168 research outputs found
Variations in marine microbiomes: from habitat to host
No full textSubmitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution September 2022.Microorganisms are the dominant life form on Earth and inextricably tied to the ecology and evolution of all multicellular life, including marine animals. As the importance of microorganisms to our conception of life gains prominence, animals (and other macroorganisms) are increasingly viewed as “holobionts”, an assemblage of the host plus all its symbiotic microbes. This dissertation examines holobiont biology from the perspective of the microbial communities that live in and around marine
hosts. Using both amplicon and metagenomic sequencing, I study the microbiomes of reef-associated seawater and Atlantic killifish to better understand habitat and host effects on microbiome structure. In two Caribbean reef systems, I used examined the
biogeography of reef water microbes. I found that the microbiome of reef seawater varies with reef system and individual reefs but that microbiomes within individual reefs were similar to each other and did not vary with benthic composition. The regionalism of reef seawater microbiomes was further assessed upon incorporation of global scale data from five additional studies, which revealed that microbial communities were more distinct with increasing geographic distance. These results contribute to our understanding of the coral holobiont’s microbial environment and can inform monitoring efforts for reef health. Atlantic killifish populations can be categorized as sensitive or tolerant to industrial pollutants based on history of pollutant exposure. Thus, they are an excellent “natural laboratory” for understanding the combined effect of environment and host on microbiome composition. I examined the gut microbiomes of two populations of wild fish as well as captive fish originating from each of these wild populations. I found that living in and adapting to polluted waters can impact microbiome composition and structure, resulting in a microbiome that appears more disordered. Additionally, captivity resulted in a complete turnover of dominant microbial taxa, indicating the environment plays a large role in shaping killifish gut microbiomes. This dissertation demonstrates that diverse systems, from coral reefs to killifish, can benefit from a better understanding of its associated microorganisms. For holobiont studies, these results highlight the importance of considering the context of microbial communities, from environment to host population.My time in the MIT-WHOI Joint Program was supported by the Civil and Environmental Engineering department at MIT, the Schoettler scholarship fund, the National Science Foundation, and the Academic Programs Office at WHOI. The research presented here was supported by Rockefeller Philanthropy Advisors, the Dalio Foundation, and NSF awards OCE-1938147 and NSF OCE-1928761 to Amy Apprill; Joint Initiative Funds from the W. Andrew Mellon Foundation to Amy Apprill and Mark Hahn; and Ocean Venture Fund to Lei Ma
Pour une géographie du pluralisme thérapeutique dans les grandes villes d'Afrique noire.
No full textFor a Geography of Therapy Pluralism in the Great Cities of Tropical Africa.
Based on the concrete example of Brazzaville and on the first results of a workteam (ORSTOM-CNRS, «Citizens and Religion»), the author questions the very notion of «medical geography» about African towns, and suggests a more global approach considering the cultural heterogeneity of medical care in the African urban environment.A partir de l'exemple concret de Brazzaville, et en s'appuyant sur les premiers résultats d'un travail d'équipe (équipe ORSTOM-CNRS «citadins et religions»), l'auteur remet en question la stricte notion de «géographie médicale» à propos des villes africaines, et suggère une approche plus globale tenant compte de l'hétérogénéité culturelle de l'offre de soins en milieu urbain africain.Dorier-Apprill Elisabeth. Pour une géographie du pluralisme thérapeutique dans les grandes villes d'Afrique noire.. In: Espace, populations, sociétés, 1995-1. La géographie de la santé en question. pp. 135-141
Extracellular reef metabolites across the protected Jardines de la Reina, Cuba Reef System
No full text© The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Weber, L., Armenteros, M., Soule, M. K., Longnecker, K., Kujawinski, E. B., & Apprill, A. Extracellular reef metabolites across the protected Jardines de la Reina, Cuba Reef System. Frontiers in Marine Science, 7, (2020): 582161, https://doi.org/10.3389/fmars.2020.582161.Coral reef ecosystems are incredibly diverse marine biomes that rely on nutrient cycling by microorganisms to sustain high productivity in generally oligotrophic regions of the ocean. Understanding the composition of extracellular reef metabolites in seawater, the small organic molecules that serve as the currency for microorganisms, may provide insight into benthic-pelagic coupling as well as the complexity of nutrient cycling in coral reef ecosystems. Jardines de la Reina (JR), Cuba is an ideal environment to examine extracellular metabolites across protected and high-quality reefs. Here, we used liquid chromatography mass spectrometry (LC-MS) to quantify specific known metabolites of interest (targeted metabolomics approach) and to survey trends in metabolite feature composition (untargeted metabolomics approach) from surface and reef depth (6 – 14 m) seawater overlying nine forereef sites in JR. We found that untargeted metabolite feature composition was surprisingly similar between reef depth and surface seawater, corresponding with other biogeochemical and physicochemical measurements and suggesting that environmental conditions were largely homogenous across forereefs within JR. Additionally, we quantified 32 of 53 detected metabolites using the targeted approach, including amino acids, nucleosides, vitamins, and other metabolic intermediates. Two of the quantified metabolites, riboflavin and xanthosine, displayed interesting trends by depth. Riboflavin concentrations were higher in reef depth compared to surface seawater, suggesting that riboflavin may be produced by reef organisms at depth and degraded in the surface through photochemical oxidation. Xanthosine concentrations were significantly higher in surface reef seawater. 