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Utzman PH, Mays VP, Miller BC, Fairbanks MC, Brazelton WJ, Horvath MP. Metagenome mining and functional analysis reveal oxidized guanine DNA repair at the Lost City Hydrothermal Field. PLoS One 2024; 19:e0284642. [PMID: 38718041 PMCID: PMC11078426 DOI: 10.1371/journal.pone.0284642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 04/16/2024] [Indexed: 05/12/2024] Open
Abstract
The GO DNA repair system protects against GC → TA mutations by finding and removing oxidized guanine. The system is mechanistically well understood but its origins are unknown. We searched metagenomes and abundantly found the genes encoding GO DNA repair at the Lost City Hydrothermal Field (LCHF). We recombinantly expressed the final enzyme in the system to show MutY homologs function to suppress mutations. Microbes at the LCHF thrive without sunlight, fueled by the products of geochemical transformations of seafloor rocks, under conditions believed to resemble a young Earth. High levels of the reductant H2 and low levels of O2 in this environment raise the question, why are resident microbes equipped to repair damage caused by oxidative stress? MutY genes could be assigned to metagenome-assembled genomes (MAGs), and thereby associate GO DNA repair with metabolic pathways that generate reactive oxygen, nitrogen and sulfur species. Our results indicate that cell-based life was under evolutionary pressure to cope with oxidized guanine well before O2 levels rose following the great oxidation event.
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Affiliation(s)
- Payton H. Utzman
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, United States of America
| | - Vincent P. Mays
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, United States of America
| | - Briggs C. Miller
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, United States of America
| | - Mary C. Fairbanks
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, United States of America
| | - William J. Brazelton
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, United States of America
| | - Martin P. Horvath
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, United States of America
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2
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Heterologous expression and biochemical comparison of two homologous SoxX proteins of endosymbiontic Candidatus Vesicomyosocius okutanii and free-living Hydrogenovibrio crunogenus from deep-sea vent environments. Protein Expr Purif 2022; 200:106157. [PMID: 35987324 DOI: 10.1016/j.pep.2022.106157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 08/11/2022] [Accepted: 08/12/2022] [Indexed: 11/21/2022]
Abstract
Candidatus Vesicomyosocius okutanii is a currently uncultured endosymbiotic bacterium of the clam Pheragena okutanii, which lives in deep-sea vent environments. The genome of Ca. V. okutanii encodes a sulfur-oxidizing (Sox) enzyme complex, presumably generating biological energy for the host from inorganic sulfur compounds. Here, Ca. V. okutanii SoxX (VoSoxX), a mono-heme cytochrome c component of the Sox complex, was shown to be phylogenetically related to its homologous counterpart (HcSoxX) from a free-living deep-sea vent bacterium, Hydrogenovibrio crunogenus. Both proteins were heterologously expressed in Escherichia coli cells with co-expressing cytochrome c maturation genes. Biochemical analysis using the recombinant proteins showed that VoSoxX had a significantly lower thermal stability than HcSoxX, possibly due to structural differences. For example, the Asn-60 residue in VoSoxX may be hydrophobically disadvantageous compared with the spatially corresponding Val-73 residue in HcSoxX. This study represents the first successful case of heterologous expression of genes from Ca. V. okutanii, suggesting that the endosymbiotic VoSoxX protein does not require stabilization, unlike the free-living HcSoxX protein.
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3
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Perez M, Breusing C, Angers B, Beinart RA, Won YJ, Young CR. Divergent paths in the evolutionary history of maternally transmitted clam symbionts. Proc Biol Sci 2022; 289:20212137. [PMID: 35259985 PMCID: PMC8905170 DOI: 10.1098/rspb.2021.2137] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Vertical transmission of bacterial endosymbionts is accompanied by virtually irreversible gene loss that results in a progressive reduction in genome size. While the evolutionary processes of genome reduction have been well described in some terrestrial symbioses, they are less understood in marine systems where vertical transmission is rarely observed. The association between deep-sea vesicomyid clams and chemosynthetic Gammaproteobacteria is one example of maternally inherited symbioses in the ocean. Here, we assessed the contributions of drift, recombination and selection to genome evolution in two extant vesicomyid symbiont clades by comparing 15 representative symbiont genomes (1.017-1.586 Mb) to those of closely related bacteria and the hosts' mitochondria. Our analyses suggest that drift is a significant force driving genome evolution in vesicomyid symbionts, though selection and interspecific recombination appear to be critical for maintaining symbiont functional integrity and creating divergent patterns of gene conservation. Notably, the two symbiont clades possess putative functional differences in sulfide physiology, anaerobic respiration and dependency on environmental vitamin B12, which probably reflect adaptations to different ecological habitats available to each symbiont group. Overall, these results contribute to our understanding of the eco-evolutionary processes shaping reductive genome evolution in vertically transmitted symbioses.
