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Zhang Y, Chen H, Lian C, Cao L, Guo Y, Wang M, Zhong Z, Li M, Zhang H, Li C. Insights into phage-bacteria interaction in cold seep Gigantidas platifrons through metagenomics and transcriptome analyses. Sci Rep 2024; 14:10540. [PMID: 38719945 PMCID: PMC11078923 DOI: 10.1038/s41598-024-61272-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 05/03/2024] [Indexed: 05/12/2024] Open
Abstract
Viruses are crucial for regulating deep-sea microbial communities and biogeochemical cycles. However, their roles are still less characterized in deep-sea holobionts. Bathymodioline mussels are endemic species inhabiting cold seeps and harboring endosymbionts in gill epithelial cells for nutrition. This study unveiled a diverse array of viruses in the gill tissues of Gigantidas platifrons mussels and analyzed the viral metagenome and transcriptome from the gill tissues of Gigantidas platifrons mussels collected from a cold seep in the South Sea. The mussel gills contained various viruses including Baculoviridae, Rountreeviridae, Myoviridae and Siphovirdae, but the active viromes were Myoviridae, Siphoviridae, and Podoviridae belonging to the order Caudovirales. The overall viral community structure showed significant variation among environments with different methane concentrations. Transcriptome analysis indicated high expression of viral structural genes, integrase, and restriction endonuclease genes in a high methane concentration environment, suggesting frequent virus infection and replication. Furthermore, two viruses (GP-phage-contig14 and GP-phage-contig72) interacted with Gigantidas platifrons methanotrophic gill symbionts (bathymodiolin mussels host intracellular methanotrophic Gammaproteobacteria in their gills), showing high expression levels, and have huge different expression in different methane concentrations. Additionally, single-stranded DNA viruses may play a potential auxiliary role in the virus-host interaction using indirect bioinformatics methods. Moreover, the Cro and DNA methylase genes had phylogenetic similarity between the virus and Gigantidas platifrons methanotrophic gill symbionts. This study also explored a variety of viruses in the gill tissues of Gigantidas platifrons and revealed that bacteria interacted with the viruses during the symbiosis with Gigantidas platifrons. This study provides fundamental insights into the interplay of microorganisms within Gigantidas platifrons mussels in deep sea.
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Affiliation(s)
- Yan Zhang
- Center of Deep Sea Research, and CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Hao Chen
- Center of Deep Sea Research, and CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Chao Lian
- Center of Deep Sea Research, and CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Lei Cao
- Center of Deep Sea Research, and CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Yang Guo
- Center of Deep Sea Research, and CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Minxiao Wang
- Center of Deep Sea Research, and CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.
| | - Zhaoshan Zhong
- Center of Deep Sea Research, and CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Mengna Li
- Center of Deep Sea Research, and CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- National Deep Sea Center, Qingdao, 266071, China
| | - Huan Zhang
- Center of Deep Sea Research, and CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- National Deep Sea Center, Qingdao, 266071, China
| | - Chaolun Li
- Center of Deep Sea Research, and CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.
- Laboratory for Marine Ecology and Environmental Science, Laoshan Laboratory, Qingdao, 266237, China.
- South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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Gheibzadeh MS, Manyumwa CV, Tastan Bishop Ö, Shahbani Zahiri H, Parkkila S, Zolfaghari Emameh R. Genome Study of α-, β-, and γ-Carbonic Anhydrases from the Thermophilic Microbiome of Marine Hydrothermal Vent Ecosystems. BIOLOGY 2023; 12:770. [PMID: 37372055 DOI: 10.3390/biology12060770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 05/17/2023] [Accepted: 05/17/2023] [Indexed: 06/29/2023]
Abstract
Carbonic anhydrases (CAs) are metalloenzymes that can help organisms survive in hydrothermal vents by hydrating carbon dioxide (CO2). In this study, we focus on alpha (α), beta (β), and gamma (γ) CAs, which are present in the thermophilic microbiome of marine hydrothermal vents. The coding genes of these enzymes can be transferred between hydrothermal-vent organisms via horizontal gene transfer (HGT), which is an important tool in natural biodiversity. We performed big data mining and bioinformatics studies on α-, β-, and γ-CA coding genes from the thermophilic microbiome of marine hydrothermal vents. The results showed a reasonable association between thermostable α-, β-, and γ-CAs in the microbial population of the hydrothermal vents. This relationship could be due to HGT. We found evidence of HGT of α- and β-CAs between Cycloclasticus sp., a symbiont of Bathymodiolus heckerae, and an endosymbiont of Riftia pachyptila via Integrons. Conversely, HGT of β-CA genes from the endosymbiont Tevnia jerichonana to the endosymbiont Riftia pachyptila was detected. In addition, Hydrogenovibrio crunogenus SP-41 contains a β-CA gene on genomic islands (GIs). This gene can be transferred by HGT to Hydrogenovibrio sp. MA2-6, a methanotrophic endosymbiont of Bathymodiolus azoricus, and a methanotrophic endosymbiont of Bathymodiolus puteoserpentis. The endosymbiont of R. pachyptila has a γ-CA gene in the genome. If α- and β-CA coding genes have been derived from other microorganisms, such as endosymbionts of T. jerichonana and Cycloclasticus sp. as the endosymbiont of B. heckerae, through HGT, the theory of the necessity of thermostable CA enzymes for survival in the extreme ecosystem of hydrothermal vents is suggested and helps the conservation of microbiome natural diversity in hydrothermal vents. These harsh ecosystems, with their integral players, such as HGT and endosymbionts, significantly impact the enrichment of life on Earth and the carbon cycle in the ocean.
