Publications by authors named "Benjamin J Tully"

19 Publications

  • Page 1 of 1

NCBI's Virus Discovery Codeathon: Building "FIVE" -The Federated Index of Viral Experiments API Index.

Viruses 2020 12 10;12(12). Epub 2020 Dec 10.

National Center for Biotechnology Information, U.S. National Library of Medicine, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20894, USA.

Viruses represent important test cases for data federation due to their genome size and the rapid increase in sequence data in publicly available databases. However, some consequences of previously decentralized (unfederated) data are lack of consensus or comparisons between feature annotations. Unifying or displaying alternative annotations should be a priority both for communities with robust entry representation and for nascent communities with burgeoning data sources. To this end, during this three-day continuation of the Virus Hunting Toolkit codeathon series (VHT-2), a new integrated and federated viral index was elaborated. This Federated Index of Viral Experiments (FIVE) integrates pre-existing and novel functional and taxonomy annotations and virus-host pairings. Variability in the context of viral genomic diversity is often overlooked in virus databases. As a proof-of-concept, FIVE was the first attempt to include viral genome variation for HIV, the most well-studied human pathogen, through viral genome diversity graphs. As per the publication of this manuscript, FIVE is the first implementation of a virus-specific federated index of such scope. FIVE is coded in BigQuery for optimal access of large quantities of data and is publicly accessible. Many projects of database or index federation fail to provide easier alternatives to access or query information. To this end, a Python API query system was developed to enhance the accessibility of FIVE.
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http://dx.doi.org/10.3390/v12121424DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7764237PMC
December 2020

Time-series transcriptomics from cold, oxic subseafloor crustal fluids reveals a motile, mixotrophic microbial community.

ISME J 2020 Dec 3. Epub 2020 Dec 3.

Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, USA.

The oceanic crustal aquifer is one of the largest habitable volumes on Earth, and it harbors a reservoir of microbial life that influences global-scale biogeochemical cycles. Here, we use time series metagenomic and metatranscriptomic data from a low-temperature, ridge flank environment representative of the majority of global hydrothermal fluid circulation in the ocean to reconstruct microbial metabolic potential, transcript abundance, and community dynamics. We also present metagenome-assembled genomes from recently collected fluids that are furthest removed from drilling disturbances. Our results suggest that the microbial community in the North Pond aquifer plays an important role in the oxidation of organic carbon within the crust. This community is motile and metabolically flexible, with the ability to use both autotrophic and organotrophic pathways, as well as function under low oxygen conditions by using alternative electron acceptors such as nitrate and thiosulfate. Anaerobic processes are most abundant in subseafloor horizons deepest in the aquifer, furthest from connectivity with the deep ocean, and there was little overlap in the active microbial populations between sampling horizons. This work highlights the heterogeneity of microbial life in the subseafloor aquifer and provides new insights into biogeochemical cycling in ocean crust.
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http://dx.doi.org/10.1038/s41396-020-00843-4DOI Listing
December 2020

Marine Dadabacteria exhibit genome streamlining and phototrophy-driven niche partitioning.

ISME J 2020 Nov 23. Epub 2020 Nov 23.

Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA.

The remineralization of organic material via heterotrophy in the marine environment is performed by a diverse and varied group of microorganisms that can specialize in the type of organic material degraded and the niche they occupy. The marine Dadabacteria are cosmopolitan in the marine environment and belong to a candidate phylum for which there has not been a comprehensive assessment of the available genomic data to date. Here in, we assess the functional potential of the marine pelagic Dadabacteria in comparison to members of the phylum that originate from terrestrial, hydrothermal, and subsurface environments. Our analysis reveals that the marine pelagic Dadabacteria have streamlined genomes, corresponding to smaller genome sizes and lower nitrogen content of their DNA and predicted proteome, relative to their phylogenetic counterparts. Collectively, the Dadabacteria have the potential to degrade microbial dissolved organic matter, specifically peptidoglycan and phospholipids. The marine Dadabacteria belong to two clades with apparent distinct ecological niches in global metagenomic data: a clade with the potential for photoheterotrophy through the use of proteorhodopsin, present predominantly in surface waters up to 100 m depth; and a clade lacking the potential for photoheterotrophy that is more abundant in the deep photic zone.
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http://dx.doi.org/10.1038/s41396-020-00834-5DOI Listing
November 2020

Biases in genome reconstruction from metagenomic data.

