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Rondon R, Cosseau C, Bergami E, Cárdenas CA, Pérez-Toledo C, Alvarez D, Aldridge J, Font A, Garrido I, Santa Cruz F, Perrois G, Balbi T, Corsi I, González-Aravena M. Exposure to nanoplastics and nanomaterials either single and combined affects the gill-associated microbiome of the Antarctic soft-shelled clam Laternula elliptica. MARINE ENVIRONMENTAL RESEARCH 2024; 198:106539. [PMID: 38718522 DOI: 10.1016/j.marenvres.2024.106539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 04/23/2024] [Accepted: 05/01/2024] [Indexed: 06/11/2024]
Abstract
Nanoplastics and engineering nanomaterials (ENMs) are contaminants of emerging concern (CECs), increasingly being detected in the marine environment and recognized as a potential threat for marine biota at the global level including in polar areas. Few studies have assessed the impact of these anthropogenic nanoparticles in the microbiome of marine invertebrates, however combined exposure resembling natural scenarios has been overlooked. The present study aimed to evaluate the single and combined effects of polystyrene nanoparticles (PS NP) as proxy for nanoplastics and nanoscale titanium dioxide (nano-TiO2) on the prokaryotic communities associated with the gill tissue of the Antarctic soft-shell clam Laternula elliptica, a keystone species of marine benthos Wild-caught specimens were exposed to two environmentally relevant concentrations of carboxylated PS NP (PS-COOH NP, ∼62 nm size) and nano-TiO2 (Aeroxide P25, ∼25 nm) as 5 and 50 μg/L either single and combined for 96h in a semi-static condition.Our findings show a shift in microbiome composition in gills of soft-shell clams exposed to PS NP and nano-TiO2 either alone and in combination with a decrease in the relative abundance of OTU1 (Spirochaetaceae). In addition, an increase of gammaproteobacterial OTUs affiliated to MBAE14 and Methylophagaceae (involved in ammonia denitrification and associated with low-quality water), and the OTU Colwellia rossensis (previously recorded in polluted waters) was observed. Our results suggest that nanoplastics and nano-TiO2 alone and in combination induce alterations in microbiome composition by promoting the increase of negative taxa over beneficial ones in the gills of the Antarctic soft-shell clam. An increase of two low abundance OTUs in PS-COOH NPs exposed clams was also observed. A predicted gene function analysis revealed that sugar, lipid, protein and DNA metabolism were the main functions affected by either PS-COOH NP and nano-TiO2 exposure. The molecular functions involved in the altered affiliated OTUs are novel for nano-CEC exposures.
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Affiliation(s)
- Rodolfo Rondon
- Departamento Científico, Instituto Antártico Chileno, Punta Arenas, Chile.
| | - Céline Cosseau
- IHPE, Univ. Montpellier, CNRS, Ifremer, Univ. Perpignan Via Domitia, Perpignan, France
| | - Elisa Bergami
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - César A Cárdenas
- Departamento Científico, Instituto Antártico Chileno, Punta Arenas, Chile; Millenium Institute Biodiversity of Antarctic and Subantarctic Ecosystems (BASE), Santiago, Chile
| | | | - Diego Alvarez
- Centro Asistencial Docente y de Investigación, Universidad de Magallanes, Punta Arenas, Chile
| | - Jacqueline Aldridge
- Departamento de Ingeniería en Computación, Universidad de Magallanes, Punta Arenas, Chile
| | - Alejandro Font
- Departamento Científico, Instituto Antártico Chileno, Punta Arenas, Chile
| | - Ignacio Garrido
- Centro de Investigaciones Dinámica de Ecosistemas Marinos de Altas Latitudes, Valdivia, Chile; Instituto de Ciencias Marinas y Limnológicas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | | | - Garance Perrois
- Departamento Científico, Instituto Antártico Chileno, Punta Arenas, Chile; Tropical & Subtropical Research Center, Korea Institute of Ocean Science and Technology, Jeju, 63349, Republic of Korea
| | - Teresa Balbi
- Department of Earth Environment and Life Sciences, University of Genoa, Genoa, Italy
| | - Ilaria Corsi
- Department of Physical, Earth and Environmental Sciences, University of Siena, Siena, Italy
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2
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Morel-Letelier I, Yuen B, Kück AC, Camacho-García YE, Petersen JM, Lara M, Leray M, Eisen JA, Osvatic JT, Gros O, Wilkins LGE. Adaptations to nitrogen availability drive ecological divergence of chemosynthetic symbionts. PLoS Genet 2024; 20:e1011295. [PMID: 38820540 PMCID: PMC11168628 DOI: 10.1371/journal.pgen.1011295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 06/12/2024] [Accepted: 05/08/2024] [Indexed: 06/02/2024] Open
Abstract
Bacterial symbionts, with their shorter generation times and capacity for horizontal gene transfer (HGT), play a critical role in allowing marine organisms to cope with environmental change. The closure of the Isthmus of Panama created distinct environmental conditions in the Tropical Eastern Pacific (TEP) and Caribbean, offering a "natural experiment" for studying how closely related animals evolve and adapt under environmental change. However, the role of bacterial symbionts in this process is often overlooked. We sequenced the genomes of endosymbiotic bacteria in two sets of sister species of chemosymbiotic bivalves from the genera Codakia and Ctena (family Lucinidae) collected on either side of the Isthmus, to investigate how differing environmental conditions have influenced the selection of symbionts and their metabolic capabilities. The lucinid sister species hosted different Candidatus Thiodiazotropha symbionts and only those from the Caribbean had the genetic potential for nitrogen fixation, while those from the TEP did not. Interestingly, this nitrogen-fixing ability did not correspond to symbiont phylogeny, suggesting convergent evolution of nitrogen fixation potential under nutrient-poor conditions. Reconstructing the evolutionary history of the nifHDKT operon by including other lucinid symbiont genomes from around the world further revealed that the last common ancestor (LCA) of Ca. Thiodiazotropha lacked nif genes, and populations in oligotrophic habitats later re-acquired the nif operon through HGT from the Sedimenticola symbiont lineage. Our study suggests that HGT of the nif operon has facilitated niche diversification of the globally distributed Ca. Thiodiazotropha endolucinida species clade. It highlights the importance of nitrogen availability in driving the ecological diversification of chemosynthetic symbiont species and the role that bacterial symbionts may play in the adaptation of marine organisms to changing environmental conditions.
