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Wei TS, Gao ZM, Gong L, Li QM, Zhou YL, Chen HG, He LS, Wang Y. Genome-centric view of the microbiome in a new deep-sea glass sponge species Bathydorus sp. Front Microbiol 2023; 14:1078171. [PMID: 36846759 PMCID: PMC9944714 DOI: 10.3389/fmicb.2023.1078171] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 01/12/2023] [Indexed: 02/10/2023] Open
Abstract
Sponges are widely distributed in the global ocean and harbor diverse symbiotic microbes with mutualistic relationships. However, sponge symbionts in the deep sea remain poorly studied at the genome level. Here, we report a new glass sponge species of the genus Bathydorus and provide a genome-centric view of its microbiome. We obtained 14 high-quality prokaryotic metagenome-assembled genomes (MAGs) affiliated with the phyla Nitrososphaerota, Pseudomonadota, Nitrospirota, Bdellovibrionota, SAR324, Bacteroidota, and Patescibacteria. In total, 13 of these MAGs probably represent new species, suggesting the high novelty of the deep-sea glass sponge microbiome. An ammonia-oxidizing Nitrososphaerota MAG B01, which accounted for up to 70% of the metagenome reads, dominated the sponge microbiomes. The B01 genome had a highly complex CRISPR array, which likely represents an advantageous evolution toward a symbiotic lifestyle and forceful ability to defend against phages. A sulfur-oxidizing Gammaproteobacteria species was the second most dominant symbiont, and a nitrite-oxidizing Nitrospirota species could also be detected, but with lower relative abundance. Bdellovibrio species represented by two MAGs, B11 and B12, were first reported as potential predatory symbionts in deep-sea glass sponges and have undergone dramatic genome reduction. Comprehensive functional analysis indicated that most of the sponge symbionts encoded CRISPR-Cas systems and eukaryotic-like proteins for symbiotic interactions with the host. Metabolic reconstruction further illustrated their essential roles in carbon, nitrogen, and sulfur cycles. In addition, diverse putative phages were identified from the sponge metagenomes. Our study expands the knowledge of microbial diversity, evolutionary adaption, and metabolic complementarity in deep-sea glass sponges.
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Affiliation(s)
- Tao-Shu Wei
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, China,University of Chinese Academy of Sciences, Beijing, China
| | - Zhao-Ming Gao
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, China,*Correspondence: Zhao-Ming Gao ✉
| | - Lin Gong
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, Shandong, China
| | - Qing-Mei Li
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, China
| | - Ying-Li Zhou
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, China
| | - Hua-Guan Chen
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, China,University of Chinese Academy of Sciences, Beijing, China
| | - Li-Sheng He
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, China
| | - Yong Wang
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, China,Institute for Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen, China,Yong Wang ✉
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2
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Wang P, Li M, Dong L, Zhang C, Xie W. Comparative Genomics of Thaumarchaeota From Deep-Sea Sponges Reveal Their Niche Adaptation. Front Microbiol 2022; 13:869834. [PMID: 35859738 PMCID: PMC9289680 DOI: 10.3389/fmicb.2022.869834] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Accepted: 05/30/2022] [Indexed: 11/17/2022] Open
Abstract
Thaumarchaeota account for a large portion of microbial symbionts in deep-sea sponges and are even dominant in some cases. In this study, we investigated three new sponge-associated Thaumarchaeota from the deep West Pacific Ocean. Thaumarchaeota were found to be the most dominant phylum in this sponge by both prokaryotic 16S rRNA amplicons and metagenomic sequencing. Fifty-seven published Thaumarchaeota genomes from sponges and other habitats were included for genomic comparison. Similar to shallow sponge-associated Thaumarchaeota, those Thaumarchaeota in deep-sea sponges have extended genome sizes and lower coding density compared with their free-living lineages. Thaumarchaeota in deep-sea sponges were specifically enriched in genes related to stress adapting, symbiotic adhesion and stability, host–microbe interaction and protein transportation. The genes involved in defense mechanisms, such as the restriction-modification system, clustered regularly interspaced short palindromic repeats (CRISPR)/Cas system, and toxin-antitoxin system were commonly enriched in both shallow and deep sponge-associated Thaumarchaeota. Our study demonstrates the significant effects of both depth and symbiosis on forming genomic characteristics of Thaumarchaeota, and provides novel insights into their niche adaptation in deep-sea sponges.
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Affiliation(s)
- Peng Wang
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, China
| | - Minchun Li
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, China
| | - Liang Dong
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, China
| | - Cheng Zhang
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, China
| | - Wei Xie
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
- *Correspondence: Wei Xie,
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3
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DeLong EF. Genome-enabled exploration of microbial ecology and evolution in the sea: a rising tide lifts all boats. Environ Microbiol 2021; 23:1301-1321. [PMID: 33459471 PMCID: PMC8049014 DOI: 10.1111/1462-2920.15403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 01/15/2021] [Indexed: 11/26/2022]
Abstract
As a young bacteriologist just launching my career during the early days of the 'microbial revolution' in the 1980s, I was fortunate to participate in some early discoveries, and collaborate in the development of cross-disciplinary methods now commonly referred to as "metagenomics". My early scientific career focused on applying phylogenetic and genomic approaches to characterize 'wild' bacteria, archaea and viruses in their natural habitats, with an emphasis on marine systems. These central interests have not changed very much for me over the past three decades, but knowledge, methodological advances and new theoretical perspectives about the microbial world certainly have. In this invited 'How we did it' perspective, I trace some of the trajectories of my lab's collective efforts over the years, including phylogenetic surveys of microbial assemblages in marine plankton and sediments, development of microbial community gene- and genome-enabled surveys, and application of genome-guided, cultivation-independent functional characterization of novel enzymes, pathways and their relationships to in situ biogeochemistry. Throughout this short review, I attempt to acknowledge, all the mentors, students, postdocs and collaborators who enabled this research. Inevitably, a brief autobiographical review like this cannot be fully comprehensive, so sincere apologies to any of my great colleagues who are not explicitly mentioned herein. I salute you all as well!
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Affiliation(s)
- Edward F DeLong
- Daniel K. Inouye Centre for Microbial Oceanography: Research and Education, University of Hawaii, Manoa, Honolulu, HI, 96822, USA
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4
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DeLong EF. Exploring Marine Planktonic Archaea: Then and Now. Front Microbiol 2021; 11:616086. [PMID: 33519774 PMCID: PMC7838436 DOI: 10.3389/fmicb.2020.616086] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Accepted: 12/18/2020] [Indexed: 12/24/2022] Open
Abstract
In 1977, Woese and Fox leveraged molecular phylogenetic analyses of ribosomal RNAs and identified a new microbial domain of life on Earth, the Archaebacteria (now known as Archaea). At the time of their discovery, only one archaebacterial group, the strictly anaerobic methanogens, was known. But soon, other phenotypically unrelated microbial isolates were shown to belong to the Archaea, many originating from extreme habitats, including extreme halophiles, extreme thermophiles, and thermoacidophiles. Since most Archaea seemed to inhabit extreme or strictly anoxic habitats, it came as a surprise in 1992 when two new lineages of archaea were reported to be abundant in oxygen rich, temperate marine coastal waters and the deep ocean. Since that time, studies of marine planktonic archaea have revealed many more surprises, including their unexpected ubiquity, unusual symbiotic associations, unpredicted physiologies and biogeochemistry, and global abundance. In this Perspective, early work conducted on marine planktonic Archaea by my lab group and others is discussed in terms of the relevant historical context, some of the original research motivations, and surprises and discoveries encountered along the way.
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Affiliation(s)
- Edward F DeLong
- Daniel K. Inouye Center for Microbial Oceanography Research and Education, University of Hawai'i at Mănoa, Honolulu, HI, United States
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5
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Mahfouz S, Mansour G, Murphy DJ, Hanano A. Dioxin impacts on lipid metabolism of soil microbes: towards effective detection and bioassessment strategies. BIORESOUR BIOPROCESS 2020. [DOI: 10.1186/s40643-020-00347-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
AbstractDioxins are the most toxic known environmental pollutants and are mainly formed by human activities. Due to their structural stability, dioxins persist for extended periods and can be transported over long distances from their emission sources. Thus, dioxins can be accumulated to considerable levels in both human and animal food chains. Along with sediments, soils are considered the most important reservoirs of dioxins. Soil microorganisms are therefore highly exposed to dioxins, leading to a range of biological responses that can impact the diversity, genetics and functional of such microbial communities. Dioxins are very hydrophobic with a high affinity to lipidic macromolecules in exposed organisms, including microbes. This review summarizes the genetic, molecular and biochemical impacts of dioxins on the lipid metabolism of soil microbial communities and especially examines modifications in the composition and architecture of cell membranes. This will provide a useful scientific benchmark for future attempts at soil ecological risk assessment, as well as in identifying potential dioxin-specific-responsive lipid biomarkers. Finally, potential uses of lipid-sequestering microorganisms as a part of biotechnological approaches to the bio-management of environmental contamination with dioxins are discussed.
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Santiago Á, Razo-Hernández RS, Pastor N. Revealing the Structural Contributions to Thermal Adaptation of the TATA-Box Binding Protein: Molecular Dynamics and QSPR Analyses. J Chem Inf Model 2020; 60:866-879. [PMID: 31917925 DOI: 10.1021/acs.jcim.9b00824] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The TATA-box binding protein (TBP) is an important element of the transcription machinery in archaea and eukaryotic organisms. TBP is expressed in organisms adapted to different temperatures, indicating a robust structure, and experimental studies have shown that the mid-unfolding temperature (Tm) of TBP is directly correlated with the optimal growth temperature (OGT) of the organism. To understand which are the relevant structural requirements for its stability, we present the first structural and dynamic computational study of TBPs, combining molecular dynamics (MD) simulations and a quantitative structure-property relationship (QSPR) over a set of TBPs of organisms adapted to different temperatures. We found that the main structural properties of TBP used to adapt to high temperatures are an increase in the ease of desolvation of charged residues at the surface, an increase in the local resiliency, the presence of Leu clusters in the protein core, and an increase in the loss of hydrophobic packing in the N-terminal subdomain. In view of our results, we consider that TBP is a good model to study thermal adaptation, and our analysis opens the possibility of performing protein engineering on TBPs to study transcription at high or low temperatures.
