1
|
Oliver A, Podell S, Wegley Kelly L, Sparagon WJ, Plominsky AM, Nelson RS, Laurens LML, Augyte S, Sims NA, Nelson CE, Allen EE. Enrichable consortia of microbial symbionts degrade macroalgal polysaccharides in Kyphosus fish. mBio 2024; 15:e0049624. [PMID: 38534158 PMCID: PMC11077953 DOI: 10.1128/mbio.00496-24] [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: 02/21/2024] [Accepted: 03/06/2024] [Indexed: 03/28/2024] Open
Abstract
Coastal herbivorous fishes consume macroalgae, which is then degraded by microbes along their digestive tract. However, there is scarce genomic information about the microbiota that perform this degradation. This study explores the potential of Kyphosus gastrointestinal microbial symbionts to collaboratively degrade and ferment polysaccharides from red, green, and brown macroalgae through in silico study of carbohydrate-active enzyme and sulfatase sequences. Recovery of metagenome-assembled genomes (MAGs) from previously described Kyphosus gut metagenomes and newly sequenced bioreactor enrichments reveals differences in enzymatic capabilities between the major microbial taxa in Kyphosus guts. The most versatile of the recovered MAGs were from the Bacteroidota phylum, whose MAGs house enzyme collections able to decompose a variety of algal polysaccharides. Unique enzymes and predicted degradative capacities of genomes from the Bacillota (genus Vallitalea) and Verrucomicrobiota (order Kiritimatiellales) highlight the importance of metabolic contributions from multiple phyla to broaden polysaccharide degradation capabilities. Few genomes contain the required enzymes to fully degrade any complex sulfated algal polysaccharide alone. The distribution of suitable enzymes between MAGs originating from different taxa, along with the widespread detection of signal peptides in candidate enzymes, is consistent with cooperative extracellular degradation of these carbohydrates. This study leverages genomic evidence to reveal an untapped diversity at the enzyme and strain level among Kyphosus symbionts and their contributions to macroalgae decomposition. Bioreactor enrichments provide a genomic foundation for degradative and fermentative processes central to translating the knowledge gained from this system to the aquaculture and bioenergy sectors.IMPORTANCESeaweed has long been considered a promising source of sustainable biomass for bioenergy and aquaculture feed, but scalable industrial methods for decomposing terrestrial compounds can struggle to break down seaweed polysaccharides efficiently due to their unique sulfated structures. Fish of the genus Kyphosus feed on seaweed by leveraging gastrointestinal bacteria to degrade algal polysaccharides into simple sugars. This study reconstructs metagenome-assembled genomes for these gastrointestinal bacteria to enhance our understanding of herbivorous fish digestion and fermentation of algal sugars. Investigations at the gene level identify Kyphosus guts as an untapped source of seaweed-degrading enzymes ripe for further characterization. These discoveries set the stage for future work incorporating marine enzymes and microbial communities in the industrial degradation of algal polysaccharides.
Collapse
Affiliation(s)
- Aaron Oliver
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| | - Sheila Podell
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| | - Linda Wegley Kelly
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| | - Wesley J. Sparagon
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, School of Ocean and Earth Science and Technology, University of Hawai’i at Mānoa, Honolulu, Hawaii, USA
| | - Alvaro M. Plominsky
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| | | | | | | | | | - Craig E. Nelson
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, School of Ocean and Earth Science and Technology, University of Hawai’i at Mānoa, Honolulu, Hawaii, USA
| | - Eric E. Allen
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, California, USA
- Department of Molecular Biology, School of Biological Sciences, University of California San Diego, La Jolla, California, USA
| |
Collapse
|
2
|
Oliver A, Podell S, Kelly LW, Sparagon WJ, Plominsky AM, Nelson RS, Laurens LML, Augyte S, Sims NA, Nelson CE, Allen EE. Enrichable consortia of microbial symbionts degrade macroalgal polysaccharides in Kyphosus fish. bioRxiv 2023:2023.11.28.568905. [PMID: 38076955 PMCID: PMC10705383 DOI: 10.1101/2023.11.28.568905] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/20/2023]
Abstract
Coastal herbivorous fishes consume macroalgae, which is then degraded by microbes along their digestive tract. However, there is scarce foundational genomic work on the microbiota that perform this degradation. This study explores the potential of Kyphosus gastrointestinal microbial symbionts to collaboratively degrade and ferment polysaccharides from red, green, and brown macroalgae through in silico study of carbohydrate-active enzyme and sulfatase sequences. Recovery of metagenome-assembled genomes (MAGs) reveals differences in enzymatic capabilities between the major microbial taxa in Kyphosus guts. The most versatile of the recovered MAGs were from the Bacteroidota phylum, whose MAGs house enzymes able to decompose a variety of algal polysaccharides. Unique enzymes and predicted degradative capacities of genomes from the Bacillota (genus Vallitalea) and Verrucomicrobiota (order Kiritimatiellales) suggest the potential for microbial transfer between marine sediment and Kyphosus digestive tracts. Few genomes contain the required enzymes to fully degrade any complex sulfated algal polysaccharide alone. The distribution of suitable enzymes between MAGs originating from different taxa, along with the widespread detection of signal peptides in candidate enzymes, is consistent with cooperative extracellular degradation of these carbohydrates. This study leverages genomic evidence to reveal an untapped diversity at the enzyme and strain level among Kyphosus symbionts and their contributions to macroalgae decomposition. Bioreactor enrichments provide a genomic foundation for degradative and fermentative processes central to translating the knowledge gained from this system to the aquaculture and bioenergy sectors.
Collapse
Affiliation(s)
- Aaron Oliver
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Sheila Podell
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Linda Wegley Kelly
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Wesley J. Sparagon
- Daniel K. Inouye Center for Microbial Oceanography, School of Ocean and Earth Science and Technology, University of Hawai’i at Mānoa, Honolulu, HI, USA
| | - Alvaro M. Plominsky
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | | | | | | | | | - Craig E. Nelson
- Daniel K. Inouye Center for Microbial Oceanography, School of Ocean and Earth Science and Technology, University of Hawai’i at Mānoa, Honolulu, HI, USA
| | - Eric E. Allen
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
- Department of Molecular Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| |
Collapse
|
3
|
Singh HW, Creamer KE, Chase AB, Klau LJ, Podell S, Jensen PR. Metagenomic data reveals type I polyketide synthase distributions across biomes. mSystems 2023:e0001223. [PMID: 37272717 DOI: 10.1128/msystems.00012-23] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023] Open
Abstract
Microbial polyketide synthase (PKS) genes encode the biosynthesis of many biomedically or otherwise commercially important natural products. Despite extensive discovery efforts, metagenomic analyses suggest that only a small fraction of nature's polyketide biosynthetic potential has been realized. Much of this potential originates from type I PKSs (T1PKSs), which can be further delineated based on their domain organization and the structural features of the compounds they encode. Notably, phylogenetic relationships among ketosynthase (KS) domains provide an effective method to classify the larger and more complex T1PKS genes in which they occur. Increased access to large metagenomic data sets from diverse habitats provides opportunities to assess T1PKS biosynthetic diversity and distributions through their smaller and more tractable KS domain sequences. Here, we used the web tool NaPDoS2 to detect and classify over 35,000 type I KS domains from 137 metagenomic data sets reported from eight diverse, globally distributed biomes. We found biome-specific separation with soils enriched in KSs from modular cis-acetyltransferase (AT) and hybrid cis-AT KSs relative to other biomes and marine sediments enriched in KSs associated with polyunsaturated fatty acid and enediyne biosynthesis. We linked the phylum Actinobacteria to soil-derived enediyne and cis-AT KSs while marine-derived KSs associated with enediyne and monomodular PKSs were linked to phyla from which the compounds produced by these biosynthetic enzymes have not been reported. These KSs were phylogenetically distinct from those associated with experimentally characterized PKSs suggesting they may be associated with novel structures or enzyme functions. Finally, we employed our metagenome-extracted KS domains to evaluate the PCR primers commonly used to amplify type I KSs and identified modifications that could increase the KS sequence diversity recovered from amplicon libraries.IMPORTANCEPolyketides are a crucial source of medicines, agrichemicals, and other commercial products. Advances in our understanding of polyketide biosynthesis, coupled with the increased availability of metagenomic sequence data, provide new opportunities to assess polyketide biosynthetic potential across biomes. Here, we used the web tool NaPDoS2 to assess type I polyketide synthase (PKS) diversity and distributions by detecting and classifying ketosynthase (KS) domains across 137 metagenomes. We show that biomes are differentially enriched in type I KS domains, providing a roadmap for future biodiscovery strategies. Furthermore, KS phylogenies reveal biome-specific clades that do not include biochemically characterized PKSs, highlighting the biosynthetic potential of poorly explored environments. The large metagenome-derived KS data set allowed us to identify regions of commonly used type I KS PCR primers that could be modified to capture a larger extent of environmental KS diversity. These results facilitate both the search for novel polyketides and our understanding of the biogeographical distribution of PKSs across Earth's major biomes.
Collapse
Affiliation(s)
- Hans W Singh
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| | - Kaitlin E Creamer
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| | - Alexander B Chase
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| | - Leesa J Klau
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| | - Sheila Podell
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| | - Paul R Jensen
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| |
Collapse
|
4
|
Podell S, Oliver A, Kelly LW, Sparagon WJ, Plominsky AM, Nelson RS, Laurens LML, Augyte S, Sims NA, Nelson CE, Allen EE. Herbivorous Fish Microbiome Adaptations to Sulfated Dietary Polysaccharides. Appl Environ Microbiol 2023; 89:e0215422. [PMID: 37133385 DOI: 10.1128/aem.02154-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2023] Open
Abstract
Marine herbivorous fish that feed primarily on macroalgae, such as those from the genus Kyphosus, are essential for maintaining coral health and abundance on tropical reefs. Here, deep metagenomic sequencing and assembly of gut compartment-specific samples from three sympatric, macroalgivorous Hawaiian kyphosid species have been used to connect host gut microbial taxa with predicted protein functional capacities likely to contribute to efficient macroalgal digestion. Bacterial community compositions, algal dietary sources, and predicted enzyme functionalities were analyzed in parallel for 16 metagenomes spanning the mid- and hindgut digestive regions of wild-caught fishes. Gene colocalization patterns of expanded carbohydrate (CAZy) and sulfatase (SulfAtlas) digestive enzyme families on assembled contigs were used to identify likely polysaccharide utilization locus associations and to visualize potential cooperative networks of extracellularly exported proteins targeting complex sulfated polysaccharides. These insights into the gut microbiota of herbivorous marine fish and their functional capabilities improve our understanding of the enzymes and microorganisms involved in digesting complex macroalgal sulfated polysaccharides. IMPORTANCE This work connects specific uncultured bacterial taxa with distinct polysaccharide digestion capabilities lacking in their marine vertebrate hosts, providing fresh insights into poorly understood processes for deconstructing complex sulfated polysaccharides and potential evolutionary mechanisms for microbial acquisition of expanded macroalgal utilization gene functions. Several thousand new marine-specific candidate enzyme sequences for polysaccharide utilization have been identified. These data provide foundational resources for future investigations into suppression of coral reef macroalgal overgrowth, fish host physiology, the use of macroalgal feedstocks in terrestrial and aquaculture animal feeds, and the bioconversion of macroalgae biomass into value-added commercial fuel and chemical products.
