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Van Den Berghe M, Walworth NG, Dalvie NC, Dupont CL, Springer M, Andrews MG, Romaniello SJ, Hutchins DA, Montserrat F, Silver PA, Nealson KH. Microbial Catalysis for CO 2 Sequestration: A Geobiological Approach. Cold Spring Harb Perspect Biol 2024; 16:a041673. [PMID: 37788887 PMCID: PMC11065169 DOI: 10.1101/cshperspect.a041673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
One of the greatest threats facing the planet is the continued increase in excess greenhouse gasses, with CO2 being the primary driver due to its rapid increase in only a century. Excess CO2 is exacerbating known climate tipping points that will have cascading local and global effects including loss of biodiversity, global warming, and climate migration. However, global reduction of CO2 emissions is not enough. Carbon dioxide removal (CDR) will also be needed to avoid the catastrophic effects of global warming. Although the drawdown and storage of CO2 occur naturally via the coupling of the silicate and carbonate cycles, they operate over geological timescales (thousands of years). Here, we suggest that microbes can be used to accelerate this process, perhaps by orders of magnitude, while simultaneously producing potentially valuable by-products. This could provide both a sustainable pathway for global drawdown of CO2 and an environmentally benign biosynthesis of materials. We discuss several different approaches, all of which involve enhancing the rate of silicate weathering. We use the silicate mineral olivine as a case study because of its favorable weathering properties, global abundance, and growing interest in CDR applications. Extensive research is needed to determine both the upper limit of the rate of silicate dissolution and its potential to economically scale to draw down significant amounts (Mt/Gt) of CO2 Other industrial processes have successfully cultivated microbial consortia to provide valuable services at scale (e.g., wastewater treatment, anaerobic digestion, fermentation), and we argue that similar economies of scale could be achieved from this research.
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Affiliation(s)
| | - Nathan G Walworth
- Vesta, San Francisco, California 94114, USA
- University of Southern California, Los Angeles, California 90007, USA
- Department of Environment and Sustainability, J. Craig Venter Institute, La Jolla, California 92037, USA
| | - Neil C Dalvie
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Chris L Dupont
- Department of Environment and Sustainability, J. Craig Venter Institute, La Jolla, California 92037, USA
- Department of Human Biology and Genomic Medicine, J. Craig Venter Institute, La Jolla, California 92037, USA
| | - Michael Springer
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | | | | | - David A Hutchins
- University of Southern California, Los Angeles, California 90007, USA
| | | | - Pamela A Silver
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Kenneth H Nealson
- Vesta, San Francisco, California 94114, USA
- University of Southern California, Los Angeles, California 90007, USA
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2
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Gambogi CW, Birchak GJ, Mer E, Brown DM, Yankson G, Kixmoeller K, Gavade JN, Espinoza JL, Kashyap P, Dupont CL, Logsdon GA, Heun P, Glass JI, Black BE. Efficient formation of single-copy human artificial chromosomes. Science 2024; 383:1344-1349. [PMID: 38513017 PMCID: PMC11059994 DOI: 10.1126/science.adj3566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 01/23/2024] [Indexed: 03/23/2024]
Abstract
Large DNA assembly methodologies underlie milestone achievements in synthetic prokaryotic and budding yeast chromosomes. While budding yeast control chromosome inheritance through ~125-base pair DNA sequence-defined centromeres, mammals and many other eukaryotes use large, epigenetic centromeres. Harnessing centromere epigenetics permits human artificial chromosome (HAC) formation but is not sufficient to avoid rampant multimerization of the initial DNA molecule upon introduction to cells. We describe an approach that efficiently forms single-copy HACs. It employs a ~750-kilobase construct that is sufficiently large to house the distinct chromatin types present at the inner and outer centromere, obviating the need to multimerize. Delivery to mammalian cells is streamlined by employing yeast spheroplast fusion. These developments permit faithful chromosome engineering in the context of metazoan cells.
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Affiliation(s)
- Craig W. Gambogi
- Department of Biochemistry and Biophysics
- Graduate Program in Biochemistry and Molecular Biophysics
- Penn Center for Genome Integrity
- Epigenetics Institute
| | - Gabriel J. Birchak
- Department of Biochemistry and Biophysics
- Graduate Program in Biochemistry and Molecular Biophysics
- Penn Center for Genome Integrity
- Graduate Program in Cell and Molecular Biology Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104 USA
| | - Elie Mer
- Department of Biochemistry and Biophysics
- Graduate Program in Biochemistry and Molecular Biophysics
- Penn Center for Genome Integrity
- Epigenetics Institute
| | | | - George Yankson
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Kathryn Kixmoeller
- Department of Biochemistry and Biophysics
- Graduate Program in Biochemistry and Molecular Biophysics
- Penn Center for Genome Integrity
- Epigenetics Institute
| | - Janardan N. Gavade
- Department of Biochemistry and Biophysics
- Penn Center for Genome Integrity
- Epigenetics Institute
| | | | - Prakriti Kashyap
- Department of Biochemistry and Biophysics
- Penn Center for Genome Integrity
- Epigenetics Institute
| | | | - Glennis A. Logsdon
- Department of Biochemistry and Biophysics
- Graduate Program in Biochemistry and Molecular Biophysics
- Penn Center for Genome Integrity
- Epigenetics Institute
| | - Patrick Heun
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | | | - Ben E. Black
- Department of Biochemistry and Biophysics
- Graduate Program in Biochemistry and Molecular Biophysics
- Penn Center for Genome Integrity
- Epigenetics Institute
- Graduate Program in Cell and Molecular Biology Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104 USA
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3
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Espinoza JL, Phillips A, Prentice MB, Tan GS, Kamath PL, Lloyd KG, Dupont CL. Unveiling the Microbial Realm with VEBA 2.0: A modular bioinformatics suite for end-to-end genome-resolved prokaryotic, (micro)eukaryotic, and viral multi-omics from either short- or long-read sequencing. bioRxiv 2024:2024.03.08.583560. [PMID: 38559265 PMCID: PMC10979853 DOI: 10.1101/2024.03.08.583560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
The microbiome is a complex community of microorganisms, encompassing prokaryotic (bacterial and archaeal), eukaryotic, and viral entities. This microbial ensemble plays a pivotal role in influencing the health and productivity of diverse ecosystems while shaping the web of life. However, many software suites developed to study microbiomes analyze only the prokaryotic community and provide limited to no support for viruses and microeukaryotes. Previously, we introduced the Viral Eukaryotic Bacterial Archaeal (VEBA) open-source software suite to address this critical gap in microbiome research by extending genome-resolved analysis beyond prokaryotes to encompass the understudied realms of eukaryotes and viruses. Here we present VEBA 2.0 with key updates including a comprehensive clustered microeukaryotic protein database, rapid genome/protein-level clustering, bioprospecting, non-coding/organelle gene modeling, genome-resolved taxonomic/pathway profiling, long-read support, and containerization. We demonstrate VEBA's versatile application through the analysis of diverse case studies including marine water, Siberian permafrost, and white-tailed deer lung tissues with the latter showcasing how to identify integrated viruses. VEBA represents a crucial advancement in microbiome research, offering a powerful and accessible platform that bridges the gap between genomics and biotechnological solutions.
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Affiliation(s)
- Josh L. Espinoza
- Department of Environment and Sustainability, J. Craig Venter Institute, La Jolla, CA 92037, USA
- Department of Genomic Medicine and Infectious Diseases, J. Craig Venter Institute, La Jolla, CA 92037, USA
| | - Allan Phillips
- Department of Environment and Sustainability, J. Craig Venter Institute, La Jolla, CA 92037, USA
- Department of Genomic Medicine and Infectious Diseases, J. Craig Venter Institute, La Jolla, CA 92037, USA
| | | | - Gene S. Tan
- Department of Genomic Medicine and Infectious Diseases, J. Craig Venter Institute, La Jolla, CA 92037, USA
| | - Pauline L. Kamath
- School of Food and Agriculture, University of Maine, Orono, ME 04469, USA
| | - Karen G. Lloyd
- Microbiology Department, University of Tennessee, Knoxville, TN 37917, USA
| | - Chris L. Dupont
- Department of Environment and Sustainability, J. Craig Venter Institute, La Jolla, CA 92037, USA
- Department of Genomic Medicine and Infectious Diseases, J. Craig Venter Institute, La Jolla, CA 92037, USA
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4
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Walworth NG, Espinoza JL, Argyle PA, Hinners J, Levine NM, Doblin MA, Dupont CL, Collins S. Genus-Wide Transcriptional Landscapes Reveal Correlated Gene Networks Underlying Microevolutionary Divergence in Diatoms. Mol Biol Evol 2023; 40:msad218. [PMID: 37874344 PMCID: PMC10595192 DOI: 10.1093/molbev/msad218] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 08/24/2023] [Accepted: 09/21/2023] [Indexed: 10/25/2023] Open
Abstract
Marine microbes like diatoms make up the base of marine food webs and drive global nutrient cycles. Despite their key roles in ecology, biogeochemistry, and biotechnology, we have limited empirical data on how forces other than adaptation may drive diatom diversification, especially in the absence of environmental change. One key feature of diatom populations is frequent extreme reductions in population size, which can occur both in situ and ex situ as part of bloom-and-bust growth dynamics. This can drive divergence between closely related lineages, even in the absence of environmental differences. Here, we combine experimental evolution and transcriptome landscapes (t-scapes) to reveal repeated evolutionary divergence within several species of diatoms in a constant environment. We show that most of the transcriptional divergence can be captured on a reduced set of axes, and that repeatable evolution can occur along a single major axis of variation defined by core ortholog expression comprising common metabolic pathways. Previous work has associated specific transcriptional changes in gene networks with environmental factors. Here, we find that these same gene networks diverge in the absence of environmental change, suggesting these pathways may be central in generating phenotypic diversity as a result of both selective and random evolutionary forces. If this is the case, these genes and the functions they encode may represent universal axes of variation. Such axes that capture suites of interacting transcriptional changes during diversification improve our understanding of both global patterns in local adaptation and microdiversity, as well as evolutionary forces shaping algal cultivation.
