Gut-associated microbial symbionts of the marsh fiddler crab, Uca pugnax

Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Insitution September 2004Digestive associations between marine invertebrates and resident (attached) microbial communities may playa critical role in host physiology and involve previously unidentified microbial species. The overarching goal of this thesis was to characterize the ecology and genetic diversity of resident gut microbes to advance our understanding of their interactions with their host, the marsh fiddler crab, Uca pugnax. Furthermore, we assessed whether microbes benefit the host by contributing extracellular enzymes along the digestive tract. This is the first report of the eccrinid protists, Enteromyces callanassae and Enterobryus sp., inhabiting U. pugnax. The greatest abundances of both bacteria and protists were documented in the host stomach and hindgut. For these sections, we have described morphologies, measured abundances and characterized the genetic diversity (bacteria) of resident microbes. Presence and abundance of the Eccrinales protists depends on host molt stage as all eccrinid biomass is shed with the host's molt. In intermolt crabs, both bacterial and protozoan symbionts appear to be consistent features of the stomach and hindgut. Furthermore, bacterial diversity patterns seem to be comparable among individuals and over time, as assessed by denaturing gradient gel electrophoresis (DGGE). Community composition, however, does differ between stomach and hindgut populations, as resolved by DGGE and clone libraries of the 16S rRNA gene. Many recovered clones were most closely related to other symbiotic or gut-associated bacteria. Few identified clones, however, shared more than 95% 16S rRNA gene sequence similarity with their nearest known relatives, indicating that this environment may support novel bacterial phylotypes. An exception was the U. pugnax hindgut phylotype most closely related to a phylotype identified from hindguts of the detritivorous shrimp Neotrypaea californiensis. This finding suggests that detritivorous crustacean hindguts may provide an ecological niche for specific bacterial phylotypes. Functionally, resident bacteria, particularly in the hindgut, may contribute to total enzyme activity in the gut of their host.Financial support was provided by an ONR NDSEG fellowship, an Ocean Ventures Fund grant, a Sea Grant New-Initiatives grant, and the Academic Programs Office

Fluid flow stimulates chemoautotrophy in hydrothermally influenced coastal sediments

© The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Sievert, S. M., Buehring, S., Gulmann, L. K., Hinrichs, K.-U., Ristova, P. P., & Gomez-Saez, G. Fluid flow stimulates chemoautotrophy in hydrothermally influenced coastal sediments. Communications Earth & Environment, 3(1), (2022): 96, https://doi.org/10.1038/s43247-022-00426-5.Hydrothermalism in coastal sediments strongly impacts biogeochemical processes and supports chemoautotrophy. Yet, the effect of fluid flow on microbial community composition and rates of chemoautotrophic production is unknown because rate measurements under natural conditions are difficult, impeding an assessment of the importance of these systems. Here, in situ incubations controlling fluid flow along a transect of three geochemically distinct locations at a shallow-water hydrothermal system off Milos (Greece) show that Campylobacteria dominated chemoautotrophy in the presence of fluid flow. Based on injected 13C-labelled dissolved inorganic carbon and its incorporation into fatty acids, we constrained carbon fixation to be as high as 12 µmol C cm−3 d−1, corresponding to areal rates up to 10-times higher than previously reported for coastal sediments, and showed the importance of fluid flow for supplying the necessary substrates to support chemoautotrophy. Without flow, rates were substantially lower and microbial community composition markedly shifted. Our results highlight the importance of fluid flow in shaping the composition and activity of microbial communities of shallow-water hydrothermal vents, identifying them as hotspots of microbial productivity.Open Access funding enabled and organized by Projekt DEAL

Single cell genomics-based analysis of gene content and expression of prophages in a diffuse-flow deep-sea hydrothermal system

© The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Labonte, J. M., Pachiadaki, M., Fergusson, E., McNichol, J., Grosche, A., Gulmann, L. K., Vetriani, C., Sievert, S. M., & Stepanauskas, R. Single cell genomics-based analysis of gene content and expression of prophages in a diffuse-flow deep-sea hydrothermal system. Frontiers in Microbiology, 10, (2019): 1262, doi:10.3389/fmicb.2019.01262.Phage–host interactions likely play a major role in the composition and functioning of many microbiomes, yet remain poorly understood. Here, we employed single cell genomics to investigate phage–host interactions in a diffuse-flow, low-temperature hydrothermal vent that may be reflective of a broadly distributed biosphere in the subseafloor. We identified putative prophages in 13 of 126 sequenced single amplified genomes (SAGs), with no evidence for lytic infections, which is in stark contrast to findings in the surface ocean. Most were distantly related to known prophages, while their hosts included bacterial phyla Campylobacterota, Bacteroidetes, Chlorobi, Proteobacteria, Lentisphaerae, Spirochaetes, and Thermotogae. Our results suggest the predominance of lysogeny over lytic interaction in diffuse-flow, deep-sea hydrothermal vents, despite the high activity of the dominant Campylobacteria that would favor lytic infections. We show that some of the identified lysogens have co-evolved with their host over geological time scales and that their genes are transcribed in the environment. Functional annotations of lysogeny-related genes suggest involvement in horizontal gene transfer enabling host’s protection against toxic metals and antibacterial compounds.This work was supported by the U.S. National Science Foundation’s Dimensions of Biodiversity Program [OCE-1136488 (to RS), OCE-1136727 (to SMS) and OCE-1136451 (to CV)], as well as DEB-1441717 and OCE-1335810 (to RS), and the DOE JGI CSP project 1477

Bacterial diversity and successional patterns during biofilm formation on freshly exposed basalt surfaces at diffuse-flow deep-sea vents

Many deep-sea hydrothermal vent systems are regularly impacted by volcanic eruptions, leaving fresh basalt where abundant animal and microbial communities once thrived. After an eruption, microbial biofilms are often the first visible evidence of biotic re-colonization. The present study is the first to investigate microbial colonization of newly exposed basalt surfaces in the context of vent fluid chemistry over an extended period of time (4 to 293 days) by deploying basalt blocks within an established diffuse-flow vent at the 9o50’N vent field on the East Pacific Rise (EPR). Additionally, samples obtained after a recent eruption at the same vent field allowed for comparison between experimental results and those from natural microbial re-colonization. Over 9 months, the community changed from being composed almost exclusively of Epsilonproteobacteria to a more diverse assemblage, corresponding with a potential expansion of metabolic capabilities. The process of biofilm formation appears to generate similar surface-associated communities within and across sites by selecting for a subset of fluid-associated microbes, via species sorting. Furthermore, the high incidence of shared operational taxonomic units (OTUs) over time and across different vent sites suggests that the microbial communities colonizing new surfaces at diffuse-flow vent sites might follow a predictable successional pattern