Biology

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    Interactions with a Complex Microbiota Mediate a Trade-Off between the Host Development Rate and Heat Stress Resistance
    (MDPI, 2020-11-13) Slowinski, Samuel; Ramirez, Isabella; Narayan, Vivek; Somayaji, Medha; Para, Maya; Pi, Sarah; Jadeja, Niharika; Karimzadegan, Siavash; Pees, Barbara; Shapira, Michael
    Animals and plants host diverse communities of microorganisms, and these microbiotas have been shown to influence host life history traits. Much has been said about the benefits that host-associated microbiotas bestow on the host. However, life history traits often demonstrate tradeoffs among one another. Raising Caenorhabditis elegans nematodes in compost microcosms emulating their natural environment, we examined how complex microbiotas affect host life history traits. We show that soil microbes usually increase the host development rate but decrease host resistance to heat stress, suggesting that interactions with complex microbiotas may mediate a tradeoff between host development and stress resistance. What element in these interactions is responsible for these effects is yet unknown, but experiments with live versus dead bacteria suggest that such effects may depend on bacterially provided signals.
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    METHOD VALIDATION AND DEVELOPMENT FOR THE METAGENOMIC EXPLORATION OF MICROBIAL COMMUNITIES
    (2022) Commichaux, Seth; Pop, Mihai; Rand, Hugh; Biology; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
    Our world is inhabited and shaped by diverse and complex microbial communities which we are only beginning to characterize and understand. With the advent of affordable high-throughput sequencing, the study of the genomic content of microbial communities, metagenomics, has accelerated our understanding of their impact on human and environmental health. The increasing number of datasets produced by metagenomic studies provide many opportunities for novel bioinformatic analyses and for the development of computational methods. However, careful benchmarking and validation are also important undertakings to ensure the integrity of methods and research in such a rapidly developing field. Here, we explored several problems in metagenomics by benchmarking existing methods and technologies, developing new methods, recommending best practices, and highlighting opportunities for future work. First, microbial gene catalogs document and organize the genes found in microbial communities and provide a reference for the standardized analysis of metagenomic data. Although commonly used to explore the intersection between microbiomes, humans, and ecosystems, the methods used for their construction and effectiveness for metagenomic analyses had not been critically evaluated. Our analysis highlighted important limitations of gene catalogs, opportunities for future research, and allowed us to recommend best practices. Second, we assessed if nanopore long read sequencing could expedite the accurate reconstruction of a pathogen genome from a microbial community. The investigation of foodborne illness outbreaks routinely uses short-read whole genome sequencing of pure culture pathogen colonies. However, culturing is a bottleneck and short reads cannot span all bacterial genomic repeats, often leading to fragmented assemblies. Our results showed that the integration of long-read sequencing could expedite the public health response by reconstructing complete pathogen genomes from a microbial community after limited culturing. Additionally, our evaluation of state-of-the-art assembly tools identified biases and areas for improvement. Third, we describe taxaTarget, a supervised learning approach for the taxonomic classification of microeukaryotes in metagenomic data. Metagenomics has been underutilized for microeukaryotes due to the many computational challenges they present. Existing tools often implement universal sequence similarity cutoffs which ignore that sequences can evolve at different rates and, thus, have different discriminatory power. We show that a data-driven approach to determining classification thresholds can result in higher sensitivity and precision than existing tools. Fourth, we explored the use of horizontally transferred plasmids to relate an outbreak strain to the microbiome of a suspected environmental source. The investigation of the 2020 red onion outbreak recovered the outbreak strain from patients but not the farms implicated as the likely source of contamination. Our analysis identified highly similar plasmids in the outbreak strain and environmental isolates collected from the farms, which supported a connection between the outbreak strain and the implicated farms. Additionally, we highlighted the need for more detailed and accurate metadata, more extensive environmental sampling, and a better understanding of plasmid molecular evolution before such analyses can be added to the public health response.
