastal zones encompass a complex spectrum of environmental gradients that each impact the composition of bacterioplankton communities. Few studies have attempted to address these gradients comprehensively. We generated a synoptic, 16S rRNA gene-based bacterioplankton community profile of a coastal zone by applying the fingerprinting technique denaturing gradient gel electrophoresis to water samples collected from the Columbia River, estuary, and plume, and along coastal transects covering 360 km of the Oregon and Washington coasts and extending to the deep ocean (>2,000 m). Communities were found to cluster into five distinct groups based on location in the system (ANOSIM, p < 0.003): estuary, plume, epipelagic, shelf bottom (depth < 150 m), and slope bottom (depth > 650 m). Across all environments, abiotic factors (salinity, temperature, depth) explained most of the community variability (ρ = 0.734). But within each coastal environment, biotic factors explained most of the variability. Thus, structuring physical factors in coastal zones, such as salinity and temperature, define the boundaries of many distinct microbial habitats, but within these habitats variability in microbial communities is explained by biological gradients in primary and secondary productivity.
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Affiliation(s)
- Caroline S Fortunato
- Horn Point Laboratory, University of Maryland Center for Environmental Science, Cambridge, MD, USA.
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Repeating patterns of virioplankton production within an estuarine ecosystem. Proc Natl Acad Sci U S A 2011; 108:11506-11. [PMID: 21709214 DOI: 10.1073/pnas.1101907108] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The Chesapeake Bay, a seasonally variable temperate estuary, provides a natural laboratory for examining the fluctuations and impacts of viral lysis on aquatic microorganisms. Viral abundance (VA) and viral production (VP) were monitored in the Chesapeake Bay over 4 1/2 annual cycles, producing a unique, long-term, interannual study of virioplankton production. High and dynamic VP rates, averaging 7.9 × 10(6) viruses per mL per h, indicate that viral lysis impacts a significant fraction of microorganisms in the Chesapeake. Viral-mediated bacterial mortality, VA, VP, and organic carbon release all displayed similar interannual and seasonal trends with higher values in 2003 and 2006 than in 2004 and 2005 and peaks in early spring and summer. Surprisingly, higher rates of viral lysis occurred in winter, resulting in a magnified effect of viral lysis on bacterioplankton during times of reduced productivity. Viral lysis directly impacted the organic carbon pool, contributing on average 76 μg of C per L per d, an amount capable of sustaining ∼55% of Chesapeake Bay bacterial production. The observed repeating interannual patterns of VP and lysis are likely interlinked with seasonal cycles of host abundance and diversity, which are in turn driven by annual cycles in environmental conditions, emphasizing the complex interplay of seasonality and microbial ecology in the Chesapeake Bay.
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Berdjeb L, Ghiglione JF, Domaizon I, Jacquet S. A 2-year assessment of the main environmental factors driving the free-living bacterial community structure in Lake Bourget (France). MICROBIAL ECOLOGY 2011; 61:941-954. [PMID: 21082178 DOI: 10.1007/s00248-010-9767-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2010] [Accepted: 10/21/2010] [Indexed: 05/30/2023]
Abstract
Despite the considerable attention that has been paid to bacterioplankton over recent decades, the dynamic of aquatic bacterial community structure is still poorly understood, and long-term studies are particularly lacking. Moreover, how the environment governs diversity patterns remains a key issue in aquatic microbial ecology. In this study, we used denaturing gradient gel electrophoresis of PCR-amplified partial 16S rRNA gene fragments and multivariable statistical approaches to explore the patterns of change in the free-living bacterial community in the mesotrophic and mono-meromictic Lake Bourget (France). A monthly sampling was conducted over two consecutive years (2007 and 2008) and at two different depths characterizing the epi- and hypolimnion of the lake (2 and 50 m, respectively). Temporal shifts in the bacterial community structure followed different patterns according to depth, and no seasonal reproducibility was recorded from 1 year to the next. Our results showed that the bacterial community structure displayed lower diversity at 2 m (22 bands) compared to 50 m (32 bands) and that bacterial community structure dynamics followed dissimilar trends between the two depths. At 2 m, five shifts in the bacterial community structure occurred, with the temporal scale varying between 2 and 8 months whereas, at 50 m, four shifts in the bacterial community structure took place at 50 m, with the temporal scale fluctuating between 3 and 13 months. More than 60% of the bacterial community structure variance was explained by seven variables at 2 m against eight at 50 m. Nutrients (PO(4)-P, NH(4)-N and NO(3)-N) and temperature were responsible for 49.6% of the variance at 2 m whereas these nutrients, with dissolved oxygen and chlorophyll a accounting for 59.6% of the variance at 50 m. Grazing by ciliates played also a critical role on the bacterial community structure at both depths. Our results suggest that the free-living bacterial community structure in the epi- and hypolimnion of Lake Bourget is mainly driven by combined, but differently weighted, top-down and bottom-up factors at 2 and 50 m.
