Abstract
Coral microbial flora has been attracting attention because of their potential to protect corals from environmental stresses or pathogens. Although coral-associated bacteria are considered to be acquired from seawater, little is known about the relationships between microbial composition in corals and its surrounding seawater. Here, we tested several methods to identify coral-associated bacteria in coral and its surrounding seawater to detect specific types of Ruegeria species, some of which exhibit growth inhibition activities against the coral pathogen Vibrio coralliilyticus. We first isolated coral-associated bacteria from the reef-building coral Galaxea fascicularis collected at Sesoko Island, Okinawa, Japan, via random colony picking, which showed the existence of varieties of bacteria including Ruegeria species. Using newly constructed primers for colony PCR, several Ruegeria species were successfully isolated from G. fascicularis and seawater. We further investigated the seawater microbiome in association with the distance from coral reefs. By seasonal sampling, it was suggested that the seawater microbiome is more affected by seasonality than the distance from coral reefs. These methods and results may contribute to investigating and understanding the relationships between the presence of corals and microbial diversity in seawater, in addition to the efficient isolation of specific bacterial species from coral or its surrounding seawater.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
Availability of Data and Material
The data and materials that support the findings of this study are available on request from the corresponding author.
References
Ben-Haim Y, Zicherman-Keren M, Rosenberg E (2003) Temperature-regulated bleaching and lysis of the coral Pocillopora damicornis by the novel pathogen Vibrio coralliilyticus. Appl Environ Microbiol 69:4236–4242
Bernasconi R, Stat M, Koenders A, Paparini A, Bunce M, Huggett MJ (2019) Establishment of coral-bacteria symbioses reveal changes in the core bacterial community with host ontogeny. Front Microbiol 10:1529
Bourne DG, Morrow KM, Webster NS (2016) Insights into the coral microbiome: underpinning the health and resilience of reef ecosystems. Annu Rev Microbiol 70:317–340
Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJ, Holmes SP (2016) DADA2: high-resolution sample inference from Illumina amplicon data. Nat Methods 13:581–583
Carpenter KE et al (2008) One-third of reef-building corals face elevated extinction risk from climate change and local impacts. Science 321:560–563
Descombes P et al (2015) Forecasted coral reef decline in marine biodiversity hotspots under climate change. Glob Chang Biol 21:2479–2487
Dietzel A, Bode M, Connolly SR, Hughes TP (2021) The population sizes and global extinction risk of reef-building coral species at biogeographic scales. Nat Ecol Evol
Dungan AM, Bulach D, Lin H, van Oppen MJH, Blackall LL (2020) Development of a free radical scavenging probiotic to mitigate coral bleaching. bioRxiv. https://doi.org/10.1101/2020.07.02.185645
Durham BP et al (2015) Cryptic carbon and sulfur cycling between surface ocean plankton. Proc Natl Acad Sci U S A 112:453–457
Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791
Frank JA, Reich CI, Sharma S, Weisbaum JS, Wilson BA, Olsen GJ (2008) Critical evaluation of two primers commonly used for amplification of bacterial 16S rRNA genes. Appl Environ Microbiol 74:2461–2470
Gignoux-Wolfsohn SA, Aronson FM, Vollmer SV (2017) Complex interactions between potentially pathogenic, opportunistic, and resident bacteria emerge during infection on a reef-building coral. FEMS Microbiol Ecol 93(7). https://doi.org/10.1093/femsec/fix080
Glasl B, Bourne DG, Frade PR, Thomas T, Schaffelke B, Webster NS (2019) Microbial indicators of environmental perturbations in coral reef ecosystems. Microbiome 7:94