PeerJ 2020 30;8:e10119. Epub 2020 Oct 30.

Chemical and Biological Signature Science Group, Pacific Northwest National Laboratory, Richland, WA, USA.

Background: Advances in sequencing, assembly, and assortment of contigs into species-specific bins has enabled the reconstruction of genomes from metagenomic data (MAGs). Though a powerful technique, it is difficult to determine whether assembly and binning techniques are accurate when applied to environmental metagenomes due to a lack of complete reference genome sequences against which to check the resulting MAGs.

Methods: We compared MAGs derived from an enrichment culture containing ~20 organisms to complete genome sequences of 10 organisms isolated from the enrichment culture. Factors commonly considered in binning software-nucleotide composition and sequence repetitiveness-were calculated for both the correctly binned and not-binned regions. This direct comparison revealed biases in sequence characteristics and gene content in the not-binned regions. Additionally, the composition of three public data sets representing MAGs reconstructed from the Oceans metagenomic data was compared to a set of representative genomes available through NCBI RefSeq to verify that the biases identified were observable in more complex data sets and using three contemporary binning software packages.

Results: Repeat sequences were frequently not binned in the genome reconstruction processes, as were sequence regions with variant nucleotide composition. Genes encoded on the not-binned regions were strongly biased towards ribosomal RNAs, transfer RNAs, mobile element functions and genes of unknown function. Our results support genome reconstruction as a robust process and suggest that reconstructions determined to be >90% complete are likely to effectively represent organismal function; however, population-level genotypic heterogeneity in natural populations, such as uneven distribution of plasmids, can lead to incorrect inferences.
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http://dx.doi.org/10.7717/peerj.10119DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7605220PMC
October 2020

MetaSanity: an integrated microbial genome evaluation and annotation pipeline.

Bioinformatics 2020 08;36(15):4341-4344

Department of Biological Sciences, Los Angeles, CA 90089, USA.

Summary: As the importance of microbiome research continues to become more prevalent and essential to understanding a wide variety of ecosystems (e.g. marine, built, host associated, etc.), there is a need for researchers to be able to perform highly reproducible and quality analysis of microbial genomes. MetaSanity incorporates analyses from 11 existing and widely used genome evaluation and annotation suites into a single, distributable workflow, thereby decreasing the workload of microbiologists by allowing for a flexible, expansive data analysis pipeline. MetaSanity has been designed to provide separate, reproducible workflows that (i) can determine the overall quality of a microbial genome, while providing a putative phylogenetic assignment, and (ii) can assign structural and functional gene annotations with varying degrees of specificity to suit the needs of the researcher. The software suite combines the results from several tools to provide broad insights into overall metabolic function. Importantly, this software provides built-in optimization for 'big data' analysis by storing all relevant outputs in an SQL database, allowing users to query all the results for the elements that will most impact their research.

Availability And Implementation: MetaSanity is provided under the GNU General Public License v.3.0 and is available for download at https://github.com/cjneely10/MetaSanity. This application is distributed as a Docker image. MetaSanity is implemented in Python3/Cython and C++. Instructions for its installation and use are available within the GitHub wiki page at https://github.com/cjneely10/MetaSanity/wiki, and additional instructions are available at https://cjneely10.github.io/year-archive/. MetaSanity is optimized for users with limited programing experience.