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Affiliation(s)
- Lyria Berdjeb
- INRA, UMR CARRTEL, 75 avenue de Corzent, 74200, Thonon-les-Bains, France
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Nogales B, Lanfranconi MP, Piña-Villalonga JM, Bosch R. Anthropogenic perturbations in marine microbial communities. FEMS Microbiol Rev 2011; 35:275-98. [DOI: 10.1111/j.1574-6976.2010.00248.x] [Citation(s) in RCA: 229] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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Aaen KN, Holm PE, Priemé A, Hung NN, Brandt KK. Comparison of aerobic and anaerobic [3H]leucine incorporation assays for determining pollution-induced bacterial community tolerance in copper-polluted, irrigated soils. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY 2011; 30:588-595. [PMID: 21298704 DOI: 10.1002/etc.420] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2010] [Revised: 08/12/2010] [Accepted: 10/04/2010] [Indexed: 05/30/2023]
Abstract
Pollution-induced community tolerance (PICT) constitutes a sensitive and ecologically relevant impact parameter in ecotoxicology. We report the development and application of a novel anaerobic [(3) H]leucine incorporation assay and its comparison with the conventional aerobic [(3) H]leucine incorporation assay for PICT detection in soil bacterial communities. Selection of bacterial communities was performed over 42 d in bulk soil microcosms (no plants) and in rice (Oryza sativa) rhizosphere soil mesocosms. The following experimental treatments were imposed using a full factorial design: two soil types, two soil water regimes, and four Cu application rates (0, 30, 120, or 280 µg g(-1)). Bacterial communities in bulk soil microcosms exhibited similar Cu tolerance patterns when assessed by aerobic and anaerobic PICT assays, whereas aerobic microorganisms tended to be more strongly selected for Cu tolerance than anaerobic microorganisms in rhizosphere soil. Despite similar levels of water-extractable Cu, bacterial Cu tolerance was significantly higher in acid sulfate soil than in alluvial soil. Copper amendment selected for significant PICT development in soils subjected to alternate wetting and drying, but not in continuously flooded soils. Our results demonstrate that soil bacterial communities subjected to alternate wetting and drying may be more affected by Cu than bacterial communities subjected to continuous flooding. We conclude that the parallel use of anaerobic and aerobic [(3) H]leucine PICT assays constitutes a valuable improvement over existing procedures for PICT detection in irrigated soils and other redox gradient environments such as sediments and wetlands.
