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  • American Society for Microbiology  (5)
  • Nelson, William C.  (5)
  • 1
    Online Resource
    Online Resource
    Three Genomes from the Phylum Acidobacteria Provide Insight into the Lifestyles of These Microorganisms in Soils
    American Society for Microbiology ; 2009
    In:  Applied and Environmental Microbiology Vol. 75, No. 7 ( 2009-04), p. 2046-2056
    Details
    In: Applied and Environmental Microbiology, American Society for Microbiology, Vol. 75, No. 7 ( 2009-04), p. 2046-2056
    Abstract: The complete genomes of three strains from the phylum Acidobacteria were compared. Phylogenetic analysis placed them as a unique phylum. They share genomic traits with members of the Proteobacteria , the Cyanobacteria , and the Fungi. The three strains appear to be versatile heterotrophs. Genomic and culture traits indicate the use of carbon sources that span simple sugars to more complex substrates such as hemicellulose, cellulose, and chitin. The genomes encode low-specificity major facilitator superfamily transporters and high-affinity ABC transporters for sugars, suggesting that they are best suited to low-nutrient conditions. They appear capable of nitrate and nitrite reduction but not N 2 fixation or denitrification. The genomes contained numerous genes that encode siderophore receptors, but no evidence of siderophore production was found, suggesting that they may obtain iron via interaction with other microorganisms. The presence of cellulose synthesis genes and a large class of novel high-molecular-weight excreted proteins suggests potential traits for desiccation resistance, biofilm formation, and/or contribution to soil structure. Polyketide synthase and macrolide glycosylation genes suggest the production of novel antimicrobial compounds. Genes that encode a variety of novel proteins were also identified. The abundance of acidobacteria in soils worldwide and the breadth of potential carbon use by the sequenced strains suggest significant and previously unrecognized contributions to the terrestrial carbon cycle. Combining our genomic evidence with available culture traits, we postulate that cells of these isolates are long-lived, divide slowly, exhibit slow metabolic rates under low-nutrient conditions, and are well equipped to tolerate fluctuations in soil hydration.
    Type of Medium: Online Resource
    ISSN: 0099-2240 , 1098-5336
    URL: Article
    DOI: 10.1128/AEM.02294-08
    RVK:
    WA 15000
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2009
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    detail.hit.zdb_id: 1478346-0
    SSG: 12
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  • 2
    Online Resource
    Online Resource
    A Histoplasma capsulatum Lipid Metabolic Map Identifies Antifungal Targets
    American Society for Microbiology ; 2021
    In:  mBio Vol. 12, No. 6 ( 2021-12-21)
    Details
    In: mBio, American Society for Microbiology, Vol. 12, No. 6 ( 2021-12-21)
    Abstract: Lipids play a fundamental role in fungal cell biology, being essential cell membrane components and major targets of antifungal drugs. A deeper knowledge of lipid metabolism is key for developing new drugs and a better understanding of fungal pathogenesis. Here, we built a comprehensive map of the Histoplasma capsulatum lipid metabolic pathway by incorporating proteomic and lipidomic analyses. We performed genetic complementation and overexpression of H. capsulatum genes in Saccharomyces cerevisiae to validate reactions identified in the map and to determine enzymes responsible for catalyzing orphan reactions. The map led to the identification of both the fatty acid desaturation and the sphingolipid biosynthesis pathways as targets for drug development. We found that the sphingolipid biosynthesis inhibitor myriocin, the fatty acid desaturase inhibitor thiocarlide, and the fatty acid analog 10-thiastearic acid inhibit H. capsulatum growth in nanomolar to low-micromolar concentrations. These compounds also reduced the intracellular infection in an alveolar macrophage cell line. Overall, this lipid metabolic map revealed pathways that can be targeted for drug development. IMPORTANCE It is estimated that 150 people die per hour due to the insufficient therapeutic treatments to combat fungal infections. A major hurdle to developing antifungal therapies is the scarce knowledge on the fungal metabolic pathways and mechanisms of virulence. In this context, fungal lipid metabolism is an excellent candidate for developing drugs due to its essential roles in cellular scaffolds, energy storage, and signaling transductors. Here, we provide a detailed map of Histoplasma capsulatum lipid metabolism. The map revealed points of this fungus lipid metabolism that can be targeted for developing antifungal drugs.
