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Zhu W, Zhao H, Ke J, Zhang J, Liu X, Zhou Y, Chen R, Wang A, Li X. Deciphering the environmental adaptation and functional trait of core and noncore bacterial communities in impacted coral reef seawater. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 931:172897. [PMID: 38697527 DOI: 10.1016/j.scitotenv.2024.172897] [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: 06/26/2023] [Revised: 11/01/2023] [Accepted: 04/28/2024] [Indexed: 05/05/2024]
Abstract
Microorganisms play pivotal roles in different biogeochemical cycles within coral reef waters. Nevertheless, our comprehension of the microbially mediated processes following environmental perturbation is still limited. To gain a deeper insight into the environmental adaptation and nutrient cycling, particularly within core and noncore bacterial communities, it is crucial to understand reef ecosystem functioning. In this study, we delved into the microbial community structure and function of seawater in a coral reef under different degrees of anthropogenic disturbance. To achieve this, we harnessed the power of 16S rRNA gene high-throughput sequencing and metagenomics techniques. The results showed that a continuous temporal succession but little spatial heterogeneity in the bacterial communities of core and noncore taxa and functional profiles involved in nitrogen (N) and phosphorus (P) cycling. Eutrophication state (i.e., nutrient concentration and turbidity) and temperature played pivotal roles in shaping both the microbial community composition and functional traits of coral reef seawater. Within this context, the core subcommunity exhibited a remarkably broader habitat niche breadth, stronger phylogenetic signal and lower environmental sensitivity when compared to the noncore taxa. Null model analysis further revealed that the core subcommunity was governed primarily by stochastic processes, while deterministic processes played a more significant role in shaping the noncore subcommunity. Furthermore, our observations indicated that changes in function related to N cycling were correlated to the variations in noncore taxa, while core taxa played a more substantial role in critical processes such as P cycling. Collectively, these findings facilitated our knowledge about environmental adaptability of core and noncore bacterial taxa and shed light on their respective roles in maintaining diverse nutrient cycling within coral reef ecosystems.
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Affiliation(s)
- Wentao Zhu
- College of Ecology and Environment, Hainan University, Haikou, China; State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, China
| | - He Zhao
- College of Ecology and Environment, Hainan University, Haikou, China; State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, China
| | - Jingzhao Ke
- College of Marine Biology and Fisheries, Hainan University, Haikou, China; State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, China
| | - Junling Zhang
- College of Marine Biology and Fisheries, Hainan University, Haikou, China; State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, China
| | - Xiangbo Liu
- College of Marine Biology and Fisheries, Hainan University, Haikou, China; State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, China
| | - Yinyin Zhou
- College of Marine Biology and Fisheries, Hainan University, Haikou, China; State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, China
| | - Rouwen Chen
- College of Marine Biology and Fisheries, Hainan University, Haikou, China; State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, China
| | - Aimin Wang
- College of Marine Biology and Fisheries, Hainan University, Haikou, China; State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, China
| | - Xiubao Li
- College of Marine Biology and Fisheries, Hainan University, Haikou, China; State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, China.
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Delgadillo-Ordoñez N, Garcias-Bonet N, Raimundo I, García FC, Villela H, Osman EO, Santoro EP, Curdia J, Rosado JGD, Cardoso P, Alsaggaf A, Barno A, Antony CP, Bocanegra C, Berumen ML, Voolstra CR, Benzoni F, Carvalho S, Peixoto RS. Probiotics reshape the coral microbiome in situ without detectable off-target effects in the surrounding environment. Commun Biol 2024; 7:434. [PMID: 38594357 PMCID: PMC11004148 DOI: 10.1038/s42003-024-06135-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 04/02/2024] [Indexed: 04/11/2024] Open
Abstract
Beneficial microorganisms for corals (BMCs), or probiotics, can enhance coral resilience against stressors in laboratory trials. However, the ability of probiotics to restructure the coral microbiome in situ is yet to be determined. As a first step to elucidate this, we inoculated putative probiotic bacteria (pBMCs) on healthy colonies of Pocillopora verrucosa in situ in the Red Sea, three times per week, during 3 months. pBMCs significantly influenced the coral microbiome, while bacteria of the surrounding seawater and sediment remained unchanged. The inoculated genera Halomonas, Pseudoalteromonas, and Bacillus were significantly enriched in probiotic-treated corals. Furthermore, the probiotic treatment also correlated with an increase in other beneficial groups (e.g., Ruegeria and Limosilactobacillus), and a decrease in potential coral pathogens, such as Vibrio. As all corals (treated and non-treated) remained healthy throughout the experiment, we could not track health improvements or protection against stress. Our data indicate that healthy, and therefore stable, coral microbiomes can be restructured in situ, although repeated and continuous inoculations may be required in these cases. Further, our study provides supporting evidence that, at the studied scale, pBMCs have no detectable off-target effects on the surrounding microbiomes of seawater and sediment near inoculated corals.
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Affiliation(s)
- Nathalia Delgadillo-Ordoñez
- Red Sea Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Marine Science and Bioscience Programs, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Neus Garcias-Bonet
- Red Sea Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Inês Raimundo
- Red Sea Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Marine Science and Bioscience Programs, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Francisca C García
- Red Sea Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Helena Villela
- Red Sea Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Eslam O Osman
- Red Sea Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Erika P Santoro
- Red Sea Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Joao Curdia
- Red Sea Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Joao G D Rosado
- Red Sea Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Marine Science and Bioscience Programs, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Pedro Cardoso
- Red Sea Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Marine Science and Bioscience Programs, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Ahmed Alsaggaf
- Red Sea Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Marine Science and Bioscience Programs, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Adam Barno
- Red Sea Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Marine Science and Bioscience Programs, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Chakkiath Paul Antony
- Red Sea Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Carolina Bocanegra
- Red Sea Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Michael L Berumen
- Red Sea Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Marine Science and Bioscience Programs, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | | | - Francesca Benzoni
- Red Sea Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Marine Science and Bioscience Programs, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Susana Carvalho
- Red Sea Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Marine Science and Bioscience Programs, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Raquel S Peixoto
- Red Sea Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia.
- Marine Science and Bioscience Programs, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia.
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Sparagon WJ, Arts MGI, Quinlan ZA, Wegley Kelly L, Koester I, Comstock J, Bullington JA, Carlson CA, Dorrestein PC, Aluwihare LI, Haas AF, Nelson CE. Coral thermal stress and bleaching enrich and restructure reef microbial communities via altered organic matter exudation. Commun Biol 2024; 7:160. [PMID: 38351328 PMCID: PMC10864316 DOI: 10.1038/s42003-023-05730-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 12/16/2023] [Indexed: 02/16/2024] Open
Abstract
Coral bleaching is a well-documented and increasingly widespread phenomenon in reefs across the globe, yet there has been relatively little research on the implications for reef water column microbiology and biogeochemistry. A mesocosm heating experiment and bottle incubation compared how unbleached and bleached corals alter dissolved organic matter (DOM) exudation in response to thermal stress and subsequent effects on microbial growth and community structure in the water column. Thermal stress of healthy corals tripled DOM flux relative to ambient corals. DOM exudates from stressed corals (heated and/or previously bleached) were compositionally distinct from healthy corals and significantly increased growth of bacterioplankton, enriching copiotrophs and putative pathogens. Together these results demonstrate how the impacts of both short-term thermal stress and long-term bleaching may extend into the water column, with altered coral DOM exudation driving microbial feedbacks that influence how coral reefs respond to and recover from mass bleaching events.
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Affiliation(s)
- Wesley J Sparagon
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, Department of Oceanography and Sea Grant College Program, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Honolulu, HI, 96822, USA.
| | - Milou G I Arts
- Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, Texel, The Netherlands
| | - Zachary A Quinlan
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, USA
- San Diego State University, San Diego, USA
| | - Linda Wegley Kelly
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, USA
- San Diego State University, San Diego, USA
| | - Irina Koester
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, USA
| | - Jacqueline Comstock
- Department of Ecology, Evolution and Marine Biology, The Marine Science Institute, University of California Santa Barbara, Santa Barbara, USA
| | - Jessica A Bullington
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, Department of Oceanography and Sea Grant College Program, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Honolulu, HI, 96822, USA
| | - Craig A Carlson
- Department of Ecology, Evolution and Marine Biology, The Marine Science Institute, University of California Santa Barbara, Santa Barbara, USA
| | | | - Lihini I Aluwihare
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, USA
| | - Andreas F Haas
- Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, Texel, The Netherlands
- San Diego State University, San Diego, USA
| | - Craig E Nelson
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, Department of Oceanography and Sea Grant College Program, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Honolulu, HI, 96822, USA
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Montaño-Salazar S, Quintanilla E, Sánchez JA. Microbial shifts associated to ENSO-derived thermal anomalies reveal coral acclimation at holobiont level. Sci Rep 2023; 13:22049. [PMID: 38087002 PMCID: PMC10716379 DOI: 10.1038/s41598-023-49049-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 12/04/2023] [Indexed: 12/18/2023] Open
Abstract
The coral microbiome conforms a proxy to study effects of changing environmental conditions. However, scarce information exists regarding microbiome dynamics and host acclimation in response to environmental changes associated to global-scale disturbances. We assessed El Niño Southern Oscillation (ENSO)-derived thermal anomalies shifts in the bacterial microbiome of Pacifigorgia cairnsi (Gorgoniidae: Octocorallia) from the remote island of Malpelo in the Tropical Eastern Pacific. Malpelo is a hot spot of biodiversity and lacks direct coastal anthropogenic impacts. We evaluated the community composition and predicted functional profiles of the microbiome during 2015, 2017 and 2018, including different phases of ENSO cycle. The bacterial community diversity and composition between the warming and cooling phase were similar, but differed from the neutral phase. Relative abundances of different microbiome core members such as Endozoicomonas and Mycoplasma mainly drove these differences. An acclimated coral holobiont is suggested not just to warm but also to cold stress by embracing similar microbiome shifts and functional redundancy that allow maintaining coral's viability under thermal stress. Responses of the microbiome of unperturbed sea fans such as P. cairnsi in Malpelo could be acting as an extended phenotype facilitating the acclimation at the holobiont level.
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Affiliation(s)
- Sandra Montaño-Salazar
- Division of Microbial Ecology, Department for Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Elena Quintanilla
- Department of Soil and Water Sciences, University of Florida, 2033 Mowry Rd, Gainesville, FL, 32610, USA.
| | - Juan A Sánchez
- Laboratory of Marine Molecular Biology (BIOMMAR), Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
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Zhao W, Chen X, Liu R, Tian P, Niu W, Zhang XH, Liu J, Wang X. Distinct coral environments shape the dynamic of planktonic Vibrio spp. ENVIRONMENTAL MICROBIOME 2023; 18:77. [PMID: 37872593 PMCID: PMC10594878 DOI: 10.1186/s40793-023-00532-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Accepted: 10/04/2023] [Indexed: 10/25/2023]
Abstract
BACKGROUND Coral reefs are one of the most biodiverse and productive ecosystems, providing habitat for a vast of species. Reef-building scleractinian corals with a symbiotic microbiome, including bacteria, archaea, viruses and eukaryotic microbes, are referred to coral holobionts. Among them, coral diseases, mainly caused by Vibrio spp., have significantly contributed to the loss of coral cover and diversity. Habitat filtering across the globe has led to a variety structure of marine bacterial communities. Coral species, quantity and characteristics are significant differences between the Xisha Islands and Daya Bay (Guangdong Province). Thus, the Vibrio communities may be distinct between coral rich and poor areas. RESULTS Through comparison of Vibrio dynamics between coral-rich (Xisha Islands) and coral-poor (Daya Bay) locations, we uncovered differences in Vibrio abundance, diversity, community composition and assembly mechanisms associated with corals. The higher abundance of Vibrio in coral rich areas may indicate a strong interaction between vibrios and corals. V. campbellii, Paraphotobacterium marinum and V. caribbeanicus were widely distributed in both coral rich and poor areas, likely indicating weak species specificity in the coral-stimulated growth of Vibrio. Random-forest prediction revealed Vibrio species and Photobacterium species as potential microbial indicators in the coral rich and coral poor areas, respectively. Ecological drift rather than selection governed the Vibrio community assembly in the Xisha Islands. Comparatively, homogenizing selection was more important for the Daya Bay community, which may reflect a role of habitat filtration. CONCLUSION This study revealed the different distribution pattern and assembly mechanism of Vibrio spp. between coral rich and poor areas, providing the background data for the research of Vibrio community in coral reef areas and may help the protection of coral reef at the biological level. The main reasons for the difference were different number and species of corals, environmental (e.g., temperature) and spatial factors. It reflected the strong interaction between Vibrio and corals, and provided a new perspective for the investigation of Vibrio in coral reef ecosystem.
