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The Woods Hole Oceanographic Institution is a private, independent, not-for-profit corporation dedicated to research and higher education at the frontiers of ocean science.
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Browsing Woods Hole Oceanographic Institution by Subject "16S rRNA gene"
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ArticleMicrobial and nutrient dynamics in mangrove, reef, and seagrass waters over tidal and diurnal time scales(Inter Research, 2020-10-08) Becker, Cynthia ; Weber, Laura ; Suca, Justin J. ; Llopiz, Joel K. ; Mooney, T. Aran ; Apprill, AmyIn coral reefs and adjacent seagrass meadow and mangrove environments, short temporal scales (i.e. tidal, diurnal) may have important influences on ecosystem processes and community structure, but these scales are rarely investigated. This study examines how tidal and diurnal forcings influence pelagic microorganisms and nutrient dynamics in 3 important and adjacent coastal biomes: mangroves, coral reefs, and seagrass meadows. We sampled for microbial (Bacteria and Archaea) community composition, cell abundances and environmental parameters at 9 coastal sites on St. John, US Virgin Islands that spanned 4 km in distance (4 coral reefs, 2 seagrass meadows and 3 mangrove locations within 2 larger bays). Eight samplings occurred over a 48 h period, capturing day and night microbial dynamics over 2 tidal cycles. The seagrass and reef biomes exhibited relatively consistent environmental conditions and microbial community structure but were dominated by shifts in picocyanobacterial abundances that were most likely attributed to diel dynamics. In contrast, mangrove ecosystems exhibited substantial daily shifts in environmental parameters, heterotrophic cell abundances and microbial community structure that were consistent with the tidal cycle. Differential abundance analysis of mangrove-associated microorganisms revealed enrichment of pelagic oligotrophic taxa during high tide and enrichment of putative sediment-associated microbes during low tide. Our study underpins the importance of tidal and diurnal time scales in structuring coastal microbial and nutrient dynamics, with diel and tidal cycles contributing to a highly dynamic microbial environment in mangroves, and time of day likely contributing to microbial dynamics in seagrass and reef biomes.
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ArticleThe microbiological drivers of temporally dynamic Dimethylsulfoniopropionate cycling processes in Australian coastal shelf waters(Frontiers Media, 2022-06-15) O’Brien, James ; McParland, Erin L. ; Bramucci, Anna R. ; Ostrowski, Martin ; Siboni, Nachshon ; Ingleton, Timothy ; Brown, Mark V. ; Levine, Naomi M. ; Laverock, Bonnie ; Petrou, Katherina ; Seymour, JustinThe organic sulfur compounds dimethylsulfoniopropionate (DMSP) and dimethyl sulfoxide (DMSO) play major roles in the marine microbial food web and have substantial climatic importance as sources and sinks of dimethyl sulfide (DMS). Seasonal shifts in the abundance and diversity of the phytoplankton and bacteria that cycle DMSP are likely to impact marine DMS (O) (P) concentrations, but the dynamic nature of these microbial interactions is still poorly resolved. Here, we examined the relationships between microbial community dynamics with DMS (O) (P) concentrations during a 2-year oceanographic time series conducted on the east Australian coast. Heterogenous temporal patterns were apparent in chlorophyll a (chl a) and DMSP concentrations, but the relationship between these parameters varied over time, suggesting the phytoplankton and bacterial community composition were affecting the net DMSP concentrations through differential DMSP production and degradation. Significant increases in DMSP were regularly measured in spring blooms dominated by predicted high DMSP-producing lineages of phytoplankton (Heterocapsa, Prorocentrum, Alexandrium, and Micromonas), while spring blooms that were dominated by predicted low DMSP-producing phytoplankton (Thalassiosira) demonstrated negligible increases in DMSP concentrations. During elevated DMSP concentrations, a significant increase in the relative abundance of the key copiotrophic bacterial lineage Rhodobacterales was accompanied by a three-fold increase in the gene, encoding the first step of DMSP demethylation (dmdA). Significant temporal shifts in DMS concentrations were measured and were significantly correlated with both fractions (0.2–2 μm and >2 μm) of microbial DMSP lyase activity. Seasonal increases of the bacterial DMSP biosynthesis gene (dsyB) and the bacterial DMS oxidation gene (tmm) occurred during the spring-summer and coincided with peaks in DMSP and DMSO concentration, respectively. These findings, along with significant positive relationships between dsyB gene abundance and DMSP, and tmm gene abundance with DMSO, reinforce the significant role planktonic bacteria play in producing DMSP and DMSO in ocean surface waters. Our results highlight the highly dynamic nature and myriad of microbial interactions that govern sulfur cycling in coastal shelf waters and further underpin the importance of microbial ecology in mediating important marine biogeochemical processes.
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DatasetMicrobiome dynamics of coral reef and cleanerfish from ecological surveys, in situ manipulations, and laboratory experiments conducted from 2020-2021(Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu, 2023-10-25) Apprill, Amy ; Sikkel, Paul C. ; Brown, Anya L.Coral reefs host some of the most iconic symbiotic interactions in nature and are host to the highest diversity of life on the planet. Cleaning symbiosis, wherein small fish or shrimp remove external parasites and associated microorganisms from specific clients, is common on coral reefs. Sites on the reef occupied by cleaners, or "cleaning stations", attract a wide variety of fish species that engage in direct physical contact with the cleaner. In this study, we used a combination of ecological surveys, in situ manipulations, and laboratory experiments to examine the unique features of cleaning stations to understand transfer of bacterial and archaeal symbionts amongst fish and within coral reef environment. We used microbial 16S rRNA gene amplicons, environmental parameters, and other molecular tools to evaluate the dynamics between coral microbiomes, cleanerfish skin microbiomes, and the environment. This dataset contains metadata describing sequenced samples, including sample name, data deposition accession records, and measurements at the time of sample collection. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/906740