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

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.

DUNE Software and Computing Challenges

The DUNE experiment will begin running in the late 2020’s. The goals of the experiment include 1) studying neutrino oscillations using a beam of neutrinos from Fermilab in Illinois to the Sanford Underground Research Facility, 2) studying astrophysical neutrino sources and rare processes and 3) understanding the physics of neutrino interactions in matter. The DUNE Far Detector, consisting of four 17 kt LArTPC modules, will produce “events” ranging in size from 6 GBs to more than 100 TBs, posing unique challenges for DUNE software and computing. The data processing algorithms, particularly for raw data, drive the requirements for the future DUNE software framework documented here.

Rectinema subterraneum sp. nov, a chemotrophic spirochaete isolated from the deep terrestrial subsurface

A novel, obligately anaerobic bacterium (strain SURF-ANA1T) was isolated from deep continental subsurface fluids at a depth of 1500 m below surface in the former Homestake Gold Mine (now Sanford Underground Research Facility, in Lead, South Dakota, USA). Cells of strain SURF-ANA1T were Gram-negative, helical, non-spore-forming and were 0.25–0.55×5.0–75.0 µm with a wavelength of 0.5–0.62 µm. Strain SURF-ANA1T grew at 15–50 °C (optimally at 40 °C), at pH 4.8–9.0 (pH 7.2) and in 1.0–40.0 g l−1 NaCl (10 g l−1 NaCl). The strain grew chemoheterotrophically with hydrogen or mono-, di- and polysaccharides as electron donors. The major cellular fatty acids in order of decreasing abundance (comprising >5% of total) were 10-methyl C16:0, iso-C15:0, C18:2 and C18:0 dimethyl acetal (DMA) and C20:0 methylene-nonadecanoic acid. Phylogenetic analysis based on the 16S rRNA gene sequence of strain SURF-ANA1T indicated a closest relationship with the recently characterized Rectinema cohabitans (99%). Despite high sequence identity, because of its distinct physiology, morphology and fatty acid profile, strain SURF-ANA1T is considered to represent a novel species within the genus Rectinema , for which the name Rectinema subterraneum sp. nov. is proposed. To our knowledge, this is the first report of an isolate within the phylum Spirochaetes from the deep (>100 m) terrestrial subsurface. The GenBank/EMBL/DDBJ accession numbers for the 16S rRNA gene and genomic sequences of strain SURF-ANA1T are KU359248 and GCF 009768935.1, respectively. The type strain of Rectinema subterraneum is SURF-ANA1T (=ATCC TSD-67=JCM 32656).

Latest results of the LUX dark matter experiment

LUX (Large Underground Xenon) was a dark matter experiment, which was housed at the Sanford Underground Research Facility (SURF) in South Dakota until late 2016, and previously set world-leading limits on Weakly Interacting Massive Particles (WIMPs), axions and axion-like particles (ALPs). This proceeding presents an overview of the LUX experiment and discusses the most recent analysis efforts, which are probing various dark matter models and detection techniques. In particular, studies of signals from inelastic scattering processes and of single scintillation photon events have improved the sensitivity of the experiment to low mass WIMPs. Additionally, a model-independent search for modulations in the LUX electron recoil rate is presented, demonstrating the most sensitive annual modulation search to date.

In Situ Electrochemical Studies of the Terrestrial Deep Subsurface Biosphere at the Sanford Underground Research Facility, South Dakota, USA

ABSTRACTThe terrestrial deep subsurface is host to significant and diverse microbial populations. However, these microbial populations remain poorly characterized, partially due to the inherent difficulty of sampling,in situstudies, and isolating of thein situmicrobes. Motivated by the ability of microbes to gain energy from redox reactions at mineral interfaces, we here presentin situelectrochemical colonization (ISEC) as a method to directly study microbial electron transfer activity and to enable the capture and isolation of electrochemically active microbes. We installed a potentiostatically controlled ISEC reactor containing four working electrodes 1500 m below the surface at the Sanford Underground Research Facility. The working electrodes were poised at different redox potentials, spanning anodic to cathodic, to mimic energy-yielding mineral reducing and oxidizing reactions predicted to occur at this site. We present a 16S rRNA analysis of thein situelectrode-associated microbial communities, revealing the dominance of novel bacterial lineages under cathodic conditions. We also demonstrate that thein situelectrodes can be further used for downstream electrochemical laboratory enrichment and isolation of novel strains. Using this workflow, we isolatedBacillus,Anaerospora,Comamonas,Cupriavidus, andAzonexusstrains from the electrode-attached biomass. Finally, the extracellular electron transfer activity of the electrode-oxidizingComamonasstrain (isolated at −0.19 V vs. SHE and designated WE1-1D1) and the electrode-reducingBacillusstrain (isolated at +0.53 V vs. SHE and designated WE4-1A1-BC) were confirmed in electrochemical reactors. Our study highlights the utility ofin situelectrodes and electrochemical enrichment workflows to shed light on microbial activity in the deep terrestrial subsurface.SIGNIFICANCEA large section of microbial life resides in the deep subsurface, but an organized effort to explore this deep biosphere has only recently begun. A detailed characterization of the resident microbes remains scientifically and technologically challenging due to difficulty in access, sampling, and emulating the complex interactions and energetic landscapes of subsurface communities with standard laboratory techniques. Here we describe an in situ approach that exploits the ability of many microbes to perform extracellular electron transfer to/from solid surfaces such as mineral interfaces in the terrestrial subsurface. By deploying and controlling the potential of in situ electrodes 4850 ft below the surface at the Sanford Underground Research Facility (South Dakota, USA), we highlight the promise of electrochemical techniques for studying active terrestrial subsurface microbial communities and enabling the isolation of electrochemically active microbes.

The LZ UK Data Centre

LUX-ZEPLIN (LZ) is a Dark Matter experiment based at the Sanford Underground Research Facility in South Dakota, USA. It is currently under construction and aims to start data taking in 2020. Its computing model stipulates two independent data centres, one in the USA and one in the UK. Both data centres will hold a complete copy of the experiment’s data and are expected to handle all aspects of data processing and user analysis. Here we discuss the set-up of the UK data centre within the context of the existing UK Grid infrastructure and show that a mature distributed computing system such as the Grid can be extended to serve as a central data centre for a reasonably large non-LHC experiment.