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Affiliation(s)
- Maëva Perez
- Department of Biological Sciences, Université de Montréal, Montreal, Canada
| | - Corinna Breusing
- Graduate School of Oceanography, University of Rhode Island, Narragansett, RI, USA
| | - Bernard Angers
- Department of Biological Sciences, Université de Montréal, Montreal, Canada
| | - Roxanne A Beinart
- Graduate School of Oceanography, University of Rhode Island, Narragansett, RI, USA
| | - Yong-Jin Won
- Division of EcoScience, Ewha Womans University, Seoul, South Korea
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4
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Hu EZ, Lan XR, Liu ZL, Gao J, Niu DK. A positive correlation between GC content and growth temperature in prokaryotes. BMC Genomics 2022; 23:110. [PMID: 35139824 PMCID: PMC8827189 DOI: 10.1186/s12864-022-08353-7] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 01/31/2022] [Indexed: 01/27/2023] Open
Abstract
Background GC pairs are generally more stable than AT pairs; GC-rich genomes were proposed to be more adapted to high temperatures than AT-rich genomes. Previous studies consistently showed positive correlations between growth temperature and the GC contents of structural RNA genes. However, for the whole genome sequences and the silent sites of the codons in protein-coding genes, the relationship between GC content and growth temperature is in a long-lasting debate. Results With a dataset much larger than previous studies (681 bacteria and 155 archaea with completely assembled genomes), our phylogenetic comparative analyses showed positive correlations between optimal growth temperature (Topt) and GC content both in bacterial and archaeal structural RNA genes and in bacterial whole genome sequences, chromosomal sequences, plasmid sequences, core genes, and accessory genes. However, in the 155 archaea, we did not observe a significant positive correlation of Topt with whole-genome GC content (GCw) or GC content at four-fold degenerate sites. We randomly drew 155 samples from the 681 bacteria for 1000 rounds. In most cases (> 95%), the positive correlations between Topt and genomic GC contents became statistically nonsignificant (P > 0.05). This result suggested that the small sample sizes might account for the lack of positive correlations between growth temperature and genomic GC content in the 155 archaea and the bacterial samples of previous studies. Comparing the GC content among four categories (psychrophiles/psychrotrophiles, mesophiles, thermophiles, and hyperthermophiles) also revealed a positive correlation between GCw and growth temperature in bacteria. By including the GCw of incompletely assembled genomes, we expanded the sample size of archaea to 303. Positive correlations between GCw and Topt appear especially after excluding the halophilic archaea whose GC contents might be strongly shaped by intense UV radiation. Conclusions This study explains the previous contradictory observations and ends a long debate. Prokaryotes growing in high temperatures have higher GC contents. Thermal adaptation is one possible explanation for the positive association. Meanwhile, we propose that the elevated efficiency of DNA repair in response to heat mutagenesis might have the by-product of increasing GC content like that happens in intracellular symbionts and marine bacterioplankton. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08353-7.
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Affiliation(s)
- En-Ze Hu
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering and Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Xin-Ran Lan
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering and Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Zhi-Ling Liu
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering and Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Jie Gao
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering and Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Deng-Ke Niu
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering and Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, 100875, China.
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5
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Kinjo Y, Lo N, Martín PV, Tokuda G, Pigolotti S, Bourguignon T. Enhanced Mutation Rate, Relaxed Selection, and the "Domino Effect" are associated with Gene Loss in Blattabacterium, A Cockroach Endosymbiont. Mol Biol Evol 2021; 38:3820-3831. [PMID: 34426845 PMCID: PMC8382890 DOI: 10.1093/molbev/msab159] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Intracellular endosymbionts have reduced genomes that progressively lose genes at a timescale of tens of million years. We previously reported that gene loss rate is linked to mutation rate in Blattabacterium, however, the mechanisms causing gene loss are not yet fully understood. Here, we carried out comparative genomic analyses on the complete genome sequences of a representative set of 67 Blattabacterium strains, with sizes ranging between 511 and 645 kb. We found that 200 of the 566 analyzed protein-coding genes were lost in at least one lineage of Blattabacterium, with the most extreme case being one gene that was lost independently in 24 lineages. We found evidence for three mechanisms influencing gene loss in Blattabacterium. First, gene loss rates were found to increase exponentially with the accumulation of substitutions. Second, genes involved in vitamin and amino acid metabolism experienced relaxed selection in Cryptocercus and Mastotermes, possibly triggered by their vertically inherited gut symbionts. Third, we found evidence of epistatic interactions among genes leading to a "domino effect" of gene loss within pathways. Our results highlight the complexity of the process of genome erosion in an endosymbiont.