Collapse
Affiliation(s)
- Sheila Podell
- Center for Marine Biotechnology & Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California, USA
| | - Aaron Oliver
- Center for Marine Biotechnology & Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California, USA
| | - Linda Wegley Kelly
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California, USA
| | - Wesley J Sparagon
- Daniel K. Inouye Center for Microbial Oceanography, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Honolulu, Hawaii, USA
| | - Alvaro M Plominsky
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California, USA
| | | | | | | | | | - Craig E Nelson
- Daniel K. Inouye Center for Microbial Oceanography, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Honolulu, Hawaii, USA
| | - Eric E Allen
- Center for Marine Biotechnology & Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California, USA
- Department of Molecular Biology, School of Biological Sciences, University of California, San Diego, La Jolla, California, USA
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, California, USA
| |
Collapse
|
5
|
Wilson K, de Rond T, Burkhardt I, Steele TS, Schäfer RJB, Podell S, Allen EE, Moore BS. Terpene biosynthesis in marine sponge animals. Proc Natl Acad Sci U S A 2023; 120:e2220934120. [PMID: 36802428 PMCID: PMC9992776 DOI: 10.1073/pnas.2220934120] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [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: 12/11/2022] [Accepted: 01/25/2023] [Indexed: 02/23/2023] Open
Abstract
Sea sponges are the largest marine source of small-molecule natural products described to date. Sponge-derived molecules, such as the chemotherapeutic eribulin, the calcium-channel blocker manoalide, and antimalarial compound kalihinol A, are renowned for their impressive medicinal, chemical, and biological properties. Sponges contain microbiomes that control the production of many natural products isolated from these marine invertebrates. In fact, all genomic studies to date investigating the metabolic origins of sponge-derived small molecules concluded that microbes-not the sponge animal host-are the biosynthetic producers. However, early cell-sorting studies suggested the sponge animal host may play a role particularly in the production of terpenoid molecules. To investigate the genetic underpinnings of sponge terpenoid biosynthesis, we sequenced the metagenome and transcriptome of an isonitrile sesquiterpenoid-containing sponge of the order Bubarida. Using bioinformatic searches and biochemical validation, we identified a group of type I terpene synthases (TSs) from this sponge and multiple other species, the first of this enzyme class characterized from the sponge holobiome. The Bubarida TS-associated contigs consist of intron-containing genes homologous to sponge genes and feature GC percentage and coverage consistent with other eukaryotic sequences. We identified and characterized TS homologs from five different sponge species isolated from geographically distant locations, thereby suggesting a broad distribution amongst sponges. This work sheds light on the role of sponges in secondary metabolite production and speaks to the possibility that other sponge-specific molecules originate from the animal host.
Collapse
Affiliation(s)
- Kayla Wilson
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA92093
| | - Tristan de Rond
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA92093
- School of Chemical Sciences, University of Auckland, Auckland1142, New Zealand
| | - Immo Burkhardt
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA92093
| | - Taylor S. Steele
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA92093
- Department of Chemistry & Biochemistry, University of California, San Diego, La Jolla, CA92093
| | - Rebecca J. B. Schäfer
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA92093
| | - Sheila Podell
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA92093
| | - Eric E. Allen
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA92093
| | - Bradley S. Moore
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA92093
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA92093
| |
Collapse
|
6
|
Singh HW, Creamer KE, Chase AB, Klau LJ, Podell S, Jensen PR. Metagenomic Data Reveal Type I Polyketide Synthase Distributions Across Biomes. bioRxiv 2023:2023.01.09.523365. [PMID: 36711755 PMCID: PMC9882069 DOI: 10.1101/2023.01.09.523365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Microbial polyketide synthase (PKS) genes encode the biosynthesis of many biomedically important natural products, yet only a small fraction of nature's polyketide biosynthetic potential has been realized. Much of this potential originates from type I PKSs (T1PKSs), which can be delineated into different classes and subclasses based on domain organization and structural features of the compounds encoded. Notably, phylogenetic relationships among PKS ketosynthase (KS) domains provide a method to classify the larger and more complex genes in which they occur. Increased access to large metagenomic datasets from diverse habitats provides opportunities to assess T1PKS biosynthetic diversity and distributions through the analysis of KS domain sequences. Here, we used the webtool NaPDoS2 to detect and classify over 35,000 type I KS domains from 137 metagenomic data sets reported from eight diverse biomes. We found biome-specific separation with soils enriched in modular cis -AT and hybrid cis -AT KSs relative to other biomes and marine sediments enriched in KSs associated with PUFA and enediyne biosynthesis. By extracting full-length KS domains, we linked the phylum Actinobacteria to soil-specific enediyne and cis -AT clades and identified enediyne and monomodular KSs in phyla from which the associated compound classes have not been reported. These sequences were phylogenetically distinct from those associated with experimentally characterized PKSs suggesting novel structures or enzyme functions remain to be discovered. Lastly, we employed our metagenome-extracted KS domains to evaluate commonly used type I KS PCR primers and identified modifications that could increase the KS sequence diversity recovered from amplicon libraries. Importance Polyketides are a crucial source of medicines, agrichemicals, and other commercial products. Advances in our understanding of polyketide biosynthesis coupled with the accumulation of metagenomic sequence data provide new opportunities to assess polyketide biosynthetic potential across biomes. Here, we used the webtool NaPDoS2 to assess type I PKS diversity and distributions by detecting and classifying KS domains across 137 metagenomes. We show that biomes are differentially enriched in KS domain classes, providing a roadmap for future biodiscovery strategies. Further, KS phylogenies reveal both biome-specific clades that do not include biochemically characterized PKSs, highlighting the biosynthetic potential of poorly explored environments. The large metagenome-derived KS dataset allowed us to identify regions of commonly used type I KS PCR primers that could be modified to capture a larger extent of KS diversity. These results facilitate both the search for novel polyketides and our understanding of the biogeographical distribution of PKSs across earth's major biomes.
Collapse
|
7
|
Oliver A, Cavalheri HB, Lima TG, Jones NT, Podell S, Zarate D, Allen E, Burton RS, Shurin JB. Phenotypic and transcriptional response of Daphnia pulicaria to the combined effects of temperature and predation. PLoS One 2022; 17:e0265103. [PMID: 35834446 PMCID: PMC9282536 DOI: 10.1371/journal.pone.0265103] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 06/09/2022] [Indexed: 11/18/2022] Open
Abstract
Daphnia, an ecologically important zooplankton species in lakes, shows both genetic adaptation and phenotypic plasticity in response to temperature and fish predation, but little is known about the molecular basis of these responses and their potential interactions. We performed a factorial experiment exposing laboratory-propagated Daphnia pulicaria clones from two lakes in the Sierra Nevada mountains of California to normal or high temperature (15°C or 25°C) in the presence or absence of fish kairomones, then measured changes in life history and gene expression. Exposure to kairomones increased upper thermal tolerance limits for physiological activity in both clones. Cloned individuals matured at a younger age in response to higher temperature and kairomones, while size at maturity, fecundity and population intrinsic growth were only affected by temperature. At the molecular level, both clones expressed more genes differently in response to temperature than predation, but specific genes involved in metabolic, cellular, and genetic processes responded differently between the two clones. Although gene expression differed more between clones from different lakes than experimental treatments, similar phenotypic responses to predation risk and warming arose from these clone-specific patterns. Our results suggest that phenotypic plasticity responses to temperature and kairomones interact synergistically, with exposure to fish predators increasing the tolerance of Daphnia pulicaria to stressful temperatures, and that similar phenotypic responses to temperature and predator cues can be produced by divergent patterns of gene regulation.
Collapse
Affiliation(s)
- Aaron Oliver
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California, United States of America
| | - Hamanda B. Cavalheri
- Department of Biological Sciences, Ecology Behavior and Evolution Section, University of California, San Diego, La Jolla, California, United States of America
| | - Thiago G. Lima
- Department of Biological Sciences, Ecology Behavior and Evolution Section, University of California, San Diego, La Jolla, California, United States of America
| | - Natalie T. Jones
- Department of Biological Sciences, Ecology Behavior and Evolution Section, University of California, San Diego, La Jolla, California, United States of America
| | - Sheila Podell
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California, United States of America
| | - Daniela Zarate
- Department of Biological Sciences, Ecology Behavior and Evolution Section, University of California, San Diego, La Jolla, California, United States of America
| | - Eric Allen
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California, United States of America
| | - Ronald S. Burton
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California, United States of America
| | - Jonathan B. Shurin
- Department of Biological Sciences, Ecology Behavior and Evolution Section, University of California, San Diego, La Jolla, California, United States of America
- * E-mail:
| |
Collapse
|
8
|
Oliver A, Podell S, Pinowska A, Traller JC, Smith SR, McClure R, Beliaev A, Bohutskyi P, Hill EA, Rabines A, Zheng H, Allen LZ, Kuo A, Grigoriev IV, Allen AE, Hazlebeck D, Allen EE. Diploid genomic architecture of Nitzschia inconspicua, an elite biomass production diatom. Sci Rep 2021; 11:15592. [PMID: 34341414 PMCID: PMC8329260 DOI: 10.1038/s41598-021-95106-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [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: 04/05/2021] [Accepted: 07/14/2021] [Indexed: 01/13/2023] Open
Abstract
A near-complete diploid nuclear genome and accompanying circular mitochondrial and chloroplast genomes have been assembled from the elite commercial diatom species Nitzschia inconspicua. The 50 Mbp haploid size of the nuclear genome is nearly double that of model diatom Phaeodactylum tricornutum, but 30% smaller than closer relative Fragilariopsis cylindrus. Diploid assembly, which was facilitated by low levels of allelic heterozygosity (2.7%), included 14 candidate chromosome pairs composed of long, syntenic contigs, covering 93% of the total assembly. Telomeric ends were capped with an unusual 12-mer, G-rich, degenerate repeat sequence. Predicted proteins were highly enriched in strain-specific marker domains associated with cell-surface adhesion, biofilm formation, and raphe system gliding motility. Expanded species-specific families of carbonic anhydrases suggest potential enhancement of carbon concentration efficiency, and duplicated glycolysis and fatty acid synthesis pathways across cytosolic and organellar compartments may enhance peak metabolic output, contributing to competitive success over other organisms in mixed cultures. The N. inconspicua genome delivers a robust new reference for future functional and transcriptomic studies to illuminate the physiology of benthic pennate diatoms and harness their unique adaptations to support commercial algae biomass and bioproduct production.
Collapse
Affiliation(s)
- Aaron Oliver
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA
| | - Sheila Podell
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA.
| | | | | | - Sarah R Smith
- Microbial and Environmental Genomics Group, J. Craig Venter Institute, La Jolla, CA, USA
| | - Ryan McClure
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Alex Beliaev
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Pavlo Bohutskyi
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Eric A Hill
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Ariel Rabines
- Microbial and Environmental Genomics Group, J. Craig Venter Institute, La Jolla, CA, USA
| | - Hong Zheng
- Microbial and Environmental Genomics Group, J. Craig Venter Institute, La Jolla, CA, USA
| | - Lisa Zeigler Allen
- Microbial and Environmental Genomics Group, J. Craig Venter Institute, La Jolla, CA, USA
| | - Alan Kuo
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, USA
| | - Igor V Grigoriev
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, USA.,Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA
| | - Andrew E Allen
- Microbial and Environmental Genomics Group, J. Craig Venter Institute, La Jolla, CA, USA
| | | | - Eric E Allen
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA. .,Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA. .,Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA.