5′-methylthioadenosine (MTA) concentrations increased significantly within the central region of the archipelago, displaying biogeographic patterns that warrant further investigation. Here we lay the groundwork for future investigations of variations in metabolite composition across reefs, sources and sinks of reef metabolites, and changes in metabolites over environmental, temporal, and reef health gradients.This work was supported by the Dalio Foundation (now “OceanX”) and the National Science Foundation (OCE-1736288) (award to Amy Apprill). The mass spectrometry samples were analyzed at the WHOI FT-MS Users’ Facility with instrumentation funded by the National Science Foundation (grant OCE-1058448 to EK and MK) and the Simons Foundation (Award ID #509042, EK). Lastly, a portion of the publication fees was supported by the Massachusetts Institute of Technology (MIT) Open Access Article Publication Subvention fund from MIT Libraries
Microbial bioindicators of Stony Coral Tissue Loss Disease identified in corals and overlying waters using a rapid field-based sequencing approach
No full textAuthor Posting. © The Author(s), 2021. This is the author's version of the work. It is posted here by permission of Society for Applied Microbiology for personal use, not for redistribution. The definitive version was published in Becker, C. C., Brandt, M., Miller, C. A., & Apprill, A. Microbial bioindicators of Stony Coral Tissue Loss Disease identified in corals and overlying waters using a rapid field-based sequencing approach. Environmental Microbiology, (2021), https://doi.org/10.1111/1462-2920.15718.Stony Coral Tissue Loss Disease (SCTLD) is a devastating disease. Since 2014, it has spread along the entire Florida Reef Tract and into the greater Caribbean. It was first detected in the United States Virgin Islands in January 2019. To more quickly identify microbial bioindicators of disease, we developed a rapid pipeline for microbiome sequencing. Over a span of 10 days we collected, processed and sequenced coral and near-coral seawater microbiomes from diseased and apparently healthy Colpophyllia natans, Montastraea cavernosa, Meandrina meandrites and Orbicella franksi. Analysis of bacterial and archaeal 16S ribosomal RNA gene sequences revealed 25 bioindicator amplicon sequence variants (ASVs) enriched in diseased corals. These bioindicator ASVs were additionally recovered in near-coral seawater (<5 cm of coral surface), a potential reservoir for pathogens. Phylogenetic analysis of microbial bioindicators with sequences from the Coral Microbiome Database revealed that Vibrio, Arcobacter, Rhizobiaceae and Rhodobacteraceae sequences were related to disease-associated coral bacteria and lineages novel to corals. Additionally, four ASVs (Algicola, Cohaesibacter, Thalassobius and Vibrio) were matches to microbes previously associated with SCTLD that should be targets for future research. Overall, this work suggests that a rapid sequencing framework paired with specialized databases facilitates identification of microbial disease bioindicators.This work was funded by The Tiffany & Co. Foundation, NSF EEID-2109622, OCE-1928753, OCE-1928761 and OCE-1938147, the Rockefeller Philanthropy Advisors, Dalio Foundation, and other generous donors of the Oceans 5 project. Samples were collected under permit DFW19057U.2022-08-2
Incidence of lesions on Fungiidae corals in the eastern Red Sea is related to water temperature and coastal pollution
No full textAuthor Posting. © The Author(s), 2014. This is the author's version of the work. It is posted here by permission of Elsevier for personal use, not for redistribution. The definitive version was published in Marine Environmental Research 98 (2014): 29-38, doi:10.1016/j.marenvres.2014.04.002.As sea surface temperatures rise and the global human population increases, large-scale
field observations of marine organism health and water quality are increasingly
necessary. We investigated the health of corals from the family Fungiidae using visual
observations in relation to water quality and microbial biogeochemistry parameters along
1300 km of the Red Sea coast of Saudi Arabia. At large scales, incidence of lesions
caused by unidentified etiology showed consistent signs, increasing significantly from the
northern to southern coast and positively correlated to annual mean seawater
temperatures. Lesion abundance also increased to a maximum of 96% near the populous
city of Jeddah. The presence of lesioned corals in the region surrounding Jeddah was strongly correlated with elevated concentrations of ammonium and changes in microbial
communities that are linked to decreased water quality. This study suggests that both high
seawater temperatures and nutrient pollution may play an indirect role in the formation of
lesions on corals.This research was supported by Award No. USA 00002 to K. Hughen by King Abdullah
University of Science and Technology (KAUST) and a WHOI Ocean Life Institute
postdoctoral scholar fellowship to A. Apprill