Supplementary Information: Supplementary data are available at Bioinformatics online.
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http://dx.doi.org/10.1093/bioinformatics/btaa512DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7520038PMC
August 2020

Author Correction: A distinct and active bacterial community in cold oxygenated fluids circulating beneath the western flank of the Mid-Atlantic ridge.

Sci Rep 2020 Apr 16;10(1):6691. Epub 2020 Apr 16.

Josephine Bay Paul Center, Marine Biological Laboratory, 7 MBL St., Woods Hole, MA, 02543, USA.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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http://dx.doi.org/10.1038/s41598-020-63127-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7162844PMC
April 2020

Genome Sequence of sp. Strain EBB-1, a Novel Marine Autotroph Isolated from an Iron-Sulfur Mineral.

Microbiol Resour Announc 2019 Sep 26;8(39). Epub 2019 Sep 26.

Department of Earth Sciences, University of Southern California, Los Angeles, California, USA.

sp. strain EBB-1 was isolated from a pyrrhotite biofilm incubated in seawater from East Boothbay (ME, USA). Strain EBB-1 is an autotrophic member of the class with the ability to form iron oxide biominerals. Here, we present the 2.88-Mb genome sequence of EBB-1, which contains 2,656 putative protein-coding sequences.
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http://dx.doi.org/10.1128/MRA.00995-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6763651PMC
September 2019

Metabolic diversity within the globally abundant Marine Group II Euryarchaea offers insight into ecological patterns.

Authors:
Benjamin J Tully

Nat Commun 2019 01 17;10(1):271. Epub 2019 Jan 17.

Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA.

Despite their discovery over 25 years ago, the Marine Group II Euryarchaea (MGII) remain a difficult group of organisms to study, lacking cultured isolates and genome references. The MGII have been identified in marine samples from around the world, and evidence supports a photoheterotrophic lifestyle combining phototrophy via proteorhodopsins with the remineralization of high molecular weight organic matter. Divided between two clades, the MGII have distinct ecological patterns that are not understood based on the limited number of available genomes. Here, I present a comparative genomic analysis of 250 MGII genomes, providing a comprehensive investigation of these mesophilic archaea. This analysis identifies 17 distinct subclades including nine subclades that previously lacked reference genomes. The metabolic potential and distribution of the MGII genera reveals distinct roles in the environment, identifying algal-saccharide-degrading coastal subclades, protein-degrading oligotrophic surface ocean subclades, and mesopelagic subclades lacking proteorhodopsins, common in all other subclades.
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http://dx.doi.org/10.1038/s41467-018-07840-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6336850PMC
January 2019

The reconstruction of 2,631 draft metagenome-assembled genomes from the global oceans.

Sci Data 2018 01 16;5:170203. Epub 2018 Jan 16.

Center for Dark Energy Biosphere Investigations, University of Southern California, Los Angeles, CA 90089, USA.

Microorganisms play a crucial role in mediating global biogeochemical cycles in the marine environment. By reconstructing the genomes of environmental organisms through metagenomics, researchers are able to study the metabolic potential of Bacteria and Archaea that are resistant to isolation in the laboratory. Utilizing the large metagenomic dataset generated from 234 samples collected during the Tara Oceans circumnavigation expedition, we were able to assemble 102 billion paired-end reads into 562 million contigs, which in turn were co-assembled and consolidated in to 7.2 million contigs ≥2 kb in length. Approximately 1 million of these contigs were binned to reconstruct draft genomes. In total, 2,631 draft genomes with an estimated completion of ≥50% were generated (1,491 draft genomes >70% complete; 603 genomes >90% complete). A majority of the draft genomes were manually assigned phylogeny based on sets of concatenated phylogenetic marker genes and/or 16S rRNA gene sequences. The draft genomes are now publically available for the research community at-large.
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http://dx.doi.org/10.1038/sdata.2017.203DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5769542PMC
January 2018

A dynamic microbial community with high functional redundancy inhabits the cold, oxic subseafloor aquifer.