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Affiliation(s)
- Nathan G Walworth
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089-0371, USA
- J.Craig Venter Institute, La Jolla, CA 92037, USA
| | | | - Phoebe A Argyle
- Climate Change Cluster, University of Technology Sydney, Sydney, New South Wales 2007, Australia
| | - Jana Hinners
- School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
- Helmholtz-Zentrum Hereon, 21502 Geesthacht, Germany
| | - Naomi M Levine
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089-0371, USA
| | - Martina A Doblin
- Climate Change Cluster, University of Technology Sydney, Sydney, New South Wales 2007, Australia
| | | | - Sinéad Collins
- School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
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5
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Espinoza JL, Torralba M, Leong P, Saffery R, Bockmann M, Kuelbs C, Singh S, Hughes T, Craig JM, Nelson KE, Dupont CL. Differential network analysis of oral microbiome metatranscriptomes identifies community scale metabolic restructuring in dental caries. PNAS Nexus 2022; 1:pgac239. [PMID: 36712365 PMCID: PMC9802336 DOI: 10.1093/pnasnexus/pgac239] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 10/14/2022] [Indexed: 11/05/2022]
Abstract
Dental caries is a microbial disease and the most common chronic health condition, affecting nearly 3.5 billion people worldwide. In this study, we used a multiomics approach to characterize the supragingival plaque microbiome of 91 Australian children, generating 658 bacterial and 189 viral metagenome-assembled genomes with transcriptional profiling and gene-expression network analysis. We developed a reproducible pipeline for clustering sample-specific genomes to integrate metagenomics and metatranscriptomics analyses regardless of biosample overlap. We introduce novel feature engineering and compositionally-aware ensemble network frameworks while demonstrating their utility for investigating regime shifts associated with caries dysbiosis. These methods can be applied when differential abundance modeling does not capture statistical enrichments or the results from such analysis are not adequate for providing deeper insight into disease. We identified which organisms and metabolic pathways were central in a coexpression network as well as how these networks were rewired between caries and caries-free phenotypes. Our findings provide evidence of a core bacterial microbiome that was transcriptionally active in the supragingival plaque of all participants regardless of phenotype, but also show highly diagnostic changes in the ways that organisms interact. Specifically, many organisms exhibit high connectedness with central carbon metabolism to Cardiobacterium and this shift serves a bridge between phenotypes. Our evidence supports the hypothesis that caries is a multifactorial ecological disease.
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Affiliation(s)
- Josh L Espinoza
- Department of Environment and Sustainability, J. Craig Venter Institute, La Jolla, CA 92037, USA,Department of Human Biology and Genomic Medicine, J. Craig Venter Institute, La Jolla, CA 92037, USA,Department of Human Biology and Genomic Medicine, J. Craig Venter Institute, Rockville, MD 20850, USA
| | - Manolito Torralba
- Department of Human Biology and Genomic Medicine, J. Craig Venter Institute, Rockville, MD 20850, USA
| | - Pamela Leong
- Epigenetics, Murdoch Children's Research Institute and Department of Paediatrics, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Richard Saffery
- Epigenetics, Murdoch Children's Research Institute and Department of Paediatrics, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Michelle Bockmann
- Adelaide Dental School, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Claire Kuelbs
- Department of Human Biology and Genomic Medicine, J. Craig Venter Institute, La Jolla, CA 92037, USA
| | - Suren Singh
- Department of Human Biology and Genomic Medicine, J. Craig Venter Institute, Rockville, MD 20850, USA
| | - Toby Hughes
- Adelaide Dental School, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Jeffrey M Craig
- Epigenetics, Murdoch Children's Research Institute and Department of Paediatrics, The University of Melbourne, Parkville, VIC 3052, Australia,IMPACT Strategic Research Centre, Deakin University School of Medicine, Geelong, VIC 3220, Australia
| | - Karen E Nelson
- Department of Human Biology and Genomic Medicine, J. Craig Venter Institute, La Jolla, CA 92037, USA,Department of Human Biology and Genomic Medicine, J. Craig Venter Institute, Rockville, MD 20850, USA
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6
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Espinoza JL, Dupont CL. VEBA: a modular end-to-end suite for in silico recovery, clustering, and analysis of prokaryotic, microeukaryotic, and viral genomes from metagenomes. BMC Bioinformatics 2022; 23:419. [PMID: 36224545 PMCID: PMC9554839 DOI: 10.1186/s12859-022-04973-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 09/27/2022] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND With the advent of metagenomics, the importance of microorganisms and how their interactions are relevant to ecosystem resilience, sustainability, and human health has become evident. Cataloging and preserving biodiversity is paramount not only for the Earth's natural systems but also for discovering solutions to challenges that we face as a growing civilization. Metagenomics pertains to the in silico study of all microorganisms within an ecological community in situ, however, many software suites recover only prokaryotes and have limited to no support for viruses and eukaryotes. RESULTS In this study, we introduce the Viral Eukaryotic Bacterial Archaeal (VEBA) open-source software suite developed to recover genomes from all domains. To our knowledge, VEBA is the first end-to-end metagenomics suite that can directly recover, quality assess, and classify prokaryotic, eukaryotic, and viral genomes from metagenomes. VEBA implements a novel iterative binning procedure and hybrid sample-specific/multi-sample framework that yields more genomes than any existing methodology alone. VEBA includes a consensus microeukaryotic database containing proteins from existing databases to optimize microeukaryotic gene modeling and taxonomic classification. VEBA also provides a unique clustering-based dereplication strategy allowing for sample-specific genomes and genes to be directly compared across non-overlapping biological samples. Finally, VEBA is the only pipeline that automates the detection of candidate phyla radiation bacteria and implements the appropriate genome quality assessments. VEBA's capabilities are demonstrated by reanalyzing 3 existing public datasets which recovered a total of 948 MAGs (458 prokaryotic, 8 eukaryotic, and 482 viral) including several uncharacterized organisms and organisms with no public genome representatives. CONCLUSIONS The VEBA software suite allows for the in silico recovery of microorganisms from all domains of life by integrating cutting edge algorithms in novel ways. VEBA fully integrates both end-to-end and task-specific metagenomic analysis in a modular architecture that minimizes dependencies and maximizes productivity. The contributions of VEBA to the metagenomics community includes seamless end-to-end metagenomics analysis but also provides users with the flexibility to perform specific analytical tasks. VEBA allows for the automation of several metagenomics steps and shows that new information can be recovered from existing datasets.
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Affiliation(s)
- Josh L. Espinoza
- Department of Environment and Sustainability, J. Craig Venter Institute, 4120 Capricorn Ln, La Jolla, CA 92037 USA
- Department of Human Biology and Genomic Medicine, J. Craig Venter Institute, La Jolla, CA 92037 USA
| | - Chris L. Dupont
- Department of Environment and Sustainability, J. Craig Venter Institute, 4120 Capricorn Ln, La Jolla, CA 92037 USA
- Department of Human Biology and Genomic Medicine, J. Craig Venter Institute, La Jolla, CA 92037 USA
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7
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Espinoza JL, Dupont CL, O’Rourke A, Beyhan S, Morales P, Spoering A, Meyer KJ, Chan AP, Choi Y, Nierman WC, Lewis K, Nelson KE. Predicting antimicrobial mechanism-of-action from transcriptomes: A generalizable explainable artificial intelligence approach. PLoS Comput Biol 2021; 17:e1008857. [PMID: 33780444 PMCID: PMC8031737 DOI: 10.1371/journal.pcbi.1008857] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 04/08/2021] [Accepted: 03/08/2021] [Indexed: 12/13/2022] Open
Abstract
To better combat the expansion of antibiotic resistance in pathogens, new compounds, particularly those with novel mechanisms-of-action [MOA], represent a major research priority in biomedical science. However, rediscovery of known antibiotics demonstrates a need for approaches that accurately identify potential novelty with higher throughput and reduced labor. Here we describe an explainable artificial intelligence classification methodology that emphasizes prediction performance and human interpretability by using a Hierarchical Ensemble of Classifiers model optimized with a novel feature selection algorithm called Clairvoyance; collectively referred to as a CoHEC model. We evaluated our methods using whole transcriptome responses from Escherichia coli challenged with 41 known antibiotics and 9 crude extracts while depositing 122 transcriptomes unique to this study. Our CoHEC model can properly predict the primary MOA of previously unobserved compounds in both purified forms and crude extracts at an accuracy above 99%, while also correctly identifying darobactin, a newly discovered antibiotic, as having a novel MOA. In addition, we deploy our methods on a recent E. coli transcriptomics dataset from a different strain and a Mycobacterium smegmatis metabolomics timeseries dataset showcasing exceptionally high performance; improving upon the performance metrics of the original publications. We not only provide insight into the biological interpretation of our model but also that the concept of MOA is a non-discrete heuristic with diverse effects for different compounds within the same MOA, suggesting substantial antibiotic diversity awaiting discovery within existing MOA.
