ORCID Profile
0000-0002-6131-0462
Current Organisations
E O Lawrence Berkeley National Laboratory
,
DOE Joint Genome Institute
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Enzymes | Microbial Ecology | Genome Structure | Genetics
Environmental health | Living resources (flora and fauna) | Biological sciences |
Publisher: Springer Science and Business Media LLC
Date: 17-12-2013
DOI: 10.4056/SIGS.5068949
Publisher: Elsevier BV
Date: 06-2021
Publisher: Springer Science and Business Media LLC
Date: 22-01-2020
DOI: 10.1038/S41586-020-1957-X
Abstract: Our current knowledge about nucleocytoplasmic large DNA viruses (NCLDVs) is largely derived from viral isolates that are co-cultivated with protists and algae. Here we reconstructed 2,074 NCLDV genomes from s ling sites across the globe by building on the rapidly increasing amount of publicly available metagenome data. This led to an 11-fold increase in phylogenetic ersity and a parallel 10-fold expansion in functional ersity. Analysis of 58,023 major capsid proteins from large and giant viruses using metagenomic data revealed the global distribution patterns and cosmopolitan nature of these viruses. The discovered viral genomes encoded a wide range of proteins with putative roles in photosynthesis and erse substrate transport processes, indicating that host reprogramming is probably a common strategy in the NCLDVs. Furthermore, inferences of horizontal gene transfer connected viral lineages to erse eukaryotic hosts. We anticipate that the global ersity of NCLDVs that we describe here will establish giant viruses—which are associated with most major eukaryotic lineages—as important players in ecosystems across Earth’s biomes.
Publisher: Springer Science and Business Media LLC
Date: 06-2012
DOI: 10.1038/NATURE11234
Publisher: Wiley
Date: 06-2018
Abstract: Pseudomonas is a large and erse genus of Gammaproteobacteria. To provide a framework for discovery of evolutionary and taxonomic relationships of these bacteria, we compared the genomes of type strains of 163 species and 3 additional subspecies of Pseudomonas, including 118 genomes sequenced herein. A maximum likelihood phylogeny of the 166 type strains based on protein sequences of 100 single-copy orthologous genes revealed thirteen groups of Pseudomonas, composed of two to sixty three species each. Pairwise average nucleotide identities and alignment fractions were calculated for the data set of the 166 type strains and 1224 genomes of Pseudomonas available in public databases. Results revealed that 394 of the 1224 genomes were distinct from any type strain, suggesting that the type strains represent only a fraction of the genomic ersity of the genus. The core genome of Pseudomonas was determined to contain 794 genes conferring primarily housekeeping functions. The results of this study provide a phylogenetic framework for future studies aiming to resolve the classification and phylogenetic relationships, identify new gene functions and phenotypes, and explore the ecological and metabolic potential of the Pseudomonas spp.
Publisher: Springer Science and Business Media LLC
Date: 09-11-2020
DOI: 10.1038/S41587-020-0718-6
Abstract: The reconstruction of bacterial and archaeal genomes from shotgun metagenomes has enabled insights into the ecology and evolution of environmental and host-associated microbiomes. Here we applied this approach to ,000 metagenomes collected from erse habitats covering all of Earth’s continents and oceans, including metagenomes from human and animal hosts, engineered environments, and natural and agricultural soils, to capture extant microbial, metabolic and functional potential. This comprehensive catalog includes 52,515 metagenome-assembled genomes representing 12,556 novel candidate species-level operational taxonomic units spanning 135 phyla. The catalog expands the known phylogenetic ersity of bacteria and archaea by 44% and is broadly available for streamlined comparative analyses, interactive exploration, metabolic modeling and bulk download. We demonstrate the utility of this collection for understanding secondary-metabolite biosynthetic potential and for resolving thousands of new host linkages to uncultivated viruses. This resource underscores the value of genome-centric approaches for revealing genomic properties of uncultivated microorganisms that affect ecosystem processes.
