Dataset Information

Metagenomics and Culture Dependent Insights into the Distribution of Firmicutes across Two Different Sample Types Located in the Black Hills Region of South Dakota, USA.

ABSTRACT: Firmicutes is almost a ubiquitous phylum. Several genera of this group, for instance, Geobacillus, are recognized for decomposing plant organic matter and for producing thermostable ligninolytic enzymes. Amplicon sequencing was used in this study to determine the prevalence and genetic diversity of the Firmicutes in two distinctly related environmental samples-South Dakota Landfill Compost (SDLC, 60 °C), and Sanford Underground Research Facility sediments (SURF, 45 °C). Although distinct microbial community compositions were observed, there was a dominance of Firmicutes in both the SDLC and SURF samples, followed by Proteobacteria. The abundant classes of bacteria in the SDLC site, within the phylum Firmicutes, were Bacilli (83.2%), and Clostridia (2.9%). In comparison, the sample from the SURF mine was dominated by the Clostridia (45.8%) and then Bacilli (20.1%). Within the class Bacilli, the SDLC sample had more diversity (a total of 11 genera with more than 1% operational taxonomic unit, OTU). On the other hand, SURF samples had just three genera, about 1% of the total population: Bacilli, Paenibacillus, and Solibacillus. With specific regard to Geobacillus, it was found to be present at a level of 0.07% and 2.5% in SURF and SDLC, respectively. Subsequently, culture isolations of endospore-forming Firmicutes members from these samples led to the isolation of a total of 117 isolates. According to colony morphologies, and identification based upon 16S rRNA and gyrB gene sequence analysis, we obtained 58 taxonomically distinct strains. Depending on the similarity indexes, a gyrB sequence comparison appeared more useful than 16S rRNA sequence analysis for inferring intra- and some intergeneric relationships between the isolates.

SUBMITTER: Govil T

PROVIDER: S-EPMC7825136 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:We report here the first dinosaur skeletal material described from the marine Fox Hills Formation (Maastrichtian) of western South Dakota. The find consists of two theropod pedal phalanges: one recovered from the middle part of the Fairpoint Member in Meade County, South Dakota; and the other from the Iron Lightning Member in Ziebach County, South Dakota. Comparison with pedal phalanges of other theropods suggests strongly that the Fairpoint specimen is a right pedal phalanx, possibly III-2, from a large ornithomimid. The Iron Lightning specimen we cautiously identify as an ornithomimid left pedal phalanx II-2. The Fairpoint bone comes from thinly bedded and cross-bedded marine sandstones containing large hematitic concretions and concretionary horizons. Associated fossils include osteichthyan teeth, fin spines and otoliths, and abundant teeth of common Cretaceous nearshore and pelagic chondrichthyans. Leaf impressions and other plant debris, blocks of fossilized wood, and Ophiomorpha burrows are also common. The Iron Lightning bone comes from a channel deposit composed of fine to coarse sandstone beds, some of which contain bivalves, and a disseminated assemblage of mammal teeth, chondrichthyan teeth, and fragmentary dinosaur teeth and claws. We interpret the depositional environment of the two specimens as marginal marine. The Fairpoint bone derives from a nearshore foreset setting, above wave base subject to tidal flux and storm activity. The Iron Lightning specimen comes from a topset channel infill probably related to deposition on a tidal flat or associated coastal setting. The taphonomic history and ages of the two bones differ. Orthogonal cracks in the cortical bone of the Fairpoint specimen suggest post-mortem desiccation in a dryland coastal setting prior to transport and preservation in the nearby nearshore setting described above. The pristine surface of the Iron Lightning specimen indicates little transport before incorporation into the channel deposit in which it was found. The Fairpoint bone bed most probably lies within the Hoploscaphites nicolletii Ammonite Zone of the early late Maastrichtian, and would therefore have an approximate age of 69 Ma. The Iron Lightning bone is from the overlying H. nebrascensis Ammonite Zone, and is thus about one million years younger.

Project description:Iron-bearing minerals are key components of the Earth's crust and potentially critical energy sources for subsurface microbial life. The Deep Mine Microbial Observatory (DeMMO) is situated in a range of iron-rich lithologies, and fracture fluids here reach concentrations as high as 8.84 mg/liter. Iron cycling is likely an important process, given the high concentrations of iron in fracture fluids and detection of putative iron-cycling taxa via marker gene surveys. However, a previous metagenomic survey detected no iron cycling potential at two DeMMO localities. Here, we revisited the potential for iron cycling at DeMMO using a new metagenomic data set including all DeMMO sites and FeGenie, a new annotation pipeline that is optimized for the detection of iron cycling genes. We annotated functional genes from whole metagenomic assemblies and metagenome-assembled genomes and characterized putative iron cycling pathways and taxa in the context of local geochemical conditions and available metabolic energy estimated from thermodynamic models. We reannotated previous metagenomic data, revealing iron cycling potential that was previously missed. Across both metagenomic data sets, we found that not only is there genetic potential for iron cycling at DeMMO, but also, iron is likely an important source of energy across the system. In response to the dramatic differences we observed between annotation approaches, we recommend the use of optimized pipelines where the detection of iron cycling genes is a major goal. IMPORTANCE We investigated iron cycling potential among microbial communities inhabiting iron-rich fracture fluids to a depth of 1.5 km in the continental crust. A previous study found no iron cycling potential in the communities despite the iron-rich nature of the system. A new tool for detecting iron cycling genes was recently published, which we used on a new data set. We combined this with a number of other approaches to get a holistic view of metabolic strategies across the communities, revealing iron cycling to be an important process here. In addition, we used the tool on the data from the previous study, revealing previously missed iron cycling potential. Iron is common in continental crust; thus, our findings are likely not unique to our study site. Our new view of important metabolic strategies underscores the importance of choosing optimized tools for detecting the potential for metabolisms like iron cycling that may otherwise be missed.

Dataset Information

Metagenomics and Culture Dependent Insights into the Distribution of Firmicutes across Two Different Sample Types Located in the Black Hills Region of South Dakota, USA.

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