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Affiliation(s)
- Mohammad Sadegh Gheibzadeh
- Department of Energy and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran 14965/161, Iran
| | - Colleen Varaidzo Manyumwa
- Research Unit in Bioinformatics (Rubi), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown 6140, South Africa
| | - Özlem Tastan Bishop
- Research Unit in Bioinformatics (Rubi), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown 6140, South Africa
| | - Hossein Shahbani Zahiri
- Department of Energy and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran 14965/161, Iran
| | - Seppo Parkkila
- Faculty of Medicine and Health Technology, Tampere University, 33520 Tampere, Finland
- Fimlab Ltd., Tampere University Hospital, 33520 Tampere, Finland
| | - Reza Zolfaghari Emameh
- Department of Energy and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran 14965/161, Iran
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Conservation of Genomic Information in Multiple Displacement Amplified Low-Quantity Metagenomic Material from Marine Invertebrates. Mar Drugs 2023; 21:md21030165. [PMID: 36976214 PMCID: PMC10054348 DOI: 10.3390/md21030165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 02/21/2023] [Accepted: 02/28/2023] [Indexed: 03/06/2023] Open
Abstract
Marine invertebrate microbiomes have been a rich source of bioactive compounds and interesting genomic features. In cases where the achievable amounts of metagenomic DNA are too low for direct sequencing, multiple displacement amplification (MDA) can be used for whole genome amplification. However, MDA has known limitations which can affect the quality of the resulting genomes and metagenomes. In this study, we evaluated the conservation of biosynthetic gene clusters (BGCs) and enzymes in MDA products from low numbers of prokaryotic cells (estimated 2–850). Marine invertebrate microbiomes collected from Arctic and sub-Arctic areas served as source material. The cells were separated from the host tissue, lysed, and directly subjected to MDA. The MDA products were sequenced by Illumina sequencing. Corresponding numbers of bacteria from a set of three reference strains were treated the same way. The study demonstrated that useful information on taxonomic, BGC, and enzyme diversities was obtainable from such marginal quantities of metagenomic material. Although high levels of assembly fragmentation resulted in most BGCs being incomplete, we conclude that this genome mining approach has the potential to reveal interesting BGCs and genes from hard-to-reach biological sources.
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Osvatic JT, Yuen B, Kunert M, Wilkins L, Hausmann B, Girguis P, Lundin K, Taylor J, Jospin G, Petersen JM. Gene loss and symbiont switching during adaptation to the deep sea in a globally distributed symbiosis. THE ISME JOURNAL 2023; 17:453-466. [PMID: 36639537 PMCID: PMC9938160 DOI: 10.1038/s41396-022-01355-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 12/16/2022] [Accepted: 12/21/2022] [Indexed: 01/14/2023]
Abstract
Chemosynthetic symbioses between bacteria and invertebrates occur worldwide from coastal sediments to the deep sea. Most host groups are restricted to either shallow or deep waters. In contrast, Lucinidae, the most species-rich family of chemosymbiotic invertebrates, has both shallow- and deep-sea representatives. Multiple lucinid species have independently colonized the deep sea, which provides a unique framework for understanding the role microbial symbionts play in evolutionary transitions between shallow and deep waters. Lucinids acquire their symbionts from their surroundings during early development, which may allow them to flexibly acquire symbionts that are adapted to local environments. Via metagenomic analyses of museum and other samples collected over decades, we investigated the biodiversity and metabolic capabilities of the symbionts of 22 mostly deep-water lucinid species. We aimed to test the theory that the symbiont played a role in adaptation to life in deep-sea habitats. We identified 16 symbiont species, mostly within the previously described genus Ca. Thiodiazotropha. Most genomic functions were shared by both shallow-water and deep-sea Ca. Thiodiazotropha, though nitrogen fixation was exclusive to shallow-water species. We discovered multiple cases of symbiont switching near deep-sea hydrothermal vents and cold seeps, where distantly related hosts convergently acquired novel symbionts from a different bacterial order. Finally, analyses of selection revealed consistently stronger purifying selection on symbiont genomes in two extreme habitats - hydrothermal vents and an oxygen-minimum zone. Our findings reveal that shifts in symbiont metabolic capability and, in some cases, acquisition of a novel symbiont accompanied adaptation of lucinids to challenging deep-sea habitats.
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Affiliation(s)
- Jay T. Osvatic
- grid.10420.370000 0001 2286 1424University of Vienna, Centre for Microbiology and Environmental Systems Science, Department for Microbiology and Ecosystem Science, Division of Microbial Ecology, Djerassiplatz 1, 1030 Vienna, Austria ,University of Venna, Doctoral School in Microbiology and Environmental Science, Djerassiplatz 1, 1030 Vienna, Austria
| | - Benedict Yuen
- grid.10420.370000 0001 2286 1424University of Vienna, Centre for Microbiology and Environmental Systems Science, Department for Microbiology and Ecosystem Science, Division of Microbial Ecology, Djerassiplatz 1, 1030 Vienna, Austria
| | - Martin Kunert
- grid.10420.370000 0001 2286 1424University of Vienna, Centre for Microbiology and Environmental Systems Science, Department for Microbiology and Ecosystem Science, Division of Microbial Ecology, Djerassiplatz 1, 1030 Vienna, Austria
| | - Laetitia Wilkins
- grid.419529.20000 0004 0491 3210Eco-Evolutionary Interactions Group, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, 28209 Bremen, Germany
| | - Bela Hausmann
- grid.10420.370000 0001 2286 1424Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, 1030 Vienna, Austria ,grid.22937.3d0000 0000 9259 8492Department of Laboratory Medicine, Medical University of Vienna, 1090 Vienna, Austria
| | - Peter Girguis
- grid.38142.3c000000041936754XDepartment of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138 USA
| | - Kennet Lundin
- grid.516430.50000 0001 0059 3334Gothenburg Natural History Museum, Box 7283, 40235 Gothenburg, Sweden ,grid.8761.80000 0000 9919 9582Gothenburg Global Biodiversity Centre, Box 461, 40530 Gothenburg, Sweden
| | - John Taylor
- grid.35937.3b0000 0001 2270 9879Natural History Museum, Cromwell Rd, London, SW7 5BD UK
| | | | - Jillian M. Petersen
- grid.10420.370000 0001 2286 1424University of Vienna, Centre for Microbiology and Environmental Systems Science, Department for Microbiology and Ecosystem Science, Division of Microbial Ecology, Djerassiplatz 1, 1030 Vienna, Austria
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Lin YT, Xu T, Ip JCH, Sun Y, Fang L, Luan T, Zhang Y, Qian PY, Qiu JW, Qian PY, Qiu JW. Interactions among deep-sea mussels and their epibiotic and endosymbiotic chemoautotrophic bacteria: Insights from multi-omics analysis. Zool Res 2023; 44:106-125. [PMID: 36419378 PMCID: PMC9841196 DOI: 10.24272/j.issn.2095-8137.2022.279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Endosymbiosis with Gammaproteobacteria is fundamental for the success of bathymodioline mussels in deep-sea chemosynthesis-based ecosystems. However, the recent discovery of Campylobacteria on the gill surfaces of these mussels suggests that these host-bacterial relationships may be more complex than previously thought. Using the cold-seep mussel ( Gigantidas haimaensis) as a model, we explored this host-bacterial system by assembling the host transcriptome and genomes of its epibiotic Campylobacteria and endosymbiotic Gammaproteobacteria and quantifying their gene and protein expression levels. We found that the epibiont applies a sulfur oxidizing (SOX) multienzyme complex with the acquisition of soxB from Gammaproteobacteria for energy production and switched from a reductive tricarboxylic acid (rTCA) cycle to a Calvin-Benson-Bassham (CBB) cycle for carbon assimilation. The host provides metabolic intermediates, inorganic carbon, and thiosulfate to satisfy the materials and energy requirements of the epibiont, but whether the epibiont benefits the host is unclear. The endosymbiont adopts methane oxidation and the ribulose monophosphate pathway (RuMP) for energy production, providing the major source of energy for itself and the host. The host obtains most of its nutrients, such as lysine, glutamine, valine, isoleucine, leucine, histidine, and folate, from the endosymbiont. In addition, host pattern recognition receptors, including toll-like receptors, peptidoglycan recognition proteins, and C-type lectins, may participate in bacterial infection, maintenance, and population regulation. Overall, this study provides insights into the complex host-bacterial relationships that have enabled mussels and bacteria to thrive in deep-sea chemosynthetic ecosystems.