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Affiliation(s)
- Yukihiro Kinjo
- Okinawa Institute of Science & Technology Graduate University, Tancha, Onna-son, Okinawa, Japan
| | - Nathan Lo
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
| | - Paula Villa Martín
- Okinawa Institute of Science & Technology Graduate University, Tancha, Onna-son, Okinawa, Japan
| | - Gaku Tokuda
- Tropical Biosphere Research Center, University of the Ryukyus, Nishihara, Okinawa, Japan
| | - Simone Pigolotti
- Okinawa Institute of Science & Technology Graduate University, Tancha, Onna-son, Okinawa, Japan
| | - Thomas Bourguignon
- Okinawa Institute of Science & Technology Graduate University, Tancha, Onna-son, Okinawa, Japan
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6
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Russell SL, Pepper-Tunick E, Svedberg J, Byrne A, Ruelas Castillo J, Vollmers C, Beinart RA, Corbett-Detig R. Horizontal transmission and recombination maintain forever young bacterial symbiont genomes. PLoS Genet 2020; 16:e1008935. [PMID: 32841233 PMCID: PMC7473567 DOI: 10.1371/journal.pgen.1008935] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2019] [Revised: 09/04/2020] [Accepted: 06/16/2020] [Indexed: 12/30/2022] Open
Abstract
Bacterial symbionts bring a wealth of functions to the associations they participate in, but by doing so, they endanger the genes and genomes underlying these abilities. When bacterial symbionts become obligately associated with their hosts, their genomes are thought to decay towards an organelle-like fate due to decreased homologous recombination and inefficient selection. However, numerous associations exist that counter these expectations, especially in marine environments, possibly due to ongoing horizontal gene flow. Despite extensive theoretical treatment, no empirical study thus far has connected these underlying population genetic processes with long-term evolutionary outcomes. By sampling marine chemosynthetic bacterial-bivalve endosymbioses that range from primarily vertical to strictly horizontal transmission, we tested this canonical theory. We found that transmission mode strongly predicts homologous recombination rates, and that exceedingly low recombination rates are associated with moderate genome degradation in the marine symbionts with nearly strict vertical transmission. Nonetheless, even the most degraded marine endosymbiont genomes are occasionally horizontally transmitted and are much larger than their terrestrial insect symbiont counterparts. Therefore, horizontal transmission and recombination enable efficient natural selection to maintain intermediate symbiont genome sizes and substantial functional genetic variation.
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Affiliation(s)
- Shelbi L. Russell
- Department of Molecular Cellular and Developmental Biology. University of California Santa Cruz, Santa Cruz, California, United States of America
- Department of Biomolecular Engineering. University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Evan Pepper-Tunick
- Department of Biomolecular Engineering. University of California Santa Cruz, Santa Cruz, California, United States of America
- Genomics Institute, University of California, Santa Cruz, California, United States of America
| | - Jesper Svedberg
- Department of Biomolecular Engineering. University of California Santa Cruz, Santa Cruz, California, United States of America
- Genomics Institute, University of California, Santa Cruz, California, United States of America
| | - Ashley Byrne
- Department of Molecular Cellular and Developmental Biology. University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Jennie Ruelas Castillo
- Department of Molecular Cellular and Developmental Biology. University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Christopher Vollmers
- Department of Biomolecular Engineering. University of California Santa Cruz, Santa Cruz, California, United States of America
- Genomics Institute, University of California, Santa Cruz, California, United States of America
| | - Roxanne A. Beinart
- Graduate School of Oceanography. University of Rhode Island, Narragansett, Rhode Island, United States of America
| | - Russell Corbett-Detig
- Department of Biomolecular Engineering. University of California Santa Cruz, Santa Cruz, California, United States of America
- Genomics Institute, University of California, Santa Cruz, California, United States of America
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7
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McCuaig B, Peña-Castillo L, Dufour SC. Metagenomic analysis suggests broad metabolic potential in extracellular symbionts of the bivalve Thyasira cf. gouldi. Anim Microbiome 2020; 2:7. [PMID: 33499960 PMCID: PMC7807488 DOI: 10.1186/s42523-020-00025-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 02/20/2020] [Indexed: 11/26/2022] Open
Abstract
Background Next-generation sequencing has opened new avenues for studying metabolic capabilities of bacteria that cannot be cultured. Here, we provide a metagenomic description of chemoautotrophic gammaproteobacterial symbionts associated with Thyasira cf. gouldi, a sediment-dwelling bivalve from the family Thyasiridae. Thyasirid symbionts differ from those of other bivalves by being extracellular, and recent work suggests that they are capable of living freely in the environment. Results Thyasira cf. gouldi symbionts appear to form mixed, non-clonal populations in the host, show no signs of genomic reduction and contain many genes that would only be useful outside the host, including flagellar and chemotaxis genes. The thyasirid symbionts may be capable of sulfur oxidation via both the sulfur oxidation and reverse dissimilatory sulfate reduction pathways, as observed in other bivalve symbionts. In addition, genes for hydrogen oxidation and dissimilatory nitrate reduction were found, suggesting varied metabolic capabilities under a range of redox conditions. The genes of the tricarboxylic acid cycle are also present, along with membrane bound sugar importer channels, suggesting that the bacteria may be mixotrophic. Conclusions In this study, we have generated the first thyasirid symbiont genomic resources. In Thyasira cf. gouldi, symbiont populations appear non-clonal and encode genes for a plethora of metabolic capabilities; future work should examine whether symbiont heterogeneity and metabolic breadth, which have been shown in some intracellular chemosymbionts, are signatures of extracellular chemosymbionts in bivalves.