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Affiliation(s)
- Ángel Santiago
- Laboratorio de Dinámica de Proteínas, Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas , Universidad Autónoma del Estado de Morelos , Av. Universidad 1001, Col. Chamilpa , Cuernavaca , Morelos 62209 , México
| | - Rodrigo Said Razo-Hernández
- Laboratorio de Dinámica de Proteínas, Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas , Universidad Autónoma del Estado de Morelos , Av. Universidad 1001, Col. Chamilpa , Cuernavaca , Morelos 62209 , México
| | - Nina Pastor
- Laboratorio de Dinámica de Proteínas, Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas , Universidad Autónoma del Estado de Morelos , Av. Universidad 1001, Col. Chamilpa , Cuernavaca , Morelos 62209 , México.,Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología , Universidad Nacional Autónoma de México , Av. Universidad 2001, Col. Chamilpa , Cuernavaca , Morelos 62210 , México
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7
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Moeller FU, Webster NS, Herbold CW, Behnam F, Domman D, Albertsen M, Mooshammer M, Markert S, Turaev D, Becher D, Rattei T, Schweder T, Richter A, Watzka M, Nielsen PH, Wagner M. Characterization of a thaumarchaeal symbiont that drives incomplete nitrification in the tropical sponge Ianthella basta. Environ Microbiol 2019; 21:3831-3854. [PMID: 31271506 PMCID: PMC6790972 DOI: 10.1111/1462-2920.14732] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 06/14/2019] [Accepted: 06/17/2019] [Indexed: 12/25/2022]
Abstract
Marine sponges represent one of the few eukaryotic groups that frequently harbour symbiotic members of the Thaumarchaeota, which are important chemoautotrophic ammonia-oxidizers in many environments. However, in most studies, direct demonstration of ammonia-oxidation by these archaea within sponges is lacking, and little is known about sponge-specific adaptations of ammonia-oxidizing archaea (AOA). Here, we characterized the thaumarchaeal symbiont of the marine sponge Ianthella basta using metaproteogenomics, fluorescence in situ hybridization, qPCR and isotope-based functional assays. 'Candidatus Nitrosospongia ianthellae' is only distantly related to cultured AOA. It is an abundant symbiont that is solely responsible for nitrite formation from ammonia in I. basta that surprisingly does not harbour nitrite-oxidizing microbes. Furthermore, this AOA is equipped with an expanded set of extracellular subtilisin-like proteases, a metalloprotease unique among archaea, as well as a putative branched-chain amino acid ABC transporter. This repertoire is strongly indicative of a mixotrophic lifestyle and is (with slight variations) also found in other sponge-associated, but not in free-living AOA. We predict that this feature as well as an expanded and unique set of secreted serpins (protease inhibitors), a unique array of eukaryotic-like proteins, and a DNA-phosporothioation system, represent important adaptations of AOA to life within these ancient filter-feeding animals.
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Affiliation(s)
- Florian U. Moeller
- Centre for Microbiology and Environmental Systems Science, Division of Microbial EcologyUniversity of ViennaAustria
| | - Nicole S. Webster
- Australian Institute of Marine ScienceTownsvilleQueenslandAustralia
- Australian Centre for Ecogenomics, School of Chemistry and Molecular BiosciencesUniversity of QueenslandSt LuciaQueenslandAustralia
| | - Craig W. Herbold
- Centre for Microbiology and Environmental Systems Science, Division of Microbial EcologyUniversity of ViennaAustria
| | - Faris Behnam
- Centre for Microbiology and Environmental Systems Science, Division of Microbial EcologyUniversity of ViennaAustria
| | - Daryl Domman
- Centre for Microbiology and Environmental Systems Science, Division of Microbial EcologyUniversity of ViennaAustria
| | - Mads Albertsen
- Center for Microbial Communities, Department of Chemistry and BioscienceAalborg University9220AalborgDenmark
| | - Maria Mooshammer
- Centre for Microbiology and Environmental Systems Science, Division of Microbial EcologyUniversity of ViennaAustria
| | - Stephanie Markert
- Institute of Marine Biotechnology e.VGreifswaldGermany
- Institute of Pharmacy, Pharmaceutical BiotechnologyUniversity of GreifswaldGreifswaldGermany
| | - Dmitrij Turaev
- Centre for Microbiology and Environmental Systems Science, Division of Computational Systems BiologyUniversity of ViennaAustria
| | - Dörte Becher
- Institute of Microbiology, Microbial ProteomicsUniversity of GreifswaldGreifswaldGermany
| | - Thomas Rattei
- Centre for Microbiology and Environmental Systems Science, Division of Computational Systems BiologyUniversity of ViennaAustria
| | - Thomas Schweder
- Institute of Marine Biotechnology e.VGreifswaldGermany
- Institute of Pharmacy, Pharmaceutical BiotechnologyUniversity of GreifswaldGreifswaldGermany
| | - Andreas Richter
- Centre for Microbiology and Environmental Systems Science, Division of Terrestrial Ecosystem ResearchUniversity of ViennaAustria
| | - Margarete Watzka
- Centre for Microbiology and Environmental Systems Science, Division of Terrestrial Ecosystem ResearchUniversity of ViennaAustria
| | - Per Halkjaer Nielsen
- Center for Microbial Communities, Department of Chemistry and BioscienceAalborg University9220AalborgDenmark
| | - Michael Wagner
- Centre for Microbiology and Environmental Systems Science, Division of Microbial EcologyUniversity of ViennaAustria
- Center for Microbial Communities, Department of Chemistry and BioscienceAalborg University9220AalborgDenmark
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8
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Zhang S, Song W, Wemheuer B, Reveillaud J, Webster N, Thomas T. Comparative Genomics Reveals Ecological and Evolutionary Insights into Sponge-Associated Thaumarchaeota. mSystems 2019; 4:e00288-19. [PMID: 31409660 PMCID: PMC6697440 DOI: 10.1128/msystems.00288-19] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 07/22/2019] [Indexed: 01/25/2023] Open
Abstract
Thaumarchaeota are frequently reported to associate with marine sponges (phylum Porifera); however, little is known about the features that distinguish them from their free-living thaumarchaeal counterparts. In this study, thaumarchaeal metagenome-assembled genomes (MAGs) were reconstructed from metagenomic data sets derived from the marine sponges Hexadella detritifera, Hexadella cf. detritifera, and Stylissa flabelliformis Phylogenetic and taxonomic analyses revealed that the three thaumarchaeal MAGs represent two new species within the genus Nitrosopumilus and one novel genus, for which we propose the names "Candidatus UNitrosopumilus hexadellus," "Candidatus UNitrosopumilus detritiferus," and "Candidatus UCenporiarchaeum stylissum" (the U superscript indicates that the taxon is uncultured). Comparison of these genomes to data from the Sponge Earth Microbiome Project revealed that "Ca UCenporiarchaeum stylissum" has been exclusively detected in sponges and can hence be classified as a specialist, while "Ca UNitrosopumilus detritiferus" and "Ca UNitrosopumilus hexadellus" are also detected outside the sponge holobiont and likely lead a generalist lifestyle. Comparison of the sponge-associated MAGs to genomes of free-living Thaumarchaeota revealed signatures that indicate functional features of a sponge-associated lifestyle, and these features were related to nutrient transport and metabolism, restriction-modification, defense mechanisms, and host interactions. Each species exhibited distinct functional traits, suggesting that they have reached different stages of evolutionary adaptation and/or occupy distinct ecological niches within their sponge hosts. Our study therefore offers new evolutionary and ecological insights into the symbiosis between sponges and their thaumarchaeal symbionts.IMPORTANCE Sponges represent ecologically important models to understand the evolution of symbiotic interactions of metazoans with microbial symbionts. Thaumarchaeota are commonly found in sponges, but their potential adaptations to a host-associated lifestyle are largely unknown. Here, we present three novel sponge-associated thaumarchaeal species and compare their genomic and predicted functional features with those of closely related free-living counterparts. We found different degrees of specialization of these thaumarchaeal species to the sponge environment that is reflected in their host distribution and their predicted molecular and metabolic properties. Our results indicate that Thaumarchaeota may have reached different stages of evolutionary adaptation in their symbiosis with sponges.
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Affiliation(s)
- Shan Zhang
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
- Center for Marine Science & Innovation, University of New South Wales, Sydney, Australia
| | - Weizhi Song
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
- Center for Marine Science & Innovation, University of New South Wales, Sydney, Australia
| | - Bernd Wemheuer
- Center for Marine Science & Innovation, University of New South Wales, Sydney, Australia
- School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, Australia
| | - Julie Reveillaud
- ASTRE, INRA, CIRAD, University of Montpellier, Montpellier, France
| | - Nicole Webster
- Australian Institute of Marine Science, Townsville, Australia
- Australian Centre for Ecogenomics, The University of Queensland, Brisbane, Australia
| | - Torsten Thomas
- Center for Marine Science & Innovation, University of New South Wales, Sydney, Australia
- School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, Australia
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Lu J, Salzberg SL. Removing contaminants from databases of draft genomes. PLoS Comput Biol 2018; 14:e1006277. [PMID: 29939994 PMCID: PMC6034898 DOI: 10.1371/journal.pcbi.1006277] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 07/06/2018] [Accepted: 06/06/2018] [Indexed: 12/22/2022] Open
Abstract
Metagenomic sequencing of patient samples is a very promising method for the diagnosis of human infections. Sequencing has the ability to capture all the DNA or RNA from pathogenic organisms in a human sample. However, complete and accurate characterization of the sequence, including identification of any pathogens, depends on the availability and quality of genomes for comparison. Thousands of genomes are now available, and as these numbers grow, the power of metagenomic sequencing for diagnosis should increase. However, recent studies have exposed the presence of contamination in published genomes, which when used for diagnosis increases the risk of falsely identifying the wrong pathogen. To address this problem, we have developed a bioinformatics system for eliminating contamination as well as low-complexity genomic sequences in the draft genomes of eukaryotic pathogens. We applied this software to identify and remove human, bacterial, archaeal, and viral sequences present in a comprehensive database of all sequenced eukaryotic pathogen genomes. We also removed low-complexity genomic sequences, another source of false positives. Using this pipeline, we have produced a database of “clean” eukaryotic pathogen genomes for use with bioinformatics classification and analysis tools. We demonstrate that when attempting to find eukaryotic pathogens in metagenomic samples, the new database provides better sensitivity than one using the original genomes while offering a dramatic reduction in false positives. Infectious diseases afflict a majority of the human population around the world, from the common cold to the devastating malaria parasite. As technology has evolved, DNA sequencing emerged as a revolutionary and rapid method for diagnosing human infections. As part of our efforts to boost the ability of scientists to identify the source of an infection by sequencing, we present here a computational method for removing erroneous or misleading sequences from existing DNA databases. When we applied this method to a database of more than 200 eukaryotic pathogens, we were able to successfully and accurately identify the true pathogens infecting real human samples.