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Affiliation(s)
- Wenbin Zhao
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266100, China
| | - Xing Chen
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266100, China
| | - Ronghua Liu
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266100, China
| | - Peng Tian
- Laboratory of Marine Biodiversity Research, Third Institute of Oceanography, Ministry of Natural Resources, 178 Daxue Road, Xiamen, 361005, China
- Nansha Islands Coral Reef Ecosystem National Observation and Research Station, Guangzhou, 510000, China
| | - Wentao Niu
- Laboratory of Marine Biodiversity Research, Third Institute of Oceanography, Ministry of Natural Resources, 178 Daxue Road, Xiamen, 361005, China
- Nansha Islands Coral Reef Ecosystem National Observation and Research Station, Guangzhou, 510000, China
| | - Xiao-Hua Zhang
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266100, China
| | - Jiwen Liu
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China.
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266100, China.
| | - Xiaolei Wang
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China.
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266100, China.
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Sun H, Miao Z, Liu S, Liu X, Chen B, Liao B, Xiao B. Neorhizobium turbinariae sp. nov., a coral-beneficial bacterium isolated from Turbinaria peltata. Int J Syst Evol Microbiol 2023; 73. [PMID: 37750757 DOI: 10.1099/ijsem.0.006057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/27/2023] Open
Abstract
Coral reef ecosystems are facing decline due to climate change, overfishing, habitat destruction and pollution. Bacteria play an essential role in maintaining the stability of coral reef ecosystems, influencing the well-being and fitness of coral hosts. The exploitation of coral probiotics has become an urgent issue. A short-rod shaped aerobic bacterium, designated NTR19T, was isolated in a healthy coral Turbinaria peltata from Daya Bay, Shenzhen, PR China. Its cells were Gram-negative, motile with a polar flagellum. The activities of catalase and oxidase were positive. Strain NTR19T grew at 10-41 °C (optimum, 28 °C), with NaCl concentrations of 0-4 % (w/v; optimum, 0.5 %) and at pH 5.0-9.5 (optimum, pH 7.0-7.5). The predominant fatty acids (>10 %) were summed feature 8 (57.6 %), C19 : 0 cyclo ω8c (12.6 %) and C16 : 0 (12.0 %). The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phospholipid and phosphatidylcholine. The major respiratory quinone was Q-10. The draft genome was 4.68 Mbp with 61.2 mol% DNA G+C content. In total, 4477 coding sequences were annotated and there were 64 RNA genes. The average nucleotide identity (ANI) and average amino acid identity (AAI) values between strain NTR19T and the related Neorhizobium species were 78.23-79.70% and 80.26-80.50 %, respectively. This strain encoded many proteins for the activities of catalase and oxidase in the genome. Strain NTR19T was clearly distinct from its closest neighbours Rhizobium oryzicola ACCC 05753T and Neorhizobium petrolearium ACCC 11238T with the 16S rRNA gene sequence similarity values of 96.86 and 96.36 %, respectively. The results of phylogenetic analysis, as well as ANI and AAI values, revealed that strain NTR19T belongs to Neorhizobium and was distinct from other species of this genus. The physiological, biochemical and chemotaxonomic characteristics also supported the species novelty of strain NTR19T. Thus, strain NTR19T is considered to be classified as a novel species in the genus Neorhizobium, for which the name Neorhizobium turbinariae sp. nov. is proposed. The type strain is NTR19T (=JCM 35342T=MCCC 1K07226T).
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Affiliation(s)
- Hao Sun
- School of Ocean, Yantai University, Yantai, 264005, PR China
| | - Zhiyuan Miao
- Shenzhen Institute of Guangdong Ocean University, Binhai 2 Road, Shenzhen, 518120, PR China
| | - Shuai Liu
- School of Ocean, Yantai University, Yantai, 264005, PR China
| | - Xuerui Liu
- School of Ocean, Yantai University, Yantai, 264005, PR China
| | - Bogui Chen
- Shenzhen Institute of Guangdong Ocean University, Binhai 2 Road, Shenzhen, 518120, PR China
| | - Baolin Liao
- Shenzhen Institute of Guangdong Ocean University, Binhai 2 Road, Shenzhen, 518120, PR China
| | - Baohua Xiao
- Shenzhen Institute of Guangdong Ocean University, Binhai 2 Road, Shenzhen, 518120, PR China
- College of Fisheries, Guangdong Ocean University, Zhanjiang, 524088, PR China
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Villela H, Modolon F, Schultz J, Delgadillo-Ordoñez N, Carvalho S, Soriano AU, Peixoto RS. Genome analysis of a coral-associated bacterial consortium highlights complementary hydrocarbon degradation ability and other beneficial mechanisms for the host. Sci Rep 2023; 13:12273. [PMID: 37507453 PMCID: PMC10382565 DOI: 10.1038/s41598-023-38512-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 07/09/2023] [Indexed: 07/30/2023] Open
Abstract
Here we report the oil degradation genetic potential of six oil-degrading bacteria (ODB), previously used as a bioremediation consortium, isolated from the hydrocoral Millepora alcicornis and seawater. The strains were identified as Halomonas sp. (LC_1), Cobetia sp. (LC_6), Pseudoalteromonas shioyasakiensis (LC_2), Halopseudomonas aestusnigri (LC_3), Shewanella algae (LC_4), and Brucella intermedia (LC_5). The taxonomic identification differed from that of the original paper when we used whole genome gene markers instead of just 16S rRNA gene. Genes responsible for the degradation of aromatic hydrocarbons and n-alkanes were found in all genomes, although different (and complementary) steps of the metabolic pathways were unique to each strain. Genes for naphthalene and toluene degradation were found in various strains. We annotated quinate degradation genes in LC_6, while LC_3 and LC_5 presented genes for biosurfactant and rhamnolipid biosynthesis. We also annotated genes related to beneficial mechanisms for corals, such as genes involved in nitrogen and DMSP metabolism, cobalamin biosynthesis and antimicrobial compounds production. Our findings reinforce the importance of using bacterial consortia for bioremediation approaches instead of single strains, due to their complementary genomic arsenals. We also propose a genome-based framework to select complementary ODB that can provide additional benefits to coral health.
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Affiliation(s)
- Helena Villela
- Red Sea Research Center, Biological and Environmental Science and Engineering Division King, Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
- Laboratory of Molecular Microbial Ecology, Institute of Microbiology, Federal University of Rio de Janeiro, Rio de Janeiro, 21941-902, Brazil
| | - Flúvio Modolon
- Red Sea Research Center, Biological and Environmental Science and Engineering Division King, Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
- Laboratory of Molecular Microbial Ecology, Institute of Microbiology, Federal University of Rio de Janeiro, Rio de Janeiro, 21941-902, Brazil
| | - Júnia Schultz
- Red Sea Research Center, Biological and Environmental Science and Engineering Division King, Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
- Computational Biology Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
| | - Nathalia Delgadillo-Ordoñez
- Red Sea Research Center, Biological and Environmental Science and Engineering Division King, Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
| | - Susana Carvalho
- Red Sea Research Center, Biological and Environmental Science and Engineering Division King, Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
- Marine Science and Bioscience Programs, Biological, Environmental and Engineering Sciences Division, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
| | | | - Raquel Silva Peixoto
- Red Sea Research Center, Biological and Environmental Science and Engineering Division King, Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia.
- Computational Biology Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia.
- Marine Science and Bioscience Programs, Biological, Environmental and Engineering Sciences Division, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia.
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Xu M, Cheng K, Xiao B, Tong M, Cai Z, Jong MC, Chen G, Zhou J. Bacterial Communities Vary from Different Scleractinian Coral Species and between Bleached and Non-Bleached Corals. Microbiol Spectr 2023; 11:e0491022. [PMID: 37191552 PMCID: PMC10269541 DOI: 10.1128/spectrum.04910-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 04/07/2023] [Indexed: 05/17/2023] Open
Abstract
Bleaching is one of the most relevant factors implicated in the integrity of coral reef ecosystems, with the increasing frequency and intensity of damaging events representing a serious threat to reef biodiversity. Here, we analyzed changes in coral-associated bacteria from three types of non-bleached and bleached scleractinian corals (Acropora digitifera, Galaxea fascicularis, and Porites pukoensis) in Hainan Luhuitou peninsula coastal areas. The community structure of symbiotic bacteria differed significantly among the three apparently healthy corals. The bleached corals had higher bacterial alpha diversity and some specific bacteria genera, including Ruegeria, Methyloceanibacter, Filomicrobium, Halioglobus, Rubripirellula, Rhodopirellula, Silicimonas, Blastopirellula, Sva0996 marine group, Woeseia, and unclassified_c_Gammaproteobacteria, were consistently increased in bleached groups. Network analysis revealed significantly different degrees of modularity between bleached and non-bleached groups at the bacterial genus level, and a higher proportion of links was dominated by positive co-occurrences. Functional prediction analysis illustrated that coral-associated bacteria remained relatively consistent in the bleached and non-bleached groups. Structure equation modeling revealed that the bacterial community diversity and function were directly influenced by host and environment factors. These findings suggested that coral-associated bacterial responses to bleaching occur in a host-dependent manner, informing novel strategies for restoring coral and aiding adaption to bleaching stress. IMPORTANCE Accumulating evidence indicates that coral-associated bacteria play an important role in the health of holobionts. However, the variability of the symbiotic bacterial community structure among coral species with different coral health statuses remains largely unknown. Here, we investigated three apparent non-bleached (healthy) and bleached coral species (sampled in situ), involving related symbiotic bacterial profiles, including composition, alpha diversity, network relationship, and potential function. Structural equation modeling analysis was used to analyze the relationship between coral status and abiotic and biotic factors. The bacterial community structure of different groups was shown to exhibit host-specific traits. Both host and environmental impacts had primary effects on coral-associated microbial communities. Future studies are needed to identify the mechanisms that mediate divergent microbial consortia.
