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  • 1
    Online Resource
    Online Resource
    New Approaches Indicate Constant Viral Diversity despite Shifts in Assemblage Structure in an Australian Hypersaline Lake
    American Society for Microbiology ; 2013
    In:  Applied and Environmental Microbiology Vol. 79, No. 21 ( 2013-11), p. 6755-6764
    Details
    In: Applied and Environmental Microbiology, American Society for Microbiology, Vol. 79, No. 21 ( 2013-11), p. 6755-6764
    Abstract: It is widely stated that viruses represent the most significant source of biodiversity on Earth, yet characterizing the diversity of viral assemblages in natural systems remains difficult. Viral diversity studies are challenging because viruses lack universally present, phylogenetically informative genes. Here, we developed an approach to estimate viral diversity using a series of functional and novel conserved genes. This approach provides direct estimates of viral assemblage diversity while retaining resolution at the level of individual viral populations in a natural system. We characterized viral assemblages in eight samples from hypersaline Lake Tyrrell (LT), Victoria, Australia, using 39,636 viral contigs. We defined viral operational taxonomic units (OTUs) in two ways. First, we used genes with three different functional predictions that were abundantly represented in the data set. Second, we clustered proteins of unknown function based on sequence similarity, and we chose genes represented by three clusters with numerous members to define OTUs. In combination, diversity metrics indicated between 412 and 735 sampled populations, and the number of populations remained relatively constant across samples. We determined the relative representation of each viral OTU in each sample and found that viral assemblage structures correlate with salinity and solution chemistry. LT viral assemblages were near-replicates from the same site sampled a few days apart but differed significantly on other spatial and temporal scales. The OTU definition approach proposed here paves the way for metagenomics-based analyses of viral assemblages using ecological models previously applied to bacteria and archaea.
    Type of Medium: Online Resource
    ISSN: 0099-2240 , 1098-5336
    URL: Article
    DOI: 10.1128/AEM.01946-13
    RVK:
    WA 15000
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2013
    detail.hit.zdb_id: 223011-2
    detail.hit.zdb_id: 1478346-0
    SSG: 12
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  • 2
    Online Resource
    Online Resource
    Differential depth distribution of microbial function and putative symbionts through sediment-hosted aquifers in the deep terrestrial subsurface
    Springer Science and Business Media LLC ; 2018
    In:  Nature Microbiology Vol. 3, No. 3 ( 2018-01-29), p. 328-336
    Details
    In: Nature Microbiology, Springer Science and Business Media LLC, Vol. 3, No. 3 ( 2018-01-29), p. 328-336
    Abstract: An enormous diversity of previously unknown bacteria and archaea has been discovered recently, yet their functional capacities and distributions in the terrestrial subsurface remain uncertain. Here, we continually sampled a CO 2 -driven geyser (Colorado Plateau, Utah, USA) over its 5-day eruption cycle to test the hypothesis that stratified, sandstone-hosted aquifers sampled over three phases of the eruption cycle have microbial communities that differ both in membership and function. Genome-resolved metagenomics, single-cell genomics and geochemical analyses confirmed this hypothesis and linked microorganisms to groundwater compositions from different depths. Autotrophic Candidatus “Altiarchaeum sp.” and phylogenetically deep-branching nanoarchaea dominate the deepest groundwater. A nanoarchaeon with limited metabolic capacity is inferred to be a potential symbiont of the Ca . “Altiarchaeum”. Candidate Phyla Radiation bacteria are also present in the deepest groundwater and they are relatively abundant in water from intermediate depths. During the recovery phase of the geyser, microaerophilic Fe- and S-oxidizers have high in situ genome replication rates. Autotrophic Sulfurimonas sustained by aerobic sulfide oxidation and with the capacity for N 2 fixation dominate the shallow aquifer. Overall, 104 different phylum-level lineages are present in water from these subsurface environments, with uncultivated archaea and bacteria partitioned to the deeper subsurface.
    Type of Medium: Online Resource
    ISSN: 2058-5276
    URL: Article
    DOI: 10.1038/s41564-017-0098-y
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2018
    detail.hit.zdb_id: 2845610-5
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  • 3
    Online Resource
    Online Resource
    Dynamic Viral Populations in Hypersaline Systems as Revealed by Metagenomic Assembly
    American Society for Microbiology ; 2012
    In:  Applied and Environmental Microbiology Vol. 78, No. 17 ( 2012-09), p. 6309-6320
    Details
    In: Applied and Environmental Microbiology, American Society for Microbiology, Vol. 78, No. 17 ( 2012-09), p. 6309-6320
    Abstract: Viruses of the Bacteria and Archaea play important roles in microbial evolution and ecology, and yet viral dynamics in natural systems remain poorly understood. Here, we created de novo assemblies from 6.4 Gbp of metagenomic sequence from eight community viral concentrate samples, collected from 12 h to 3 years apart from hypersaline Lake Tyrrell (LT), Victoria, Australia. Through extensive manual assembly curation, we reconstructed 7 complete and 28 partial novel genomes of viruses and virus-like entities (VLEs, which could be viruses or plasmids). We tracked these 35 populations across the eight samples and found that they are generally stable on the timescale of days and transient on the timescale of years, with some exceptions. Cross-detection of the 35 LT populations in three previously described haloviral metagenomes was limited to a few genes, and most previously sequenced haloviruses were not detected in our samples, though 3 were detected upon reducing our detection threshold from 90% to 75% nucleotide identity. Similar results were obtained when we applied our methods to haloviral metagenomic data previously reported from San Diego, CA: 10 contigs that we assembled from that system exhibited a variety of detection patterns on a timescale of weeks to 1 month but were generally not detected in LT. Our results suggest that most haloviral populations have a limited or, possibly, a temporally variable global distribution. This study provides high-resolution insight into viral biogeography and dynamics and it places “snapshot” viral metagenomes, collected at a single time and location, in context.
