Identifying potential introduced and natural sources of pollution in Delaware watersheds.

Managing water quality with microbial impairment caused by poses unique challenges regarding the determination of fecal host origin. Most water monitoring is performed based on counts that neither detect the location of the introduction of pollution nor identify the type of contaminating . The use of sequenced-based microbial source tracking could allow for identification of fecal origin and potential remediation of pollution.

Comparative metagenomics of tropical reef fishes show conserved core gut functions across hosts and diets with diet-related functional gene enrichments.

Fish gut microbial communities are important for the breakdown and energy harvesting of the host diet. Microbes within the fish gut are selected by environmental and evolutionary factors. To understand how fish gut microbial communities are shaped by diet, three tropical fish species (hawkfish, ; yellow tang, ; and triggerfish, ) were fed piscivorous (fish meal pellets), herbivorous (seaweed), and invertivorous (shrimp) diets, respectively.

Archaeal blooms and busts in an estuarine time series.

Coastal bays, such as Delaware Bay, are highly productive, ecologically important transitions between rivers and the coastal ocean. They offer opportunities to investigate archaeal assemblages across seasons, with the exchange of water masses that occurs with tidal cycles, and in the context of variable organic matter quality. For a year-long estuarine, size-fractionated time series, we used amplicon sequencing, chemical measurements, and qPCR to follow archaeal groups through the seasons.

High methane concentrations in tidal salt marsh soils: Where does the methane go?

Tidal salt marshes produce and emit CH . Therefore, it is critical to understand the biogeochemical controls that regulate CH spatial and temporal dynamics in wetlands. The prevailing paradigm assumes that acetoclastic methanogenesis is the dominant pathway for CH production, and higher salinity concentrations inhibit CH production in salt marshes.

Reference library for microbial source tracking in the mid-Atlantic United States.

Microbial source tracking can determine fecal contamination but requires a relevant, sizable reference library for analysis. We provide a reference library of 100+ fecal microbiome samples relevant to mid-Atlantic United States ecosystems. Included are wild and domesticated fauna, wastewater, and septic samples applicable to Delaware source tracking studies.

Occurrence, Diversity, and Genomes of " Patescibacteria" along the Early Diagenesis of Marine Sediments.

The phylum " Patescibacteria" (or Candidate Phyla Radiation [CPR]) accounts for roughly one-quarter of microbial diversity on Earth, but the presence and diversity of these bacteria in marine sediments have been rarely charted. Here, we investigate the abundance, diversity, and metabolic capacities of CPR bacteria in three sediment sites (Mohns Ridge, North Pond, and Costa Rica Margin) with samples covering a wide range of redox zones formed during the early diagenesis of organic matter. Through metagenome sequencing, we found that all investigated sediment horizons contain " Patescibacteria" (0.

Introducing Candidatus Bathyanammoxibiaceae, a family of bacteria with the anammox potential present in both marine and terrestrial environments.

Anaerobic ammonium oxidation (Anammox) bacteria are a group of extraordinary bacteria exerting a major impact on the global nitrogen cycle. Their phylogenetic breadth and diversity, however, are not well constrained. Here we describe a new, deep-branching family in the order of Candidatus Brocadiales, Candidatus Bathyanammoxibiaceae, members of which have genes encoding the key enzymes of the anammox metabolism.

Helarchaeota and co-occurring sulfate-reducing bacteria in subseafloor sediments from the Costa Rica Margin.

Deep sediments host many archaeal lineages, including the Asgard superphylum which contains lineages predicted to require syntrophic partnerships. Our knowledge about sedimentary archaeal diversity and their metabolic pathways and syntrophic partners is still very limited. We present here new genomes of Helarchaeota and the co-occurring sulfate-reducing bacteria (SRB) recovered from organic-rich sediments off Costa Rica Margin.

Expanding the repertoire of electron acceptors for the anaerobic oxidation of methane in carbonates in the Atlantic and Pacific Ocean.

Authigenic carbonates represent a significant microbial sink for methane, yet little is known about the microbiome responsible for the methane removal. We identify carbonate microbiomes distributed over 21 locations hosted by seven different cold seeps in the Pacific and Atlantic Oceans by carrying out a gene-based survey using 16S rRNA- and mcrA gene sequencing coupled with metagenomic analyses. Based on 16S rRNA gene amplicon analyses, these sites were dominated by bacteria affiliated to the Firmicutes, Alpha- and Gammaproteobacteria.

"," a Novel Asgard Phylum from Costa Rican Sediment Capable of Polysaccharide Degradation and Anaerobic Methylotrophy.

The Asgard superphylum is a deeply branching monophyletic group of , recently described as some of the closest relatives of the eukaryotic ancestor. The wide application of genomic analyses from metagenome sequencing has established six distinct phyla, whose genomes encode diverse metabolic capacities and which play important biogeochemical and ecological roles in marine sediments. Here, we describe two metagenome-assembled genomes (MAGs) recovered from deep marine sediments off the Costa Rica margin, defining a novel lineage phylogenetically married to " Thorarchaeota"; as such, we propose the name "" for this phylum.

Methanogens Within a High Salinity Oil Reservoir From the Gulf of Mexico.

Oil reservoirs contain microbial populations that are both autochthonously and allochthonously introduced by industrial development. These microbial populations are greatly influenced by external factors including, but not limited to, salinity and temperature. In this study, we used metagenomics to examine the microbial populations within five wells of the same hydrocarbon reservoir system in the Gulf of Mexico.