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Affiliation(s)
- Yi-Tao Lin
- Department of Biology, Hong Kong Baptist University, Hong Kong SAR, China,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, Guangdong 511458, China
| | - Ting Xu
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, Guangdong 511458, China,Department of Ocean Science, Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Jack Chi-Ho Ip
- Department of Biology, Hong Kong Baptist University, Hong Kong SAR, China,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, Guangdong 511458, China
| | - Yanan Sun
- Department of Biology, Hong Kong Baptist University, Hong Kong SAR, China,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, Guangdong 511458, China
| | - Ling Fang
- Instrumental Analysis & Research Center, Sun Yat-Sen University, Guangzhou, Guangdong 510875, China
| | - Tiangang Luan
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, Guangdong 510875, China,Institute of Environmental and Ecological Engineering, Guangdong University of Technology, Guangzhou, Guangdong 510006, China
| | - Yu Zhang
- College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong 518060, China,E-mail:
| | - Pei-Yuan Qian
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, Guangdong 511458, China,Department of Ocean Science, Hong Kong University of Science and Technology, Hong Kong SAR, China,
| | - Jian-Wen Qiu
- Department of Biology, Hong Kong Baptist University, Hong Kong SAR, China,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, Guangdong 511458, China,
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Molecular Characterization and Assessment of Risk Factors Associated with Theileria annulata Infection. Microorganisms 2022; 10:microorganisms10081614. [PMID: 36014032 PMCID: PMC9412660 DOI: 10.3390/microorganisms10081614] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 08/05/2022] [Accepted: 08/07/2022] [Indexed: 11/16/2022] Open
Abstract
Theileria annulata is a tick-associated parasite that causes tropical theileriosis in livestock and is responsible for huge economic losses. Studies have been neglected on the effect of Theileria spp. on cattle in Khyber Pakhtunkhwa (KP), Pakistan. The present study was designed to determine the genetic diversity and assess the risk factors associated with Theileria infection in selected districts of KP. Information on the risk factors related to the Theileria infection was collected through a questionnaire. Blood samples were collected from symptomatic cattle from January 2019 to February 2020, identified morphologically through microscopic examination, and processed for molecular characterization using the 18S rRNA gene as a genetic marker. Of the 555 cattle examined (136, 24.5%) and (294, 53%) were found positive for Theileria spp. by microscopic examination and a PCR test, respectively. Based on the PCR test, the highest prevalence of infection was found in district Upper Dir (46/75, 61.3%), followed by Lower Dir (54/90, 60%); Malakand (51/88, 57.9%); Peshawar (40/80, 50%); and Charsadda (52/112, 46.4%), with the lowest in Bajaur (51/110, 46.34%). A BLAST analysis of the 18S rDNA sequences showed 99.5% identity with T. annulata. In a phylogenetic tree, the 18S rDNA sequence of T. annulata clustered with sequences from Pakistan, China, and Italy. A significant association was observed between the prevalence of infection and different host characteristics. The highest infection was found in adult cattle (216/360, 60%); females (218/377, 57.8%); and Holstein Friesian (120/180, 66.6%). Theileria infection was significantly associated with management practices. Higher infection rates were observed in free-grazing cattle (190/412, 42.2%); those kept in unhygienic conditions (246/405, 60.7%); cattle in combined farming systems (165/255, 64.8%); and those in congested stall systems (150/218, 68.8%). Seasonal patterns were found to be significantly associated with infection, and a higher infection rate was observed in summer (215/350, 61.4%) than in winter (79/205, 38.5%). Identified risk factors should be considered in designing practical control approaches to reduce the burden of Theileria infection. Large scale studies are required to explore the diversity of Theileria species in KP, Pakistan.
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Abstract
The SUP05 clade of gammaproteobacteria (Thioglobaceae) comprises both primary producers and primary consumers of organic carbon in the oceans. Host-associated autotrophs are a principal source of carbon and other nutrients for deep-sea eukaryotes at hydrothermal vents, and their free-living relatives are a primary source of organic matter in seawater at vents and in marine oxygen minimum zones. Similar to other abundant marine heterotrophs, such as SAR11 and Roseobacter, heterotrophic Thioglobaceae use the dilute pool of osmolytes produced by phytoplankton for growth, including methylated amines and sulfonates. Heterotrophic members are common throughout the ocean, and autotrophic members are abundant at hydrothermal vents and in anoxic waters; combined, they can account for more than 50% of the total bacterial community. Studies of both cultured and uncultured representatives from this diverse family are providing novel insights into the shifting biogeochemical roles of autotrophic and heterotrophic bacteria that cross oxic-anoxic boundary layers in the ocean.