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Affiliation(s)
- Isidora Morel-Letelier
- Eco-Evolutionary Interactions Group, Max Planck Institute for Marine Microbiology (MPIMM), Bremen, Germany
| | - Benedict Yuen
- Eco-Evolutionary Interactions Group, Max Planck Institute for Marine Microbiology (MPIMM), Bremen, Germany
| | - A. Carlotta Kück
- Eco-Evolutionary Interactions Group, Max Planck Institute for Marine Microbiology (MPIMM), Bremen, Germany
| | - Yolanda E. Camacho-García
- Centro de Investigación en Ciencias del Mar y Limnología (CIMAR), Universidad de Costa Rica, San Pedro, San José, Costa Rica
- Centro de Investigación en Biodiversidad y Ecología Tropical (CIBET), Universidad de Costa Rica, San Pedro, San José, Costa Rica
- Escuela de Biología, Universidad de Costa Rica, San Pedro, San José, Costa Rica
| | - Jillian M. Petersen
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Minor Lara
- Diving Center Cuajiniquil, Provincia de Guanacaste, Cuajiniquil, Costa Rica
| | - Matthieu Leray
- Smithsonian Tropical Research Institute, Balboa, Ancon, Republic of Panamá
| | - Jonathan A. Eisen
- Department of Evolution and Ecology, University of California, Davis, Davis, California, United States of America
- Department of Medical Microbiology and Immunology, University of California, Davis, Davis, California, United States of America
| | - Jay T. Osvatic
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria
- Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | - Olivier Gros
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d’Histoire Naturelle, CNRS, Sorbonne Université, Université des Antilles, Pointe-à-Pitre, France
| | - Laetitia G. E. Wilkins
- Eco-Evolutionary Interactions Group, Max Planck Institute for Marine Microbiology (MPIMM), Bremen, Germany
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3
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Rolando JL, Kolton M, Song T, Liu Y, Pinamang P, Conrad R, Morris JT, Konstantinidis KT, Kostka JE. Sulfur oxidation and reduction are coupled to nitrogen fixation in the roots of the salt marsh foundation plant Spartina alterniflora. Nat Commun 2024; 15:3607. [PMID: 38684658 PMCID: PMC11059160 DOI: 10.1038/s41467-024-47646-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 04/09/2024] [Indexed: 05/02/2024] Open
Abstract
Heterotrophic activity, primarily driven by sulfate-reducing prokaryotes, has traditionally been linked to nitrogen fixation in the root zone of coastal marine plants, leaving the role of chemolithoautotrophy in this process unexplored. Here, we show that sulfur oxidation coupled to nitrogen fixation is a previously overlooked process providing nitrogen to coastal marine macrophytes. In this study, we recovered 239 metagenome-assembled genomes from a salt marsh dominated by the foundation plant Spartina alterniflora, including diazotrophic sulfate-reducing and sulfur-oxidizing bacteria. Abundant sulfur-oxidizing bacteria encode and highly express genes for carbon fixation (RuBisCO), nitrogen fixation (nifHDK) and sulfur oxidation (oxidative-dsrAB), especially in roots stressed by sulfidic and reduced sediment conditions. Stressed roots exhibited the highest rates of nitrogen fixation and expression level of sulfur oxidation and sulfate reduction genes. Close relatives of marine symbionts from the Candidatus Thiodiazotropha genus contributed ~30% and ~20% of all sulfur-oxidizing dsrA and nitrogen-fixing nifK transcripts in stressed roots, respectively. Based on these findings, we propose that the symbiosis between S. alterniflora and sulfur-oxidizing bacteria is key to ecosystem functioning of coastal salt marshes.
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Affiliation(s)
- J L Rolando
- Georgia Institute of Technology, School of Biological Sciences, Atlanta, GA, 30332, USA
| | - M Kolton
- Georgia Institute of Technology, School of Biological Sciences, Atlanta, GA, 30332, USA
- French Associates Institute for Agriculture and Biotechnology of Drylands, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - T Song
- Georgia Institute of Technology, School of Biological Sciences, Atlanta, GA, 30332, USA
| | - Y Liu
- Georgia Institute of Technology, School of Biological Sciences, Atlanta, GA, 30332, USA
- The Pennsylvania State University, Department of Civil & Environmental Engineering, University Park, PA, 16802, USA
| | - P Pinamang
- Georgia Institute of Technology, School of Biological Sciences, Atlanta, GA, 30332, USA
| | - R Conrad
- Georgia Institute of Technology, School of Biological Sciences, Atlanta, GA, 30332, USA
| | - J T Morris
- Belle Baruch Institute for Marine & Coastal Sciences, University of South Carolina, Columbia, SC, 29201, USA
| | - K T Konstantinidis
- Georgia Institute of Technology, School of Biological Sciences, Atlanta, GA, 30332, USA
- Georgia Institute of Technology, School of Civil and Environmental Engineering, Atlanta, GA, 30332, USA
| | - J E Kostka
- Georgia Institute of Technology, School of Biological Sciences, Atlanta, GA, 30332, USA.
- Georgia Institute of Technology, School of Earth and Atmospheric Sciences, Atlanta, GA, 30332, USA.
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA, 30332, USA.