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Affiliation(s)
- Bonita McCuaig
- Department of Biology, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Lourdes Peña-Castillo
- Department of Biology, Memorial University of Newfoundland, St. John's, NL, Canada.,Department of Computer Science, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Suzanne C Dufour
- Department of Biology, Memorial University of Newfoundland, St. John's, NL, Canada.
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8
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Breusing C, Johnson SB, Vrijenhoek RC, Young CR. Host hybridization as a potential mechanism of lateral symbiont transfer in deep-sea vesicomyid clams. Mol Ecol 2019; 28:4697-4708. [PMID: 31478269 PMCID: PMC7004080 DOI: 10.1111/mec.15224] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 08/01/2019] [Accepted: 08/06/2019] [Indexed: 12/16/2022]
Abstract
Deep-sea vesicomyid clams live in mutualistic symbiosis with chemosynthetic bacteria that are inherited through the maternal germ line. On evolutionary timescales, strictly vertical transmission should lead to cospeciation of host mitochondrial and symbiont lineages; nonetheless, examples of incongruent phylogenies have been reported, suggesting that symbionts are occasionally horizontally transmitted between host species. The current paradigm for vesicomyid clams holds that direct transfers cause host shifts or mixtures of symbionts. An alternative hypothesis suggests that hybridization between host species might explain symbiont transfers. Two clam species, Archivesica gigas and Phreagena soyoae, frequently co-occur at deep-sea hydrocarbon seeps in the eastern Pacific Ocean. Although the two species typically host gammaproteobacterial symbiont lineages marked by divergent 16S rRNA phylotypes, we identified a number of clams with the A. gigas mitotype that hosted symbionts with the P. soyoae phylotype. Demographic inference models based on genome-wide SNP data and three Sanger sequenced gene markers provided evidence that A. gigas and P. soyoae hybridized in the past, supporting the hypothesis that hybridization might be a viable mechanism of interspecific symbiont transfer. These findings provide new perspectives on the evolution of vertically transmitted symbionts and their hosts in deep-sea chemosynthetic environments.
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Affiliation(s)
- Corinna Breusing
- Monterey Bay Aquarium Research Institute, Moss Landing, CA, USA.,National Oceanography Centre, Southampton, UK
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9
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Single-cell genomics unveiled a cryptic cyanobacterial lineage with a worldwide distribution hidden by a dinoflagellate host. Proc Natl Acad Sci U S A 2019; 116:15973-15978. [PMID: 31235587 DOI: 10.1073/pnas.1902538116] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Cyanobacteria are one of the most important contributors to oceanic primary production and survive in a wide range of marine habitats. Much effort has been made to understand their ecological features, diversity, and evolution, based mainly on data from free-living cyanobacterial species. In addition, symbiosis has emerged as an important lifestyle of oceanic microbes and increasing knowledge of cyanobacteria in symbiotic relationships with unicellular eukaryotes suggests their significance in understanding the global oceanic ecosystem. However, detailed characteristics of these cyanobacteria remain poorly described. To gain better insight into marine cyanobacteria in symbiosis, we sequenced the genome of cyanobacteria collected from a cell of a pelagic dinoflagellate that is known to host cyanobacterial symbionts within a specialized chamber. Phylogenetic analyses using the genome sequence revealed that the cyanobacterium represents an underdescribed lineage within an extensively studied, ecologically important group of marine cyanobacteria. Metagenomic analyses demonstrated that this cyanobacterial lineage is globally distributed and strictly coexists with its host dinoflagellates, suggesting that the intimate symbiotic association allowed the cyanobacteria to escape from previous metagenomic studies. Furthermore, a comparative analysis of the protein repertoire with related species indicated that the lineage has independently undergone reductive genome evolution to a similar extent as Prochlorococcus, which has the most reduced genomes among free-living cyanobacteria. Discovery of this cyanobacterial lineage, hidden by its symbiotic lifestyle, provides crucial insights into the diversity, ecology, and evolution of marine cyanobacteria and suggests the existence of other undiscovered cryptic cyanobacterial lineages.
