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Remple KL, Silbiger NJ, Quinlan ZA, Fox MD, Kelly LW, Donahue MJ, Nelson CE. Coral reef biofilm bacterial diversity and successional trajectories are structured by reef benthic organisms and shift under chronic nutrient enrichment. NPJ Biofilms Microbiomes 2021; 7:84. [PMID: 34853316 PMCID: PMC8636626 DOI: 10.1038/s41522-021-00252-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 10/21/2021] [Indexed: 12/21/2022] Open
Abstract
Work on marine biofilms has primarily focused on host-associated habitats for their roles in larval recruitment and disease dynamics; little is known about the factors regulating the composition of reef environmental biofilms. To contrast the roles of succession, benthic communities and nutrients in structuring marine biofilms, we surveyed bacteria communities in biofilms through a six-week succession in aquaria containing macroalgae, coral, or reef sand factorially crossed with three levels of continuous nutrient enrichment. Our findings demonstrate how biofilm successional trajectories diverge from temporal dynamics of the bacterioplankton and how biofilms are structured by the surrounding benthic organisms and nutrient enrichment. We identify a suite of biofilm-associated bacteria linked with the orthogonal influences of corals, algae and nutrients and distinct from the overlying water. Our results provide a comprehensive characterization of marine biofilm successional dynamics and contextualize the impact of widespread changes in reef community composition and nutrient pollution on biofilm community structure.
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Affiliation(s)
- Kristina L. Remple
- grid.410445.00000 0001 2188 0957Daniel K. Inouye Center for Microbial Oceanography: Research and Education, Department of Oceanography and Sea Grant College Program, University of Hawaiʻi at Mānoa, Honolulu, HI USA
| | - Nyssa J. Silbiger
- grid.253563.40000 0001 0657 9381Department of Biology, California State University, Northridge, CA USA
| | - Zachary A. Quinlan
- grid.263081.e0000 0001 0790 1491Department of Biology, San Diego State University, San Diego, CA USA ,grid.266100.30000 0001 2107 4242Scripps Institution of Oceanography, University of California, San Diego, CA USA
| | - Michael D. Fox
- grid.56466.370000 0004 0504 7510Woods Hole Oceanographic Institution, Woods Hole, MA USA
| | - Linda Wegley Kelly
- grid.263081.e0000 0001 0790 1491Department of Biology, San Diego State University, San Diego, CA USA ,grid.266100.30000 0001 2107 4242Scripps Institution of Oceanography, University of California, San Diego, CA USA
| | - Megan J. Donahue
- grid.410445.00000 0001 2188 0957Hawaiʻi Institute of Marine Biology, University of Hawaiʻi at Mānoa, Honolulu, HI USA
| | - Craig E. Nelson
- grid.410445.00000 0001 2188 0957Daniel K. Inouye Center for Microbial Oceanography: Research and Education, Department of Oceanography and Sea Grant College Program, University of Hawaiʻi at Mānoa, Honolulu, HI USA
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2
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Ares Á, Brisbin MM, Sato KN, Martín JP, Iinuma Y, Mitarai S. Extreme storms cause rapid but short-lived shifts in nearshore subtropical bacterial communities. Environ Microbiol 2021; 22:4571-4588. [PMID: 33448616 DOI: 10.1111/1462-2920.15178] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 06/27/2020] [Accepted: 07/24/2020] [Indexed: 01/04/2023]
Abstract
Climate change scenarios predict tropical cyclones will increase in both frequency and intensity, which will escalate the amount of terrestrial run-off and mechanical disruption affecting coastal ecosystems. Bacteria are key contributors to ecosystem functioning, but relatively little is known about how they respond to extreme storm events, particularly in nearshore subtropical regions. In this study, we combine field observations and mesocosm experiments to assess bacterial community dynamics and changes in physicochemical properties during early- and late-season tropical cyclones affecting Okinawa, Japan. Storms caused large and fast influxes of freshwater and terrestrial sediment - locally known as red soil pollution - and caused moderate increases of macronutrients, especially SiO2 and PO4 3-, with up to 25 and 0.5 μM respectively. We detected shifts in relative abundances of marine and terrestrially derived bacteria, including putative coral and human pathogens, during storm events. Soil input alone did not substantially affect marine bacterial communities in mesocosms, indicating that other components of run-off or other storm effects likely exert a larger influence on bacterial communities. The storm effects were short-lived and bacterial communities quickly recovered following both storm events. The early- and late-season storms caused different physicochemical and bacterial community changes, demonstrating the context-dependency of extreme storm responses in a subtropical coastal ecosystem.