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Ratinskaia L, Malavin S, Zvi-Kedem T, Vintila S, Kleiner M, Rubin-Blum M. Metabolically-versatile Ca. Thiodiazotropha symbionts of the deep-sea lucinid clam Lucinoma kazani have the genetic potential to fix nitrogen. ISME COMMUNICATIONS 2024; 4:ycae076. [PMID: 38873029 PMCID: PMC11171427 DOI: 10.1093/ismeco/ycae076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 05/06/2024] [Accepted: 05/31/2024] [Indexed: 06/15/2024]
Abstract
Lucinid clams are one of the most diverse and widespread symbiont-bearing animal groups in both shallow and deep-sea chemosynthetic habitats. Lucinids harbor Ca. Thiodiazotropha symbionts that can oxidize inorganic and organic substrates such as hydrogen sulfide and formate to gain energy. The interplay between these key metabolic functions, nutrient uptake and biotic interactions in Ca. Thiodiazotropha is not fully understood. We collected Lucinoma kazani individuals from next to a deep-sea brine pool in the eastern Mediterranean Sea, at a depth of 1150 m and used Oxford Nanopore and Illumina sequencing to obtain high-quality genomes of their Ca. Thiodiazotropha gloverae symbiont. The genomes served as the basis for transcriptomic and proteomic analyses to characterize the in situ gene expression, metabolism and physiology of the symbionts. We found genes needed for N2 fixation in the deep-sea symbiont's genome, which, to date, were only found in shallow-water Ca. Thiodiazotropha. However, we did not detect the expression of these genes and thus the potential role of nitrogen fixation in this symbiosis remains to be determined. We also found the high expression of carbon fixation and sulfur oxidation genes, which indicate chemolithoautotrophy as the key physiology of Ca. Thiodiazotropha. However, we also detected the expression of pathways for using methanol and formate as energy sources. Our findings highlight the key traits these microbes maintain to support the nutrition of their hosts and interact with them.
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Affiliation(s)
- Lina Ratinskaia
- Biology Department, National Institute of Oceanography, Israel Oceanographic and Limnological Research (IOLR), Haifa 3108000Israel
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa 3498838Israel
| | - Stas Malavin
- Biology Department, National Institute of Oceanography, Israel Oceanographic and Limnological Research (IOLR), Haifa 3108000Israel
- Department of Environmental Hydrology and Microbiology, Zuckerberg Institute for Water Research, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sde Boker 8499000, Israel
| | - Tal Zvi-Kedem
- Biology Department, National Institute of Oceanography, Israel Oceanographic and Limnological Research (IOLR), Haifa 3108000Israel
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa 3498838Israel
| | - Simina Vintila
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, United States
| | - Manuel Kleiner
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, United States
| | - Maxim Rubin-Blum
- Biology Department, National Institute of Oceanography, Israel Oceanographic and Limnological Research (IOLR), Haifa 3108000Israel
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa 3498838Israel
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Cleary DFR, de Voogd NJ, Stuij TM, Swierts T, Oliveira V, Polónia ARM, Louvado A, Gomes NCM, Coelho FJRC. A Study of Sponge Symbionts from Different Light Habitats. MICROBIAL ECOLOGY 2023; 86:2819-2837. [PMID: 37597041 PMCID: PMC10640470 DOI: 10.1007/s00248-023-02267-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Accepted: 07/07/2023] [Indexed: 08/21/2023]
Abstract
The amount of available light plays a key role in the growth and development of microbial communities. In the present study, we tested to what extent sponge-associated prokaryotic communities differed between specimens of the sponge species Cinachyrella kuekenthali and Xestospongia muta collected in dimly lit (caves and at greater depths) versus illuminated (shallow water) habitats. In addition to this, we also collected samples of water, sediment, and another species of Cinachyrella, C. alloclada. Overall, the biotope (sponge host species, sediment, and seawater) proved the major driver of variation in prokaryotic community composition. The light habitat, however, also proved a predictor of compositional variation in prokaryotic communities of both C. kuekenthali and X. muta. We used an exploratory technique based on machine learning to identify features (classes, orders, and OTUs), which distinguished X. muta specimens sampled in dimly lit versus illuminated habitat. We found that the classes Alphaproteobacteria and Rhodothermia and orders Puniceispirillales, Rhodospirillales, Rhodobacterales, and Thalassobaculales were associated with specimens from illuminated, i.e., shallow water habitat, while the classes Dehalococcoidia, Spirochaetia, Entotheonellia, Nitrospiria, Schekmanbacteria, and Poribacteria, and orders Sneathiellales and Actinomarinales were associated with specimens sampled from dimly lit habitat. There was, however, considerable variation within the different light habitats highlighting the importance of other factors in structuring sponge-associated bacterial communities.
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Affiliation(s)
- D F R Cleary
- CESAM & Department of Biology, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal.
| | - N J de Voogd
- Naturalis Biodiversity Center, Leiden, The Netherlands.
- Institute of Environmental Sciences (CML), Leiden University, Leiden, The Netherlands.