    Type of Medium: Online Resource
    ISSN: 0099-2240 , 1098-5336
    URL: Article
    DOI: 10.1128/AEM.01212-12
    RVK:
    WA 15000
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2012
    detail.hit.zdb_id: 223011-2
    detail.hit.zdb_id: 1478346-0
    SSG: 12
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  • 4
    Online Resource
    Online Resource
    Metagenomic analysis of a high carbon dioxide subsurface microbial community populated by chemolithoautotrophs and bacteria and archaea from candidate phyla
    Wiley ; 2016
    In:  Environmental Microbiology Vol. 18, No. 6 ( 2016-06), p. 1686-1703
    Details
    In: Environmental Microbiology, Wiley, Vol. 18, No. 6 ( 2016-06), p. 1686-1703
    Abstract: Research on geologic carbon sequestration raises questions about potential impacts of subsurface microbiota on carbon cycling and biogeochemistry. Subsurface, high‐ CO 2 systems are poorly biologically characterized, partly because of difficulty accessing high‐volume, uncontaminated samples. CO 2 ‐driven C rystal G eyser ( CG , U tah, USA ), an established geologic carbon sequestration analogue, provides high volumes of deep (∼ 200–500 m) subsurface fluids. We explored microbial diversity and metabolic potential in this high‐ CO 2 environment by assembly and analysis of metagenomes recovered from geyser water filtrate. The system is dominated by neutrophilic, iron‐oxidizing bacteria, including ‘marine’ M ariprofundus ( Z etaproteobacteria ) and ‘freshwater’ Gallionellales , sulfur‐oxidizing T hiomicrospira crunogena and T hiobacillus ‐like Hydrogenophilales . Near‐complete genomes were reconstructed for these bacteria. CG is notably populated by a wide diversity of bacteria and archaea from phyla lacking isolated representatives (candidate phyla) and from as‐yet undefined lineages. Many bacteria affiliate with OD 1, OP 3, OP 9, PER , ACD 58, WWE 3, BD 1‐5, OP 11, TM 7 and ZB 2. The recovery of nearly 100 genes encoding ribulose‐1,5 bisphosphate carboxylase‐oxygenase subunit proteins of the C alvin cycle and AMP salvage pathways suggests a strong biological role in high‐ CO 2 subsurface carbon cycling. Overall, we predict microbial impacts on subsurface biogeochemistry via iron, sulfur, and complex carbon oxidation, carbon and nitrogen fixation, fermentation, hydrogen metabolism, and aerobic and anaerobic respiration.
    Type of Medium: Online Resource
    ISSN: 1462-2912 , 1462-2920
    URL: Issue
    URL: Article
    DOI: 10.1111/emi.2016.18.issue-6
    DOI: 10.1111/1462-2920.12817
    Language: English
    Publisher: Wiley
    Publication Date: 2016
    detail.hit.zdb_id: 2020213-1
    SSG: 12
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  • 5
    Online Resource
    Online Resource
    Genomic resolution of a cold subsurface aquifer community provides metabolic insights for novel microbes adapted to high CO 2 concentrations
    Wiley ; 2017
    In:  Environmental Microbiology Vol. 19, No. 2 ( 2017-02), p. 459-474
    Details
    In: Environmental Microbiology, Wiley, Vol. 19, No. 2 ( 2017-02), p. 459-474
    Abstract: As in many deep underground environments, the microbial communities in subsurface high‐CO 2 ecosystems remain relatively unexplored. Recent investigations based on single‐gene assays revealed a remarkable variety of organisms from little studied phyla in Crystal Geyser (Utah, USA), a site where deeply sourced CO 2 ‐saturated fluids are erupted at the surface. To provide genomic resolution of the metabolisms of these organisms, we used a novel metagenomic approach to recover 227 high‐quality genomes from 150 microbial species affiliated with 46 different phylum‐level lineages. Bacteria from two novel phylum‐level lineages have the capacity for CO 2 fixation. Analyses of carbon fixation pathways in all studied organisms revealed that the Wood‐Ljungdahl pathway and the Calvin‐Benson‐Bassham Cycle occurred with the highest frequency, whereas the reverse TCA cycle was little used. We infer that this, and selection for form II RuBisCOs, are adaptions to high CO 2 ‐concentrations. However, many autotrophs can also grow mixotrophically, a strategy that confers metabolic versatility. The assignment of 156 hydrogenases to 90 different organisms suggests that H 2 is an important inter‐species energy currency even under gaseous CO 2 ‐saturation. Overall, metabolic analyses at the organism level provided insight into the biochemical cycles that support subsurface life under the extreme condition of CO 2 saturation.