ISME J 2018 01 3;12(1):1-16. Epub 2017 Nov 3.

Josephine Bay Paul Center, Marine Biological Laboratory, Woods Hole, MA, USA.

The rock-hosted subseafloor crustal aquifer harbors a reservoir of microbial life that may influence global marine biogeochemical cycles. Here we utilized metagenomic libraries of crustal fluid samples from North Pond, located on the flanks of the Mid-Atlantic Ridge, a site with cold, oxic subseafloor fluid circulation within the upper basement to query microbial diversity. Twenty-one samples were collected during a 2-year period to examine potential microbial metabolism and community dynamics. We observed minor changes in the geochemical signatures over the 2 years, yet the microbial community present in the crustal fluids underwent large shifts in the dominant taxonomic groups. An analysis of 195 metagenome-assembled genomes (MAGs) were generated from the data set and revealed a connection between litho- and autotrophic processes, linking carbon fixation to the oxidation of sulfide, sulfur, thiosulfate, hydrogen, and ferrous iron in members of the Proteobacteria, specifically the Alpha-, Gamma- and Zetaproteobacteria, the Epsilonbacteraeota and the Planctomycetes. Despite oxic conditions, analysis of the MAGs indicated that members of the microbial community were poised to exploit hypoxic or anoxic conditions through the use of microaerobic cytochromes, such as cbb- and bd-type cytochromes, and alternative electron acceptors, like nitrate and sulfate. Temporal and spatial trends from the MAGs revealed a high degree of functional redundancy that did not correlate with the shifting microbial community membership, suggesting functional stability in mediating subseafloor biogeochemical cycles. Collectively, the repeated sampling at multiple sites, together with the successful binning of hundreds of genomes, provides an unprecedented data set for investigation of microbial communities in the cold, oxic crustal aquifer.
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http://dx.doi.org/10.1038/ismej.2017.187DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5739024PMC
January 2018

290 metagenome-assembled genomes from the Mediterranean Sea: a resource for marine microbiology.

PeerJ 2017 10;5:e3558. Epub 2017 Jul 10.

Center for Dark Energy Biosphere Investigations, University of Southern California, Los Angeles, CA, USA.

The Expedition has provided large, publicly-accessible microbial metagenomic datasets from a circumnavigation of the globe. Utilizing several size fractions from the samples originating in the Mediterranean Sea, we have used current assembly and binning techniques to reconstruct 290 putative draft metagenome-assembled bacterial and archaeal genomes, with an estimated completion of ≥50%, and an additional 2,786 bins, with estimated completion of 0-50%. We have submitted our results, including initial taxonomic and phylogenetic assignments, for the putative draft genomes to open-access repositories for the scientific community to use in ongoing research.
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http://dx.doi.org/10.7717/peerj.3558DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5507172PMC
July 2017

BinSanity: unsupervised clustering of environmental microbial assemblies using coverage and affinity propagation.

PeerJ 2017 8;5:e3035. Epub 2017 Mar 8.

Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA; Center for Dark Energy Biosphere Investigations, Los Angeles, CA, USA.

Metagenomics has become an integral part of defining microbial diversity in various environments. Many ecosystems have characteristically low biomass and few cultured representatives. Linking potential metabolisms to phylogeny in environmental microorganisms is important for interpreting microbial community functions and the impacts these communities have on geochemical cycles. However, with metagenomic studies there is the computational hurdle of 'binning' contigs into phylogenetically related units or putative genomes. Binning methods have been implemented with varying approaches such as k-means clustering, Gaussian mixture models, hierarchical clustering, neural networks, and two-way clustering; however, many of these suffer from biases against low coverage/abundance organisms and closely related taxa/strains. We are introducing a new binning method, BinSanity, that utilizes the clustering algorithm affinity propagation (AP), to cluster assemblies using coverage with compositional based refinement (tetranucleotide frequency and percent GC content) to optimize bins containing multiple source organisms. This separation of composition and coverage based clustering reduces bias for closely related taxa. BinSanity was developed and tested on artificial metagenomes varying in size and complexity. Results indicate that BinSanity has a higher precision, recall, and Adjusted Rand Index compared to five commonly implemented methods. When tested on a previously published environmental metagenome, BinSanity generated high completion and low redundancy bins corresponding with the published metagenome-assembled genomes.
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http://dx.doi.org/10.7717/peerj.3035DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5345454PMC
March 2017

Potential Mechanisms for Microbial Energy Acquisition in Oxic Deep-Sea Sediments.