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Affiliation(s)
- Ángela Ares
- Marine Biophysics Unit, Okinawa Institute of Science and Technology (OIST), Okinawa, Japan
| | - Margaret Mars Brisbin
- Marine Biophysics Unit, Okinawa Institute of Science and Technology (OIST), Okinawa, Japan
| | - Kirk N Sato
- Marine Biophysics Unit, Okinawa Institute of Science and Technology (OIST), Okinawa, Japan.,Friday Harbor Laboratories, University of Washington, WA, USA
| | - Juan P Martín
- Marine Biophysics Unit, Okinawa Institute of Science and Technology (OIST), Okinawa, Japan
| | - Yoshiteru Iinuma
- Instrumental Analysis Section, Okinawa Institute of Science and Technology (OIST), Okinawa, Japan
| | - Satoshi Mitarai
- Marine Biophysics Unit, Okinawa Institute of Science and Technology (OIST), Okinawa, Japan
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3
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He J, Guo J, Fu X, Cai J. Potential use of high-throughput sequencing of bacterial communities for postmortem submersion interval estimation. Braz J Microbiol 2019; 50:999-1010. [PMID: 31364013 DOI: 10.1007/s42770-019-00119-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 07/11/2019] [Indexed: 02/06/2023] Open
Abstract
Microorganisms play vital roles in the natural decomposition of carcasses in aquatic systems. Using high-throughput sequencing techniques, we evaluated the composition and succession of microbial communities throughout the decomposition of rat carcasses in freshwater. A total of 4,428,781 high-quality 16S rRNA gene sequences and 2144 operational taxonomic units were obtained. Further analysis revealed that the microbial composition differed significantly between the epinecrotic (rat skins) and the epilithic (rocks) samples. During the carcass decomposition process, Proteobacteria became the dominant phylum in the epinecrotic, epilithic, and environmental (water) samples, followed by Firmicutes in the epinecrotic samples and Bacteroidetes in the epilithic and water samples. Microbial communities were influenced by numerous environmental factors, such as dissolved oxygen content and conductivity. Our study provides new insight about postmortem submersion interval (PMSI) estimation in aquatic environments.
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Affiliation(s)
- Jing He
- Department of Forensic Medicine, School of Basic Medical Sciences, Central South University, Changsha, 410013, Hunan, People's Republic of China
| | - Juanjuan Guo
- Department of Forensic Medicine, School of Basic Medical Sciences, Central South University, Changsha, 410013, Hunan, People's Republic of China
| | - Xiaoliang Fu
- Department of Forensic Medicine, School of Basic Medical Sciences, Central South University, Changsha, 410013, Hunan, People's Republic of China
| | - Jifeng Cai
- Department of Forensic Medicine, School of Basic Medical Sciences, Central South University, Changsha, 410013, Hunan, People's Republic of China.
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4
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Hadaidi G, Ziegler M, Shore-Maggio A, Jensen T, Aeby G, Voolstra CR. Ecological and molecular characterization of a coral black band disease outbreak in the Red Sea during a bleaching event. PeerJ 2018; 6:e5169. [PMID: 30013839 PMCID: PMC6046197 DOI: 10.7717/peerj.5169] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 06/16/2018] [Indexed: 11/20/2022] Open
Abstract
Black Band Disease (BBD) is a widely distributed and destructive coral disease that has been studied on a global scale, but baseline data on coral diseases is missing from many areas of the Arabian Seas. Here we report on the broad distribution and prevalence of BBD in the Red Sea in addition to documenting a bleaching-associated outbreak of BBD with subsequent microbial community characterization of BBD microbial mats at this reef site in the southern central Red Sea. Coral colonies with BBD were found at roughly a third of our 22 survey sites with an overall prevalence of 0.04%. Nine coral genera were infected including Astreopora, Coelastrea, Dipsastraea, Gardineroseris, Goniopora, Montipora, Pavona, Platygyra, and Psammocora. For a southern central Red Sea outbreak site, overall prevalence was 40 times higher than baseline (1.7%). Differential susceptibility to BBD was apparent among coral genera with Dipsastraea (prevalence 6.1%), having more diseased colonies than was expected based on its abundance within transects. Analysis of the microbial community associated with the BBD mat showed that it is dominated by a consortium of cyanobacteria and heterotrophic bacteria. We detected the three main indicators for BBD (filamentous cyanobacteria, sulfate-reducing bacteria (SRB), and sulfide-oxidizing bacteria (SOB)), with high similarity to BBD-associated microbes found worldwide. More specifically, the microbial consortium of BBD-diseased coral colonies in the Red Sea consisted of Oscillatoria sp. (cyanobacteria), Desulfovibrio sp. (SRB), and Arcobacter sp. (SOB). Given the similarity of associated bacteria worldwide, our data suggest that BBD represents a global coral disease with predictable etiology. Furthermore, we provide a baseline assessment of BBD disease prevalence in the Red Sea, a still understudied region.