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Affiliation(s)
- Meiting Xu
- School of Environment, Harbin Institute of Technology, Harbin, People’s Republic of China
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Weihai, Shandong Province, People’s Republic of China
| | - Keke Cheng
- Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Institute for Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen, People’s Republic of China
| | - Baohua Xiao
- Shenzhen Institute of Guangdong Ocean University, Shenzhen, People’s Republic of China
| | - Mengmeng Tong
- Ocean College, Zhejiang University, Zhoushan, People’s Republic of China
| | - Zhonghua Cai
- Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Institute for Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen, People’s Republic of China
| | - Mui-Choo Jong
- Institute of Environment and Ecology, Shenzhen International Graduate School, Tsinghua University, Shenzhen, People’s Republic of China
| | - Guofu Chen
- School of Environment, Harbin Institute of Technology, Harbin, People’s Republic of China
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Weihai, Shandong Province, People’s Republic of China
| | - Jin Zhou
- Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Institute for Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen, People’s Republic of China
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9
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Padayhag BM, Nada MAL, Baquiran JIP, Sison-Mangus MP, San Diego-McGlone ML, Cabaitan PC, Conaco C. Microbial community structure and settlement induction capacity of marine biofilms developed under varied reef conditions. MARINE POLLUTION BULLETIN 2023; 193:115138. [PMID: 37321001 DOI: 10.1016/j.marpolbul.2023.115138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 05/27/2023] [Accepted: 06/01/2023] [Indexed: 06/17/2023]
Abstract
Coral larval settlement relies on biogenic cues such as those elicited by microbial biofilm communities, a crucial element of coral recruitment. Eutrophication can modify these biofilm-associated communities, but studies on how this affects coral larval settlement are limited. In this study, we developed biofilm communities on glass slides at four sites with increasing distance from a mariculture zone. Biofilms farthest from the mariculture area were more effective at inducing the settlement of Acropora tenuis larvae. These biofilms were characterized by a greater proportion of crustose coralline algae (CCA) and gammaproteobacterial taxa compared to biofilms from sites closer to the mariculture zone, which had a greater proportion of cyanobacteria and no CCA. These findings suggest that nutrient enrichment due to mariculture activities alters the composition of biofilm-associated microbiome at nearby reef sites and indirectly causes poor coral larval settlement.
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Affiliation(s)
- Blaire M Padayhag
- Marine Science Institute, University of the Philippines Diliman, Quezon City, Philippines
| | - Michael Angelou L Nada
- Marine Science Institute, University of the Philippines Diliman, Quezon City, Philippines
| | - Jake Ivan P Baquiran
- Marine Science Institute, University of the Philippines Diliman, Quezon City, Philippines
| | | | | | - Patrick C Cabaitan
- Marine Science Institute, University of the Philippines Diliman, Quezon City, Philippines
| | - Cecilia Conaco
- Marine Science Institute, University of the Philippines Diliman, Quezon City, Philippines.
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10
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Dong K, Qiu Y, Wang X, Yu D, Yu Z, Feng J, Wang J, Gu R, Zhao J. Towards low carbon demand and highly efficient nutrient removal: Establishing denitrifying phosphorus removal in a biofilm-based system. BIORESOURCE TECHNOLOGY 2023; 372:128658. [PMID: 36690218 DOI: 10.1016/j.biortech.2023.128658] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 01/14/2023] [Accepted: 01/18/2023] [Indexed: 06/17/2023]
Abstract
The combined denitrifying phosphorus removal (DPR) and Anammox process is expected to achieve advanced nutrient removal with low carbon consumption. However, exchanging ammonia/nitrate between them is one limitation. This study investigated the feasibility of conducting DPR in a biofilm reactor to solve that problem. After 46-day anaerobic/aerobic operation, high phosphorus removal efficiency (PRE, 83.15 %) was obtained in the activated sludge (AS) and biofilm co-existed system, in which the AS performed better. Phosphate-accumulating organisms might quickly adapt to the anoxic introduced nitrate, but the following aerobic stage ensured a low effluent orthophosphate (<1.03 mg/L). Because of waste sludge discharging and AS transforming to biofilm, the suspended solids dropped below 60 mg/L on Day 100, resulting in PRE decline (17.17 %) and effluent orthophosphate rise (4.23 mg/L). Metagenomes analysis revealed that Pseudomonas and Thiothrix had genes for denitrification and encoding Pit phosphate transporter, and Candidatus_Competibacter was necessary for biofilm formation.
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Affiliation(s)
- Kaiyue Dong
- School of Environmental Science and Engineering, Qingdao University, Qingdao 266071, China
| | - Yanling Qiu
- School of Environmental Science and Engineering, Qingdao University, Qingdao 266071, China
| | - Xiaoxia Wang
- School of Environmental Science and Engineering, Qingdao University, Qingdao 266071, China; Efficient Intelligent Sewage Treatment Technology Innovation Center of Shandong Province, Linyi 276000, China; Carbon Neutrality and Eco-Environmental Technology Innovation Center of Qingdao, Qingdao 266071, China
| | - Deshuang Yu
- School of Environmental Science and Engineering, Qingdao University, Qingdao 266071, China
| | - Zhengda Yu
- School of Environmental Science and Engineering, Qingdao University, Qingdao 266071, China; Carbon Neutrality and Eco-Environmental Technology Innovation Center of Qingdao, Qingdao 266071, China
| | - Juan Feng
- Science and Technology Department, Qingdao University, Qingdao 266071, China
| | - Jimiao Wang
- Qingdao Water Group Co. Ltd., Qingdao 266071, China
| | - Ruihuan Gu
- Qingdao Water Group Co. Ltd., Qingdao 266071, China
| | - Ji Zhao
- School of Environmental Science and Engineering, Qingdao University, Qingdao 266071, China; Efficient Intelligent Sewage Treatment Technology Innovation Center of Shandong Province, Linyi 276000, China; Carbon Neutrality and Eco-Environmental Technology Innovation Center of Qingdao, Qingdao 266071, China.
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11
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Mohamed HF, Abd‐Elgawad A, Cai R, Luo Z, Xu C. The bacterial signature offers vision into the machinery of coral fitness across high-latitude coral reef in the South China Sea. ENVIRONMENTAL MICROBIOLOGY REPORTS 2023; 15:13-30. [PMID: 36054576 PMCID: PMC10103774 DOI: 10.1111/1758-2229.13119] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 08/15/2022] [Indexed: 05/20/2023]
Abstract
Coral-bacterial interaction is a major driver in coral acclimatization to the stressful environment. 16S rRNA High-throughput sequencing was used to classify the role of different coral reef compartments; sediment, water, and tissue; in the South China Sea (SCS), as well as different locations in shaping the microbial community. The majority of OTUs significantly shifted at impacted sites and indicated distinction in the relative abundance of bacteria compartment/site-wise. Richness and diversity were higher, and more taxa were enriched in the sediment communities. Proteobacteria dominated sediment samples, while Cyanobacteria dominated water samples. Coral tissue showed a shift among different sites with Proteobacteria remaining the dominant Phylum. Moreover, we report a dominance of Chlorobium genus in the healthy coral tissue sample collected from the severely damaged Site B, suggesting a contribution to tolerance and adaptation to the disturbing environment. Thus, revealing the complex functionally diverse microbial patterns associated with biotic and abiotic disturbed coral reefs will deliver understanding of the symbiotic connections and competitive benefit inside the hosts niche and can reveal a measurable footprint of the environmental impacts on coral ecosystems. We hence, urge scientists to draw more attention towards using coral microbiome as a self-sustaining tool in coral restoration.
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Affiliation(s)
- Hala F. Mohamed
- Third Institute of OceanographyMinistry of Natural ResourcesXiamenPeople's Republic of China
- Al‐Azhar University (Girls Branch)Faculty of Science, Botany & Microbiology DepartmentCairoEgypt
| | - Amro Abd‐Elgawad
- Third Institute of OceanographyMinistry of Natural ResourcesXiamenPeople's Republic of China
- Tourism Developing AuthorityCentral Adminstration for Environmental AffairsCairoEgypt
| | - Rongshuo Cai
- Third Institute of OceanographyMinistry of Natural ResourcesXiamenPeople's Republic of China
| | - Zhaohe Luo
- Third Institute of OceanographyMinistry of Natural ResourcesXiamenPeople's Republic of China
| | - Changan Xu
- Third Institute of OceanographyMinistry of Natural ResourcesXiamenPeople's Republic of China
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12
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Nelson CE, Wegley Kelly L, Haas AF. Microbial Interactions with Dissolved Organic Matter Are Central to Coral Reef Ecosystem Function and Resilience. ANNUAL REVIEW OF MARINE SCIENCE 2023; 15:431-460. [PMID: 36100218 DOI: 10.1146/annurev-marine-042121-080917] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
To thrive in nutrient-poor waters, coral reefs must retain and recycle materials efficiently. This review centers microbial processes in facilitating the persistence and stability of coral reefs, specifically the role of these processes in transforming and recycling the dissolved organic matter (DOM) that acts as an invisible currency in reef production, nutrient exchange, and organismal interactions. The defining characteristics of coral reefs, including high productivity, balanced metabolism, high biodiversity, nutrient retention, and structural complexity, are inextricably linked to microbial processing of DOM. The composition of microbes and DOM in reefs is summarized, and the spatial and temporal dynamics of biogeochemical processes carried out by microorganisms in diverse reef habitats are explored in a variety of key reef processes, including decomposition, accretion, trophictransfer, and macronutrient recycling. Finally, we examine how widespread habitat degradation of reefs is altering these important microbe-DOM interactions, creating feedbacks that reduce reef resilience to global change.
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Affiliation(s)
- Craig E Nelson
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, Department of Oceanography, and Sea Grant College Program, School of Ocean and Earth Sciences and Technology, University of Hawai'i at Mānoa, Honolulu, Hawai'i, USA;
| | - Linda Wegley Kelly
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California, USA;
| | - Andreas F Haas
- Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research (NIOZ), Texel, The Netherlands;
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13
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Park J, Davis K, Lajoie G, Parfrey LW. Alternative approaches to identify core bacteria in Fucus distichus microbiome and assess their distribution and host-specificity. ENVIRONMENTAL MICROBIOME 2022; 17:55. [PMID: 36384808 PMCID: PMC9670562 DOI: 10.1186/s40793-022-00451-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 11/09/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Identifying meaningful ecological associations between host and components of the microbiome is challenging. This is especially true for hosts such as marine macroalgae where the taxonomic composition of the microbiome is highly diverse and variable in space and time. Identifying core taxa is one way forward but there are many methods and thresholds in use. This study leverages a large dataset of microbial communities associated with the widespread brown macroalga, Fucus distichus, across sites and years on one island in British Columbia, Canada. We compare three different methodological approaches to identify core taxa at the amplicon sequence variant (ASV) level from this dataset: (1) frequency analysis of taxa on F. distichus performed over the whole dataset, (2) indicator species analysis (IndVal) over the whole dataset that identifies frequent taxa that are enriched on F. distichus in comparison to the local environment, and (3) a two-step IndVal method that identifies taxa that are consistently enriched on F. distichus across sites and time points. We then investigated a F. distichus time-series dataset to see if those core taxa are seasonally consistent on another remote island in British Columbia, Canada. We then evaluate host-specificity of the identified F. distichus core ASVs using comparative data from 32 other macroalgal species sampled at one of the sites. RESULTS We show that a handful of core ASVs are consistently identified by both frequency analysis and IndVal approaches with alternative definitions, although no ASVs were always present on F. distichus and IndVal identified a diverse array of F. distichus indicator taxa across sites on Calvert Island in multiple years. Frequency analysis captured a broader suit of taxa, while IndVal was better at identifying host-specific microbes. Finally, two-step IndVal identified hundreds of indicator ASVs for particular sites/timepoints but only 12 that were indicators in a majority (> 6 out of 11) of sites/timepoints. Ten of these ASVs were also indicators on Quadra Island, 250 km away. Many F. distichus-core ASVs are generally found on multiple macroalgal species, while a few ASVs are highly specific to F. distichus. CONCLUSIONS Different methodological approaches with variable set thresholds influence core identification, but a handful of core taxa are apparently identifiable as they are widespread and temporally associated with F. distichus and enriched in comparison to the environment. Moreover, we show that many of these core ASVs of F. distichus are found on multiple macroalgal hosts, indicating that most occupy a macroalgal generalist niche rather than forming highly specialized associations with F. distichus. Further studies should test whether macroalgal generalists or specialists are more likely to engage in biologically important exchanges with host.
