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At least 469 records · Page 26
All sourcesNASA NTRSDOE OSTI
DOE OSTI2013

Kallotenue papyrolyticum gen. nov., sp. nov., a cellulolytic and filamentous thermophile that represents a novel lineage (Kallotenuales ord. nov., Kallotenuaceae fam. nov.) within the class Chloroflexia

Several closely-related, thermophilic, and cellulolytic bacterial strains, designated JKG1T, JKG2, JKG3, JKG4, and JKG5, were isolated from a cellulolytic enrichment (corn stover) incubated in the water column of Great Boiling Spring, NV. Strain JKG1T had cells of a diameter of 0.7 - 0.9 μm and length of ~2.0 μm that formed non-branched multicellular filaments reaching >300 μm. Spores were not formed and dense liquid cultures were red. The temperature range for growth was 45-65 °C, with an optimum of 55 °C. The pH range for growth was 5.6-9.0, with an optimum of 7.5. JKG1T grew as an aerobic heterotroph, utilizing glucose, sucrose, xylose, arabinose, cellobiose, carboxymethylcellulose, filter paper, microcrystalline cellulose, xylan, starch, casamino acids, tryptone, peptone, yeast extract, acetate, citrate, lactate, pyruvate, and glycerol as sole carbon sources, and was not observed to photosynthesize. The cells stained Gram-negative. Phylogenetic analysis using 16S rRNA gene sequences placed the new isolates in the class Chloroflexia, but distant from other cultivated members, with the highest sequence identity of 82.5% to Roseiflexus castenholzii. The major quinone was menaquinone-9; no ubiquinones were detected. The major cellular fatty acids (>5%) were C18:0, anteiso-C17:0, iso-C18:0, and iso-C17:0. C16:0, iso-C16:0, and C17:0. The peptidoglycan amino acids were alanine, ornithine, glutamic acid, serine, and asparagine. Whole-cell sugars included mannose, rhamnose, glucose, galactose, ribose, arabinose, and xylose. Morphological, phylogenetic, and chemotaxonomic results suggest that JKG1T is representative of a new lineage within the class Chloroflexia, which we propose to designate Kallotenue papyrolyticum gen. nov., sp. nov., Kallotenuaceae fam. nov., Kallotenuales ord. nov.

Environmental Molecular Sciences Laboratory↗
DOE OSTI2014

Thermoflexus hugenholtzii gen. nov., sp. nov., a thermophilic, microaerophilic, filamentous bacterium representing a novel class in the Chloroflexi, Thermoflexia classis nov., and description of Thermoflexaceae fam. nov. and Thermoflexales ord. nov.

A thermophilic, filamentous, heterotrophic bacterium designated strain JAD2T was isolated from sediment of Great Boiling Spring in Nevada, USA. Cells had an average diameter of 0.3 µm and length of 4.0 µm, and formed filaments typically ranging in length from 20 µm to 200 µm. Filaments were negative for the Gram stain reaction, spores were not formed, and motility was not observed. The optimum temperature for growth was 75 °C with a range from 67.5-75 °C, and the optimum pH for growth was 6.75 with a range from 6.5-7.75. Peptone, tryptone or yeast extract were able to support growth when supplemented with a vitamin solution, but no growth was observed using a variety of defined organic substrates. Strain JAD2T was a facultative microaerophile, with optimal growth at 1% v/v O2 and an upper limit of 8% O2, and anaerobic growth was stimulated by fumarate but inhibited by sulfite and elemental sulfur. The major cellular fatty acids (>5%) were C16:0, C19:0, C18:0, C20:0, and C19:1. The genomic DNA G+C content was 69.3%. Phylogenetic and phylogenomic analyses using 16S rRNA gene sequences and other conserved genes placed JAD2T and other members of the yet-uncultivated GAL35 group within the phylum Chloroflexi, but not within any existing class in this phylum. These results indicate that strain JAD2T is the first cultivated representative of a new lineage within the phylum Chloroflexi, for which we propose the name Thermoflexus hugenholtzii gen. nov., sp. nov., type strain JAD2T, within Thermoflexia classis nov., Thermoflexales ord. nov., and Thermoflexaceae fam. nov.