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Affiliation(s)
- Jennifer Lu
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, United States of America
- Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD, United States of America
- * E-mail: ,
| | - Steven L. Salzberg
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, United States of America
- Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD, United States of America
- Departments of Computer Science and Biostatistics, Johns Hopkins University, Baltimore, MD, United States of America
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10
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Garcia SL, Buck M, McMahon KD, Grossart HP, Eiler A, Warnecke F. Auxotrophy and intrapopulation complementary in the ‘interactome’ of a cultivated freshwater model community. Mol Ecol 2015; 24:4449-59. [DOI: 10.1111/mec.13319] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Revised: 07/09/2015] [Accepted: 07/10/2015] [Indexed: 01/05/2023]
Affiliation(s)
- Sarahi L. Garcia
- Department of Ecology and Genetics; Limnology and Science for Life Laboratory; Uppsala University; Norbyvägen 18D 752 36 Uppsala Sweden
| | - Moritz Buck
- Department of Ecology and Genetics; Limnology and Science for Life Laboratory; Uppsala University; Norbyvägen 18D 752 36 Uppsala Sweden
- BILS; Swedish Bioinformatics Infrastructure for Life Sciences; Husargatan 3 751 23 Uppsala Sweden
| | - Katherine D. McMahon
- Department of Bacteriology and Department of Civil and Environmental Engineering; University of Wisconsin-Madison; 5552 Microbial Sciences Building 1550 Linden Drive Madison WI 53706 USA
| | - Hans-Peter Grossart
- Department Experimental Limnology; Leibniz-Institute for Freshwater Ecology and Inland Fisheries; Alte Fischerhütte 2 OT Neuglobsow 16775 Stechlin Germany
- Institute for Biochemistry and Biology; Potsdam University; Karl-Liebknecht-Straße 24-25 Haus 25 14476 Potsdam Germany
| | - Alexander Eiler
- Department of Ecology and Genetics; Limnology and Science for Life Laboratory; Uppsala University; Norbyvägen 18D 752 36 Uppsala Sweden
| | - Falk Warnecke
- Jena School for Microbial Communication at Friedrich Schiller University Jena; Philosophenweg 12 07743 Jena Germany
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11
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Sipkema D, de Caralt S, Morillo JA, Al-Soud WA, Sørensen SJ, Smidt H, Uriz MJ. Similar sponge-associated bacteria can be acquired via both vertical and horizontal transmission. Environ Microbiol 2015; 17:3807-21. [PMID: 25732544 DOI: 10.1111/1462-2920.12827] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Revised: 02/19/2015] [Accepted: 02/22/2015] [Indexed: 11/29/2022]
Abstract
Marine sponges host diverse communities of microorganisms that are often vertically transmitted from mother to oocyte or embryo. Horizontal transmission has often been proposed to co-occur in marine sponges, but the mechanism is poorly understood. To assess the impact of the mode of transmission on the microbial assemblages of sponges, we analysed the microbiota in sympatric sponges that have previously been reported to acquire bacteria via either vertical (Corticium candelabrum and Crambe crambe) or horizontal transmission (Petrosia ficiformis). The comparative study was performed by polymerase chain reaction-denaturing gradient gel electrophoresis and pyrosequencing of barcoded PCR-amplified 16S rRNA gene fragments. We found that P. ficiformis and C. candelabrum each harbour their own species-specific bacteria, but they are similar to other high-microbial-abundance sponges, while the low-microbial-abundance sponge C. crambe hosts microbiota of a very different phylogenetic signature. In addition, nearly 50% of the reads obtained from P. ficiformis were most closely related to bacteria that were previously reported to be vertically transmitted in other sponges and comprised vertical-horizontal transmission phylogenetic clusters (VHT clusters). Therefore, our results provide evidence for the hypothesis that similar sponge-associated bacteria can be acquired via both vertical and horizontal transmission.
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Affiliation(s)
- Detmer Sipkema
- Centre d'Estudis Avançats de Blanes (CEAB), CSIC, Accés a la Cala Sant Francesc 14, 17300, Blanes, Spain.,Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB, Wageningen, The Netherlands
| | - Sònia de Caralt
- Centre d'Estudis Avançats de Blanes (CEAB), CSIC, Accés a la Cala Sant Francesc 14, 17300, Blanes, Spain
| | - Jose A Morillo
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB, Wageningen, The Netherlands.,Institute of Water Research, Department of Microbiology, University of Granada, c/Ramon y Cajal 4, 18071, Granada, Spain
| | - Waleed Abu Al-Soud
- Molecular Microbial Ecology Group, University of Copenhagen, Sølvgade 83H, 1307K, Copenhagen, Denmark
| | - Søren J Sørensen
- Molecular Microbial Ecology Group, University of Copenhagen, Sølvgade 83H, 1307K, Copenhagen, Denmark
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB, Wageningen, The Netherlands
| | - María J Uriz
- Centre d'Estudis Avançats de Blanes (CEAB), CSIC, Accés a la Cala Sant Francesc 14, 17300, Blanes, Spain
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Hardoim CCP, Costa R. Temporal dynamics of prokaryotic communities in the marine spongeSarcotragus spinosulus. Mol Ecol 2014; 23:3097-112. [DOI: 10.1111/mec.12789] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Revised: 04/30/2014] [Accepted: 05/05/2014] [Indexed: 02/01/2023]
Affiliation(s)
- Cristiane C. P. Hardoim
- Microbial Ecology and Evolution Research Group; Centre of Marine Sciences (CCMar); University of Algarve (UAlg); Gambelas 8005-139 Faro Portugal
| | - Rodrigo Costa
- Microbial Ecology and Evolution Research Group; Centre of Marine Sciences (CCMar); University of Algarve (UAlg); Gambelas 8005-139 Faro Portugal
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Hong JK, Kim HJ, Cho JC. Novel PCR primers for the archaeal phylum Thaumarchaeota designed based on the comparative analysis of 16S rRNA gene sequences. PLoS One 2014; 9:e96197. [PMID: 24805255 PMCID: PMC4013054 DOI: 10.1371/journal.pone.0096197] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2013] [Accepted: 04/03/2014] [Indexed: 02/01/2023] Open
Abstract
Based on comparative phylogenetic analysis of 16S rRNA gene sequences deposited in an RDP database, we constructed a local database of thaumarchaeotal 16S rRNA gene sequences and developed a novel PCR primer specific for the archaeal phylum Thaumarchaeota. Among 9,727 quality-filtered (chimeral-checked, size >1.2 kb) archaeal sequences downloaded from the RDP database, 1,549 thaumarchaeotal sequences were identified and included in our local database. In our study, Thaumarchaeota included archaeal groups MG-I, SAGMCG-I, SCG, FSCG, RC, and HWCG-III, forming a monophyletic group in the phylogenetic tree. Cluster analysis revealed 114 phylotypes for Thaumarchaeota. The majority of the phylotypes (66.7%) belonged to the MG-I and SCG, which together contained most (93.9%) of the thaumarchaeotal sequences in our local database. A phylum-directed primer was designed from a consensus sequence of the phylotype sequences, and the primer's specificity was evaluated for coverage and tolerance both in silico and empirically. The phylum-directed primer, designated THAUM-494, showed >90% coverage for Thaumarchaeota and <1% tolerance to non-target taxa, indicating high specificity. To validate this result experimentally, PCRs were performed with THAUM-494 in combination with a universal archaeal primer (ARC917R or 1017FAR) and DNAs from five environmental samples to construct clone libraries. THAUM-494 showed a satisfactory specificity in empirical studies, as expected from the in silico results. Phylogenetic analysis of 859 cloned sequences obtained from 10 clone libraries revealed that >95% of the amplified sequences belonged to Thaumarchaeota. The most frequently sampled thaumarchaeotal subgroups in our samples were SCG, MG-I, and SAGMCG-I. To our knowledge, THAUM-494 is the first phylum-level primer for Thaumarchaeota. Furthermore, the high coverage and low tolerance of THAUM-494 will make it a potentially valuable tool in understanding the phylogenetic diversity and ecological niche of Thaumarchaeota.
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Affiliation(s)
- Jin-Kyung Hong
- Institute of Environmental Sciences and Department of Environmental Sciences, Hankuk University of Foreign Studies, Yong-In, Korea
| | - Hye-Jin Kim
- Institute of Environmental Sciences and Department of Environmental Sciences, Hankuk University of Foreign Studies, Yong-In, Korea
| | - Jae-Chang Cho
- Institute of Environmental Sciences and Department of Environmental Sciences, Hankuk University of Foreign Studies, Yong-In, Korea
- * E-mail:
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Eme L, Reigstad LJ, Spang A, Lanzén A, Weinmaier T, Rattei T, Schleper C, Brochier-Armanet C. Metagenomics of Kamchatkan hot spring filaments reveal two new major (hyper)thermophilic lineages related to Thaumarchaeota. Res Microbiol 2013; 164:425-38. [DOI: 10.1016/j.resmic.2013.02.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2012] [Accepted: 02/11/2013] [Indexed: 10/27/2022]
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15
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Galm U, Shen B. Expression of biosynthetic gene clusters in heterologous hosts for natural product production and combinatorial biosynthesis. Expert Opin Drug Discov 2013; 1:409-37. [PMID: 23495943 DOI: 10.1517/17460441.1.5.409] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Expression of biosynthetic gene clusters in heterologous hosts for natural product production and combinatorial biosynthesis is playing an increasingly important role in natural product-based drug discovery and development programmes. This review highlights the requirements and challenges associated with this conceptually simple strategy of using surrogate hosts for the production of natural products in good yields and for the generation of novel analogues by combinatorial biosynthesis methods, taking advantage of the recombinant DNA technologies and tools available in the model hosts. Specific topics addressed include: i) the mobilisation of biosynthetic gene clusters using different vector systems; ii) the selection of suitable model heterologous hosts; iii) the requirement of post-translational protein modifications and precursor supply within the model hosts; iv) the influence of promoters and pathway regulators; and v) the choice of suitable fermentation conditions. Lastly, the use of heterologous expression in combinatorial biosynthesis is addressed. Future directions for model heterologous host engineering and the optimisation of natural product biosynthetic gene cluster expression in heterologous hosts are also discussed.
