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At least 55 records · Page 3
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Desiccation induces varied responses within a soil bacterial genus

Abstract Desiccation impacts a suite of physiological processes in microbes by elevating levels of damaging reactive oxygen species and inducing DNA strand breaks. In response to desiccation‐induced stress, microbes have evolved specialized mechanisms to help them survive. Here, we performed a 128‐day lab desiccation experiment on nine strains from three clades of an abundant soil bacterium, Curtobacterium . We sequenced RNA from each strain at three time points to investigate their response. Curtobacterium was highly resistant to desiccation, outlasting both Escherichia coli and a famously DNA damage‐resistant bacterium, Deinococcus radiodurans . However, within the genus, there were also 10‐fold differences in survival rates among strains. Transcriptomic profiling revealed responses shared within the genus including up‐regulation of genes involved in DNA damage repair, osmolyte production, and efflux pumps, but also up‐regulation of pathways and genes unique to the three clades. For example, trehalose synthesis gene otsB , the chaperone groEL , and the oxygen scavenger katA were all found in either one or two clades but not the third. Here, we provide evidence of considerable variation in closely related strains, and further elucidation of the phylogenetic conservation of desiccation tolerance remains an important goal for microbial ecologists.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Refinement of the “ Candidatus Accumulibacter” genus based on metagenomic analysis of biological nutrient removal (BNR) pilot-scale plants operated with reduced aeration

Members of the “Candidatus Accumulibacter” genus are widely studied as key polyphosphate-accumulating organisms (PAOs) in biological nutrient removal (BNR) facilities performing enhanced biological phosphorus removal (EBPR). This diverse lineage includes 18 “Ca. Accumulibacter” species, which have been proposed based on the phylogenetic divergence of the polyphosphate kinase 1 (ppk1) gene and genome-scale comparisons of metagenome-assembled genomes (MAGs). Phylogenetic classification based on the 16S rRNA genetic marker has been difficult to attain because most “Ca. Accumulibacter” MAGs are incomplete and often do not include the rRNA operon. Here, we investigate the “Ca. Accumulibacter” diversity in pilot-scale treatment trains performing BNR under low dissolved oxygen (DO) conditions using genome-resolved metagenomics. Using long-read sequencing, we recovered medium- and high-quality MAGs for 5 of the 18 “Ca. Accumulibacter” species, all with rRNA operons assembled, which allowed a reassessment of the 16S rRNA-based phylogeny of this genus and an analysis of phylogeny based on the 23S rRNA gene.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

A new genus and species of xanthoid crab (Decapoda: Brachyura) from offshore hard bank habitats in the Gulf of Mexico

Speciose populations of small xanthoid crabs on offshore banks and reefs of the northern Gulf of Mexico include a new species that is not assignable to presently named genera. Morphological diagnoses of the new genus and species are underpinned by previously published gene sequence analyses, originally misattributed to another species but now known to apply to this taxon. Herein named Guinope tiara n. gen., n. sp., the species shows molecular phylogenetic affinities with the family Linnaeoxanthidae Stevcic, 2005, an ally of panopeid and pseudorhombilid crabs. Specimens from Occulina banks off the Florida Atlantic coast, previously regarded to represent Garthiope barbadensis (Rathbun, 1921), are not that species but instead morphologically assignable to Guinope n. gen. Whether they represent variants of Guinope tiara n. gen, n. sp. or a second species of the genus awaits the collection of fresh materials for DNA analyses.

Zoology↗
DOE OSTI2023

A new mud shrimp of the genus Paragourretia Sakai, 2004, from the Gulf of Mexico (Crustacea: Decapoda: Ctenochelidae)

A new western Atlantic member of the ctenochelid genus Paragourretia Sakai, 2004 is described to accommodate a single unique specimen collected by dredge on muddy rubble substrates of the continental shelf in the southwestern Gulf of Mexico. Paragourretia sandrae n. sp. closely resembles Paragourretia biffari, another regionally reported species for which photographs and additional illustrations are herein provided. While P. biffari and P. sandrae n. sp. are similar in habitus and known habitat o the more commonly encountered confamilial Dawsonius latispina, the third maxillipeds in Paragourretia bear distinct exopods that are absent in Dawsonius. As in eight other world congeners, P. sandrae n. sp. differs from both P. biffari and Dawsonius in lacking triangular ventrolateral projections on the sixth pleomere. It is further distinguished from P. biffari by lacking a distinctly incised notch in the anterodistal margin of the uropodal exopod and by absence of a median terminal spine on the telson. Additional sequence-quality specimens of P. sandrae n. sp. are required to clarify its relationships within the polyphyletic genus Paragourretia on a molecular genetic basis.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Complete genome sequence of Jiangella gansuensis strain YIM 002T (DSM 44835T), the type species of the genus Jiangella and source of new antibiotic compounds