Chloroflexi↗
DOE OSTI2018

Description of Alicyclobacillus montanus sp. nov., a mixotrophic bacterium isolated from acidic hot springs

Three morphologically similar thermo-acidophilic strains, USBA-GBX-501, USBA-GBX-502 and USBA-GBX-503T, were isolated from acidic thermal springs at the National Natural Park Los Nevados (Colombia). All isolates were spore-forming, Gram-stain-positive and motile, growing aerobically at 25–55°C (optimum ~45°C) and at pH 1.5–4.5 (optimum pH ~3.0). Phylogenetic analysis of the 16S rRNA gene sequences of these isolates showed an almost identical sequence (99.0% similarity) and they formed a robust cluster with the closest relative Alicyclobacillus tolerans DSM 16297 T with a sequence similarity of 99.0%. Average similarity to other species of the genus Alicyclobacillus was 93.0% and average similarity to species of the genus Effusibacillus was 90%. In addition, the level of DNA–DNA hybridization between strain USBA-GBX-503 T and Alicyclobacillus tolerans DSM 16297 T was 31.7 %. The genomic DNA G+C content of strain USBA-GBX-503 T was 44.6 mol%. The only menaquinone was MK-7 (100.0%). No ω-alicyclic fatty acids were detected in strain USBA-GBX-503 T , and the major cellular fatty acids were C18:1ω7c, anteiso-C17:0 and iso-C17:0. Based on phenotypic and chemotaxonomic characteristics, phylogenetic analysis and DNA–DNA relatedness values, along with low levels of identity at the whole genome level (ANIb and ANIm values of <67.0 and <91.0%, respectively), it can be concluded that strain USBA-GBX-503 T represents a novel species of the genus Alicyclobacillus , for which the name Alicyclobacillus montanus sp. nov. is proposed. The type strain is USBA-GBX-503 T (=CMPUJ UGB U503 T =CBMAI1927 T ).

López, G.↗
DOE OSTI2023

Sulfurospirillum diekertiae sp. nov., a tetrachloroethene-respiring bacterium isolated from contaminated soil

Two anaerobic, tetrachloroethene- (PCE-) respiring bacterial isolates, designated strain ACS DCE T and strain ACS TCE , were characterized using a polyphasic approach. Cells were Gram-stain-negative, motile, non-spore-forming and shared a vibrioid- to spirillum-shaped morphology. Optimum growth occurred at 30°C and 0.1–0.4% salinity. The pH range for growth was pH 5.5–7.5, with an optimum at pH 7.2. Hydrogen, formate, pyruvate and lactate as electron donors supported respiratory reductive dechlorination of PCE to cis-1,2-dichloroethene (cDCE) in strain ACS DCE T and of PCE to trichloroethene (TCE) in strain ACS TCE . Both strains were able to grow with pyruvate under microaerobic conditions. Nitrate, elemental sulphur, and thiosulphate were alternative electron acceptors. Autotrophic growth was not observed and acetate served as carbon source for both strains. The major cellular fatty acids were C 16:1 ω7c, C 16:0 , C 14:0 and C 18:1 ω7c. Both genomes feature a circular plasmid. Strains ACS DCE T and ACS TCE were previously assigned to the candidate species 'Sulfurospirillum acididehalogenans'. Here, based on key genomic features and pairwise comparisons of whole-genome sequences, including average nucleotide identity, digital DNA–DNA hybridization and average amino acid identity, strains ACS DCE T and ACS TCE , 'Ca. Sulfurospirillum diekertiae' strains SL2-1 and SL2-2, and the unclassified Sulfurospirillum sp. strain SPD-1 are grouped into one distinct species separate from previously described Sulfurospirillum species. Compared to Sulfurospirillum multivorans and Sulfurospirillum halorespirans, which dechlorinate PCE to cDCE without substantial TCE accumulation, these five strains produce TCE or cDCE as the end product. In addition, some cellular fatty acids (e.g., C 16:0 3OH, C 17:0 iso 3OH, C 17:0 2OH) were detected in strains ACS DCE T and ACS TCE but not in other Sulfurospirillum species. On the basis of phylogenetic, physiological and phenotypic characteristics, 'Ca. Sulfurospirillum acididehalogenans' and 'Ca. Sulfurospirillum diekertiae' are proposed to be merged into one novel species within the genus Sulfurospirillum, for which the name Sulfurospirillum diekertiae sp. nov. is proposed. Finally, the type strain is ACS DCE T (=JCM 33349 T = KCTC 15819 T =CGMCC 1.5292 T ).