| | - T M Stuij
- CESAM & Department of Biology, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
| | - T Swierts
- Naturalis Biodiversity Center, Leiden, The Netherlands
| | - V Oliveira
- CESAM & Department of Biology, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
| | - A R M Polónia
- CESAM & Department of Biology, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
| | - A Louvado
- CESAM & Department of Biology, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
| | - N C M Gomes
- CESAM & Department of Biology, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
| | - F J R C Coelho
- CESAM & Department of Biology, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
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Slobodkina G, Merkel A, Ratnikova N, Kuchierskaya A, Slobodkin A. Sedimenticola hydrogenitrophicus sp. nov. a chemolithoautotrophic bacterium isolated from a terrestrial mud volcano, and proposal of Sedimenticolaceae fam. nov. in the order Chromatiales. Syst Appl Microbiol 2023; 46:126451. [PMID: 37562281 DOI: 10.1016/j.syapm.2023.126451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 07/27/2023] [Accepted: 08/02/2023] [Indexed: 08/12/2023]
Abstract
Chemolithoautotrophic microorganisms can play a significant role in the biogeochemical cycling of elements in deep-subsurface-associated environments. A novel facultatively anaerobic lithoautotrophic bacteria (strains SB48T and SN1189) were isolated from terrestrial mud volcanoes (Krasnodar Krai, Russia). Cells of the strains were straight motile rods. Growth was observed at temperatures up to 35 °C (optimum at 30 °C), pH 6.0-8.5 (optimum at pH 7.5) and NaCl concentrations of 0.5-4.0% (w/v) (optimum at 1.5-2.0% (w/v)). The isolates grew chemolithoautotrophically with molecular hydrogen or thiosulfate as an electron donor, nitrate as an electron acceptor and CO2/HCO3- as a carbon source. They also grew with organic acids, ethanol, yeast extract and peptone. The isolates were capable of either anaerobic respiration with nitrate or nitrous oxide as the electron acceptors or aerobic respiration under microaerobic condition. The total size of the genome of strains SB48T and SN1189 was 4.71 and 5.13 Mbp, respectively. Based on phenotypic and phylogenetic characteristics, strains SB48T and SN1189 represent a novel species of the genus Sedimenticola, S. hydrogenitrophicus (the type strain is SB48T = KCTC 25568 T = VKM B-3680 T). The new isolates are the first representatives of the genus Sedimenticola isolated from a terrestrial ecosystem. Based on phylogenomic reconstruction we propose to include the genus Sedimenticola and the related genera into a new family Sedimenticolaceae fam. nov. within the order Chromatiales.
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Affiliation(s)
- Galina Slobodkina
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Leninskiy Prospect, 33, bld. 2, 119071 Moscow, Russia.
| | - Alexander Merkel
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Leninskiy Prospect, 33, bld. 2, 119071 Moscow, Russia
| | - Nataliya Ratnikova
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Leninskiy Prospect, 33, bld. 2, 119071 Moscow, Russia
| | | | - Alexander Slobodkin
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Leninskiy Prospect, 33, bld. 2, 119071 Moscow, Russia
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7
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Gao ZM, Xu T, Chen HG, Lu R, Tao J, Wang HB, Qiu JW, Wang Y. Early genome erosion and internal phage-symbiont-host interaction in the endosymbionts of a cold-seep tubeworm. iScience 2023; 26:107033. [PMID: 37389180 PMCID: PMC10300362 DOI: 10.1016/j.isci.2023.107033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 03/11/2023] [Accepted: 05/31/2023] [Indexed: 07/01/2023] Open
Abstract
Endosymbiosis with chemosynthetic Gammaproteobacteria is widely recognized as an adaptive mechanism of siboglinid tubeworms, yet evolution of these endosymbionts and their driving forces remain elusive. Here, we report a finished endosymbiont genome (HMS1) of the cold-seep tubeworm Sclerolinum annulatum. The HMS1 genome is small in size, with abundant prophages and transposable elements but lacking gene sets coding for denitrification, hydrogen oxidization, oxidative phosphorylation, vitamin biosynthesis, cell pH and/or sodium homeostasis, environmental sensing, and motility, indicative of early genome erosion and adaptive evolution toward obligate endosymbiosis. Unexpectedly, a prophage embedded in the HMS1 genome undergoes lytic cycle. Highly expressed ROS scavenger and LexA repressor genes indicate that the tubeworm host likely activates the lysogenic phage into lytic cycle through the SOS response to regulate endosymbiont population and harvest nutrients. Our findings indicate progressive evolution of Sclerolinum endosymbionts toward obligate endosymbiosis and expand the knowledge about phage-symbiont-host interaction in deep-sea tubeworms.
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Affiliation(s)
- Zhao-Ming Gao
- Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China
- HKUST-CAS Sanya Joint Laboratory of Marine Science Research, Chinese Academy of Sciences, Sanya 572000, China
| | - Ting Xu
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Hua-Guan Chen
- Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China
- University of Chinese Academy of Sciences, Beijing 101408, China
| | - Rui Lu
- Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China
- University of Chinese Academy of Sciences, Beijing 101408, China
| | - Jun Tao
- MLR Key Laboratory of Marine Mineral Resources, Guangzhou Marine Geological Survey, China Geological Survey, Guangzhou 511458, China
| | - Hong-Bin Wang
- MLR Key Laboratory of Marine Mineral Resources, Guangzhou Marine Geological Survey, China Geological Survey, Guangzhou 511458, China
| | - Jian-Wen Qiu
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Yong Wang
- Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China
- HKUST-CAS Sanya Joint Laboratory of Marine Science Research, Chinese Academy of Sciences, Sanya 572000, China
- Institute for Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518000, China
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8
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Shu Y, Wang Y, Wei Z, Gao N, Wang S, Li C, Xing Q, Hu X, Zhang X, Zhang Y, Zhang W, Bao Z, Ding W. A bacterial symbiont in the gill of the marine scallop Argopecten irradians irradians metabolizes dimethylsulfoniopropionate. MLIFE 2023; 2:178-189. [PMID: 38817626 PMCID: PMC10989825 DOI: 10.1002/mlf2.12072] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 04/23/2023] [Accepted: 05/15/2023] [Indexed: 06/01/2024]
Abstract
Microbial lysis of dimethylsulfoniopropionate (DMSP) is a key step in marine organic sulfur cycling and has been recently demonstrated to play an important role in mediating interactions between bacteria, algae, and zooplankton. To date, microbes that have been found to lyse DMSP are largely confined to free-living and surface-attached bacteria. In this study, we report for the first time that a symbiont (termed "Rhodobiaceae bacterium HWgs001") in the gill of the marine scallop Argopecten irradians irradians can lyse and metabolize DMSP. Analysis of 16S rRNA gene sequences suggested that HWgs001 accounted for up to 93% of the gill microbiota. Microscopic observations suggested that HWgs001 lived within the gill tissue. Unlike symbionts of other bivalves, HWgs001 belongs to Alphaproteobacteria rather than Gammaproteobacteria, and no genes for carbon fixation were identified in its small genome. Moreover, HWgs001 was found to possess a dddP gene, responsible for the lysis of DMSP to acrylate. The enzymatic activity of dddP was confirmed using the heterologous expression, and in situ transcription of the gene in scallop gill tissues was demonstrated using reverse-transcription PCR. Together, these results revealed a taxonomically and functionally unique symbiont, which represents the first-documented DMSP-metabolizing symbiont likely to play significant roles in coastal marine ecosystems.