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Affiliation(s)
- Ute Galm
- Divison of Pharmaceutical Sciences, School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, WI 53705, USA.
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Bayer K, Scheuermayer M, Fieseler L, Hentschel U. Genomic mining for novel FADH₂-dependent halogenases in marine sponge-associated microbial consortia. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2013; 15:63-72. [PMID: 22562484 DOI: 10.1007/s10126-012-9455-2] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2011] [Accepted: 04/15/2012] [Indexed: 05/31/2023]
Abstract
Many marine sponges (Porifera) are known to contain large amounts of phylogenetically diverse microorganisms. Sponges are also known for their large arsenal of natural products, many of which are halogenated. In this study, 36 different FADH₂-dependent halogenase gene fragments were amplified from various Caribbean and Mediterranean sponges using newly designed degenerate PCR primers. Four unique halogenase-positive fosmid clones, all containing the highly conserved amino acid motif "GxGxxG", were identified in the microbial metagenome of Aplysina aerophoba. Sequence analysis of one halogenase-bearing fosmid revealed notably two open reading frames with high homologies to efflux and multidrug resistance proteins. Single cell genomic analysis allowed for a taxonomic assignment of the halogenase genes to specific symbiotic lineages. Specifically, the halogenase cluster S1 is predicted to be produced by a deltaproteobacterial symbiont and halogenase cluster S2 by a poribacterial sponge symbiont. An additional halogenase gene is possibly produced by an actinobacterial symbiont of marine sponges. The identification of three novel, phylogenetically, and possibly also functionally distinct halogenase gene clusters indicates that the microbial consortia of sponges are a valuable resource for novel enzymes involved in halogenation reactions.
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Affiliation(s)
- Kristina Bayer
- Julius-von-Sachs Institute for Biological Sciences, University of Wuerzburg, Julius-von-Sachs Platz 3, D-97082 Wuerzburg, Germany
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Nishizawa T, Komatsuzaki M, Kaneko N, Ohta H. Archaeal Diversity of Upland Rice Field Soils Assessed by the Terminal Restriction Fragment Length Polymorphism Method Combined with Real Time Quantitative-PCR and a Clone Library Analysis. Microbes Environ 2012; 23:237-43. [PMID: 21558714 DOI: 10.1264/jsme2.23.237] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The PCR amplification-based analysis of microbial diversity is subject to potential problems. In this study, to minimize the bias toward a 1:1 ratio in multitemplate PCR, a real-time PCR assay was carried out using a quenching fluorescence dye primer and amplification efficiency was monitored. Then terminal-restriction fragment length polymorphism (T-RFLP) profiling was performed using the PCR product with minimized PCR bias. This method was applied to an analysis of the diversity of the archaeal community in an upland rice field under different tillage systems and winter cover cropping. Terminal restriction fragments (T-RFs) of PCR-amplified archaeal 16S rRNA genes were assigned to the gene sequences recovered from the same soil by using an archaeal 16S rRNA gene clone library. Our results indicated that soil archaeal members were not influenced but the relative abundance of archaeal species particularly those belonging to Crenarchaeota which changed between the tillage and non-tillage treatments.
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18
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Temperton B, Giovannoni SJ. Metagenomics: microbial diversity through a scratched lens. Curr Opin Microbiol 2012; 15:605-12. [PMID: 22831844 DOI: 10.1016/j.mib.2012.07.001] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2012] [Revised: 07/04/2012] [Accepted: 07/06/2012] [Indexed: 01/07/2023]
Abstract
Since nucleic acids were first extracted directly from the environment and sequenced, metagenomics has grown to one of the most data-rich and pervasive techniques for understanding the taxonomic and functional diversity of microbial communities. In the last decade, cheaper sequencing has democratized the application of metagenomics and generated billions of reads, revealing staggering microbial diversity and functional complexity. However, cheaper sequencing has come at the cost of reduced sequence length, resulting in poor gene annotation and overestimates of bacterial richness and abundance. Recent improvements in sequencing technology are beginning to provide reads of sufficient length for accurate annotation and assembly of whole operons and beyond, that will once again enable experimental testing of gene function and re-capture the early successes of metagenomic investigations.
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Affiliation(s)
- Ben Temperton
- Department of Microbiology, Oregon State University, Corvallis, OR 97331, United States.
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19
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Abstract
Carbonate chimneys at the Lost City hydrothermal field are coated in biofilms dominated by a single phylotype of archaea known as Lost City Methanosarcinales. In this study, we have detected surprising physiological complexity in single-species biofilms, which is typically indicative of multispecies biofilm communities. Multiple cell morphologies were visible within the biofilms by transmission electron microscopy, and some cells contained intracellular membranes that may facilitate methane oxidation. Both methane production and oxidation were detected at 70 to 80°C and pH 9 to 10 in samples containing the single-species biofilms. Both processes were stimulated by the presence of hydrogen (H2), indicating that methane production and oxidation are part of a syntrophic interaction. Metagenomic data included a sequence encoding AMP-forming acetyl coenzyme A synthetase, indicating that acetate may play a role in the methane-cycling syntrophy. A wide range of nitrogen fixation genes were also identified, many of which were likely acquired via lateral gene transfer (LGT). Our results indicate that cells within these single-species biofilms may have differentiated into multiple physiological roles to form multicellular communities linked by metabolic interactions and LGT. Communities similar to these Lost City biofilms are likely to have existed early in the evolution of life, and we discuss how the multicellular characteristics of ancient hydrogen-fueled biofilm communities could have stimulated ecological diversification, as well as unity of biochemistry, during the earliest stages of cellular evolution. Our previous work at the Lost City hydrothermal field has shown that its carbonate chimneys host microbial biofilms dominated by a single uncultivated “species” of archaea. In this paper, we integrate evidence from these previous studies with new data on the metabolic activity and cellular morphology of these archaeal biofilms. We conclude that the archaeal biofilm must contain cells that are physiologically and possibly genetically differentiated with respect to each other. These results are especially interesting considering the possibility that the first cells originated and evolved in hydrothermal systems similar to Lost City.
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20
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Reigstad LJ, Bartossek R, Schleper C. Preparation of high-molecular weight DNA and metagenomic libraries from soils and hot springs. Methods Enzymol 2011; 496:319-44. [PMID: 21514470 DOI: 10.1016/b978-0-12-386489-5.00013-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/14/2023]
Abstract
Metagenomics has become an important tool for the characterization of microorganisms, as it is independent of their enrichment or cultivation in the laboratory. Its application has led to the discovery of metabolisms from widespread, yet uncharacterized organisms such as the ammonia-oxidizing archaea. Different approaches ranging from the generation of short sequence reads by direct use of high-throughput sequencing technologies to the construction and sequencing of large-insert DNA libraries are being employed. For these purposes, DNA of high quality needs to be prepared from an environmental sample, which is a particular challenge for soils and sediments. Here we describe the methods used for the isolation of high-molecular weight (hmw) DNA from soil and hot spring samples, the subsequent production of large-insert metagenomic libraries, and the analysis of the resulting genomic fragments. Detailed step-by-step procedures include (1) how to isolate good-quality hmw DNA from soils and mud; (2) how to prepare the DNA for cloning; (3) how to efficiently establish, grow, pick, replicate, and store the large-insert metagenomic fosmid library; and finally, (4) how to screen the library for genes of interest.
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Affiliation(s)
- Laila J Reigstad
- Centre for Geobiology, Department of Biology, University of Bergen, Bergen, Norway
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21
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Abstract
Nitrification is a microbially mediated process that plays a central role in the global cycling of nitrogen and is also of economic importance in agriculture and wastewater treatment. The first step in nitrification is performed by ammonia-oxidising microorganisms, which convert ammonia into nitrite ions. Ammonia-oxidising bacteria (AOB) have been known for more than 100 years. However, metagenomic studies and subsequent cultivation efforts have recently demonstrated that microorganisms of the domain archaea are also capable of performing this process. Astonishingly, members of this group of ammonia-oxidising archaea (AOA), which was overlooked for so long, are present in almost every environment on Earth and typically outnumber the known bacterial ammonia oxidisers by orders of magnitudes in common environments such as the marine plankton, soils, sediments and estuaries. Molecular studies indicate that AOA are amongst the most abundant organisms on this planet, adapted to the most common environments, but are also present in those considered extreme, such as hot springs. The ecological distribution and community dynamics of these archaea are currently the subject of intensive study by many research groups who are attempting to understand the physiological diversity and the ecosystem function of these organisms. The cultivation of a single marine isolate and two enrichments from hot terrestrial environments has demonstrated a chemolithoautotrophic mode of growth. Both pure culture-based and environmental studies indicate that at least some AOA have a high substrate affinity for ammonia and are able to grow under extremely oligotrophic conditions. Information from the first available genomes of AOA indicate that their metabolism is fundamentally different from that of their bacterial counterparts, involving a highly copper-dependent system for ammonia oxidation and electron transport, as well as a novel carbon fixation pathway that has recently been discovered in hyperthermophilic archaea. A distinct set of informational processing genes of AOA indicates that they are members of a distinct and novel phylum within the archaea, the 'Thaumarchaeota', which may even be a more ancient lineage than the established Cren- and Euryarchaeota lineages, raising questions about the evolutionary origins of archaea and the origins of ammonia-oxidising metabolism.