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

The Enterprise , a massive transposon carrying Spok meiotic drive genes

The genomes of eukaryotes are full of parasitic sequences known as transposable elements (TEs). Here, we report the discovery of a putative giant tyrosine-recombinase-mobilized DNA transposon, Enterprise, from the model fungus Podospora anserina. Previously, we described a large genomic feature called the Spok block which is notable due to the presence of meiotic drive genes of the Spok gene family. The Spok block ranges from 110 kb to 247 kb and can be present in at least four different genomic locations within P. anserina, despite what is an otherwise highly conserved genome structure. We propose that the reason for its varying positions is that the Spok block is not only capable of meiotic drive but is also capable of transposition. More precisely, the Spok block represents a unique case where the Enterprise has captured the Spoks, thereby parasitizing a resident genomic parasite to become a genomic hyperparasite. Furthermore, we demonstrate that Enterprise (without the Spoks) is found in other fungal lineages, where it can be as large as 70 kb. Lastly, we provide experimental evidence that the Spok block is deleterious, with detrimental effects on spore production in strains which carry it. This union of meiotic drivers and a transposon has created a selfish element of impressive size in Podospora, challenging our perception of how TEs influence genome evolution and broadening the horizons in terms of what the upper limit of transposition may be.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Crystal structure of CotA laccase complexed with 2,2-azinobis-(3-ethylbenzothiazoline-6-sulfonate) at a novel binding site

The crystal structure of CotA complexed with 2,2-azinobis-(3-ethylbenzothiazoline-6-sulfonate) in a hole motif has been solved; this novel binding site could be a potential structure-based target for protein engineering of CotA laccase. The CotA laccase from Bacillus subtilis is an abundant component of the spore outer coat and has been characterized as a typical laccase. The crystal structure of CotA complexed with 2,2-azinobis-(3-ethylbenzothiazoline-6-sulfonate) (ABTS) in a hole motif has been solved. The novel binding site was about 26 Å away from the T1 binding pocket. Comparison with known structures of other laccases revealed that the hole is a specific feature of CotA. The key residues Arg476 and Ser360 were directly bound to ABTS. Site-directed mutagenesis studies revealed that the residues Arg146, Arg429 and Arg476, which are located at the bottom of the novel binding site, are essential for the oxidation of ABTS and syringaldazine. Specially, a Thr480Phe variant was identified to be almost 3.5 times more specific for ABTS than for syringaldazine compared with the wild type. These results suggest this novel binding site for ABTS could be a potential target for protein engineering of CotA laccases.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2017

Structure of the Bacillus anthracis dTDP- L -rhamnose-biosynthetic enzyme dTDP-4-dehydrorhamnose 3,5-epimerase (RfbC)

The exosporium layer of Bacillus anthracis spores is rich in L-rhamnose, a common bacterial cell-wall component, which often contributes to the virulence of pathogens by increasing their adherence and immune evasion. The biosynthetic pathway used to form the activated L-rhamnose donor dTDP-L-rhamnose consists of four enzymes (RfbA, RfbB, RfbC and RfbD) and is an attractive drug target because there are no homologs in mammals. It was found that co-purifying and screening RfbC (dTDP-6-deoxy-D- xylo -4-hexulose 3,5-epimerase) from B. anthracis in the presence of the other three B. anthracis enzymes of the biosynthetic pathway yielded crystals that were suitable for data collection. RfbC crystallized as a dimer and its structure was determined at 1.63 Å resolution. Two different ligands were bound in the protein structure: pyrophosphate in the active site of one monomer and dTDP in the other monomer. A structural comparison with RfbC homologs showed that the key active-site residues are conserved across kingdoms.