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Affiliation(s)
- Karoline Nolsø Aaen
- Department of Agriculture and Ecology, University of Copenhagen, Frederiksberg, Denmark
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Fontes MLS, Suzuki MT, Cottrell MT, Abreu PC. Primary production in a subtropical stratified coastal lagoon--contribution of anoxygenic phototrophic bacteria. MICROBIAL ECOLOGY 2011; 61:223-237. [PMID: 20809289 DOI: 10.1007/s00248-010-9739-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2010] [Accepted: 08/08/2010] [Indexed: 05/29/2023]
Abstract
Anaerobic anoxygenic phototrophic bacteria can be found in the suboxic waters of shallow stratified coastal systems, and may play important roles in the total primary production of subtropical stratified coastal lagoons. We investigated the spatiotemporal variability of light CO(2) fixation and net oxygen production in the stratified Conceição Lagoon (Brazil) in summer and fall of 2007, as well as the contribution of bacteriochlorophyll a (BChl a)-containing bacteria to photosynthetically driven electron transfer. Both chlorophyll a (Chl a) and BChl a varied in space, while only BChl a varied in time (three-fold increase from summer to fall). In summer, net oxygen production and light CO(2) fixation were correlated, with both having higher rates with higher Chl a concentrations in the enclosed region of the lagoon. In fall, CO(2) fixation was decoupled from oxygen production. Denaturing gradient gel electrophoresis revealed that bacterial communities of oxic site 12 and suboxic site 33 formed one cluster, different from other oxic samples within the lagoon. In addition, BChl a/Chl a ratios at these sites were high, 40% and 45%, respectively. Light acted as the main factor controlling the BChl a concentration and CO(2) fixation rates. High turbidity within the enclosed area of the lagoon explained high BChl a and decoupling between CO(2) fixation and oxygen production in oxygenated waters. Contribution of purple sulfur bacteria to total bacterial density in suboxic waters was 1.2%, and their biomass contributed to a much higher percentage (12.2%) due to their large biovolume. Our results indicate a significant contribution of anaerobic anoxygenic bacteria to the primary production of the "dead zone" of Conceição Lagoon.
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Affiliation(s)
- Maria Luiza S Fontes
- Institute of Oceanography, Federal University of Rio Grande, Av. Itália km 8, Campus Carreiros, Rio Grande, Rio Grande do Sul, Brazil.
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Lavin P, González B, Santibáñez JF, Scanlan DJ, Ulloa O. Novel lineages of Prochlorococcus thrive within the oxygen minimum zone of the eastern tropical South Pacific. ENVIRONMENTAL MICROBIOLOGY REPORTS 2010; 2:728-38. [PMID: 23766277 DOI: 10.1111/j.1758-2229.2010.00167.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
The eastern tropical Pacific Ocean holds two of the main oceanic oxygen minimum zones of the global ocean. The presence of an oxygen-depleted layer at intermediate depths, which also impinges on the seafloor and in some cases the euphotic zone, plays a significant role in structuring both pelagic and benthic communities, and also in the vertical partitioning of microbial assemblages. Here, we assessed the genetic diversity and distribution of natural populations of the cyanobacteria Prochlorococcus and Synechococcus within oxic and suboxic waters of the eastern tropical Pacific using cloning and sequencing, and terminal restriction fragment length polymorphism (T-RFLP) analyses applied to the 16S-23S rRNA internal transcribed spacer region. With the T-RFLP approach we could discriminate 19 cyanobacterial clades, of which 18 were present in the study region. Synechococcus was more abundant in the surface oxic waters of the eastern South Pacific, while Prochlorococcus dominated the subsurface low-oxygen waters. Two of the dominant clades in the oxygen-deficient waters belong to novel and yet uncultivated lineages of low-light adapted Prochlorococcus.
