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Krinos AI, Cohen NR, Follows MJ, Alexander H. Reverse engineering environmental metatranscriptomes clarifies best practices for eukaryotic assembly. BMC Bioinformatics 2023; 24:74. [PMID: 36869298 PMCID: PMC9983209 DOI: 10.1186/s12859-022-05121-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 12/21/2022] [Indexed: 03/05/2023] Open
Abstract
BACKGROUND Diverse communities of microbial eukaryotes in the global ocean provide a variety of essential ecosystem services, from primary production and carbon flow through trophic transfer to cooperation via symbioses. Increasingly, these communities are being understood through the lens of omics tools, which enable high-throughput processing of diverse communities. Metatranscriptomics offers an understanding of near real-time gene expression in microbial eukaryotic communities, providing a window into community metabolic activity. RESULTS Here we present a workflow for eukaryotic metatranscriptome assembly, and validate the ability of the pipeline to recapitulate real and manufactured eukaryotic community-level expression data. We also include an open-source tool for simulating environmental metatranscriptomes for testing and validation purposes. We reanalyze previously published metatranscriptomic datasets using our metatranscriptome analysis approach. CONCLUSION We determined that a multi-assembler approach improves eukaryotic metatranscriptome assembly based on recapitulated taxonomic and functional annotations from an in-silico mock community. The systematic validation of metatranscriptome assembly and annotation methods provided here is a necessary step to assess the fidelity of our community composition measurements and functional content assignments from eukaryotic metatranscriptomes.
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Affiliation(s)
- Arianna I Krinos
- MIT-WHOI Joint Program in Oceanography and Applied Ocean Science and Engineering, Cambridge and Woods Hole, MA, USA. .,Department of Biology, Woods Hole Oceanographic Institution, Woods Hole, MA, USA. .,Department of Earth, Atmospheric, and Planetary Science, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Natalie R Cohen
- Skidaway Institute of Oceanography, University of Georgia, Savannah, GA, USA
| | - Michael J Follows
- Department of Earth, Atmospheric, and Planetary Science, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Harriet Alexander
- Department of Biology, Woods Hole Oceanographic Institution, Woods Hole, MA, USA.
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Berta-Thompson JW, Thomas E, Cubillos-Ruiz A, Hackl T, Becker JW, Coe A, Biller SJ, Berube PM, Chisholm SW. Draft genomes of three closely related low light-adapted Prochlorococcus. BMC Genom Data 2023; 24:11. [PMID: 36829130 PMCID: PMC9951446 DOI: 10.1186/s12863-022-01103-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Accepted: 12/21/2022] [Indexed: 02/26/2023] Open
Abstract
OBJECTIVES The marine cyanobacterium Prochlorococcus is a critical part of warm ocean ecosystems and a model for studying microbial evolution and ecology. To expand the representation of this organism's vast wild diversity in sequence collections, we performed a set of isolation efforts targeting low light-adapted Prochlorococcus. Three genomes resulting from this larger body of work are described here. DATA DESCRIPTION We present draft-quality Prochlorococcus genomes from enrichment cultures P1344, P1361, and P1363, sampled in the North Pacific. The genomes were built from Illumina paired reads assembled de novo. Supporting datasets of raw reads, assessments, and sequences from co-enriched heterotrophic marine bacteria are also provided. These three genomes represent members of the low light-adapted LLIV Prochlorococcus clade that are closely related, with 99.9% average nucleotide identity between pairs, yet vary in gene content. Expanding the powerful toolkit of Prochlorococcus genomes, these sequences provide an opportunity to study fine-scale variation and microevolutionary processes.