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10
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Ozawa G, Shimamura S, Takaki Y, Takishita K, Ikuta T, Barry JP, Maruyama T, Fujikura K, Yoshida T. Ancient Occasional Host Switching of Maternally Transmitted Bacterial Symbionts of Chemosynthetic Vesicomyid Clams. Genome Biol Evol 2018; 9:2226-2236. [PMID: 28922872 PMCID: PMC5604134 DOI: 10.1093/gbe/evx166] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/22/2017] [Indexed: 11/22/2022] Open
Abstract
Vesicomyid clams in deep-sea chemosynthetic ecosystems harbor sulfur-oxidizing bacteria in their gill epithelial cells. These symbionts, which are vertically transmitted, are species-specific and thought to have cospeciated with their hosts. However, recent studies indicate incongruent phylogenies between some vesicomyid clams and their symbionts, suggesting that symbionts are horizontally transmitted. To more precisely understand the evolution of vesicomyid clams and their symbionts, we compared the evolution of vesicomyid clams and their symbionts through phylogenetic analyses using multi-gene data sets. Many clades in the phylogenetic trees of 13 host species (Abyssogena mariana, Ab. phaseoliformis, Akebiconcha kawamurai, Calyptogena fausta, C. laubieri, C. magnifica, C. nautilei, C. pacifica, Isorropodon fossajaponicum, Phreagena kilmeri, Ph. okutanii, Ph. soyoae, and Pliocardia stearnsii) and their symbionts were well resolved. Six of the 13 host-symbiont pairs (C. fausta, C. magnifica, C. pacifica, Ph. kilmeri, Ph. okutanii, and Ph. soyoae, and their respective symbionts) showed topological congruence. However, the remaining seven pairs (Ak. kawamurai, Ab mariana, Ab. phaseoliformis, C. laubieri, C. nautilei, I. fossajaponicum, and Pl. stearnsii and their corresponding symbionts) showed incongruent topologies, which were supported by the approximately unbiased and Bayes factor tests. Coevolution analyses indicated that six pairs cospeciated, whereas host switching events occurred in the remaining seven pairs. Markedly, multiple host switching events may have occurred in the lineages from the common ancestral symbiont of C. pacifica and C. fausta. Our phylogenetic and coevolution analyses provide additional evidence for host switching during the evolution of vesicomyids.
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Affiliation(s)
- Genki Ozawa
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Natsushima-cho, Yokosuka, Kanagawa, Japan.,Department of Marine Biosciences, School of Marine Biosciences, Kitasato University, Minami-ku, Sagamihara, Kanagawa, Japan
| | - Shigeru Shimamura
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Natsushima-cho, Yokosuka, Kanagawa, Japan
| | - Yoshihiro Takaki
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Natsushima-cho, Yokosuka, Kanagawa, Japan
| | - Kiyotaka Takishita
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Natsushima-cho, Yokosuka, Kanagawa, Japan
| | - Tetsuro Ikuta
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Natsushima-cho, Yokosuka, Kanagawa, Japan
| | - James P Barry
- Monterey Bay Aquarium Research Institute, Moss Landing, Monterey, California
| | - Tadashi Maruyama
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Natsushima-cho, Yokosuka, Kanagawa, Japan
| | - Katsunori Fujikura
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Natsushima-cho, Yokosuka, Kanagawa, Japan
| | - Takao Yoshida
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Natsushima-cho, Yokosuka, Kanagawa, Japan.,Department of Marine Biosciences, School of Marine Biosciences, Kitasato University, Minami-ku, Sagamihara, Kanagawa, Japan
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11
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Shimamura S, Kaneko T, Ozawa G, Matsumoto MN, Koshiishi T, Takaki Y, Kato C, Takai K, Yoshida T, Fujikura K, Barry JP, Maruyama T. Loss of genes related to Nucleotide Excision Repair (NER) and implications for reductive genome evolution in symbionts of deep-sea vesicomyid clams. PLoS One 2017; 12:e0171274. [PMID: 28199404 PMCID: PMC5310779 DOI: 10.1371/journal.pone.0171274] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Accepted: 01/17/2017] [Indexed: 01/08/2023] Open
Abstract
Intracellular thioautotrophic symbionts of deep-sea vesicomyid clams lack some DNA repair genes and are thought to be undergoing reductive genome evolution (RGE). In this study, we addressed two questions, 1) how these symbionts lost their DNA repair genes and 2) how such losses affect RGE. For the first question, we examined genes associated with nucleotide excision repair (NER; uvrA, uvrB, uvrC, uvrD, uvrD paralog [uvrDp] and mfd) in 12 symbionts of vesicomyid clams belonging to two clades (5 clade I and 7 clade II symbionts). While uvrA, uvrDp and mfd were conserved in all symbionts, uvrB and uvrC were degraded in all clade I symbionts but were apparently intact in clade II symbionts. UvrD was disrupted in two clade II symbionts. Among the intact genes in Ca. Vesicomyosocius okutanii (clade I), expressions of uvrD and mfd were detected by reverse transcription-polymerase chain reaction (RT-PCR), but those of uvrA and uvrDp were not. In contrast, all intact genes were expressed in the symbiont of Calyptogena pacifica (clade II). To assess how gene losses affect RGE (question 2), genetic distances of the examined genes in symbionts from Bathymodiolus septemdierum were shown to be larger in clade I than clade II symbionts. In addition, these genes had lower guanine+cytosine (GC) content and higher repeat sequence densities in clade I than measured in clade II. Our results suggest that NER genes are currently being lost from the extant lineages of vesicomyid clam symbionts. The loss of NER genes and mutY in these symbionts is likely to promote increases in genetic distance and repeat sequence density as well as reduced GC content in genomic genes, and may have facilitated reductive evolution of the genome.