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Affiliation(s)
- Ghaida Hadaidi
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Maren Ziegler
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Amanda Shore-Maggio
- Institute of Marine and Environmental Technology (IMET), University of Maryland, Baltimore County, Baltimore, MD, United States of America
| | - Thor Jensen
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Greta Aeby
- Hawai'i Institute of Marine Biology, Kāne'ohe, HI, United States of America
| | - Christian R Voolstra
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
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Kegler HF, Hassenrück C, Kegler P, Jennerjahn TC, Lukman M, Jompa J, Gärdes A. Small tropical islands with dense human population: differences in water quality of near-shore waters are associated with distinct bacterial communities. PeerJ 2018; 6:e4555. [PMID: 29761035 PMCID: PMC5944435 DOI: 10.7717/peerj.4555] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 03/09/2018] [Indexed: 12/30/2022] Open
Abstract
Water quality deterioration caused by an enrichment in inorganic and organic matter due to anthropogenic inputs is one of the major local threats to coral reefs in Indonesia. However, even though bacteria are important mediators in coral reef ecosystems, little is known about the response of individual taxa and whole bacterial communities to these anthropogenic inputs. The present study is the first to investigate how bacterial community composition responds to small-scale changes in water quality in several coral reef habitats of the Spermonde Archipelago including the water column, particles, and back-reef sediments, on a densely populated and an uninhabited island. The main aims were to elucidate if (a) water quality indicators and organic matter concentrations differ between the uninhabited and the densely populated island of the archipelago, and (b) if there are differences in bacterial community composition in back-reef sediments and in the water column, which are associated with differences in water quality. Several key water quality parameters, such as inorganic nitrate and phosphate, chlorophyll a, and transparent exopolymer particles (TEP) were significantly higher at the inhabited than at the uninhabited island. Bacterial communities in sediments and particle-attached communities were significantly different between the two islands with bacterial taxa commonly associated with nutrient and organic matter-rich conditions occurring in higher proportions at the inhabited island. Within the individual reef habitats, variations in bacterial community composition between the islands were associated with differences in water quality. We also observed that copiotrophic, opportunistic bacterial taxa were enriched at the inhabited island with its higher chlorophyll a, dissolved organic carbon and TEP concentrations. Given the increasing strain on tropical coastal ecosystems, this study suggests that effluents from densely populated islands lacking sewage treatment can alter bacterial communities that may be important for coral reef ecosystem function.
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Affiliation(s)
- Hauke F. Kegler
- Department of Biogeochemistry and Geology, Leibniz-Centre for Tropical Marine Research, Bremen, Germany
- Faculty of Biology and Chemistry (FB2), University of Bremen, Bremen, Germany
| | - Christiane Hassenrück
- Department of Biogeochemistry and Geology, Leibniz-Centre for Tropical Marine Research, Bremen, Germany
| | - Pia Kegler
- Department of Ecology, Leibniz-Centre for Tropical Marine Research, Bremen, Germany
| | - Tim C. Jennerjahn
- Department of Biogeochemistry and Geology, Leibniz-Centre for Tropical Marine Research, Bremen, Germany
| | - Muhammad Lukman
- Department of Marine Science, Universitas Hasanuddin, Makassar, Indonesia
| | - Jamaluddin Jompa
- Department of Marine Science, Universitas Hasanuddin, Makassar, Indonesia
| | - Astrid Gärdes
- Department of Biogeochemistry and Geology, Leibniz-Centre for Tropical Marine Research, Bremen, Germany
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6
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Kegler HF, Lukman M, Teichberg M, Plass-Johnson J, Hassenrück C, Wild C, Gärdes A. Bacterial Community Composition and Potential Driving Factors in Different Reef Habitats of the Spermonde Archipelago, Indonesia. Front Microbiol 2017; 8:662. [PMID: 28473810 PMCID: PMC5397486 DOI: 10.3389/fmicb.2017.00662] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Accepted: 03/31/2017] [Indexed: 12/04/2022] Open
Abstract
Coastal eutrophication is a key driver of shifts in bacterial communities on coral reefs. With fringing and patch reefs at varying distances from the coast the Spermonde Archipelago in southern Sulawesi, Indonesia offers ideal conditions to study the effects of coastal eutrophication along a spatially defined gradient. The present study investigated bacterial community composition of three coral reef habitats: the water column, sediments, and mucus of the hard coral genus Fungia, along that cross-shelf environmental and water quality gradient. The main research questions were: (1) How do water quality and bacterial community composition change along a coastal shelf gradient? (2) Which water quality parameters influence bacterial community composition? (3) Is there a difference in bacterial community composition among the investigated habitats? For this purpose, a range of key water parameters were measured at eight stations in distances from 2 to 55 km from urban Makassar. This was supplemented by sampling of bacterial communities of important microbial habitats using 454 pyrosequencing. Findings revealed that the population center Makassar had a strong effect on the concentrations of Chlorophyll a, suspended particulate matter (SPM), and transparent exopolymer particles (TEP), which were all significantly elevated at the inshore compared the other seven sites. Shifts in the bacterial communities were specific to each sampled habitat. Two OTUs, belonging to the genera Escherichia/Shigella (Gammaproteobacteria) and Ralstonia (Betaproteobacteria), respectively, both dominated the bacterial community composition of the both size fractions of the water column and coral mucus. The sampled reef sediments were more diverse, and no single OTUs was dominant. There was no gradual shift in bacterial classes or OTUs within the sampled habitats. In addition, we observed very distinct communities between the investigated habitats. Our data show strong changes in the bacterial community composition at the inshore site for water column and sediment samples. Alarmingly, there was generally a high prevalence of potentially pathogenic bacteria across the entire gradient.