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Affiliation(s)
- Paris Lavin
- Programa de Doctorado, Departamento de Botánica, Universidad de Concepción, Concepción, Chile. Departamento de Oceanografía and Centro de Investigación Oceanográfica en el Pacifico Sudoriental, Universidad de Concepción, Concepción, Chile. Departamento de Genética Molecular y Microbiología, Center for Advanced Studies in Ecology and Biodiversity, and Millennium Nucleus on Microbial Ecology and Environmental Microbiology and Biotechnology, Pontificia Universidad Católica de Chile, Santiago, Chile. Facultad de Ingeniería y Ciencia, Universidad Adolfo Ibáñez, Santiago, Chile. Department of Biological Sciences, University of Warwick, Coventry CV4 7AL, UK
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Breitburg DL, Crump BC, Dabiri JO, Gallegos CL. Ecosystem engineers in the pelagic realm: alteration of habitat by species ranging from microbes to jellyfish. Integr Comp Biol 2010; 50:188-200. [PMID: 21558198 DOI: 10.1093/icb/icq051] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Ecosystem engineers are species that alter the physical environment in ways that create new habitat or change the suitability of existing habitats for themselves or other organisms. In marine systems, much of the focus has been on species such as corals, oysters, and macrophytes that add physical structure to the environment, but organisms ranging from microbes to jellyfish and finfish that reside in the water column of oceans, estuaries, and coastal seas alter the chemical and physical environment both within the water column and on the benthos. By causing hypoxia, changing light regimes, and influencing physical mixing, these organisms may have as strong an effect as species that fall more clearly within the classical category of ecosystem engineer. In addition, planktonic species, such as jellyfish, may indirectly alter the physical environment through predator-mediated landscape structure. By creating spatial patterns of habitats that vary in their rates of mortality due to predation, planktonic predators may control spatial patterns and abundances of species that are the direct creators or modifiers of physical habitat.
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Korenblum E, Valoni E, Penna M, Seldin L. Bacterial diversity in water injection systems of Brazilian offshore oil platforms. Appl Microbiol Biotechnol 2010; 85:791-800. [PMID: 19830416 DOI: 10.1007/s00253-009-2281-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2009] [Revised: 09/26/2009] [Accepted: 09/28/2009] [Indexed: 10/20/2022]
Abstract
Biogenic souring and microbial-influenced corrosion is a common scenario in water-flooded petroleum reservoirs. Water injection systems are continuously treated to control bacterial contamination, but some bacteria that cause souring and corrosion can persist even after different treatments have been applied. Our aim was to increase our knowledge of the bacterial communities that persist in the water injection systems of three offshore oil platforms in Brazil. To achieve this goal, we used a culture-independent molecular approach (16S ribosomal RNA gene clone libraries) to analyze seawater samples that had been subjected to different treatments. Phylogenetic analyses revealed that the bacterial communities from the different platforms were taxonomically different. A predominance of bacterial clones affiliated with Gammaproteobacteria, mostly belonging to the genus Marinobacter (60.7%), were observed in the platform A samples. Clones from platform B were mainly related to the genera Colwellia (37.9%) and Achromobacter (24.6%), whereas clones obtained from platform C were all related to unclassified bacteria. Canonical correspondence analyses showed that different treatments such as chlorination, deoxygenation, and biocide addition did not significantly influence the bacterial diversity in the platforms studied. Our results demonstrated that the injection water used in secondary oil recovery procedures contained potentially hazardous bacteria, which may ultimately cause souring and corrosion.