Publisher: Public Library of Science (PLoS)
Date: 05-08-2014
Publisher: Oxford University Press (OUP)
Date: 10-2016
DOI: 10.1093/NAR/GKW1030
Abstract: Viruses represent the most abundant life forms on the planet. Recent experimental and computational improvements have led to a dramatic increase in the number of viral genome sequences identified primarily from metagenomic s les. As a result of the expanding catalog of metagenomic viral sequences, there exists a need for a comprehensive computational platform integrating all these sequences with associated metadata and analytical tools. Here we present IMG/VR (r/), the largest publicly available database of 3908 isolate reference DNA viruses with 264 413 computationally identified viral contigs from & ecologically erse metagenomic s les. Approximately half of the viral contigs are grouped into genetically distinct quasi-species clusters. Microbial hosts are predicted for 20 000 viral sequences, revealing nine microbial phyla previously unreported to be infected by viruses. Viral sequences can be queried using a variety of associated metadata, including habitat type and geographic location of the s les, or taxonomic classification according to hallmark viral genes. IMG/VR has a user-friendly interface that allows users to interrogate all integrated data and interact by comparing with external sequences, thus serving as an essential resource in the viral genomics community.
Publisher: American Association for the Advancement of Science (AAAS)
Date: 09-10-2009
Abstract: More detailed sequence standards that keep up with revolutionary sequencing technologies will aid the research community in evaluating data.
Publisher: Springer Science and Business Media LLC
Date: 04-2021
DOI: 10.1038/S41587-021-00898-4
Abstract: A Correction to this paper has been published: 0.1038/s41587-021-00898-4.
Publisher: Springer Science and Business Media LLC
Date: 10-09-2009
Abstract: Dinoroseobacter shibae DFL12(T), a member of the globally important marine Roseobacter clade, comprises symbionts of cosmopolitan marine microalgae, including toxic dinoflagellates. Its annotated 4 417 868 bp genome sequence revealed a possible advantage of this symbiosis for the algal host. D. shibae DFL12(T) is able to synthesize the vitamins B(1) and B(12) for which its host is auxotrophic. Two pathways for the de novo synthesis of vitamin B(12) are present, one requiring oxygen and the other an oxygen-independent pathway. The de novo synthesis of vitamin B(12) was confirmed to be functional, and D. shibae DFL12(T) was shown to provide the growth-limiting vitamins B(1) and B(12) to its dinoflagellate host. The Roseobacter clade has been considered to comprise obligate aerobic bacteria. However, D. shibae DFL12(T) is able to grow anaerobically using the alternative electron acceptors nitrate and dimethylsulfoxide it has the arginine deiminase survival fermentation pathway and a complex oxygen-dependent Fnr (fumarate and nitrate reduction) regulon. Many of these traits are shared with other members of the Roseobacter clade. D. shibae DFL12(T) has five plasmids, showing ex les for vertical recruitment of chromosomal genes (thiC) and horizontal gene transfer (cox genes, gene cluster of 47 kb) possibly by conjugation (vir gene cluster). The long-range (80%) synteny between two sister plasmids provides insights into the emergence of novel plasmids. D. shibae DFL12(T) shows the most complex viral defense system of all Rhodobacterales sequenced to date.
Publisher: Wiley
Date: 09-01-2017
DOI: 10.1111/MMI.13592
Abstract: Most Ensifer strains are comparatively acid sensitive, compromising their persistence in low pH soils. In the acid-tolerant strain Ensifer medicae WSM419, the acid-activated expression of lpiA is essential for enhancing survival in lethal acidic conditions. Here we characterise a multi-step phosphorelay signal transduction pathway consisting of TcsA, TcrA, FsrR, RpoN and its cognate enhancer-binding protein EbpA, which is required for the induction of lpiA and the downstream acvB gene. The fsrR, tcrA, tcsA and rpoN genes were constitutively expressed, whereas lpiA and acvB were strongly acid-induced. RACE mapping revealed that lpiA/acvB were co-transcribed as an operon from an RpoN promoter. In most Ensifer species, lpiA/acvB is located on the chromosome and the sequence upstream of lpiA lacks an RpoN-binding site. Nearly all Ensifer meliloti strains completely lack ebpA, tcrA, tcsA and fsrR regulatory loci. In contrast, E. medicae strains have lpiA/acvB and ebpA/tcrA/tcsA/fsrR co-located on the pSymA megaplasmid, with lpiA/acvB expression coupled to an RpoN promoter. Here we provide a model for the expression of lpiA/acvB in E. medicae. This unique acid-activated regulatory system provides insights into an evolutionary process which may assist the adaptation of E. medicae to acidic environmental niches.