Grottoli AG et al (2018) Coral physiology and microbiome dynamics under combined warming and ocean acidification. PLOS ONE 13:e0191156
Jones GP, McCormick MI, Srinivasan M, Eagle JV (2004) Coral decline threatens fish biodiversity in marine reserves. Proc Natl Acad Sci U S A 101:8251–8253
Kitamura R, Miura N, Okada K, Motone K, Takagi T, Ueda M, Kataoka M (2020) Design of novel primer sets for easy detection of Ruegeria species from seawater. Biosci Biotechnol Biochem 84:854–864
Kumar S, Stecher G, Li M, Knyaz C, Tamura K (2018) MEGA X: Molecular Evolutionary Genetics Analysis across computing platforms. Mol Biol Evol 35:1547–1549
Lane DJ (1991) 16S/23S rRNA sequencing. In: Nucleic acid techniques in bacterial systematics. In: Stackebrandt E, Goodfellow M (eds) Nucleic Acid Techniques in Bacterial Systematic. John Wiley and Sons, New York, pp 115–175
Liang J et al (2017) Distinct bacterial communities associated with massive and branching scleractinian corals and potential linkages to coral susceptibility to thermal or cold stress. Front Microbiol 8:979
Loya Y, Sakai K, Yamazato K, Nakano Y, Sambali H, van Woesik R (2001) Coral bleaching: the winners and the losers. Ecology Letters 4:122–131
Maher RL, Rice MM, McMinds R, Burkepile DE, Vega Thurber R (2019) Multiple stressors interact primarily through antagonism to drive changes in the coral microbiome. Sci Rep 9:6834
Martin M (2011) Cutadapt removes adapter sequences from high-throughput sequencing reads. Embnetjournal 17:10–1
McMurdie PJ, Holmes S (2013) phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. PLOS ONE 8:e61217
Meyer JL, Castellanos-Gell J, Aeby GS, Hase CC, Ushijima B, Paul VJ (2019) Microbial community shifts associated with the ongoing stony coral tissue loss disease outbreak on the Florida reef tract. Front Microbiol 10:2244
Miura N, Motone K, Takagi T, Aburaya S, Watanabe S, Aoki W, Ueda M (2019) Ruegeria sp. strains isolated from the reef-building coral Galaxea fascicularis inhibit growth of the temperature-dependent pathogen Vibrio coralliilyticus. Mar Biotechnol (NY) 21:1–8
Motone K, Takagi T, Aburaya S, Miura N, Aoki W, Ueda M (2020) A zeaxanthin-producing bacterium isolated from the algal phycosphere protects coral endosymbionts from environmental stress. mBio 11:e01019-19
Nichols PK, Marko PB (2019) Rapid assessment of coral cover from environmental DNA in Hawai’i. Environmental DNA 1:40–53
Peixoto RS, Rosado PM, Leite DC, Rosado AS, Bourne DG (2017) Beneficial microorganisms for corals (BMC): proposed mechanisms for coral health and resilience. Front Microbiol 8:34
Peixoto RS et al (2021) Coral probiotics: premise, promise, prospects. Annu Rev Anim Biosci 9:265–288
Pootakham W et al (2018) Dynamics of coral-associated microbiomes during a thermal bleaching event. Microbiologyopen 7:e00604
Pootakham W et al (2019) Heat-induced shift in coral microbiome reveals several members of the Rhodobacteraceae family as indicator species for thermal stress in Porites lutea. Microbiologyopen 8:e935
Raina JB et al (2016) Isolation of an antimicrobial compound produced by bacteria associated with reef-building corals. PeerJ 4:e2275
Raina JB, Tapiolas D, Willis BL, Bourne DG (2009) Coral-associated bacteria and their role in the biogeochemical cycling of sulfur. Appl Environ Microbiol 75:3492–3501
Reshef L, Koren O, Loya Y, Zilber-Rosenberg I, Rosenberg E (2006) The coral probiotic hypothesis. Environ Microbiol 8:2068–2073
Rognes T, Flouri T, Nichols B, Quince C, Mahe F (2016) VSEARCH: a versatile open source tool for metagenomics. PeerJ 4:e2584
Rosado PM et al (2019) Marine probiotics: increasing coral resistance to bleaching through microbiome manipulation. ISME J 13:921–936
Rosales SM, Miller MW, Williams DE, Traylor-Knowles N, Young B, Serrano XM (2019) Microbiome differences in disease-resistant vs. susceptible Acropora corals subjected to disease challenge assays. Sci Rep 9:18279
Rosenberg E, Koren O, Reshef L, Efrony R, Zilber-Rosenberg I (2007) The role of microorganisms in coral health, disease and evolution. Nat Rev Microbiol 5:355–36
Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425
Shinzato C, Zayasu Y, Kanda M, Kawamitsu M, Satoh N, Yamashita H, Suzuki G (2018) Using seawater to document coral-zoothanthella diversity: a new approach to coral reef monitoring using environmental DNA. Front Mar Sci 5:1–12
Sonnenschein EC et al (2017) Global occurrence and heterogeneity of the Roseobacter-clade species Ruegeria mobilis. ISME J 11:569–583
Sunagawa S et al (2009) Bacterial diversity and White Plague Disease-associated community changes in the Caribbean coral Montastraea faveolata. ISME J 3:512–521
Sweet M, Burian A, Fifer J, Bulling M, Elliott D, Raymundo L (2019) Compositional homogeneity in the pathobiome of a new, slow-spreading coral disease. Microbiome 7:139
Tamura K, Nei M, Kumar S (2004) Prospects for inferring very large phylogenies by using the neighbor-joining method. Proc Natl Acad Sci U S A 101:11030–11035
Tang K, Zhan W, Zhou Y, Xu T, Chen X, Wang W, Zeng Z, Wang Y, Wang X (2020) Antagonism between coral pathogen Vibrio coralliilyticus and other bacteria in the gastric cavity of scleractinian coral Galaxea fascicularis. Sci China Earth Sci 63:157–166
Vega Thurber R et al (2009) Metagenomic analysis of stressed coral holobionts. Environ Microbiol 11:2148–2163
von Scheibner M, Sommer U, Jurgens K (2017) Tight coupling of Glaciecola spp. and diatoms during cold-water phytoplankton spring blooms. Front Microbiol 8:27
West KM et al (2020) eDNA metabarcoding survey reveals fine-scale coral reef community variation across a remote, tropical island ecosystem. Mol Ecol 29:1069–1086
Yuyama I, Harii S, Hidaka M (2012) Algal symbiont type affects gene expression in juveniles of the coral Acropora tenuis exposed to thermal stress. Mar Environ Res 76:41–47
Ziegler M, Seneca FO, Yum LK, Palumbi SR, Voolstra CR (2017) Bacterial community dynamics are linked to patterns of coral heat tolerance. Nat Commun 8:14213
Acknowledgements
We thank Mr. Yoshikatsu Nakano of the University of the Ryukyus for the helpful discussions and suggestions regarding the determination of sampling locations. We also thank Mr. Shohei Kadena of the University of the Ryukyus for the assistance in field sampling. Coral sampling was carried out with the approval of the authorities of Okinawa Prefecture, Japan.
Funding
This study was supported by the Collaborative Research of Tropical Biosphere Research Center, University of the Ryukyus, as well as Grants-in-Aid for Young Scientists (JSPS KAKENHI) (NM, JP19K15739; MI, JP17K15402; TT, JP18K14479, JP21K14766), a Grant for Environmental Research Projects from Nippon Life Insurance Foundation (NM), a Research Grant from Sugiyama Chemical & Industrial Laboratory (NM), and JST, ACT-X Grant Number JPMJAX20B9, Japan (TT).
Author information
Authors and Affiliations
Contributions
Conceptualization: NM, MI, TT; design of experiments: NM, RK, MI, TT; experiments: RK, Y Nishikawa, Y Nishimura, NM, MI, TT; collection of seawater: MI, TT, NM; collection of corals: TT, HY; data analysis: RK, NM, MI, KK; writing original draft: RK, NM; reviewing and editing the manuscript: NM, MI, TT, HY, MK; reviewing and approving the final manuscript: RK, NM, MI, TT, HY, Y Nishikawa, Y Nishimura, KK, MK.
Corresponding author
Ethics declarations
Conflict of Interest
The authors declare no competing interests.
Additional information
Publisher's Note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Supplementary Information
Below is the link to the electronic supplementary material.
Rights and permissions
About this article
Cite this article
Kitamura, R., Miura, N., Ito, M. et al. Specific Detection of Coral-Associated Ruegeria, a Potential Probiotic Bacterium, in Corals and Subtropical Seawater. Mar Biotechnol 23, 576–589 (2021). https://doi.org/10.1007/s10126-021-10047-2
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s10126-021-10047-2