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Affiliation(s)
- Shigeru Shimamura
- Department of Marine Biodiversity Research, Japan Agency for Marine-Earth Science and Technology, 2–15, Natsushima-cho, Yokosuka-shi, Kanagawa, Japan
- Department of Subsurface Geobiological Analysis and Research, Japan Agency for Marine-Earth Science and Technology, Natsushima-cho, Yokosuka-shi, Kanagawa, Japan
| | - Takashi Kaneko
- Department of Marine Biodiversity Research, Japan Agency for Marine-Earth Science and Technology, 2–15, Natsushima-cho, Yokosuka-shi, Kanagawa, Japan
- Tokyo College of Biotechnology, Kitakoujiya, Ota-ku,Tokyo, Japan
| | - Genki Ozawa
- Department of Marine Biodiversity Research, Japan Agency for Marine-Earth Science and Technology, 2–15, Natsushima-cho, Yokosuka-shi, Kanagawa, Japan
- Kitasato University, School of Marine Biosciences, Kitasato Minami-ku Sagamihara-shi Kanagawa, Japan
| | - Mamiko Nishino Matsumoto
- Department of Marine Biodiversity Research, Japan Agency for Marine-Earth Science and Technology, 2–15, Natsushima-cho, Yokosuka-shi, Kanagawa, Japan
| | - Takeru Koshiishi
- Department of Marine Biodiversity Research, Japan Agency for Marine-Earth Science and Technology, 2–15, Natsushima-cho, Yokosuka-shi, Kanagawa, Japan
| | - Yoshihiro Takaki
- Department of Subsurface Geobiological Analysis and Research, Japan Agency for Marine-Earth Science and Technology, Natsushima-cho, Yokosuka-shi, Kanagawa, Japan
| | - Chiaki Kato
- Department of Marine Biodiversity Research, Japan Agency for Marine-Earth Science and Technology, 2–15, Natsushima-cho, Yokosuka-shi, Kanagawa, Japan
| | - Ken Takai
- Department of Subsurface Geobiological Analysis and Research, Japan Agency for Marine-Earth Science and Technology, Natsushima-cho, Yokosuka-shi, Kanagawa, Japan
| | - Takao Yoshida
- Department of Marine Biodiversity Research, Japan Agency for Marine-Earth Science and Technology, 2–15, Natsushima-cho, Yokosuka-shi, Kanagawa, Japan
- Kitasato University, School of Marine Biosciences, Kitasato Minami-ku Sagamihara-shi Kanagawa, Japan
| | - Katsunori Fujikura
- Department of Marine Biodiversity Research, Japan Agency for Marine-Earth Science and Technology, 2–15, Natsushima-cho, Yokosuka-shi, Kanagawa, Japan
| | - James P. Barry
- Monterey Bay Aquarium Research Institute, Moss Landing, California, United States of America
| | - Tadashi Maruyama
- Kitasato University, School of Marine Biosciences, Kitasato Minami-ku Sagamihara-shi Kanagawa, Japan
- Research and Development Center for Submarine Resources, Japan Agency for Marine-Earth Science and Technology, Natsushima-cho, Yokosuka-shi, Kanagawa, Japan
- * E-mail:
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12
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Ikuta T, Igawa K, Tame A, Kuroiwa T, Kuroiwa H, Aoki Y, Takaki Y, Nagai Y, Ozawa G, Yamamoto M, Deguchi R, Fujikura K, Maruyama T, Yoshida T. Surfing the vegetal pole in a small population: extracellular vertical transmission of an 'intracellular' deep-sea clam symbiont. ROYAL SOCIETY OPEN SCIENCE 2016; 3:160130. [PMID: 27293794 PMCID: PMC4892456 DOI: 10.1098/rsos.160130] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Accepted: 04/21/2016] [Indexed: 06/06/2023]
Abstract
Symbiont transmission is a key event for understanding the processes underlying symbiotic associations and their evolution. However, our understanding of the mechanisms of symbiont transmission remains still fragmentary. The deep-sea clam Calyptogena okutanii harbours obligate sulfur-oxidizing intracellular symbiotic bacteria in the gill epithelial cells. In this study, we determined the localization of their symbiont associating with the spawned eggs, and the population size of the symbiont transmitted via the eggs. We show that the symbionts are located on the outer surface of the egg plasma membrane at the vegetal pole, and that each egg carries approximately 400 symbiont cells, each of which contains close to 10 genomic copies. The very small population size of the symbiont transmitted via the eggs might narrow the bottleneck and increase genetic drift, while polyploidy and its transient extracellular lifestyle might slow the rate of genome reduction. Additionally, the extracellular localization of the symbiont on the egg surface may increase the chance of symbiont exchange. This new type of extracellular transovarial transmission provides insights into complex interactions between the host and symbiont, development of both host and symbiont, as well as the population dynamics underlying genetic drift and genome evolution in microorganisms.