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Affiliation(s)
- Jungsoo Park
- Department of Botany, Biodiversity Research Centre, University of British Columbia, Vancouver, BC Canada
| | - Katherine Davis
- Department of Botany, Biodiversity Research Centre, University of British Columbia, Vancouver, BC Canada
| | - Geneviève Lajoie
- Department of Botany, Biodiversity Research Centre, University of British Columbia, Vancouver, BC Canada
- Institut de Recherche en Biologie Végétale, Département de Sciences Biologiques, Université de Montréal, Montréal, QC Canada
| | - Laura Wegener Parfrey
- Department of Botany, Biodiversity Research Centre, University of British Columbia, Vancouver, BC Canada
- Department of Zoology, University of British Columbia, Vancouver, BC Canada
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14
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Arjunwadkar CV, Tebbett SB, Bellwood DR, Bourne DG, Smith HA. Algal turf structure and composition vary with particulate loads on coral reefs. MARINE POLLUTION BULLETIN 2022; 181:113903. [PMID: 35843165 DOI: 10.1016/j.marpolbul.2022.113903] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 05/10/2022] [Accepted: 06/26/2022] [Indexed: 06/15/2023]
Abstract
Algal turfs trap and retain particulates, however, little is known about the relationship between particulate accumulation and taxonomic composition of algal turfs. We investigated how particulate mass related to algal turf structure (length and density) and community composition (taxonomic and functional) on two disparate reefs. Particulate mass was positively related to algal turf length. By contrast, the relationship between particulate mass and turf density was more complex and followed a negative parabolic shape; density increased with particulate mass before stabilising and then declining. Community analyses showed taxonomic, but not functional group compositions differed significantly between reefs and with increasing particulate mass. Our results suggest high loads of particulates accumulated in algal turfs are related to a longer, lower density turf structure, typified by filamentous forms such as Cladophora. Changes in algal turf structure and composition could have a variety of bottom-up influences on coral reef ecosystems.
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Affiliation(s)
| | - Sterling B Tebbett
- College of Science and Engineering, James Cook University, Townsville, QLD, Australia; Research Hub for Coral Reef Ecosystem Functions, James Cook University, Townsville, QLD, Australia; ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD, Australia
| | - David R Bellwood
- College of Science and Engineering, James Cook University, Townsville, QLD, Australia; Research Hub for Coral Reef Ecosystem Functions, James Cook University, Townsville, QLD, Australia; ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD, Australia
| | - David G Bourne
- College of Science and Engineering, James Cook University, Townsville, QLD, Australia; Australian Institute of Marine Science, Townsville, QLD, Australia
| | - Hillary A Smith
- College of Science and Engineering, James Cook University, Townsville, QLD, Australia; Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, University of New South Wales, Kensington, NSW, Australia.
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15
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Roth F, El-Khaled YC, Karcher DB, Rädecker N, Carvalho S, Duarte CM, Silva L, Calleja ML, Morán XAG, Jones BH, Voolstra CR, Wild C. Nutrient pollution enhances productivity and framework dissolution in algae- but not in coral-dominated reef communities. MARINE POLLUTION BULLETIN 2021; 168:112444. [PMID: 33984578 DOI: 10.1016/j.marpolbul.2021.112444] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 04/26/2021] [Accepted: 04/28/2021] [Indexed: 06/12/2023]
Abstract
Ecosystem services provided by coral reefs may be susceptible to the combined effects of benthic species shifts and anthropogenic nutrient pollution, but related field studies are scarce. We thus investigated in situ how dissolved inorganic nutrient enrichment, maintained for two months, affected community-wide biogeochemical functions of intact coral- and degraded algae-dominated reef patches in the central Red Sea. Results from benthic chamber incubations revealed 87% increased gross productivity and a shift from net calcification to dissolution in algae-dominated communities after nutrient enrichment, but the same processes were unaffected by nutrients in neighboring coral communities. Both community types changed from net dissolved organic nitrogen sinks to sources, but the increase in net release was 56% higher in algae-dominated communities. Nutrient pollution may, thus, amplify the effects of community shifts on key ecosystem services of coral reefs, possibly leading to a loss of structurally complex habitats with carbonate dissolution and altered nutrient recycling.
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Affiliation(s)
- Florian Roth
- Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia; Baltic Sea Centre, Stockholm University, Stockholm, Sweden; Tvärminne Zoological Station, University of Helsinki, Helsinki, Finland.
| | - Yusuf C El-Khaled
- Marine Ecology, Faculty of Biology and Chemistry, University of Bremen, Bremen, Germany
| | - Denis B Karcher
- Marine Ecology, Faculty of Biology and Chemistry, University of Bremen, Bremen, Germany; Australian National Centre for the Public Awareness of Science, Australian National University, Canberra, Australia
| | - Nils Rädecker
- Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia; Laboratory for Biological Geochemistry, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland; Department of Biology, University of Konstanz, Konstanz, Germany
| | - Susana Carvalho
- Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Carlos M Duarte
- Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia; Computational Biology Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Luis Silva
- Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Maria Ll Calleja
- Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia; Department of Climate Geochemistry, Max Planck Institute for Chemistry (MPIC), Mainz, Germany
| | - Xosé Anxelu G Morán
- Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Burton H Jones
- Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Christian R Voolstra
- Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia; Department of Biology, University of Konstanz, Konstanz, Germany
| | - Christian Wild
- Marine Ecology, Faculty of Biology and Chemistry, University of Bremen, Bremen, Germany
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16
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Wambua S, Gourlé H, de Villiers EP, Karlsson-Lindsjö O, Wambiji N, Macdonald A, Bongcam-Rudloff E, de Villiers S. Cross-Sectional Variations in Structure and Function of Coral Reef Microbiome With Local Anthropogenic Impacts on the Kenyan Coast of the Indian Ocean. Front Microbiol 2021; 12:673128. [PMID: 34248882 PMCID: PMC8260691 DOI: 10.3389/fmicb.2021.673128] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 05/31/2021] [Indexed: 11/13/2022] Open
Abstract
Coral reefs face an increased number of environmental threats from anthropomorphic climate change and pollution from agriculture, industries and sewage. Because environmental changes lead to their compositional and functional shifts, coral reef microbial communities can serve as indicators of ecosystem impacts through development of rapid and inexpensive molecular monitoring tools. Little is known about coral reef microbial communities of the Western Indian Ocean (WIO). We compared taxonomic and functional diversity of microbial communities inhabiting near-coral seawater and sediments from Kenyan reefs exposed to varying impacts of human activities. Over 19,000 species (bacterial, viral and archaeal combined) and 4,500 clusters of orthologous groups of proteins (COGs) were annotated. The coral reefs showed variations in the relative abundances of ecologically significant taxa, especially copiotrophic bacteria and coliphages, corresponding to the magnitude of the neighboring human impacts in the respective sites. Furthermore, the near-coral seawater and sediment metagenomes had an overrepresentation of COGs for functions related to adaptation to diverse environments. Malindi and Mombasa marine parks, the coral reef sites closest to densely populated settlements were significantly enriched with genes for functions suggestive of mitigation of environment perturbations including the capacity to reduce intracellular levels of environmental contaminants and repair of DNA damage. Our study is the first metagenomic assessment of WIO coral reef microbial diversity which provides a much-needed baseline for the region, and points to a potential area for future research toward establishing indicators of environmental perturbations.
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Affiliation(s)
- Sammy Wambua
- Pwani University Bioscience Research Centre (PUBReC), Pwani University, Kilifi, Kenya.,Department of Biological Sciences, Pwani University, Kilifi, Kenya
| | - Hadrien Gourlé
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Etienne P de Villiers
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya.,Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Oskar Karlsson-Lindsjö
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Nina Wambiji
- Kenya Marine and Fisheries Research Institute, Mombasa, Kenya
| | - Angus Macdonald
- School of Life Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Erik Bongcam-Rudloff
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Santie de Villiers
- Pwani University Bioscience Research Centre (PUBReC), Pwani University, Kilifi, Kenya.,Department of Biochemistry and Biotechnology, Pwani University, Kilifi, Kenya
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17
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Dai H, Gao J, Li D, Wang Z, Duan W. Metagenomics combined with DNA-based stable isotope probing provide comprehensive insights of active triclosan-degrading bacteria in wastewater treatment. JOURNAL OF HAZARDOUS MATERIALS 2021; 404:124192. [PMID: 33069997 DOI: 10.1016/j.jhazmat.2020.124192] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 10/02/2020] [Accepted: 10/04/2020] [Indexed: 06/11/2023]
Abstract
The biotransformation of triclosan (TCS) during wastewater treatment occurred frequently, while little researches are known the identity of microorganisms involved in the biodegradation process. In this work, DNA-based stable isotope probing (DNA-SIP) was occupied to investigate the TCS assimilation microbes originated from a full-scale cyclic activated sludge system in Beijing. Results of TCS removal pathway showed that the TCS removal in nitrification process was mainly contributed by the metabolism of heterotrophic bacteria, accounting for about 18.54%. DNA-SIP assay indicated that Sphingobium dominated the degradation of TCS. Oligotyping analysis further indicated that oligotype GCTAAT and ATGTTA of Sphingobium played important roles in degrading TCS. Furthermore, the Kyoto Encyclopedia of Genes and Genomes functional abundance statistics based on PICRUSt2 showed that glutathione transferase was the most prevalent enzyme involved in TCS metabolism, and TCS might be removed through microbial carbon metabolism. Metagenomics made clear that Sphingobium might play irrelevant role on the propagation of antibiotics resistance genes (ARGs), even though, it could degrade TCS. Thauera and Dechloromonas were identified as the key hosts of most ARGs. This study revealed the potential metabolic pathway and microbial ecology of TCS biodegradation in nitrification process of wastewater treatment system.
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Affiliation(s)
- Huihui Dai
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Beijing University of Technology, Beijing 100124, China
| | - Jingfeng Gao
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Beijing University of Technology, Beijing 100124, China.
| | - Dingchang Li
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Beijing University of Technology, Beijing 100124, China
| | - Zhiqi Wang
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Beijing University of Technology, Beijing 100124, China
| | - Wanjun Duan
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Beijing University of Technology, Beijing 100124, China
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18
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Jones AG, Denis L, Fournier J, Desroy N, Duong G, Dubois SF. Linking multiple facets of biodiversity and ecosystem functions in a coastal reef habitat. MARINE ENVIRONMENTAL RESEARCH 2020; 162:105092. [PMID: 32892150 DOI: 10.1016/j.marenvres.2020.105092] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 07/20/2020] [Accepted: 07/23/2020] [Indexed: 06/11/2023]
Abstract
Reef-building species play key roles in promoting local species richness and regulating ecosystem functions like biogeochemical fluxes. We evaluated the functioning of a habitat engineered by the reef-building polychaete Sabellaria alveolata, by measuring oxygen and nutrient fluxes in the reef structures and in the soft-sediments nearby. Then, we investigated the relative importance of temperature, the engineer S. alveolata, and different facets of macrofauna diversity (taxonomic, functional diversity and identity), on the reef biogeochemical fluxes using multiple linear regressions and effect sizes. The reef fluxes were more intense than the soft-sediment fluxes and mainly driven by the engineer biomass and abundance, stressing the importance of these biogenic structures. Higher water temperatures and an intermediate level of associated macrofauna functional dispersion weighted only by abundance (i.e. intermediate biological trait variability) maximized the reef's global biogeochemical functioning. Ultimately, the physical degradation of the reefs could lead to lower levels of functioning.