| |
Collapse
|
9
|
Podell S, Blanton JM, Oliver A, Schorn MA, Agarwal V, Biggs JS, Moore BS, Allen EE. A genomic view of trophic and metabolic diversity in clade-specific Lamellodysidea sponge microbiomes. Microbiome 2020; 8:97. [PMID: 32576248 PMCID: PMC7313196 DOI: 10.1186/s40168-020-00877-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [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: 11/06/2019] [Accepted: 05/28/2020] [Indexed: 05/09/2023]
Abstract
BACKGROUND Marine sponges and their microbiomes contribute significantly to carbon and nutrient cycling in global reefs, processing and remineralizing dissolved and particulate organic matter. Lamellodysidea herbacea sponges obtain additional energy from abundant photosynthetic Hormoscilla cyanobacterial symbionts, which also produce polybrominated diphenyl ethers (PBDEs) chemically similar to anthropogenic pollutants of environmental concern. Potential contributions of non-Hormoscilla bacteria to Lamellodysidea microbiome metabolism and the synthesis and degradation of additional secondary metabolites are currently unknown. RESULTS This study has determined relative abundance, taxonomic novelty, metabolic capacities, and secondary metabolite potential in 21 previously uncharacterized, uncultured Lamellodysidea-associated microbial populations by reconstructing near-complete metagenome-assembled genomes (MAGs) to complement 16S rRNA gene amplicon studies. Microbial community compositions aligned with sponge host subgroup phylogeny in 16 samples from four host clades collected from multiple sites in Guam over a 3-year period, including representatives of Alphaproteobacteria, Gammaproteobacteria, Oligoflexia, and Bacteroidetes as well as Cyanobacteria (Hormoscilla). Unexpectedly, microbiomes from one host clade also included Cyanobacteria from the prolific secondary metabolite-producer genus Prochloron, a common tunicate symbiont. Two novel Alphaproteobacteria MAGs encoded pathways diagnostic for methylotrophic metabolism as well as type III secretion systems, and have been provisionally assigned to a new order, designated Candidatus Methylospongiales. MAGs from other taxonomic groups encoded light-driven energy production pathways using not only chlorophyll, but also bacteriochlorophyll and proteorhodopsin. Diverse heterotrophic capabilities favoring aerobic versus anaerobic conditions included pathways for degrading chitin, eukaryotic extracellular matrix polymers, phosphonates, dimethylsulfoniopropionate, trimethylamine, and benzoate. Genetic evidence identified an aerobic catabolic pathway for halogenated aromatics that may enable endogenous PBDEs to be used as a carbon and energy source. CONCLUSIONS The reconstruction of high-quality MAGs from all microbial taxa comprising greater than 0.1% of the sponge microbiome enabled species-specific assignment of unique metabolic features that could not have been predicted from taxonomic data alone. This information will promote more representative models of marine invertebrate microbiome contributions to host bioenergetics, the identification of potential new sponge parasites and pathogens based on conserved metabolic and physiological markers, and a better understanding of biosynthetic and degradative pathways for secondary metabolites and halogenated compounds in sponge-associated microbiota. Video Abstract.
Collapse
Affiliation(s)
- Sheila Podell
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA
| | - Jessica M Blanton
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA
| | - Aaron Oliver
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA
| | - Michelle A Schorn
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Vinayak Agarwal
- School of Chemistry and Biochemistry and School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Jason S Biggs
- University of Guam Marine Laboratory, UoG Station, Mangilao, GU, USA
| | - Bradley S Moore
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA
| | - Eric E Allen
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA.
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA.
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA.
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA.
| |
Collapse
|
10
|
Mohanty I, Podell S, Biggs JS, Garg N, Allen EE, Agarwal V. Multi-Omic Profiling of Melophlus Sponges Reveals Diverse Metabolomic and Microbiome Architectures that Are Non-overlapping with Ecological Neighbors. Mar Drugs 2020; 18:E124. [PMID: 32092934 PMCID: PMC7074536 DOI: 10.3390/md18020124] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [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: 01/31/2020] [Revised: 02/14/2020] [Accepted: 02/17/2020] [Indexed: 12/11/2022] Open
Abstract
Marine sponge holobionts, defined as filter-feeding sponge hosts together with their associated microbiomes, are prolific sources of natural products. The inventory of natural products that have been isolated from marine sponges is extensive. Here, using untargeted mass spectrometry, we demonstrate that sponges harbor a far greater diversity of low-abundance natural products that have evaded discovery. While these low-abundance natural products may not be feasible to isolate, insights into their chemical structures can be gleaned by careful curation of mass fragmentation spectra. Sponges are also some of the most complex, multi-organismal holobiont communities in the oceans. We overlay sponge metabolomes with their microbiome structures and detailed metagenomic characterization to discover candidate gene clusters that encode production of sponge-derived natural products. The multi-omic profiling strategy for sponges that we describe here enables quantitative comparison of sponge metabolomes and microbiomes to address, among other questions, the ecological relevance of sponge natural products and for the phylochemical assignment of previously undescribed sponge identities.
Collapse
Affiliation(s)
- Ipsita Mohanty
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA; (I.M.); (N.G.)
| | - Sheila Podell
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92093, USA; (S.P.); (E.E.A.)
| | - Jason S. Biggs
- University of Guam Marine Laboratory, UOG Station, Mangilao 96913, Guam;
| | - Neha Garg
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA; (I.M.); (N.G.)
| | - Eric E. Allen
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92093, USA; (S.P.); (E.E.A.)
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Vinayak Agarwal
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA; (I.M.); (N.G.)
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| |
Collapse
|
11
|
Zhu Q, Mai U, Pfeiffer W, Janssen S, Asnicar F, Sanders JG, Belda-Ferre P, Al-Ghalith GA, Kopylova E, McDonald D, Kosciolek T, Yin JB, Huang S, Salam N, Jiao JY, Wu Z, Xu ZZ, Cantrell K, Yang Y, Sayyari E, Rabiee M, Morton JT, Podell S, Knights D, Li WJ, Huttenhower C, Segata N, Smarr L, Mirarab S, Knight R. Phylogenomics of 10,575 genomes reveals evolutionary proximity between domains Bacteria and Archaea. Nat Commun 2019; 10:5477. [PMID: 31792218 PMCID: PMC6889312 DOI: 10.1038/s41467-019-13443-4] [Citation(s) in RCA: 121] [Impact Index Per Article: 24.2] [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: 06/08/2019] [Accepted: 11/06/2019] [Indexed: 11/10/2022] Open
Abstract
Rapid growth of genome data provides opportunities for updating microbial evolutionary relationships, but this is challenged by the discordant evolution of individual genes. Here we build a reference phylogeny of 10,575 evenly-sampled bacterial and archaeal genomes, based on a comprehensive set of 381 markers, using multiple strategies. Our trees indicate remarkably closer evolutionary proximity between Archaea and Bacteria than previous estimates that were limited to fewer "core" genes, such as the ribosomal proteins. The robustness of the results was tested with respect to several variables, including taxon and site sampling, amino acid substitution heterogeneity and saturation, non-vertical evolution, and the impact of exclusion of candidate phyla radiation (CPR) taxa. Our results provide an updated view of domain-level relationships.
Collapse
Affiliation(s)
- Qiyun Zhu
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Uyen Mai
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
| | - Wayne Pfeiffer
- San Diego Supercomputer Center, University of California San Diego, La Jolla, CA, USA
| | - Stefan Janssen
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Algorithmic Bioinformatics, Department of Biology and Chemistry, Justus Liebig University Gießen, Giessen, Germany
| | | | - Jon G Sanders
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Pedro Belda-Ferre
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Gabriel A Al-Ghalith
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Evguenia Kopylova
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Daniel McDonald
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Tomasz Kosciolek
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - John B Yin
- Department of Electrical and Computer Engineering, University of California San Diego, La Jolla, CA, USA
- Department of Mathematics, University of California San Diego, La Jolla, CA, USA
| | - Shi Huang
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Single-Cell Center, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China
| | - Nimaichand Salam
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Jian-Yu Jiao
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Zijun Wu
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Zhenjiang Z Xu
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Kalen Cantrell
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Yimeng Yang
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Erfan Sayyari
- Department of Electrical and Computer Engineering, University of California San Diego, La Jolla, CA, USA
| | - Maryam Rabiee
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
| | - James T Morton
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
| | - Sheila Podell
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Dan Knights
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Curtis Huttenhower
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Nicola Segata
- Department CIBIO, University of Trento, Trento, Italy
| | - Larry Smarr
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
- California Institute for Telecommunications and Information Technology, University of California San Diego, La Jolla, CA, USA
| | - Siavash Mirarab
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA.
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA.
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA.
| |
Collapse
|
12
|
Podell S, Blanton JM, Neu A, Agarwal V, Biggs JS, Moore BS, Allen EE. Pangenomic comparison of globally distributed Poribacteria associated with sponge hosts and marine particles. ISME J 2018; 13:468-481. [PMID: 30291328 DOI: 10.1038/s41396-018-0292-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 09/12/2018] [Accepted: 09/15/2018] [Indexed: 01/10/2023]
Abstract
Candidatus Poribacteria is a little-known bacterial phylum, previously characterized by partial genomes from a single sponge host, but never isolated in culture. We have reconstructed multiple genome sequences from four different sponge genera and compared them to recently reported, uncharacterized Poribacteria genomes from the open ocean, discovering shared and unique functional characteristics. Two distinct, habitat-linked taxonomic lineages were identified, designated Entoporibacteria (sponge-associated) and Pelagiporibacteria (free-living). These lineages differed in flagellar motility and chemotaxis genes unique to Pelagiporibacteria, and highly expanded families of restriction endonucleases, DNA methylases, transposases, CRISPR repeats, and toxin-antitoxin gene pairs in Entoporibacteria. Both lineages shared pathways for facultative anaerobic metabolism, denitrification, fermentation, organosulfur compound utilization, type IV pili, cellulosomes, and bacterial proteosomes. Unexpectedly, many features characteristic of eukaryotic host association were also shared, including genes encoding the synthesis of eukaryotic-like cell adhesion molecules, extracellular matrix digestive enzymes, phosphoinositol-linked membrane glycolipids, and exopolysaccharide capsules. Complete Poribacteria 16S rRNA gene sequences were found to contain multiple mismatches to "universal" 16S rRNA gene primer sets, substantiating concerns about potential amplification failures in previous studies. A newly designed primer set corrects these mismatches, enabling more accurate assessment of Poribacteria abundance in diverse marine habitats where it may have previously been overlooked.
Collapse
Affiliation(s)
- Sheila Podell
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, La Jolla, San Diego, CA, USA
| | - Jessica M Blanton
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, La Jolla, San Diego, CA, USA
| | - Alexander Neu
- Division of Biological Sciences, University of California, La Jolla, San Diego, CA, USA
| | - Vinayak Agarwal
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA.,Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, La Jolla, San Diego, CA, USA
| | - Jason S Biggs
- University of Guam Marine Laboratory, UOG Station, Mangilao, Guam, USA
| | - Bradley S Moore
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, La Jolla, San Diego, CA, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, La Jolla, San Diego, CA, USA
| | - Eric E Allen
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, La Jolla, San Diego, CA, USA. .,Division of Biological Sciences, University of California, La Jolla, San Diego, CA, USA. .,Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, La Jolla, San Diego, CA, USA.
| |
Collapse
|
13
|
Plominsky AM, Henríquez-Castillo C, Delherbe N, Podell S, Ramirez-Flandes S, Ugalde JA, Santibañez JF, van den Engh G, Hanselmann K, Ulloa O, De la Iglesia R, Allen EE, Trefault N. Distinctive Archaeal Composition of an Artisanal Crystallizer Pond and Functional Insights Into Salt-Saturated Hypersaline Environment Adaptation. Front Microbiol 2018; 9:1800. [PMID: 30154761 PMCID: PMC6102401 DOI: 10.3389/fmicb.2018.01800] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [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: 12/29/2017] [Accepted: 07/17/2018] [Indexed: 11/23/2022] Open
Abstract
Hypersaline environments represent some of the most challenging settings for life on Earth. Extremely halophilic microorganisms have been selected to colonize and thrive in these extreme environments by virtue of a broad spectrum of adaptations to counter high salinity and osmotic stress. Although there is substantial data on microbial taxonomic diversity in these challenging ecosystems and their primary osmoadaptation mechanisms, less is known about how hypersaline environments shape the genomes of microbial inhabitants at the functional level. In this study, we analyzed the microbial communities in five ponds along the discontinuous salinity gradient from brackish to salt-saturated environments and sequenced the metagenome of the salt (halite) precipitation pond in the artisanal Cáhuil Solar Saltern system. We combined field measurements with spectrophotometric pigment analysis and flow cytometry to characterize the microbial ecology of the pond ecosystems, including primary producers and applied metagenomic sequencing for analysis of archaeal and bacterial taxonomic diversity of the salt crystallizer harvest pond. Comparative metagenomic analysis of the Cáhuil salt crystallizer pond against microbial communities from other salt-saturated aquatic environments revealed a dominance of the archaeal genus Halorubrum and showed an unexpectedly low abundance of Haloquadratum in the Cáhuil system. Functional comparison of 26 hypersaline microbial metagenomes revealed a high proportion of sequences associated with nucleotide excision repair, helicases, replication and restriction-methylation systems in all of them. Moreover, we found distinctive functional signatures between the microbial communities from salt-saturated (>30% [w/v] total salinity) compared to sub-saturated hypersaline environments mainly due to a higher representation of sequences related to replication, recombination and DNA repair in the former. The current study expands our understanding of the diversity and distribution of halophilic microbial populations inhabiting salt-saturated habitats and the functional attributes that sustain them.