Publisher: American Association for the Advancement of Science (AAAS)
Date: 25-01-2019
Abstract: Publication interests should not limit access to public data
Publisher: Wiley
Date: 03-2009
Publisher: Springer Science and Business Media LLC
Date: 21-12-2021
DOI: 10.1038/S41587-020-00774-7
Abstract: Millions of new viral sequences have been identified from metagenomes, but the quality and completeness of these sequences vary considerably. Here we present CheckV, an automated pipeline for identifying closed viral genomes, estimating the completeness of genome fragments and removing flanking host regions from integrated proviruses. CheckV estimates completeness by comparing sequences with a large database of complete viral genomes, including 76,262 identified from a systematic search of publicly available metagenomes, metatranscriptomes and metaviromes. After validation on mock datasets and comparison to existing methods, we applied CheckV to large and erse collections of metagenome-assembled viral sequences, including IMG/VR and the Global Ocean Virome. This revealed 44,652 high-quality viral genomes (that is, % complete), although the vast majority of sequences were small fragments, which highlights the challenge of assembling viral genomes from short-read metagenomes. Additionally, we found that removal of host contamination substantially improved the accurate identification of auxiliary metabolic genes and interpretation of viral-encoded functions.
Publisher: Springer Science and Business Media LLC
Date: 30-12-2021
DOI: 10.1038/S41396-021-01178-4
Abstract: With advances in DNA sequencing and miniaturized molecular biology workflows, rapid and affordable sequencing of single-cell genomes has become a reality. Compared to 16S rRNA gene surveys and shotgun metagenomics, large-scale application of single-cell genomics to whole microbial communities provides an integrated snapshot of community composition and function, directly links mobile elements to their hosts, and enables analysis of population heterogeneity of the dominant community members. To that end, we sequenced nearly 500 single-cell genomes from a low ersity hot spring sediment s le from Dewar Creek, British Columbia, and compared this approach to 16S rRNA gene licon and shotgun metagenomics applied to the same s le. We found that the broad taxonomic profiles were similar across the three sequencing approaches, though several lineages were missing from the 16S rRNA gene licon dataset, likely the result of primer mismatches. At the functional level, we detected a large array of mobile genetic elements present in the single-cell genomes but absent from the corresponding same species metagenome-assembled genomes. Moreover, we performed a single-cell population genomic analysis of the three most abundant community members, revealing differences in population structure based on mutation and recombination profiles. While the average pairwise nucleotide identities were similar across the dominant species-level lineages, we observed differences in the extent of recombination between these dominant populations. Most intriguingly, the creek’s Hydrogenobacter sp . population appeared to be so recombinogenic that it more closely resembled a sexual species than a clonally evolving microbe. Together, this work demonstrates that a randomized single-cell approach can be useful for the exploration of previously uncultivated microbes from community composition to population structure.
Publisher: Springer Science and Business Media LLC
Date: 07-2011
DOI: 10.4056/SIGS.2004648
Publisher: Springer Science and Business Media LLC
Date: 17-10-2017
Publisher: Cold Spring Harbor Laboratory
Date: 19-09-2019
DOI: 10.1101/762682
Abstract: Comprehensive reference data is essential for accurate taxonomic and functional characterization of the human gut microbiome. Here we present the Unified Human Gastrointestinal Genome (UHGG) collection, a resource combining 286,997 genomes representing 4,644 prokaryotic species from the human gut. These genomes contain over 625 million protein sequences used to generate the Unified Human Gastrointestinal Protein (UHGP) catalogue, a collection that more than doubles the number of gut protein clusters over the Integrated Gene Catalogue. We find that a large portion of the human gut microbiome remains to be fully explored, with over 70% of the UHGG species lacking cultured representatives, and 40% of the UHGP missing meaningful functional annotations. Intra-species genomic variation analyses revealed a large reservoir of accessory genes and single-nucleotide variants, many of which were specific to in idual human populations. These freely available genomic resources should greatly facilitate investigations into the human gut microbiome.