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Affiliation(s)
- Josh L. Espinoza
- J. Craig Venter Institute, La Jolla, CA, United States of America
- Department of Applied Sciences, Durban University of Technology, Durban, South Africa
| | - Chris L. Dupont
- J. Craig Venter Institute, La Jolla, CA, United States of America
| | - Aubrie O’Rourke
- J. Craig Venter Institute, La Jolla, CA, United States of America
| | - Sinem Beyhan
- J. Craig Venter Institute, La Jolla, CA, United States of America
| | - Pavel Morales
- J. Craig Venter Institute, La Jolla, CA, United States of America
| | - Amy Spoering
- NovoBiotic Pharmaceuticals, Cambridge, MA, United States of America
| | - Kirsten J. Meyer
- Department of Biology, Northeastern University, Boston, MA, United States of America
| | - Agnes P. Chan
- J. Craig Venter Institute, Rockville, MD, United States of America
| | - Yongwook Choi
- J. Craig Venter Institute, Rockville, MD, United States of America
| | | | - Kim Lewis
- Department of Biology, Northeastern University, Boston, MA, United States of America
| | - Karen E. Nelson
- J. Craig Venter Institute, La Jolla, CA, United States of America
- Department of Applied Sciences, Durban University of Technology, Durban, South Africa
- J. Craig Venter Institute, Rockville, MD, United States of America
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8
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Lee MD, O'Rourke A, Lorenzi H, Bebout BM, Dupont CL, Everroad RC. Reference-guided metagenomics reveals genome-level evidence of potential microbial transmission from the ISS environment to an astronaut's microbiome. iScience 2021; 24:102114. [PMID: 33659879 PMCID: PMC7892915 DOI: 10.1016/j.isci.2021.102114] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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: 10/08/2020] [Revised: 11/22/2020] [Accepted: 01/22/2021] [Indexed: 11/16/2022] Open
Abstract
Monitoring microbial communities aboard the International Space Station (ISS) is essential to maintaining astronaut health and the integrity of life-support systems. Using assembled genomes of ISS-derived microbial isolates as references, recruiting metagenomic reads from an astronaut's nasal microbiome revealed no recruitment to a Staphylococcus aureus isolate from samples before launch, yet systematic recruitment across the genome when sampled after 3 months aboard the ISS, with a median percent identity of 100%. This suggests that either a highly similar S. aureus population colonized the astronaut's nasal microbiome while the astronaut was aboard the ISS or that it may have been below detection before spaceflight, instead supporting a shift in community composition. This work highlights the value in generating genomic libraries of microbes from built-environments such as the ISS and demonstrates one way such data can be integrated with metagenomics to facilitate the tracking and monitoring of astronaut microbiomes and health. Understanding built-environment microbiomes is critical for human space exploration Reference-guided metagenomics is a powerful approach for monitoring microbiomes We show potential microbial colonization of an astronaut microbiome while aboard the ISS
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Affiliation(s)
- Michael D Lee
- Exobiology Branch, NASA Ames Research Center, Mountain View, CA, USA.,Blue Marble Space Institute of Science, Seattle, WA, USA
| | - Aubrie O'Rourke
- Space Life Sciences, NASA Kennedy Space Center, Merritt Island, FL, USA
| | - Hernan Lorenzi
- Department of Infectious Diseases, J. Craig Venter Institute, Rockville, MD, USA
| | - Brad M Bebout
- Exobiology Branch, NASA Ames Research Center, Mountain View, CA, USA
| | | | - R Craig Everroad
- Exobiology Branch, NASA Ames Research Center, Mountain View, CA, USA
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9
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Breier JA, Jakuba MV, Saito MA, Dick GJ, Grim SL, Chan EW, McIlvin MR, Moran DM, Alanis BA, Allen AE, Dupont CL, Johnson R. Revealing ocean-scale biochemical structure with a deep-diving vertical profiling autonomous vehicle. Sci Robot 2020; 5:5/48/eabc7104. [PMID: 33239321 DOI: 10.1126/scirobotics.abc7104] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 10/21/2020] [Indexed: 12/25/2022]
Abstract
Vast and diverse microbial communities exist within the ocean. To better understand the global influence of these microorganisms on Earth's climate, we developed a robot capable of sampling dissolved and particulate seawater biochemistry across ocean basins while still capturing the fine-scale biogeochemical processes therein. Carbon and other nutrients are acquired and released by marine microorganisms as they build and break down organic matter. The scale of the ocean makes these processes globally relevant and, at the same time, challenging to fully characterize. Microbial community composition and ocean biochemistry vary across multiple physical scales up to that of the ocean basins. Other autonomous underwater vehicles are optimized for moving continuously and, primarily, horizontally through the ocean. In contrast, Clio, the robot that we describe, is designed to efficiently and precisely move vertically through the ocean, drift laterally in a Lagrangian manner to better observe water masses, and integrate with research vessel operations to map large horizontal scales to a depth of 6000 meters. We present results that show how Clio conducts high-resolution sensor surveys and sample return missions, including a mapping of 1144 kilometers of the Sargasso Sea to a depth of 1000 meters. We further show how the samples obtain filtered biomass from seawater that enable genomic and proteomic measurements not possible through in situ sensing. These results demonstrate a robotic oceanography approach for global-scale surveys of ocean biochemistry.
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Affiliation(s)
- John A Breier
- School of Earth, Environmental, and Marine Sciences, The University of Texas Rio Grande Valley, Edinburg, TX 78539, USA.
| | | | - Mak A Saito
- Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA
| | - Gregory J Dick
- Department of Earth and Environmental Sciences, University of Michigan, Ann Arbor, MI 48109, USA.,Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA.,Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Sharon L Grim
- Department of Earth and Environmental Sciences, University of Michigan, Ann Arbor, MI 48109, USA
| | - Eric W Chan
- School of Earth, Environmental, and Marine Sciences, The University of Texas Rio Grande Valley, Edinburg, TX 78539, USA
| | | | - Dawn M Moran
- Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA
| | - Brianna A Alanis
- School of Earth, Environmental, and Marine Sciences, The University of Texas Rio Grande Valley, Edinburg, TX 78539, USA
| | - Andrew E Allen
- Microbial and Environmental Genomics, J. Craig Venter Institute, San Diego, CA 92121, USA.,Integrative Oceanography Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92093, USA
| | - Chris L Dupont
- Microbial and Environmental Genomics, J. Craig Venter Institute, San Diego, CA 92121, USA
| | - Rod Johnson
- Bermuda Institute of Ocean Sciences, St. George's, GE 01, Bermuda
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10
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Espinoza JL, Shah N, Singh S, Nelson KE, Dupont CL. Applications of weighted association networks applied to compositional data in biology. Environ Microbiol 2020; 22:3020-3038. [PMID: 32436334 DOI: 10.1111/1462-2920.15091] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 05/15/2020] [Accepted: 05/18/2020] [Indexed: 12/14/2022]
Abstract
Next-generation sequencing technologies have generated, and continue to produce, an increasingly large corpus of biological data. The data generated are inherently compositional as they convey only relative information dependent upon the capacity of the instrument, experimental design and technical bias. There is considerable information to be gained through network analysis by studying the interactions between components within a system. Network theory methods using compositional data are powerful approaches for quantifying relationships between biological components and their relevance to phenotype, environmental conditions or other external variables. However, many of the statistical assumptions used for network analysis are not designed for compositional data and can bias downstream results. In this mini-review, we illustrate the utility of network theory in biological systems and investigate modern techniques while introducing researchers to frameworks for implementation. We overview (1) compositional data analysis, (2) data transformations and (3) network theory along with insight on a battery of network types including static-, temporal-, sample-specific- and differential-networks. The intention of this mini-review is not to provide a comprehensive overview of network methods, rather to introduce microbiology researchers to (semi)-unsupervised data-driven approaches for inferring latent structures that may give insight into biological phenomena or abstract mechanics of complex systems.
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Affiliation(s)
- Josh L Espinoza
- J. Craig Venter Institute, La Jolla, USA.,Applied Sciences, Durban University of Technology, Durban, South Africa
| | | | - Suren Singh
- Applied Sciences, Durban University of Technology, Durban, South Africa
| | - Karen E Nelson
- J. Craig Venter Institute, La Jolla, USA.,Applied Sciences, Durban University of Technology, Durban, South Africa.,J. Craig Venter Institute, Rockville, USA
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11
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O’Rourke A, Lee MD, Nierman WC, Everroad RC, Dupont CL. Genomic and phenotypic characterization of Burkholderia isolates from the potable water system of the International Space Station. PLoS One 2020; 15:e0227152. [PMID: 32074104 PMCID: PMC7029842 DOI: 10.1371/journal.pone.0227152] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 12/11/2019] [Indexed: 12/27/2022] Open
Abstract
The opportunistic pathogens Burkholderia cepacia and Burkholderia contaminans, both genomovars of the Burkholderia cepacia complex (BCC), are frequently cultured from the potable water dispenser (PWD) of the International Space Station (ISS). Here, we sequenced the genomes and conducted phenotypic assays to characterize these Burkholderia isolates. All recovered isolates of the two species fall within monophyletic clades based on phylogenomic trees of conserved single-copy core genes. Within species, the ISS-derived isolates all demonstrate greater than 99% average nucleotide identity (with 95-99% of genomes aligning) and share around 90% of the identified gene clusters from a pangenomic analysis-suggesting that the two groups are each composed of highly similar genomic lineages and their members may have all stemmed from the same two founding populations. The differences that can be observed between the recovered isolates at the pangenomic level are primarily located within putative plasmids. Phenotypically, macrophage intracellularization and lysis occurred at generally similar rates between all ISS-derived isolates, as well as with their respective type-terrestrial strain references. All ISS-derived isolates exhibited antibiotic sensitivity similar to that of the terrestrial reference strains, and minimal differences between isolates were observed. With a few exceptions, biofilm formation rates were generally consistent across each species. And lastly, though isolation date does not necessarily provide any insight into how long a given isolate had been aboard the ISS, none of the assayed physiology correlated with either date of isolation or distances based on nucleotide variation. Overall, we find that while the populations of Burkholderia present in the ISS PWS each maintain virulence, they are likely are not more virulent than those that might be encountered on planet and remain susceptible to clinically used antibiotics.
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Affiliation(s)
- Aubrie O’Rourke
- J. Craig Venter Institute, San Diego, CA, United States of America
| | - Michael D. Lee
- Exobiology Branch, NASA Ames Research Center, Mountain View, CA, United States of America
- Blue Marble Space Institute of Science, Seattle, WA, United States of America
| | | | - R. Craig Everroad
- Exobiology Branch, NASA Ames Research Center, Mountain View, CA, United States of America
| | - Chris L. Dupont
- J. Craig Venter Institute, San Diego, CA, United States of America
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12
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Pollak B, Matute T, Nuñez I, Cerda A, Lopez C, Vargas V, Kan A, Bielinski V, von Dassow P, Dupont CL, Federici F. Universal loop assembly: open, efficient and cross-kingdom DNA fabrication. Synth Biol (Oxf) 2020; 5:ysaa001. [PMID: 32161816 PMCID: PMC7052795 DOI: 10.1093/synbio/ysaa001] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [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: 10/14/2019] [Revised: 12/04/2019] [Accepted: 12/23/2019] [Indexed: 01/22/2023] Open
Abstract
Standardized type IIS DNA assembly methods are becoming essential for biological engineering and research. These methods are becoming widespread and more accessible due to the proposition of a 'common syntax' that enables higher interoperability between DNA libraries. Currently, Golden Gate (GG)-based assembly systems, originally implemented in host-specific vectors, are being made compatible with multiple organisms. We have recently developed the GG-based Loop assembly system for plants, which uses a small library and an intuitive strategy for hierarchical fabrication of large DNA constructs (>30 kb). Here, we describe 'universal Loop' (uLoop) assembly, a system based on Loop assembly for use in potentially any organism of choice. This design permits the use of a compact number of plasmids (two sets of four odd and even vectors), which are utilized repeatedly in alternating steps. The elements required for transformation/maintenance in target organisms are also assembled as standardized parts, enabling customization of host-specific plasmids. Decoupling of the Loop assembly logic from the host-specific propagation elements enables universal DNA assembly that retains high efficiency regardless of the final host. As a proof-of-concept, we show the engineering of multigene expression vectors in diatoms, yeast, plants and bacteria. These resources are available through the OpenMTA for unrestricted sharing and open access.