Appl Environ Microbiol 2016 07 30;82(14):4232-43. Epub 2016 Jun 30.

Center for Dark Energy Biosphere Investigations, University of Southern California, Los Angeles, California, USA Department of Biological Sciences, University of Southern California, Los Angeles, California, USA.

Unlabelled: The South Pacific Gyre (SPG) possesses the lowest rates of sedimentation, surface chlorophyll concentration, and primary productivity in the global oceans. As a direct result, deep-sea sediments are thin and contain small amounts of labile organic carbon. It was recently shown that the entire SPG sediment column is oxygenated and may be representative of up to a third of the global marine environment. To understand the microbial processes that contribute to the removal of the labile organic matter at the water-sediment interface, a sediment sample was collected and subjected to metagenomic sequencing and analyses. Analysis of nine partially reconstructed environmental genomes, which represent approximately one-third of the microbial community, revealed that the members of the SPG surface sediment microbial community are phylogenetically distinct from surface/upper-ocean organisms. These genomes represent a wide distribution of novel organisms, including deep-branching Alphaproteobacteria, two novel organisms within the Proteobacteria, and new members of the Nitrospirae, Nitrospinae, and candidate phylum NC10. These genomes contain evidence for microbially mediated metal (iron/manganese) oxidation and carbon fixation linked to nitrification. Additionally, despite hypothesized energy limitation, members of the SPG microbial community had motility and chemotaxis genes and possessed mechanisms for the degradation of high-molecular-weight organic matter. This study contributes to our understanding of the metabolic potential of microorganisms in deep-sea oligotrophic sediments and their impact on local carbon geochemistry.

Importance: This research provides insight into the microbial metabolic potential of organisms inhabiting oxygenated deep-sea marine sediments. Current estimates suggest that these environments account for up to a third of the global marine sediment habitat. Nine novel deep-sea microbial genomes were reconstructed from a metagenomic data set and expand the limited number of environmental genomes from deep-sea sediment environments. This research provides phylogeny-linked insight into critical metabolisms, including carbon fixation associated with nitrification, which is assignable to members of the marine group 1 Thaumarchaeota, Nitrospinae, and Nitrospirae and neutrophilic metal (iron/manganese) oxidation assignable to a novel proteobacterium.
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http://dx.doi.org/10.1128/AEM.01023-16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4959193PMC
July 2016

A distinct and active bacterial community in cold oxygenated fluids circulating beneath the western flank of the Mid-Atlantic ridge.

Sci Rep 2016 Mar 3;6:22541. Epub 2016 Mar 3.

Josephine Bay Paul Center, Marine Biological Laboratory, 7 MBL St., Woods Hole, MA 02543.

The rock-hosted, oceanic crustal aquifer is one of the largest ecosystems on Earth, yet little is known about its indigenous microorganisms. Here we provide the first phylogenetic and functional description of an active microbial community residing in the cold oxic crustal aquifer. Using subseafloor observatories, we recovered crustal fluids and found that the geochemical composition is similar to bottom seawater, as are cell abundances. However, based on relative abundances and functional potential of key bacterial groups, the crustal fluid microbial community is heterogeneous and markedly distinct from seawater. Potential rates of autotrophy and heterotrophy in the crust exceeded those of seawater, especially at elevated temperatures (25 °C) and deeper in the crust. Together, these results reveal an active, distinct, and diverse bacterial community engaged in both heterotrophy and autotrophy in the oxygenated crustal aquifer, providing key insight into the role of microbial communities in the ubiquitous cold dark subseafloor biosphere.
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http://dx.doi.org/10.1038/srep22541DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4776111PMC
March 2016

De novo sequences of Haloquadratum walsbyi from Lake Tyrrell, Australia, reveal a variable genomic landscape.