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Affiliation(s)
- Yi Shu
- MOE Key Laboratory of Marine Genetics and BreedingOcean University of ChinaQingdaoChina
- Laboratory of Tropical Marine Germplasm Resources and Breeding Engineering, Sanya Oceanographic InstitutionOcean University of ChinaSanyaChina
| | - Yongming Wang
- MOE Key Laboratory of Marine Genetics and BreedingOcean University of ChinaQingdaoChina
- Laboratory of Tropical Marine Germplasm Resources and Breeding Engineering, Sanya Oceanographic InstitutionOcean University of ChinaSanyaChina
| | - Zhongcheng Wei
- MOE Key Laboratory of Marine Genetics and BreedingOcean University of ChinaQingdaoChina
| | - Ning Gao
- MOE Key Laboratory of Marine Genetics and BreedingOcean University of ChinaQingdaoChina
- Laboratory of Tropical Marine Germplasm Resources and Breeding Engineering, Sanya Oceanographic InstitutionOcean University of ChinaSanyaChina
| | - Shuyan Wang
- College of Marine Life SciencesOcean University of ChinaQingdaoChina
| | - Chun‐Yang Li
- College of Marine Life SciencesOcean University of ChinaQingdaoChina
| | - Qiang Xing
- MOE Key Laboratory of Marine Genetics and BreedingOcean University of ChinaQingdaoChina
- College of Marine Life SciencesOcean University of ChinaQingdaoChina
| | - Xiaoli Hu
- MOE Key Laboratory of Marine Genetics and BreedingOcean University of ChinaQingdaoChina
- Laboratory of Tropical Marine Germplasm Resources and Breeding Engineering, Sanya Oceanographic InstitutionOcean University of ChinaSanyaChina
| | - Xiao‐Hua Zhang
- College of Marine Life SciencesOcean University of ChinaQingdaoChina
| | - Yu‐Zhong Zhang
- College of Marine Life SciencesOcean University of ChinaQingdaoChina
| | - Weipeng Zhang
- Institute of Evolution & Marine BiodiversityOcean University of ChinaQingdaoChina
| | - Zhenmin Bao
- MOE Key Laboratory of Marine Genetics and BreedingOcean University of ChinaQingdaoChina
- Laboratory of Tropical Marine Germplasm Resources and Breeding Engineering, Sanya Oceanographic InstitutionOcean University of ChinaSanyaChina
| | - Wei Ding
- MOE Key Laboratory of Marine Genetics and BreedingOcean University of ChinaQingdaoChina
- College of Marine Life SciencesOcean University of ChinaQingdaoChina
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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: 0] [Impact Index Per Article: 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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10
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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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11
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Arboleda-Baena C, Pareja CB, Pla I, Logares R, De la Iglesia R, Navarrete SA. Hidden interactions in the intertidal rocky shore: variation in pedal mucus microbiota among marine grazers that feed on epilithic biofilm communities. PeerJ 2022; 10:e13642. [PMID: 36172502 PMCID: PMC9512015 DOI: 10.7717/peerj.13642] [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] [Received: 08/23/2021] [Accepted: 06/07/2022] [Indexed: 01/17/2023] Open
Abstract
In marine ecosystems, most invertebrates possess diverse microbiomes on their external surfaces, such as those found in the pedal mucus of grazing gastropods and chitons that aids displacement on different surfaces. The microbes are then transported around and placed in contact with free-living microbial communities of micro and other macro-organisms, potentially exchanging species and homogenizing microbial composition and structure among grazer hosts. Here, we characterize the microbiota of the pedal mucus of five distantly related mollusk grazers, quantify differences in microbial community structure, mucus protein and carbohydrate content, and, through a simple laboratory experiment, assess their effects on integrated measures of biofilm abundance. Over 665 Amplicon Sequence Variants (ASVs) were found across grazers, with significant differences in abundance and composition among grazer species and epilithic biofilms. The pulmonate limpet Siphonaria lessonii and the periwinkle Echinolittorina peruviana shared similar microbiota. The microbiota of the chiton Chiton granosus, keyhole limpet Fissurella crassa, and scurrinid limpet Scurria araucana differed markedly from one another, and form those of the pulmonate limpet and periwinkle. Flavobacteriaceae (Bacteroidia) and Colwelliaceae (Gammaproteobacteria) were the most common among microbial taxa. Microbial strict specialists were found in only one grazer species. The pedal mucus pH was similar among grazers, but carbohydrate and protein concentrations differed significantly. Yet, differences in mucus composition were not reflected in microbial community structure. Only the pedal mucus of F. crassa and S. lessonii negatively affected the abundance of photosynthetic microorganisms in the biofilm, demonstrating the specificity of the pedal mucus effects on biofilm communities. Thus, the pedal mucus microbiota are distinct among grazer hosts and can affect and interact non-trophically with the epilithic biofilms on which grazers feed, potentially leading to microbial community coalescence mediated by grazer movement. Further studies are needed to unravel the myriad of non-trophic interactions and their reciprocal impacts between macro- and microbial communities.