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Affiliation(s)
- Bernardo Pollak
- Microbial and Environmental Genomics Department, J. Craig Venter Institute, La Jolla, CA 92037, USA
- Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Fundación Ciencia y Vida, Santiago, Chile
| | - Tamara Matute
- Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Department of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Isaac Nuñez
- Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Department of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Ariel Cerda
- Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Constanza Lopez
- Departamento de Ecología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Valentina Vargas
- Departamento de Ecología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Anton Kan
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Vincent Bielinski
- Microbial and Environmental Genomics Department, J. Craig Venter Institute, La Jolla, CA 92037, USA
| | - Peter von Dassow
- Departamento de Ecología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
- Instituto Milenio de Oceanografía de Chile, Concepción, Chile
- UMI 3614 Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Université, Pontificia Universidad Católica de Chile, Universidad Austral de Chile, Station Biologique de Roscoff, 29680 Roscoff, France
| | - Chris L Dupont
- Microbial and Environmental Genomics Department, J. Craig Venter Institute, La Jolla, CA 92037, USA
| | - Fernán Federici
- Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
- Fondo de Desarrollo de Áreas Prioritarias, Center for Genome Regulation, Santiago, Chile
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13
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Okie JG, Poret-Peterson AT, Lee ZM, Richter A, Alcaraz LD, Eguiarte LE, Siefert JL, Souza V, Dupont CL, Elser JJ. Genomic adaptations in information processing underpin trophic strategy in a whole-ecosystem nutrient enrichment experiment. eLife 2020; 9:49816. [PMID: 31989922 PMCID: PMC7028357 DOI: 10.7554/elife.49816] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [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: 07/01/2019] [Accepted: 01/27/2020] [Indexed: 01/03/2023] Open
Abstract
Several universal genomic traits affect trade-offs in the capacity, cost, and efficiency of the biochemical information processing that underpins metabolism and reproduction. We analyzed the role of these traits in mediating the responses of a planktonic microbial community to nutrient enrichment in an oligotrophic, phosphorus-deficient pond in Cuatro Ciénegas, Mexico. This is one of the first whole-ecosystem experiments to involve replicated metagenomic assessment. Mean bacterial genome size, GC content, total number of tRNA genes, total number of rRNA genes, and codon usage bias in ribosomal protein sequences were all higher in the fertilized treatment, as predicted on the basis of the assumption that oligotrophy favors lower information-processing costs whereas copiotrophy favors higher processing rates. Contrasting changes in trait variances also suggested differences between traits in mediating assembly under copiotrophic versus oligotrophic conditions. Trade-offs in information-processing traits are apparently sufficiently pronounced to play a role in community assembly because the major components of metabolism-information, energy, and nutrient requirements-are fine-tuned to an organism's growth and trophic strategy.
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Affiliation(s)
- Jordan G Okie
- School of Earth and Space Exploration, Arizona State University, Tempe, United States
| | | | - Zarraz Mp Lee
- School of Life Sciences, Arizona State University, Tempe, United States
| | | | - Luis D Alcaraz
- Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Luis E Eguiarte
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Janet L Siefert
- Department of Statistics, Rice University, Houston, United States
| | - Valeria Souza
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | | | - James J Elser
- School of Life Sciences, Arizona State University, Tempe, United States.,Flathead Lake Biological Station, University of Montana, Polson, United States
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14
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Broddrick JT, Du N, Smith SR, Tsuji Y, Jallet D, Ware MA, Peers G, Matsuda Y, Dupont CL, Mitchell BG, Palsson BO, Allen AE. Cross-compartment metabolic coupling enables flexible photoprotective mechanisms in the diatom Phaeodactylum tricornutum. New Phytol 2019; 222:1364-1379. [PMID: 30636322 PMCID: PMC6594073 DOI: 10.1111/nph.15685] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 12/20/2018] [Indexed: 05/07/2023]
Abstract
Photoacclimation consists of short- and long-term strategies used by photosynthetic organisms to adapt to dynamic light environments. Observable photophysiology changes resulting from these strategies have been used in coarse-grained models to predict light-dependent growth and photosynthetic rates. However, the contribution of the broader metabolic network, relevant to species-specific strategies and fitness, is not accounted for in these simple models. We incorporated photophysiology experimental data with genome-scale modeling to characterize organism-level, light-dependent metabolic changes in the model diatom Phaeodactylum tricornutum. Oxygen evolution and photon absorption rates were combined with condition-specific biomass compositions to predict metabolic pathway usage for cells acclimated to four different light intensities. Photorespiration, an ornithine-glutamine shunt, and branched-chain amino acid metabolism were hypothesized as the primary intercompartment reductant shuttles for mediating excess light energy dissipation. Additionally, simulations suggested that carbon shunted through photorespiration is recycled back to the chloroplast as pyruvate, a mechanism distinct from known strategies in photosynthetic organisms. Our results suggest a flexible metabolic network in P. tricornutum that tunes intercompartment metabolism to optimize energy transport between the organelles, consuming excess energy as needed. Characterization of these intercompartment reductant shuttles broadens our understanding of energy partitioning strategies in this clade of ecologically important primary producers.
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Affiliation(s)
- Jared T. Broddrick
- Division of Biological SciencesUC San DiegoLa JollaCA92093USA
- Department of BioengineeringUC San DiegoLa JollaCA92093USA
| | - Niu Du
- Scripps Institution of OceanographyUC San DiegoLa JollaCA92093USA
- J. Craig Venter InstituteLa JollaCA92037USA
| | | | - Yoshinori Tsuji
- Department of Environmental BioscienceKwansei Gakuin UniversitySanda669‐1337Japan
| | - Denis Jallet
- Department of BiologyColorado State UniversityFort CollinsCO80523USA
| | - Maxwell A. Ware
- Department of BiologyColorado State UniversityFort CollinsCO80523USA
| | - Graham Peers
- Department of BiologyColorado State UniversityFort CollinsCO80523USA
| | - Yusuke Matsuda
- Department of Environmental BioscienceKwansei Gakuin UniversitySanda669‐1337Japan
| | | | - B. Greg Mitchell
- Scripps Institution of OceanographyUC San DiegoLa JollaCA92093USA
| | | | - Andrew E. Allen
- Scripps Institution of OceanographyUC San DiegoLa JollaCA92093USA
- J. Craig Venter InstituteLa JollaCA92037USA
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15
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Gomez A, Espinoza JL, Harkins DM, Leong P, Saffery R, Bockmann M, Torralba M, Kuelbs C, Kodukula R, Inman J, Hughes T, Craig JM, Highlander SK, Jones MB, Dupont CL, Nelson KE. Host Genetic Control of the Oral Microbiome in Health and Disease. Cell Host Microbe 2018; 22:269-278.e3. [PMID: 28910633 DOI: 10.1016/j.chom.2017.08.013] [Citation(s) in RCA: 120] [Impact Index Per Article: 20.0] [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: 04/24/2017] [Revised: 06/30/2017] [Accepted: 08/18/2017] [Indexed: 12/11/2022]
Abstract
Host-associated microbial communities are influenced by both host genetics and environmental factors. However, factors controlling the human oral microbiome and their impact on disease remain to be investigated. To determine the combined and relative effects of host genotype and environment on oral microbiome composition and caries phenotypes, we profiled the supragingival plaque microbiome of 485 dizygotic and monozygotic twins aged 5-11. Oral microbiome similarity always increased with shared host genotype, regardless of caries state. Additionally, although most of the variation in the oral microbiome was determined by environmental factors, highly heritable oral taxa were identified. The most heritable oral bacteria were not associated with caries state, did not tend to co-occur with other taxa, and decreased in abundance with age and sugar consumption frequency. Thus, while the human oral microbiome composition is influenced by host genetic background, potentially cariogenic taxa are likely not controlled by genetic factors.
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Affiliation(s)
- Andres Gomez
- Departments of Human Biology and Genomic Medicine, J. Craig Venter Institute, La Jolla, CA 92037, USA
| | - Josh L Espinoza
- Department of Microbial and Environmental Genomics, J. Craig Venter Institute, La Jolla, CA 92037, USA
| | - Derek M Harkins
- Departments of Human Biology and Genomic Medicine, J. Craig Venter Institute, Rockville, MD 20850, USA
| | - Pamela Leong
- Murdoch Children's Research Institute and Department of Pediatrics, University of Melbourne, Royal Children's Hospital, Parkville, VIC 3052, Australia
| | - Richard Saffery
- Murdoch Children's Research Institute and Department of Pediatrics, University of Melbourne, Royal Children's Hospital, Parkville, VIC 3052, Australia
| | - Michelle Bockmann
- School of Dentistry, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Manolito Torralba
- Departments of Human Biology and Genomic Medicine, J. Craig Venter Institute, La Jolla, CA 92037, USA
| | - Claire Kuelbs
- Departments of Human Biology and Genomic Medicine, J. Craig Venter Institute, La Jolla, CA 92037, USA
| | - Rohith Kodukula
- JCVI Summer Intern Program, Torrey Pines High School, San Diego, CA 9213, USA
| | - Jason Inman
- Departments of Human Biology and Genomic Medicine, J. Craig Venter Institute, Rockville, MD 20850, USA
| | - Toby Hughes
- School of Dentistry, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Jeffrey M Craig
- Murdoch Children's Research Institute and Department of Pediatrics, University of Melbourne, Royal Children's Hospital, Parkville, VIC 3052, Australia
| | - Sarah K Highlander
- Departments of Human Biology and Genomic Medicine, J. Craig Venter Institute, La Jolla, CA 92037, USA
| | | | - Chris L Dupont
- Department of Microbial and Environmental Genomics, J. Craig Venter Institute, La Jolla, CA 92037, USA
| | - Karen E Nelson
- Departments of Human Biology and Genomic Medicine, J. Craig Venter Institute, La Jolla, CA 92037, USA; Departments of Human Biology and Genomic Medicine, J. Craig Venter Institute, Rockville, MD 20850, USA.
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16
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Lee ZMP, Poret-Peterson AT, Siefert JL, Kaul D, Moustafa A, Allen AE, Dupont CL, Eguiarte LE, Souza V, Elser JJ. Nutrient Stoichiometry Shapes Microbial Community Structure in an Evaporitic Shallow Pond. Front Microbiol 2017; 8:949. [PMID: 28611750 PMCID: PMC5447685 DOI: 10.3389/fmicb.2017.00949] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [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: 12/13/2016] [Accepted: 05/11/2017] [Indexed: 11/20/2022] Open
Abstract
Nutrient availability and ratios can play an important role in shaping microbial communities of freshwater ecosystems. The Cuatro Ciénegas Basin (CCB) in Mexico is a desert oasis where, perhaps paradoxically, high microbial diversity coincides with extreme oligotrophy. To better understand the effects of nutrients on microbial communities in CCB, a mesocosm experiment was implemented in a stoichiometrically imbalanced pond, Lagunita, which has an average TN:TP ratio of 122 (atomic). The experiment had four treatments, each with five spatial replicates – unamended controls and three fertilization treatments with different nitrogen:phosphorus (N:P) regimes (P only, N:P = 16 and N:P = 75 by atoms). In the water column, quantitative PCR of the 16S rRNA gene indicated that P enrichment alone favored proliferation of bacterial taxa with high rRNA gene copy number, consistent with a previously hypothesized but untested connection between rRNA gene copy number and P requirement. Bacterial and microbial eukaryotic community structure was investigated by pyrosequencing of 16S and 18S rRNA genes from the planktonic and surficial sediment samples. Nutrient enrichment shifted the composition of the planktonic community in a treatment-specific manner and promoted the growth of previously rare bacterial taxa at the expense of the more abundant, potentially endemic, taxa. The eukaryotic community was highly enriched with phototrophic populations in the fertilized treatment. The sediment microbial community exhibited high beta diversity among replicates within treatments, which obscured any changes due to fertilization. Overall, these results showed that nutrient stoichiometry can be an important factor in shaping microbial community structure.