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Affiliation(s)
- Robert M Morris
- School of Oceanography, University of Washington, Seattle, Washington 98195, USA;
| | - Rachel L Spietz
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, Montana 59717, USA;
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Chen H, Wang M, Zhang H, Wang H, Zhou L, Zhong Z, Cao L, Lian C, Sun Y, Li C. microRNAs facilitate comprehensive responses of Bathymodiolinae mussel against symbiotic and nonsymbiotic bacteria stimulation. FISH & SHELLFISH IMMUNOLOGY 2021; 119:420-431. [PMID: 34687882 DOI: 10.1016/j.fsi.2021.10.025] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 10/08/2021] [Accepted: 10/16/2021] [Indexed: 06/13/2023]
Abstract
Bathymodiolinae mussels are dominant species in cold seeps and hydrothermal vents and could harbor endosymbionts in gill bacteriocytes. However, mechanisms underlying the symbiosis have remained largely undisclosed for years. In the present study, the global expression pattern of immune-related genes and miRNAs were surveyed in Gigantidas platifrons during bacterial challenges using enriched symbiotic methane oxidation bacteria MOBs or nonsymbiotic Vibrio. As a result, multiple pattern recognition receptors were found differentially expressed at 12 h and 24 h post bacteria challenges and distinctly clustered between stimulations. Dozens of immune effectors along with signal transducers were also modulated simultaneously during MOB or Vibrio challenge. A total of 459 miRNAs were identified in the gill while some were differentially expressed post MOB or nonsymbiotic bacteria challenge. A variety of immune-related genes were annotated as target genes of aforesaid differentially expressed miRNAs. As a result, biological processes including the immune recognition, lysosome activity and bacteria engulfment were suggested to be dynamically modulated by miRNAs in either symbiotic or nonsymbiotic bacteria challenge. It was suggested that G. platifrons mussels could maintain a robust immune response against invading pathogens while establishing symbiosis with chemosynthetic bacteria with the orchestra of immune-related genes and miRNAs.
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Affiliation(s)
- Hao Chen
- Center of Deep Sea Research, And CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Minxiao Wang
- Center of Deep Sea Research, And CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Huan Zhang
- Center of Deep Sea Research, And CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Hao Wang
- Center of Deep Sea Research, And CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Li Zhou
- Center of Deep Sea Research, And CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Zhaoshan Zhong
- Center of Deep Sea Research, And CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China; University of Chinese Academy of Sciences, Beijing, 10049, China
| | - Lei Cao
- Center of Deep Sea Research, And CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Chao Lian
- Center of Deep Sea Research, And CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Yan Sun
- Center of Deep Sea Research, And CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Chaolun Li
- Center of Deep Sea Research, And CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China; University of Chinese Academy of Sciences, Beijing, 10049, China.
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Lin G, Lu J, Sun Z, Xie J, Huang J, Su M, Wu N. Characterization of tissue-associated bacterial community of two Bathymodiolus species from the adjacent cold seep and hydrothermal vent environments. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 796:149046. [PMID: 34328889 DOI: 10.1016/j.scitotenv.2021.149046] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 07/08/2021] [Accepted: 07/10/2021] [Indexed: 06/13/2023]
Abstract
Deep-sea mussels are widely distributed in marine chemosynthetic ecosystems. Bathymodiolus platifrons and B. japonicus, occurring at both cold seeps and hydrothermal vents, have been reported to house exclusively methanotrophic symbionts in the gill. However, the comparison of microbiota associated with different tissues between these two species from two contrasting habitats is still limited. In this study, using B. platifrons and B. japonicus collected from the adjacent cold seep and hydrothermal vent environments, we sampled different tissues (gill, adductor muscle, mantle, foot, and visceral mass including the gut) to decipher the microbial community structure at the tissue scale by employing 16S rRNA gene sequencing strategy. In the gill of both seep mussels and vent mussels, the symbiont gammaproteobacterial Methylomonaceae was the predominant lineage, and methane oxidation was identified as one of the most abundant putative function. In comparison, abundant families in other tissues were Pseudomonadaceae and Enterobacteriaceae in seep mussels and vent mussels, respectively, which may get involved in element cycling. The results revealed high similarity of community structure between two mussel species from the same habitat. The gill showed distinctive bacterial community structure compared with other tissues within the same environment, while the gill communities from two environments were more similar. Remarkably structural variations of adductor muscle, mantle, foot, and visceral mass were observed between two environments. This study can extend the understanding on the characteristics of tissue-associated microbiota of deep-sea mussels from the adjacent cold seep and hydrothermal vent environments.
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Affiliation(s)
- Genmei Lin
- School of Marine Sciences, Sun Yat-sen University, Zhuhai 519082, China
| | - Jianguo Lu
- School of Marine Sciences, Sun Yat-sen University, Zhuhai 519082, China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519080, China.
| | - Zhilei Sun
- Key Laboratory of Gas Hydrate, Ministry of Natural Resources, Institute of Marine Geology, China Geological Survey, Qingdao 266071, China; Laboratory for Mineral Resources, Qingdao Pilot National Laboratory for Marine Sciences and Technology, Qingdao 266071, China
| | - Jingui Xie
- School of Marine Sciences, Sun Yat-sen University, Zhuhai 519082, China
| | - Junrou Huang
- School of Marine Sciences, Sun Yat-sen University, Zhuhai 519082, China
| | - Ming Su
- School of Marine Sciences, Sun Yat-sen University, Zhuhai 519082, China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519080, China
| | - Nengyou Wu
- Key Laboratory of Gas Hydrate, Ministry of Natural Resources, Institute of Marine Geology, China Geological Survey, Qingdao 266071, China; Laboratory for Mineral Resources, Qingdao Pilot National Laboratory for Marine Sciences and Technology, Qingdao 266071, China.