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Affiliation(s)
- Jessie W Berta-Thompson
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA. .,Department of Research and Conservation, Denver Botanic Gardens, Denver, CO, 80206, USA.
| | - Elaina Thomas
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.,School of Oceanography, University of Washington, Seattle, WA, 98195, USA
| | - Andrés Cubillos-Ruiz
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Thomas Hackl
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.,Groningen Institute of Evolutionary Life Sciences, University of Groningen, Groningen, 9700 CC, The Netherlands
| | - Jamie W Becker
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.,Department of Science and Mathematics, Alvernia University, Reading, PA, 19607, USA
| | - Allison Coe
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Steven J Biller
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.,Department of Biological Sciences, Wellesley College, Wellesley, MA, 02481, USA
| | - Paul M Berube
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Sallie W Chisholm
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA. .,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
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Doss JH, Barekzi N, Gauthier DT. Improving high-throughput techniques for bacteriophage discovery in multi-well plates. J Microbiol Methods 2022; 200:106542. [PMID: 35882287 DOI: 10.1016/j.mimet.2022.106542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 06/21/2022] [Accepted: 07/16/2022] [Indexed: 10/16/2022]
Abstract
Bacteriophages (also called phages) are viruses of bacteria that have numerous applications in medicine, agriculture, ecology, and molecular biology. With the increasing interest in phages for their many uses, it is now especially important to make phage discovery more efficient and economical. Using the host Mycobacterium smegmatis mc2155, which is a model organism for phage discovery research and is closely related to important pathogens of humans and other animals, we investigated three procedures that are an integral part of phage discovery: enrichment of environmental samples, phage isolation and detection (which can also be used for host range determination), and phage purification. Enrichment in 6-well plates was successful with most environmental samples, and enrichment in 24- and 96-well plates was successful with some environmental samples, demonstrating that larger sample volumes are preferred when possible, but smaller sample volumes may be acceptable if the starting concentration of phages is sufficiently high. Measuring absorbance in multi-well plates was at least as sensitive as the traditional plaque assay for the detection of phages. We also demonstrated a technique for the purification of single phage types from mixed cultures in liquid medium. Multi-well techniques can be used as alternatives or complementary approaches to traditional methods of phage discovery and characterization depending on the needs of the researcher in terms of time, available resources, host species, phage-bacteria matches, and specific goals. In the future, these techniques could be applied to the discovery of phages of aquatic mycobacteria and other hosts for which few phages have currently been isolated.
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Affiliation(s)
- Janis H Doss
- The Association of Public Health Laboratories, Silver Spring, MD, USA.
| | - Nazir Barekzi
- Department of Biology, Norfolk State University, Norfolk, VA, USA.
| | - David T Gauthier
- Department of Biological Sciences, Old Dominion University, Norfolk, VA, USA.
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Fernandes L, Jesus H, Almeida P, Sandrini J, Bianchini A, Santos H. The influence of the Doce River mouth on the microbiome of nearby coastal areas three years after the Fundão Dam failure, Brazil. Sci Total Environ 2022; 807:151777. [PMID: 34808168 DOI: 10.1016/j.scitotenv.2021.151777] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 10/14/2021] [Accepted: 11/14/2021] [Indexed: 06/13/2023]
Abstract
The failure of the Fundão Dam, considered the world's largest mining disaster, released more than 55 million m3 of ore tailings into the environment. The sediment plume formed by water and tailings spread along approximately 663 km of water bodies of the Doce River basin. It reached the Atlantic Ocean sixteen days after the dam failure. However, the effects of the dam failure in the marine coastal areas years after the disaster are still unknown. This study aims to evaluate water and sediment microbial communities of nearby coastal areas three years after the Fundão Dam failure, using 16S rRNA gene amplicon sequencing. A total of 441 samples from 25 locations were collected during two different seasons (dry and rainy). The results showed that the Doce River mouth seems to divide the microbial communities from the southern and northern stations into two groups. The plume of sediments from the Doce River seems to be impacting the marine microbiome even at the furthest sampling stations. Bacterial (Anaerolineaceae, Thermodesulfovibrionia and Rhodopirellula) and Archaeal (Bathyarchaeia and Woesearchaeia) taxa, found in high abundance in the sediment of the Doce River mouth, have been previously described in high abundance in heavy metal contaminated sediments, including the Doce River itself and in mine tailing sediments. Cyanobium, found in great abundance in the water samples from the Doce River mouth, was also reported as the most abundant in the water of the Doce River after the Fundão Dam failure. Overall, the farther from the Doce River mouth the sample was, the lower the relative abundances of these taxa were. These results provide strong evidence that the sediment plume released by the Fundão Dam failure is probably impacting the marine microbiome of nearby coastal areas, even three years after the dam failure.