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Affiliation(s)
- Zarraz M-P Lee
- School of Life Sciences, Arizona State University, TempeAZ, United States
| | | | - Janet L Siefert
- Department of Statistics, Rice University, HoustonTX, United States
| | - Drishti Kaul
- J. Craig Venter Institute, La JollaCA, United States
| | - Ahmed Moustafa
- Department of Biology and Biotechnology Graduate Program, American University in CairoNew Cairo, Egypt
| | - Andrew E Allen
- J. Craig Venter Institute, La JollaCA, United States.,Integrative Oceanography Division, Scripps Institution of Oceanography, University of California, San Diego, La JollaCA, United States
| | | | - Luis E Eguiarte
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de MéxicoCiudad de México, Mexico
| | - Valeria Souza
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de MéxicoCiudad de México, Mexico
| | - James J Elser
- School of Life Sciences, Arizona State University, TempeAZ, United States.,Flathead Lake Biological Station, University of Montana, PolsonMT, United States
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17
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Smith SR, Gillard JTF, Kustka AB, McCrow JP, Badger JH, Zheng H, New AM, Dupont CL, Obata T, Fernie AR, Allen AE. Correction: Transcriptional Orchestration of the Global Cellular Response of a Model Pennate Diatom to Diel Light Cycling under Iron Limitation. PLoS Genet 2017; 13:e1006688. [PMID: 28355217 PMCID: PMC5371279 DOI: 10.1371/journal.pgen.1006688] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
[This corrects the article DOI: 10.1371/journal.pgen.1006490.].
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18
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Celepli N, Sundh J, Ekman M, Dupont CL, Yooseph S, Bergman B, Ininbergs K. Meta-omic analyses of Baltic Sea cyanobacteria: diversity, community structure and salt acclimation. Environ Microbiol 2017; 19:673-686. [PMID: 27871145 DOI: 10.1111/1462-2920.13592] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 11/16/2016] [Indexed: 01/08/2023]
Abstract
Cyanobacteria are important phytoplankton in the Baltic Sea, an estuarine-like environment with pronounced north to south gradients in salinity and nutrient concentrations. Here, we present a metagenomic and -transcriptomic survey, with subsequent analyses targeting the genetic identity, phylogenetic diversity, and spatial distribution of Baltic Sea cyanobacteria. The cyanobacterial community constituted close to 12% of the microbial population sampled during a pre-bloom period (June-July 2009). The community was dominated by unicellular picocyanobacteria, specifically a few highly abundant taxa (Synechococcus and Cyanobium) with a long tail of low abundance representatives, and local peaks of bloom-forming heterocystous taxa. Cyanobacteria in the Baltic Sea differed genetically from those in adjacent limnic and marine waters as well as from cultivated and sequenced picocyanobacterial strains. Diversity peaked at brackish salinities 3.5-16 psu, with low N:P ratios. A shift in community composition from brackish to marine strains was accompanied by a change in the repertoire and expression of genes involved in salt acclimation. Overall, the pre-bloom cyanobacterial population was more genetically diverse, widespread and abundant than previously documented, with unicellular picocyanobacteria being the most abundant clade along the entire Baltic Sea salinity gradient.
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Affiliation(s)
- Narin Celepli
- Department of Ecology, Environment and Plant Sciences, Stockholm University/Science for Life Laboratory, Solna, 17121, Sweden
| | - John Sundh
- Centre for Ecology and Evolution in Microbial model Systems, Linnaeus University, Kalmar, 391 82, Sweden
| | - Martin Ekman
- Department of Ecology, Environment and Plant Sciences, Stockholm University/Science for Life Laboratory, Solna, 17121, Sweden
| | - Chris L Dupont
- Microbial and Environmental Genomics, J. Craig Venter Institute, San Diego, CA, 92037, USA
| | - Shibu Yooseph
- Department of Computer Science, University of Central Florida, Orlando, FL, USA
| | - Birgitta Bergman
- Department of Ecology, Environment and Plant Sciences, Stockholm University/Science for Life Laboratory, Solna, 17121, Sweden
| | - Karolina Ininbergs
- Department of Ecology, Environment and Plant Sciences, Stockholm University/Science for Life Laboratory, Solna, 17121, Sweden
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19
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Smith SR, Gillard JTF, Kustka AB, McCrow JP, Badger JH, Zheng H, New AM, Dupont CL, Obata T, Fernie AR, Allen AE. Transcriptional Orchestration of the Global Cellular Response of a Model Pennate Diatom to Diel Light Cycling under Iron Limitation. PLoS Genet 2016; 12:e1006490. [PMID: 27973599 PMCID: PMC5156380 DOI: 10.1371/journal.pgen.1006490] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 11/16/2016] [Indexed: 11/23/2022] Open
Abstract
Environmental fluctuations affect distribution, growth and abundance of diatoms in nature, with iron (Fe) availability playing a central role. Studies on the response of diatoms to low Fe have either utilized continuous (24 hr) illumination or sampled a single time of day, missing any temporal dynamics. We profiled the physiology, metabolite composition, and global transcripts of the pennate diatom Phaeodactylum tricornutum during steady-state growth at low, intermediate, and high levels of dissolved Fe over light:dark cycles, to better understand fundamental aspects of genetic control of physiological acclimation to growth under Fe-limitation. We greatly expand the catalog of genes involved in the low Fe response, highlighting the importance of intracellular trafficking in Fe-limited diatoms. P. tricornutum exhibited transcriptomic hallmarks of slowed growth leading to prolonged periods of cell division/silica deposition, which could impact biogeochemical carbon sequestration in Fe-limited regions. Light harvesting and ribosome biogenesis transcripts were generally reduced under low Fe while transcript levels for genes putatively involved in the acquisition and recycling of Fe were increased. We also noted shifts in expression towards increased synthesis and catabolism of branched chain amino acids in P. tricornutum grown at low Fe whereas expression of genes involved in central core metabolism were relatively unaffected, indicating that essential cellular function is protected. Beyond the response of P. tricornutum to low Fe, we observed major coordinated shifts in transcript control of primary and intermediate metabolism over light:dark cycles which contribute to a new view of the significance of distinctive diatom pathways, such as mitochondrial glycolysis and the ornithine-urea cycle. This study provides new insight into transcriptional modulation of diatom physiology and metabolism across light:dark cycles in response to Fe availability, providing mechanistic understanding for the ability of diatoms to remain metabolically poised to respond quickly to Fe input and revealing strategies underlying their ecological success. Oceanic diatoms live in constantly fluctuating environments to which they must adapt in order to survive. During sunlit hours, photosynthesis occurs allowing diatoms to store energy used at night to sustain energy demands. Cellular and molecular mechanisms for regulation of phytoplankton growth are important to understand because of their environmental roles at the base of food webs and in regulating carbon flux out of the atmosphere. In ocean ecosystems, the availability of iron (Fe) commonly limits phytoplankton growth and diatoms typically outcompete other phytoplankton when Fe is added, indicating they have adaptations allowing them to both survive at low Fe and rapidly respond to Fe additions. These adaptations may be unique depending on isolation from coastal or oceanic locations. To identify adaptive strategies, we characterized the response of a model diatom, Phaeodactylum tricornutum, to limiting Fe conditions over day:night cycles using a combination of gene expression analyses, metabolite, and physiology measurements. Major coordinated shifts in metabolism and growth were documented over diel cycles, with peak expression of low Fe expressed genes in the dark phase. Diatoms respond to limiting Fe by increasing Fe acquisition, while decreasing growth rate through slowed cell cycle progression, reduced energy acquisition, and subtle metabolic remodeling.
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Affiliation(s)
- Sarah R. Smith
- Integrative Oceanography Division, Scripps Institution of Oceanography, UC San Diego, La Jolla, California, United States of America
- J. Craig Venter Institute, La Jolla, California, United States of America
| | - Jeroen T. F. Gillard
- J. Craig Venter Institute, La Jolla, California, United States of America
- Department of Biology, CSU Bakersfield, Bakersfield, California, United States of America
| | - Adam B. Kustka
- Department of Earth and Environmental Sciences, Rutgers University, Newark, New Jersey, United States of America
| | - John P. McCrow
- J. Craig Venter Institute, La Jolla, California, United States of America
| | - Jonathan H. Badger
- J. Craig Venter Institute, La Jolla, California, United States of America
| | - Hong Zheng
- J. Craig Venter Institute, La Jolla, California, United States of America
| | - Ashley M. New
- Department of Earth and Environmental Sciences, Rutgers University, Newark, New Jersey, United States of America
| | - Chris L. Dupont
- J. Craig Venter Institute, La Jolla, California, United States of America
| | - Toshihiro Obata
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam, Germany
| | - Alisdair R. Fernie
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam, Germany
| | - Andrew E. Allen
- Integrative Oceanography Division, Scripps Institution of Oceanography, UC San Diego, La Jolla, California, United States of America
- J. Craig Venter Institute, La Jolla, California, United States of America
- * E-mail: ,
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Asplund-Samuelsson J, Sundh J, Dupont CL, Allen AE, McCrow JP, Celepli NA, Bergman B, Ininbergs K, Ekman M. Diversity and Expression of Bacterial Metacaspases in an Aquatic Ecosystem. Front Microbiol 2016; 7:1043. [PMID: 27458440 PMCID: PMC4933709 DOI: 10.3389/fmicb.2016.01043] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [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: 02/26/2016] [Accepted: 06/22/2016] [Indexed: 11/13/2022] Open
Abstract
Metacaspases are distant homologs of metazoan caspase proteases, implicated in stress response, and programmed cell death (PCD) in bacteria and phytoplankton. While the few previous studies on metacaspases have relied on cultured organisms and sequenced genomes, no studies have focused on metacaspases in a natural setting. We here present data from the first microbial community-wide metacaspase survey; performed by querying metagenomic and metatranscriptomic datasets from the brackish Baltic Sea, a water body characterized by pronounced environmental gradients and periods of massive cyanobacterial blooms. Metacaspase genes were restricted to ~4% of the bacteria, taxonomically affiliated mainly to Bacteroidetes, Alpha- and Betaproteobacteria and Cyanobacteria. The gene abundance was significantly higher in larger or particle-associated bacteria (>0.8 μm), and filamentous Cyanobacteria dominated metacaspase gene expression throughout the bloom season. Distinct seasonal expression patterns were detected for the three metacaspase genes in Nodularia spumigena, one of the main bloom-formers. Clustering of normalized gene expression in combination with analyses of genomic and assembly data suggest functional diversification of these genes, and possible roles of the metacaspase genes related to stress responses, i.e., sulfur metabolism in connection to oxidative stress, and nutrient stress induced cellular differentiation. Co-expression of genes encoding metacaspases and nodularin toxin synthesis enzymes was also observed in Nodularia spumigena. The study shows that metacaspases represent an adaptation of potentially high importance for several key organisms in the Baltic Sea, most prominently Cyanobacteria, and open up for further exploration of their physiological roles in microbes and assessment of their ecological impact in aquatic habitats.