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Affiliation(s)
- Christa Schleper
- Department of Genetics in Ecology, University of Vienna, Vienna, Austria
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Heidelberg KB, Gilbert JA, Joint I. Marine genomics: at the interface of marine microbial ecology and biodiscovery. Microb Biotechnol 2010; 3:531-43. [PMID: 20953417 PMCID: PMC2948669 DOI: 10.1111/j.1751-7915.2010.00193.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2010] [Accepted: 05/15/2010] [Indexed: 11/29/2022] Open
Abstract
The composition and activities of microbes from diverse habitats have been the focus of intense research during the past decade with this research being spurred on largely by advances in molecular biology and genomic technologies. In recent years environmental microbiology has entered very firmly into the age of the 'omics' – (meta)genomics, proteomics, metabolomics, transcriptomics – with probably others on the rise. Microbes are essential participants in all biogeochemical processes on our planet, and the practical applications of what we are learning from the use of molecular approaches has altered how we view biological systems. In addition, there is considerable potential to use information about uncultured microbes in biodiscovery research as microbes provide a rich source of discovery for novel genes, enzymes and metabolic pathways. This review explores the brief history of genomic and metagenomic approaches to study environmental microbial assemblages and describes some of the future challenges involved in broadening our approaches – leading to new insights for understanding environmental problems and enabling biodiscovery research.
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Affiliation(s)
- Karla B Heidelberg
- Department of Biological Sciences, University of Southern California, 3616 Trousdale Parkway, Los Angeles, CA 90089-0371, USA.
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Brazelton WJ, Sogin ML, Baross JA. Multiple scales of diversification within natural populations of archaea in hydrothermal chimney biofilms. ENVIRONMENTAL MICROBIOLOGY REPORTS 2010; 2:236-242. [PMID: 23766074 DOI: 10.1111/j.1758-2229.2009.00097.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Corroborative data collected from 16S rRNA clone libraries, intergenic transcribed spacer (ITS) region clone libraries, and 16S rRNA hypervariable region tag pyrosequencing demonstrate microdiversity within single-species archaeal biofilms of the Lost City Hydrothermal Field. Both 16S rRNA clone libraries and pyrosequencing of the V6 hypervariable region show that Lost City Methanosarcinales (LCMS) biofilms are dominated by a single sequence, but the pyrosequencing data set also reveals the presence of an additional 1654 rare sequences. Clone libraries constructed with DNA spanning the V6 hypervariable region and ITS show that multiple ITS sequences are associated with the same dominant V6 sequence. Furthermore, ITS variability differed among three chimney samples, and the sample with the highest ITS diversity also contained the highest V6 diversity as measured by clone libraries as well as tag pyrosequencing. These results indicate that the extensive microdiversity detected in V6 tag sequences is an underestimate of genetic diversity within the archaeal biofilms.
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Affiliation(s)
- William J Brazelton
- School of Oceanography and Center for Astrobiology and Early Evolution, University of Washington, Seattle, WA, USA. Josephine Bay Paul Center, Marine Biological Laboratory at Woods Hole, Woods Hole, MA, USA
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Sipkema D, Holmes B, Nichols SA, Blanch HW. Biological characterisation of Haliclona (?gellius) sp.: sponge and associated microorganisms. MICROBIAL ECOLOGY 2009; 58:903-920. [PMID: 19471996 PMCID: PMC2772955 DOI: 10.1007/s00248-009-9534-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2009] [Accepted: 05/07/2009] [Indexed: 05/27/2023]
Abstract
We have characterised the northern Pacific undescribed sponge Haliclona (?gellius) sp. based on rDNA of the sponge and its associated microorganisms. The sponge is closely related to Amphimedon queenslandica from the Great Barrier Reef as the near-complete 18S rDNA sequences of both sponges were identical. The microbial fingerprint of three specimens harvested at different times and of a transplanted specimen was compared to identify stably associated microorganisms. Most bacterial phyla were detected in each sample, but only a few bacterial species were determined to be stably associated with the sponge. A sponge-specific beta- and gamma-Proteobacterium were abundant clones and both of them were present in three of the four specimens analysed. In addition, a Planctomycete and a Crenarchaea were detected in all sponge individuals. Both were closely related to operational taxonomic units that have been found in other sponges, but not exclusively in sponges. Interestingly, also a number of clones that are closely related to intracellular symbionts from insects and amoeba were detected.
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Affiliation(s)
- Detmer Sipkema
- Department of Chemical Engineering, University of California Berkeley, 201 Gilman Hall, Berkeley, CA 94720, USA.
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Singh J, Behal A, Singla N, Joshi A, Birbian N, Singh S, Bali V, Batra N. Metagenomics: Concept, methodology, ecological inference and recent advances. Biotechnol J 2009; 4:480-94. [PMID: 19288513 DOI: 10.1002/biot.200800201] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Microorganisms constitute two third of the Earth's biological diversity. As many as 99% of the microorganisms present in certain environments cannot be cultured by standard techniques. Culture-independent methods are required to understand the genetic diversity, population structure and ecological roles of the majority of organisms. Metagenomics is the genomic analysis of microorganisms by direct extraction and cloning of DNA from their natural environment. Protocols have been developed to capture unexplored microbial diversity to overcome the existing barriers in estimation of diversity. New screening methods have been designed to select specific functional genes within metagenomic libraries to detect novel biocatalysts as well as bioactive molecules applicable to mankind. To study the complete gene or operon clusters, various vectors including cosmid, fosmid or bacterial artificial chromosomes are being developed. Bioinformatics tools and databases have added much to the study of microbial diversity. This review describes the various methodologies and tools developed to understand the biology of uncultured microbes including bacteria, archaea and viruses through metagenomic analysis.
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Affiliation(s)
- Jagtar Singh
- Department of Biotechnology, Panjab University, Chandigarh, India
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Temperton B, Field D, Oliver A, Tiwari B, Mühling M, Joint I, Gilbert JA. Bias in assessments of marine microbial biodiversity in fosmid libraries as evaluated by pyrosequencing. ISME JOURNAL 2009; 3:792-6. [PMID: 19340085 DOI: 10.1038/ismej.2009.32] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
On the basis of 16S rRNA gene sequencing, the SAR11 clade of marine bacteria has an almost universal distribution, being detected as abundant sequences in all marine provinces. Yet, SAR11 sequences are rarely detected in fosmid libraries, suggesting that the widespread abundance may be an artefact of PCR cloning and that SAR11 has a relatively low abundance. Here the relative abundance of SAR11 is explored in both a fosmid library and a metagenomic sequence data set from the same biological community taken from fjord surface water from Bergen, Norway. Pyrosequenced data and 16S clone data confirmed an 11-15% relative abundance of SAR11 within the community. In contrast, not a single SAR11 fosmid was identified in a pooled shotgun sequence data set of 100 fosmid clones. This underrepresentation was evidenced by comparative abundances of SAR11 sequences assessed by taxonomic annotation and fragment recruitment. Analysis revealed a similar underrepresentation of low-GC Flavobacteriaceae. We speculate that a contributing factor towards the fosmid bias may be DNA fragmentation during preparation because of the low GC content of SAR11 sequences and other underrepresented taxa. This study suggests that, although fosmid libraries can be extremely useful, caution must be taken when directly inferring community composition from metagenomic fosmid libraries.
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Wilmes P, Simmons SL, Denef VJ, Banfield JF. The dynamic genetic repertoire of microbial communities. FEMS Microbiol Rev 2008; 33:109-32. [PMID: 19054116 PMCID: PMC2704941 DOI: 10.1111/j.1574-6976.2008.00144.x] [Citation(s) in RCA: 84] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Community genomic data have revealed multiple levels of variation between and within microbial consortia. This variation includes large-scale differences in gene content between ecosystems as well as within-population sequence heterogeneity. In the present review, we focus specifically on how fine-scale variation within microbial and viral populations is apparent from community genomic data. A major unresolved question is how much of the observed variation is due to neutral vs. adaptive processes. Limited experimental data hint that some of this fine-scale variation may be in part functionally relevant, whereas sequence-based and modeling analyses suggest that much of it may be neutral. While methods for interpreting population genomic data are still in their infancy, we discuss current interpretations of existing datasets in the light of evolutionary processes and models. Finally, we highlight the importance of virus–host dynamics in generating and shaping within-population diversity.
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Affiliation(s)
- Paul Wilmes
- Department of Earth and Planetary Science, University of California at Berkeley, Berkeley, CA 94720, USA
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Metagenome analysis of an extreme microbial symbiosis reveals eurythermal adaptation and metabolic flexibility. Proc Natl Acad Sci U S A 2008; 105:17516-21. [PMID: 18987310 DOI: 10.1073/pnas.0802782105] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Hydrothermal vent ecosystems support diverse life forms, many of which rely on symbiotic associations to perform functions integral to survival in these extreme physicochemical environments. Epsilonproteobacteria, found free-living and in intimate associations with vent invertebrates, are the predominant vent-associated microorganisms. The vent-associated polychaete worm, Alvinella pompejana, is host to a visibly dense fleece of episymbionts on its dorsal surface. The episymbionts are a multispecies consortium of Epsilonproteobacteria present as a biofilm. We unraveled details of these enigmatic, uncultivated episymbionts using environmental genome sequencing. They harbor wide-ranging adaptive traits that include high levels of strain variability analogous to Epsilonproteobacteria pathogens such as Helicobacter pylori, metabolic diversity of free-living bacteria, and numerous orthologs of proteins that we hypothesize are each optimally adapted to specific temperature ranges within the 10-65 degrees C fluctuations characteristic of the A. pompejana habitat. This strategic combination enables the consortium to thrive under diverse thermal and chemical regimes. The episymbionts are metabolically tuned for growth in hydrothermal vent ecosystems with genes encoding the complete rTCA cycle, sulfur oxidation, and denitrification; in addition, the episymbiont metagenome also encodes capacity for heterotrophic and aerobic metabolisms. Analysis of the environmental genome suggests that A. pompejana may benefit from the episymbionts serving as a stable source of food and vitamins. The success of Epsilonproteobacteria as episymbionts in hydrothermal vent ecosystems is a product of adaptive capabilities, broad metabolic capacity, strain variance, and virulent traits in common with pathogens.