Archaea 2015 1;2015:875784. Epub 2015 Feb 1.

Department of Biological Sciences, Dornsife College of Letters, Arts and Sciences, University of Southern California, 3616 Trousdale Parkway, Los Angeles, CA 90089, USA.

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.
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http://dx.doi.org/10.1155/2015/875784DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4330952PMC
November 2015

Comparative genomics of planktonic Flavobacteriaceae from the Gulf of Maine using metagenomic data.

Microbiome 2014 5;2:34. Epub 2014 Sep 5.

Biological Science, Marine & Environmental Biology, Dornsife College of Letters, Arts and Sciences, University of Southern California, 3616 Trousdale Parkway, Los Angeles CA 90089, USA.

Background: The Gulf of Maine is an important biological province of the Northwest Atlantic with high productivity year round. From an environmental Sanger-based metagenome, sampled in summer and winter, we were able to assemble and explore the partial environmental genomes of uncultured members of the class Flavobacteria. Each of the environmental genomes represents organisms that compose less than 1% of the total microbial metagenome.

Results: Four partial environmental genomes were assembled with varying degrees of estimated completeness (37%-84% complete) and were analyzed from a perspective of gathering information regarding niche partitioning between co-occurring organisms. Comparative genomics revealed potentially important niche partitioning genomic variations, including iron transporters and genes associated with cell attachment and polymer degradation. Analysis of large syntenic regions helped reveal potentially ecologically relevant variations for Flavobacteriaceae in the Gulf of Maine, such as arginine biosynthesis, and identify a putative genomic island incorporating novel exogenous genes from the environment.

Conclusions: Biogeographic analysis revealed flavobacteria species with distinct abundance patterns suggesting the presence of local blooms relative to the other species, as well as seasonally selected organisms. The analysis of genomic content for the Gulf of Maine Flavobacteria supports the hypothesis of a particle-associated lifestyle and specifically highlights a number of putative coding sequences that may play a role in the remineralization of particulate organic matter. And lastly, analysis of the underlying sequences for each assembled genome revealed seasonal and nonseasonal variants of specific genes implicating a dynamic interaction between individuals within the species.
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http://dx.doi.org/10.1186/2049-2618-2-34DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4164334PMC
September 2014

Microbial communities associated with ferromanganese nodules and the surrounding sediments.

Front Microbiol 2013 25;4:161. Epub 2013 Jun 25.

Department of Biological Science, Marine and Environmental Biology, Dornsife College of Letters, Arts, and Sciences, University of Southern California Los Angeles, CA, USA.

The formation and maintenance of deep-sea ferromanganese/polymetallic nodules still remains a mystery 140 years after their discovery. The wealth of rare metals concentrated in these nodules has spurred global interest in exploring the mining potential of these resources. The prevailing theory of abiotic formation has been called into question and the role of microbial metabolisms in nodule development is now an area of active research. To understand the community structure of microbes associated with nodules and their surrounding sediment, we performed targeted sequencing of the V4 hypervariable region of the 16S rRNA gene from three nodules collected from the central South Pacific. Results have shown that the microbial communities of the nodules are significantly distinct from the communities in the surrounding sediments, and that the interiors of the nodules harbor communities different from the exterior. This suggests not only differences in potential metabolisms between the nodule and sediment communities, but also differences in the dominant metabolisms of interior and exterior communities. We identified several operational taxonomic units (OTUs) unique to both the nodule and sediment environments. The identified OTUs were assigned putative taxonomic identifications, including two OTUs only found associated with the nodules, which were assigned to the α-Proteobacteria. Finally, we explored the diversity of the most assigned taxonomic group, the Thaumarchaea MG-1, which revealed novel OTUs compared to previous research from the region and suggests a potential role as a source of fixed carbon for ammonia oxidizing archaea in the environment.
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http://dx.doi.org/10.3389/fmicb.2013.00161DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3691505PMC
June 2013

Prospects for the study of evolution in the deep biosphere.