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Affiliation(s)
- Tetsuro Ikuta
- Department of Marine Biodiversity Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima, Yokosuka, Kanagawa 237-0061, Japan
| | - Kanae Igawa
- Department of Marine Biodiversity Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima, Yokosuka, Kanagawa 237-0061, Japan
- Graduate School of Marine Science and Technology, Tokyo University of Marine Science and Technology, 4-5-7 Konan, Minato-ku, Tokyo 108-8477, Japan
| | - Akihiro Tame
- Marine Works Japan, Ltd, 3-54-1 Oppamahigashi, Yokosuka, Kanagawa 237-0063, Japan
| | - Tsuneyoshi Kuroiwa
- Department of Chemical and Biological Sciences, Japan Women's University, 2-8-1 Mejirodai, Bunkyo-ku, Tokyo 112-8681, Japan
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency, Gobancho, Chiyoda-ku, Tokyo 102-0076, Japan
| | - Haruko Kuroiwa
- Department of Chemical and Biological Sciences, Japan Women's University, 2-8-1 Mejirodai, Bunkyo-ku, Tokyo 112-8681, Japan
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency, Gobancho, Chiyoda-ku, Tokyo 102-0076, Japan
| | - Yui Aoki
- Department of Marine Biodiversity Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima, Yokosuka, Kanagawa 237-0061, Japan
| | - Yoshihiro Takaki
- Department of Subsurface Geobiological Analysis and Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima, Yokosuka, Kanagawa 237-0061, Japan
| | - Yukiko Nagai
- Department of Marine Biodiversity Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima, Yokosuka, Kanagawa 237-0061, Japan
| | - Genki Ozawa
- Department of Marine Biodiversity Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima, Yokosuka, Kanagawa 237-0061, Japan
- Department of Marine Biosciences, School of Marine Biosciences, Kitasato University, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa 252-0373, Japan
| | - Masahiro Yamamoto
- Department of Subsurface Geobiological Analysis and Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima, Yokosuka, Kanagawa 237-0061, Japan
| | - Ryusaku Deguchi
- Department of Biology, Miyagi University of Education, Aoba-ku, Sendai, Miyagi 980-0845, Japan
| | - Katsunori Fujikura
- Department of Marine Biodiversity Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima, Yokosuka, Kanagawa 237-0061, Japan
| | - Tadashi Maruyama
- Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima, Yokosuka, Kanagawa 237-0061, Japan
| | - Takao Yoshida
- Department of Marine Biodiversity Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima, Yokosuka, Kanagawa 237-0061, Japan
- Graduate School of Marine Science and Technology, Tokyo University of Marine Science and Technology, 4-5-7 Konan, Minato-ku, Tokyo 108-8477, Japan
- Department of Marine Biosciences, School of Marine Biosciences, Kitasato University, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa 252-0373, Japan
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13
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Decker C, Olu K, Arnaud-Haond S, Duperron S. Physical proximity may promote lateral acquisition of bacterial symbionts in vesicomyid clams. PLoS One 2013; 8:e64830. [PMID: 23861734 PMCID: PMC3704533 DOI: 10.1371/journal.pone.0064830] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2012] [Accepted: 04/18/2013] [Indexed: 11/19/2022] Open
Abstract
Vesicomyid clams harbor intracellular sulfur-oxidizing bacteria that are predominantly maternally inherited and co-speciate with their hosts. Genome recombination and the occurrence of non-parental strains were recently demonstrated in symbionts. However, mechanisms favoring such events remain to be identified. In this study, we investigated symbionts in two phylogenetically distant vesicomyid species, Christineconcha regab and Laubiericoncha chuni, which sometimes co-occur at a cold-seep site in the Gulf of Guinea. We showed that each of the two species harbored a single dominant bacterial symbiont strain. However, for both vesicomyid species, the symbiont from the other species was occasionally detected in the gills using fluorescence in situ hybridization and gene sequences analyses based on six symbiont marker genes. Symbiont strains co-occurred within a single host only at sites where both host species were found; whereas one single symbiont strain was detected in C. regab specimens from a site where no L. chuni individuals had been observed. These results suggest that physical proximity favored the acquisition of non-parental symbiont strains in Vesicomyidae. Over evolutionary time, this could potentially lead to genetic exchanges among symbiont species and eventually symbiont displacement. Symbiont densities estimated using 3D fluorescence in situ hybridization varied among host species and sites, suggesting flexibility in the association despite the fact that a similar type of metabolism is expected in all symbionts.