Collapse
Affiliation(s)
- Alvaro M Plominsky
- Department of Oceanography, Faculty of Natural and Oceanographic Sciences, Universidad de Concepción, Concepción, Chile.,Instituto Milenio de Oceanografía, Concepción, Chile
| | - Carlos Henríquez-Castillo
- Department of Oceanography, Faculty of Natural and Oceanographic Sciences, Universidad de Concepción, Concepción, Chile.,Instituto Milenio de Oceanografía, Concepción, Chile
| | - Nathalie Delherbe
- Biology Department, Cell and Molecular Biology Joint Doctoral Program with UC San Diego, San Diego State University, San Diego, CA, United States
| | - Sheila Podell
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, United States
| | - Salvador Ramirez-Flandes
- Instituto Milenio de Oceanografía, Concepción, Chile.,Programa de Doctorado en Ingeniería de Sistemas Complejos, Universidad Adolfo Ibáñez, Santiago, Chile
| | - Juan A Ugalde
- uBiome, Inc., San Francisco, CA, United States.,Center for Bioinformatics and Integrative Biology, Facultad de Ciencias Biológicas, Universidad Andrés Bello, Santiago, Chile
| | - Juan F Santibañez
- Department of Oceanography, Faculty of Natural and Oceanographic Sciences, Universidad de Concepción, Concepción, Chile
| | | | - Kurt Hanselmann
- Department of Earth Sciences, ETH Zürich, Zurich, Switzerland
| | - Osvaldo Ulloa
- Department of Oceanography, Faculty of Natural and Oceanographic Sciences, Universidad de Concepción, Concepción, Chile.,Instituto Milenio de Oceanografía, Concepción, Chile
| | - Rodrigo De la Iglesia
- Department of Molecular Genetics and Microbiology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Eric E Allen
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, United States.,Division of Biological Sciences, University of California, San Diego, La Jolla, CA, United States
| | - Nicole Trefault
- GEMA Center for Genomics, Ecology and Environment, Faculty of Sciences, Universidad Mayor, Santiago, Chile
| |
Collapse
|
14
|
Plominsky AM, Trefault N, Podell S, Blanton JM, De la Iglesia R, Allen EE, von Dassow P, Ulloa O. Metabolic potential andin situtranscriptomic profiles of previously uncharacterized key microbial groups involved in coupled carbon, nitrogen and sulfur cycling in anoxic marine zones. Environ Microbiol 2018; 20:2727-2742. [DOI: 10.1111/1462-2920.14109] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Revised: 02/27/2018] [Accepted: 03/07/2018] [Indexed: 01/05/2023]
Affiliation(s)
- Alvaro M. Plominsky
- Departamento de Oceanografía; Universidad de Concepción, P.O. Box 160-C; Concepción 4070386 Chile
- Instituto Milenio de Oceanografía, Universidad de Concepción; Concepción Chile
| | - Nicole Trefault
- GEMA Center for Genomics, Ecology & Environment, Universidad Mayor; Santiago 8580745 Chile
| | - Sheila Podell
- Marine Biology Research Division; Scripps Institution of Oceanography, University of California San Diego; San Diego CA 92093-0202 USA
| | - Jessica M. Blanton
- Marine Biology Research Division; Scripps Institution of Oceanography, University of California San Diego; San Diego CA 92093-0202 USA
| | - Rodrigo De la Iglesia
- Department of Molecular Genetics and Microbiology; Pontificia Universidad Católica de Chile; Santiago 8331150 Chile
| | - Eric E. Allen
- Marine Biology Research Division; Scripps Institution of Oceanography, University of California San Diego; San Diego CA 92093-0202 USA
- Division of Biological Sciences; University of California; San Diego CA USA
| | - Peter von Dassow
- Instituto Milenio de Oceanografía, Universidad de Concepción; Concepción Chile
- Department of Ecology; Pontificia Universidad Católica de Chile; Santiago 8331150 Chile
- Research Department UMI 3614, Evolutionary Biology and Ecology of Algae; CNRS UPMC; Roscoff 29680 France
| | - Osvaldo Ulloa
- Departamento de Oceanografía; Universidad de Concepción, P.O. Box 160-C; Concepción 4070386 Chile
- Instituto Milenio de Oceanografía, Universidad de Concepción; Concepción Chile
| |
Collapse
|
15
|
León-Zayas R, Peoples L, Biddle JF, Podell S, Novotny M, Cameron J, Lasken RS, Bartlett DH. The metabolic potential of the single cell genomes obtained from the Challenger Deep, Mariana Trench within the candidate superphylum Parcubacteria (OD1). Environ Microbiol 2017; 19:2769-2784. [PMID: 28474498 DOI: 10.1111/1462-2920.13789] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2016] [Revised: 04/27/2017] [Accepted: 04/27/2017] [Indexed: 11/28/2022]
Abstract
Candidate phyla (CP) are broad phylogenetic clusters of organisms that lack cultured representatives. Included in this fraction is the candidate Parcubacteria superphylum. Specific characteristics that have been ascribed to the Parcubacteria include reduced genome size, limited metabolic potential and exclusive reliance on fermentation for energy acquisition. The study of new environmental niches, such as the marine versus terrestrial subsurface, often expands the understanding of the genetic potential of taxonomic groups. For this reason, we analyzed 12 Parcubacteria single amplified genomes (SAGs) from sediment samples collected within the Challenger Deep of the Mariana Trench, obtained during the Deepsea Challenge (DSC) Expedition. Many of these SAGs are closely related to environmental sequences obtained from deep-sea environments based on 16S rRNA gene similarity and BLAST matches to predicted proteins. DSC SAGs encode features not previously identified in Parcubacteria obtained from other habitats. These include adaptation to oxidative stress, polysaccharide modification and genes associated with respiratory nitrate reduction. The DSC SAGs are also distinguished by relative greater abundance of genes for nucleotide and amino acid biosynthesis, repair of alkylated DNA and the synthesis of mechanosensitive ion channels. These results present an expanded view of the Parcubacteria, among members residing in an ultra-deep hadal environment.
Collapse
Affiliation(s)
- Rosa León-Zayas
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, 92093, USA.,School of Marine Science and Policy, University of Delaware, Lewes, DE, 19958, USA
| | - Logan Peoples
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, 92093, USA
| | - Jennifer F Biddle
- School of Marine Science and Policy, University of Delaware, Lewes, DE, 19958, USA
| | - Sheila Podell
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, 92093, USA
| | - Mark Novotny
- Microbial and Environmental Genomics, J. Craig Venter Institute, San Diego, CA, 92121, USA
| | - James Cameron
- Earthship Productions, 3806 Cross Creek Rd. Suite D, Malibu, CA, 90265-4975, USA
| | - Roger S Lasken
- Microbial and Environmental Genomics, J. Craig Venter Institute, San Diego, CA, 92121, USA
| | - Douglas H Bartlett
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, 92093, USA
| |
Collapse
|
16
|
Schorn MA, Alanjary MM, Aguinaldo K, Korobeynikov A, Podell S, Patin N, Lincecum T, Jensen PR, Ziemert N, Moore BS. Sequencing rare marine actinomycete genomes reveals high density of unique natural product biosynthetic gene clusters. Microbiology (Reading) 2016; 162:2075-2086. [PMID: 27902408 DOI: 10.1099/mic.0.000386] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Traditional natural product discovery methods have nearly exhausted the accessible diversity of microbial chemicals, making new sources and techniques paramount in the search for new molecules. Marine actinomycete bacteria have recently come into the spotlight as fruitful producers of structurally diverse secondary metabolites, and remain relatively untapped. In this study, we sequenced 21 marine-derived actinomycete strains, rarely studied for their secondary metabolite potential and under-represented in current genomic databases. We found that genome size and phylogeny were good predictors of biosynthetic gene cluster diversity, with larger genomes rivalling the well-known marine producers in the Streptomyces and Salinispora genera. Genomes in the Micrococcineae suborder, however, had consistently the lowest number of biosynthetic gene clusters. By networking individual gene clusters into gene cluster families, we were able to computationally estimate the degree of novelty each genus contributed to the current sequence databases. Based on the similarity measures between all actinobacteria in the Joint Genome Institute's Atlas of Biosynthetic gene Clusters database, rare marine genera show a high degree of novelty and diversity, with Corynebacterium, Gordonia, Nocardiopsis, Saccharomonospora and Pseudonocardia genera representing the highest gene cluster diversity. This research validates that rare marine actinomycetes are important candidates for exploration, as they are relatively unstudied, and their relatives are historically rich in secondary metabolites.
Collapse
Affiliation(s)
- Michelle A Schorn
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, USA
| | - Mohammad M Alanjary
- German Centre for Infection Research (DZIF), Interfaculty Institute for Microbiology and Infection Medicine Tuebingen (IMIT), University of Tuebingen, Tuebingen, Germany
| | | | - Anton Korobeynikov
- Center for Algorithmic Biotechnology, St. Petersburg State University, St. Petersburg, Russia.,Department of Statistical Modeling, St. Petersburg State University, St. Petersburg, Russia
| | - Sheila Podell
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, USA
| | - Nastassia Patin
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, USA
| | | | - Paul R Jensen
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, USA.,Center for Microbiome Innovation, University of California, San Diego, USA
| | - Nadine Ziemert
- German Centre for Infection Research (DZIF), Interfaculty Institute for Microbiology and Infection Medicine Tuebingen (IMIT), University of Tuebingen, Tuebingen, Germany
| | - Bradley S Moore
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, USA.,Center for Microbiome Innovation, University of California, San Diego, USA
| |
Collapse
|
17
|
Traller JC, Cokus SJ, Lopez DA, Gaidarenko O, Smith SR, McCrow JP, Gallaher SD, Podell S, Thompson M, Cook O, Morselli M, Jaroszewicz A, Allen EE, Allen AE, Merchant SS, Pellegrini M, Hildebrand M. Genome and methylome of the oleaginous diatom Cyclotella cryptica reveal genetic flexibility toward a high lipid phenotype. Biotechnol Biofuels 2016; 9:258. [PMID: 27933100 PMCID: PMC5124317 DOI: 10.1186/s13068-016-0670-3] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 11/15/2016] [Indexed: 05/08/2023]
Abstract
BACKGROUND Improvement in the performance of eukaryotic microalgae for biofuel and bioproduct production is largely dependent on characterization of metabolic mechanisms within the cell. The marine diatom Cyclotella cryptica, which was originally identified in the Aquatic Species Program, is a promising strain of microalgae for large-scale production of biofuel and bioproducts, such as omega-3 fatty acids. RESULTS We sequenced the nuclear genome and methylome of this oleaginous diatom to identify the genetic traits that enable substantial accumulation of triacylglycerol. The genome is comprised of highly methylated repetitive sequence, which does not significantly change under silicon starved lipid induction, and data further suggests the primary role of DNA methylation is to suppress DNA transposition. Annotation of pivotal glycolytic, lipid metabolism, and carbohydrate degradation processes reveal an expanded enzyme repertoire in C. cryptica that would allow for an increased metabolic capacity toward triacylglycerol production. Identification of previously unidentified genes, including those involved in carbon transport and chitin metabolism, provide potential targets for genetic manipulation of carbon flux to further increase its lipid phenotype. New genetic tools were developed, bringing this organism on a par with other microalgae in terms of genetic manipulation and characterization approaches. CONCLUSIONS Functional annotation and detailed cross-species comparison of key carbon rich processes in C. cryptica highlights the importance of enzymatic subcellular compartmentation for regulation of carbon flux, which is often overlooked in photosynthetic microeukaryotes. The availability of the genome sequence, as well as advanced genetic manipulation tools enable further development of this organism for deployment in large-scale production systems.