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Affiliation(s)
- Clara Arboleda-Baena
- Estación Costera de Investigaciones Marinas and Center for Applied Ecology and Sustainability (CAPES), Pontificia Universidad Católica de Chile, El Tabo, Chile,Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago de Chile, Región Metropolitana, Chile
| | - Claudia Belén Pareja
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago de Chile, Región Metropolitana, Chile
| | - Isadora Pla
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago de Chile, Región Metropolitana, Chile
| | - Ramiro Logares
- Institut de Ciències del Mar (ICM), CSIC, Barcelona, Catalonia, Spain
| | - Rodrigo De la Iglesia
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago de Chile, Región Metropolitana, Chile,Marine Energy Research & Innovation Center (MERIC), Santiago de Chile, Chile
| | - Sergio Andrés Navarrete
- Estación Costera de Investigaciones Marinas and Center for Applied Ecology and Sustainability (CAPES), Pontificia Universidad Católica de Chile, El Tabo, Chile,Marine Energy Research & Innovation Center (MERIC), Santiago de Chile, Chile,Centro Basal COPAS-COASTAL, Universidad de Concepción
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12
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Chemoautotrophy, symbiosis and sedimented diatoms support high biomass of benthic molluscs in the Namibian shelf. Sci Rep 2022; 12:9731. [PMID: 35697901 PMCID: PMC9192762 DOI: 10.1038/s41598-022-13571-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 05/17/2022] [Indexed: 11/26/2022] Open
Abstract
The molluscs Lucinoma capensis, Lembulus bicuspidatus and Nassarius vinctus are highly abundant in Namibian oxygen minimum zone sediments. To understand which nutritional strategies allow them to reach such impressive abundances in this extreme habitat we investigated their trophic diversity, including a chemosymbiosis in L. capensis, focussing on nitrogen biochemical pathways of the symbionts. We combined results of bulk nitrogen and carbon (δ13C and δ15N) and of compound-specific isotope analyses of amino acid nitrogen (AAs—δ15NPhe and δ15NGlu), with 16S rRNA gene sequencing of L. capensis tissues and also with exploratory results of ammonium, nitrate and nitrite turnover. The trophic position (TP) of the bivalve L. capensis is placed between autotrophy and mixotrophy, consistent with its proposed symbiosis with sulfur-oxidizing Candidatus Thiodiazotropha sp. symbionts. The symbionts are here revealed to perform nitrate reduction and ammonium uptake, with clear indications of ammonium host-symbionts recycling, but surprisingly unable to fix nitrogen. The TP of the bivalve L. bicuspidatus is placed in between mixotrophy and herbivory. The TP of the gastropod N. vinctus reflected omnivory. Multiple lines of evidences in combination with current ecosystem knowledge point to sedimented diatoms as important components of L. bicuspidatus and N. vinctus’ diet, likely supplemented at times with chemoautotrophic bacteria. This study highlights the importance of benthic-pelagic coupling that fosters the dietary base for macrozoobenthos in the OMZ. It further unveils that, in contrast to all shallow water lucinid symbionts, deeper water lucinid symbionts rely on ammonium assimilation rather than dinitrogen fixation to obtain nitrogen for growth.
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13
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Clavere-Graciette AG, McWhirt ME, Hoopes LA, Bassos-Hull K, Wilkinson KA, Stewart FJ, Pratte ZA. Microbiome differences between wild and aquarium whitespotted eagle rays (Aetobatus narinari). Anim Microbiome 2022; 4:34. [PMID: 35606841 PMCID: PMC9128078 DOI: 10.1186/s42523-022-00187-8] [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] [Received: 08/24/2021] [Accepted: 05/09/2022] [Indexed: 11/15/2022] Open
Abstract
Background Animal-associated microbiomes can be influenced by both host and environmental factors. Comparing wild animals to those in zoos or aquariums can help disentangle the effects of host versus environmental factors, while also testing whether managed conditions foster a ‘natural’ host microbiome. Focusing on an endangered elasmobranch species—the whitespotted eagle ray Aetobatus narinari—we compared the skin, gill, and cloaca microbiomes of wild individuals to those at Georgia Aquarium. Whitespotted eagle ray microbiomes from Georgia Aquarium were also compared to those of cownose rays (Rhinoptera bonasus) in the same exhibit, allowing us to explore the effect of host identity on the ray microbiome.
Results Long-term veterinary monitoring indicated that the rays in managed care did not have a history of disease and maintained health parameters consistent with those of wild individuals, with one exception. Aquarium whitespotted eagle rays were regularly treated to control parasite loads, but the effects on animal health were subclinical. Microbiome α- and β-diversity differed between wild versus aquarium whitespotted eagle rays at all body sites, with α-diversity significantly higher in wild individuals. β-diversity differences in wild versus aquarium whitespotted eagle rays were greater for skin and gill microbiomes compared to those of the cloaca. At each body site, we also detected microbial taxa shared between wild and aquarium eagle rays. Additionally, the cloaca, skin, and gill microbiomes of aquarium eagle rays differed from those of cownose rays in the same exhibit. Potentially pathogenic bacteria were at low abundance in all wild and aquarium rays.
Conclusion For whitespotted eagle rays, managed care was associated with a microbiome differing significantly from that of wild individuals. These differences were not absolute, as the microbiome of aquarium rays shared members with that of wild counterparts and was distinct from that of a cohabitating ray species. Eagle rays under managed care appear healthy, suggesting that their microbiomes are not associated with compromised host health. However, the ray microbiome is dynamic, differing with both environmental factors and host identity. Monitoring of aquarium ray microbiomes over time may identify taxonomic patterns that co-vary with host health. Supplementary Information The online version contains supplementary material available at 10.1186/s42523-022-00187-8.