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Affiliation(s)
- Auriane G Jones
- IFREMER, Laboratoire Centre de Bretagne, DYNECO, Laboratoire d'Ecologie Benthique Côtière (LEBCO), 29280, Plouzané, France; IFREMER, Laboratoire Environnement et Ressources Bretagne nord, BP 80108, 35801, Dinard cedex, France; ESE, Ecology and Ecosystem Health, AGROCAMPUS OUEST, INRA, 65 rue de Saint-Brieuc, 35042, Rennes, France.
| | - Lionel Denis
- Univ. Lille, CNRS, Univ. Littoral Côte d'Opale, UMR 8187, LOG, Laboratoire d'Océanologie et de Géosciences, F 62930, Wimereux, France
| | - Jérôme Fournier
- CNRS, UMR 7204 CESCO, 75005, Paris, France; MNHN, Station de Biologie Marine, BP 225, 29182, Concarneau cedex, France
| | - Nicolas Desroy
- IFREMER, Laboratoire Environnement et Ressources Bretagne nord, BP 80108, 35801, Dinard cedex, France
| | - Gwendoline Duong
- Univ. Lille, CNRS, Univ. Littoral Côte d'Opale, UMR 8187, LOG, Laboratoire d'Océanologie et de Géosciences, F 62930, Wimereux, France
| | - Stanislas F Dubois
- IFREMER, Laboratoire Centre de Bretagne, DYNECO, Laboratoire d'Ecologie Benthique Côtière (LEBCO), 29280, Plouzané, France
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19
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Weber L, Apprill A. Diel, daily, and spatial variation of coral reef seawater microbial communities. PLoS One 2020; 15:e0229442. [PMID: 32160233 PMCID: PMC7065756 DOI: 10.1371/journal.pone.0229442] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2019] [Accepted: 02/06/2020] [Indexed: 01/02/2023] Open
Abstract
Reef organisms influence microorganisms within the surrounding seawater, yet the spatial and temporal dynamics of seawater microbial communities located in proximity to corals are rarely investigated. To better understand reef seawater microbial community dynamics over time and space, we collected small-volume seawater samples during the day and night over a 72 hour period from three locations that differed in spatial distance from 5 Porites astreoides coral colonies on a shallow reef in St. John, U.S. Virgin Islands: near-coral (sampled 5 cm horizontally from each colony), reef-depth (sampled 2 m above each colony) and surface seawater (sampled 1 m from the seawater surface). At all time points and locations, we quantified abundances of microbial cells, sequenced small subunit rRNA genes of bacterial and archaeal communities, and measured inorganic nutrient concentrations. Prochlorococcus and Synechococcus cells were consistently elevated at night compared to day and these abundances changed over time, corresponding with temperature, nitrite, and silicate concentrations. During the day, bacterial and archaeal alpha diversity was significantly higher in reef-depth and near-coral seawater compared to the surface seawater, signifying that the reef influences the diversity of the seawater microorganisms. At night, alpha diversity decreased across all samples, suggesting that photosynthesis may favor a more taxonomically diverse community. While Prochlorococcus exhibited consistent temporal rhythmicity, additional taxa were enriched in reef seawater at night compared to day or in reef-depth compared to surface seawater based on their normalized sequence counts. There were some significant differences in nutrient concentrations and cell abundances between reef-depth and near-coral seawater but no clear trends. This study demonstrates that temporal variation supersedes small-scale spatial variation in proximity to corals in reef seawater microbial communities. As coral reefs continue to change in benthic composition worldwide, monitoring microbial composition in response to temporal changes and environmental fluctuations will help discern normal variability from longer lasting changes attributed to anthropogenic stressors and global climate change.
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Affiliation(s)
- Laura Weber
- Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, MA, United States of America
- MIT-WHOI Joint PhD Program in Biological Oceanography, Woods Hole, MA, United States of America
| | - Amy Apprill
- Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, MA, United States of America
- * E-mail:
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20
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Lima LFO, Weissman M, Reed M, Papudeshi B, Alker AT, Morris MM, Edwards RA, de Putron SJ, Vaidya NK, Dinsdale EA. Modeling of the Coral Microbiome: the Influence of Temperature and Microbial Network. mBio 2020; 11:e02691-19. [PMID: 32127450 PMCID: PMC7064765 DOI: 10.1128/mbio.02691-19] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 01/14/2020] [Indexed: 12/12/2022] Open
Abstract
Host-associated microbial communities are shaped by extrinsic and intrinsic factors to the holobiont organism. Environmental factors and microbe-microbe interactions act simultaneously on the microbial community structure, making the microbiome dynamics challenging to predict. The coral microbiome is essential to the health of coral reefs and sensitive to environmental changes. Here, we develop a dynamic model to determine the microbial community structure associated with the surface mucus layer (SML) of corals using temperature as an extrinsic factor and microbial network as an intrinsic factor. The model was validated by comparing the predicted relative abundances of microbial taxa to the relative abundances of microbial taxa from the sample data. The SML microbiome from Pseudodiploria strigosa was collected across reef zones in Bermuda, where inner and outer reefs are exposed to distinct thermal profiles. A shotgun metagenomics approach was used to describe the taxonomic composition and the microbial network of the coral SML microbiome. By simulating the annual temperature fluctuations at each reef zone, the model output is statistically identical to the observed data. The model was further applied to six scenarios that combined different profiles of temperature and microbial network to investigate the influence of each of these two factors on the model accuracy. The SML microbiome was best predicted by model scenarios with the temperature profile that was closest to the local thermal environment, regardless of the microbial network profile. Our model shows that the SML microbiome of P. strigosa in Bermuda is primarily structured by seasonal fluctuations in temperature at a reef scale, while the microbial network is a secondary driver.IMPORTANCE Coral microbiome dysbiosis (i.e., shifts in the microbial community structure or complete loss of microbial symbionts) caused by environmental changes is a key player in the decline of coral health worldwide. Multiple factors in the water column and the surrounding biological community influence the dynamics of the coral microbiome. However, by including only temperature as an external factor, our model proved to be successful in describing the microbial community associated with the surface mucus layer (SML) of the coral P. strigosa The dynamic model developed and validated in this study is a potential tool to predict the coral microbiome under different temperature conditions.
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Affiliation(s)
- Laís F O Lima
- Department of Biology, San Diego State University, San Diego, California, USA
- College of Biological Sciences, University of California Davis, Davis, California, USA
| | - Maya Weissman
- Department of Mathematics and Statistics, San Diego State University, San Diego, California, USA
| | - Micheal Reed
- Department of Biology, San Diego State University, San Diego, California, USA
| | - Bhavya Papudeshi
- National Center for Genome Analysis Support, Pervasive Institute of Technology, Indiana University, Bloomington, Indiana, USA
| | - Amanda T Alker
- Department of Biology, San Diego State University, San Diego, California, USA
| | - Megan M Morris
- Department of Biology, San Diego State University, San Diego, California, USA
| | - Robert A Edwards
- Department of Biology, San Diego State University, San Diego, California, USA
- Viral Information Institute, San Diego State University, San Diego, California, USA
| | | | - Naveen K Vaidya
- Department of Mathematics and Statistics, San Diego State University, San Diego, California, USA
- Viral Information Institute, San Diego State University, San Diego, California, USA
| | - Elizabeth A Dinsdale
- Department of Biology, San Diego State University, San Diego, California, USA
- Viral Information Institute, San Diego State University, San Diego, California, USA
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Hernandez-Agreda A, Leggat W, Ainsworth TD. A place for taxonomic profiling in the study of the coral prokaryotic microbiome. FEMS Microbiol Lett 2020; 366:5426210. [PMID: 30939203 DOI: 10.1093/femsle/fnz063] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 04/01/2019] [Indexed: 12/29/2022] Open
Abstract
The enormous variability in richness, abundance and diversity of unknown bacterial organisms inhabiting the coral microbiome have challenged our understanding of their functional contribution to coral health. Identifying the attributes of the healthy meta-organism is paramount for contemporary approaches aiming to manipulate dysbiotic stages of the coral microbiome. This review evaluates the current knowledge on the structure and mechanisms driving bacterial communities in the coral microbiome and discusses two topics requiring further research to define the healthy coral microbiome. (i) We examine the necessity to establish microbial baselines to understand the spatial and temporal dynamics of the healthy coral microbiome and summarise conceptual and logistic challenges to consider in the design of these baselines. (ii) We propose potential mechanical, physical and chemical mechanisms driving bacterial distribution within coral compartments and suggest experiments to test them. Finally, we highlight aspects of the use of 16S amplicon sequencing requiring standardization and discuss its contribution to other multi-omics approaches.
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Affiliation(s)
- Alejandra Hernandez-Agreda
- Australian Research Council Centre of Excellence for Coral Reef Studies, James Cook University, 1 James Cook Dr, Townsville, Queensland, 4811, Australia.,The College of Public Health, Medical and Veterinary Sciences, James Cook University, 1 James Cook Dr, Townsville, Queensland, 4811, Australia.,Invertebrate Zoology and Geology, California Academy of Sciences, 55 Music Concourse Drive, San Francisco, California, 94118, USA
| | - William Leggat
- Australian Research Council Centre of Excellence for Coral Reef Studies, James Cook University, 1 James Cook Dr, Townsville, Queensland, 4811, Australia.,The College of Public Health, Medical and Veterinary Sciences, James Cook University, 1 James Cook Dr, Townsville, Queensland, 4811, Australia.,School of Environmental and Life Sciences, The University of Newcastle, 10 Chittaway Road, Ourimbah, New South Wales, 2258, Australia
| | - Tracy D Ainsworth
- Australian Research Council Centre of Excellence for Coral Reef Studies, James Cook University, 1 James Cook Dr, Townsville, Queensland, 4811, Australia.,School of Biological, Earth and Environmental Sciences, The University of New South Wales, Biological Sciences Building (D26), Randwick, New South Wales, 2052, Australia
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22
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Gut Microbiomes of the Eastern Oyster ( Crassostrea virginica) and the Blue Mussel ( Mytilus edulis): Temporal Variation and the Influence of Marine Aggregate-Associated Microbial Communities. mSphere 2019; 4:4/6/e00730-19. [PMID: 31826972 PMCID: PMC6908423 DOI: 10.1128/msphere.00730-19] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
This work investigates the influence that extrinsic factors, diet, and the environment can have on the microbiomes of shellfish. Over the course of a year, the gut microbial communities of two species of bivalves, oysters and mussels, held under identical conditions in coastal marine waters were compared. While the mussels and oysters harbored gut microbial communities with similar composition, on a functional level, they exhibited species and temporal variation. These results indicate that intrinsic factors influence the bivalve microbiome, resulting in species variability, even when environmental conditions, feeding mechanism, and particle diet are constant. Seasonal and multispecies comparisons for bivalve-associated microbial communities are rare, and we believe this research represents an important contribution. The results presented here advance our understanding of the symbiotic interactions between marine invertebrates, the microbial communities they harbor, and the environment. Gut microbial community structure was evaluated for two species of bivalve molluscs, the eastern oyster (Crassostrea virginica) and the blue mussel (Mytilus edulis) collected from Long Island Sound, Connecticut, over the course of a year. These bivalves utilize a shared feeding mechanism, which may result in similar gut microbial communities. Their particle diet, marine aggregates, and surrounding environment, aggregate-free seawater (AFSW), were also collected for comparison. Due to the suspension-feeding activities of bivalves, the potential for aggregate- and AFSW-associated microbiota to influence their microbial communities may be significant. Both taxonomic and functional diversity of the samples were assessed. 16S rRNA gene amplicon sequencing indicated that oysters and mussels maintained similar, but not identical, gut microbiomes, with some temporal variation. Throughout the year, bivalve species had gut microbial community compositions that were more similar to one another than to aggregates. Within a month, bivalves shared on average a quarter of their total operational taxonomic units (OTUs) with each other and a 10th of their total OTUs with aggregates. During months with warm water temperatures, individuals within each of the four sample types had similar alpha diversity, but again, temporal variation was observed. On a functional level, bivalve gut microbial communities exhibited variation attributed to host species and season. Unlike oysters, mussel gut bacterial communities maintained high richness and evenness values throughout the year, even when values for the particle diet and AFSW were reduced. Overall, a core gut bivalve microbiome was present, and it was partially influenced by the marine aggregate microbial community. IMPORTANCE This work investigates the influence that extrinsic factors, diet, and the environment can have on the microbiomes of shellfish. Over the course of a year, the gut microbial communities of two species of bivalves, oysters and mussels, held under identical conditions in coastal marine waters were compared. While the mussels and oysters harbored gut microbial communities with similar composition, on a functional level, they exhibited species and temporal variation. These results indicate that intrinsic factors influence the bivalve microbiome, resulting in species variability, even when environmental conditions, feeding mechanism, and particle diet are constant. Seasonal and multispecies comparisons for bivalve-associated microbial communities are rare, and we believe this research represents an important contribution. The results presented here advance our understanding of the symbiotic interactions between marine invertebrates, the microbial communities they harbor, and the environment.