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10
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Paredes GF, Viehboeck T, Lee R, Palatinszky M, Mausz MA, Reipert S, Schintlmeister A, Maier A, Volland JM, Hirschfeld C, Wagner M, Berry D, Markert S, Bulgheresi S, König L. Anaerobic Sulfur Oxidation Underlies Adaptation of a Chemosynthetic Symbiont to Oxic-Anoxic Interfaces. mSystems 2021; 6:e0118620. [PMID: 34058098 PMCID: PMC8269255 DOI: 10.1128/msystems.01186-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 04/20/2021] [Indexed: 11/23/2022] Open
Abstract
Chemosynthetic symbioses occur worldwide in marine habitats, but comprehensive physiological studies of chemoautotrophic bacteria thriving on animals are scarce. Stilbonematinae are coated by thiotrophic Gammaproteobacteria. As these nematodes migrate through the redox zone, their ectosymbionts experience varying oxygen concentrations. However, nothing is known about how these variations affect their physiology. Here, by applying omics, Raman microspectroscopy, and stable isotope labeling, we investigated the effect of oxygen on "Candidatus Thiosymbion oneisti." Unexpectedly, sulfur oxidation genes were upregulated in anoxic relative to oxic conditions, but carbon fixation genes and incorporation of 13C-labeled bicarbonate were not. Instead, several genes involved in carbon fixation were upregulated under oxic conditions, together with genes involved in organic carbon assimilation, polyhydroxyalkanoate (PHA) biosynthesis, nitrogen fixation, and urea utilization. Furthermore, in the presence of oxygen, stress-related genes were upregulated together with vitamin biosynthesis genes likely necessary to withstand oxidative stress, and the symbiont appeared to proliferate less. Based on its physiological response to oxygen, we propose that "Ca. T. oneisti" may exploit anaerobic sulfur oxidation coupled to denitrification to proliferate in anoxic sand. However, the ectosymbiont would still profit from the oxygen available in superficial sand, as the energy-efficient aerobic respiration would facilitate carbon and nitrogen assimilation. IMPORTANCE Chemoautotrophic endosymbionts are famous for exploiting sulfur oxidization to feed marine organisms with fixed carbon. However, the physiology of thiotrophic bacteria thriving on the surface of animals (ectosymbionts) is less understood. One longstanding hypothesis posits that attachment to animals that migrate between reduced and oxic environments would boost sulfur oxidation, as the ectosymbionts would alternatively access sulfide and oxygen, the most favorable electron acceptor. Here, we investigated the effect of oxygen on the physiology of "Candidatus Thiosymbion oneisti," a gammaproteobacterium which lives attached to marine nematodes inhabiting shallow-water sand. Surprisingly, sulfur oxidation genes were upregulated under anoxic relative to oxic conditions. Furthermore, under anoxia, the ectosymbiont appeared to be less stressed and to proliferate more. We propose that animal-mediated access to oxygen, rather than enhancing sulfur oxidation, would facilitate assimilation of carbon and nitrogen by the ectosymbiont.
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Affiliation(s)
- Gabriela F. Paredes
- University of Vienna, Department of Functional and Evolutionary Ecology, Environmental Cell Biology Group, Vienna, Austria
| | - Tobias Viehboeck
- University of Vienna, Department of Functional and Evolutionary Ecology, Environmental Cell Biology Group, Vienna, Austria
- University of Vienna, Center for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Vienna, Austria
| | - Raymond Lee
- Washington State University, School of Biological Sciences, Pullman, Washington, USA
| | - Marton Palatinszky
- University of Vienna, Center for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Vienna, Austria
| | - Michaela A. Mausz
- University of Warwick, School of Life Sciences, Coventry, United Kingdom
| | - Siegfried Reipert
- University of Vienna, Core Facility Cell Imaging and Ultrastructure Research, Vienna, Austria
| | - Arno Schintlmeister
- University of Vienna, Center for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Vienna, Austria
- University of Vienna, Center for Microbiology and Environmental Systems Science, Large-Instrument Facility for Environmental and Isotope Mass Spectrometry, Vienna, Austria
| | - Andreas Maier
- University of Vienna, Faculty of Geosciences, Geography, and Astronomy, Department of Geography and Regional Research, Geoecology, Vienna, Austria
| | - Jean-Marie Volland
- University of Vienna, Department of Functional and Evolutionary Ecology, Environmental Cell Biology Group, Vienna, Austria
| | - Claudia Hirschfeld
- University of Greifswald, Institute of Pharmacy, Department of Pharmaceutical Biotechnology, Greifswald, Germany
| | - Michael Wagner
- University of Vienna, Center for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Vienna, Austria
- Aalborg University, Department of Chemistry and Bioscience, Aalborg, Denmark
| | - David Berry
- University of Vienna, Center for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Vienna, Austria
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria
| | - Stephanie Markert
- University of Greifswald, Institute of Pharmacy, Department of Pharmaceutical Biotechnology, Greifswald, Germany
| | - Silvia Bulgheresi
- University of Vienna, Department of Functional and Evolutionary Ecology, Environmental Cell Biology Group, Vienna, Austria
| | - Lena König
- University of Vienna, Department of Functional and Evolutionary Ecology, Environmental Cell Biology Group, Vienna, Austria
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11
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Petersen JM, Yuen B. The symbiotic 'all-rounders': Partnerships between marine animals and chemosynthetic nitrogen-fixing bacteria. Appl Environ Microbiol 2021; 87:AEM.02129-20. [PMID: 33355107 PMCID: PMC8090883 DOI: 10.1128/aem.02129-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Nitrogen fixation is a widespread metabolic trait in certain types of microorganisms called diazotrophs. Bioavailable nitrogen is limited in various habitats on land and in the sea, and accordingly, a range of plant, animal, and single-celled eukaryotes have evolved symbioses with diverse diazotrophic bacteria, with enormous economic and ecological benefits. Until recently, all known nitrogen-fixing symbionts were heterotrophs such as nodulating rhizobia, or photoautotrophs such as cyanobacteria. In 2016, the first chemoautotrophic nitrogen-fixing symbionts were discovered in a common family of marine clams, the Lucinidae. Chemosynthetic nitrogen-fixing symbionts use the chemical energy stored in reduced sulfur compounds to power carbon and nitrogen fixation, making them metabolic 'all-rounders' with multiple functions in the symbiosis. This distinguishes them from heterotrophic symbionts that require a source of carbon from their host, and their chemosynthetic metabolism distinguishes them from photoautotrophic symbionts that produce oxygen, a potent inhibitor of nitrogenase. In this review, we consider evolutionary aspects of this discovery, by comparing strategies that have evolved for hosting intracellular nitrogen-fixing symbionts in plants and animals. The symbiosis between lucinid clams and chemosynthetic nitrogen-fixing bacteria also has important ecological impacts, as they form a nested symbiosis with endangered marine seagrasses. Notably, nitrogen fixation by lucinid symbionts may help support seagrass health by providing a source of nitrogen in seagrass habitats. These discoveries were enabled by new techniques for understanding the activity of microbial populations in natural environments. However, an animal (or plant) host represents a diverse landscape of microbial niches due to its structural, chemical, immune and behavioural properties. In future, methods that resolve microbial activity at the single cell level will provide radical new insights into the regulation of nitrogen fixation in chemosynthetic symbionts, shedding new light on the evolution of nitrogen-fixing symbioses in contrasting hosts and environments.