Publisher: Springer Science and Business Media LLC
Date: 22-07-2019
DOI: 10.1038/S41564-019-0510-X
Abstract: Bacteriophages from the Inoviridae family (inoviruses) are characterized by their unique morphology, genome content and infection cycle. One of the most striking features of inoviruses is their ability to establish a chronic infection whereby the viral genome resides within the cell in either an exclusively episomal state or integrated into the host chromosome and virions are continuously released without killing the host. To date, a relatively small number of inovirus isolates have been extensively studied, either for biotechnological applications, such as phage display, or because of their effect on the toxicity of known bacterial pathogens including Vibrio cholerae and Neisseria meningitidis . Here, we show that the current 56 members of the Inoviridae family represent a minute fraction of a highly erse group of inoviruses. Using a machine learning approach leveraging a combination of marker gene and genome features, we identified 10,295 inovirus-like sequences from microbial genomes and metagenomes. Collectively, our results call for reclassification of the current Inoviridae family into a viral order including six distinct proposed families associated with nearly all bacterial phyla across virtually every ecosystem. Putative inoviruses were also detected in several archaeal genomes, suggesting that, collectively, members of this supergroup infect hosts across the domains Bacteria and Archaea. Finally, we identified an expansive ersity of inovirus-encoded toxin–antitoxin and gene expression modulation systems, alongside evidence of both synergistic (CRISPR evasion) and antagonistic (superinfection exclusion) interactions with co-infecting viruses, which we experimentally validated in a Pseudomonas model. Capturing this previously obscured component of the global virosphere may spark new avenues for microbial manipulation approaches and innovative biotechnological applications.
Publisher: Springer Science and Business Media LLC
Date: 02-10-2017
DOI: 10.1038/NMETH.4458
Publisher: Springer Science and Business Media LLC
Date: 19-03-2018
DOI: 10.1038/NBT.4110
Publisher: Springer Science and Business Media LLC
Date: 20-09-2016
DOI: 10.1038/S41587-020-0603-3
Abstract: Comprehensive, high-quality reference genomes are required for functional characterization and taxonomic assignment of the human gut microbiota. We present the Unified Human Gastrointestinal Genome (UHGG) collection, comprising 204,938 nonredundant genomes from 4,644 gut prokaryotes. These genomes encode million protein sequences, which we collated in the Unified Human Gastrointestinal Protein (UHGP) catalog. The UHGP more than doubles the number of gut proteins in comparison to those present in the Integrated Gene Catalog. More than 70% of the UHGG species lack cultured representatives, and 40% of the UHGP lack functional annotations. Intraspecies genomic variation analyses revealed a large reservoir of accessory genes and single-nucleotide variants, many of which are specific to in idual human populations. The UHGG and UHGP collections will enable studies linking genotypes to phenotypes in the human gut microbiome.
Publisher: Springer Science and Business Media LLC
Date: 19-06-2020
Publisher: Proceedings of the National Academy of Sciences
Date: 15-09-2009
Abstract: Many marine bacteria have evolved to grow optimally at either high (copiotrophic) or low (oligotrophic) nutrient concentrations, enabling different species to colonize distinct trophic habitats in the oceans. Here, we compare the genome sequences of two bacteria, Photobacterium angustum S14 and Sphingopyxis alaskensis RB2256, that serve as useful model organisms for copiotrophic and oligotrophic modes of life and specifically relate the genomic features to trophic strategy for these organisms and define their molecular mechanisms of adaptation. We developed a model for predicting trophic lifestyle from genome sequence data and tested ,000 proteins representing million nucleotides of sequence data from 126 genome sequences with metagenome data of whole environmental s les. When applied to available oceanic metagenome data (e.g., the Global Ocean Survey data) the model demonstrated that oligotrophs, and not the more readily isolatable copiotrophs, dominate the ocean's free-living microbial populations. Using our model, it is now possible to define the types of bacteria that specific ocean niches are capable of sustaining.
Publisher: Springer Science and Business Media LLC
Date: 30-06-2015
Publisher: American Society for Microbiology
Date: 07-2011
DOI: 10.1128/JB.05109-11
Abstract: Nocardioides sp. strain JS614 grows on ethene and vinyl chloride (VC) as sole carbon and energy sources and is of interest for bioremediation and biocatalysis. Sequencing of the complete genome of JS614 provides insight into the genetic basis of alkene oxidation, supports ongoing research into the physiology and biochemistry of growth on ethene and VC, and provides biomarkers to facilitate detection of VC/ethene oxidizers in the environment. This is the first genome sequence from the genus Nocardioides and the first genome of a VC/ethene-oxidizing bacterium.
