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      Different nitrogen sources speed recovery from corallivory and uniquely alter the microbiome of a reef-building coral

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          Abstract

          Corals are in decline worldwide due to local anthropogenic stressors, such as nutrient loading, and global stressors, such as ocean warming. Anthropogenic nutrient loading, which is often rich in nitrate, inhibits coral growth and worsens corals’ response to warming while natural sources of nitrogen, such as ammonium from fish excretion, promotes coral growth. Although the effects of nutrient loading and ocean warming have been well-studied, it remains unclear how these factors may interact with biotic processes, such as corallivory, to alter coral health and the coral microbiome. This study examined how nitrate vs. ammonium enrichment altered the effects of increased seawater temperature and simulated parrotfish corallivory on the health of Pocillopora meandrina and its microbial community. We tested the effects of nitrogen source on the response to corallivory under contrasting temperatures (control: 26 °C, warming: 29 °C) in a factorial mesocosm experiment in Moorea, French Polynesia. Corals were able to maintain growth rates despite simultaneous stressors. Seawater warming suppressed wound healing rates by nearly 66%. However, both ammonium and nitrate enrichment counteracted the effect of higher temperatures on would healing rates. Elevated seawater temperature and ammonium enrichment independently increased Symbiodiniaceae densities relative to controls, yet there was no effect of nitrate enrichment on algal symbiont densities. Microbiome variability increased with the addition of nitrate or ammonium. Moreover, microbial indicator analysis showed that Desulfovibrionaceae Operational taxonomic units (OTUs) are indicators of exclusively temperature stress while Rhodobacteraceae and Saprospiraceae OTUs were indicators of high temperature, wounding, and nitrogen enrichment. Overall, our results suggest that nitrogen source may not alter the response of the coral host to simultaneous stressors, but that the associated microbial community may be distinct depending on the source of enrichment.

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          Improving indicator species analysis by combining groups of sites

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            Subsampled open-reference clustering creates consistent, comprehensive OTU definitions and scales to billions of sequences

            We present a performance-optimized algorithm, subsampled open-reference OTU picking, for assigning marker gene (e.g., 16S rRNA) sequences generated on next-generation sequencing platforms to operational taxonomic units (OTUs) for microbial community analysis. This algorithm provides benefits over de novo OTU picking (clustering can be performed largely in parallel, reducing runtime) and closed-reference OTU picking (all reads are clustered, not only those that match a reference database sequence with high similarity). Because more of our algorithm can be run in parallel relative to “classic” open-reference OTU picking, it makes open-reference OTU picking tractable on massive amplicon sequence data sets (though on smaller data sets, “classic” open-reference OTU clustering is often faster). We illustrate that here by applying it to the first 15,000 samples sequenced for the Earth Microbiome Project (1.3 billion V4 16S rRNA amplicons). To the best of our knowledge, this is the largest OTU picking run ever performed, and we estimate that our new algorithm runs in less than 1/5 the time than would be required of “classic” open reference OTU picking. We show that subsampled open-reference OTU picking yields results that are highly correlated with those generated by “classic” open-reference OTU picking through comparisons on three well-studied datasets. An implementation of this algorithm is provided in the popular QIIME software package, which uses uclust for read clustering. All analyses were performed using QIIME’s uclust wrappers, though we provide details (aided by the open-source code in our GitHub repository) that will allow implementation of subsampled open-reference OTU picking independently of QIIME (e.g., in a compiled programming language, where runtimes should be further reduced). Our analyses should generalize to other implementations of these OTU picking algorithms. Finally, we present a comparison of parameter settings in QIIME’s OTU picking workflows and make recommendations on settings for these free parameters to optimize runtime without reducing the quality of the results. These optimized parameters can vastly decrease the runtime of uclust-based OTU picking in QIIME.
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              The microbiome of coral surface mucus has a key role in mediating holobiont health and survival upon disturbance

              Microbes are well-recognized members of the coral holobiont. However, little is known about the short-term dynamics of mucus-associated microbial communities under natural conditions and after disturbances, and how these dynamics relate to the host's health. Here we examined the natural variability of prokaryotic communities (based on 16S ribosomal RNA gene amplicon sequencing) associating with the surface mucus layer (SML) of Porites astreoides, a species exhibiting cyclical mucus aging and shedding. Shifts in the prokaryotic community composition during mucus aging led to the prevalence of opportunistic and potentially pathogenic bacteria (Verrucomicrobiaceae and Vibrionaceae) in aged mucus and to a twofold increase in prokaryotic abundance. After the release of aged mucus sheets, the community reverted to its original state, dominated by Endozoicimonaceae and Oxalobacteraceae. Furthermore, we followed the fate of the coral holobiont upon depletion of its natural mucus microbiome through antibiotics treatment. After re-introduction to the reef, healthy-looking microbe-depleted corals started exhibiting clear signs of bleaching and necrosis. Recovery versus mortality of the P. astreoides holobiont was related to the degree of change in abundance distribution of the mucus microbiome. We conclude that the natural prokaryotic community inhabiting the coral SML contributes to coral health and that cyclical mucus shedding has a key role in coral microbiome dynamics.
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                Author and article information

                Contributors
                Journal
                PeerJ
                PeerJ
                PeerJ
                PeerJ
                PeerJ
                PeerJ Inc. (San Diego, USA )
                2167-8359
                15 November 2019
                2019
                : 7
                : e8056
                Affiliations
                [1 ]Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara , Santa Barbara, CA, USA
                [2 ]Department of Microbiology, Oregon State University , Corvallis, OR, USA
                [3 ]Marine Science Institute, University of California, Santa Barbara , Santa Barbara, CA, USA
                Author information
                http://orcid.org/0000-0002-8975-652X
                http://orcid.org/0000-0003-3108-8503
                http://orcid.org/0000-0002-0427-0484
                Article
                8056
                10.7717/peerj.8056
                6859885
                31741802
                e99d3894-d9b3-4d45-bccf-3e15ba7c2094
                © 2019 Rice et al.

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited.

                History
                : 6 March 2019
                : 18 October 2019
                Funding
                Funded by: U.S. National Science Foundation (NSF) CAREER
                Award ID: #OCE-1547952
                Funded by: Dimensions of Biodiversity NSF
                Award ID: #1442306
                Funded by: NSF Ocean Sciences
                Award ID: #1635913
                Funded by: NSF GRFP to both Mallory M. Rice (#1650114) and Rebecca L. Maher (#1314109-DGE)
                Funded by: Riverbanks Conservation Fund
                Funded by: NSF grant OCE
                Award ID: 16-37396
                Funded by: Gordon and Betty Moore Foundation to the Moorea Coral Reef LTER
                This work was supported by a U.S. National Science Foundation (NSF) CAREER grant to Deron E. Burkepile (#OCE-1547952), a Dimensions of Biodiversity NSF grant (#1442306) to Rebecca Vega Thurber, an NSF Ocean Sciences grant (#1635913) to Rebecca Vega Thurber, the NSF GRFP to both Mallory M. Rice (#1650114) and Rebecca L. Maher (#1314109-DGE), and the Riverbanks Conservation Fund Grant to Mallory M. Rice. This research was facilitated by the NSF grant OCE 16-37396 as well as a grant from the Gordon and Betty Moore Foundation to the Moorea Coral Reef LTER. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
                Categories
                Ecology
                Marine Biology
                Microbiology

                corallivory,seawater warming,nitrate,ammonium,coral microbiome,nutrient loading

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