Shornikov, Aleksander↗
DOE OSTI2021

Cryptic genetic structure and copy-number variation in the ubiquitous forest symbiotic fungus Cenococcum geophilum

Ectomycorrhizal (ECM) fungi associated with plants constitute one of the most successful symbiotic interactions in forest ecosystems. ECM support trophic exchanges with host plants and are important factors for the survival and stress resilience of trees. However, ECM clades often harbour morpho-species and cryptic lineages, with weak morphological differentiation. How this relates to intraspecific genome variability and ecological functioning is poorly known. Here, we analysed 16 European isolates of the ascomycete Cenococcum geophilum, an extremely ubiquitous forest symbiotic fungus with no known sexual or asexual spore-forming structures but with a massively enlarged genome. We carried out whole-genome sequencing to identify single-nucleotide polymorphisms. We found no geographic structure at the European scale but divergent lineages within sampling sites. Evidence for recombination was restricted to specific cryptic lineages. Lineage differentiation was supported by extensive copy-number variation. Finally, we confirmed heterothallism with a single MAT1 idiomorph per genome. Synteny analyses of the MAT1 locus revealed substantial rearrangements and a pseudogene of the opposite MAT1 idiomorph. Our study provides the first evidence for substantial genome-wide structural variation, lineage-specific recombination and low continent-wide genetic differentiation in C. geophilum. Our study provides a foundation for targeted analyses of intra-specific functional variation in this major symbiosis.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2014

Does aspartic acid racemization constrain the depth limit of the subsurface biosphere?

Previous studies of the subsurface biosphere have deduced average cellular doubling times of hundreds to thousands of years based upon geochemical models. We have directly constrained the in situ average cellular protein turnover or doubling times for metabolically active micro-organisms based on cellular amino acid abundances, D/L values of cellular aspartic acid, and the in vivo aspartic acid racemization rate. Application of this method to planktonic microbial communities collected from deep fractures in South Africa yielded maximum cellular amino acid turnover times of ~89 years for 1 km depth and 27 C and 1 2 years for 3 km depth and 54 C. The latter turnover times are much shorter than previously estimated cellular turnover times based upon geochemical arguments. The aspartic acid racemization rate at higher temperatures yields cellular protein doubling times that are consistent with the survival times of hyperthermophilic strains and predicts that at temperatures of 85 C, cells must replace proteins every couple of days to maintain enzymatic activity. Such a high maintenance requirement may be the principal limit on the abundance of living micro-organisms in the deep, hot subsurface biosphere, as well as a potential limit on their activity. The measurement of the D/L of aspartic acid in biological samples is a potentially powerful tool for deep, fractured continental and oceanic crustal settings where geochemical models of carbon turnover times are poorly constrained. Experimental observations on the racemization rates of aspartic acid in living thermophiles and hyperthermophiles could test this hypothesis. The development of corrections for cell wall peptides and spores will be required, however, to improve the accuracy of these estimates for environmental samples.

Onstott, T. C.↗
DOE OSTI2021

A critical review of 25 years of glomalin research: a better mechanical understanding and robust quantification techniques are required

Arbuscular mycorrhizal fungi (AMF) are important contributors to both plant and soil health. Twenty-five years ago, researchers discovered ‘glomalin’, a soil component potentially produced by AMF, which was unconventionally extracted from soil and bound by a monoclonal antibody raised against Rhizophagus irregularis spores. ‘Glomalin’ can resist boiling, strong acids and bases, and protease treatment. Researchers proposed that ‘glomalin’ is a 60 kDa heat shock protein produced by AMF, while others suggested that it is a mixture of soil organic materials that are not unique to AMF. Despite disagreements on the nature of ‘glomalin’, it has been consistently associated with a long list of plant and soil health benefits, including soil aggregation, soil carbon storage and enhancing growth under abiotic stress. The benefits attributed to ‘glomalin’ have caused much excitement in the plant and soil health community; however, the mechanism(s) for these benefits have yet to be established. This review provides insights into the current understanding of the identity of ‘glomalin’, ‘glomalin’ quantification, and the associated benefits of ‘glomalin’. We invite the community to think more critically about how glomalin-associated benefits are generated. We suggest a series of experiments to test hypotheses regarding the nature of ‘glomalin’ and associated health benefits.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Efficacy of atmospheric pressure dielectric barrier discharge for inactivating airborne pathogens