Jiangella gansuensis strain YIM 002 T is the type strain of the type species of the genus Jiangella, which is at the present time composed of five species, and was isolated from desert soil sample in Gansu Province (China). The five strains of this genus are clustered in a monophyletic group when closer actinobacterial genera are used to infer a 16S rRNA gene sequence phylogeny. The study of this genome is part of the Genomic Encyclopedia of Bacteria and Archaea project, and here we describe the complete genome sequence and annotation of this taxon. The genome of J. gansuensis strain YIM 002T contains a single scaffold of size 5,585,780 bp, which involves 149 pseudogenes, 4905 protein-coding genes and 50 RNA genes, including 2520 hypothetical proteins and 4 rRNA genes. From the investigation of genome sizes of Jiangella species, J. gansuensis shows a smaller size, which indicates this strain might have discarded too much genetic information to adapt to desert environment. Seven new compounds from this bacterium have recently been described; however, its potential should be higher, as secondary metabolite gene cluster analysis predicted 60 gene clusters, including the potential to produce the pristinamycin.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

Genus‐wide microsatellite primers for the goldenrods ( Solidago ; Asteraceae)

• Premise of the study: Microsatellite primers were developed for studies of polyploid evolution, ecological genetics, conservation genetics, and species delimitation in the genus Solidago . • Methods and Results: Illumina sequencing of a shotgun library from S. gigantea identified ca. 1900 putative single‐copy loci. Fourteen loci were subsequently shown to be amplifiable, single‐copy, and variable in a broad range of Solidago species. • Conclusions: The utility of these markers both across the genus and in herbarium specimens of a wide age range will facilitate numerous inter‐ and intraspecific studies in the ca. 120 Solidago species.

Beck, James B.↗
DOE OSTI2025

A double copy from twisted (co)homology at genus g

We study a family of generalized hypergeometric integrals defined on punctured Riemann surfaces of genus g. These integrals are closely related to g-loop string amplitudes in chiral splitting, where one leaves the loop-momenta, moduli and all but one puncture un-integrated. We study the twisted homology groups associated to these integrals, and determine their intersection numbers. We make use of these homology intersection numbers to write a double-copy formula for the "complex" version of these integrals -- their closed-string analogues. To verify our findings, we develop numerical tools for the evaluation of the integrals in this work. This includes the recently introduced Enriquez kernels -- integration kernels for higher-genus polylogarithms.

Pokraka, Andrejz [Brown University; Amsterdam Univ↗
NASA NTRS2003

Aerobic growth of Anoxybacillus pushchinoensis K1(T): emended descriptions of A. pushchinoensis and the genus Anoxybacillus

In this work, corrections are made to the descriptions of the species Anoxybacillus pushchinoensis corrig. and the genus ANOXYBACILLUS: Experiments to determine the relationship of A. pushchinoensis K1(T) to oxygen showed that it was capable of aerobic growth, but preferred to grow anaerobically. During aerobic growth, the redox indicator resazurin was reduced as a result of hydrogen gas production. The facultatively anaerobic nature of K1(T) was ascertained by cultivation in aerobic liquid medium, where growth began at the bottom of the tube. The anaerobic nature of K1(T) was also indicated by a negative catalase reaction. This work is submitted to correct the description of the species A. pushchinoensis from obligate anaerobe to aerotolerant anaerobe and to emend the description of the genus Anoxybacillus from obligate anaerobes or facultative anaerobes to aerotolerant anaerobes or facultative anaerobes.