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Affiliation(s)
- Jillian M Petersen
- Centre for Microbiology and Environmental Systems Science, University of Vienna
| | - Benedict Yuen
- Centre for Microbiology and Environmental Systems Science, University of Vienna
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12
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Wang H, Zhang H, Zhong Z, Sun Y, Wang M, Chen H, Zhou L, Cao L, Lian C, Li C. Molecular analyses of the gill symbiosis of the bathymodiolin mussel Gigantidas platifrons. iScience 2020; 24:101894. [PMID: 33364583 PMCID: PMC7750550 DOI: 10.1016/j.isci.2020.101894] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 10/07/2020] [Accepted: 12/02/2020] [Indexed: 11/29/2022] Open
Abstract
Although the deep-sea bathymodiolin mussels have been intensively studied as a model of animal-bacteria symbiosis, it remains challenging to assess the host-symbiont interactions due to the complexity of the symbiotic tissue-the gill. Using cold-seep mussel Gigantidas platifrons as a model, we isolated the symbiont harboring bacteriocytes and profiled the transcriptomes of the three major parts of the symbiosis-the gill, the bacteriocyte, and the symbiont. This breakdown of the complex symbiotic tissue allowed us to characterize the host-symbiont interactions further. Our data showed that the gill's non-symbiotic parts play crucial roles in maintaining and protecting the symbiosis; the bacteriocytes supply the symbiont with metabolites, control symbiont population, and shelter the symbiont from phage infection; the symbiont dedicates to the methane oxidation and energy production. This study demonstrates that the bathymodiolin symbiosis interacts at the tissue, cellular, and molecular level, maintaining high efficiency and harmonic chemosynthetic micro niche.
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Affiliation(s)
- Hao Wang
- Center of Deep-Sea Research, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, P. R. China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, P. R. China
| | - Huan Zhang
- Center of Deep-Sea Research, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, P. R. China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, P. R. China
| | - Zhaoshan Zhong
- Center of Deep-Sea Research, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, P. R. China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, P. R. China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yan Sun
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, P. R. China.,Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, P. R. China
| | - Minxiao Wang
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, P. R. China.,Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, P. R. China
| | - Hao Chen
- Center of Deep-Sea Research, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, P. R. China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, P. R. China
| | - Li Zhou
- Center of Deep-Sea Research, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, P. R. China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, P. R. China
| | - Lei Cao
- Center of Deep-Sea Research, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, P. R. China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, P. R. China
| | - Chao Lian
- Center of Deep-Sea Research, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, P. R. China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, P. R. China
| | - Chaolun Li
- Center of Deep-Sea Research, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, P. R. China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, P. R. China.,Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, P. R. China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,University of Chinese Academy of Sciences, Beijing, China
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13
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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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14
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Mat AM, Sarrazin J, Markov GV, Apremont V, Dubreuil C, Eché C, Fabioux C, Klopp C, Sarradin PM, Tanguy A, Huvet A, Matabos M. Biological rhythms in the deep-sea hydrothermal mussel Bathymodiolus azoricus. Nat Commun 2020; 11:3454. [PMID: 32651383 PMCID: PMC7351958 DOI: 10.1038/s41467-020-17284-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 06/17/2020] [Indexed: 11/22/2022] Open
Abstract
Biological rhythms are a fundamental property of life. The deep ocean covers 66% of our planet surface and is one of the largest biomes. The deep sea has long been considered as an arrhythmic environment because sunlight is totally absent below 1,000 m depth. In the present study, we have sequenced the temporal transcriptomes of a deep-sea species, the ecosystem-structuring vent mussel Bathymodiolus azoricus. We reveal that tidal cycles predominate in the transcriptome and physiology of mussels fixed directly at hydrothermal vents at 1,688 m depth at the Mid-Atlantic Ridge, whereas daily cycles prevail in mussels sampled after laboratory acclimation. We identify B. azoricus canonical circadian clock genes, and show that oscillations observed in deep-sea mussels could be either a direct response to environmental stimulus, or be driven endogenously by one or more biological clocks. This work generates in situ insights into temporal organisation in a deep-sea organism. Little is known about gene expression of organisms in the deep sea, partially owing to constraints on sampling these organisms in situ. Here the authors circumvent this problem, fixing tissue of a deep-sea mussel at 1,688 m in depth, and later analyzing transcriptomes to reveal gene expression patterns showing tidal oscillations.
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Affiliation(s)
- Audrey M Mat
- Univ Brest, Ifremer, CNRS, IRD, LEMAR, F-29280, Plouzané, France. .,Ifremer, EEP, F-29280, Plouzané, France.
| | | | - Gabriel V Markov
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), 29680, Roscoff, France
| | - Vincent Apremont
- Univ Brest, Ifremer, CNRS, IRD, LEMAR, F-29280, Plouzané, France.,Ifremer, EEP, F-29280, Plouzané, France
| | | | - Camille Eché
- GeT-PlaGe, Genotoul, INRA Auzeville, Auzeville, France
| | - Caroline Fabioux
- Univ Brest, Ifremer, CNRS, IRD, LEMAR, F-29280, Plouzané, France
| | | | | | - Arnaud Tanguy
- Sorbonne Université, CNRS, Lab. Adaptation et Diversité en Milieu Marin, Team ABICE, Station Biologique de Roscoff, 29680, Roscoff, France
| | - Arnaud Huvet
- Univ Brest, Ifremer, CNRS, IRD, LEMAR, F-29280, Plouzané, France
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15
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Oren A, Garrity GM, Parker CT, Chuvochina M, Trujillo ME. Lists of names of prokaryotic Candidatus taxa. Int J Syst Evol Microbiol 2020; 70:3956-4042. [DOI: 10.1099/ijsem.0.003789] [Citation(s) in RCA: 782] [Impact Index Per Article: 195.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
We here present annotated lists of names of Candidatus taxa of prokaryotes with ranks between subspecies and class, proposed between the mid-1990s, when the provisional status of Candidatus taxa was first established, and the end of 2018. Where necessary, corrected names are proposed that comply with the current provisions of the International Code of Nomenclature of Prokaryotes and its Orthography appendix. These lists, as well as updated lists of newly published names of Candidatus taxa with additions and corrections to the current lists to be published periodically in the International Journal of Systematic and Evolutionary Microbiology, may serve as the basis for the valid publication of the Candidatus names if and when the current proposals to expand the type material for naming of prokaryotes to also include gene sequences of yet-uncultivated taxa is accepted by the International Committee on Systematics of Prokaryotes.