Atmospheric pressure plasmas have gained attention in recent years for several environmental applications. This technology could potentially be used to deactivate airborne microorganisms, surface-bound microorganisms, and biofilms. Here, the authors explore the efficacy of the atmospheric pressure dielectric barrier discharge (DBD) to inactivate airborne Staphylococcus epidermidis and Aspergillus niger that are opportunistic pathogens associated with nosocomial infections. This technology uses air as the source of gas and does not require any process gas such as helium, argon, nitrogen, or hydrogen. Moreover, the effect of DBD was studied on aerosolized S. epidermidis and aerosolized A. niger spores via scanning electron microscopy (SEM). The morphology observed on the SEM micrographs showed deformations in the cellular structure of both microorganisms. Cell structure damage upon interaction with the DBD suggests leakage of vital cellular materials, which is a key mechanism for microbial inactivation. The chemical structure of the cell surface of S. epidermidis was also analyzed by near edge x-ray absorption fine structure spectroscopy before and after DBD exposure. Our results from surface analysis revealed that reactive oxygen species from the DBD discharge contributed to alterations on the chemistry of the cell membrane/cell wall of S. epidermidis.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

Combined LIBS-Raman for remote detection and characterization of biological samples

Laser-Induced Breakdown Spectroscopy (LIBS) and Raman Spectroscopy have rich histories in the analysis of a wide variety of samples in both in situ and remote configurations. Our team is working on building a deployable, integrated Raman and LIBS spectrometer (RLS) for the parallel elucidation of elemental and molecular signatures under Earth and Martian surface conditions. Herein, results from remote LIBS and Raman analysis of biological samples such as amino acids, small peptides, mono- and disaccharides, and nucleic acids acquired under terrestrial and Mars conditions are reported, giving rise to some interesting differences. A library of spectra and peaks of interest were compiled, and will be used to inform the analysis of more complex systems, such as large peptides, dried bacterial spores, and biofilms. Lastly, these results will be presented and future applications will be discussed, including the assembly of a combined RLS spectroscopic system and stand-off detection in a variety of environments.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

SU-E-J-248: Contributions of Tumor and Stroma Phenotyping in Computer-Aided Diagnosis

Purpose: To gain insight into the role of parenchyma stroma in the characterization of breast tumors by incorporating computerized mammographic parenchyma assessment into breast CADx in the task of distinguishing between malignant and benign lesions. Methods: This study was performed on 182 biopsy-proven breast mass lesions, including 76 benign and 106 malignant lesions. For each full-field digital mammogram (FFDM) case, our quantitative imaging analysis was performed on both the tumor and a region-of-interest (ROI) from the normal contralateral breast. The lesion characterization includes automatic lesion segmentation and feature extraction. Radiographic texture analysis (RTA) was applied on the normal ROIs to assess the mammographic parenchymal patterns of these contralateral normal breasts. Classification performance of both individual computer extracted features and the output from a Bayesian artificial neural network (BANN) were evaluated with a leave-one-lesion-out method using receiver operating characteristic (ROC) analysis with area under the curve (AUC) as the figure of merit. Results: Lesion characterization included computer-extracted phenotypes of spiculation, size, shape, and margin. For parenchymal pattern characterization, five texture features were selected, including power law beta, contrast, and edge gradient. Merging of these computer-selected features using BANN classifiers yielded AUC values of 0.79 (SE=0.03) and 0.67 (SE=0.04) in the task of distinguishing between malignant and benign lesions using only tumor phenotypes and texture features from the contralateral breasts, respectively. Incorporation of tumor phenotypes with parenchyma texture features into the BANN yielded improved classification performance with an AUC value of 0.83 (SE=0.03) in the task of differentiating malignant from benign lesions. Conclusion: Combining computerized tumor and parenchyma phenotyping was found to significantly improve breast cancer diagnostic accuracy highlighting the need to consider both tumor and stroma in decision making. Funding: University of Chicago Dean Bridge Fund, NCI U24-CA143848-05, P50-CA58223 Breast SPORE program, and Breast Cancer Research Foundation. COI: MLG is a stockholder in R2 technology/Hologic and receives royalties from Hologic, GE Medical Systems, MEDIAN Technologies, Riverain Medical, Mitsubishi, and Toshiba. MLG is a cofounder and stockholder in Quantitative Insights.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