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Affiliation(s)
- Johannes Asplund-Samuelsson
- Science for Life Laboratory, Department of Ecology, Environment and Plant Sciences, Stockholm UniversitySolna, Sweden
| | - John Sundh
- Science for Life Laboratory, Department of Biology and Environmental Science, Linnaeus UniversitySolna, Sweden
| | - Chris L. Dupont
- Microbial and Environmental Genomics, J. Craig Venter InstituteSan Diego, CA, USA
| | - Andrew E. Allen
- Microbial and Environmental Genomics, J. Craig Venter InstituteSan Diego, CA, USA
| | - John P. McCrow
- Microbial and Environmental Genomics, J. Craig Venter InstituteSan Diego, CA, USA
| | - Narin A. Celepli
- Science for Life Laboratory, Department of Ecology, Environment and Plant Sciences, Stockholm UniversitySolna, Sweden
| | - Birgitta Bergman
- Science for Life Laboratory, Department of Ecology, Environment and Plant Sciences, Stockholm UniversitySolna, Sweden
| | - Karolina Ininbergs
- Science for Life Laboratory, Department of Ecology, Environment and Plant Sciences, Stockholm UniversitySolna, Sweden
| | - Martin Ekman
- Science for Life Laboratory, Department of Ecology, Environment and Plant Sciences, Stockholm UniversitySolna, Sweden
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21
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Llorens-Marès T, Triadó-Margarit X, Borrego CM, Dupont CL, Casamayor EO. High Bacterial Diversity and Phylogenetic Novelty in Dark Euxinic Freshwaters Analyzed by 16S Tag Community Profiling. Microb Ecol 2016; 71:566-574. [PMID: 26552395 DOI: 10.1007/s00248-015-0696-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [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: 08/12/2015] [Accepted: 10/26/2015] [Indexed: 06/05/2023]
Abstract
Microbial communities growing under extreme low redox conditions are present in anoxic and sulfide-rich (euxinic) environments such as karstic lakes and experience limitation of electron acceptors. The fine natural chemical gradients and the large diversity of organic and inorganic compounds accumulated in bottom waters are impossible to mimic under laboratory conditions, and only a few groups have been cultured. We investigated the bacterial composition in the oxic-anoxic interface and in the deep waters of three sulfurous lakes from the Lake Banyoles karstic area (NE Spain) through 16S rRNA gene tag sequencing and identified the closest GenBank counterpart. High diversity indices were found in most of the samples with >15 phyla/classes and >45 bacterial orders. A higher proportion of operational taxonomic units (OTUs) of the "highest novelty" was found in the hypolimnia (38 % of total sequences) than in the metalimnia (17 %), whereas the percentage of OTUs closer to cultured counterparts (i.e., 97 % identity in the 16S rRNA gene) was 6 to 21 %, respectively. Elusimicrobia, Chloroflexi, Fibrobacteres, and Spirochaetes were the taxa with the highest proportion of novel sequences. Interestingly, tag sequencing results comparison with metagenomics data available from the same dataset, showed a systematic underestimation of sulfur-oxidizing Epsilonproteobacteria with the currently available 907R "universal" primer. Overall, despite the limitation of electron acceptors, a highly diverse and novel assemblage was present in dark and euxinic hypolimnetic freshwaters, unveiling a hotspot of microbial diversity with a remarkable gap with cultured counterparts.
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Affiliation(s)
- Tomàs Llorens-Marès
- Integrative Freshwater Ecology Group, Centro de Estudios Avanzados de Blanes, CEAB-CSIC, Accés Cala Sant Francesc, 14, 17300, Blanes, Girona, Spain
| | - Xavier Triadó-Margarit
- Integrative Freshwater Ecology Group, Centro de Estudios Avanzados de Blanes, CEAB-CSIC, Accés Cala Sant Francesc, 14, 17300, Blanes, Girona, Spain
| | - Carles M Borrego
- Water Quality and Microbial Diversity, Catalan Institute for Water Research (ICRA), Girona, Spain
- Group of Molecular Microbial Ecology, Institute of Aquatic Ecology, University of Girona, Girona, Spain
| | - Chris L Dupont
- Microbial and Environmental Genomics Group, J. Craig Venter Institute, San Diego, CA, USA
| | - Emilio O Casamayor
- Integrative Freshwater Ecology Group, Centro de Estudios Avanzados de Blanes, CEAB-CSIC, Accés Cala Sant Francesc, 14, 17300, Blanes, Girona, Spain.
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22
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Kent AG, Dupont CL, Yooseph S, Martiny AC. Global biogeography of Prochlorococcus genome diversity in the surface ocean. ISME J 2016; 10:1856-65. [PMID: 26836261 DOI: 10.1038/ismej.2015.265] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Revised: 12/05/2015] [Accepted: 12/15/2015] [Indexed: 01/08/2023]
Abstract
Prochlorococcus, the smallest known photosynthetic bacterium, is abundant in the ocean's surface layer despite large variation in environmental conditions. There are several genetically divergent lineages within Prochlorococcus and superimposed on this phylogenetic diversity is extensive gene gain and loss. The environmental role in shaping the global ocean distribution of genome diversity in Prochlorococcus is largely unknown, particularly in a framework that considers the vertical and lateral mechanisms of evolution. Here we show that Prochlorococcus field populations from a global circumnavigation harbor extensive genome diversity across the surface ocean, but this diversity is not randomly distributed. We observed a significant correspondence between phylogenetic and gene content diversity, including regional differences in both phylogenetic composition and gene content that were related to environmental factors. Several gene families were strongly associated with specific regions and environmental factors, including the identification of a set of genes related to lower nutrient and temperature regions. Metagenomic assemblies of natural Prochlorococcus genomes reinforced this association by providing linkage of genes across genomic backbones. Overall, our results show that the phylogeography in Prochlorococcus taxonomy is echoed in its genome content. Thus environmental variation shapes the functional capabilities and associated ecosystem role of the globally abundant Prochlorococcus.
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Affiliation(s)
- Alyssa G Kent
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, USA
| | - Chris L Dupont
- Microbial and Environmental Genomics Group, J. Craig Venter Institute, San Diego, CA, USA
| | - Shibu Yooseph
- Informatics Group, J. Craig Venter Institute, San Diego, CA, USA
| | - Adam C Martiny
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, USA.,Department of Earth System Science, University of California, Irvine, CA, USA
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23
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Roitman S, Flores-Uribe J, Philosof A, Knowles B, Rohwer F, Ignacio-Espinoza JC, Sullivan MB, Cornejo-Castillo FM, Sánchez P, Acinas SG, Dupont CL, Béjà O. Closing the gaps on the viral photosystem-I psaDCAB gene organization. Environ Microbiol 2015; 17:5100-8. [PMID: 26310718 PMCID: PMC5019241 DOI: 10.1111/1462-2920.13036] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Accepted: 08/20/2015] [Indexed: 11/30/2022]
Abstract
Marine photosynthesis is largely driven by cyanobacteria, namely Synechococcus and Prochlorococcus. Genes encoding for photosystem (PS) I and II reaction centre proteins are found in cyanophages and are believed to increase their fitness. Two viral PSI gene arrangements are known, psaJF→C→A→B→K→E→D and psaD→C→A→B. The shared genes between these gene cassettes and their encoded proteins are distinguished by %G + C and protein sequence respectively. The data on the psaD→C→A→B gene organization were reported from only two partial gene cassettes coming from Global Ocean Sampling stations in the Pacific and Indian oceans. Now we have extended our search to 370 marine stations from six metagenomic projects. Genes corresponding to both PSI gene arrangements were detected in the Pacific, Indian and Atlantic oceans, confined to a strip along the equator (30°N and 30°S). In addition, we found that the predicted structure of the viral PsaA protein from the psaD→C→A→B organization contains a lumenal loop conserved in PsaA proteins from Synechococcus, but is completely absent in viral PsaA proteins from the psaJF→C→A→B→K→E→D gene organization and most Prochlorococcus strains. This may indicate a co-evolutionary scenario where cyanophages containing either of these gene organizations infect cyanobacterial ecotypes biogeographically restricted to the 30°N and 30°S equatorial strip.