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Martin-Cuadrado AB, Rodriguez-Valera F, Moreira D, Alba JC, Ivars-Martínez E, Henn MR, Talla E, López-García P. Hindsight in the relative abundance, metabolic potential and genome dynamics of uncultivated marine archaea from comparative metagenomic analyses of bathypelagic plankton of different oceanic regions. ISME JOURNAL 2008; 2:865-86. [DOI: 10.1038/ismej.2008.40] [Citation(s) in RCA: 98] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Rusch DB, Halpern AL, Sutton G, Heidelberg KB, Williamson S, Yooseph S, Wu D, Eisen JA, Hoffman JM, Remington K, Beeson K, Tran B, Smith H, Baden-Tillson H, Stewart C, Thorpe J, Freeman J, Andrews-Pfannkoch C, Venter JE, Li K, Kravitz S, Heidelberg JF, Utterback T, Rogers YH, Falcón LI, Souza V, Bonilla-Rosso G, Eguiarte LE, Karl DM, Sathyendranath S, Platt T, Bermingham E, Gallardo V, Tamayo-Castillo G, Ferrari MR, Strausberg RL, Nealson K, Friedman R, Frazier M, Venter JC. The Sorcerer II Global Ocean Sampling expedition: northwest Atlantic through eastern tropical Pacific. PLoS Biol 2007; 5:e77. [PMID: 17355176 PMCID: PMC1821060 DOI: 10.1371/journal.pbio.0050077] [Citation(s) in RCA: 1309] [Impact Index Per Article: 77.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2006] [Accepted: 01/16/2007] [Indexed: 11/19/2022] Open
Abstract
The world's oceans contain a complex mixture of micro-organisms that are for the most part, uncharacterized both genetically and biochemically. We report here a metagenomic study of the marine planktonic microbiota in which surface (mostly marine) water samples were analyzed as part of the Sorcerer II Global Ocean Sampling expedition. These samples, collected across a several-thousand km transect from the North Atlantic through the Panama Canal and ending in the South Pacific yielded an extensive dataset consisting of 7.7 million sequencing reads (6.3 billion bp). Though a few major microbial clades dominate the planktonic marine niche, the dataset contains great diversity with 85% of the assembled sequence and 57% of the unassembled data being unique at a 98% sequence identity cutoff. Using the metadata associated with each sample and sequencing library, we developed new comparative genomic and assembly methods. One comparative genomic method, termed “fragment recruitment,” addressed questions of genome structure, evolution, and taxonomic or phylogenetic diversity, as well as the biochemical diversity of genes and gene families. A second method, termed “extreme assembly,” made possible the assembly and reconstruction of large segments of abundant but clearly nonclonal organisms. Within all abundant populations analyzed, we found extensive intra-ribotype diversity in several forms: (1) extensive sequence variation within orthologous regions throughout a given genome; despite coverage of individual ribotypes approaching 500-fold, most individual sequencing reads are unique; (2) numerous changes in gene content some with direct adaptive implications; and (3) hypervariable genomic islands that are too variable to assemble. The intra-ribotype diversity is organized into genetically isolated populations that have overlapping but independent distributions, implying distinct environmental preference. We present novel methods for measuring the genomic similarity between metagenomic samples and show how they may be grouped into several community types. Specific functional adaptations can be identified both within individual ribotypes and across the entire community, including proteorhodopsin spectral tuning and the presence or absence of the phosphate-binding gene PstS. Marine microbes remain elusive and mysterious, even though they are the most abundant life form in the ocean, form the base of the marine food web, and drive energy and nutrient cycling. We know so little about the vast majority of microbes because only a small percentage can be cultivated and studied in the lab. Here we report on the Global Ocean Sampling expedition, an environmental metagenomics project that aims to shed light on the role of marine microbes by sequencing their DNA without first needing to isolate individual organisms. A total of 41 different samples were taken from a wide variety of aquatic habitats collected over 8,000 km. The resulting 7.7 million sequencing reads provide an unprecedented look at the incredible diversity and heterogeneity in naturally occurring microbial populations. We have developed new bioinformatic methods to reconstitute large portions of both cultured and uncultured microbial genomes. Organism diversity is analyzed in relation to sampling locations and environmental pressures. Taken together, these data and analyses serve as a foundation for greatly expanding our understanding of individual microbial lineages and their evolution, the nature of marine microbial communities, and how they are impacted by and impact our world. TheSorcerer II GOS expedition, data sampling, and analysis is described. The immense diversity in the sequence data required novel comparative genomic assembly methods, which uncovered genomic differences that marker-based methods could not.
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Affiliation(s)
- Douglas B Rusch
- J. Craig Venter Institute, Rockville, Maryland, United States of America.
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Taylor MW, Radax R, Steger D, Wagner M. Sponge-associated microorganisms: evolution, ecology, and biotechnological potential. Microbiol Mol Biol Rev 2007; 71:295-347. [PMID: 17554047 PMCID: PMC1899876 DOI: 10.1128/mmbr.00040-06] [Citation(s) in RCA: 788] [Impact Index Per Article: 46.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Marine sponges often contain diverse and abundant microbial communities, including bacteria, archaea, microalgae, and fungi. In some cases, these microbial associates comprise as much as 40% of the sponge volume and can contribute significantly to host metabolism (e.g., via photosynthesis or nitrogen fixation). We review in detail the diversity of microbes associated with sponges, including extensive 16S rRNA-based phylogenetic analyses which support the previously suggested existence of a sponge-specific microbiota. These analyses provide a suitable vantage point from which to consider the potential evolutionary and ecological ramifications of these widespread, sponge-specific microorganisms. Subsequently, we examine the ecology of sponge-microbe associations, including the establishment and maintenance of these sometimes intimate partnerships, the varied nature of the interactions (ranging from mutualism to host-pathogen relationships), and the broad-scale patterns of symbiont distribution. The ecological and evolutionary importance of sponge-microbe associations is mirrored by their enormous biotechnological potential: marine sponges are among the animal kingdom's most prolific producers of bioactive metabolites, and in at least some cases, the compounds are of microbial rather than sponge origin. We review the status of this important field, outlining the various approaches (e.g., cultivation, cell separation, and metagenomics) which have been employed to access the chemical wealth of sponge-microbe associations.
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Affiliation(s)
- Michael W Taylor
- Department of Microbial Ecology, University of Vienna, Althanstr. 14, A-1090 Vienna, Austria.
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Grozdanov L, Hentschel U. An environmental genomics perspective on the diversity and function of marine sponge-associated microbiota. Curr Opin Microbiol 2007; 10:215-20. [PMID: 17574904 DOI: 10.1016/j.mib.2007.05.012] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2007] [Accepted: 05/29/2007] [Indexed: 10/23/2022]
Abstract
Numerous marine demosponges serve as habitats to phylogenetically complex microbial communities, with population densities exceeding those of seawater by several orders of magnitude. 16S rRNA gene-based studies have enabled a detailed phylogenetic description of the microorganisms associated with sponges, whereas environmental genomics analyses are beginning to reveal insights into their metabolic and physiological properties. Additionally, metagenomic approaches provide access to functional genes and gene clusters, thereby paving the way for the heterologous expression of novel bioactive substances from microbial symbionts of marine invertebrates.
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Affiliation(s)
- Lubomir Grozdanov
- Research Center for Infectious Diseases, University of Wuerzburg, Roentgenring 11, D-97070 Wuerzburg, Germany
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35
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Ward DM, Cohan FM, Bhaya D, Heidelberg JF, Kühl M, Grossman A. Genomics, environmental genomics and the issue of microbial species. Heredity (Edinb) 2007; 100:207-19. [PMID: 17551524 DOI: 10.1038/sj.hdy.6801011] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
A microbial species concept is crucial for interpreting the variation detected by genomics and environmental genomics among cultivated microorganisms and within natural microbial populations. Comparative genomic analyses of prokaryotic species as they are presently described and named have led to the provocative idea that prokaryotes may not form species as we think about them for plants and animals. There are good reasons to doubt whether presently recognized prokaryotic species are truly species. To achieve a better understanding of microbial species, we believe it is necessary to (i) re-evaluate traditional approaches in light of evolutionary and ecological theory, (ii) consider that different microbial species may have evolved in different ways and (iii) integrate genomic, metagenomic and genome-wide expression approaches with ecological and evolutionary theory. Here, we outline how we are using genomic methods to (i) identify ecologically distinct populations (ecotypes) predicted by theory to be species-like fundamental units of microbial communities, and (ii) test their species-like character through in situ distribution and gene expression studies. By comparing metagenomic sequences obtained from well-studied hot spring cyanobacterial mats with genomic sequences of two cultivated cyanobacterial ecotypes, closely related to predominant native populations, we can conduct in situ population genetics studies that identify putative ecotypes and functional genes that determine the ecotypes' ecological distinctness. If individuals within microbial communities are found to be grouped into ecologically distinct, species-like populations, knowing about such populations should guide us to a better understanding of how genomic variation is linked to community function.
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Affiliation(s)
- D M Ward
- Department of Land Resources and Environmental Science, Montana State University, Bozeman, MT 59715, USA.
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Konstantinidis KT, Ramette A, Tiedje JM. The bacterial species definition in the genomic era. Philos Trans R Soc Lond B Biol Sci 2006; 361:1929-40. [PMID: 17062412 PMCID: PMC1764935 DOI: 10.1098/rstb.2006.1920] [Citation(s) in RCA: 399] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The bacterial species definition, despite its eminent practical significance for identification, diagnosis, quarantine and diversity surveys, remains a very difficult issue to advance. Genomics now offers novel insights into intra-species diversity and the potential for emergence of a more soundly based system. Although we share the excitement, we argue that it is premature for a universal change to the definition because current knowledge is based on too few phylogenetic groups and too few samples of natural populations. Our analysis of five important bacterial groups suggests, however, that more stringent standards for species may be justifiable when a solid understanding of gene content and ecological distinctiveness becomes available. Our analysis also reveals what is actually encompassed in a species according to the current standards, in terms of whole-genome sequence and gene-content diversity, and shows that this does not correspond to coherent clusters for the environmental Burkholderia and Shewanella genera examined. In contrast, the obligatory pathogens, which have a very restricted ecological niche, do exhibit clusters. Therefore, the idea of biologically meaningful clusters of diversity that applies to most eukaryotes may not be universally applicable in the microbial world, or if such clusters exist, they may be found at different levels of distinction.