WE-FG-BRA-10: Radiodosimetry of a Novel Alpha Particle Therapy Targeted to Uveal Melanoma: Absorbed Dose to Organs in Mice

Purpose: The melanocortin-1 receptor (MC1R) is expressed in 94% of uveal melanomas and is described as an ideal target for this untreatable disease. MC1RL is a high affinity MC1R specific peptidomimetic ligand that can serve as a scaffold for therapeutic conjugates such as alpha particle emitting isotopes. The purpose of this study was to assess normal tissue distribution and risk as a result of using the DOTA chelator conjugated to MC1RL to deliver {sup 225}Ac: MC1RL-DOTA-{sup 225}Ac. Methods: 17 non-tumor bearing BALB/c mice were intravenously injected with the novel MC1RL-DOTA-{sup 225}Ac radiopharmaceutical with an average initial administered activity of 2.5 µCi. After the injection, three groups of animals (6, 6, and 5 per group) were euthanized at 24, 48, and 96 hour time points. A total of 11 organs of interest were harvested at each time point including kidneys and liver. Since the emitted alpha particles from {sup 225}Ac and its daughter products are not easy to detect directly, the isomeric gamma spectra were measured instead in the tissue samples using a modified Atomlab™ Gamma Counter (Biodex Medical Systems, Inc) and converted using factors for gamma ray abundance per alpha decay. Dosimetry was performed using measured radioactivity distribution in organs and the generalized internal dosimetry schema of MIRD pamphlet #21. Results: Our calculations have shown that the maximum absorbed dose was delivered to the liver with a total of 47 cGy per 96 hour period. The average dose per kidney was calculated to be 21 cGy. Heart, brain, lung, spleen, skin doses ranged from 0.01 to 1 cGy over the same time period. All animals gained weight over the 110 day decay period and no organ damage was observed by pathology. Conclusion: Based on our results, the risk of using the MC1RL-DOTA-{sup 225}Ac compound is relatively small in terms of deterministic radiation effects. Funding Support: NIH/NCI P50CA168536-03 Skin SPORE; NIH/NCI Phase I SBIR Contract #HHSN261201500067C; Imaging and Technology Center of Excellence at Moffitt. Disclosures and Conflict of Interest: Collaboration with Modulation Therapeutics, Inc.(MTI) and has been partially funded by sub-contracts from MTI via collaboration on a NIH/NCI phase I SBIR contract.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2017

Iron-Dependent Enzyme Catalyzes the Initial Step in Biodegradation of N -Nitroglycine by Variovorax sp. Strain JS1663

Nitramines are key constituents of most of the explosives currently in use and consequently contaminate soil and groundwater at many military facilities around the world. Toxicity from nitramine contamination poses a health risk to plants and animals. Thus, understanding how nitramines are biodegraded is critical to environmental remediation. The biodegradation of synthetic nitramine compounds such as hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) has been studied for decades, but little is known about the catabolism of naturally produced nitramine compounds. Here in this study, we report the isolation of a soil bacterium, Variovorax sp. strain JS1663, that degrades N-nitroglycine (NNG), a naturally produced nitramine, and the key enzyme involved in its catabolism. Variovorax sp. JS1663 is a Gram-negative, non-spore-forming motile bacterium isolated from activated sludge based on its ability to use NNG as a sole growth substrate under aerobic conditions. A single gene (nnlA) encodes an iron-dependent enzyme that releases nitrite from NNG through a proposed β-elimination reaction. Bioinformatics analysis of the amino acid sequence of NNG lyase identified a PAS (Per-Arnt-Sim) domain. PAS domains can be associated with heme cofactors and function as signal sensors in signaling proteins. Finally, this is the first instance of a PAS domain present in a denitration enzyme. The NNG biodegradation pathway should provide the basis for the identification of other enzymes that cleave the N—N bond and facilitate the development of enzymes to cleave similar bonds in RDX, nitroguanidine, and other nitramine explosives.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2017