    Type of Medium: Online Resource
    ISSN: 1462-2912 , 1462-2920
    URL: Issue
    URL: Article
    DOI: 10.1111/emi.2017.19.issue-2
    DOI: 10.1111/1462-2920.13362
    Language: English
    Publisher: Wiley
    Publication Date: 2017
    detail.hit.zdb_id: 2020213-1
    SSG: 12
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  • 6
    Online Resource
    Online Resource
    Biology of a widespread uncultivated archaeon that contributes to carbon fixation in the subsurface
    Springer Science and Business Media LLC ; 2014
    In:  Nature Communications Vol. 5, No. 1 ( 2014-11-26)
    Details
    In: Nature Communications, Springer Science and Business Media LLC, Vol. 5, No. 1 ( 2014-11-26)
    Type of Medium: Online Resource
    ISSN: 2041-1723
    URL: Article
    DOI: 10.1038/ncomms6497
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2014
    detail.hit.zdb_id: 2553671-0
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  • 7
    Online Resource
    Online Resource
    Virus-Host and CRISPR Dynamics in Archaea-Dominated Hypersaline Lake Tyrrell, Victoria, Australia
    Hindawi Limited ; 2013
    In:  Archaea Vol. 2013 ( 2013), p. 1-12
    Details
    In: Archaea, Hindawi Limited, Vol. 2013 ( 2013), p. 1-12
    Abstract: The study of natural archaeal assemblages requires community context, namely, a concurrent assessment of the dynamics of archaeal, bacterial, and viral populations. Here, we use filter size-resolved metagenomic analyses to report the dynamics of 101 archaeal and bacterial OTUs and 140 viral populations across 17 samples collected over different timescales from 2007–2010 from Australian hypersaline Lake Tyrrell (LT). All samples were dominated by Archaea (75–95%). Archaeal, bacterial, and viral populations were found to be dynamic on timescales of months to years, and different viral assemblages were present in planktonic, relative to host-associated (active and provirus) size fractions. Analyses of clustered regularly interspaced short palindromic repeat (CRISPR) regions indicate that both rare and abundant viruses were targeted, primarily by lower abundance hosts. Although very few spacers had hits to the NCBI nr database or to the 140 LT viral populations, 21% had hits to unassembled LT viral concentrate reads. This suggests local adaptation to LT-specific viruses and/or undersampling of haloviral assemblages in public databases, along with successful CRISPR-mediated maintenance of viral populations at abundances low enough to preclude genomic assembly. This is the first metagenomic report evaluating widespread archaeal dynamics at the population level on short timescales in a hypersaline system.
    Type of Medium: Online Resource
    ISSN: 1472-3646 , 1472-3654
    URL: Article
    DOI: 10.1155/2013/370871
    Language: English
    Publisher: Hindawi Limited
    Publication Date: 2013
    detail.hit.zdb_id: 2133011-6
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  • 8
    Online Resource
    Online Resource
    De Novo Sequences of Haloquadratum walsbyi from Lake Tyrrell, Australia, Reveal a Variable Genomic Landscape
    Hindawi Limited ; 2015
    In:  Archaea Vol. 2015 ( 2015), p. 1-12
    Details
    In: Archaea, Hindawi Limited, Vol. 2015 ( 2015), p. 1-12
    Abstract: Hypersaline systems near salt saturation levels represent an extreme environment, in which organisms grow and survive near the limits of life. One of the abundant members of the microbial communities in hypersaline systems is the square archaeon, Haloquadratum walsbyi . Utilizing a short-read metagenome from Lake Tyrrell, a hypersaline ecosystem in Victoria, Australia, we performed a comparative genomic analysis of H. walsbyi to better understand the extent of variation between strains/subspecies. Results revealed that previously isolated strains/subspecies do not fully describe the complete repertoire of the genomic landscape present in H. walsbyi . Rearrangements, insertions, and deletions were observed for the Lake Tyrrell derived Haloquadratum genomes and were supported by environmental de novo sequences, including shifts in the dominant genomic landscape of the two most abundant strains. Analysis pertaining to halomucins indicated that homologs for this large protein are not a feature common for all species of Haloquadratum . Further, we analyzed ATP-binding cassette transporters (ABC-type transporters) for evidence of niche partitioning between different strains/subspecies. We were able to identify unique and variable transporter subunits from all five genomes analyzed and the de novo environmental sequences, suggesting that differences in nutrient and carbon source acquisition may play a role in maintaining distinct strains/subspecies.
    Type of Medium: Online Resource
    ISSN: 1472-3646 , 1472-3654
    URL: Article
    DOI: 10.1155/2015/875784
    Language: English
    Publisher: Hindawi Limited
    Publication Date: 2015
    detail.hit.zdb_id: 2133011-6
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