    Type of Medium: Online Resource
    ISSN: 2150-7511
    URL: Article
    DOI: 10.1128/mBio.02972-21
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2021
    detail.hit.zdb_id: 2557172-2
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  • 3
    Online Resource
    Online Resource
    Complete Genome Sequence of the Broad-Host-Range Vibriophage KVP40: Comparative Genomics of a T4-Related Bacteriophage
    American Society for Microbiology ; 2003
    In:  Journal of Bacteriology Vol. 185, No. 17 ( 2003-09), p. 5220-5233
    Details
    In: Journal of Bacteriology, American Society for Microbiology, Vol. 185, No. 17 ( 2003-09), p. 5220-5233
    Abstract: The complete genome sequence of the T4-like, broad-host-range vibriophage KVP40 has been determined. The genome sequence is 244,835 bp, with an overall G+C content of 42.6%. It encodes 386 putative protein-encoding open reading frames (CDSs), 30 tRNAs, 33 T4-like late promoters, and 57 potential rho-independent terminators. Overall, 92.1% of the KVP40 genome is coding, with an average CDS size of 587 bp. While 65% of the CDSs were unique to KVP40 and had no known function, the genome sequence and organization show specific regions of extensive conservation with phage T4. At least 99 KVP40 CDSs have homologs in the T4 genome (Blast alignments of 45 to 68% amino acid similarity). The shared CDSs represent 36% of all T4 CDSs but only 26% of those from KVP40. There is extensive representation of the DNA replication, recombination, and repair enzymes as well as the viral capsid and tail structural genes. KVP40 lacks several T4 enzymes involved in host DNA degradation, appears not to synthesize the modified cytosine (hydroxymethyl glucose) present in T-even phages, and lacks group I introns. KVP40 likely utilizes the T4-type sigma-55 late transcription apparatus, but features of early- or middle-mode transcription were not identified. There are 26 CDSs that have no viral homolog, and many did not necessarily originate from Vibrio spp., suggesting an even broader host range for KVP40. From these latter CDSs, an NAD salvage pathway was inferred that appears to be unique among bacteriophages. Features of the KVP40 genome that distinguish it from T4 are presented, as well as those, such as the replication and virion gene clusters, that are substantially conserved.
    Type of Medium: Online Resource
    ISSN: 0021-9193 , 1098-5530
    URL: Article
    DOI: 10.1128/JB.185.17.5220-5233.2003
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2003
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    SSG: 12
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  • 4
    Online Resource
    Online Resource
    A Mineral-Doped Micromodel Platform Demonstrates Fungal Bridging of Carbon Hot Spots and Hyphal Transport of Mineral-Derived Nutrients
    American Society for Microbiology ; 2022
    In:  mSystems Vol. 7, No. 6 ( 2022-12-20)
    Details
    In: mSystems, American Society for Microbiology, Vol. 7, No. 6 ( 2022-12-20)
    Abstract: Soil fungi facilitate the translocation of inorganic nutrients from soil minerals to other microorganisms and plants. This ability is particularly advantageous in impoverished soils because fungal mycelial networks can bridge otherwise spatially disconnected and inaccessible nutrient hot spots. However, the molecular mechanisms underlying fungal mineral weathering and transport through soil remains poorly understood primarily due to the lack of a platform for spatially resolved analysis of biotic-driven mineral weathering. Here, we addressed this knowledge gap by demonstrating a mineral-doped soil micromodel platform where mineral weathering mechanisms can be studied. We directly visualize acquisition and transport of inorganic nutrients from minerals through fungal hyphae in the micromodel using a multimodal imaging approach. We found that Fusarium sp. strain DS 682, a representative of common saprotrophic soil fungus, exhibited a mechanosensory response (thigmotropism) around obstacles and through pore spaces (~12 μm) in the presence of minerals. The fungus incorporated and translocated potassium (K) from K-rich mineral interfaces, as evidenced by visualization of mineral-derived nutrient transport and unique K chemical moieties following fungus-induced mineral weathering. Specific membrane transport proteins were expressed in the fungus in the presence of minerals, including those involved in oxidative phosphorylation pathways and the transmembrane transport of small-molecular-weight organic acids. This study establishes the significance of