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Affiliation(s)
- Sheila Roitman
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, Israel
| | - José Flores-Uribe
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, Israel
| | - Alon Philosof
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, Israel
| | - Ben Knowles
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Forest Rohwer
- Department of Biology, San Diego State University, San Diego, CA, USA
| | | | - Matthew B Sullivan
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
| | | | - Pablo Sánchez
- Departament of Marine Biology and Oceanography, Institute of Marine Sciences (ICM), CSIC, Barcelona, Spain
| | - Silvia G Acinas
- Departament of Marine Biology and Oceanography, Institute of Marine Sciences (ICM), CSIC, Barcelona, Spain
| | - Chris L Dupont
- Microbial and Environmental Genomics Group, J Craig Venter Institute, San Diego, CA, USA
| | - Oded Béjà
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, Israel
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24
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Dupont CL, McCrow JP, Valas R, Moustafa A, Walworth N, Goodenough U, Roth R, Hogle SL, Bai J, Johnson ZI, Mann E, Palenik B, Barbeau KA, Venter JC, Allen AE. Genomes and gene expression across light and productivity gradients in eastern subtropical Pacific microbial communities. ISME J 2014; 9:1076-92. [PMID: 25333462 PMCID: PMC4410273 DOI: 10.1038/ismej.2014.198] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Revised: 08/20/2014] [Accepted: 09/01/2014] [Indexed: 12/16/2022]
Abstract
Transitions in community genomic features and biogeochemical processes were examined in surface and subsurface chlorophyll maximum (SCM) microbial communities across a trophic gradient from mesotrophic waters near San Diego, California to the oligotrophic Pacific. Transect end points contrasted in thermocline depth, rates of nitrogen and CO2 uptake, new production and SCM light intensity. Relative to surface waters, bacterial SCM communities displayed greater genetic diversity and enrichment in putative sulfur oxidizers, multiple actinomycetes, low-light-adapted Prochlorococcus and cell-associated viruses. Metagenomic coverage was not correlated with transcriptional activity for several key taxa within Bacteria. Low-light-adapted Prochlorococcus, Synechococcus, and low abundance gamma-proteobacteria enriched in the>3.0-μm size fraction contributed disproportionally to global transcription. The abundance of these groups also correlated with community functions, such as primary production or nitrate uptake. In contrast, many of the most abundant bacterioplankton, including SAR11, SAR86, SAR112 and high-light-adapted Prochlorococcus, exhibited low levels of transcriptional activity and were uncorrelated with rate processes. Eukaryotes such as Haptophytes and non-photosynthetic Aveolates were prevalent in surface samples while Mamielles and Pelagophytes dominated the SCM. Metatranscriptomes generated with ribosomal RNA-depleted mRNA (total mRNA) coupled to in vitro polyadenylation compared with polyA-enriched mRNA revealed a trade-off in detection eukaryotic organelle and eukaryotic nuclear origin transcripts, respectively. Gene expression profiles of SCM eukaryote populations, highly similar in sequence identity to the model pelagophyte Pelagomonas sp. CCMP1756, suggest that pelagophytes are responsible for a majority of nitrate assimilation within the SCM.
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Affiliation(s)
- Chris L Dupont
- Microbial and Environmental Genomics Group, J. Craig Venter Institute, La Jolla, CA, USA
| | - John P McCrow
- Microbial and Environmental Genomics Group, J. Craig Venter Institute, La Jolla, CA, USA
| | - Ruben Valas
- Microbial and Environmental Genomics Group, J. Craig Venter Institute, La Jolla, CA, USA
| | - Ahmed Moustafa
- Department of Biology and Biotechnology Graduate Program, American University in Cairo, New Cairo, Egypt
| | - Nathan Walworth
- Microbial and Environmental Genomics Group, J. Craig Venter Institute, La Jolla, CA, USA
| | | | - Robyn Roth
- Department of Biology, Washington University, St Louis, MO, USA
| | - Shane L Hogle
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA
| | - Jing Bai
- Microbial and Environmental Genomics Group, J. Craig Venter Institute, La Jolla, CA, USA
| | - Zackary I Johnson
- 1] Marine Laboratory, Nicholas School of the Environment, Beaufort, NC, USA [2] Biology Department, Duke University, Durham, NC, USA
| | | | - Brian Palenik
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA
| | - Katherine A Barbeau
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA
| | - J Craig Venter
- Microbial and Environmental Genomics Group, J. Craig Venter Institute, La Jolla, CA, USA
| | - Andrew E Allen
- 1] Microbial and Environmental Genomics Group, J. Craig Venter Institute, La Jolla, CA, USA [2] Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA
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25
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Dupont CL, Larsson J, Yooseph S, Ininbergs K, Goll J, Asplund-Samuelsson J, McCrow JP, Celepli N, Allen LZ, Ekman M, Lucas AJ, Hagström Å, Thiagarajan M, Brindefalk B, Richter AR, Andersson AF, Tenney A, Lundin D, Tovchigrechko A, Nylander JAA, Brami D, Badger JH, Allen AE, Rusch DB, Hoffman J, Norrby E, Friedman R, Pinhassi J, Venter JC, Bergman B. Functional tradeoffs underpin salinity-driven divergence in microbial community composition. PLoS One 2014; 9:e89549. [PMID: 24586863 PMCID: PMC3937345 DOI: 10.1371/journal.pone.0089549] [Citation(s) in RCA: 113] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Accepted: 01/23/2014] [Indexed: 11/23/2022] Open
Abstract
Bacterial community composition and functional potential change subtly across gradients in the surface ocean. In contrast, while there are significant phylogenetic divergences between communities from freshwater and marine habitats, the underlying mechanisms to this phylogenetic structuring yet remain unknown. We hypothesized that the functional potential of natural bacterial communities is linked to this striking divide between microbiomes. To test this hypothesis, metagenomic sequencing of microbial communities along a 1,800 km transect in the Baltic Sea area, encompassing a continuous natural salinity gradient from limnic to fully marine conditions, was explored. Multivariate statistical analyses showed that salinity is the main determinant of dramatic changes in microbial community composition, but also of large scale changes in core metabolic functions of bacteria. Strikingly, genetically and metabolically different pathways for key metabolic processes, such as respiration, biosynthesis of quinones and isoprenoids, glycolysis and osmolyte transport, were differentially abundant at high and low salinities. These shifts in functional capacities were observed at multiple taxonomic levels and within dominant bacterial phyla, while bacteria, such as SAR11, were able to adapt to the entire salinity gradient. We propose that the large differences in central metabolism required at high and low salinities dictate the striking divide between freshwater and marine microbiomes, and that the ability to inhabit different salinity regimes evolved early during bacterial phylogenetic differentiation. These findings significantly advance our understanding of microbial distributions and stress the need to incorporate salinity in future climate change models that predict increased levels of precipitation and a reduction in salinity.
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Affiliation(s)
- Chris L. Dupont
- Microbial and Environmental Genomics, J. Craig Venter Institute, San Diego, California, United States of America
- * E-mail: (CLD); (JL)
| | - John Larsson
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
- * E-mail: (CLD); (JL)
| | - Shibu Yooseph
- Informatics Group, J. Craig Venter Institute, San Diego, California, United States of America
| | - Karolina Ininbergs
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| | - Johannes Goll
- Informatics Group, J. Craig Venter Institute, Rockville, Maryland, United States of America
| | | | - John P. McCrow
- Microbial and Environmental Genomics, J. Craig Venter Institute, San Diego, California, United States of America
| | - Narin Celepli
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| | - Lisa Zeigler Allen
- Microbial and Environmental Genomics, J. Craig Venter Institute, San Diego, California, United States of America
| | - Martin Ekman
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| | - Andrew J. Lucas
- Marine Physical Laboratory, Scripps Institution of Oceanography, University of California San Diego, San Diego, California, United States of America
| | - Åke Hagström
- Swedish Institute for the Marine Environment (SIME), University of Gothenburg, Gothenburg, Sweden
| | - Mathangi Thiagarajan
- Informatics Group, J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Björn Brindefalk
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| | - Alexander R. Richter
- Informatics Group, J. Craig Venter Institute, San Diego, California, United States of America
| | - Anders F. Andersson
- KTH Royal Institute of Technology, Science for Life Laboratory, School of Biotechnology, Solna, Sweden
| | - Aaron Tenney
- Informatics Group, J. Craig Venter Institute, San Diego, California, United States of America
| | - Daniel Lundin
- KTH Royal Institute of Technology, Science for Life Laboratory, School of Biotechnology, Solna, Sweden
| | - Andrey Tovchigrechko
- Informatics Group, J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Johan A. A. Nylander
- Department of Biodiversity Informatics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Daniel Brami
- Informatics Group, J. Craig Venter Institute, San Diego, California, United States of America
| | - Jonathan H. Badger
- Informatics Group, J. Craig Venter Institute, San Diego, California, United States of America
| | - Andrew E. Allen
- Microbial and Environmental Genomics, J. Craig Venter Institute, San Diego, California, United States of America
| | - Douglas B. Rusch
- Informatics Group, J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Jeff Hoffman
- Microbial and Environmental Genomics, J. Craig Venter Institute, San Diego, California, United States of America
| | - Erling Norrby
- Center for History of Science, The Royal Swedish Academy of Sciences, Stockholm, Sweden
| | - Robert Friedman
- Microbial and Environmental Genomics, J. Craig Venter Institute, San Diego, California, United States of America
| | - Jarone Pinhassi
- Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Kalmar, Sweden
| | - J. Craig Venter
- Microbial and Environmental Genomics, J. Craig Venter Institute, San Diego, California, United States of America
| | - Birgitta Bergman
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
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Tetu SG, Johnson DA, Varkey D, Phillippy K, Stuart RK, Dupont CL, Hassan KA, Palenik B, Paulsen IT. Impact of DNA damaging agents on genome-wide transcriptional profiles in two marine Synechococcus species. Front Microbiol 2013; 4:232. [PMID: 23966990 PMCID: PMC3744912 DOI: 10.3389/fmicb.2013.00232] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [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: 04/26/2013] [Accepted: 07/29/2013] [Indexed: 11/21/2022] Open
Abstract
Marine microorganisms, particularly those residing in coastal areas, may come in contact with any number of chemicals of environmental or xenobiotic origin. The sensitivity and response of marine cyanobacteria to such chemicals is, at present, poorly understood. We have looked at the transcriptional response of well characterized Synechococcus open ocean (WH8102) and coastal (CC9311) isolates to two DNA damaging agents, mitomycin C and ethidium bromide, using whole-genome expression microarrays. The coastal strain showed differential regulation of a larger proportion of its genome following “shock” treatment with each agent. Many of the orthologous genes in these strains, including those encoding sensor kinases, showed different transcriptional responses, with the CC9311 genes more likely to show significant changes in both treatments. While the overall response of each strain was considerably different, there were distinct transcriptional responses common to both strains observed for each DNA damaging agent, linked to the mode of action of each chemical. In both CC9311 and WH8102 there was evidence of SOS response induction under mitomycin C treatment, with genes recA, lexA and umuC significantly upregulated in this experiment but not under ethidium bromide treatment. Conversely, ethidium bromide treatment tended to result in upregulation of the DNA-directed RNA polymerase genes, not observed following mitomycin C treatment. Interestingly, a large number of genes residing on putative genomic island regions of each genome also showed significant upregulation under one or both chemical treatments.