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Affiliation(s)
- Hauke F Kegler
- Tropical Marine Microbiology, Department of Biogeochemistry and Geology, Leibniz Center for Tropical Marine ResearchBremen, Germany.,Faculty of Biology and Chemistry (FB 2), University of BremenBremen, Germany
| | - Muhammad Lukman
- Marine Science Department, Faculty of Marine Science and Fisheries, Hasanuddin UniversitySouth Sulawesi, Indonesia
| | - Mirta Teichberg
- Algae and Seagrass Ecology, Department of Ecology, Leibniz Center for Tropical Marine ResearchBremen, Germany
| | - Jeremiah Plass-Johnson
- Algae and Seagrass Ecology, Department of Ecology, Leibniz Center for Tropical Marine ResearchBremen, Germany.,Centre for Ocean Life, National Institute of Aquatic Resources (DTU-Aqua), Technical University of DenmarkCharlottenlund, Denmark
| | - Christiane Hassenrück
- Tropical Marine Microbiology, Department of Biogeochemistry and Geology, Leibniz Center for Tropical Marine ResearchBremen, Germany.,HGF MPG Joint Research Group for Deep-Sea Ecology and Technology, Max Planck Institute for Marine MicrobiologyBremen, Germany
| | - Christian Wild
- Faculty of Biology and Chemistry (FB 2), University of BremenBremen, Germany
| | - Astrid Gärdes
- Tropical Marine Microbiology, Department of Biogeochemistry and Geology, Leibniz Center for Tropical Marine ResearchBremen, Germany
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7
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Prazeres M, Ainsworth T, Roberts TE, Pandolfi JM, Leggat W. Symbiosis and microbiome flexibility in calcifying benthic foraminifera of the Great Barrier Reef. MICROBIOME 2017; 5:38. [PMID: 28335814 PMCID: PMC5364595 DOI: 10.1186/s40168-017-0257-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 03/15/2017] [Indexed: 05/16/2023]
Abstract
BACKGROUND Symbiosis is a phenomenon that allows organisms to colonise a wide range of environments and occupy a variety of ecological niches in marine environments. Large benthic foraminifera (LBF) are crucial marine calcifiers that rely on photo-endosymbionts for growth and calcification, yet the influence of environmental conditions in shaping their interactions with prokaryotic and eukaryotic associates is poorly known. RESULTS Here, we used next-generation sequencing to identify eukaryotic photosynthesizing and prokaryotic microbes associated with the common LBF Amphistegina lobifera across a physio-chemical gradient on the Great Barrier Reef (GBR). We collected samples from three reef sites located in the inner-, mid- and outer-shelf regions of the northern section of the GBR. Results showed the consistent presence of Bacillaryophyta as the main eukaryotic taxa associated with A. lobifera across all reef sites analysed; however, the abundance and the diversity of prokaryotic organisms varied among reef sites. Inner-shelf specimens showed the highest diversity of prokaryote associates, with a total of 231 genotypes in their core microbiome. A total of 30 taxa were identified in the core microbiome across all reef sites. Within these taxa, Proteobacteria was the most abundant bacteria present. The presence of groups such as Actinobacteria was significantly correlated with inner-shelf populations, whereas the abundance of Bacteroidetes and Firmicutes was associated with A. lobifera collected from mid- and outer-shelf reef sites. CONCLUSIONS We found that benthic foraminifera form stable and persistent symbiosis with eukaryotic partners, but flexible and site-specific associations with prokaryotic microbes that likely influence the ecological success of these crucial calcifying organisms on the GBR.