Major similarities in the bacterial communities associated with lesioned and healthy Fungiidae corals
No full textCultivation-based studies have demonstrated that yellow-band disease (YBD), a lesion-producing ailment affecting diverse species of coral, is caused by a consortium of Vibrio spp. This study takes the first cultivation-independent approach to examine the whole bacterial community associated with YBD-like lesioned corals. Two species of Fungiidae corals, Ctenactis crassa and Herpolitha limax, displaying YBD-like lesions were examined across diverse reefs throughout the Red Sea. Using a pyrosequencing approach targeting the V1-V3 regions of the SSU rRNA gene, no major differences in bacterial community composition or diversity were identified between healthy and lesioned corals of either species. Indicator species analysis did not find Vibrio significantly associated with the lesioned corals. However, operational taxonomic units belonging to the Ruegeria genus of Alphaproteobacteria and NS9 marine group of Flavobacteria were significantly associated with the lesioned corals. The most striking trend of this dataset was that reef location was found to be the most significant influence on the coral-bacterial community. It is possible that more pronounced lesion-specific bacterial signatures might have been concealed by the strong influence of environmental conditions on coral-bacteria. Overall, this study demonstrates inconsistencies between cultivation-independent and cultivation-based studies regarding the role of specific bacteria in coral diseases. © 2013 John Wiley & Sons Ltd and Society for Applied Microbiology.We are grateful to J. Cervino for lesion identification, K. Furby, J. Ossolinski, J. Kneeland and W. Bernstein for sample collections, and the crew of the M/V Dream Island. We thank K. Selph of the UH SOEST flow cytometry facility for cell enumeration, J. Jennings of Oregon State University for inorganic nutrient analysis, and C. Wright and the University of Illinois W. M. Keck Center for Comparative and Functional Genomics for sequencing. The authors acknowledge the faculty of the 2011 MBL hosted STAMPS course for insight into sequencing data analysis and two insightful reviewers for their comments on this manuscript. This research was supported by a WHOI Ocean Life Institute postdoctoral scholar fellowship to A. Apprill, and by Award No. USA 00002 to K. Hughen made by King Abdullah University of Science and Technology (KAUST)
Flow cytometry and nutrient analyses data from a tidal study over 48 hours of mangrove, seagrass, and seawater from the US Virgin Islands in July of 2017
No full textDataset: Tidal study of seawater microbial communitiesData from a tidal study over 48 hours of mangrove, seagrass, and seawater from the US Virgin Islands in 2017. These data include tidal height, depth, temperature, salinity, Prochlorococcus counts, Synechococcus counts, Picoeukaryote abundances, nutrient concentrations at accession numbers for sequences at The National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA).
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/783679NSF Division of Ocean Sciences (NSF OCE) OCE-173628
Marine Animal Microbiomes: Toward Understanding Host–Microbiome Interactions in a Changing Ocean
No full textAll animals on Earth form associations with microorganisms, including protists, bacteria, archaea, fungi, and viruses. In the ocean, animal–microbial relationships were historically explored in single host–symbiont systems. However, new explorations into the diversity of microorganisms associating with diverse marine animal hosts is moving the field into studies that address interactions between the animal host and a more multi-member microbiome. The potential for microbiomes to influence the health, physiology, behavior, and ecology of marine animals could alter current understandings of how marine animals adapt to change, and especially the growing climate-related and anthropogenic-induced changes already impacting the ocean environment. This review explores the nature of marine animal–microbiome relationships and interactions, and possible factors that may shift associations from symbiotic to dissociated states. I present a brief review of current microbiome research and opportunities, using examples of select marine animals that span diverse phyla within the Animalia, including systems that are more and less developed for symbiosis research, including two represented in my own research program. Lastly, I consider challenges and emerging solutions for moving these and other study systems into a more detailed understanding of host–microbiome interactions within a changing ocean
Diel, daily, and spatial variation of coral reef seawater microbial communities from US Virgin Islands, 2017
No full textDataset: Coral reef seawater microbial communitiesBacterial and archaeal diversity and composition, microbial cell abundances, inorganic nutrient concentrations, and physicochemical conditions were determined and measured in coral reef seawater over a three-day, diel time series on one reef in St. John, U.S. Virgin Islands.
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/775229NSF Division of Ocean Sciences (NSF OCE) OCE-173628
Bacterioplankton data from coral and coral mucus aquaria experiments conducted at Bermuda Institute of Ocean Sciences in 2013
No full textDataset: Coral-bacterioplankton data from mesocosm experimentsBacterioplankton data from coral and coral mucus aquaria experiments conducted at Bermuda Institute of Ocean Sciences in 2013
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/652849NSF Division of Ocean Sciences (NSF OCE) OCE-123361
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