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Affiliation(s)
- Sasha G Tetu
- Department of Chemistry and Biomolecular Sciences, Macquarie University Sydney, NSW, Australia
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Robbins LJ, Lalonde SV, Saito MA, Planavsky NJ, Mloszewska AM, Pecoits E, Scott C, Dupont CL, Kappler A, Konhauser KO. Authigenic iron oxide proxies for marine zinc over geological time and implications for eukaryotic metallome evolution. Geobiology 2013; 11:295-306. [PMID: 23601652 DOI: 10.1111/gbi.12036] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2012] [Accepted: 03/08/2013] [Indexed: 06/02/2023]
Abstract
Here, we explore enrichments in paleomarine Zn as recorded by authigenic iron oxides including Precambrian iron formations, ironstones, and Phanerozoic hydrothermal exhalites. This compilation of new and literature-based iron formation analyses track dissolved Zn abundances and constrain the magnitude of the marine reservoir over geological time. Overall, the iron formation record is characterized by a fairly static range in Zn/Fe ratios throughout the Precambrian, consistent with the shale record (Scott et al., 2013, Nature Geoscience, 6, 125-128). When hypothetical partitioning scenarios are applied to this record, paleomarine Zn concentrations within about an order of magnitude of modern are indicated. We couple this examination with new chemical speciation models to interpret the iron formation record. We present two scenarios: first, under all but the most sulfidic conditions and with Zn-binding organic ligand concentrations similar to modern oceans, the amount of bioavailable Zn remained relatively unchanged through time. Late proliferation of Zn in eukaryotic metallomes has previously been linked to marine Zn biolimitation, but under this scenario the expansion in eukaryotic Zn metallomes may be better linked to biologically intrinsic evolutionary factors. In this case, zinc's geochemical and biological evolution may be decoupled and viewed as a function of increasing need for genome regulation and diversification of Zn-binding transcription factors. In the second scenario, we consider Archean organic ligand complexation in such excess that it may render Zn bioavailability low. However, this is dependent on Zn-organic ligand complexes not being bioavailable, which remains unclear. In this case, although bioavailability may be low, sphalerite precipitation is prevented, thereby maintaining a constant Zn inventory throughout both ferruginous and euxinic conditions. These results provide new perspectives and constraints on potential couplings between the trajectory of biological and marine geochemical coevolution.
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Affiliation(s)
- L J Robbins
- Department of Earth & Atmospheric Sciences, University of Alberta, Edmonton, AB, Canada.
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Dupont CL, Rusch DB, Yooseph S, Lombardo MJ, Richter RA, Valas R, Novotny M, Yee-Greenbaum J, Selengut JD, Haft DH, Halpern AL, Lasken RS, Nealson K, Friedman R, Venter JC. Genomic insights to SAR86, an abundant and uncultivated marine bacterial lineage. ISME J 2011; 6:1186-99. [PMID: 22170421 PMCID: PMC3358033 DOI: 10.1038/ismej.2011.189] [Citation(s) in RCA: 349] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Bacteria in the 16S rRNA clade SAR86 are among the most abundant uncultivated constituents of microbial assemblages in the surface ocean for which little genomic information is currently available. Bioinformatic techniques were used to assemble two nearly complete genomes from marine metagenomes and single-cell sequencing provided two more partial genomes. Recruitment of metagenomic data shows that these SAR86 genomes substantially increase our knowledge of non-photosynthetic bacteria in the surface ocean. Phylogenomic analyses establish SAR86 as a basal and divergent lineage of γ-proteobacteria, and the individual genomes display a temperature-dependent distribution. Modestly sized at 1.25-1.7 Mbp, the SAR86 genomes lack several pathways for amino-acid and vitamin synthesis as well as sulfate reduction, trends commonly observed in other abundant marine microbes. SAR86 appears to be an aerobic chemoheterotroph with the potential for proteorhodopsin-based ATP generation, though the apparent lack of a retinal biosynthesis pathway may require it to scavenge exogenously-derived pigments to utilize proteorhodopsin. The genomes contain an expanded capacity for the degradation of lipids and carbohydrates acquired using a wealth of tonB-dependent outer membrane receptors. Like the abundant planktonic marine bacterial clade SAR11, SAR86 exhibits metabolic streamlining, but also a distinct carbon compound specialization, possibly avoiding competition.
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Affiliation(s)
- Chris L Dupont
- Microbial and Environmental Genomics, J Craig Venter Institute, San Diego, CA 92121, USA.
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Todd JD, Curson ARJ, Dupont CL, Nicholson P, Johnston AWB. The dddP gene, encoding a novel enzyme that converts dimethylsulfoniopropionate into dimethyl sulfide, is widespread in ocean metagenomes and marine bacteria and also occurs in some Ascomycete fungi. Environ Microbiol 2009; 11:1376-85. [PMID: 19220400 DOI: 10.1111/j.1462-2920.2009.01864.x] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The marine alphaproteobacterium Roseovarius nubinhibens ISM can produce the gas dimethyl sulfide (DMS) from dimethylsulfoniopropionate (DMSP), a widespread secondary metabolite that occurs in many phytoplankton. Roseovarius possesses a novel gene, termed dddP, which when cloned, confers on Escherichia coli the ability to produce DMS. The DddP polypeptide is in the large family of M24 metallopeptidases and is wholly different from two other enzymes, DddD and DddL, which were previously shown to generate DMS from dimethylsulfoniopropionate. Close homologues of DddP occur in other alphaproteobacteria and more surprisingly, in some Ascomycete fungi. These were the biotechnologically important Aspergillus oryzae and the plant pathogen, Fusarium graminearum. The dddP gene is abundant in the bacterial metagenomic sequences in the Global Ocean Sampling Expedition. Thus, dddP has several novel features and is widely dispersed, both taxonomically and geographically.
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Affiliation(s)
- J D Todd
- School of Biological Sciences, University of East Anglia, Norwich, UK
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Dupont CL, Neupane K, Shearer J, Palenik B. Diversity, function and evolution of genes coding for putative Ni-containing superoxide dismutases. Environ Microbiol 2008; 10:1831-43. [PMID: 18412551 DOI: 10.1111/j.1462-2920.2008.01604.x] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
We examined the phylogenetic distribution, functionality and evolution of the sodN gene family, which has been shown to code for a unique Ni-containing isoform of superoxide dismutase (Ni-SOD) in Streptomyces. Many of the putative sodN sequences retrieved from public domain genomic and metagenomic databases are quite divergent from structurally and functionally characterized Ni-SOD. Structural bioinformatics studies verified that the divergent members of the sodN protein family code for similar three-dimensional structures and identified evolutionarily conserved amino acid residues. Structural and biochemical studies of the N-terminus 'Ni-hook' motif coded for by the putative sodN sequences confirmed both Ni (II) ligating and superoxide dismutase activity. Both environmental and organismal genomes expanded the previously noted phylogenetic distribution of sodN, and the sequences form four well-separated clusters, with multiple subclusters. The phylogenetic distribution of sodN suggests that the gene has been acquired via horizontal gene transfer by numerous organisms of diverse phylogenetic background, including both Eukaryotes and Prokaryotes. The presence of sodN correlates with the genomic absence of the gene coding for Fe-SOD, a structurally and evolutionarily distinct isoform of SOD. Given the low levels of Fe found in the marine environment from where many sequences were attained, we suggest that the replacement of Fe-SOD with Ni-SOD may be an evolutionary adaptation to reduce iron requirements.
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Affiliation(s)
- C L Dupont
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92039, USA
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Palenik B, Ren Q, Dupont CL, Myers GS, Heidelberg JF, Badger JH, Madupu R, Nelson WC, Brinkac LM, Dodson RJ, Durkin AS, Daugherty SC, Sullivan SA, Khouri H, Mohamoud Y, Halpin R, Paulsen IT. Genome sequence of Synechococcus CC9311: Insights into adaptation to a coastal environment. Proc Natl Acad Sci U S A 2006; 103:13555-9. [PMID: 16938853 PMCID: PMC1569201 DOI: 10.1073/pnas.0602963103] [Citation(s) in RCA: 154] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2006] [Indexed: 11/18/2022] Open
Abstract
Coastal aquatic environments are typically more highly productive and dynamic than open ocean ones. Despite these differences, cyanobacteria from the genus Synechococcus are important primary producers in both types of ecosystems. We have found that the genome of a coastal cyanobacterium, Synechococcus sp. strain CC9311, has significant differences from an open ocean strain, Synechococcus sp. strain WH8102, and these are consistent with the differences between their respective environments. CC9311 has a greater capacity to sense and respond to changes in its (coastal) environment. It has a much larger capacity to transport, store, use, or export metals, especially iron and copper. In contrast, phosphate acquisition seems less important, consistent with the higher concentration of phosphate in coastal environments. CC9311 is predicted to have differences in its outer membrane lipopolysaccharide, and this may be characteristic of the speciation of some cyanobacterial groups. In addition, the types of potentially horizontally transferred genes are markedly different between the coastal and open ocean genomes and suggest a more prominent role for phages in horizontal gene transfer in oligotrophic environments.
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Affiliation(s)
- Brian Palenik
- *Scripps Institution of Oceanography, University of California at San Diego, La Jolla, CA 92093; and
| | - Qinghu Ren
- The Institute for Genomic Research, Rockville, MD 20850
| | - Chris L. Dupont
- *Scripps Institution of Oceanography, University of California at San Diego, La Jolla, CA 92093; and
| | | | | | | | - Ramana Madupu
- The Institute for Genomic Research, Rockville, MD 20850
| | | | | | | | | | | | | | - Hoda Khouri
- The Institute for Genomic Research, Rockville, MD 20850
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Abstract
Manganese deficiency syndromes have been well described in animals and include among a wide variety of metabolic aberrations the heightened susceptibility to convulsions induced by electroshock or drugs. We have measured manganese blood levels in two populations of children: (1) a reference group of 120 ambulatory patients without neurologic disease, (2) 197 patients with convulsive disorder. Blood manganese was found to be age related in infants under 1 year of age. Highly significant was the lower mean blood manganese found in the convulsive disorder group as compared to the reference group. There was also a slight trend in the convulsive group for blood manganese to decrease from 1 to 22 years of age. No significant differences in manganese levels were found related to sex, type of seizure disorder, type of anticonvulsant drug therapy, or serum level of drug. Although this study does not demonstrate a causal relation between manganese and seizure disorder, and cannot be used as the basis for altering current approaches to therapy, it provides insight into the potentially important role of previously unrecognized factors in the pathophysiology of this syndrome.
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Abstract
The LaBrosse spot test, in our experience, is not very useful as a screening procedure since the majority of specimens give an intermediate reaction, representing a heterogeneous group which may include many patients with abnormal 24-hour VMA excretion. The test is helpful only if either "positive" or "negative" in the individual patient who presents symptoms or signs compatible with abnormal catecholamine excretion. It is also of value in following patients with catecholamine-secreting tumors. The clinician should be aware of the limitations of VMA screening tests as they exist to date, and should assure himself, as well, that a specific quantitative assay is used to confirm doubtful or positive screening test results.
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