a spatial visualization platform for investigating microbial induced mineral weathering at microbially relevant scales. Moreover, we demonstrate the importance of fungal biology and nutrient translocation in maintaining fungal growth under water and carbon limitations in a reduced-complexity soil-like microenvironment. IMPORTANCE Fungal species are foundational members of soil microbiomes, where their contributions in accessing and transporting vital nutrients is key for community resilience. To date, the molecular mechanisms underlying fungal mineral weathering and nutrient translocation in low-nutrient environments remain poorly resolved due to the lack of a platform for spatial analysis of biotic weathering processes. Here, we addressed this knowledge gap by developing a mineral-doped soil micromodel platform. We demonstrate the function of this platform by directly probing fungal growth using spatially resolved optical and chemical imaging methodologies. We found the presence of minerals was required for fungal thigmotropism around obstacles and through soil-like pore spaces, and this was related to fungal transport of potassium (K) and corresponding K speciation from K-rich minerals. These findings provide new evidence and visualization into hyphal transport of mineral-derived nutrients under nutrient and water stresses.
    Type of Medium: Online Resource
    ISSN: 2379-5077
    URL: Article
    DOI: 10.1128/msystems.00913-22
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2022
    detail.hit.zdb_id: 2844333-0
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  • 5
    Online Resource
    Online Resource
    DNA Viral Diversity, Abundance, and Functional Potential Vary across Grassland Soils with a Range of Historical Moisture Regimes
    American Society for Microbiology ; 2021
    In:  mBio Vol. 12, No. 6 ( 2021-12-21)
    Details
    In: mBio, American Society for Microbiology, Vol. 12, No. 6 ( 2021-12-21)
    Abstract: Soil viruses are abundant, but the influence of the environment and climate on soil viruses remains poorly understood. Here, we addressed this gap by comparing the diversity, abundance, lifestyle, and metabolic potential of DNA viruses in three grassland soils with historical differences in average annual precipitation, low in eastern Washington (WA), high in Iowa (IA), and intermediate in Kansas (KS). Bioinformatics analyses were applied to identify a total of 2,631 viral contigs, including 14 complete viral genomes from three deep metagenomes (1 terabase [Tb] each) that were sequenced from bulk soil DNA. An additional three replicate metagenomes (∼0.5 Tb each) were obtained from each location for statistical comparisons. Identified viruses were primarily bacteriophages targeting dominant bacterial taxa. Both viral and host diversity were higher in soil with lower precipitation. Viral abundance was also significantly higher in the arid WA location than in IA and KS. More lysogenic markers and fewer clustered regularly interspaced short palindromic repeats (CRISPR) spacer hits were found in WA, reflecting more lysogeny in historically drier soil. More putative auxiliary metabolic genes (AMGs) were also detected in WA than in the historically wetter locations. The AMGs occurring in 18 pathways could potentially contribute to carbon metabolism and energy acquisition in their hosts. Structural equation modeling (SEM) suggested that historical precipitation influenced viral life cycle and selection of AMGs. The observed and predicted relationships between soil viruses and various biotic and abiotic variables have value for predicting viral responses to environmental change. IMPORTANCE Soil viruses are abundant but poorly understood. Because soil viruses regulate the dynamics of their hosts and potentially key processes in soil ecology, it is important to understand them better. Here, we leveraged massive DNA sequencing to unearth previously unknown soil viruses. We found that soil viruses differed across a historical gradient of precipitation. We compared soil viruses from Iowa, which is traditionally wetter, to those from Washington, which is traditionally drier, and from Kansas, which is intermediate. This study provides strong evidence that changes in historical precipitation impact not only the types of soil viruses but also their functional potential.
    Type of Medium: Online Resource
    ISSN: 2150-7511
    URL: Article
    DOI: 10.1128/mBio.02595-21
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2021
    detail.hit.zdb_id: 2557172-2
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