Publisher: Springer Science and Business Media LLC
Date: 08-2017
DOI: 10.1038/NBT.3893
Abstract: We present two standards developed by the Genomic Standards Consortium (GSC) for reporting bacterial and archaeal genome sequences. Both are extensions of the Minimum Information about Any (x) Sequence (MIxS). The standards are the Minimum Information about a Single Amplified Genome (MISAG) and the Minimum Information about a Metagenome-Assembled Genome (MIMAG), including, but not limited to, assembly quality, and estimates of genome completeness and contamination. These standards can be used in combination with other GSC checklists, including the Minimum Information about a Genome Sequence (MIGS), Minimum Information about a Metagenomic Sequence (MIMS), and Minimum Information about a Marker Gene Sequence (MIMARKS). Community-wide adoption of MISAG and MIMAG will facilitate more robust comparative genomic analyses of bacterial and archaeal ersity.
Publisher: Springer Science and Business Media LLC
Date: 17-12-2019
DOI: 10.1038/NBT.4306
Publisher: Wiley
Date: 31-05-2009
Publisher: Proceedings of the National Academy of Sciences
Date: 10-06-2008
Abstract: The candidate ision Korarchaeota comprises a group of uncultivated microorganisms that, by their small subunit rRNA phylogeny, may have erged early from the major archaeal phyla Crenarchaeota and Euryarchaeota . Here, we report the initial characterization of a member of the Korarchaeota with the proposed name, “ Candidatus Korarchaeum cryptofilum,” which exhibits an ultrathin filamentous morphology. To investigate possible ancestral relationships between deep-branching Korarchaeota and other phyla, we used whole-genome shotgun sequencing to construct a complete composite korarchaeal genome from enriched cells. The genome was assembled into a single contig 1.59 Mb in length with a G + C content of 49%. Of the 1,617 predicted protein-coding genes, 1,382 (85%) could be assigned to a revised set of archaeal Clusters of Orthologous Groups (COGs). The predicted gene functions suggest that the organism relies on a simple mode of peptide fermentation for carbon and energy and lacks the ability to synthesize de novo purines, CoA, and several other cofactors. Phylogenetic analyses based on conserved single genes and concatenated protein sequences positioned the korarchaeote as a deep archaeal lineage with an apparent affinity to the Crenarchaeota . However, the predicted gene content revealed that several conserved cellular systems, such as cell ision, DNA replication, and tRNA maturation, resemble the counterparts in the Euryarchaeota . In light of the known composition of archaeal genomes, the Korarchaeota might have retained a set of cellular features that represents the ancestral archaeal form.
Publisher: American Association for the Advancement of Science (AAAS)
Date: 07-04-2017
Abstract: Viral evolution is revealed by giant viruses encoding multiple components of the protein translation machinery.
Publisher: Oxford University Press (OUP)
Date: 2006
DOI: 10.1093/NAR/GKJ145
Publisher: Springer Science and Business Media LLC
Date: 05-08-2010
Publisher: Springer Science and Business Media LLC
Date: 05-2008
DOI: 10.1038/NBT1360
Publisher: Oxford University Press (OUP)
Date: 30-07-2101
DOI: 10.1093/NAR/GKP848
Publisher: Cold Spring Harbor Laboratory
Date: 06-03-2023
DOI: 10.1101/2023.03.05.531206
Abstract: Identifying and characterizing mobile genetic elements (MGEs) in sequencing data is essential for understanding their ersity, ecology, biotechnological applications, and impact on public health. Here, we introduce geNomad, a classification and annotation framework that combines information from gene content and a deep neural network to identify sequences of plasmids and viruses. geNomad uses a large dataset of marker proteins to provide functional gene annotation and taxonomic assignment of viral genomes. Using a conditional random field model, geNomad also detects proviruses integrated into host genomes with high precision. In benchmarks that included erse MGE and chromosome sequences, geNomad significantly outperformed other tools in all evaluated clades of plasmids and viruses. Leveraging geNomad's speed and scalability, we were able to process public metagenomes and metatranscriptomes, leading to the discovery of millions of new viruses and plasmids that are available through the IMG/VR and IMG/PR databases. We anticipate that geNomad will enable further advancements in MGE research, and it is available at enomad.