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Affiliation(s)
- Martina Prazeres
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, QLD 4811 Australia
| | - Tracy Ainsworth
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD 4811 Australia
| | - T. Edward Roberts
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD 4811 Australia
| | - John M. Pandolfi
- ARC Centre of Excellence for Coral Reef Studies and School of Biological Sciences, The University of Queensland, St. Lucia, QLD 4072 Australia
| | - William Leggat
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, QLD 4811 Australia
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD 4811 Australia
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8
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Roik A, Röthig T, Roder C, Ziegler M, Kremb SG, Voolstra CR. Year-Long Monitoring of Physico-Chemical and Biological Variables Provide a Comparative Baseline of Coral Reef Functioning in the Central Red Sea. PLoS One 2016; 11:e0163939. [PMID: 27828965 PMCID: PMC5102394 DOI: 10.1371/journal.pone.0163939] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 09/16/2016] [Indexed: 11/26/2022] Open
Abstract
Coral reefs in the central Red Sea are sparsely studied and in situ data on physico-chemical and key biotic variables that provide an important comparative baseline are missing. To address this gap, we simultaneously monitored three reefs along a cross-shelf gradient for an entire year over four seasons, collecting data on currents, temperature, salinity, dissolved oxygen (DO), chlorophyll-a, turbidity, inorganic nutrients, sedimentation, bacterial communities of reef water, and bacterial and algal composition of epilithic biofilms. Summer temperature (29–33°C) and salinity (39 PSU) exceeded average global maxima for coral reefs, whereas DO concentration was low (2–4 mg L-1). While temperature and salinity differences were most pronounced between seasons, DO, chlorophyll-a, turbidity, and sedimentation varied most between reefs. Similarly, biotic communities were highly dynamic between reefs and seasons. Differences in bacterial biofilms were driven by four abundant families: Rhodobacteraceae, Flavobacteriaceae, Flammeovirgaceae, and Pseudanabaenaceae. In algal biofilms, green crusts, brown crusts, and crustose coralline algae were most abundant and accounted for most of the variability of the communities. Higher bacterial diversity of biofilms coincided with increased algal cover during spring and summer. By employing multivariate matching, we identified temperature, salinity, DO, and chlorophyll-a as the main contributing physico-chemical drivers of biotic community structures. These parameters are forecast to change most with the progression of ocean warming and increased nutrient input, which suggests an effect on the recruitment of Red Sea benthic communities as a result of climate change and anthropogenic influence. In conclusion, our study provides insight into coral reef functioning in the Red Sea and a comparative baseline to support coral reef studies in the region.
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Affiliation(s)
- Anna Roik
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955–6900, Saudi Arabia
| | - Till Röthig
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955–6900, Saudi Arabia
| | - Cornelia Roder
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955–6900, Saudi Arabia
| | - Maren Ziegler
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955–6900, Saudi Arabia
| | - Stephan G. Kremb
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955–6900, Saudi Arabia
| | - Christian R. Voolstra
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955–6900, Saudi Arabia
- * E-mail:
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9
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Säwström C, Hyndes GA, Eyre BD, Huggett MJ, Fraser MW, Lavery PS, Thomson PG, Tarquinio F, Steinberg PD, Laverock B. Coastal connectivity and spatial subsidy from a microbial perspective. Ecol Evol 2016; 6:6662-6671. [PMID: 27777738 PMCID: PMC5058536 DOI: 10.1002/ece3.2408] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 08/06/2016] [Indexed: 01/04/2023] Open
Abstract
The transfer of organic material from one coastal environment to another can increase production in recipient habitats in a process known as spatial subsidy. Microorganisms drive the generation, transformation, and uptake of organic material in shallow coastal environments, but their significance in connecting coastal habitats through spatial subsidies has received limited attention. We address this by presenting a conceptual model of coastal connectivity that focuses on the flow of microbially mediated organic material in key coastal habitats. Our model suggests that it is not the difference in generation rates of organic material between coastal habitats but the amount of organic material assimilated into microbial biomass and respiration that determines the amount of material that can be exported from one coastal environment to another. Further, the flow of organic material across coastal habitats is sensitive to environmental change as this can alter microbial remineralization and respiration rates. Our model highlights microorganisms as an integral part of coastal connectivity and emphasizes the importance of including a microbial perspective in coastal connectivity studies.
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Affiliation(s)
- Christin Säwström
- School of Science Centre for Marine Ecosystems Research Edith Cowan University Joondalup WA Australia
| | - Glenn A Hyndes
- School of Science Centre for Marine Ecosystems Research Edith Cowan University Joondalup WA Australia
| | - Bradley D Eyre
- School of Environment Science and Engineering Centre for Coastal Biogeochemistry Research Southern Cross University Lismore NSW Australia
| | - Megan J Huggett
- School of Science Centre for Marine Ecosystems Research Edith Cowan University Joondalup WA Australia