Collapse
Affiliation(s)
- Jesse C. Traller
- Scripps Institution of Oceanography, University California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0202 USA
| | - Shawn J. Cokus
- Institute for Genomics and Proteomics, University of California, Los Angeles, CA 90095 USA
| | - David A. Lopez
- Institute for Genomics and Proteomics, University of California, Los Angeles, CA 90095 USA
| | - Olga Gaidarenko
- Scripps Institution of Oceanography, University California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0202 USA
| | - Sarah R. Smith
- Scripps Institution of Oceanography, University California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0202 USA
- J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA 92037 USA
| | - John P. McCrow
- J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA 92037 USA
| | - Sean D. Gallaher
- Institute for Genomics and Proteomics, University of California, Los Angeles, CA 90095 USA
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095 USA
| | - Sheila Podell
- Scripps Institution of Oceanography, University California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0202 USA
| | - Michael Thompson
- Institute for Genomics and Proteomics, University of California, Los Angeles, CA 90095 USA
| | - Orna Cook
- Scripps Institution of Oceanography, University California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0202 USA
| | - Marco Morselli
- Institute for Genomics and Proteomics, University of California, Los Angeles, CA 90095 USA
| | - Artur Jaroszewicz
- Institute for Genomics and Proteomics, University of California, Los Angeles, CA 90095 USA
| | - Eric E. Allen
- Scripps Institution of Oceanography, University California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0202 USA
| | - Andrew E. Allen
- Scripps Institution of Oceanography, University California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0202 USA
- J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA 92037 USA
| | - Sabeeha S. Merchant
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095 USA
| | - Matteo Pellegrini
- Institute for Genomics and Proteomics, University of California, Los Angeles, CA 90095 USA
| | - Mark Hildebrand
- Scripps Institution of Oceanography, University California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0202 USA
| |
Collapse
|
18
|
Bräuer S, Cadillo-Quiroz H, Kyrpides N, Woyke T, Goodwin L, Detter C, Podell S, Yavitt JB, Zinder SH. Genome of Methanoregula boonei 6A8 reveals adaptations to oligotrophic peatland environments. Microbiology (Reading) 2015; 161:1572-1581. [PMID: 25998264 DOI: 10.1099/mic.0.000117] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Analysis of the genome sequence of Methanoregula boonei strain 6A8, an acidophilic methanogen isolated from an ombrotrophic (rain-fed) peat bog, has revealed unique features that likely allow it to survive in acidic, nutrient-poor conditions. First, M. boonei is predicted to generate ATP using protons that are abundant in peat, rather than sodium ions that are scarce, and the sequence of a membrane-bound methyltransferase, believed to pump Na+ in all methanogens, shows differences in key amino acid residues. Further, perhaps reflecting the hypokalemic status of many peat bogs, M. boonei demonstrates redundancy in the predicted potassium uptake genes trk, kdp and kup, some of which may have been horizontally transferred to methanogens from bacteria, possibly Geobacter spp. Overall, the putative functions of the potassium uptake, ATPase and methyltransferase genes may, at least in part, explain the cosmopolitan success of group E1/E2 and related methanogenic archaea in acidic peat bogs.
Collapse
Affiliation(s)
- Suzanna Bräuer
- Department of Biology, Appalachian State University, Boone, NC 28608, USA
| | - Hinsby Cadillo-Quiroz
- Swette Center for Environmental Biotechnology at the Biodesign Institute, Arizona State University, Tempe, AZ 85287-4501, USA
| | - Nikos Kyrpides
- Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Tanja Woyke
- Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Lynne Goodwin
- Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Chris Detter
- Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Sheila Podell
- Scripps Institution of Oceanography, La Jolla, CA 92093, USA
| | - Joseph B Yavitt
- Department of Natural Resources, Cornell University, Ithaca, NY 14853, USA
| | - Stephen H Zinder
- Department of Microbiology, Cornell University, Ithaca, NY 14853, USA
| |
Collapse
|
19
|
Coates RC, Podell S, Korobeynikov A, Lapidus A, Pevzner P, Sherman DH, Allen EE, Gerwick L, Gerwick WH. Characterization of cyanobacterial hydrocarbon composition and distribution of biosynthetic pathways. PLoS One 2014; 9:e85140. [PMID: 24475038 PMCID: PMC3903477 DOI: 10.1371/journal.pone.0085140] [Citation(s) in RCA: 101] [Impact Index Per Article: 10.1] [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: 07/12/2013] [Accepted: 11/22/2013] [Indexed: 12/20/2022] Open
Abstract
Cyanobacteria possess the unique capacity to naturally produce hydrocarbons from fatty acids. Hydrocarbon compositions of thirty-two strains of cyanobacteria were characterized to reveal novel structural features and insights into hydrocarbon biosynthesis in cyanobacteria. This investigation revealed new double bond (2- and 3-heptadecene) and methyl group positions (3-, 4- and 5-methylheptadecane) for a variety of strains. Additionally, results from this study and literature reports indicate that hydrocarbon production is a universal phenomenon in cyanobacteria. All cyanobacteria possess the capacity to produce hydrocarbons from fatty acids yet not all accomplish this through the same metabolic pathway. One pathway comprises a two-step conversion of fatty acids first to fatty aldehydes and then alkanes that involves a fatty acyl ACP reductase (FAAR) and aldehyde deformylating oxygenase (ADO). The second involves a polyketide synthase (PKS) pathway that first elongates the acyl chain followed by decarboxylation to produce a terminal alkene (olefin synthase, OLS). Sixty-one strains possessing the FAAR/ADO pathway and twelve strains possessing the OLS pathway were newly identified through bioinformatic analyses. Strains possessing the OLS pathway formed a cohesive phylogenetic clade with the exception of three Moorea strains and Leptolyngbya sp. PCC 6406 which may have acquired the OLS pathway via horizontal gene transfer. Hydrocarbon pathways were identified in one-hundred-forty-two strains of cyanobacteria over a broad phylogenetic range and there were no instances where both the FAAR/ADO and the OLS pathways were found together in the same genome, suggesting an unknown selective pressure maintains one or the other pathway, but not both.
Collapse
Affiliation(s)
- R. Cameron Coates
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, United States of America
| | - Sheila Podell
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, United States of America
| | - Anton Korobeynikov
- Algorithmic Biology Laboratory, St. Petersburg Academic University, Russian Academy of Sciences, St. Petersburg, Russia
- Department of Mathematics and Mechanics, St. Petersburg State University, St. Petersburg, Russia
| | - Alla Lapidus
- Algorithmic Biology Laboratory, St. Petersburg Academic University, Russian Academy of Sciences, St. Petersburg, Russia
- Theodosius Dobzhansky Center for Genome Bionformatics, St. Petersburg State University, St. Petersburg, Russia
| | - Pavel Pevzner
- Algorithmic Biology Laboratory, St. Petersburg Academic University, Russian Academy of Sciences, St. Petersburg, Russia
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, California, United States of America
| | - David H. Sherman
- Life Sciences Institute and Department of Medical Chemistry, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Eric E. Allen
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, United States of America
| | - Lena Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, United States of America
| | - William H. Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, United States of America
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, United States of America
- * E-mail:
| |
Collapse
|
20
|
Podell S, Ugalde JA, Narasingarao P, Banfield JF, Heidelberg KB, Allen EE. Assembly-driven community genomics of a hypersaline microbial ecosystem. PLoS One 2013; 8:e61692. [PMID: 23637883 PMCID: PMC3630111 DOI: 10.1371/journal.pone.0061692] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [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: 12/21/2012] [Accepted: 03/13/2013] [Indexed: 01/10/2023] Open
Abstract
Microbial populations inhabiting a natural hypersaline lake ecosystem in Lake Tyrrell, Victoria, Australia, have been characterized using deep metagenomic sampling, iterative de novo assembly, and multidimensional phylogenetic binning. Composite genomes representing habitat-specific microbial populations were reconstructed for eleven different archaea and one bacterium, comprising between 0.6 and 14.1% of the planktonic community. Eight of the eleven archaeal genomes were from microbial species without previously cultured representatives. These new genomes provide habitat-specific reference sequences enabling detailed, lineage-specific compartmentalization of predicted functional capabilities and cellular properties associated with both dominant and less abundant community members, including organisms previously known only by their 16S rRNA sequences. Together, these data provide a comprehensive, culture-independent genomic blueprint for ecosystem-wide analysis of protein functions, population structure, and lifestyles of co-existing, co-evolving microbial groups within the same natural habitat. The “assembly-driven” community genomic approach demonstrated in this study advances our ability to push beyond single gene investigations, and promotes genome-scale reconstructions as a tangible goal in the quest to define the metabolic, ecological, and evolutionary dynamics that underpin environmental microbial diversity.
Collapse
Affiliation(s)
- Sheila Podell
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, United States of America
| | - Juan A. Ugalde
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, United States of America
| | - Priya Narasingarao
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, United States of America
| | - Jillian F. Banfield
- Department of Earth and Planetary Sciences, University of California, Berkeley, California, United States of America
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, California, United States of America
| | - Karla B. Heidelberg
- Department of Biological Sciences, University of Southern California, Los Angeles, California, United States of America
| | - Eric E. Allen
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, United States of America
- Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
- * E-mail:
| |
Collapse
|
21
|
Baudoux AC, Hendrix RW, Lander GC, Bailly X, Podell S, Paillard C, Johnson JE, Potter CS, Carragher B, Azam F. Genomic and functional analysis of Vibrio phage SIO-2 reveals novel insights into ecology and evolution of marine siphoviruses. Environ Microbiol 2012; 14:2071-86. [PMID: 22225728 PMCID: PMC3338904 DOI: 10.1111/j.1462-2920.2011.02685.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [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] [Indexed: 02/05/2023]
Abstract
We report on a genomic and functional analysis of a novel marine siphovirus, the Vibrio phage SIO-2. This phage is lytic for related Vibrio species of great ecological interest including the broadly antagonistic bacterium Vibrio sp. SWAT3 as well as notable members of the Harveyi clade (V.harveyi ATTC BAA-1116 and V.campbellii ATCC 25920). Vibrio phage SIO-2 has a circularly permuted genome of 80598 bp, which displays unusual features. This genome is larger than that of most known siphoviruses and only 38 of the 116 predicted proteins had homologues in databases. Another divergence is manifest by the origin of core genes, most of which share robust similarities with unrelated viruses and bacteria spanning a wide range of phyla. These core genes are arranged in the same order as in most bacteriophages but they are unusually interspaced at two places with insertions of DNA comprising a high density of uncharacterized genes. The acquisition of these DNA inserts is associated with morphological variation of SIO-2 capsid, which assembles as a large (80 nm) shell with a novel T=12 symmetry. These atypical structural features confer on SIO-2 a remarkable stability to a variety of physical, chemical and environmental factors. Given this high level of functional and genomic novelty, SIO-2 emerges as a model of considerable interest in ecological and evolutionary studies.