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Affiliation(s)
- Luanny Fernandes
- Department of Marine Biology, Fluminense Federal University - UFF, St. Professor Marcos Waldemar de Freitas Reis, Niterói, RJ 24210-201, Brazil
| | - Hugo Jesus
- Department of Marine Biology, Fluminense Federal University - UFF, St. Professor Marcos Waldemar de Freitas Reis, Niterói, RJ 24210-201, Brazil
| | - Pedro Almeida
- Department of Marine Biology, Fluminense Federal University - UFF, St. Professor Marcos Waldemar de Freitas Reis, Niterói, RJ 24210-201, Brazil
| | - Juliana Sandrini
- Instituto de Ciências Biológicas, Universidade Federal do Rio Grande - FURG, Av. Itália, s/n, Carreiros, Rio Grande, RS 96203-900, Brazil
| | - Adalto Bianchini
- Instituto de Ciências Biológicas, Universidade Federal do Rio Grande - FURG, Av. Itália, s/n, Carreiros, Rio Grande, RS 96203-900, Brazil; Coral Vivo Institute, Rio de Janeiro, Brazil
| | - Henrique Santos
- Department of Marine Biology, Fluminense Federal University - UFF, St. Professor Marcos Waldemar de Freitas Reis, Niterói, RJ 24210-201, Brazil; Coral Vivo Institute, Rio de Janeiro, Brazil.
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Lydon KA, Lipp EK. Taxonomic annotation errors incorrectly assign the family Pseudoalteromonadaceae to the order Vibrionales in Greengenes: implications for microbial community assessments. PeerJ 2018; 6:e5248. [PMID: 30018864 PMCID: PMC6044269 DOI: 10.7717/peerj.5248] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 06/26/2018] [Indexed: 02/01/2023] Open
Abstract
Next-generation sequencing has provided powerful tools to conduct microbial ecology studies. Analysis of community composition relies on annotated databases of curated sequences to provide taxonomic assignments; however, these databases occasionally have errors with implications for downstream analyses. Systemic taxonomic errors were discovered in Greengenes database (v13_5 and 13_8) related to orders Vibrionales and Alteromonadales. These orders have family level annotations that were erroneous at least one taxonomic level, e.g., 100% of sequences assigned to the Pseudoalteromonadaceae family were placed improperly in Vibrionales (rather than Alteromonadales) and >20% of these sequences were indeed Vibrio spp. but were improperly assigned to the Pseudoalteromonadaceae family (rather than to Vibrionaceae). Use of this database is common; we identified 68 peer-reviewed papers since 2013 that likely included erroneous annotations specifically associated with Vibrionales and Pseudoalteromonadaceae, with 20 explicitly stating the incorrect taxonomy. Erroneous assignments using these specific versions of Greengenes can lead to incorrect conclusions, especially in marine systems where these taxa are commonly encountered as conditionally rare organisms and potential pathogens.
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Affiliation(s)
- Keri Ann Lydon
- Department of Environmental Health Science, University of Georgia, Athens, GA, USA
| | - Erin K. Lipp
- Department of Environmental Health Science, University of Georgia, Athens, GA, USA
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Abstract
In the late nineteenth century, French naturalists were global leaders in microbial research. Louis Pasteur advanced sterilization techniques and demonstrated that dust particles in the air could contaminate a putrefiable liquid. Pasteur's discoveries prompted a new research program for the naturalists of the Talisman and Travailleur expeditions: to recover uncontaminated water and mud samples from the deep sea. French naturalists Adrien Certes and Paul Regnard both independently conducted experiments to address the question of whether microorganisms inhabited the oceans and whether organic material in the deep sea was subject to decomposition. The experiments of Certes and Regnard have largely been omitted from histories of microbiology and marine science. However, an examination of their work is crucial for understanding the context in which marine microbiology first developed. At the end of the nineteenth century, marine microbiology emerged from the disciplinary melding of terrestrial microbial ecology, experimental physiology, and the then-nascent field of deep-sea biology.
