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White, Richard A.

Publications and source records attributed to White, Richard A..

13 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2019

Gut anatomical properties and microbial functional assembly promote lignocellulose deconstruction and colony subsistence of a wood-feeding beetle

Beneficial microbial associations enhance the fitness of most living organisms, and wood-feeding insects offer some of the most striking examples of this. Odontotaenius disjunctus is a wood-feeding beetle that possesses a digestive tract with four main compartments, each of which contains well-differentiated microbial populations, suggesting that anatomical properties and separation of these compartments may enhance energy extraction from woody biomass. In this work, using integrated chemical analyses, we demonstrate that lignocellulose deconstruction and fermentation occur sequentially across compartments, and that selection for microbial groups and their metabolic pathways is facilitated by gut anatomical features. Metaproteogenomics showed that higher oxygen concentration in the midgut drives lignocellulose depolymerization, while a thicker gut wall in the anterior hindgut reduces oxygen diffusion and favours hydrogen accumulation, facilitating fermentation, homoacetogenesis and nitrogen fixation. We demonstrate that depolymerization continues in the posterior hindgut, and that the beetle excretes an energy- and nutrient-rich product on which its offspring subsist and develop. Our results show that the establishment of beneficial microbial partners within a host requires both the acquisition of the microorganisms and the formation of specific habitats within the host to promote key microbial metabolic functions. Together, gut anatomical properties and microbial functional assembly enable lignocellulose deconstruction and colony subsistence on an extremely nutrient-poor diet.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

The Complete Genome and Physiological Analysis of the Microbialite-Dwelling Agrococcus pavilionensis sp. nov; Reveals Genetic Promiscuity and Predicted Adaptations to Environmental Stress

Members of the bacterial genus Agrococcus are globally distributed and found across highly diverse environments including forests, deserts, potatoes, coal mines, and cheese. Despite their widespread occurrence, the extent of their genetic diversity is poorly explored and no complete reference genomes are available. Using whole-genome analysis, chemotaxonomic markers, morphology, and 16S rDNA phylogeny we characterize the new species Agrococcus pavilionensis strain RW1, and provide the first complete genome from a member of the genus Agrococcus. The A. pavilionensis genome consists of one chromosome (2,627,177 bp) as well as two plasmids (HC-CG1 1,427 bp, and LC-RRW783 31,795 bp) that reveal considerable genetic promiscuity, and include a prophage-like element on the main chromosome, and plasmid genes involved in integration, transposition, and heavy-metal stress. Agrococcus pavilionensis strain RW1 differs from other members of the genus in having a novel phospholipid fatty acid iso-C15:1Δ 4 , ß-galactosidase activity, filamentous growth under carbon stress, and amygdalin utilization. Both Agrococcus pavilionensis and Agrococcus lahaulensis encode a gene cluster that is likely involved in the synthesis of carotenoids and the production of the characteristic yellow pigmentation found in Agrococcus spp. The widespread occurrence of this genus across a remarkable range of diverse environments, and its genetic plasticity, hints at the ecological significance of Agrococcus spp.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

The MPLEx Protocol for Multi-omic Analyses of Soil Samples

Mass spectrometry (MS)-based integrated metaproteomic, metabolomic and lipidomic (multi-omic) studies are transforming our ability to understand and characterize microbial communities in environmental and biological systems. These measurements are even enabling enhanced analyses of complex soil microbial communities, which are the most complex microbial systems known to date. Multi-omic analyses, however, do have sample preparation challenges since separate extractions are typically needed for each omic study, thereby greatly amplifying the preparation time and amount of sample required. To address this limitation, a 3-in-1 method for simultaneous metabolite, protein, and lipid extraction (MPLEx) from the exact same soil sample was created by adapting a solvent-based approach. This MPLEx protocol has proven to be simple yet robust for many sample types and even when utilized for limited quantities of complex soil samples. The MPLEx method also greatly enabled the rapid multi-omic measurements needed to gain a better understanding of the members of each microbial community, while evaluating the changes taking place upon biological and environmental perturbations.

Environmental Molecular Sciences Laboratory↗
DOE OSTI2017

ATLAS (Automatic Tool for Local Assembly Structures) - A Comprehensive Infrastructure for Assembly, Annotation, and Genomic Binning of Metagenomic and Metaranscripomic Data

ATLAS (Automatic Tool for Local Assembly Structures) is a comprehensive multiomics data analysis pipeline that is massively parallel and scalable. ATLAS contains a modular analysis pipeline for assembly, annotation, quantification and genome binning of metagenomics and metatranscriptomics data and a framework for reference metaproteomic database construction. ATLAS transforms raw sequence data into functional and taxonomic data at the microbial population level and provides genome-centric resolution through genome binning. ATLAS provides robust taxonomy based on majority voting of protein coding open reading frames rolled-up at the contig level using modified lowest common ancestor (LCA) analysis. ATLAS provides robust taxonomy based on majority voting of protein coding open reading frames rolled-up at the contig level using modified lowest common ancestor (LCA) analysis. ATLAS is user-friendly, easy install through bioconda maintained as open-source on GitHub, and is implemented in Snakemake for modular customizable workflows.