Collapse
Affiliation(s)
- A-C Baudoux
- Scripps Institution of Oceanography, Marine Biology Research Division, University of California San Diego, La Jolla, CA 92093, USA.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
22
|
Ugalde JA, Podell S, Narasingarao P, Allen EE. Xenorhodopsins, an enigmatic new class of microbial rhodopsins horizontally transferred between archaea and bacteria. Biol Direct 2011; 6:52. [PMID: 21985229 PMCID: PMC3198991 DOI: 10.1186/1745-6150-6-52] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [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: 06/27/2011] [Accepted: 10/10/2011] [Indexed: 02/26/2023] Open
Abstract
Based on unique, coherent properties of phylogenetic analysis, key amino acid substitutions and structural modeling, we have identified a new class of unusual microbial rhodopsins related to the Anabaena sensory rhodopsin (ASR) protein, including multiple homologs not previously recognized. We propose the name xenorhodopsin for this class, reflecting a taxonomically diverse membership spanning five different Bacterial phyla as well as the Euryarchaeotal class Nanohaloarchaea. The patchy phylogenetic distribution of xenorhodopsin homologs is consistent with historical dissemination through horizontal gene transfer. Shared characteristics of xenorhodopsin-containing microbes include the absence of flagellar motility and isolation from high light habitats.
Collapse
Affiliation(s)
- Juan A Ugalde
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92093-0202, USA
| | | | | | | |
Collapse
|
23
|
Narasingarao P, Podell S, Ugalde JA, Brochier-Armanet C, Emerson JB, Brocks JJ, Heidelberg KB, Banfield JF, Allen EE. De novo metagenomic assembly reveals abundant novel major lineage of Archaea in hypersaline microbial communities. ISME J 2011; 6:81-93. [PMID: 21716304 DOI: 10.1038/ismej.2011.78] [Citation(s) in RCA: 227] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
This study describes reconstruction of two highly unusual archaeal genomes by de novo metagenomic assembly of multiple, deeply sequenced libraries from surface waters of Lake Tyrrell (LT), a hypersaline lake in NW Victoria, Australia. Lineage-specific probes were designed using the assembled genomes to visualize these novel archaea, which were highly abundant in the 0.1-0.8 μm size fraction of lake water samples. Gene content and inferred metabolic capabilities were highly dissimilar to all previously identified hypersaline microbial species. Distinctive characteristics included unique amino acid composition, absence of Gvp gas vesicle proteins, atypical archaeal metabolic pathways and unusually small cell size (approximately 0.6 μm diameter). Multi-locus phylogenetic analyses demonstrated that these organisms belong to a new major euryarchaeal lineage, distantly related to halophilic archaea of class Halobacteria. Consistent with these findings, we propose creation of a new archaeal class, provisionally named 'Nanohaloarchaea'. In addition to their high abundance in LT surface waters, we report the prevalence of Nanohaloarchaea in other hypersaline environments worldwide. The simultaneous discovery and genome sequencing of a novel yet ubiquitous lineage of uncultivated microorganisms demonstrates that even historically well-characterized environments can reveal unexpected diversity when analyzed by metagenomics, and advances our understanding of the ecology of hypersaline environments and the evolutionary history of the archaea.
Collapse
Affiliation(s)
- Priya Narasingarao
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
24
|
Junier P, Junier T, Podell S, Sims DR, Detter JC, Lykidis A, Han CS, Wigginton NS, Gaasterland T, Bernier-Latmani R. The genome of the Gram-positive metal- and sulfate-reducing bacterium Desulfotomaculum reducens strain MI-1. Environ Microbiol 2011; 12:2738-54. [PMID: 20482743 DOI: 10.1111/j.1462-2920.2010.02242.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Spore-forming, Gram-positive sulfate-reducing bacteria (SRB) represent a group of SRB that dominates the deep subsurface as well as niches in which resistance to oxygen and dessication is an advantage. Desulfotomaculum reducens strain MI-1 is one of the few cultured representatives of that group with a complete genome sequence available. The metabolic versatility of this organism is reflected in the presence of genes encoding for the oxidation of various electron donors, including three- and four-carbon fatty acids and alcohols. Synteny in genes involved in sulfate reduction across all four sequenced Gram-positive SRB suggests a distinct sulfate-reduction mechanism for this group of bacteria. Based on the genomic information obtained for sulfate reduction in D. reducens, the transfer of electrons to the sulfite and APS reductases is proposed to take place via the quinone pool and heterodisulfide reductases respectively. In addition, both H(2) -evolving and H(2) -consuming cytoplasmic hydrogenases were identified in the genome, pointing to potential cytoplasmic H(2) cycling in the bacterium. The mechanism of metal reduction remains unknown.
Collapse
Affiliation(s)
- Pilar Junier
- Environmental Microbiology Laboratory, Ecole Polytechnique Fédérale de Lausanne, Lausanne 1015, Switzerland
| | | | | | | | | | | | | | | | | | | |
Collapse
|
25
|
Penn K, Jenkins C, Nett M, Udwary DW, Gontang EA, McGlinchey RP, Foster B, Lapidus A, Podell S, Allen EE, Moore BS, Jensen PR. Genomic islands link secondary metabolism to functional adaptation in marine Actinobacteria. ISME J 2009; 3:1193-203. [PMID: 19474814 PMCID: PMC2749086 DOI: 10.1038/ismej.2009.58] [Citation(s) in RCA: 150] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Genomic islands have been shown to harbor functional traits that differentiate ecologically distinct populations of environmental bacteria. A comparative analysis of the complete genome sequences of the marine Actinobacteria Salinispora tropica and S. arenicola reveals that 75% of the species-specific genes are located in 21 genomic islands. These islands are enriched in genes associated with secondary metabolite biosynthesis providing evidence that secondary metabolism is linked to functional adaptation. Secondary metabolism accounts for 8.8% and 10.9% of the genes in the S. tropica and S. arenicola genomes, respectively, and represents the major functional category of annotated genes that differentiates the two species. Genomic islands harbor all 25 of the species-specific biosynthetic pathways, the majority of which occur in S. arenicola and may contribute to the cosmopolitan distribution of this species. Genome evolution is dominated by gene duplication and acquisition, which in the case of secondary metabolism provide immediate opportunities for the production of new bioactive products. Evidence that secondary metabolic pathways are exchanged horizontally, coupled with prior evidence for fixation among globally distributed populations, supports a functional role and suggests that the acquisition of natural product biosynthetic gene clusters represents a previously unrecognized force driving bacterial diversification. Species-specific differences observed in CRISPR (clustered regularly interspaced short palindromic repeat) sequences suggest that S. arenicola may possess a higher level of phage immunity, while a highly duplicated family of polymorphic membrane proteins provides evidence of a new mechanism of marine adaptation in Gram-positive bacteria.
Collapse
Affiliation(s)
- Kevin Penn
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
26
|
Podell S, Gaasterland T, Allen EE. A database of phylogenetically atypical genes in archaeal and bacterial genomes, identified using the DarkHorse algorithm. BMC Bioinformatics 2008; 9:419. [PMID: 18840280 PMCID: PMC2573894 DOI: 10.1186/1471-2105-9-419] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [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: 05/14/2008] [Accepted: 10/07/2008] [Indexed: 01/30/2023] Open
Abstract
Background The process of horizontal gene transfer (HGT) is believed to be widespread in Bacteria and Archaea, but little comparative data is available addressing its occurrence in complete microbial genomes. Collection of high-quality, automated HGT prediction data based on phylogenetic evidence has previously been impractical for large numbers of genomes at once, due to prohibitive computational demands. DarkHorse, a recently described statistical method for discovering phylogenetically atypical genes on a genome-wide basis, provides a means to solve this problem through lineage probability index (LPI) ranking scores. LPI scores inversely reflect phylogenetic distance between a test amino acid sequence and its closest available database matches. Proteins with low LPI scores are good horizontal gene transfer candidates; those with high scores are not. Description The DarkHorse algorithm has been applied to 955 microbial genome sequences, and the results organized into a web-searchable relational database, called the DarkHorse HGT Candidate Resource . Users can select individual genomes or groups of genomes to screen by LPI score, search for protein functions by descriptive annotation or amino acid sequence similarity, or select proteins with unusual G+C composition in their underlying coding sequences. The search engine reports LPI scores for match partners as well as query sequences, providing the opportunity to explore whether potential HGT donor sequences are phylogenetically typical or atypical within their own genomes. This information can be used to predict whether or not sufficient information is available to build a well-supported phylogenetic tree using the potential donor sequence. Conclusion The DarkHorse HGT Candidate database provides a powerful, flexible set of tools for identifying phylogenetically atypical proteins, allowing researchers to explore both individual HGT events in single genomes, and large-scale HGT patterns among protein families and genome groups. Although the DarkHorse algorithm cannot, by itself, provide definitive proof of horizontal gene transfer, it is a flexible, powerful tool that can be combined with slower, more rigorous methods in situations where these other methods could not otherwise be applied.
Collapse
Affiliation(s)
- Sheila Podell
- Marine Biology Research Division, Scripps Institution of Oceanography University of California at San Diego, La Jolla, CA 92093 USA.
| | | | | |
Collapse
|
27
|
Dick GJ, Podell S, Johnson HA, Rivera-Espinoza Y, Bernier-Latmani R, McCarthy JK, Torpey JW, Clement BG, Gaasterland T, Tebo BM. Genomic insights into Mn(II) oxidation by the marine alphaproteobacterium Aurantimonas sp. strain SI85-9A1. Appl Environ Microbiol 2008; 74:2646-58. [PMID: 18344346 PMCID: PMC2394881 DOI: 10.1128/aem.01656-07] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.6] [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: 07/19/2007] [Accepted: 03/02/2008] [Indexed: 01/06/2023] Open
Abstract
Microbial Mn(II) oxidation has important biogeochemical consequences in marine, freshwater, and terrestrial environments, but many aspects of the physiology and biochemistry of this process remain obscure. Here, we report genomic insights into Mn(II) oxidation by the marine alphaproteobacterium Aurantimonas sp. strain SI85-9A1, isolated from the oxic/anoxic interface of a stratified fjord. The SI85-9A1 genome harbors the genetic potential for metabolic versatility, with genes for organoheterotrophy, methylotrophy, oxidation of sulfur and carbon monoxide, the ability to grow over a wide range of O(2) concentrations (including microaerobic conditions), and the complete Calvin cycle for carbon fixation. Although no growth could be detected under autotrophic conditions with Mn(II) as the sole electron donor, cultures of SI85-9A1 grown on glycerol are dramatically stimulated by addition of Mn(II), suggesting an energetic benefit from Mn(II) oxidation. A putative Mn(II) oxidase is encoded by duplicated multicopper oxidase genes that have a complex evolutionary history including multiple gene duplication, loss, and ancient horizontal transfer events. The Mn(II) oxidase was most abundant in the extracellular fraction, where it cooccurs with a putative hemolysin-type Ca(2+)-binding peroxidase. Regulatory elements governing the cellular response to Fe and Mn concentration were identified, and 39 targets of these regulators were detected. The putative Mn(II) oxidase genes were not among the predicted targets, indicating that regulation of Mn(II) oxidation is controlled by other factors yet to be identified. Overall, our results provide novel insights into the physiology and biochemistry of Mn(II) oxidation and reveal a genome specialized for life at the oxic/anoxic interface.
Collapse
Affiliation(s)
- Gregory J Dick
- Department of Environmental and Biomolecular Systems, OGI School of Science & Engineering, Oregon Health & Sciences University, 20000 NW Walker Rd., Beaverton, OR 97006, USA
| | | | | | | | | | | | | | | | | | | |
Collapse
|
28
|
Abstract
Phagosomal transporters (Phts), required for intracellular growth of Legionella pneumophila, comprise a novel family of multispanning alpha-helical proteins within the major facilitator superfamily (MFS). The members of this family derive exclusively from bacteria. Multiple paralogues are present in a restricted group of Alpha- and Gammaproteobacteria, but single members were also found in Chlamydia and Cyanobacteria. Their protein sequences were aligned, yielding a phylogenetic tree showing the relations of the proteins to each other. Topological analyses revealed a probable 12 alpha-helical transmembrane segment (TMS) topology. Motif identification and statistical analyses provided convincing evidence that these proteins arose from a six TMS precursor by intragenic duplication. The phylogenetic tree revealed some potential orthologous relationships, suggestive of common function. However, several probable examples of lateral transfer of the encoding genetic material between bacteria were identified and analysed. The Pht family most closely resembles a smaller MFS family (the UMF9 family) with no functionally characterized members. However, the UMF9 family occurs in a broader range of prokaryotic organism types, including Archaea. These two families differ in that organisms bearing members of the Pht family often have numerous paralogues, whereas organisms bearing members of the UMF9 family never have more than two. This work serves to characterize two novel families within the MFS and provides compelling evidence for horizontal transfer of some of the family members.