Draft Genome Sequence of Anoxybacillus ayderensis Strain MT-Cab ( Firmicutes )

ABSTRACT The draft genome of the Gram-positive spore-forming Anoxybacillus ayderensis strain MT-Cab ( Firmicutes ), isolated from an enrichment culture of Chloracidobacterium thermophilum , was sequenced and comprises 2,577,015 bp in 92 contigs. The draft genome is predicted to consist of 2,699 protein-coding genes, 73 tRNA-coding genes, and an estimated 8 rRNA operons.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

A DNA-Binding Protein Tunes Septum Placement during Bacillus subtilis Sporulation

Bacillus subtilis is a bacterium capable of differentiating into a spore form more resistant to environmental stress. Early in sporulation, each cell possesses two copies of a circular chromosome. A polar FtsZ ring (Z ring) directs septation over one of the chromosomes, generating two cell compartments. The smaller “forespore” compartment initially contains only 25 to 30% of one chromosome, and this transient genetic asymmetry is required for differentiation. Timely assembly of polar Z rings and precise capture of the chromosome in the forespore both require the DNA-binding protein RefZ. To mediate its role in chromosome capture, RefZ must bind to specific DNA motifs (RBMs) that localize near the poles at the time of septation. Cells artificially induced to express RefZ during vegetative growth cannot assemble Z rings, an effect that also requires DNA binding. We hypothesized that RefZ-RBM complexes mediate precise chromosome capture by modulating FtsZ function. To investigate, we isolated 10 RefZ loss-of-function (rLOF) variants unable to inhibit cell division yet still capable of binding RBMs. Sporulating cells expressing the rLOF variants in place of wild-type RefZ phenocopied a ΔrefZ mutant, suggesting that RefZ acts through an FtsZ-dependent mechanism. The crystal structure of RefZ was solved, and wild-type RefZ and the rLOF variants were further characterized. Our data suggest that RefZ’s oligomerization state and specificity for the RBMs are critical determinants influencing RefZ’s ability to affect FtsZ dynamics. We propose that RBM-bound RefZ complexes function as a developmentally regulated nucleoid occlusion system for fine-tuning the position of the septum relative to the chromosome during sporulation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Ecological and Genomic Attributes of Novel Bacterial Taxa That Thrive in Subsurface Soil Horizons

While most bacterial and archaeal taxa living in surface soils remain undescribed, this problem is exacerbated in deeper soils, owing to the unique oligotrophic conditions found in the subsurface. Additionally, previous studies of soil microbiomes have focused almost exclusively on surface soils, even though the microbes living in deeper soils also play critical roles in a wide range of biogeochemical processes. We examined soils collected from 20 distinct profiles across the United States to characterize the bacterial and archaeal communities that live in subsurface soils and to determine whether there are consistent changes in soil microbial communities with depth across a wide range of soil and environmental conditions. We found that bacterial and archaeal diversity generally decreased with depth, as did the degree of similarity of microbial communities to those found in surface horizons. We observed five phyla that consistently increased in relative abundance with depth across our soil profiles: Chloroflexi , Nitrospirae , Euryarchaeota , and candidate phyla GAL15 and Dormibacteraeota (formerly AD3). Leveraging the unusually high abundance of Dormibacteraeota at depth, we assembled genomes representative of this candidate phylum and identified traits that are likely to be beneficial in low-nutrient environments, including the synthesis and storage of carbohydrates, the potential to use carbon monoxide (CO) as a supplemental energy source, and the ability to form spores. Together these attributes likely allow members of the candidate phylum Dormibacteraeota to flourish in deeper soils and provide insight into the survival and growth strategies employed by the microbes that thrive in oligotrophic soil environments.

59 BASIC BIOLOGICAL SCIENCES↗