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Affiliation(s)
- Elisa Korenblum
- Instituto de Microbiologia Prof. Paulo de Góes, Universidade Federal do Rio de Janeiro, Ilha do Fundão, Rio de Janeiro, RJ, Brazil
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Cottrell MT, Ras J, Kirchman DL. Bacteriochlorophyll and community structure of aerobic anoxygenic phototrophic bacteria in a particle-rich estuary. ISME JOURNAL 2010; 4:945-54. [DOI: 10.1038/ismej.2010.13] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Zaikova E, Walsh DA, Stilwell CP, Mohn WW, Tortell PD, Hallam SJ. Microbial community dynamics in a seasonally anoxic fjord: Saanich Inlet, British Columbia. Environ Microbiol 2009; 12:172-91. [PMID: 19788414 DOI: 10.1111/j.1462-2920.2009.02058.x] [Citation(s) in RCA: 132] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Dissolved oxygen concentration plays a major role in shaping biotic interactions and nutrient flows within marine ecosystems. Throughout the global ocean, regions of low dissolved oxygen concentration (hypoxia) are a common and expanding feature of the water column, with major feedback on productivity and greenhouse gas cycling. To better understand microbial diversity underlying biogeochemical transformations within oxygen-deficient oceanic waters, we monitored and quantified bacterial and archaeal community dynamics in relation to dissolved gases and nutrients during a seasonal stratification and deep water renewal cycle in Saanich Inlet, British Columbia, a seasonally anoxic fjord. A number of microbial groups partitioned within oxygen-deficient waters including Nitrospina and SAR324 affiliated with the delta-proteobacteria, SAR406 and gamma-proteobacteria related to thiotrophic gill symbionts of deep-sea clams and mussels. Microbial diversity was highest within the hypoxic transition zone decreasing dramatically within anoxic basin waters and temporal patterns of niche partitioning were observed along defined gradients of oxygen and phosphate. These results provide a robust comparative phylogenetic framework for inferring systems metabolism of nitrogen, carbon and sulfur cycling within oxygen-deficient oceanic waters and establish Saanich Inlet as a tractable model for studying the response of microbial communities to changing levels of water column hypoxia.
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Affiliation(s)
- Elena Zaikova
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
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Zhang R, Lau SC, Ki JS, Thiyagarajan V, Qian PY. Response of bacterioplankton community structures to hydrological conditions and anthropogenic pollution in contrasting subtropical environments. FEMS Microbiol Ecol 2009; 69:449-60. [DOI: 10.1111/j.1574-6941.2009.00726.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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Fontes MLS, Abreu PC. Spatiotemporal variation of bacterial assemblages in a shallow subtropical coastal lagoon in Southern Brazil. MICROBIAL ECOLOGY 2009; 58:140-152. [PMID: 18953593 DOI: 10.1007/s00248-008-9454-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2008] [Accepted: 09/10/2008] [Indexed: 05/27/2023]
Abstract
A study on the bacterioplankton of Conceição Lagoon (27 degrees 34' S-48 degrees 27' W), Southern Brazil, was carried out in July 2005 (austral winter) and January 2006 (austral summer) to characterize the bacterial spatiotemporal distribution and to determine the heterotrophic and photoautotrophic bacterial dominance in hypoxic/oxic stratified waters. Bacterial abundance increased significantly (p < 0.05) in summer with averages of coccus cyanobacteria (CCY) ranging from 1.02 x 10(5) (winter) to 3.21 x 10(6) cells mL(-1) (summer), heterotrophic coccus/rod-shaped (HCR) cells from 7.00 x 10(4) to 3.60 x 10(6) cells mL(-1), and heterotrophic filamentous (HF) bacteria from 2.90 x 10(3) to 2.74 x 10(5) cells mL(-1). Bacterial biovolumes also increased in summer with mean biovolumes of CCY ranging from 0.38 to 1.37 microm3, HCR cells from 0.31 to 1.12 microm3, and HF from 3.32 to 11.34 microm3. Principal component analysis showed that salinity, temperature, and light were the abiotic factors that better explained the temporal variability of bacterial assemblages. Bacterial heterotrophy dominated in the lagoon, excepted by the southern and part of central sector in January 2006, when autotrophic-dominated microbial community occurred. Spatially, bacterial assemblages were influenced by nutrient gradient, oxygen, and salinity with a positive relationship between biovolumes and nutrients and a negative relationship between abundance of coccus cyanobacteria and nutrients. The stratified [corrected] area revealed a singular temporal pattern with hypoxic bottom waters in winter and oxygen-rich waters appearing in summer related with the availability of light and predominant microbes. Thus, oxygen consumption/production is likely to be regulated by the amount of light reaching the bottom, stimulating the production of oxygen by oxygenic phototrophs.
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Affiliation(s)
- Maria Luiza Schmitz Fontes
- Post-Graduation Course on Biological Oceanography, Institute of Oceanography, Federal University of Rio Grande (FURG), Av. Itália km 08, Rio Grande, RS 96201-900, Brazil.