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Hallam SJ, Konstantinidis KT, Putnam N, Schleper C, Watanabe YI, Sugahara J, Preston C, de la Torre J, Richardson PM, DeLong EF. Genomic analysis of the uncultivated marine crenarchaeote Cenarchaeum symbiosum. Proc Natl Acad Sci U S A 2006; 103:18296-301. [PMID: 17114289 PMCID: PMC1643844 DOI: 10.1073/pnas.0608549103] [Citation(s) in RCA: 306] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Crenarchaeota are ubiquitous and abundant microbial constituents of soils, sediments, lakes, and ocean waters. To further describe the cosmopolitan nonthermophilic Crenarchaeota, we analyzed the genome sequence of one representative, the uncultivated sponge symbiont Cenarchaeum symbiosum. C. symbiosum genotypes coinhabiting the same host partitioned into two dominant populations, corresponding to previously described a- and b-type ribosomal RNA variants. Although they were syntenic, overlapping a- and b-type ribotype genomes harbored significant variability. A single tiling path comprising the dominant a-type genotype was assembled and used to explore the genomic properties of C. symbiosum and its planktonic relatives. Of 2,066 ORFs, 55.6% matched genes with predicted function from previously sequenced genomes. The remaining genes partitioned between functional RNAs (2.4%) and hypotheticals (42%) with limited homology to known functional genes. The latter category included some genes likely involved in the archaeal-sponge symbiotic association. Conversely, 525 C. symbiosum ORFs were most highly similar to sequences from marine environmental genomic surveys, and they apparently represent orthologous genes from free-living planktonic Crenarchaeota. In total, the C. symbiosum genome was remarkably distinct from those of other known Archaea and shared many core metabolic features in common with its free-living planktonic relatives.
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Affiliation(s)
| | | | - Nik Putnam
- Joint Genome Institute, Walnut Creek, CA 94598
| | - Christa Schleper
- Department of Biology, University of Bergen, Jahnebakken 5, N-5020 Bergen, Norway
| | - Yoh-ichi Watanabe
- Department of Biomedical Chemistry, University of Tokyo, Tokyo 113-0033, Japan
| | - Junichi Sugahara
- Institute for Advanced Biosciences, Keio University, Tsuruoka 997-0017, Japan
| | - Christina Preston
- **Monterey Bay Aquarium Research Institute, Moss Landing, CA 95069; and
| | | | | | - Edward F. DeLong
- *Massachusetts Institute of Technology, Cambridge, MA 02139
- To whom correspondence should be addressed. E-mail:
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Moussard H, Moreira D, Cambon-Bonavita MA, López-García P, Jeanthon C. Uncultured Archaea in a hydrothermal microbial assemblage: phylogenetic diversity and characterization of a genome fragment from a euryarchaeote. FEMS Microbiol Ecol 2006; 57:452-69. [PMID: 16907759 DOI: 10.1111/j.1574-6941.2006.00128.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The polychaete Alvinella pompejana lives in organic tubes on the walls of active hydrothermal chimneys along the East Pacific Rise. To examine the diversity of the archaeal community associated with the polychaete tubes, we constructed libraries by direct PCR amplification and cloning of 16S rRNA genes. Almost half of the sequences of the 16S rRNA gene libraries clustered with uncultured archaeal groups. In an effort to access genomic information from uncultured archaeal members we further constructed a fosmid library from the same DNA source. One of the clones, Alv-FOS5, was sequenced completely. Its sequence analysis revealed an incomplete rRNA operon and 32 predicted ORFs. Seventeen of these ORFs have been assigned putative functions, including transcription and translation, cellular processes and signalling, transport systems and metabolic pathways. Phylogenetic analyses of the 16S rRNA gene suggested that Alv-FOS5 formed a new lineage related to members of Deep-Sea Hydrothermal Vent Euryarchaeota group II. Phylogenetic analyses of predicted proteins revealed the existence of likely cases of horizontal gene transfer, both between Crenarchaeota and Euryarchaeota and between Archaea and Bacteria. This study is the first step in using genomics to reveal the physiology of an as yet uncultured group of archaea from deep-sea hydrothermal vents.
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Affiliation(s)
- Hélène Moussard
- Laboratoire de Microbiologie des Environnements Extrêmes, UMR 6197, Centre National de la Recherche Scientifique, IFREMER, Université de Bretagne Occidentale, Institut Universitaire Européen de la Mer, Plouzané, France
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Whitaker RJ, Banfield JF. Population genomics in natural microbial communities. Trends Ecol Evol 2006; 21:508-16. [PMID: 16859806 DOI: 10.1016/j.tree.2006.07.001] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2005] [Revised: 05/02/2006] [Accepted: 07/03/2006] [Indexed: 11/24/2022]
Abstract
Little is known about the evolutionary processes that structure and maintain microbial diversity because, until recently, it was difficult to explore individual-level patterns of variation at the microbial scale. Now, community-genomic sequence data enable such variation to be assessed across large segments of microbial genomes. Here, we discuss how population-genomic analysis of these data can be used to determine how selection and genetic exchange shape the evolution of new microbial lineages. We show that once independent lineages have been identified, such analyses enable the identification of genome changes that drive niche differentiation and promote the coexistence of closely related lineages within the same environment. We suggest that understanding the evolutionary ecology of natural microbial populations through population-genomic analyses will enhance our understanding of genome evolution across all domains of life.
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Affiliation(s)
- Rachel J Whitaker
- Ecosystem Sciences, 137 Mulford Hall, University of California, Berkeley, CA 94720-3114, USA.
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Koch M, Rudolph C, Moissl C, Huber R. A cold-loving crenarchaeon is a substantial part of a novel microbial community in cold sulphidic marsh water. FEMS Microbiol Ecol 2006; 57:55-66. [PMID: 16819950 DOI: 10.1111/j.1574-6941.2006.00088.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
In this paper, we report the identification and first characterization of a novel, cold-loving, prokaryotic community thriving among white-greenish 'streamers' in the cold (c. 10 degrees C) sulphurous water of the marsh Sippenauer Moor near Regensburg, Bavaria, Germany. It consists of the bacterial genus Thiothrix, the bacterium 'Sip100' and one archaeal representative, forming together a unique association structure with a distinct life cycle. Fluorescence in situ hybridization studies have revealed that the archaeal member can be affiliated to the crenarchaeal kingdom ('Cre1'). This crenarchaeon was always observed attached to the bacterial community member 'Sip100'. Extended fluorescence in situ hybridization studies showed that this crenarchaeon was not detected in a free-living form, raising the idea of a probable host-dependent relationship. In line with our fluorescence in situ hybridization studies, novel crenarchaeal 16S rRNA gene sequences were identified in these samples. The design and application of a new in situ cultivation method in the sulphurous water of the marsh allowed first insights into the cohesion mechanisms, lifestyle and chronology of the microbes involved in this prokaryotic community in nature. Our results suggest that hitherto unknown Crenarchaeota thrive in cold sulphidic water and are a substantial part of a synchronized microbial community.
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Affiliation(s)
- Marcus Koch
- Lehrstuhl für Mikrobiologie und Archaeenzentrum, Universität Regensburg, Regensburg, Germany
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41
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Fieseler L, Quaiser A, Schleper C, Hentschel U. Analysis of the first genome fragment from the marine sponge-associated, novel candidate phylum Poribacteria by environmental genomics. Environ Microbiol 2006; 8:612-24. [PMID: 16584473 DOI: 10.1111/j.1462-2920.2005.00937.x] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
The novel candidate phylum Poribacteria is specifically associated with several marine demosponge genera. Because no representatives of Poribacteria have been cultivated, an environmental genomic approach was used to gain insights into genomic properties and possibly physiological/functional features of this elusive candidate division. In a large-insert library harbouring an estimated 1.1 Gb of microbial community DNA from Aplysina aerophoba, a Poribacteria-positive 16S rRNA gene locus was identified. Sequencing and sequence annotation of the 39 kb size insert revealed 27 open reading frames (ORFs) and two genes for stable RNAs. The fragment exhibited an overall G+C content of 50.5% and a coding density of 86.1%. The 16S rRNA gene was unlinked from a conventional rrn operon. Its flanking regions did not show any synteny to other 16S rRNA encoding loci from microorganisms with unlinked rrn operons. Two of the predicted hypothetical proteins were highly similar to homologues from Rhodopirellula baltica. Furthermore, a novel kind of molybdenum containing oxidoreductase was predicted as well as a series of eight ORFs encoding for unusual transporters, channel or pore forming proteins. This environmental genomics approach provides, for the first time, genomic and, by inference, functional information on the so far uncultivated, sponge-associated candidate division Poribacteria.
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Affiliation(s)
- Lars Fieseler
- Zentrum für Infektionsforschung, Universität Würzburg, Röntgenring 11, D-97070 Würzburg, Germany
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42
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Grzymski JJ, Carter BJ, DeLong EF, Feldman RA, Ghadiri A, Murray AE. Comparative genomics of DNA fragments from six Antarctic marine planktonic bacteria. Appl Environ Microbiol 2006; 72:1532-41. [PMID: 16461708 PMCID: PMC1392886 DOI: 10.1128/aem.72.2.1532-1541.2006] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Six environmental fosmid clones from Antarctic coastal water bacterioplankton were completely sequenced. The genome fragments harbored small-subunit rRNA genes that were between 85 and 91% similar to those of their nearest cultivated relatives. The six fragments span four phyla, including the Gemmatimonadetes, Proteobacteria (alpha and gamma), Bacteroidetes, and high-G+C gram-positive bacteria. Gene-finding and annotation analyses identified 244 total open reading frames. Amino acid comparisons of 123 and 113 Antarctic bacterial amino acid sequences to mesophilic homologs from G+C-specific and SwissProt/UniProt databases, respectively, revealed widespread adaptation to the cold. The most significant changes in these Antarctic bacterial protein sequences included a reduction in salt-bridge-forming residues such as arginine, glutamic acid, and aspartic acid, reduced proline contents, and a reduction in stabilizing hydrophobic clusters. Stretches of disordered amino acids were significantly longer in the Antarctic sequences than in the mesophilic sequences. These characteristics were not specific to any one phylum, COG role category, or G+C content and imply that underlying genotypic and biochemical adaptations to the cold are inherent to life in the permanently subzero Antarctic waters.