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Affiliation(s)
- Antony Adler
- History Department, Carleton College, Northfield, MN, USA.
| | - Erik Dücker
- Center for the History of Philosophy and Science, Radboud University Nijmegen, Nijmegen, The Netherlands
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Nielsen S, Wilkes Walburn J, Vergés A, Thomas T, Egan S. Microbiome patterns across the gastrointestinal tract of the rabbitfish Siganus fuscescens. PeerJ 2017; 5:e3317. [PMID: 28533966 PMCID: PMC5437856 DOI: 10.7717/peerj.3317] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Accepted: 04/14/2017] [Indexed: 12/22/2022] Open
Abstract
Most of our knowledge regarding the biodiversity of gut microbes comes from terrestrial organisms or marine species of economic value, with less emphasis on ecologically important species. Here we investigate the bacterial composition associated with the gut of Siganus fuscescens, a rabbitfish that plays an important ecological role in coastal ecosystems by consuming seaweeds. Members of Firmicutes, Bacteroidetes and delta-Proteobacteria were among the dominant taxa across samples taken from the contents and the walls (sites) of the midgut and hindgut (location). Despite the high variability among individual fish, we observed statistically significant differences in beta-diversity between gut sites and gut locations. Some bacterial taxa low in abundance in the midgut content (e.g., Desulfovibrio) were found in greater abundances on the midgut wall and within the hindgut, suggesting that the gut may select for specific groups of environmental and/or food-associated microorganisms. In contrast, some distinct taxa present in the midgut content (e.g., Synechococcus) were noticeably reduced in the midgut wall and hindgut, and are thus likely to be representative of transient microbiota. This is the first assessment of the bacterial diversity associated with the gut of S. fuscescens and highlights the need to consider the variability across different gut locations and sites when analyzing fish gut microbiomes.
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Affiliation(s)
- Shaun Nielsen
- Centre for Marine Bio-Innovation and School of Biological Earth and Environmental Sciences, University of New South Wales, Sydney, Australia
| | - Jackson Wilkes Walburn
- Centre for Marine Bio-Innovation and School of Biological Earth and Environmental Sciences, University of New South Wales, Sydney, Australia
| | - Adriana Vergés
- Centre for Marine Bio-Innovation and School of Biological Earth and Environmental Sciences, University of New South Wales, Sydney, Australia
| | - Torsten Thomas
- Centre for Marine Bio-Innovation and School of Biological Earth and Environmental Sciences, University of New South Wales, Sydney, Australia
| | - Suhelen Egan
- Centre for Marine Bio-Innovation and School of Biological Earth and Environmental Sciences, University of New South Wales, Sydney, Australia
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Abstract
Biosurfactants produced by biofilm-forming bacteria have great applications in biotechnology, pharmaceutical, food engineering, bioremediation, and biohydrometallurgy industries. This study aimed to find out the bacteria that produce novel exopolymers (EPSs) which can find potential role in oil biodegradation. A screening procedure was performed to detect EPS-producing bacteria. The EPS producing isolate was identified as Acinetobacter species by 16S rDNA analysis. The polymer produced by the isolate has shown significant emulsification and surfactant activities, and the activities were compared to some of the commercial emulsifiers. The EPS has been partially characterized by FTIR analysis and has been proved to be a glycolipoprotein. This is one of the very few reports on Acinetobacter species producing EPS with surfactant properties.