Collapse
Affiliation(s)
- Derek E Chen
- Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093-0116, USA
| | - Sheila Podell
- Scripps Genome Center, Scripps Institution of Oceanography, University of California at San Diego, La Jolla, CA 92093-0202, USA
| | - John-Demian Sauer
- Department of Biochemistry, University of California at Berkeley, Berkeley, CA, USA
| | - Michele S Swanson
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Milton H Saier
- Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093-0116, USA
| |
Collapse
|
29
|
Podell S, Gaasterland T. DarkHorse: a method for genome-wide prediction of horizontal gene transfer. Genome Biol 2007; 8:R16. [PMID: 17274820 PMCID: PMC1852411 DOI: 10.1186/gb-2007-8-2-r16] [Citation(s) in RCA: 123] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2006] [Revised: 11/09/2006] [Accepted: 02/02/2007] [Indexed: 12/14/2022] Open
Abstract
DarkHorse is a new approach to rapid, genome-wide identification and ranking of horizontal transfer candidate proteins. A new approach to rapid, genome-wide identification and ranking of horizontal transfer candidate proteins is presented. The method is quantitative, reproducible, and computationally undemanding. It can be combined with genomic signature and/or phylogenetic tree-building procedures to improve accuracy and efficiency. The method is also useful for retrospective assessments of horizontal transfer prediction reliability, recognizing orthologous sequences that may have been previously overlooked or unavailable. These features are demonstrated in bacterial, archaeal, and eukaryotic examples.
Collapse
Affiliation(s)
- Sheila Podell
- Scripps Genome Center, Scripps Institution of Oceanography, University of California at San Diego, Gilman Drive, La Jolla, CA 92093-0202, USA
| | - Terry Gaasterland
- Scripps Genome Center, Scripps Institution of Oceanography, University of California at San Diego, Gilman Drive, La Jolla, CA 92093-0202, USA
| |
Collapse
|
30
|
Palenik B, Grimwood J, Aerts A, Rouzé P, Salamov A, Putnam N, Dupont C, Jorgensen R, Derelle E, Rombauts S, Zhou K, Otillar R, Merchant SS, Podell S, Gaasterland T, Napoli C, Gendler K, Manuell A, Tai V, Vallon O, Piganeau G, Jancek S, Heijde M, Jabbari K, Bowler C, Lohr M, Robbens S, Werner G, Dubchak I, Pazour GJ, Ren Q, Paulsen I, Delwiche C, Schmutz J, Rokhsar D, Van de Peer Y, Moreau H, Grigoriev IV. The tiny eukaryote Ostreococcus provides genomic insights into the paradox of plankton speciation. Proc Natl Acad Sci U S A 2007; 104:7705-10. [PMID: 17460045 PMCID: PMC1863510 DOI: 10.1073/pnas.0611046104] [Citation(s) in RCA: 417] [Impact Index Per Article: 24.5] [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: 11/18/2022] Open
Abstract
The smallest known eukaryotes, at approximately 1-mum diameter, are Ostreococcus tauri and related species of marine phytoplankton. The genome of Ostreococcus lucimarinus has been completed and compared with that of O. tauri. This comparison reveals surprising differences across orthologous chromosomes in the two species from highly syntenic chromosomes in most cases to chromosomes with almost no similarity. Species divergence in these phytoplankton is occurring through multiple mechanisms acting differently on different chromosomes and likely including acquisition of new genes through horizontal gene transfer. We speculate that this latter process may be involved in altering the cell-surface characteristics of each species. In addition, the genome of O. lucimarinus provides insights into the unique metal metabolism of these organisms, which are predicted to have a large number of selenocysteine-containing proteins. Selenoenzymes are more catalytically active than similar enzymes lacking selenium, and thus the cell may require less of that protein. As reported here, selenoenzymes, novel fusion proteins, and loss of some major protein families including ones associated with chromatin are likely important adaptations for achieving a small cell size.
Collapse
Affiliation(s)
- Brian Palenik
- Scripps Institution of Oceanography, University of California at San Diego, La Jolla, CA 92093-0202
- To whom correspondence may be addressed. E-mail: or
| | - Jane Grimwood
- Joint Genome Institute and Stanford Human Genome Center, Stanford University School of Medicine, 975 California Avenue, Palo Alto, CA 94304
| | - Andrea Aerts
- U.S. Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598
| | - Pierre Rouzé
- Laboratoire Associé de l'Institut National de la Recherche Agronomique (France), Ghent University, Technologiepark 927, B-9052 Ghent, Belgium
| | - Asaf Salamov
- U.S. Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598
| | - Nicholas Putnam
- U.S. Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598
| | - Chris Dupont
- Scripps Institution of Oceanography, University of California at San Diego, La Jolla, CA 92093-0202
| | - Richard Jorgensen
- Department of Plant Sciences, University of Arizona, 303 Forbes Building, Tucson, AZ 85721-0036
| | - Evelyne Derelle
- Observatoire Océanologique, Laboratoire Arago, Centre National de la Recherche Scientifique/Université Pierre et Marie Curie Paris 6, Unité Mixte de Recherche 7628, BP 44, 66651 Banyuls sur Mer Cedex, France
| | - Stephane Rombauts
- Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology, Ghent University, Technologiepark 927, B-9052 Ghent, Belgium
| | - Kemin Zhou
- U.S. Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598
| | - Robert Otillar
- U.S. Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598
| | - Sabeeha S. Merchant
- Department of Chemistry and Biochemistry, University of California, Box 951569, Los Angeles, CA 90095
| | - Sheila Podell
- Scripps Genome Center, Scripps Institution of Oceanography, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0202
| | - Terry Gaasterland
- Scripps Genome Center, Scripps Institution of Oceanography, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0202
| | - Carolyn Napoli
- Department of Plant Sciences, University of Arizona, 303 Forbes Building, Tucson, AZ 85721-0036
| | - Karla Gendler
- Department of Plant Sciences, University of Arizona, 303 Forbes Building, Tucson, AZ 85721-0036
| | - Andrea Manuell
- Department of Cell Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037
| | - Vera Tai
- Scripps Institution of Oceanography, University of California at San Diego, La Jolla, CA 92093-0202
| | - Olivier Vallon
- Institut de Biologie Physico-Chimique, Centre National de la Recherche Scientifique/Université Paris 6, Unité Mixte de Recherche 7141, 13, Rue Pierre et Marie Curie, 75005 Paris, France
| | - Gwenael Piganeau
- Observatoire Océanologique, Laboratoire Arago, Centre National de la Recherche Scientifique/Université Pierre et Marie Curie Paris 6, Unité Mixte de Recherche 7628, BP 44, 66651 Banyuls sur Mer Cedex, France
| | - Séverine Jancek
- Observatoire Océanologique, Laboratoire Arago, Centre National de la Recherche Scientifique/Université Pierre et Marie Curie Paris 6, Unité Mixte de Recherche 7628, BP 44, 66651 Banyuls sur Mer Cedex, France
| | - Marc Heijde
- Département de Biologie, Ecole Normale Supérieure, Formation de Recherche en Evolution 2910, Centre National de la Recherche Scientifique, 46, Rue D'Ulm, 75230 Paris Cedex 05, France
| | - Kamel Jabbari
- Département de Biologie, Ecole Normale Supérieure, Formation de Recherche en Evolution 2910, Centre National de la Recherche Scientifique, 46, Rue D'Ulm, 75230 Paris Cedex 05, France
| | - Chris Bowler
- Département de Biologie, Ecole Normale Supérieure, Formation de Recherche en Evolution 2910, Centre National de la Recherche Scientifique, 46, Rue D'Ulm, 75230 Paris Cedex 05, France
| | - Martin Lohr
- Institut für Allgemeine Botanik, Johannes Gutenberg-Universität, D-55099 Mainz, Germany
| | - Steven Robbens
- Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology, Ghent University, Technologiepark 927, B-9052 Ghent, Belgium
| | - Gregory Werner
- U.S. Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598
| | - Inna Dubchak
- U.S. Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598
| | - Gregory J. Pazour
- Program in Molecular Medicine, University of Massachusetts Medical School, Suite 213, Biotech II, 373 Plantation Street, Worcester, MA 01605
| | - Qinghu Ren
- The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850; and
| | - Ian Paulsen
- The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850; and
| | - Chuck Delwiche
- Cell Biology and Molecular Genetics, University of Maryland, H. J. Patterson Hall, Building 073, College Park, MD 20742-5815
| | - Jeremy Schmutz
- Joint Genome Institute and Stanford Human Genome Center, Stanford University School of Medicine, 975 California Avenue, Palo Alto, CA 94304
| | - Daniel Rokhsar
- U.S. Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598
| | - Yves Van de Peer
- Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology, Ghent University, Technologiepark 927, B-9052 Ghent, Belgium
| | - Hervé Moreau
- Observatoire Océanologique, Laboratoire Arago, Centre National de la Recherche Scientifique/Université Pierre et Marie Curie Paris 6, Unité Mixte de Recherche 7628, BP 44, 66651 Banyuls sur Mer Cedex, France
| | - Igor V. Grigoriev
- U.S. Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598
- To whom correspondence may be addressed. E-mail: or
| |
Collapse
|
31
|
Li X, Wang XJ, Tannenhauser J, Podell S, Mukherjee P, Hertel M, Biane J, Masuda S, Nottebohm F, Gaasterland T. Genomic resources for songbird research and their use in characterizing gene expression during brain development. Proc Natl Acad Sci U S A 2007; 104:6834-9. [PMID: 17426146 PMCID: PMC1850020 DOI: 10.1073/pnas.0701619104] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [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] [Indexed: 11/18/2022] Open
Abstract
Vocal learning and neuronal replacement have been studied extensively in songbirds, but until recently, few molecular and genomic tools for songbird research existed. Here we describe new molecular/genomic resources developed in our laboratory. We made cDNA libraries from zebra finch (Taeniopygia guttata) brains at different developmental stages. A total of 11,000 cDNA clones from these libraries, representing 5,866 unique gene transcripts, were randomly picked and sequenced from the 3' ends. A web-based database was established for clone tracking, sequence analysis, and functional annotations. Our cDNA libraries were not normalized. Sequencing ESTs without normalization produced many developmental stage-specific sequences, yielding insights into patterns of gene expression at different stages of brain development. In particular, the cDNA library made from brains at posthatching day 30-50, corresponding to the period of rapid song system development and song learning, has the most diverse and richest set of genes expressed. We also identified five microRNAs whose sequences are highly conserved between zebra finch and other species. We printed cDNA microarrays and profiled gene expression in the high vocal center of both adult male zebra finches and canaries (Serinus canaria). Genes differentially expressed in the high vocal center were identified from the microarray hybridization results. Selected genes were validated by in situ hybridization. Networks among the regulated genes were also identified. These resources provide songbird biologists with tools for genome annotation, comparative genomics, and microarray gene expression analysis.