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Affiliation(s)
- Carole Decker
- IFREMER Centre de Brest, Laboratoire Environnement Profond, REM-EEP, Plouzané, France.
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14
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SUP05 dominates the Gammaproteobacterial sulfur oxidizer assemblages in pelagic redoxclines of the central Baltic and Black Seas. Appl Environ Microbiol 2013; 79:2767-76. [PMID: 23417000 DOI: 10.1128/aem.03777-12] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Gammaproteobacterial sulfur oxidizers (GSOs), particularly SUP05-related sequences, have been found worldwide in numerous oxygen-deficient marine environments. However, knowledge regarding their abundance, distribution, and ecological role is scarce. In this study, on the basis of phylogenetic analyses of 16S rRNA gene sequences originating from a Baltic Sea pelagic redoxcline, the in situ abundances of different GSO subgroups were quantified by CARD-FISH (catalyzed reporter fluorescence in situ hybridization) with oligonucleotide probes developed specifically for this purpose. Additionally, ribulose bisphosphate carboxylase/oxygenase form II (cbbM) gene transcript clone libraries were used to detect potential active chemolithoautotrophic GSOs in the Baltic Sea. Taken together, the results obtained by these two approaches demonstrated the existence of two major phylogenetic subclusters embedded within the GSO, one of them affiliated with sequences of the previously described SUP05 subgroup. CARD-FISH analyses revealed that only SUP05 occurred in relatively high numbers, reaching 10 to 30% of the total prokaryotes around the oxic-anoxic interface, where oxygen and sulfide concentrations are minimal. The applicability of the oligonucleotide probes was confirmed with samples from the Black Sea redoxcline, in which the SUP05 subgroup accounted for 10 to 13% of the total prokaryotic abundance. The cbbM transcripts presumably originating from SUP05 cells support previous evidence for the chemolithoautotrophic activity of this phylogenetic group. Our findings on the vertical distribution and high abundance of SUP05 suggest that this group plays an important role in marine redoxcline biogeochemistry, probably as anaerobic or aerobic sulfur oxidizers.
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Williams TJ, Wilkins D, Long E, Evans F, DeMaere MZ, Raftery MJ, Cavicchioli R. The role of planktonic Flavobacteria in processing algal organic matter in coastal East Antarctica revealed using metagenomics and metaproteomics. Environ Microbiol 2012; 15:1302-17. [PMID: 23126454 DOI: 10.1111/1462-2920.12017] [Citation(s) in RCA: 211] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2012] [Revised: 09/20/2012] [Accepted: 09/26/2012] [Indexed: 11/27/2022]
Abstract
Heterotrophic marine bacteria play key roles in remineralizing organic matter generated from primary production. However, far more is known about which groups are dominant than about the cellular processes they perform in order to become dominant. In the Southern Ocean, eukaryotic phytoplankton are the dominant primary producers. In this study we used metagenomics and metaproteomics to determine how the dominant bacterial and archaeal plankton processed bloom material. We examined the microbial community composition in 14 metagenomes and found that the relative abundance of Flavobacteria (dominated by Polaribacter) was positively correlated with chlorophyll a fluorescence, and the relative abundance of SAR11 was inversely correlated with both fluorescence and Flavobacteria abundance. By performing metaproteomics on the sample with the highest relative abundance of Flavobacteria (Newcomb Bay, East Antarctica) we defined how Flavobacteria attach to and degrade diverse complex organic material, how they make labile compounds available to Alphaproteobacteria (especially SAR11) and Gammaproteobacteria, and how these heterotrophic Proteobacteria target and utilize these nutrients. The presence of methylotrophic proteins for archaea and bacteria also indicated the importance of metabolic specialists. Overall, the study provides functional data for the microbial mechanisms of nutrient cycling at the surface of the coastal Southern Ocean.
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Affiliation(s)
- Timothy J Williams
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, New South Wales, 2052, Australia
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