Microbiomes of fish, sediment and seagrass suggest connectivity of coral reef microbial populations.

The benthic environments of coral reefs are heavily shaped by physiochemical factors, but also the ecological interactions of the animals and plants in the reef ecosystem. Microbial populations may be shared within the ecosystem of sediments, seagrasses and reef fish. In this study, we hypothesize that coral reef and seagrass environments share members of the microbial community that are rare in some habitats and enriched in others, and that animals may integrate this connectivity.

Novel clostridial lineages recovered from metagenomes of a hot oil reservoir.

Oil reservoirs have been shown to house numerous microbial lineages that differ based on the in-situ pH, salinity and temperature of the subsurface environment. Lineages of Firmicutes, including Clostridiales, have been frequently detected in oil reservoirs, but are typically not considered impactful or relevant due to their spore-forming nature. Here we show, using metagenomics, a high temperature oil reservoir of marine salinity contains a microbial population that is predominantly from within the Order Clostridiales.

Metagenomic views of microbial dynamics influenced by hydrocarbon seepage in sediments of the Gulf of Mexico.

Microbial cells in the seabed are thought to persist by slow population turnover rates and extremely low energy requirements. External stimulations such as seafloor hydrocarbon seeps have been demonstrated to significantly boost microbial growth; however, the microbial community response has not been fully understood. Here we report a comparative metagenomic study of microbial response to natural hydrocarbon seeps in the Gulf of Mexico.

Mercury geochemistry and microbial diversity in meromictic Glacier Lake, Jamesville, NY.

Meromictic lakes are stratified lakes that typically stimulate phototrophic anoxic microbial metabolism, including the transformation of sulphur. Less studied are the transformations of mercury in these environments, and the microorganisms, which mediate these reactions. In order to further an understanding of redox species, mercury and microbial populations in meromictic lakes, we examined the geochemistry and microbiology of Glacier Lake in Jamesville, NY.

Cytosine Methylation Within Marine Sediment Microbial Communities: Potential Epigenetic Adaptation to the Environment.

Marine sediments harbor a vast amount of Earth's microbial biomass, yet little is understood regarding how cells subsist in this low-energy, presumably slow-growth environment. Cells in marine sediments may require additional methods for genetic regulation, such as epigenetic modification DNA methylation. We investigated this potential phenomenon within a shallow estuary sediment core spanning 100 years of age.

An Ionic Limit to Life in the Deep Subsurface.

The physical and chemical factors that can limit or prevent microbial growth in the deep subsurface are not well defined. Brines from an evaporite sequence were sampled in the Boulby Mine, United Kingdom between 800 and 1300 m depth. Ionic, hydrogen and oxygen isotopic composition were used to identify two brine sources, an aquifer situated in strata overlying the mine, and another ambiguous source distinct from the regional groundwater.

Discerning autotrophy, mixotrophy and heterotrophy in marine TACK archaea from the North Atlantic.

DNA stable isotope probing (SIP) was used to track the uptake of organic and inorganic carbon sources for TACK archaea (Thaumarchaeota/Aigarchaeota/Crenarchaeota/Korarchaeota) on a cruise of opportunity in the North Atlantic. Due to water limitations, duplicate samples from the deep photic (60-115 m), the mesopelagic zones (local oxygen minimum; 215-835 m) and the bathypelagic zone (2085-2835 m) were amended with various combinations of 12C- or 13C-acetate/urea/bicarbonate to assess cellular carbon acquisition. The SIP results indicated the majority of TACK archaeal operational taxonomic units (OTUs) incorporated 13C from acetate and/or urea into newly synthesized DNA within 48 h.

The metabolic potential of the single cell genomes obtained from the Challenger Deep, Mariana Trench within the candidate superphylum Parcubacteria (OD1).

Candidate phyla (CP) are broad phylogenetic clusters of organisms that lack cultured representatives. Included in this fraction is the candidate Parcubacteria superphylum. Specific characteristics that have been ascribed to the Parcubacteria include reduced genome size, limited metabolic potential and exclusive reliance on fermentation for energy acquisition.

Using directed evolution to improve hydrogen production in chimeric hydrogenases from Clostridia species.

Hydrogenases are enzymes that play a key role in controlling excess reducing equivalents in both photosynthetic and anaerobic organisms. This enzyme is viewed as potentially important for the industrial generation of hydrogen gas; however, insufficient hydrogen production has impeded its use in a commercial process. Here, we explore the potential to circumvent this problem by directly evolving the Fe-Fe hydrogenase genes from two species of Clostridia bacteria.

Deep Subsurface Life from North Pond: Enrichment, Isolation, Characterization and Genomes of Heterotrophic Bacteria.

Studies of subsurface microorganisms have yielded few environmentally relevant isolates for laboratory studies. In order to address this lack of cultivated microorganisms, we initiated several enrichments on sediment and underlying basalt samples from North Pond, a sediment basin ringed by basalt outcrops underlying an oligotrophic water-column west of the Mid-Atlantic Ridge at 22°N. In contrast to anoxic enrichments, growth was observed in aerobic, heterotrophic enrichments from sediment of IODP Hole U1382B at 4 and 68 m below seafloor (mbsf).