| | - Matthew W Fraser
- The UWA Oceans Institute and the School of Plant Biology The University of Western Australia Crawley WA Australia
| | - Paul S Lavery
- School of Science Centre for Marine Ecosystems Research Edith Cowan University Joondalup WA Australia
| | - Paul G Thomson
- The School of Civil, Environmental and Mining Engineering and The UWA Oceans Institute The University of Western Australia Crawley WA Australia
| | - Flavia Tarquinio
- School of Science Centre for Marine Ecosystems Research Edith Cowan University Joondalup WA Australia
| | - Peter D Steinberg
- Sydney Institute of Marine Science Mosman NSW Australia; Centre for Marine Bio-Innovation and School of Biological, Earth and Environmental Sciences University of New South Wales Sydney NSW Australia
| | - Bonnie Laverock
- The UWA Oceans Institute and the School of Plant Biology The University of Western Australia Crawley WA Australia; Plant Functional Biology and Climate Change Cluster University of Technology Sydney Sydney NSW Australia
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10
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Staley C, Gould TJ, Wang P, Phillips J, Cotner JB, Sadowsky MJ. Sediments and Soils Act as Reservoirs for Taxonomic and Functional Bacterial Diversity in the Upper Mississippi River. MICROBIAL ECOLOGY 2016; 71:814-24. [PMID: 26879939 DOI: 10.1007/s00248-016-0729-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 01/11/2016] [Indexed: 05/25/2023]
Abstract
In this study, we utilized Illumina next-generation sequencing of 16S rDNA to characterize the bacterial communities in water, sediments, and soils at four sites along the Mississippi River and Minnesota River, in Minnesota, in order to evaluate community exchanges between these habitats. Communities in water and sediment were hypothesized to show greater taxonomic similarity than those in soil, while microbial communities in sediment and soil would show greater functional similarity. Habitat-specific communities showed significant differences in phylogenetic structure and β-diversity (P < 0.001), but site-specific differences in community structures within a single habitat type did not differ greatly (P ≥ 0.083). Community exchange among habitats generally influenced < 5% of the total community composition in a single sample, with the exception of the sediment community at the Minnesota River site, which contributed to a mean of 14% of the microbial community in the water column. Communities from all habitat types were significantly correlated with each other (r = 0.44-0.64, P ≤ 0.004). Furthermore, approximately 33% of the taxonomic units were found in all samples and comprised at least 40% of the bacterial community. Functional annotation of shotgun sequencing data revealed similar functional profiles for sediment and soil communities that were distinct from those in the water. Results of this study suggest that sediments, when disturbed, contribute significantly to bacterial communities in the water and that a core bacterial community may be supported in the soils and sediments. Furthermore, a high degree of functional redundancy results in similar functional profiles in sediment and soil communities.
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Affiliation(s)
- Christopher Staley
- BioTechnology Institute, University of Minnesota, 140 Gortner Lab, 1479 Gortner Ave, St. Paul, MN, 55108, USA
| | - Trevor J Gould
- BioTechnology Institute, University of Minnesota, 140 Gortner Lab, 1479 Gortner Ave, St. Paul, MN, 55108, USA
- Biology Program, University of Minnesota, St. Paul, MN, USA
| | - Ping Wang
- BioTechnology Institute, University of Minnesota, 140 Gortner Lab, 1479 Gortner Ave, St. Paul, MN, 55108, USA
| | - Jane Phillips
- Biology Program, University of Minnesota, St. Paul, MN, USA
| | - James B Cotner
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, MN, USA
| | - Michael J Sadowsky
- BioTechnology Institute, University of Minnesota, 140 Gortner Lab, 1479 Gortner Ave, St. Paul, MN, 55108, USA.
- Department of Soil, Water and Climate, University of Minnesota, St. Paul, MN, USA.
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Sato Y, Civiello M, Bell SC, Willis BL, Bourne DG. Integrated approach to understanding the onset and pathogenesis of black band disease in corals. Environ Microbiol 2016; 18:752-65. [PMID: 26549807 DOI: 10.1111/1462-2920.13122] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2015] [Revised: 10/27/2015] [Accepted: 11/02/2015] [Indexed: 10/22/2022]
Abstract
Emerging infectious diseases are contributing to global declines in coral reef ecosystems, highlighting a growing need for aetiological knowledge to develop effective management strategies. In this review, we focus on black band disease (BBD), one of the most virulent diseases and the only polymicrobial disease so far known to affect corals. A multipartite microbial consortium dominated by Cyanobacteria, but also including sulfur-cycling bacteria, other bacterial groups and members of the Archaea and Eukarya, forms a sulfide-rich anaerobic mat that migrates across the surface of coral colonies, killing the underlying tissues. The polymicrobial nature of the disease challenges classic aetiological approaches to unravelling disease causation. Here, we synthesize current knowledge on the range of pathogens forming the microbial consortium with recent studies on the transmission, biogeochemistry and environmental drivers of BBD to develop a conceptual model of BBD pathogenesis. The model illustrates how the development of BBD virulence factors is linked to a cascade of microbial community shifts and associated functional roles that progressively develop the microbial consortium from comparatively benign cyanobacterial patches to virulent BBD lesions. This review showcases how an approach that integrates multiple key aspects of the disease provides insights essential to elucidating the aetiology of BBD.