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Kato S, Kobayashi C, Kakegawa T, Yamagishi A. Microbial communities in iron-silica-rich microbial mats at deep-sea hydrothermal fields of the Southern Mariana Trough. Environ Microbiol 2009; 11:2094-111. [PMID: 19397679 DOI: 10.1111/j.1462-2920.2009.01930.x] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The abundance, diversity and composition of bacterial and archaeal communities in the microbial mats at deep-sea hydrothermal fields were investigated, using culture-independent 16S rRNA and functional gene analyses combined with mineralogical analysis. Microbial mats were collected at two hydrothermal areas on the ridge of the back-arc spreading centre in the Southern Mariana Trough. Scanning electron microscope and energy dispersive X-ray spectroscopic (SEM-EDS) analyses revealed that the mats were mainly composed of amorphous silica and contained numerous filamentous structures of iron hydroxides. Direct cell counting with SYBR Green I staining showed that the prokaryotic cell densities were more than 10(8) cells g(-1). Quantitative polymerase chain reaction (Q-PCR) analysis revealed that Bacteria are more abundant than Archaea in the microbial communities. Furthermore, zetaproteobacterial cells accounted for 6% and 22% of the prokaryotic cells in each mat estimated by Q-PCR with newly designed primers and TaqMan probe. Phylotypes related to iron-oxidizers, methanotrophs/methylotrophs, ammonia-oxidizers and sulfate-reducers were found in the 16S rRNA gene clone libraries constructed from each mat sample. A variety of unique archaeal 16S rRNA gene phylotypes, several pmoA, dsrAB and archaeal amoA gene phylotypes were also recovered from the microbial mats. Our results provide insights into the diversity and abundance of microbial communities within microbial mats in deep-sea hydrothermal fields.
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Affiliation(s)
- Shingo Kato
- Department of Molecular Biology, Tokyo University of Pharmacy and Life Science, Hachioji, Tokyo 192-0392, Japan
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Culture-independent characterization of bacterial communities associated with the cold-water coral Lophelia pertusa in the northeastern Gulf of Mexico. Appl Environ Microbiol 2009; 75:2294-303. [PMID: 19233949 DOI: 10.1128/aem.02357-08] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Bacteria are recognized as an important part of the total biology of shallow-water corals. Studies of shallow-water corals suggest that associated bacteria may benefit the corals by cycling carbon, fixing nitrogen, chelating iron, and producing antibiotics that protect the coral from other microbes. Cold-water or deep-sea corals have a fundamentally different ecology due to their adaptation to cold, dark, high-pressure environments and as such have novel microbiota. The goal of this study was to characterize the microbial associates of Lophelia pertusa in the northeastern Gulf of Mexico. This is the first study to collect the coral samples in individual insulated containers and to preserve coral samples at depth in an effort to minimize thermal shock and evaluate the effects of environmental gradients on the microbial diversity of samples. Molecular analysis of bacterial diversity showed a marked difference between the two study sites, Viosca Knoll 906/862 (VK906/862) and Viosca Knoll 826 (VK826). The bacterial communities from VK826 were dominated by a variety of unknown mycoplasmal members of the Tenericutes and Bacteroidetes, whereas the libraries from VK906/862 were dominated by members of the Proteobacteria. In addition to novel sequences, the 16S rRNA gene clone libraries revealed many bacterial sequences in common between Gulf of Mexico Lophelia corals and Norwegian fjord Lophelia corals, as well as shallow-water corals. Two Lophelia-specific bacterial groups were identified: a cluster of gammaproteobacteria related to sulfide-oxidizing gill symbionts of seep clams and a group of Mycoplasma spp. The presence of these groups in both Gulf and Norwegian Lophelia corals indicates that in spite of the geographic heterogeneity observed in Lophelia-associated bacterial communities, there are Lophelia-specific microbes.
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