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23
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A horizon scan of priorities for coastal marine microbiome research. Nat Ecol Evol 2019; 3:1509-1520. [PMID: 31636428 DOI: 10.1038/s41559-019-0999-7] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 09/05/2019] [Indexed: 12/21/2022]
Abstract
Research into the microbiomes of natural environments is changing the way ecologists and evolutionary biologists view the importance of microorganisms in ecosystem function. This is particularly relevant in ocean environments, where microorganisms constitute the majority of biomass and control most of the major biogeochemical cycles, including those that regulate Earth's climate. Coastal marine environments provide goods and services that are imperative to human survival and well-being (for example, fisheries and water purification), and emerging evidence indicates that these ecosystem services often depend on complex relationships between communities of microorganisms (the 'microbiome') and the environment or their hosts - termed the 'holobiont'. Understanding of coastal ecosystem function must therefore be framed under the holobiont concept, whereby macroorganisms and their associated microbiomes are considered as a synergistic ecological unit. Here, we evaluate the current state of knowledge on coastal marine microbiome research and identify key questions within this growing research area. Although the list of questions is broad and ambitious, progress in the field is increasing exponentially, and the emergence of large, international collaborative networks and well-executed manipulative experiments are rapidly advancing the field of coastal marine microbiome research.
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24
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Glasl B, Bourne DG, Frade PR, Thomas T, Schaffelke B, Webster NS. Microbial indicators of environmental perturbations in coral reef ecosystems. MICROBIOME 2019; 7:94. [PMID: 31227022 PMCID: PMC6588946 DOI: 10.1186/s40168-019-0705-7] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 05/28/2019] [Indexed: 05/27/2023]
Abstract
BACKGROUND Coral reefs are facing unprecedented pressure on local and global scales. Sensitive and rapid markers for ecosystem stress are urgently needed to underpin effective management and restoration strategies. Although the fundamental contribution of microbes to the stability and functioning of coral reefs is widely recognised, it remains unclear how different reef microbiomes respond to environmental perturbations and whether microbiomes are sensitive enough to predict environmental anomalies that can lead to ecosystem stress. However, the lack of coral reef microbial baselines hinders our ability to study the link between shifts in microbiomes and ecosystem stress. In this study, we established a comprehensive microbial reference database for selected Great Barrier Reef sites to assess the diagnostic value of multiple free-living and host-associated reef microbiomes to infer the environmental state of coral reef ecosystems. RESULTS A comprehensive microbial reference database, originating from multiple coral reef microbiomes (i.e. seawater, sediment, corals, sponges and macroalgae), was generated by 16S rRNA gene sequencing for 381 samples collected over the course of 16 months. By coupling this database to environmental parameters, we showed that the seawater microbiome has the greatest diagnostic value to infer shifts in the surrounding reef environment. In fact, 56% of the observed compositional variation in the microbiome was explained by environmental parameters, and temporal successions in the seawater microbiome were characterised by uniform community assembly patterns. Host-associated microbiomes, in contrast, were five-times less responsive to the environment and their community assembly patterns were generally less uniform. By applying a suite of indicator value and machine learning approaches, we further showed that seawater microbial community data provide an accurate prediction of temperature and eutrophication state (i.e. chlorophyll concentration and turbidity). CONCLUSION Our results reveal that free-living microbial communities have a high potential to infer environmental parameters due to their environmental sensitivity and predictability. This highlights the diagnostic value of microorganisms and illustrates how long-term coral reef monitoring initiatives could be enhanced by incorporating assessments of microbial communities in seawater. We therefore recommend timely integration of microbial sampling into current coral reef monitoring initiatives.
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Affiliation(s)
- Bettina Glasl
- Australian Institute of Marine Science, Townsville, QLD, Australia.
- College of Science and Engineering, James Cook University, Townsville, QLD, Australia.
- AIMS@JCU, Townsville, QLD, Australia.
| | - David G Bourne
- Australian Institute of Marine Science, Townsville, QLD, Australia
- College of Science and Engineering, James Cook University, Townsville, QLD, Australia
- AIMS@JCU, Townsville, QLD, Australia
| | - Pedro R Frade
- Centre of Marine Science, University of Algarve, Faro, Portugal
| | - Torsten Thomas
- Centre for Marine Bio-Innovation & School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, Australia
| | | | - Nicole S Webster
- Australian Institute of Marine Science, Townsville, QLD, Australia
- AIMS@JCU, Townsville, QLD, Australia
- Australian Centre for Ecogenomics, University of Queensland, Brisbane, QLD, Australia
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25
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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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26
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Keller-Costa T, Eriksson D, Gonçalves JMS, Gomes NCM, Lago-Lestón A, Costa R. The gorgonian coral Eunicella labiata hosts a distinct prokaryotic consortium amenable to cultivation. FEMS Microbiol Ecol 2018; 93:4563573. [PMID: 29069352 DOI: 10.1093/femsec/fix143] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 10/20/2017] [Indexed: 11/14/2022] Open
Abstract
Microbial communities inhabiting gorgonian corals are believed to benefit their hosts through nutrient provision and chemical defence; yet much remains to be learned about their phylogenetic uniqueness and cultivability. Here, we determined the prokaryotic community structure and distinctiveness in the gorgonian Eunicella labiata by Illumina sequencing of 16S rRNA genes from gorgonian and seawater metagenomic DNA. Furthermore, we used a 'plate-wash' methodology to compare the phylogenetic diversity of the 'total' gorgonian bacteriome and its 'cultivatable' fraction. With 1016 operational taxonomic units (OTUs), prokaryotic richness was higher in seawater than in E. labiata where 603 OTUs were detected, 68 of which were host-specific. Oceanospirillales and Rhodobacterales predominated in the E. labiata communities. One Oceanospirillales OTU, classified as Endozoicomonas, was particularly dominant, and closest relatives comprised exclusively uncultured clones from other gorgonians. We cultivated a remarkable 62% of the bacterial symbionts inhabiting E. labiata: Ruegeria, Sphingorhabdus, Labrenzia, other unclassified Rhodobacteraceae, Vibrio and Shewanella ranked among the 10 most abundant genera in both the cultivation-independent and dependent samples. In conclusion, the E. labiata microbiome is diverse, distinct from seawater and enriched in (gorgonian)-specific bacterial phylotypes. In contrast to current understanding, many dominant E. labiata symbionts can, indeed, be cultivated.
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Affiliation(s)
- Tina Keller-Costa
- Instituto de Bioengenharia e Biociências (iBB), Instituto Superior Técnico (IST), Universidade de Lisboa, 1049-001 Lisbon, Portugal
| | - Dominic Eriksson
- Centro de Ciências do Mar (CCMAR), Universidade do Algarve, 8005-139 Faro, Portugal
| | - Jorge M S Gonçalves
- Centro de Ciências do Mar (CCMAR), Universidade do Algarve, 8005-139 Faro, Portugal
| | - Newton C M Gomes
- Departamento de Biologia (CESAM), Universidade de Aveiro, 3810-193 Aveiro, Portugal
| | - Asunción Lago-Lestón
- Centro de Investigación Científica y de Educación Superior de Ensenada (CICESE), 22860 Ensenada, Mexico
| | - Rodrigo Costa
- Instituto de Bioengenharia e Biociências (iBB), Instituto Superior Técnico (IST), Universidade de Lisboa, 1049-001 Lisbon, Portugal
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27
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Jeffries TC, Rayu S, Nielsen UN, Lai K, Ijaz A, Nazaries L, Singh BK. Metagenomic Functional Potential Predicts Degradation Rates of a Model Organophosphorus Xenobiotic in Pesticide Contaminated Soils. Front Microbiol 2018. [PMID: 29515526 PMCID: PMC5826299 DOI: 10.3389/fmicb.2018.00147] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Chemical contamination of natural and agricultural habitats is an increasing global problem and a major threat to sustainability and human health. Organophosphorus (OP) compounds are one major class of contaminant and can undergo microbial degradation, however, no studies have applied system-wide ecogenomic tools to investigate OP degradation or use metagenomics to understand the underlying mechanisms of biodegradation in situ and predict degradation potential. Thus, there is a lack of knowledge regarding the functional genes and genomic potential underpinning degradation and community responses to contamination. Here we address this knowledge gap by performing shotgun sequencing of community DNA from agricultural soils with a history of pesticide usage and profiling shifts in functional genes and microbial taxa abundance. Our results showed two distinct groups of soils defined by differing functional and taxonomic profiles. Degradation assays suggested that these groups corresponded to the organophosphorus degradation potential of soils, with the fastest degrading community being defined by increases in transport and nutrient cycling pathways and enzymes potentially involved in phosphorus metabolism. This was against a backdrop of taxonomic community shifts potentially related to contamination adaptation and reflecting the legacy of exposure. Overall our results highlight the value of using holistic system-wide metagenomic approaches as a tool to predict microbial degradation in the context of the ecology of contaminated habitats.
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Affiliation(s)
- Thomas C Jeffries
- School of Science and Health, Western Sydney University, Penrith, NSW, Australia.,Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia
| | - Smriti Rayu
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia
| | - Uffe N Nielsen
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia
| | - Kaitao Lai
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia.,Health and Biosecurity, Commonwealth Scientific and Industrial Research Organisation, North Ryde, NSW, Australia
| | - Ali Ijaz
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia
| | - Loic Nazaries
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia
| | - Brajesh K Singh
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia.,Global Centre for Land Based Innovation, Western Sydney University, Penrith, NSW, Australia
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28
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Tout J, Astudillo-García C, Taylor MW, Tyson GW, Stocker R, Ralph PJ, Seymour JR, Webster NS. Redefining the sponge-symbiont acquisition paradigm: sponge microbes exhibit chemotaxis towards host-derived compounds. ENVIRONMENTAL MICROBIOLOGY REPORTS 2017; 9:750-755. [PMID: 28892304 DOI: 10.1111/1758-2229.12591] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Revised: 08/30/2017] [Accepted: 08/31/2017] [Indexed: 06/07/2023]
Abstract
Marine sponges host stable and species-specific microbial symbionts that are thought to be acquired and maintained by the host through a combination of vertical transmission and filtration from the surrounding seawater. To assess whether the microbial symbionts also actively contribute to the establishment of these symbioses, we performed in situ experiments on Orpheus Island, Great Barrier Reef, to quantify the chemotactic responses of natural populations of seawater microorganisms towards cellular extracts of the reef sponge Rhopaloeides odorabile. Flow cytometry analysis revealed significant levels of microbial chemotaxis towards R. odorabile extracts and 16S rRNA gene amplicon sequencing showed enrichment of 'sponge-specific' microbial phylotypes, including a cluster within the Gemmatimonadetes and another within the Actinobacteria. These findings infer a potential mechanism for how sponges can acquire bacterial symbionts from the surrounding environment and suggest an active role of the symbionts in finding their host.