Collapse
Affiliation(s)
- Xiaoching Li
- The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
32
|
Barabote RD, Tamang DG, Abeywardena SN, Fallah NS, Fu JYC, Lio JK, Mirhosseini P, Pezeshk R, Podell S, Salampessy ML, Thever MD, Saier MH. Extra domains in secondary transport carriers and channel proteins. Biochimica et Biophysica Acta (BBA) - Biomembranes 2006; 1758:1557-79. [PMID: 16905115 DOI: 10.1016/j.bbamem.2006.06.018] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2006] [Revised: 06/16/2006] [Accepted: 06/20/2006] [Indexed: 01/06/2023]
Abstract
"Extra" domains in members of the families of secondary transport carrier and channel proteins provide secondary functions that expand, amplify or restrict the functional nature of these proteins. Domains in secondary carriers include TrkA and SPX domains in DASS family members, DedA domains in TRAP-T family members (both of the IT superfamily), Kazal-2 and PDZ domains in OAT family members (of the MF superfamily), USP, IIA(Fru) and TrkA domains in ABT family members (of the APC superfamily), ricin domains in OST family members, and TrkA domains in AAE family members. Some transporters contain highly hydrophilic domains consisting of multiple repeat units that can also be found in proteins of dissimilar function. Similarly, transmembrane alpha-helical channel-forming proteins contain unique, conserved, hydrophilic domains, most of which are not found in carriers. In some cases the functions of these domains are known. They may be ligand binding domains, phosphorylation domains, signal transduction domains, protein/protein interaction domains or complex carbohydrate-binding domains. These domains mediate regulation, subunit interactions, or subcellular targeting. Phylogenetic analyses show that while some of these domains are restricted to closely related proteins derived from specific organismal types, others are nearly ubiquitous within a particular family of transporters and occur in a tremendous diversity of organisms. The former probably became associated with the transporters late in the evolutionary process; the latter probably became associated with the carriers much earlier. These domains can be located at either end of the transporter or in a central region, depending on the domain and transporter family. These studies provide useful information about the evolution of extra domains in channels and secondary carriers and provide novel clues concerning function.
Collapse
Affiliation(s)
- Ravi D Barabote
- Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093-0116, USA
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
33
|
Abstract
Background N-terminal myristoylation plays a vital role in membrane targeting and signal transduction in plant responses to environmental stress. Although N-myristoyltransferase enzymatic function is conserved across plant, animal, and fungal kingdoms, exact substrate specificities vary, making it difficult to predict protein myristoylation accurately within specific taxonomic groups. Results A new method for predicting N-terminal myristoylation sites specifically in plants has been developed and statistically tested for sensitivity, specificity, and robustness. Compared to previously available methods, the new model is both more sensitive in detecting known positives, and more selective in avoiding false positives. Scores of myristoylated and non-myristoylated proteins are more widely separated than with other methods, greatly reducing ambiguity and the number of sequences giving intermediate, uninformative results. The prediction model is available at . Conclusion Superior performance of the new model is due to the selection of a plant-specific training set, covering 266 unique sequence examples from 40 different species, the use of a probability-based hidden Markov model to obtain predictive scores, and a threshold cutoff value chosen to provide maximum positive-negative discrimination. The new model has been used to predict 589 plant proteins likely to contain N-terminal myristoylation signals, and to analyze the functional families in which these proteins occur.
Collapse
Affiliation(s)
- Sheila Podell
- San Diego Supercomputer Center, University of California San Diego, La Jolla CA 92093-0537, USA
- Department of Biology, University of California San Diego, La Jolla CA 92093-0537, USA
| | - Michael Gribskov
- San Diego Supercomputer Center, University of California San Diego, La Jolla CA 92093-0537, USA
- Department of Biology, University of California San Diego, La Jolla CA 92093-0537, USA
| |
Collapse
|
34
|
Miller JJ, Tiemann K, Podell S, Doerr Stevens JK, Kuvelas T, Greener Y, Killam AL, Goenechea J, Dittrich HC, Becher H. In vitro, animal, and human characterization of OPTISON infusions for myocardial contrast echocardiography. J Am Soc Echocardiogr 1999; 12:1027-34. [PMID: 10588777 DOI: 10.1016/s0894-7317(99)70098-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
UNLABELLED Traditionally, performing myocardial contrast echocardiography with OPTISON required maximal bolus dosing. However, sustained and consistent opacification of the myocardium would be preferable for perfusion imaging. METHODS Images of 5 anesthetized dogs and 6 human volunteers were obtained with a second harmonic ultrasound system during bolus administration of OPTISON and 2 infusion techniques. One infusion technique used diluted OPTISON, and the other used the buoyant properties of OPTISON microspheres by placing the contrast agent between an infusion source and the intravenous site in a vertically oriented extension line (ELT). Myocardial intensities and in vitro microsphere characteristics were analyzed to assess the consistency of microsphere delivery over time. RESULTS In addition to providing higher myocardial opacification intensity than diluted infusions, ELT infusions provided consistent microsphere concentration, phantom enhancement, and near-peak bolus-level myocardial opacification for 7 to 15 minutes. The myocardial intensity at 3 and 5 minutes in human subjects during ELT infusions (30 mL/h; 2.5 mL) was lower (220 arbitrary units [au] and 165 au, respectively) but not significantly different (P =.3 and.1, respectively) than the peak myocardial intensity (265 au) after bolus administration. CONCLUSION This new ELT infusion method provides an acceptable alternative to bolus administration of OPTISON for prolonged myocardial opacification.
Collapse
Affiliation(s)
- J J Miller
- Molecular Biosystems, Inc, San Diego, CA 92121, USA
| | | | | | | | | | | | | | | | | | | |
Collapse
|
35
|
Podell S, Burrascano C, Gaal M, Golec B, Maniquis J, Mehlhaff P. Physical and biochemical stability of Optison, an injectable ultrasound contrast agent. Biotechnol Appl Biochem 1999; 30:213-23. [PMID: 10574690] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/14/2023]
Abstract
Optison(R) is an ultrasound contrast agent, consisting of gas-filled microspheres surrounded by a solid shell of heat-denatured human albumin. Size-distribution measurements of these microspheres are a critical stability indicating factor, because loss of encapsulated gas eliminates ultrasound contrast activity. Composition of the encapsulated gas is also critical, because air-filled microspheres do not persist nearly as long in vivo as microspheres filled with less soluble gases. Optison(R) stability has been tested during exposure to chemical substances expected to dissolve microsphere shells. In addition, size-distribution and gas-composition measurements were used to evaluate the effects of external gas composition, elevated temperature, mixing, needle shear and pressure on product stability. Optison(R) microsphere shells dissolve only when exposed to relatively extreme chemical conditions, such as low pH (<4.0), detergents or chaotropic salts. The shells are highly gas-permeable, and microspheres lose encapsulated gas rapidly and irreversibly when exposed to gas-deficient liquids. Pressure, impact stress, and the application of ultrasound energy all cause liquids to become gas-deficient, and also cause irreversible gas loss. Pressure sensitivity differs dramatically between mixed and unmixed microspheres, further supporting the conclusion that gas diffusion is the major cause of Optison(R) instability. To preserve the efficacy of Optison(R) as an ultrasound contrast agent, it is necessary to devote special attention to minimizing opportunities for gas exchange, mixing and exposure to gas-deficient liquids, so that the size distribution and gas composition of the original product are maintained during handling.
Collapse
Affiliation(s)
- S Podell
- Molecular Biosystems Inc., 10030 Barnes Canyon Road, San Diego, CA 92121-2789, USA
| | | | | | | | | | | |
Collapse
|
36
|
Dubensky TW, Lauderdale V, Marich JE, Podell S, Pontsler AV, Rice SM, Ruth JL, Jablonski EG. Application of Nonisotopic Oligonucleotide Probes. Clin Chem 1991. [DOI: 10.1093/clinchem/37.4.611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- T W Dubensky
- Syngene, Inc., 10030 Barnes Canyon Rd., San Diego, CA 92121
| | - V Lauderdale
- Syngene, Inc., 10030 Barnes Canyon Rd., San Diego, CA 92121
| | - J E Marich
- Syngene, Inc., 10030 Barnes Canyon Rd., San Diego, CA 92121
| | - S Podell
- Syngene, Inc., 10030 Barnes Canyon Rd., San Diego, CA 92121
| | - A V Pontsler
- Syngene, Inc., 10030 Barnes Canyon Rd., San Diego, CA 92121
| | - S M Rice
- Syngene, Inc., 10030 Barnes Canyon Rd., San Diego, CA 92121
| | - J L Ruth
- Syngene, Inc., 10030 Barnes Canyon Rd., San Diego, CA 92121
| | - E G Jablonski
- Syngene, Inc., 10030 Barnes Canyon Rd., San Diego, CA 92121
| |
Collapse
|
37
|
Podell S, Maske W, Ibañez E, Jablonski E. Comparison of solution hybridization efficiencies using alkaline phosphatase-labelled and 32P-labelled oligodeoxynucleotide probes. Mol Cell Probes 1991; 5:117-24. [PMID: 2072933 DOI: 10.1016/0890-8508(91)90005-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [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: 12/30/2022]
Abstract
The hybridization efficiencies of oligonucleotide probes directly labelled with alkaline phosphatase and probes labelled with 32P were compared by quantitating the enzyme activity or radioactivity associated with hybridization targets over time. The targets tested included both synthetic oligonucleotides (53 bases in length) and single-stranded and double-stranded cloned M13 DNA (7350 bases long). Hybrid molecules were separated from unhybridized probes using size exclusion FPLC. This system allowed quantitative analysis of the time course and efficiency of hybridization for both probes and targets in complex hybridization media containing protein blocking agents, formamide, and carrier DNA. Similar maximum hybridization efficiencies were attained for probes labelled with either radioactivity or alkaline phosphatase as a marker. The reaction rate constant for oligonucleotide hybridization to long M13 targets was 3.6 x 10(5) mol-1 s-1 for a probe labelled with alkaline phosphatase, and 5.8 x 10(5) mol-1 s-1 for the same probe labelled with 32P.
Collapse
Affiliation(s)
- S Podell
- Molecular Biosystems, Inc., San Diego, CA 92121
| | | | | | | |
Collapse
|
38
|
Zheng XF, Podell S, Sefton BM, Kaplan PL. The sequence of chicken c-yes and p61c-yes. Oncogene 1989; 4:99-104. [PMID: 2464785] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
We have deduced the sequence of the protein encoded by the chicken c-yes gene from overlapping cDNA clones. The predicted protein, p61c-yes, contains 541 amino acids and has a molecular weight of 60,911 with the amino terminal methionine residue. Chicken p61c-yes differs from Y73 virus p90gag/v-yes in three respects. First, the carboxy-terminal eight amino acids of p61c-yes are replaced by three amino acids in p90gag/v-yes, which are encoded by the avian leukemia virus env gene. This alteration changes the position and context of a tyrosine residue in p61c-yes. Second, nucleotides which are present as 5' non-translated sequence in the p61c-yes mRNA, are translated in the p90gag/v-yes mRNA. Third, there are fourteen dispersed nucleotide differences in Y73 v-yes which result in six amino differences between the body of p90gag/v-yes and p61c-yes. Chicken p61c-yes differs from human p61c-yes at 43 residues, and from chicken pp60c-src at 122 residues.
Collapse
Affiliation(s)
- X F Zheng
- Dana-Farber Cancer Institute, Boston, Massachusetts 02115
| | | | | | | |
Collapse
|
39
|
Werner DL, Podell S. Interpretation of heterophoria and duction findings when using the Humphrey Vision Analyzer. Am J Optom Physiol Opt 1982; 59:878-84. [PMID: 7180929 DOI: 10.1097/00006324-198211000-00005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
|
40
|
Werner DL, Podell S. Effectiveness of hypertension screening in an urban optometric clinic. J Am Optom Assoc 1978; 49:1393-1403. [PMID: 107214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
461 randomly selected eyecare patients were screened for systemic hypertension at the clinic of the University Optometric Center, State College of Optometry, State University of New York. The results of this survey showed 52 screening failures, 30 of whom had previously been identified as having hypertension. The study showed that the screening and follow-up added $2.00 per patient to the chair cost. The authors concluded that the information provided to our patients, students and practitioners warrants this cost.
Collapse
|