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Affiliation(s)
- Yui Sato
- Australian Institute of Marine Science, PMB 3, Townsville MC, Townsville, 4810, Australia
| | - Michael Civiello
- AIMS@JCU, James Cook University, Townsville, 4811, Australia.,ARC Centre of Excellence for Coral Reef Studies and College of Marine and Environmental Sciences, James Cook University, Townsville, 4811, Australia
| | - Sara C Bell
- Australian Institute of Marine Science, PMB 3, Townsville MC, Townsville, 4810, Australia
| | - Bette L Willis
- ARC Centre of Excellence for Coral Reef Studies and College of Marine and Environmental Sciences, James Cook University, Townsville, 4811, Australia
| | - David G Bourne
- Australian Institute of Marine Science, PMB 3, Townsville MC, Townsville, 4810, Australia
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Rotini A, Mejia AY, Costa R, Migliore L, Winters G. Ecophysiological Plasticity and Bacteriome Shift in the Seagrass Halophila stipulacea along a Depth Gradient in the Northern Red Sea. FRONTIERS IN PLANT SCIENCE 2016; 7:2015. [PMID: 28119709 PMCID: PMC5221695 DOI: 10.3389/fpls.2016.02015] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 12/19/2016] [Indexed: 05/03/2023]
Abstract
Halophila stipulacea is a small tropical seagrass species. It is the dominant seagrass species in the Gulf of Aqaba (GoA; northern Red Sea), where it grows in both shallow and deep environments (1-50 m depth). Native to the Red Sea, Persian Gulf, and Indian Ocean, this species has invaded the Mediterranean and has recently established itself in the Caribbean Sea. Due to its invasive nature, there is growing interest to understand this species' capacity to adapt to new conditions, which might be attributed to its ability to thrive in a broad range of ecological niches. In this study, a multidisciplinary approach was used to depict variations in morphology, biochemistry (pigment and phenol content) and epiphytic bacterial communities along a depth gradient (4-28 m) in the GoA. Along this gradient, H. stipulacea increased leaf area and pigment contents (Chlorophyll a and b, total Carotenoids), while total phenol contents were mostly uniform. H. stipulacea displayed a well conserved core bacteriome, as assessed by 454-pyrosequencing of 16S rRNA gene reads amplified from metagenomic DNA. The core bacteriome aboveground (leaves) and belowground (roots and rhizomes), was composed of more than 100 Operational Taxonomic Units (OTUs) representing 63 and 52% of the total community in each plant compartment, respectively, with a high incidence of the classes Alphaproteobacteria, Gammaproteobacteria, and Deltaproteobacteria across all depths. Above and belowground communities were different and showed higher within-depth variability at the intermediate depths (9 and 18 m) than at the edges. Plant parts showed a clear influence in shaping the communities while depth showed a greater influence on the belowground communities. Overall, results highlighted a different ecological status of H. stipulacea at the edges of the gradient (4-28 m), where plants showed not only marked differences in morphology and biochemistry, but also the most distinct associated bacterial consortium. We demonstrated the pivotal role of morphology, biochemistry (pigment and phenol content), and epiphytic bacterial communities in helping plants to cope with environmental and ecological variations. The plant/holobiont capability to persist and adapt to environmental changes probably has an important role in its ecological resilience and invasiveness.
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Affiliation(s)
- Alice Rotini
- Department of Biology, Tor Vergata UniversityRome, Italy
- *Correspondence: Gidon Winters, Alice Rotini,
| | | | - Rodrigo Costa
- Department of Bioengineering (iBB), Instituto Superior Técnico, Universidade de LisboaLisbon, Portugal
| | | | - Gidon Winters
- The Dead Sea-Arava Science CenterNeve Zohar, Israel
- *Correspondence: Gidon Winters, Alice Rotini,
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13
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Microbial Surface Colonization and Biofilm Development in Marine Environments. Microbiol Mol Biol Rev 2015; 80:91-138. [PMID: 26700108 DOI: 10.1128/mmbr.00037-15] [Citation(s) in RCA: 488] [Impact Index Per Article: 54.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Biotic and abiotic surfaces in marine waters are rapidly colonized by microorganisms. Surface colonization and subsequent biofilm formation and development provide numerous advantages to these organisms and support critical ecological and biogeochemical functions in the changing marine environment. Microbial surface association also contributes to deleterious effects such as biofouling, biocorrosion, and the persistence and transmission of harmful or pathogenic microorganisms and their genetic determinants. The processes and mechanisms of colonization as well as key players among the surface-associated microbiota have been studied for several decades. Accumulating evidence indicates that specific cell-surface, cell-cell, and interpopulation interactions shape the composition, structure, spatiotemporal dynamics, and functions of surface-associated microbial communities. Several key microbial processes and mechanisms, including (i) surface, population, and community sensing and signaling, (ii) intraspecies and interspecies communication and interaction, and (iii) the regulatory balance between cooperation and competition, have been identified as critical for the microbial surface association lifestyle. In this review, recent progress in the study of marine microbial surface colonization and biofilm development is synthesized and discussed. Major gaps in our knowledge remain. We pose questions for targeted investigation of surface-specific community-level microbial features, answers to which would advance our understanding of surface-associated microbial community ecology and the biogeochemical functions of these communities at levels from molecular mechanistic details through systems biological integration.