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Affiliation(s)
- Jessica Tout
- Plant Functional Biology & Climate Change Cluster, University of Technology Sydney, NSW, Australia
| | | | - Michael W Taylor
- School of Biological Sciences, University of Auckland, New Zealand
| | - Gene W Tyson
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD, Australia
| | - Roman Stocker
- Department of Civil, Environmental and Geomatic Engineering, Institute of Environmental Engineering, ETH Zurich, 8093 Zurich, Switzerland
| | - Peter J Ralph
- Plant Functional Biology & Climate Change Cluster, University of Technology Sydney, NSW, Australia
| | - Justin R Seymour
- Plant Functional Biology & Climate Change Cluster, University of Technology Sydney, NSW, Australia
| | - Nicole S Webster
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD, Australia
- Australian Institute of Marine Science, Townsville, QLD, Australia
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29
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Walsh K, Haggerty JM, Doane MP, Hansen JJ, Morris MM, Moreira APB, de Oliveira L, Leomil L, Garcia GD, Thompson F, Dinsdale EA. Aura-biomes are present in the water layer above coral reef benthic macro-organisms. PeerJ 2017; 5:e3666. [PMID: 28828261 PMCID: PMC5562181 DOI: 10.7717/peerj.3666] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 07/19/2017] [Indexed: 11/20/2022] Open
Abstract
As coral reef habitats decline worldwide, some reefs are transitioning from coral- to algal-dominated benthos with the exact cause for this shift remaining elusive. Increases in the abundance of microbes in the water column has been correlated with an increase in coral disease and reduction in coral cover. Here we investigated how multiple reef organisms influence microbial communities in the surrounding water column. Our study consisted of a field assessment of microbial communities above replicate patches dominated by a single macro-organism. Metagenomes were constructed from 20 L of water above distinct macro-organisms, including (1) the coral Mussismilia braziliensis, (2) fleshy macroalgae (Stypopodium, Dictota and Canistrocarpus), (3) turf algae, and (4) the zoanthid Palythoa caribaeorum and were compared to the water microbes collected 3 m above the reef. Microbial genera and functional potential were annotated using MG-RAST and showed that the dominant benthic macro-organisms influence the taxa and functions of microbes in the water column surrounding them, developing a specific “aura-biome”. The coral aura-biome reflected the open water column, and was associated with Synechococcus and functions suggesting oligotrophic growth, while the fleshy macroalgae aura-biome was associated with Ruegeria, Pseudomonas, and microbial functions suggesting low oxygen conditions. The turf algae aura-biome was associated with Vibrio, Flavobacterium, and functions suggesting pathogenic activity, while zoanthids were associated with Alteromonas and functions suggesting a stressful environment. Because each benthic organism has a distinct aura-biome, a change in benthic cover will change the microbial community of the water, which may lead to either the stimulation or suppression of the recruitment of benthic organisms.
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Affiliation(s)
- Kevin Walsh
- Department of Biology, San Diego State University, San Diego, CA, United States of America
| | - J Matthew Haggerty
- Department of Biology, San Diego State University, San Diego, CA, United States of America
| | - Michael P Doane
- Department of Biology, San Diego State University, San Diego, CA, United States of America
| | - John J Hansen
- Department of Biology, San Diego State University, San Diego, CA, United States of America
| | - Megan M Morris
- Department of Biology, San Diego State University, San Diego, CA, United States of America
| | - Ana Paula B Moreira
- Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Louisi de Oliveira
- Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Luciana Leomil
- Macae campus, Federal University of Rio de Janeiro, Macae, Rio de Janeiro, Brazil
| | - Gizele D Garcia
- Macae campus, Federal University of Rio de Janeiro, Macae, Rio de Janeiro, Brazil.,Laboratory of Microbiology, Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Fabiano Thompson
- Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Elizabeth A Dinsdale
- Department of Biology, San Diego State University, San Diego, CA, United States of America
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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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31
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Zhou G, Yuan T, Cai L, Zhang W, Tian R, Tong H, Jiang L, Yuan X, Liu S, Qian P, Huang H. Changes in microbial communities, photosynthesis and calcification of the coral Acropora gemmifera in response to ocean acidification. Sci Rep 2016; 6:35971. [PMID: 27786309 PMCID: PMC5082368 DOI: 10.1038/srep35971] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 10/10/2016] [Indexed: 12/24/2022] Open
Abstract
With the increasing anthropogenic CO2 concentration, ocean acidification (OA) can have dramatic effects on coral reefs. However, the effects of OA on coral physiology and the associated microbes remain largely unknown. In the present study, reef-building coral Acropora gemmifera collected from a reef flat with highly fluctuating environmental condition in the South China Sea were exposed to three levels of partial pressure of carbon dioxide (pCO2) (i.e., 421, 923, and 2070 μatm) for four weeks. The microbial community structures associated with A. gemmifera under these treatments were analyzed using 16S rRNA gene barcode sequencing. The results revealed that the microbial community associated with A. gemmifera was highly diverse at the genus level and dominated by Alphaproteobacteria. More importantly, the microbial community structure remained rather stable under different pCO2 treatments. Photosynthesis and calcification in A. gemmifera, as indicated by enrichment of δ18O and increased depletion of δ13C in the coral skeleton, were significantly impaired only at the high pCO2 (2070 μatm). These results suggest that A. gemmifera can maintain a high degree of stable microbial communities despite of significant physiological changes in response to extremely high pCO2.
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Affiliation(s)
- Guowei Zhou
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, China.,Tropical Marine Biological Research Station in Hainan, Chinese Academy of Sciences, China.,Shenzhen Research Institute and Division of Life Science, Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Tao Yuan
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, China
| | - Lin Cai
- Shenzhen Research Institute and Division of Life Science, Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Weipeng Zhang
- Shenzhen Research Institute and Division of Life Science, Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Renmao Tian
- Shenzhen Research Institute and Division of Life Science, Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Haoya Tong
- Shenzhen Research Institute and Division of Life Science, Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Lei Jiang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, China
| | - Xiangcheng Yuan
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, China
| | - Sheng Liu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, China
| | - Peiyuan Qian
- Shenzhen Research Institute and Division of Life Science, Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Hui Huang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, China.,Tropical Marine Biological Research Station in Hainan, Chinese Academy of Sciences, China
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32
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Hernández-Zulueta J, Araya R, Vargas-Ponce O, Díaz-Pérez L, Rodríguez-Troncoso AP, Ceh J, Ríos-Jara E, Rodríguez-Zaragoza FA. First deep screening of bacterial assemblages associated with corals of the Tropical Eastern Pacific. FEMS Microbiol Ecol 2016; 92:fiw196. [DOI: 10.1093/femsec/fiw196] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/11/2016] [Indexed: 11/12/2022] Open
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Badhai J, Ghosh TS, Das SK. Composition and Functional Characterization of Microbiome Associated with Mucus of the Coral Fungia echinata Collected from Andaman Sea. Front Microbiol 2016; 7:936. [PMID: 27379066 PMCID: PMC4909750 DOI: 10.3389/fmicb.2016.00936] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 05/31/2016] [Indexed: 12/29/2022] Open
Abstract
This study describes the community composition and functions of the microbiome associated with the mucus of the coral Fungia echinata based on metagenomic approach. Metagenome sequence data showed a dominance of the class Gammaproteobacteria followed by Alphaproteobacteria, Betaproteobacteria, Deltaproteobacteria, Flavobacteriia, Bacilli, and Clostridia. At the order level, the most abundant groups were Pseudomonadales, Oceanospirillales, Alteromonadales, and Rhodobacterales. The genus Psychrobacter was the most predominant followed by Thalassolituus and Cobetia, although other genera were also present, such as Sulfitobacter, Pseudoalteromonas, Oleispira, Halomonas, Oceanobacter, Acinetobacter, Pseudomonas, Vibrio, and Marinobacter. The metabolic profile of the bacterial community displayed high prevalence of genes associated with core-housekeeping processes, such as carbohydrates, amino acids, proteins, and nucleic acid metabolism. Further, high abundance of genes coding for DNA replication and repair, stress response, and virulence factors in the metagenome suggested acquisition of specific environmental adaptation by the microbiota. Comparative analysis with other coral metagenome exhibits marked differences at the taxonomical and functional level. This study suggests the bacterial community compositions are influenced by the specific coral micro-niche and the oligotrophic marine environment.
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Affiliation(s)
- Jhasketan Badhai
- Department of Biotechnology, Institute of Life Sciences Bhubaneswar, India
| | - Tarini S Ghosh
- Computational and Systems Biology Group, Genome Institute of Singapore Singapore, Singapore
| | - Subrata K Das
- Department of Biotechnology, Institute of Life Sciences Bhubaneswar, India
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34
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Roth-Schulze AJ, Zozaya-Valdés E, Steinberg PD, Thomas T. Partitioning of functional and taxonomic diversity in surface-associated microbial communities. Environ Microbiol 2016; 18:4391-4402. [PMID: 27062175 DOI: 10.1111/1462-2920.13325] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Revised: 03/29/2016] [Accepted: 03/31/2016] [Indexed: 12/14/2022]
Abstract
Surfaces, including those submerged in the marine environment, are subjected to constant interactions and colonisation by surrounding microorganisms. The principles that determine the assembly of those epibiotic communities are however poorly understood. In this study, we employed a hierarchical design to assess the functionality and diversity of microbial communities on different types of host surfaces (e.g. macroalgae, seagrasses). We found that taxonomic diversity was unique to each type of host, but that the majority of functions (> 95%) could be found in any given surface community, suggesting a high degree of functional redundancy. However, some community functions were enriched on certain surfaces and were related to host-specific properties (e.g. the degradation of specific polysaccharides). Together these observations support a model, whereby communities on surfaces are assembled from guilds of microorganisms with a functionality that is partitioned into general properties for a surface-associated life-style, but also specific features that mediate host-specificity.
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Affiliation(s)
- Alexandra J Roth-Schulze
- Centre for Marine Bio-Innovation, School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW, 2052, Australia
| | - Enrique Zozaya-Valdés
- Centre for Marine Bio-Innovation, School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW, 2052, Australia
| | - Peter D Steinberg
- Centre for Marine Bio-Innovation, School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW, 2052, Australia.,Sydney Institute of Marine Science, 2 Chowder Bay Rd., Mosman, NSW, 2088, Australia
| | - Torsten Thomas
- Centre for Marine Bio-Innovation, School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW, 2052, Australia
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35
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Sousa V, Nibali L, Spratt D, Dopico J, Mardas N, Petrie A, Donos N. Peri-implant and periodontal microbiome diversity in aggressive periodontitis patients: a pilot study. Clin Oral Implants Res 2016; 28:558-570. [PMID: 27170047 DOI: 10.1111/clr.12834] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/27/2016] [Indexed: 12/29/2022]
Abstract
AIM To investigate the bacterial microbiome in periodontal and peri-implant biofilms deriving from aggressive periodontitis patients (AgP) in conditions of health and disease. MATERIAL AND METHODS Ninety-one plaque samples were collected from 18 patients previously diagnosed and treated for AgP. The samples were taken from (i) 24 residual periodontal pockets (TD) (n = 6 patients), (ii) 24 healthy periodontal sites (TH) (n = 6 patients), (iii) 24 dental sites from the same implant patients (TM) (n = 6 patients), (iv) 5 peri-implantitis sites (II) (n = 2 patients), (v) 6 peri-mucositis sites (IM) (n = 2 patients) and (vi) 8 healthy implant sites (IH) (n = 2 patients). All subjects underwent periodontal clinical and radiographic assessments. Bacterial DNA was extracted, PCR amplified using 16S rRNA gene V5-V7 primers (barcoded amplicons 785F;1175R), purified, pooled at equimolar concentrations and sequenced (MiSeq, Illumina) yielding 250 bp paired-end reads. The 16S rRNA reads were filtered, assembled and analysed. RESULTS The genera Propionibacterium, Paludibacter, Staphylococcus, Filifactor, Mogibacterium, Bradyrhizobium and Acinetobacter were unique to peri-implant sites (P = 0.05). In TM samples, different proportions and bacterial spp. were found when compared with the same patients' samples at implant sites. Specifically, Actinomyces (P = 0.013) and Corynebacterium (P = 0.030) genera showed to be significantly more abundant in the TM group when compared to the II. The highest phylogenetic diversity was observed in residual periodontal pocket sites (TD). Increased annual tooth loss rate and residual pocketing was related to high proportions of the genera Actinomyces, Porphyromonas, Prevotella, Streptococcus, Actinomycetaceae, TM7-3, Selenomonas, and Dialister, Treponema, Parvimonas and Peptostreptococcus in the TD group. CONCLUSION Within the limitations of this pilot study, the periodontal and peri-implant microbiome presents a dissimilar taxonomic composition across different niches within AgP patients. The host response, the habitat structure and the vast coexistence of strains and species surrounding implants and teeth in health and disease are likely to be shaping the heterogeneous composition of the subgingival biofilms. The TM7 phylum was found only in TD cases. The investigation of the impact of periodontal and peri-implant keystone species on these complex ecosystems in states of health and disease seems to be essential.