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    The skin microbiome of woodland salamanders and its association with hosts' taxonomy, environment and health status
    (2016) Muletz Wolz, Carly Rae; Lips, Karen R.; Behavior, Ecology, Evolution and Systematics; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
    Microbial communities play central roles in animal health. Host species, environmental conditions and presence of pathogens can affect the diversity and composition of animal-associated microbiomes. Amphibians form integral and functionally important symbioses with microbes. The amphibian microbiome interacts with pathogens, and can protect hosts from disease, including the disease chytridiomycosis, caused by skin infection by Batrachochytrium dendrobatidis (Bd). The implications of amphibian-microbiome associations are difficult to predict because little is known about the factors shaping bacterial communities or their functional traits, such as anti-Bd properties. I used culture-dependent and culture-independent methods to characterize the skin microbiome of Plethodon salamanders in field and laboratory studies. I hypothesized that the evolutionary history, environmental conditions, and health status of the hosts shape skin bacterial community assemblages. In a field study, I sampled sympatric, congeneric salamander species (Plethodon cinereus, P. glutinosus, P. cylindraceus) across three localities to quantify the distribution of both anti-Bd bacteria and the entire bacterial community. I identified 50 anti-Bd bacterial OTUs and 480 bacterial OTUs overall on the salamander skin, with high prevalence and abundance of anti-Bd bacterial genera Pseudomonas, Acinetobacter and Stenotrophomonas. Within a locality, co-occurring salamanders generally had similar microbiome diversity and composition patterns, but these differed among sites. This indicates that environment is more influential in shaping skin microbiome patterns than differences in host properties in these species. I sampled P. cinereus along an elevational gradient, as a proxy for environmental variables that co-vary with elevation. Microbiome diversity and composition changed with elevation, in which compositional changes were related to soil pH. In a laboratory experiment, I quantified the responses of P. cinereus and the skin microbiome to temperature (13, 17, 21 °C) and pathogen (Bd+, Bd-) exposure to determine whether the native microbiome affected survival at natural temperatures. Temperature changed the microbiome, but this did not prevent host mortality from Bd. Instead, Bd exposure changed the microbiome and caused 78% mortality. My results demonstrate that environmental conditions and pathogen presence are important factors determining skin microbiome structure in Plethodon salamanders. These findings contribute to our understanding of animal-microbial symbioses, microbial community ecology, and amphibian disease ecology.
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    MICROBIAL INTERACTIONS AND ECOLOGY WITHIN BLOOMS OF THE TOXIC DINOFLAGELLATE KARENIA brevis ON THE WEST FLORIDA SHELF.
    (2013) Meyer, Kevin Anthony; O'Neil, Judith M; Marine-Estuarine-Environmental Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
    The dinoflagellate Karenia brevis is capable of significant ecological and economic impacts in Florida waters where blooms typically occur. Blooms and cultures of K. brevis were sampled to determine the composition, production, and possible ecological function of bacteria and virus communities associated with K. brevis. Bacterial communities on the West Florida Shelf (WFS) were similar inside and outside K. brevis blooms, but primary and secondary (bacterial) production and bacteria and virus abundances were different depending on bloom stage. Bloom stages need to be identified so that discrete sampling events can be combined to characterize an entire bloom event. Within an initiating bloom bacterial production and mortality was high and viral abundance was low, suggesting that viral genomes were either within host cells or bacterial mortality was due to mixotrophic grazing by K. brevis or heterotrophic nanoflagellates. In a maintenance phase bloom the bacterial community was metabolically stressed, subject to increased viral infection, and most likely not being subjected to mixotrophic grazing. Bacterial communities associated with healthy K. brevis were dominated by the Cytophaga-Flavobacterium-Bacteroides (CFB) complex. As K. brevis shifted to stationary or senescing growth communities had higher proportions of Alphaproteobacteria. The SAR406 group, typically found in deep waters, was present in the surface waters of the WFS which supports existing K. brevis bloom formation hypotheses involving upwelling of deep waters from the mid to outer shelf. The CFB complex of bacteria also need to be further investigated as the consistent presence of CFB bacteria in both blooms and cultures of K. brevis suggest CFB bacteria are capable of numerous interactions with K. brevis. Furthermore, such interactions may be a vector of bloom control through viral infection; a high proportion of CFB bacteria would be ideal for density-dependent viral infection which could disrupt interactions between bacteria and K. brevis. Inoculating cultures of K. brevis, which included associated bacteria, with viral concentrates from the WFS showed differences in bacterial production and growth which indicate viruses are acting upon the bacterial community and not the dinoflagellates. Interactions between bacteria and K. brevis need to be further elucidated and explored for a better understanding of the role of each in dynamics of this harmful algal species. There may be a natural community succession amongst bacteria during blooms: utilizing certain indicator species to indicate bloom stage and transition between stages may aid in bloom forecasting and detection efforts.