Front Microbiol 2011 24;2:285. Epub 2012 Jan 24.

College of Earth, Ocean and the Environment, University of Delaware Lewes, DE, USA.

Since the days of Darwin, scientists have used the framework of the theory of evolution to explore the interconnectedness of life on Earth and adaptation of organisms to the ever-changing environment. The advent of molecular biology has advanced and accelerated the study of evolution by allowing direct examination of the genetic material that ultimately determines the phenotypes upon which selection acts. The study of evolution has been furthered through examination of microbial evolution, with large population numbers, short generation times, and easily extractable DNA. Such work has spawned the study of microbial biogeography, with the realization that concepts developed in population genetics may be applicable to microbial genomes (Martiny et al., 2006; Manhes and Velicer, 2011). Microbial biogeography and adaptation has been examined in many different environments. Here we argue that the deep biosphere is a unique environment for the study of evolution and list specific factors that can be considered and where the studies may be performed. This publication is the result of the NSF-funded Center for Dark Energy Biosphere Investigations (C-DEBI) theme team on Evolution (www.darkenergybiosphere.org).
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http://dx.doi.org/10.3389/fmicb.2011.00285DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3265032PMC
October 2012

Metagenomic analysis of a complex marine planktonic thaumarchaeal community from the Gulf of Maine.

Environ Microbiol 2012 Jan 3;14(1):254-67. Epub 2011 Nov 3.

Department of Biological Sciences, David and Dana Dornsife College of Letters, Arts and Sciences, University of Southern California, 3616 Trousdale Parkway, Los Angeles, CA 90089, USA.

Thaumarchaea, which represent as much as 20% of prokaryotic biomass in the open ocean, have been linked to environmentally relevant biogeochemical processes, such as ammonia oxidation (nitrification) and inorganic carbon fixation. We have used culture-independent methods to study this group because current cultivation limitations have proved a hindrance in studying these organisms. From a metagenomic data set obtained from surface waters from the Gulf of Maine, we have identified 36,111 sequence reads (containing 30 Mbp) likely derived from environmental planktonic Thaumarchaea. Metabolic analysis of the raw sequences and assemblies identified copies of the catalytic subunit required in aerobic ammonia oxidation. In addition, genes that comprise a nearly complete carbon assimilation pathway in the form of the 3-hyroxypropionate/4-hydroxybutyrate cycle were identified. Comparative genomics contrasting the putative environmental thaumarchaeal sequences and 'Candidatus Nitrosopumilus maritimus SCM1' revealed a number of genomic islands absent in the Gulf of Maine population. Analysis of these genomic islands revealed an integrase-associated island also found in distantly related microbial species, variations in the abundance of genes predicted to be important in thaumarchaeal respiratory chain, and the absence of a high-affinity phosphate uptake operon. Analysis of the underlying sequence diversity suggests the presence of at least two dominant environmental populations. Attempts to assemble complete environmental genomes were unsuccessful, but analysis of scaffolds revealed two diverging populations, including a thaumarchaeal-related scaffold with the full urease operon. Ultimately, the analysis revealed a number of insights into the metabolic potential of a predominantly uncultivated lineage of organisms. The predicted functions in the thaumarchaeal metagenomic sequences are directly supported by historic measurements of nutrient concentrations and provide new avenues of research in regards to understanding the role Thaumarchaea play in the environment.
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http://dx.doi.org/10.1111/j.1462-2920.2011.02628.xDOI Listing
January 2012