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Affiliation(s)
- Vanessa Sousa
- Periodontology Unit, Department of Clinical Research, UCL Eastman Dental Institute, London, UK.,Centre for Oral Clinical Research, Institute of Dentistry, Barts & The London School of Medicine & Dentistry, QMUL, London, UK
| | - Luigi Nibali
- Periodontology Unit, Department of Clinical Research, UCL Eastman Dental Institute, London, UK.,Centre for Oral Clinical Research, Institute of Dentistry, Barts & The London School of Medicine & Dentistry, QMUL, London, UK
| | - David Spratt
- Department of Microbial Diseases, UCL Eastman Dental Institute, London, UK
| | - Jose Dopico
- Periodontology Unit, Department of Clinical Research, UCL Eastman Dental Institute, London, UK
| | - Nikos Mardas
- Centre for Adult Oral Health, Institute of Dentistry, Barts & The London School of Medicine & Dentistry, QMUL, London, UK
| | - Aviva Petrie
- Biostatistics Unit, UCL Eastman Dental Institute, London, UK
| | - Nikolaos Donos
- Periodontology Unit, Department of Clinical Research, UCL Eastman Dental Institute, London, UK.,Centre for Oral Clinical Research, Institute of Dentistry, Barts & The London School of Medicine & Dentistry, QMUL, London, UK
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36
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Archaeal and Bacterial Communities Associated with the Surface Mucus of Caribbean Corals Differ in Their Degree of Host Specificity and Community Turnover Over Reefs. PLoS One 2016; 11:e0144702. [PMID: 26788724 PMCID: PMC4720286 DOI: 10.1371/journal.pone.0144702] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Accepted: 11/23/2015] [Indexed: 12/28/2022] Open
Abstract
Comparative studies on the distribution of archaeal versus bacterial communities associated with the surface mucus layer of corals have rarely taken place. It has therefore remained enigmatic whether mucus-associated archaeal and bacterial communities exhibit a similar specificity towards coral hosts and whether they vary in the same fashion over spatial gradients and between reef locations. We used microbial community profiling (terminal-restriction fragment length polymorphism, T-RFLP) and clone library sequencing of the 16S rRNA gene to compare the diversity and community structure of dominant archaeal and bacterial communities associating with the mucus of three common reef-building coral species (Porites astreoides, Siderastrea siderea and Orbicella annularis) over different spatial scales on a Caribbean fringing reef. Sampling locations included three reef sites, three reef patches within each site and two depths. Reference sediment samples and ambient water were also taken for each of the 18 sampling locations resulting in a total of 239 samples. While only 41% of the bacterial operational taxonomic units (OTUs) characterized by T-RFLP were shared between mucus and the ambient water or sediment, for archaeal OTUs this percentage was 2-fold higher (78%). About half of the mucus-associated OTUs (44% and 58% of bacterial and archaeal OTUs, respectively) were shared between the three coral species. Our multivariate statistical analysis (ANOSIM, PERMANOVA and CCA) showed that while the bacterial community composition was determined by habitat (mucus, sediment or seawater), host coral species, location and spatial distance, the archaeal community composition was solely determined by the habitat. This study highlights that mucus-associated archaeal and bacterial communities differ in their degree of community turnover over reefs and in their host-specificity.
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37
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Stable and sporadic symbiotic communities of coral and algal holobionts. ISME JOURNAL 2015; 10:1157-69. [PMID: 26555246 PMCID: PMC5029208 DOI: 10.1038/ismej.2015.190] [Citation(s) in RCA: 95] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Revised: 09/09/2015] [Accepted: 09/22/2015] [Indexed: 12/26/2022]
Abstract
Coral and algal holobionts are assemblages of macroorganisms and microorganisms, including viruses, Bacteria, Archaea, protists and fungi. Despite a decade of research, it remains unclear whether these associations are spatial–temporally stable or species-specific. We hypothesized that conflicting interpretations of the data arise from high noise associated with sporadic microbial symbionts overwhelming signatures of stable holobiont members. To test this hypothesis, the bacterial communities associated with three coral species (Acropora rosaria, Acropora hyacinthus and Porites lutea) and two algal guilds (crustose coralline algae and turf algae) from 131 samples were analyzed using a novel statistical approach termed the Abundance-Ubiquity (AU) test. The AU test determines whether a given bacterial species would be present given additional sampling effort (that is, stable) versus those species that are sporadically associated with a sample. Using the AU test, we show that coral and algal holobionts have a high-diversity group of stable symbionts. Stable symbionts are not exclusive to one species of coral or algae. No single bacterial species was ubiquitously associated with one host, showing that there is not strict heredity of the microbiome. In addition to the stable symbionts, there was a low-diversity community of sporadic symbionts whose abundance varied widely across individual holobionts of the same species. Identification of these two symbiont communities supports the holobiont model and calls into question the hologenome theory of evolution.
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38
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Blackall LL, Wilson B, van Oppen MJH. Coral-the world's most diverse symbiotic ecosystem. Mol Ecol 2015; 24:5330-47. [DOI: 10.1111/mec.13400] [Citation(s) in RCA: 118] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2015] [Revised: 09/21/2015] [Accepted: 09/24/2015] [Indexed: 12/22/2022]
Affiliation(s)
- Linda L. Blackall
- Department of Chemistry and Biotechnology; Faculty of Science, Engineering & Technology; Swinburne University of Technology; Melbourne Vic. 3122 Australia
| | - Bryan Wilson
- Marine Microbiology Research Group; Department of Biology; University of Bergen; Thormøhlensgate 53B 5020 Bergen Norway
| | - Madeleine J. H. van Oppen
- Australian Institute of Marine Science; PMB No. 3 Townsville MC Qld. 4810 Australia
- School of BioSciences; The University of Melbourne; Parkville Vic. 3010 Australia
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39
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Taxonomic and environmental variation of metabolite profiles in marine dinoflagellates of the genus symbiodinium. Metabolites 2015; 5:74-99. [PMID: 25693143 PMCID: PMC4381291 DOI: 10.3390/metabo5010074] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Revised: 02/04/2015] [Accepted: 02/09/2015] [Indexed: 11/17/2022] Open
Abstract
Microorganisms in terrestrial and marine ecosystems are essential to environmental sustainability. In the marine environment, invertebrates often depend on metabolic cooperation with their endosymbionts. Coral reefs, one of the most important marine ecosystems, are based on the symbiosis between a broad diversity of dinoflagellates of the genus Symbiodinium and a wide phyletic diversity of hosts (i.e., cnidarian, molluscan, poriferan). This diversity is reflected in the ecology and physiology of the symbionts, yet the underlying biochemical mechanisms are still poorly understood. We examined metabolite profiles of four cultured species of Symbiodinium known to form viable symbioses with reef-building corals, S. microadriaticum (cp-type A194), S. minutum (cp-type B184), S. psygmophilum (cp-type B224) and S. trenchii (cp-type D206). Metabolite profiles were shown to differ among Symbiodinium species and were found to be affected by their physiological response to growth in different temperatures and light regimes. A combined Random Forests and Bayesian analysis revealed that the four Symbiodinium species examined primarily differed in their production of sterols and sugars, including a C29 stanol and the two sterols C28Δ5 and C28Δ5,22, as well as differences in metabolite abundances of a hexose and inositol. Inositol levels were also strongly affected by changes in temperature across all Symbiodinium species. Our results offer a detailed view of the metabolite profile characteristic of marine symbiotic dinoflagellates of the genus Symbiodinium, and identify patterns of metabolites related to several growth conditions.
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40
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Tout J, Jeffries TC, Petrou K, Tyson GW, Webster NS, Garren M, Stocker R, Ralph PJ, Seymour JR. Chemotaxis by natural populations of coral reef bacteria. ISME JOURNAL 2015; 9:1764-77. [PMID: 25615440 DOI: 10.1038/ismej.2014.261] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Revised: 12/01/2014] [Accepted: 12/05/2014] [Indexed: 12/27/2022]
Abstract
Corals experience intimate associations with distinct populations of marine microorganisms, but the microbial behaviours underpinning these relationships are poorly understood. There is evidence that chemotaxis is pivotal to the infection process of corals by pathogenic bacteria, but this evidence is limited to experiments using cultured isolates under laboratory conditions. We measured the chemotactic capabilities of natural populations of coral-associated bacteria towards chemicals released by corals and their symbionts, including amino acids, carbohydrates, ammonium and dimethylsulfoniopropionate (DMSP). Laboratory experiments, using a modified capillary assay, and in situ measurements, using a novel microfabricated in situ chemotaxis assay, were employed to quantify the chemotactic responses of natural microbial assemblages on the Great Barrier Reef. Both approaches showed that bacteria associated with the surface of the coral species Pocillopora damicornis and Acropora aspera exhibited significant levels of chemotaxis, particularly towards DMSP and amino acids, and that these levels of chemotaxis were significantly higher than that of bacteria inhabiting nearby, non-coral-associated waters. This pattern was supported by a significantly higher abundance of chemotaxis and motility genes in metagenomes within coral-associated water types. The phylogenetic composition of the coral-associated chemotactic microorganisms, determined using 16S rRNA amplicon pyrosequencing, differed from the community in the seawater surrounding the coral and comprised known coral associates, including potentially pathogenic Vibrio species. These findings indicate that motility and chemotaxis are prevalent phenotypes among coral-associated bacteria, and we propose that chemotaxis has an important role in the establishment and maintenance of specific coral-microbe associations, which may ultimately influence the health and stability of the coral holobiont.
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Affiliation(s)
- Jessica Tout
- Plant Functional Biology and Climate Change Cluster, University of Technology Sydney, Sydney, New South Wales, Australia
| | - Thomas C Jeffries
- Plant Functional Biology and Climate Change Cluster, University of Technology Sydney, Sydney, New South Wales, Australia
| | - Katherina Petrou
- Plant Functional Biology and Climate Change Cluster, University of Technology Sydney, Sydney, New South Wales, Australia
| | - Gene W Tyson
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, Queensland, Australia
| | - Nicole S Webster
- Australian Institute of Marine Science, Townsville, Queensland, Australia
| | - Melissa Garren
- Department of Civil and Environmental Engineering, Ralph M. Parsons Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Roman Stocker
- Department of Civil and Environmental Engineering, Ralph M. Parsons Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Peter J Ralph
- Plant Functional Biology and Climate Change Cluster, University of Technology Sydney, Sydney, New South Wales, Australia
| | - Justin R Seymour
- Plant Functional Biology and Climate Change Cluster, University of Technology Sydney, Sydney, New South Wales, Australia
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