genome binning↗
DOE OSTI2017

MerCat: a versatile k-mer counter and diversity estimator for database-independent property analysis obtained from metagenomic and/or metatranscriptomic sequencing data

MerCat is a parallel, highly scalable and modular property software package for robust analysis of features in next-generation sequencing data. MerCat inputs include assembled contigs and raw sequence reads from any platform resulting in feature abundance counts tables. MerCat allows for direct analysis of data properties without reference sequence database dependency commonly used by search tools such as BLAST and/or DIAMOND for compositional analysis of whole community shotgun sequencing (e.g. metagenomes and metatranscriptomes).

metabolomics↗
DOE OSTI2016

The fungal cultivar of leaf-cutter ants produces specific enzymes in response to different plant substrates

Herbivores use symbiotic microbes to help gain access to energy and nutrients from plant material. Leaf-cutter ants are a paradigmatic example, having tremendous impact on their ecosystems as dominant generalist herbivores through cultivation of a fungus, Leucoagaricus gongylophorous. Here we examine how this mutualism could facilitate the flexible substrate incorporation of the ants by providing leaf-cutter ant subcolonies four substrate types: leaves, flowers, oats, and a mixture of all three. Through metaproteomic analysis of the fungus gardens, we were able to identify and quantify 1766 different fungal proteins, including 161 biomass-degrading enzymes. This analysis revealed that fungal protein profiles were significantly different between subcolonies fed different substrates with the highest abundance of cellulolytic enzymes observed in the leaf and flower treatments. When the fungus garden is provided with leaves and flowers, which contain the majority of their energy in recalcitrant material, it increases its production of proteins that break down cellulose: endoglucanases, exoglucanase and β-glucosidase. Further, the complete metaproteomes for the leaves and flowers treatments were very similar, the mixed treatment closely resembled the treatment with oats alone. This suggests that when provided a mixture of substrates, the fungus garden preferentially produces enzymes necessary for breakdown of simpler, more digestible substrates. This flexible, substrate-specific response of the fungal cultivar allows the leaf-cutter ants to derive energy from a wide range of substrates, which may contribute to their ability to be dominant generalist herbivores.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

Virology: The Next Generation from Digital PCR to Single Virion Genomics

In the past 25 years, virology has had major technology breakthroughs stemming first from the introduction of nucleic acid amplification testing, but more recently from the use of next-generation sequencing, digital PCR, and the possibility of single virion genomics. These technologies have and will improve diagnosis and disease state monitoring in clinical settings, aid in environmental monitoring, and reveal the vast genetic potential of viruses. Using the principle of limiting dilution, digital PCR amplifies single molecules of DNA in highly partitioned endpoint reactions and reads each of those reactions as either positive or negative based on the presence or absence of target fluorophore. In this review, digital PCR will be highlighted along with current studies, advantages/disadvantages, and future perspectives with regard to digital PCR, viral load testing, and the possibility of single virion genomics.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

Complete genome sequence of Bacillus amyloliquefaciens strain Co1-6, a plant growth-promoting rhizobacterium of Calendula officinalis

The genome sequence of Bacillus amyloliquefaciens strain Co1-6, a plant growth-promoting rhizobacterium (PGPR) with broad-spectrum antagonistic activities against plant pathogenic fungi, bacteria and nematodes, consists of a single 3.9 Mb circular chromosome. The genome reveals genes putatively responsible for its promising biocontrol and PGP properties.

Environmental Molecular Sciences Laboratory↗
DOE OSTI2015

Draft Genome Sequence of Streptomyces sp. Strain Wb2n-11, a Desert Isolate with Broad-Spectrum Antagonism against Soilborne Phytopathogens

Streptomyces sp. strain Wb2n-11, isolated from native desert soil, exhibited broad-spectrum antagonism against plant pathogenic fungi, bacteria and nematodes. The 8.2 Mb draft genome reveals genes putatively responsible for its promising biocontrol activity and genes which enable the soil bacterium to directly interact beneficially with plants.

Köberl, Martina↗
DOE OSTI2015

Draft genome sequence of Paenbacillus polymyxa strain Mc5Re-14, an antagonistic root endophyte of Matricaria chamomilla

Paenbacillus polymyxa strain Mc5Re-14 was isolated from the inner root tissue of Matricaria chamomilla (e.g German chamomile). The draft genome of Paenbacillus polymyxa strain Mc5Re-14 revealed promising antagonistic in vitro activity against plant and opportunistic human pathogens. Putative genes involved in plant pathogen suppression and plant growth-promotion were identified.

Environmental Molecular Sciences Laboratory↗
NASA NTRS1991

Surface photometry of radio galaxies. II - Cluster sources

R-band CCD photometric observations are reported for 52 radio galaxies in clusters for which good radio maps are available. Data obtained with the No. 1 0.9-m telescope at KPNO (following the procedures described by Owen and Laing, 1989) are presented in tables and graphs and discussed in detail. Optical and radio luminosity are found to be well correlated in twin-jet, fat-double, narrow-angle-tail, and small-twin-jet sources, all of which are clearly distinguished from the classical doubles as in the scheme of Fanaroff and Riley (1974). It is also shown that the elliptical parent galaxies of the extended radio sources form a one-parameter family with the optical luminosity as the key parameter.

Owen, Frazer N.↗