Publisher: Springer Science and Business Media LLC
Date: 22-07-2014
Publisher: Springer Science and Business Media LLC
Date: 05-06-2020
DOI: 10.1038/S41597-020-0497-4
Abstract: A synthesis of phenotypic and quantitative genomic traits is provided for bacteria and archaea, in the form of a scripted, reproducible workflow that standardizes and merges 26 sources. The resulting unified dataset covers 14 phenotypic traits, 5 quantitative genomic traits, and 4 environmental characteristics for approximately 170,000 strain-level and 15,000 species-aggregated records. It spans all habitats including soils, marine and fresh waters and sediments, host-associated and thermal. Trait data can find use in clarifying major dimensions of ecological strategy variation across species. They can also be used in conjunction with species and abundance s ling to characterize trait mixtures in communities and responses of traits along environmental gradients.
Publisher: Springer Science and Business Media LLC
Date: 24-06-2021
DOI: 10.1038/S41564-021-00928-6
Abstract: Bacteriophages have important roles in the ecology of the human gut microbiome but are under-represented in reference databases. To address this problem, we assembled the Metagenomic Gut Virus catalogue that comprises 189,680 viral genomes from 11,810 publicly available human stool metagenomes. Over 75% of genomes represent double-stranded DNA phages that infect members of the Bacteroidia and Clostridia classes. Based on sequence clustering we identified 54,118 candidate viral species, 92% of which were not found in existing databases. The Metagenomic Gut Virus catalogue improves detection of viruses in stool metagenomes and accounts for nearly 40% of CRISPR spacers found in human gut Bacteria and Archaea. We also produced a catalogue of 459,375 viral protein clusters to explore the functional potential of the gut virome. This revealed tens of thousands of ersity-generating retroelements, which use error-prone reverse transcription to mutate target genes and may be involved in the molecular arms race between phages and their bacterial hosts.
Publisher: Cold Spring Harbor Laboratory
Date: 15-02-2019
DOI: 10.1101/548222
Abstract: Bacteriophages from the Inoviridae family (inoviruses) are characterized by their unique morphology, genome content, and infection cycle. To date, a relatively small number of inovirus isolates have been extensively studied, either for biotechnological applications such as phage display, or because of their impact on the toxicity of known bacterial pathogens including Vibrio cholerae and Neisseria meningitidis . Here we show that the current 56 members of the Inoviridae family represent a minute fraction of a highly erse group of inoviruses. Using a new machine learning approach leveraging a combination of marker gene and genome features, we identified 10,295 inovirus-like genomes from microbial genomes and metagenomes. Collectively, these represent six distinct proposed inovirus families infecting nearly all bacterial phyla across virtually every ecosystem. Putative inoviruses were also detected in several archaeal genomes, suggesting that these viruses may have occasionally transferred from bacterial to archaeal hosts. Finally, we identified an expansive ersity of inovirus-encoded toxin-antitoxin and gene expression modulation systems, alongside evidence of both synergistic (CRISPR evasion) and antagonistic (superinfection exclusion) interactions with co-infecting viruses which we experimentally validated in a Pseudomonas model. Capturing this previously obscured component of the global virosphere sparks new avenues for microbial manipulation approaches and innovative biotechnological applications.
Publisher: Springer Science and Business Media LLC
Date: 13-07-2020
DOI: 10.1038/S41396-020-0705-4
Abstract: Our current knowledge of host–virus interactions in biofilms is limited to computational predictions based on laboratory experiments with a small number of cultured bacteria. However, natural biofilms are erse and chiefly composed of uncultured bacteria and archaea with no viral infection patterns and lifestyle predictions described to date. Herein, we predict the first DNA sequence-based host–virus interactions in a natural biofilm. Using single-cell genomics and metagenomics applied to a hot spring mat of the Cone Pool in Mono County, California, we provide insights into virus–host range, lifestyle and distribution across different mat layers. Thirty-four out of 130 single cells contained at least one viral contig (26%), which, together with the metagenome-assembled genomes, resulted in detection of 59 viruses linked to 34 host species. Analysis of single-cell lification kinetics revealed a lack of active viral replication on the single-cell level. These findings were further supported by mapping metagenomic reads from different mat layers to the obtained host–virus pairs, which indicated a low copy number of viral genomes compared to their hosts. Lastly, the metagenomic data revealed high layer specificity of viruses, suggesting limited diffusion to other mat layers. Taken together, these observations indicate that in low mobility environments with high microbial abundance, lysogeny is the predominant viral lifestyle, in line with the previously proposed “Piggyback-the-Winner” theory.