Bacillaceae/classification/growth & development/me↗
NASA NTRS1999

Polyphasic taxonomy of the genus Shewanella and description of Shewanella oneidensis sp. nov

The genus Shewanella has been studied since 1931 with regard to a variety of topics of relevance to both applied and environmental microbiology. Recent years have seen the introduction of a large number of new Shewanella-like isolates, necessitating a coordinated review of the genus. In this work, the phylogenetic relationships among known shewanellae were examined using a battery of morphological, physiological, molecular and chemotaxonomic characterizations. This polyphasic taxonomy takes into account all available phenotypic and genotypic data and integrates them into a consensus classification. Based on information generated from this study and obtained from the literature, a scheme for the identification of Shewanella species has been compiled. Key phenotypic characteristics were sulfur reduction and halophilicity. Fatty acid and quinone profiling were used to impart an additional layer of information. Molecular characterizations employing small-subunit 16S rDNA sequences were at the limits of resolution for the differentiation of species in some cases. As a result, DNA-DNA hybridization and sequence analyses of a more rapidly evolving molecule (gyrB gene) were performed. Species-specific PCR probes were designed for the gyrB gene and used for the rapid screening of closely related strains. With this polyphasic approach, in addition to the ten described Shewanella species, two new species, Shewanella oneidensis and 'Shewanella pealeana', were recognized; Shewanella oneidensis sp. nov. is described here for the first time.

NASA Discipline Exobiology↗
NASA NTRS1992

Comparative sequence analyses on the 16S rRNA (rDNA) of Bacillus acidocaldarius, Bacillus acidoterrestris, and Bacillus cycloheptanicus and proposal for creation of a new genus, Alicyclobacillus gen. nov

Comparative 16S rRNA (rDNA) sequence analyses performed on the thermophilic Bacillus species Bacillus acidocaldarius, Bacillus acidoterrestris, and Bacillus cycloheptanicus revealed that these organisms are sufficiently different from the traditional Bacillus species to warrant reclassification in a new genus, Alicyclobacillus gen. nov. An analysis of 16S rRNA sequences established that these three thermoacidophiles cluster in a group that differs markedly from both the obligately thermophilic organisms Bacillus stearothermophilus and the facultatively thermophilic organism Bacillus coagulans, as well as many other common mesophilic and thermophilic Bacillus species. The thermoacidophilic Bacillus species B. acidocaldarius, B. acidoterrestris, and B. cycloheptanicus also are unique in that they possess omega-alicylic fatty acid as the major natural membranous lipid component, which is a rare phenotype that has not been found in any other Bacillus species characterized to date. This phenotype, along with the 16S rRNA sequence data, suggests that these thermoacidophiles are biochemically and genetically unique and supports the proposal that they should be reclassified in the new genus Alicyclobacillus.

Non-NASA Center↗
DOE OSTI2017

Pseudo-Spectral Methods for the Laplace-Beltrami Equation and the Hodge Decomposition on Surfaces of Genus One

The inversion of the Laplace-Beltrami operator and the computation of the Hodge decomposition of a tangential vector field on smooth surfaces arise as computational tasks in many areas of science, from computer graphics to machine learning to computational physics. In this work, we present a high-order accurate pseudo-spectral approach, applicable to closed surfaces of genus one in three-dimensional space, with a view toward applications in plasma physics and fluid dynamics.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

A Genus Definition for Bacteria and Archaea Based on a Standard Genome Relatedness Index

In recent decades, the taxonomy of Bacteria and Archaea , and therefore genus designation, has been largely based on the use of a single ribosomal gene, the 16S rRNA gene, as a taxonomic marker. We propose an approach to delineate genera that excludes the direct use of the 16S rRNA gene and focuses on a standard genome relatedness index, the average nucleotide identity. Our findings are of importance to the microbiology community because the emergent properties of Bacteria and Archaea that are identified in this study will help assign genera with higher taxonomic resolution.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Prokaryotic taxa play keystone roles in the soil microbiome associated with woody perennial plants in the genus Buxus

The microbiome associated with ornamental plants has largely been neglected, despite its potential for impacting plant health. This work characterized the composition, diversity, and microbial co-associations in the soil microbiome associated with species and cultivars of plant in the genus Buxus (common name boxwood), a group of woody perennial shrubs commonly used in residential landscapes and found in native ecosystems. Soil was collected from 82 individual curated boxwood accessions at the U.S. National Arboretum National Boxwood Collection. Amplicon libraries targeting archaea, bacteria, and fungi were generated and sequenced using the Illumina MiSeq platform. Identification of individual sequence variants resulted in 275 archaeal, 15,580 bacterial, and 7,525 fungal taxa. Neither spatial distance among samples nor association with different types of boxwood were significant predictors of soil microbiome composition. However, archaeal and bacterial diversity was significantly different in soil from distinct types of boxwood. Co-association networks indicated that archaea and bacteria show greater evidence of being keystone taxa than fungi. Overall, this work demonstrates the potential for targeting specific keystone taxa to shift the soil microbiome associated with these boxwood accessions and that planting different species or cultivars in the landscape may shift the diversity of prokaryotic microorganisms.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2018