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Abstract
Many archaea are extremophiles. They thrive at high temperatures, at high pressure and in concentrated acidic environments. Nevertheless, the largest proportion and greatest diversity of archaea exist in cold environments. Most of the Earth's biosphere is cold, and archaea represent a significant fraction of the biomass. Although psychrophilic archaea have long been the neglected majority, the study of these microorganisms is beginning to come of age. This review casts a spotlight on the ecology, adaptation biology and unique science that is being realized from studies on cold-adapted archaea.
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Affiliation(s)
- Ricardo Cavicchioli
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney NSW 2052, Australia.
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44
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Hallam SJ, Mincer TJ, Schleper C, Preston CM, Roberts K, Richardson PM, DeLong EF. Pathways of carbon assimilation and ammonia oxidation suggested by environmental genomic analyses of marine Crenarchaeota. PLoS Biol 2006; 4:e95. [PMID: 16533068 PMCID: PMC1403158 DOI: 10.1371/journal.pbio.0040095] [Citation(s) in RCA: 461] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2005] [Accepted: 01/25/2006] [Indexed: 11/19/2022] Open
Abstract
Marine
Crenarchaeota represent an abundant component of oceanic microbiota with potential to significantly influence biogeochemical cycling in marine ecosystems. Prior studies using specific archaeal lipid biomarkers and isotopic analyses indicated that planktonic
Crenarchaeota have the capacity for autotrophic growth, and more recent cultivation studies support an ammonia-based chemolithoautotrophic energy metabolism. We report here analysis of fosmid sequences derived from the uncultivated marine crenarchaeote,
Cenarchaeum symbiosum, focused on the reconstruction of carbon and energy metabolism. Genes predicted to encode multiple components of a modified 3-hydroxypropionate cycle of autotrophic carbon assimilation were identified, consistent with utilization of carbon dioxide as a carbon source. Additionally, genes predicted to encode a near complete oxidative tricarboxylic acid cycle were also identified, consistent with the consumption of organic carbon and in the production of intermediates for amino acid and cofactor biosynthesis. Therefore,
C. symbiosum has the potential to function either as a strict autotroph, or as a mixotroph utilizing both carbon dioxide and organic material as carbon sources. From the standpoint of energy metabolism, genes predicted to encode ammonia monooxygenase subunits, ammonia permease, urease, and urea transporters were identified, consistent with the use of reduced nitrogen compounds as energy sources fueling autotrophic metabolism. Homologues of these genes, recovered from ocean waters worldwide, demonstrate the conservation and ubiquity of crenarchaeal pathways for carbon assimilation and ammonia oxidation. These findings further substantiate the likely global metabolic importance of
Crenarchaeota with respect to key steps in the biogeochemical transformation of carbon and nitrogen in marine ecosystems.
Sequence data reveal the presence of key genes from pathways for carbon assimilation and ammonia oxidation in marine microbiota, supporting their importance in regulating the biogeochemistry of marine ecosystems.
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Affiliation(s)
- Steven J Hallam
- 1Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Tracy J Mincer
- 1Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | | | - Christina M Preston
- 3Monterey Bay Aquarium Research Institute, Moss Landing, California, United States of America
| | - Katie Roberts
- 4Department of Geological & Environmental Sciences, Stanford University, Stanford, California, United States of America
| | - Paul M Richardson
- 5Joint Genome Institute, Walnut Creek, California, United States of America
| | - Edward F DeLong
- 1Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
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Abstract
The domain Archaea represents a third line of evolutionary descent, separate from Bacteria and Eucarya. Initial studies seemed to limit archaea to various extreme environments. These included habitats at the extreme limits that allow life on earth, in terms of temperature, pH, salinity, and anaerobiosis, which were the homes to hyper thermo philes, extreme (thermo)acidophiles, extreme halophiles, and methanogens. Typical environments from which pure cultures of archaeal species have been isolated include hot springs, hydrothermal vents, solfataras, salt lakes, soda lakes, sewage digesters, and the rumen. Within the past two decades, the use of molecular techniques, including PCR-based amplification of 16S rRNA genes, has allowed a culture-independent assessment of microbial diversity. Remarkably, such techniques have indicated a wide distribution of mostly uncultured archaea in normal habitats, such as ocean waters, lake waters, and soil. This review discusses organisms from the domain Archaea in the context of the environments where they have been isolated or detected. For organizational purposes, the domain has been separated into the traditional groups of methanogens, extreme halophiles, thermoacidophiles, and hyperthermophiles, as well as the uncultured archaea detected by molecular means. Where possible, we have correlated known energy-yielding reactions and carbon sources of the archaeal types with available data on potential carbon sources and electron donors and acceptors present in the environments. From the broad distribution, metabolic diversity, and sheer numbers of archaea in environments from the extreme to the ordinary, the roles that the Archaea play in the ecosystems have been grossly underestimated and are worthy of much greater scrutiny.Key words: Archaea, methanogen, extreme halophile, hyperthermophile, thermoacidophile, uncultured archaea, habitats.
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Affiliation(s)
- Bonnie Chaban
- Department of Microbiology and Immunology, Queen's University, Kingston, ON, Canada
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Abstract
The discovery of phylogenetically complex, yet highly sponge-specific microbial communities in marine sponges, including novel lineages and even candidate phyla, came as a surprise. At the same time, unique research opportunities opened up, because the microorganisms of sponges are in many ways more accessible than those of seawater. Accordingly, we consider sponges as microbial fermenters that provide exciting new avenues in marine microbiology and biotechnology. This review covers recent findings regarding diversity, biogeography and population dynamics of sponge-associated microbiota, and the data are discussed within the larger context of the microbiology of the ocean.
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Affiliation(s)
- Ute Hentschel
- Research Center for Infectious Diseases, University of Würzburg, Würzburg, Germany.
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47
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Affiliation(s)
- Nobutada Kimura
- Institute for Biological Resources and Functions, National Institute of Advanced Industrial Science and Technology (AIST)
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48
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Robertson CE, Harris JK, Spear JR, Pace NR. Phylogenetic diversity and ecology of environmental Archaea. Curr Opin Microbiol 2005; 8:638-42. [PMID: 16236543 DOI: 10.1016/j.mib.2005.10.003] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2005] [Accepted: 10/06/2005] [Indexed: 10/25/2022]
Abstract
On the basis of culture studies, Archaea were thought to be synonymous with extreme environments. However, the large numbers of environmental rRNA gene sequences currently flooding into databases such as GenBank show that these organisms are present in almost all environments examined to date. Large sequence databases and new fast phylogenetic software allow more precise determination of the archaeal phylogenetic tree, but also indicate that our knowledge of archaeal diversity is incomplete. Although it is apparent that Archaea can be found in all environments, the chemistry of their ecological context is mostly unknown.
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Affiliation(s)
- Charles E Robertson
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80309, USA
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Schirmer A, Gadkari R, Reeves CD, Ibrahim F, DeLong EF, Hutchinson CR. Metagenomic analysis reveals diverse polyketide synthase gene clusters in microorganisms associated with the marine sponge Discodermia dissoluta. Appl Environ Microbiol 2005; 71:4840-9. [PMID: 16085882 PMCID: PMC1183291 DOI: 10.1128/aem.71.8.4840-4849.2005] [Citation(s) in RCA: 221] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Sponge-associated bacteria are thought to produce many novel bioactive compounds, including polyketides. PCR amplification of ketosynthase domains of type I modular polyketide synthases (PKS) from the microbial community of the marine sponge Discodermia dissoluta revealed great diversity and a novel group of sponge-specific PKS ketosynthase domains. Metagenomic libraries totaling more than four gigabases of bacterial genomes associated with this sponge were screened for type I modular PKS gene clusters. More than 90% of the clones in total sponge DNA libraries represented bacterial DNA inserts, and 0.7% harbored PKS genes. The majority of the PKS hybridizing clones carried small PKS clusters of one to three modules, although some clones encoded large multimodular PKSs (more than five modules). The most abundant large modular PKS appeared to be encoded by a bacterial symbiont that made up < 1% of the sponge community. Sequencing of this PKS revealed 14 modules that, if expressed and active, is predicted to produce a multimethyl-branched fatty acid reminiscent of mycobacterial lipid components. Metagenomic libraries made from fractions enriched for unicellular or filamentous bacteria differed significantly, with the latter containing numerous nonribosomal peptide synthetase (NRPS) and mixed NRPS-PKS gene clusters. The filamentous bacterial community of D. dissoluta consists mainly of Entotheonella spp., an unculturable sponge-specific taxon previously implicated in the biosynthesis of bioactive peptides.
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Affiliation(s)
- Andreas Schirmer
- Kosan Biosciences Inc., 3832 Bay Center Place, Hayward, CA 94545, USA.
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Tyson GW, Banfield JF. Cultivating the uncultivated: a community genomics perspective. Trends Microbiol 2005; 13:411-5. [PMID: 16043355 DOI: 10.1016/j.tim.2005.07.003] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2005] [Revised: 06/16/2005] [Accepted: 07/13/2005] [Indexed: 11/15/2022]
Abstract
Current isolation methods access only a small subset of the total microbial diversity. Although an isolate traditionally has been required for genomic characterization, the advent of sequencing of entire natural microbial communities enables culture-independent genomic analysis. Information about the genetic potential of uncultivated organisms can be used to predict the form of metabolic interdependencies and nutritional requirements. We believe that this could provide the information necessary to bypass bottlenecks that have inhibited cultivation of many microorganisms. However, it might not be practical or possible to isolate all of the vast number of microbial species and strains for laboratory-based characterization. Ultimately, cultivation-independent genomic and genomically enabled approaches could provide a way to directly analyze microbial activity in its geochemical and ecological context.
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Affiliation(s)
- Gene W Tyson
- Department of Environmental Science, Policy and Management, and Department of Earth and Planetary Sciences, University of California-Berkeley, Berkeley, CA 94720, USA
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