Publisher: Springer Science and Business Media LLC
Date: 17-05-2015
Publisher: Springer Science and Business Media LLC
Date: 15-11-2017
Publisher: Springer Science and Business Media LLC
Date: 09-08-2020
DOI: 10.1186/S40168-020-00889-8
Abstract: Cold environments dominate the Earth’s biosphere and microbial activity drives ecosystem processes thereby contributing greatly to global biogeochemical cycles. Polar environments differ to all other cold environments by experiencing 24-h sunlight in summer and no sunlight in winter. The Vestfold Hills in East Antarctica contains hundreds of lakes that have evolved from a marine origin only 3000–7000 years ago. Ace Lake is a meromictic (stratified) lake from this region that has been intensively studied since the 1970s. Here, a total of 120 metagenomes representing a seasonal cycle and four summers spanning a 10-year period were analyzed to determine the effects of the polar light cycle on microbial-driven nutrient cycles. The lake system is characterized by complex sulfur and hydrogen cycling, especially in the anoxic layers, with multiple mechanisms for the breakdown of biopolymers present throughout the water column. The two most abundant taxa are phototrophs (green sulfur bacteria and cyanobacteria) that are highly influenced by the seasonal availability of sunlight. The extent of the Chlorobium biomass thriving at the interface in summer was captured in underwater video footage. The Chlorobium abundance dropped from up to 83% in summer to 6% in winter and 1% in spring, before rebounding to high levels. Predicted Chlorobium viruses and cyanophage were also abundant, but their levels did not negatively correlate with their hosts. Over-wintering expeditions in Antarctica are logistically challenging, meaning insight into winter processes has been inferred from limited data. Here, we found that in contrast to chemolithoautotrophic carbon fixation potential of Southern Ocean Thaumarchaeota, this marine-derived lake evolved a reliance on photosynthesis. While viruses associated with phototrophs also have high seasonal abundance, the negative impact of viral infection on host growth appeared to be limited. The microbial community as a whole appears to have developed a capacity to generate biomass and remineralize nutrients, sufficient to sustain itself between two rounds of sunlight-driven summer-activity. In addition, this unique metagenome dataset provides considerable opportunity for future interrogation of eukaryotes and their viruses, abundant uncharacterized taxa (i.e. dark matter), and for testing hypotheses about endemic species in polar aquatic ecosystems.
Publisher: Springer Science and Business Media LLC
Date: 12-06-2017
DOI: 10.1038/NBT.3886
Abstract: We present 1,003 reference genomes that were sequenced as part of the Genomic Encyclopedia of Bacteria and Archaea (GEBA) initiative, selected to maximize sequence coverage of phylogenetic space. These genomes double the number of existing type strains and expand their overall phylogenetic ersity by 25%. Comparative analyses with previously available finished and draft genomes reveal a 10.5% increase in novel protein families as a function of phylogenetic ersity. The GEBA genomes recruit 25 million previously unassigned metagenomic proteins from 4,650 s les, improving their phylogenetic and functional interpretation. We identify numerous biosynthetic clusters and experimentally validate a ergent phenazine cluster with potential new chemical structure and antimicrobial activity. This Resource is the largest single release of reference genomes to date. Bacterial and archaeal isolate sequence space is still far from saturated, and future endeavors in this direction will continue to be a valuable resource for scientific discovery.
Publisher: Proceedings of the National Academy of Sciences
Date: 30-09-2013
Abstract: Horizontal gene exchange across species boundaries is considered infrequent relative to vertical inheritance that maintains species coherence. However, haloarchaea living in hypersaline environments take a more relaxed approach to gene exchange. Here we demonstrate that in Deep Lake, Antarctica, haloarchaea exchange DNA between distinct genera, not just species, with some of the DNA being long (up to 35 kb) and virtually 100% conserved. With extremely low cell ision rates in the cold (e.g., six generations per year), the remarkable extent of lateral exchange could conceivably homogenize the population. It is therefore equally notable that despite the demonstrated capacity for exchange, different genera are maintained, their coexistence being linked to genomic differences conferring ecotype distinctions that enable niche adaptation.