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Affiliation(s)
| | - Mary E McWhirt
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Lisa A Hoopes
- Department of Research and Conservation, Georgia Aquarium, Atlanta, GA, USA
| | - Kim Bassos-Hull
- Sharks and Rays Conservation Research Program, Mote Marine Laboratory, Sarasota, FL, USA.,Chicago Zoological Society's Sarasota Dolphin Research Program, c/o Mote Marine Laboratory, Sarasota, FL, USA
| | - Krystan A Wilkinson
- Sharks and Rays Conservation Research Program, Mote Marine Laboratory, Sarasota, FL, USA.,Chicago Zoological Society's Sarasota Dolphin Research Program, c/o Mote Marine Laboratory, Sarasota, FL, USA
| | - Frank J Stewart
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA.,Department of Microbiology & Cell Biology, Montana State University, Bozeman, MT, USA
| | - Zoe A Pratte
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA. .,Department of Microbiology & Cell Biology, Montana State University, Bozeman, MT, USA.
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14
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Intrahabitat Differences in Bacterial Communities Associated with Corbicula fluminea in the Large Shallow Eutrophic Lake Taihu. Appl Environ Microbiol 2022; 88:e0232821. [PMID: 35285714 DOI: 10.1128/aem.02328-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The Asian clam Corbicula fluminea is a keystone zoobenthos in freshwater ecosystems. However, its associated microbiome is not well understood. We investigated the bacterial communities of this clam and its surrounding environment, including sediment and water simultaneously, in a large lake by means of 16S rRNA gene sequencing. Approximately two-thirds of the bacterial operational taxonomic units (OTUs) associated with clams were observed in the surrounding environment and mostly from particle-associated samples. The associated bacterial communities were site specific and more similar to environmental bacteria from the same site than those at other sites, suggesting a local environmental influence on host bacteria. However, the significant differences in bacterial diversities and compositions between the clam and the environment also indicated strong host selection pressure on bacteria from the surrounding environment. Bacteria affiliated with Firmicutes, Spirochaetes, Tenericutes, Bacteroidetes, Epsilonbacteraeota, Patescibacteria, and Fusobacteria were found to be significantly enriched in the clams in comparison to their local environment. Oligotyping analyses of the core-associated bacterial OTUs also demonstrated that most of the core OTUs had lower relative abundances and occurrence frequencies in environmental samples. The core bacterial OTUs were found to play an important role in maintaining the stability of the bacterial community network. These core bacteria included the two most abundant taxa Romboutsia and Paraclostridium with the potential function of fermenting polysaccharides for assisting host clams in food digestion. Overall, we demonstrate that clam-associated bacteria were spatially dynamic and site specific, which were mainly structured both by local environments and host selection. IMPORTANCE The Asian clam Corbicula fluminea is an important benthic clam in freshwater ecosystems due to its high population densities and high filtering efficiency for particulate organic matter. While the associated microbiota is believed to be vital for host living, our knowledge about the compositions, sources, and potential functions is still lacking. We found that C. fluminea offers a unique ecological niche for specific lake bacteria. We also observed high intrahabitat variation in the associated bacterial communities. Such variations were driven mainly by local environments, followed by host selection pressure. While the local microbes served as a source of the clam-associated bacteria, host selection resulted in enrichments of bacterial taxa with the potential for assisting the host in organic matter digestion. These results significantly advance our current understanding of the origins and ecological roles of the microbiota associated with a keynote clam in freshwater ecosystems.
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15
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Rolando JL, Kolton M, Song T, Kostka JE. The core root microbiome of Spartina alterniflora is predominated by sulfur-oxidizing and sulfate-reducing bacteria in Georgia salt marshes, USA. MICROBIOME 2022; 10:37. [PMID: 35227326 PMCID: PMC8886783 DOI: 10.1186/s40168-021-01187-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 10/25/2021] [Indexed: 05/12/2023]
Abstract
BACKGROUND Salt marshes are dominated by the smooth cordgrass Spartina alterniflora on the US Atlantic and Gulf of Mexico coastlines. Although soil microorganisms are well known to mediate important biogeochemical cycles in salt marshes, little is known about the role of root microbiomes in supporting the health and productivity of marsh plant hosts. Leveraging in situ gradients in aboveground plant biomass as a natural laboratory, we investigated the relationships between S. alterniflora primary productivity, sediment redox potential, and the physiological ecology of bulk sediment, rhizosphere, and root microbial communities at two Georgia barrier islands over two growing seasons. RESULTS A marked decrease in prokaryotic alpha diversity with high abundance and increased phylogenetic dispersion was found in the S. alterniflora root microbiome. Significantly higher rates of enzymatic organic matter decomposition, as well as the relative abundances of putative sulfur (S)-oxidizing, sulfate-reducing, and nitrifying prokaryotes correlated with plant productivity. Moreover, these functional guilds were overrepresented in the S. alterniflora rhizosphere and root core microbiomes. Core microbiome bacteria from the Candidatus Thiodiazotropha genus, with the metabolic potential to couple S oxidation with C and N fixation, were shown to be highly abundant in the root and rhizosphere of S. alterniflora. CONCLUSIONS The S. alterniflora root microbiome is dominated by highly active and competitive species taking advantage of available carbon substrates in the oxidized root zone. Two microbially mediated mechanisms are proposed to stimulate S. alterniflora primary productivity: (i) enhanced microbial activity replenishes nutrients and terminal electron acceptors in higher biomass stands, and (ii) coupling of chemolithotrophic S oxidation with carbon (C) and nitrogen (N) fixation by root- and rhizosphere-associated prokaryotes detoxifies sulfide in the root zone while potentially transferring fixed C and N to the host plant. Video Abstract.