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Mahmoud H. Variations in the abundance and structural diversity of microbes forming biofilms in a thermally stressed coral reef system. MARINE POLLUTION BULLETIN 2015; 100:710-718. [PMID: 26494248 DOI: 10.1016/j.marpolbul.2015.10.030] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Revised: 10/10/2015] [Accepted: 10/16/2015] [Indexed: 06/05/2023]
Abstract
Little information is known about biofilm formation in the thermally stressed coral reef systems north of the Arabian Gulf. The current study investigates the abundance and diversity of marine microbes involved in biofilm formation and their succession over a period of 14 weeks (May-August 2007) at temperatures exceeding 32 °C. The results showed variations in microbial numbers and the development of more stable biofilm communities as the biofilms aged. The culture-dependent technique and microscopic examination of the developed biofilms showed the dominance of key species known for their role in precipitating CaCO3 such as Vibrio and in facilitating coral larvae settlement and metamorphosis such as Pseudoalteromonas, Bacillariophyceae and Rhodophyceae. The results revealed biofilm formations with microbial diversities that have the potential to support the larval settlement and metamorphism of marine organisms and to consolidate and stabilize biofilms via the process of calcification in the thermally stressed coral reef system considered herein.
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Affiliation(s)
- Huda Mahmoud
- Faculty of Science, Department of Biological Sciences, Kuwait University, P.O. Box (5969), Safat, Kuwait.
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Jessen C, Voolstra CR, Wild C. In situ effects of simulated overfishing and eutrophication on settlement of benthic coral reef invertebrates in the Central Red Sea. PeerJ 2014; 2:e339. [PMID: 24765573 PMCID: PMC3994645 DOI: 10.7717/peerj.339] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2014] [Accepted: 03/21/2014] [Indexed: 11/20/2022] Open
Abstract
In the Central Red Sea, healthy coral reefs meet intense coastal development, but data on the effects of related stressors for reef functioning are lacking. This in situ study therefore investigated the independent and combined effects of simulated overfishing through predator/grazer exclusion and simulated eutrophication through fertilizer addition on settlement of reef associated invertebrates on light-exposed and -shaded tiles over 4 months. At the end of the study period invertebrates had almost exclusively colonized shaded tiles. Algae were superior settling competitors on light-exposed tiles. On the shaded tiles, simulated overfishing prevented settlement of hard corals, but significantly increased settlement of polychaetes, while simulated eutrophication only significantly decreased hard coral settlement relative to controls. The combined treatment significantly increased settlement of bryozoans and bivalves compared to controls and individual manipulations, but significantly decreased polychaetes compared to simulated overfishing. These results suggest settlement of polychaetes and hard corals as potential bioindicators for overfishing and eutrophication, respectively, and settlement of bivalves and bryozoans for a combination of both. Therefore, if the investigated stressors are not controlled, phase shifts from dominance by hard corals to that by other invertebrates may occur at shaded reef locations in the Central Red Sea.
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Affiliation(s)
- Christian Jessen
- Coral Reef Ecology Group (CORE), Leibniz Center for Tropical Marine Ecology , Bremen , Germany
| | - Christian R Voolstra
- Red Sea Research Center, King Abdullah University of Science and Technology (KAUST) , Thuwal , Saudi Arabia
| | - Christian Wild
- Coral Reef Ecology Group (CORE), Leibniz Center for Tropical Marine Ecology , Bremen , Germany ; Faculty of Biology and Chemistry, University of Bremen , Germany
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Luo J, Liang H, Yan L, Ma J, Yang Y, Li G. Microbial community structures in a closed raw water distribution system biofilm as revealed by 454-pyrosequencing analysis and the effect of microbial biofilm communities on raw water quality. BIORESOURCE TECHNOLOGY 2013; 148:189-95. [PMID: 24055963 DOI: 10.1016/j.biortech.2013.08.109] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2013] [Revised: 08/15/2013] [Accepted: 08/19/2013] [Indexed: 05/16/2023]
Abstract
This is the first report on the characterization of the microbial biofilm community structure and water quality change along a closed and stable raw water distribution system. 454-pyrosequencing was employed to investigate the microbial communities in four biofilm samples. 25,426 optimized sequences were obtained. Results showed Proteobacteria was the dominant phylum in each biofilm sample. The abundance of Nitrospiraes in M6 biofilm, Firmicutes in M8 biofilm, Actinobacteria in M9 biofilm were higher by comparing with other three biofilm samples. The M6 microbial biofilm community structure was similar to that of M7, dissimilar to that of M9. Dissolved oxygen and nitrogen was probably major factors to influence the microbial biofilm communities. Nitrospiraes in M6 biofilm and Firmicutes in M8 biofilm were crucial to remove ammonia nitrogen and nitrate in raw water. How to enrich functional microbes in biofilm to pretreat raw water is an important area of future research.
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Affiliation(s)
- Jianghan Luo
- State Key Laboratory of Urban Water Resource and Environment (SKLUWRE), Harbin Institute of Technology, 73 Huanghe Road, Nangang District, Harbin 150090, PR China; Institute of Cell and Molecular Biology, Harbin University of Commerce, No. 1 Xuehai Street, Songbei District, Harbin, Heilongjiang Province 150028, PR China.
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