Publisher: Springer Science and Business Media LLC
Date: 11-02-2020
DOI: 10.1038/S41564-020-0681-5
Abstract: An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Publisher: Springer Science and Business Media LLC
Date: 06-07-2018
DOI: 10.1038/NBT0718-660A
Publisher: Springer Science and Business Media LLC
Date: 20-02-2014
Publisher: Springer Science and Business Media LLC
Date: 04-2018
DOI: 10.1038/NBT0418-368C
Publisher: Wiley
Date: 07-2010
Publisher: Springer Science and Business Media LLC
Date: 18-06-2007
Publisher: Springer Science and Business Media LLC
Date: 15-12-2013
DOI: 10.4056/SIGS.4478252
Publisher: American Association for the Advancement of Science (AAAS)
Date: 03-05-2019
Publisher: Springer Science and Business Media LLC
Date: 29-04-2011
DOI: 10.4056/SIGS.1553865
Publisher: Springer Science and Business Media LLC
Date: 14-07-2013
DOI: 10.1038/NATURE12352
Abstract: Genome sequencing enhances our understanding of the biological world by providing blueprints for the evolutionary and functional ersity that shapes the biosphere. However, microbial genomes that are currently available are of limited phylogenetic breadth, owing to our historical inability to cultivate most microorganisms in the laboratory. We apply single-cell genomics to target and sequence 201 uncultivated archaeal and bacterial cells from nine erse habitats belonging to 29 major mostly uncharted branches of the tree of life, so-called 'microbial dark matter'. With this additional genomic information, we are able to resolve many intra- and inter-phylum-level relationships and to propose two new superphyla. We uncover unexpected metabolic features that extend our understanding of biology and challenge established boundaries between the three domains of life. These include a novel amino acid use for the opal stop codon, an archaeal-type purine synthesis in Bacteria and complete sigma factors in Archaea similar to those in Bacteria. The single-cell genomes also served to phylogenetically anchor up to 20% of metagenomic reads in some habitats, facilitating organism-level interpretation of ecosystem function. This study greatly expands the genomic representation of the tree of life and provides a systematic step towards a better understanding of biological evolution on our planet.
Publisher: Springer Science and Business Media LLC
Date: 23-12-2011
DOI: 10.4056/SIGS.1854551
Publisher: Royal Society of Chemistry (RSC)
Date: 2011
DOI: 10.1039/C1GC15193B
Publisher: Springer Science and Business Media LLC
Date: 31-07-2019
DOI: 10.1038/S41597-019-0141-3
Abstract: The rocky, seasonally-dry and nutrient-impoverished soils of the Brazilian c os rupestre s impose severe growth-limiting conditions on plants. Species of a dominant plant family, Velloziaceae, are highly specialized to low-nutrient conditions and seasonal water availability of this environment, where phosphorus (P) is the key limiting nutrient. Despite plant-microbe associations playing critical roles in stressful ecosystems, the contribution of these interactions in the c os rupestres remains poorly studied. Here we present the first microbiome data of Velloziaceae spp. thriving in contrasting substrates of c os rupestres . We assessed the microbiomes of Vellozia epidendroides , which occupies shallow patches of soil, and Barbacenia macrantha , growing on exposed rocks. The prokaryotic and fungal profiles were assessed by rRNA barcode sequencing of epiphytic and endophytic compartments of roots, stems, leaves and surrounding soil/rocks. We also generated root and substrate (rock/soil)-associated metagenomes of each plant species. We foresee that these data will contribute to decipher how the microbiome contributes to plant functioning in the c os rupestres , and to unravel new strategies for improved crop productivity in stressful environments.
Publisher: Springer Science and Business Media LLC
Date: 21-09-2023
Publisher: Springer Science and Business Media LLC
Date: 18-11-2020
DOI: 10.1038/S41587-020-00769-4
Abstract: An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Location: United States of America
Start Date: 09-2008
End Date: 09-2011
Amount: $525,000.00
Funder: Australian Research Council
View Funded Activity