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Affiliation(s)
- Aharon Oren
- The Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, 9190401 Jerusalem, Israel
| | - George M. Garrity
- NamesforLife, LLC, PO Box 769, Okemos MI 48805-0769, USA
- Department of Microbiology & Molecular Genetics, Biomedical Physical Sciences, Michigan State University, East Lansing, MI 48824-4320, USA
| | | | - Maria Chuvochina
- Australian Centre for Ecogenomics, University of Queensland, St. Lucia QLD 4072, Brisbane, Australia
| | - Martha E. Trujillo
- Departamento de Microbiología y Genética, Campus Miguel de Unamuno, Universidad de Salamanca, 37007, Salamanca, Spain
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16
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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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17
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Yang Y, Sun J, Sun Y, Kwan YH, Wong WC, Zhang Y, Xu T, Feng D, Zhang Y, Qiu JW, Qian PY. Genomic, transcriptomic, and proteomic insights into the symbiosis of deep-sea tubeworm holobionts. THE ISME JOURNAL 2020; 14:135-150. [PMID: 31595051 PMCID: PMC6908572 DOI: 10.1038/s41396-019-0520-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 08/11/2019] [Accepted: 08/25/2019] [Indexed: 12/22/2022]
Abstract
Deep-sea hydrothermal vents and methane seeps are often densely populated by animals that host chemosynthetic symbiotic bacteria, but the molecular mechanisms of such host-symbiont relationship remain largely unclear. We characterized the symbiont genome of the seep-living siboglinid Paraescarpia echinospica and compared seven siboglinid-symbiont genomes. Our comparative analyses indicate that seep-living siboglinid endosymbionts have more virulence traits for establishing infections and modulating host-bacterium interaction than the vent-dwelling species, and have a high potential to resist environmental hazards. Metatranscriptome and metaproteome analyses of the Paraescarpia holobiont reveal that the symbiont is highly versatile in its energy use and efficient in carbon fixation. There is close cooperation within the holobiont in production and supply of nutrients, and the symbiont may be able to obtain nutrients from host cells using virulence factors. Moreover, the symbiont is speculated to have evolved strategies to mediate host protective immunity, resulting in weak expression of host innate immunity genes in the trophosome. Overall, our results reveal the interdependence of the tubeworm holobiont through mutual nutrient supply, a pathogen-type regulatory mechanism, and host-symbiont cooperation in energy utilization and nutrient production, which is a key adaptation allowing the tubeworm to thrive in deep-sea chemosynthetic environments.
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Affiliation(s)
- Yi Yang
- Department of Ocean Science, Division of Life Science and Hong Kong Branch of The Southern Science and Engineering Guangdong Laboratory, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Jin Sun
- Department of Ocean Science, Division of Life Science and Hong Kong Branch of The Southern Science and Engineering Guangdong Laboratory, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Yanan Sun
- Department of Ocean Science, Division of Life Science and Hong Kong Branch of The Southern Science and Engineering Guangdong Laboratory, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Yick Hang Kwan
- Department of Ocean Science, Division of Life Science and Hong Kong Branch of The Southern Science and Engineering Guangdong Laboratory, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Wai Chuen Wong
- Department of Ocean Science, Division of Life Science and Hong Kong Branch of The Southern Science and Engineering Guangdong Laboratory, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Yanjie Zhang
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Ting Xu
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Dong Feng
- CAS Key Laboratory of Ocean and Marginal Sea Geology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 510301, Guangzhou, China
- Laboratory for Marine Geology, Qingdao National Laboratory for Marine Science and Technology, 266061, Qingdao, China
| | - Yu Zhang
- College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Jian-Wen Qiu
- Department of Biology, Hong Kong Baptist University, Hong Kong, China.
| | - Pei-Yuan Qian
- Department of Ocean Science, Division of Life Science and Hong Kong Branch of The Southern Science and Engineering Guangdong Laboratory, The Hong Kong University of Science and Technology, Hong Kong, China.
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18
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Baker LJ, Freed LL, Easson CG, Lopez JV, Fenolio D, Sutton TT, Nyholm SV, Hendry TA. Diverse deep-sea anglerfishes share a genetically reduced luminous symbiont that is acquired from the environment. eLife 2019; 8:47606. [PMID: 31571583 PMCID: PMC6773444 DOI: 10.7554/elife.47606] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 08/21/2019] [Indexed: 11/13/2022] Open
Abstract
Deep-sea anglerfishes are relatively abundant and diverse, but their luminescent bacterial symbionts remain enigmatic. The genomes of two symbiont species have qualities common to vertically transmitted, host-dependent bacteria. However, a number of traits suggest that these symbionts may be environmentally acquired. To determine how anglerfish symbionts are transmitted, we analyzed bacteria-host codivergence across six diverse anglerfish genera. Most of the anglerfish species surveyed shared a common species of symbiont. Only one other symbiont species was found, which had a specific relationship with one anglerfish species, Cryptopsaras couesii. Host and symbiont phylogenies lacked congruence, and there was no statistical support for codivergence broadly. We also recovered symbiont-specific gene sequences from water collected near hosts, suggesting environmental persistence of symbionts. Based on these results we conclude that diverse anglerfishes share symbionts that are acquired from the environment, and that these bacteria have undergone extreme genome reduction although they are not vertically transmitted. The deep sea is home to many different species of anglerfish, a group of animals in which females often display a dangling lure on the top of their heads. This organ shelters bacteria that make light, a partnership (known as symbiosis) that benefits both parties. The bacteria get a safe environment in which to grow, while the animal may use the light to confuse predators as well as attract prey and mates. The genetic information of these bacteria has changed since they became associated with their host. Their genomes have become smaller and more specialized, limiting their ability to survive outside of the fish. This phenomenon is also observed in other symbiotic bacteria, but mostly in microorganisms that are directly transmitted from parent to offspring, never having to live on their own. Yet, some evidence suggests that the bacteria in the lure of anglerfish may be spending time in the water until they find a new host, crossing thousands of meters of ocean in the process. To explore this paradox, Baker et al. looked into the type of bacteria carried by different groups of anglerfish. If each type of fish has its own kind of bacteria, this would suggest that the microorganisms are passed from one generation to the next, and are evolving with their hosts. On the other hand, if the same sort of bacteria can be found in different anglerfish species, this would imply that the bacteria pass from host to host and evolve independently from the fish. Genetic data analysis showed that amongst six groups of anglerfishes, one species of bacteria is shared across five groups while another is specific to one type of fish. The analyses also revealed that anglerfish and their bacteria are most likely not evolving together. This means that the bacteria must make the difficult journey from host to host by persisting in the deep sea, which was confirmed by finding the genetic information of these bacteria in the water near the fish. Anglerfish and the bacteria that light up their lure are hard to study, as they live so deep in the ocean. In fact, many symbiotic relationships are equally difficult to investigate. Examining genetic information can help to give an insight into how hosts and bacteria interact across the tree of life.