The topologically twisted index of $ \mathcal{N} $ = 4 super-Yang-Mills on T 2 × S 2 and the elliptic genus

We examine the topologically twisted index of $ \mathcal{N} $ = 4 super-Yang-Mills with gauge group SU(N ) on T 2 × S 2 , and demonstrate that it receives contributions from multiple sectors corresponding to the freely acting orbifolds T 2 /$ \mathbb{Z} $m × $ \mathbb{Z} $n where N = mn . After summing over these sectors, the index can be expressed as the elliptic genus of a twodimensional $ \mathcal{N} $ = (0, 2) theory resulting from Kaluza-Klein reduction on S 2 . This provides an alternate path to the ‘high-temperature’ limit of the index, and confirms the connection to the right-moving central charge of the $ \mathcal{N} $ = (0, 2) theory.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2018

Enumeration of Regular Maps on Surfaces of a Given Genus

We enumerate the labelled and unlabelled d-regular maps on two-dimensional oriented surfaces of arbitrary genus g. The case of d-regular maps with a single face is considered separately in more detail.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2017

Radiative gravitational collapse to spherical, toroidal and higher genus black holes

We derive the matching conditions between FLRW and generalised Vaidya spacetimes with spherical, planar or hyperbolic symmetry, across timelike hypersurfaces. We then construct new models of gravitational collapse of FLRW spacetimes with a negative cosmological constant having electromagnetic radiation in the exterior. The final state of the collapse are asymptotically AdS black holes with spherical, toroidal or higher genus topologies. We analyse the collapse dynamics including trapped surface formation, for various examples.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

Dairy manure acidogenic fermentation at hyperthermophilic temperature enabled superior activity of thermostable hydrolytic enzymes linked to the genus Caldicoprobacter

In this study, fermentation experiments were conducted under mesophilic, thermophilic, and hyperthermophilic conditions to investigate adaptation of microbial communities and its effect on extracellular enzyme activities toward degradation of cellulose, hemicellulose and proteins in dairy manure. Here, hyperthermophilic conditions transformed the microbiome structure and stimulated activity of extracellular proteolytic, cellulolytic, and hemicellulolytic enzymes. Specifically, the activities of protease, cellulose 1,4-β-cellobiosidase, and β-glucosidase secreted by hyperthermophilic microbes were higher by 22%, 47% and 49% compared to those produced by mesophilic and thermophilic communities. Enhanced hydrolytic activity of hyperthermophilic microbes enabled improved feedstock solubilization and production of 39% and 22% more soluble COD than mesophilic and thermophilic microbes, respectively. Connections between hydrolytic function and microbial community structure at various temperatures were assessed using the PICRUSt2 computational tool. Genus Caldicoprobacter was identified as the primary candidate responsible for increased production of thermostable endo-1,4-β-glucanase, β-glucosidase and endo-1,4-β-xylanase, and enhanced hydrolytic performance of hyperthermophilic microbial community.

09 BIOMASS FUELS↗
DOE OSTI2017

A comparative genome analysis of Cercospora sojina with other members of the pathogen genus Mycosphaerella on different plant hosts

Fungi are the causal agents of many of the world's most serious plant diseases causing disastrous consequences for large-scale agricultural production. Pathogenicity genomic basis is complex in fungi as multicellular eukaryotic pathogens. Here, we report the genome sequence of C. sojina, and comparative genome analysis with plant pathogen members of the genus Mycosphaerella (Zymoseptoria. tritici (synonyms M. graminicola), M. pini, M. populorum and M. fijiensis - pathogens of wheat, pine, poplar and banana, respectively). Synteny or collinearity was limited between genomes of major Mycosphaerella pathogens. Comparative analysis with these related pathogen genomes indicated distinct genome-wide repeat organization features. It suggests repetitive elements might be responsible for considerable evolutionary genomic changes. These results reveal the background of genomic differences and similarities between Dothideomycete species. Wide diversity as well as conservation on genome features forms the potential genomic basis of the pathogen specialization, such as pathogenicity to woody vs. herbaceous hosts. Through comparative genome analysis among five Dothideomycete species, our results have shed light on the genome features of these related fungi species. It provides insight for understanding the genomic basis of fungal pathogenicity and disease resistance in the crop hosts.

54 ENVIRONMENTAL SCIENCES↗