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Colatriano D, Ramachandran A, Yergeau E, Maranger R, Gélinas Y, Walsh DA. Metaproteomics of aquatic microbial communities in a deep and stratified estuary. Proteomics 2015. [PMID: 26223443 DOI: 10.1002/pmic.201500079] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Here we harnessed the power of metaproteomics to assess the metabolic diversity and function of stratified aquatic microbial communities in the deep and expansive Lower St. Lawrence Estuary, located in eastern Canada. Vertical profiling of the microbial communities through the stratified water column revealed differences in metabolic lifestyles and in carbon and nitrogen processing pathways. In productive surface waters, we identified heterotrophic populations involved in the processing of high and low molecular weight organic matter from both terrestrial (e.g. cellulose and xylose) and marine (e.g. organic compatible osmolytes) sources. In the less productive deep waters, chemosynthetic production coupled to nitrification by MG-I Thaumarchaeota and Nitrospina appeared to be a dominant metabolic strategy. Similar to other studies of the coastal ocean, we identified methanol oxidation proteins originating from the common OM43 marine clade. However, we also identified a novel lineage of methanol-oxidizers specifically in the particle-rich bottom (i.e. nepheloid) layer. Membrane transport proteins assigned to the uncultivated MG-II Euryarchaeota were also specifically detected in the nepheloid layer. In total, these results revealed strong vertical structure of microbial taxa and metabolic activities, as well as the presence of specific "nepheloid" taxa that may contribute significantly to coastal ocean nutrient cycling.
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Affiliation(s)
- David Colatriano
- Department of Biology, Concordia University, Montreal, Quebec, Canada
| | | | - Etienne Yergeau
- National Research Council Canada, Energy, Mining and Environment, Montreal, Quebec, Canada
| | - Roxane Maranger
- Département des Sciences Biologiques, Université de Montréal, Montréal, Quebec, Canada.,Groupe de Recherche Interuniversitaire en Limnologie (GRIL), Montreal, Quebec, Canada
| | - Yves Gélinas
- Department of Chemistry and Biochemistry, Concordia University, Montreal, Quebec, Canada.,Geochemistry and Geodynamics Research Center (GEOTOP), Montreal, Quebec, Canada
| | - David A Walsh
- Department of Biology, Concordia University, Montreal, Quebec, Canada.,Groupe de Recherche Interuniversitaire en Limnologie (GRIL), Montreal, Quebec, Canada.,Canadian Institute for Advanced Research, Integrated Microbial Biodiversity Program, Toronto ON, Canada
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Dogs M, Teshima H, Petersen J, Fiebig A, Chertkov O, Dalingault H, Chen A, Pati A, Goodwin LA, Chain P, Detter JC, Ivanova N, Lapidus A, Rohde M, Gronow S, Kyrpides NC, Woyke T, Simon M, Göker M, Klenk HP, Brinkhoff T. Genome sequence of Phaeobacter daeponensis type strain (DSM 23529(T)), a facultatively anaerobic bacterium isolated from marine sediment, and emendation of Phaeobacter daeponensis. Stand Genomic Sci 2013; 9:142-59. [PMID: 24501652 PMCID: PMC3910554 DOI: 10.4056/sigs.4287962] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
TF-218T is the type strain of the species Phaeobacter daeponensis Yoon et al. 2007, a facultatively anaerobic Phaeobacter species isolated from tidal flats. Here we describe the draft genome sequence and annotation of this bacterium together with previously unreported aspects of its phenotype. We analyzed the genome for genes involved in secondary metabolite production and its anaerobic lifestyle, which have also been described for its closest relative Phaeobacter caeruleus. The 4,642,596 bp long genome of strain TF-218T contains 4,310 protein-coding genes and 78 RNA genes including four rRNA operons and consists of five replicons: one chromosome and four extrachromosomal elements with sizes of 276 kb, 174 kb, 117 kb and 90 kb. Genome analysis showed that TF-218T possesses all of the genes for indigoidine biosynthesis, and on specific media the strain showed a blue pigmentation. We also found genes for dissimilatory nitrate reduction, gene-transfer agents, NRPS/ PKS genes and signaling systems homologous to the LuxR/I system.
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Affiliation(s)
- Marco Dogs
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Hazuki Teshima
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Jörn Petersen
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Anne Fiebig
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Olga Chertkov
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Hajnalka Dalingault
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Amy Chen
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Amrita Pati
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Lynne A Goodwin
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA ; DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Patrick Chain
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - John C Detter
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA ; DOE Joint Genome Institute, Walnut Creek, California, USA
| | | | - Alla Lapidus
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Manfred Rohde
- HZI - Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Sabine Gronow
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | | | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Meinhard Simon
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Markus Göker
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Hans-Peter Klenk
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Thorsten Brinkhoff
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
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