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Affiliation(s)
- Lydia J Baker
- Department of Microbiology, Cornell University, New York, United States
| | - Lindsay L Freed
- Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, Fort Lauderdale, United States
| | - Cole G Easson
- Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, Fort Lauderdale, United States.,Department of Biology, Middle Tennessee State University, Murfreesboro, United States
| | - Jose V Lopez
- Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, Fort Lauderdale, United States
| | - Danté Fenolio
- Center for Conservation and Research, San Antonio Zoo, San Antonio, United States
| | - Tracey T Sutton
- Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, Fort Lauderdale, United States
| | - Spencer V Nyholm
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, United States
| | - Tory A Hendry
- Department of Microbiology, Cornell University, New York, United States
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Chen H, Wang M, Zhang H, Wang H, Lv Z, Zhou L, Zhong Z, Lian C, Cao L, Li C. An LRR-domain containing protein identified in Bathymodiolus platifrons serves as intracellular recognition receptor for the endosymbiotic methane-oxidation bacteria. FISH & SHELLFISH IMMUNOLOGY 2019; 93:354-360. [PMID: 31306759 DOI: 10.1016/j.fsi.2019.07.032] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 07/03/2019] [Accepted: 07/11/2019] [Indexed: 06/10/2023]
Abstract
As domain species in seep and vent ecosystem, Bathymodioline mussels has been regarded as a model organism in investigating deep sea chemosymbiosis. However, mechanisms underlying their symbiosis with chemosynthetic bacteria, especially how the host recognizes symbionts, have remained largely unsolved. In the present study, a modified pull-down assay was conducted using enriched symbiotic methane-oxidation bacteria as bait and gill proteins of Bathymodiolus platifrons as a target to isolate pattern recognition receptors involved in the immune recognition of symbionts. As a result, a total of 47 proteins including BpLRR-1 were identified from the pull-down assay. It was found that complete cDNA sequence of BpLRR-1 contained an open reading frame of 1479 bp and could encode a protein of 492 amino acid residues with no signal peptide or transmembrane region but eight LRR motif and two EFh motif. The binding patterns of BpLRR-1 against microbial associated molecular patterns were subsequently investigated by surface plasmon resonance analysis and LPS pull-down assay. Consequently, BpLRR-1 was found with high binding affinity with LPS and suggested as a key molecule in recognizing symbionts. Besides, transcripts of BpLRR-1 were found decreased significantly during symbiont depletion assay yet increased rigorously during symbionts or nonsymbiotic Vibrio alginolyticus challenge, further demonstrating its participation in the chemosynthetic symbiosis. Collectively, these results suggest that BpLRR-1 could serve as an intracellular recognition receptor for the endosymbionts, providing new hints for understanding the immune recognition in symbiosis of B. platifrons.
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Affiliation(s)
- Hao Chen
- Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
| | - Minxiao Wang
- Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
| | - Huan Zhang
- Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
| | - Hao Wang
- Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
| | - Zhao Lv
- University of Chinese Academy of Sciences, Beijing, 10049, China
| | - Li Zhou
- Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
| | - Zhaoshan Zhong
- Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; University of Chinese Academy of Sciences, Beijing, 10049, China
| | - Chao Lian
- Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
| | - Lei Cao
- Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
| | - Chaolun Li
- Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China; University of Chinese Academy of Sciences, Beijing, 10049, China.
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Spietz RL, Lundeen RA, Zhao X, Nicastro D, Ingalls AE, Morris RM. Heterotrophic carbon metabolism and energy acquisition in Candidatus Thioglobus singularis strain PS1, a member of the SUP05 clade of marine Gammaproteobacteria. Environ Microbiol 2019; 21:2391-2401. [PMID: 30951247 DOI: 10.1111/1462-2920.14623] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 03/14/2019] [Accepted: 03/19/2019] [Indexed: 11/30/2022]
Abstract
A hallmark of the SUP05 clade of marine Gammaproteobacteria is the ability to use energy obtained from reduced inorganic sulfur to fuel autotrophic fixation of carbon using RuBisCo. However, some SUP05 also have the genetic potential for heterotrophic growth, raising questions about the roles of SUP05 in the marine carbon cycle. We used genomic reconstructions, physiological growth experiments and proteomics to characterize central carbon and energy metabolism in Candidatus Thioglobus singularis strain PS1, a representative from the SUP05 clade that has the genetic potential for autotrophy and heterotrophy. Here, we show that the addition of individual organic compounds and 0.2 μm filtered diatom lysate significantly enhanced the growth of this bacterium. This positive growth response to organic substrates, combined with expression of a complete TCA cycle, heterotrophic pathways for carbon assimilation, and methylotrophic pathways for energy conversion demonstrate strain PS1's capacity for heterotrophic growth. Further, our inability to verify the expression of RuBisCO suggests that carbon fixation was not critical for growth. These results highlight the metabolic diversity of the SUP05 clade that harbours both primary producers and consumers of organic carbon in the oceans and expand our understanding of specific pathways of organic matter oxidation by the heterotrophic SUP05.
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Affiliation(s)
- Rachel L Spietz
- School of Oceanography, University of Washington, Seattle, WA, 98195, USA
| | - Rachel A Lundeen
- School of Oceanography, University of Washington, Seattle, WA, 98195, USA
| | - Xiaowei Zhao
- Department of Cell Biology and Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Daniela Nicastro
- Department of Cell Biology and Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Anitra E Ingalls
- School of Oceanography, University of Washington, Seattle, WA, 98195, USA
| | - Robert M Morris
- School of Oceanography, University of Washington, Seattle, WA, 98195, USA
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