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Affiliation(s)
- Jose L Rolando
- Georgia Institute of Technology, School of Biological Sciences, Atlanta, GA, 30332, USA
| | - Max Kolton
- Georgia Institute of Technology, School of Biological Sciences, Atlanta, GA, 30332, USA
- French Associates Institute for Agriculture and Biotechnology of Drylands, Ben-Gurion, University of the Negev, Beer Sheva, Israel
| | - Tianze Song
- Georgia Institute of Technology, School of Biological Sciences, Atlanta, GA, 30332, USA
| | - Joel E Kostka
- Georgia Institute of Technology, School of Biological Sciences, Atlanta, GA, 30332, USA.
- Georgia Institute of Technology, School of Earth and Atmospheric Sciences, Atlanta, GA, 30332, USA.
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA, 30332, USA.
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16
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Oren A, Garrity GM. CANDIDATUS LIST No. 3. Lists of names of prokaryotic Candidatus taxa. Int J Syst Evol Microbiol 2022; 72. [PMID: 35100104 DOI: 10.1099/ijsem.0.005186] [Citation(s) in RCA: 251] [Impact Index Per Article: 125.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
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
- Department of Microbiology & Molecular Genetics, Biomedical Physical Sciences, Michigan State University, East Lansing, MI 48824-4320, USA
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Wale M, Daffonchio D, Fusi M, Marasco R, Garuglieri E, Diele K. The Importance of Larval Stages for Considering Crab Microbiomes as a Paradigm for the Evolution of Terrestrialization. Front Microbiol 2021; 12:770245. [PMID: 34721372 PMCID: PMC8555880 DOI: 10.3389/fmicb.2021.770245] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 09/15/2021] [Indexed: 11/30/2022] Open
Affiliation(s)
- Matthew Wale
- School of Applied Sciences, Edinburgh Napier University, Edinburgh, United Kingdom
| | - Daniele Daffonchio
- Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Marco Fusi
- School of Applied Sciences, Edinburgh Napier University, Edinburgh, United Kingdom
| | - Ramona Marasco
- Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Elisa Garuglieri
- Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Karen Diele
- School of Applied Sciences, Edinburgh Napier University, Edinburgh, United Kingdom
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18
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Pacor S, Benincasa M, Musso MV, Krce L, Aviani I, Pallavicini A, Scocchi M, Gerdol M, Mardirossian M. The proline-rich myticalins from Mytilus galloprovincialis display a membrane-permeabilizing antimicrobial mode of action. Peptides 2021; 143:170594. [PMID: 34118363 DOI: 10.1016/j.peptides.2021.170594] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 05/19/2021] [Accepted: 06/03/2021] [Indexed: 12/15/2022]
Abstract
Bivalve mollusks are continuously exposed to potentially pathogenic microorganisms living in the marine environment. Not surprisingly, these filter-feeders developed a robust innate immunity to protect themselves, which includes a broad panel of antimicrobial peptides. Among these, myticalins represent a recently discovered family of linear cationic peptides expressed in the gills of Mytilus galloprovincialis. Even though myticalins and insect and mammalian proline-rich antimicrobial peptides (PrAMPs) share a similar amino acid composition, we here show that none of the tested mussel peptides use a non-lytic mode of action relying on the bacterial transporter SbmA. On the other hand, all the tested myticalins perturbed and permeabilized the membranes of E. coli BW25113, as shown by flow-cytometry and atomic force microscopy. Circular dichroism spectra revealed that most myticalins did not adopt recognizable secondary structures in the presence of amphipathic environments, such as biological membranes. To explore possible uses of myticalins for biotech, we assessed their biocompatibility with a human cell line. Non-negligible cytotoxic effects displayed by myticalins indicate that their optimization would be required before their further use as lead compounds in the development of new antibiotics.
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Affiliation(s)
- Sabrina Pacor
- Department of Life Sciences, Via Licio Giorgieri 5, University of Trieste, 34127 Trieste, Italy.
| | - Monica Benincasa
- Department of Life Sciences, Via Licio Giorgieri 5, University of Trieste, 34127 Trieste, Italy.
| | - Maria Valentina Musso
- Department of Life Sciences, Via Licio Giorgieri 5, University of Trieste, 34127 Trieste, Italy.
| | - Lucija Krce
- Department of Physics, Faculty of Science, University of Split, Soba B3-18, Ruđera Boškovića 33, 21000 Split, Croatia.
| | - Ivica Aviani
- Department of Physics, Faculty of Science, University of Split, Soba B3-18, Ruđera Boškovića 33, 21000 Split, Croatia.
| | - Alberto Pallavicini
- Department of Life Sciences, Via Licio Giorgieri 5, University of Trieste, 34127 Trieste, Italy.
| | - Marco Scocchi
- Department of Life Sciences, Via Licio Giorgieri 5, University of Trieste, 34127 Trieste, Italy.
| | - Marco Gerdol
- Department of Life Sciences, Via Licio Giorgieri 5, University of Trieste, 34127 Trieste, Italy.
| | - Mario Mardirossian
- Department of Medical Sciences, University of Trieste, Laboratorio Clinica Odontostomatologica, Piazza dell'Ospitale 1, 34125 Trieste, Italy.
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19
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Sogin EM, Kleiner M, Borowski C, Gruber-Vodicka HR, Dubilier N. Life in the Dark: Phylogenetic and Physiological Diversity of Chemosynthetic Symbioses. Annu Rev Microbiol 2021; 75:695-718. [PMID: 34351792 DOI: 10.1146/annurev-micro-051021-123130] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Possibly the last discovery of a previously unknown major ecosystem on Earth was made just over half a century ago, when researchers found teaming communities of animals flourishing two and a half kilometers below the ocean surface at hydrothermal vents. We now know that these highly productive ecosystems are based on nutritional symbioses between chemosynthetic bacteria and eukaryotes and that these chemosymbioses are ubiquitous in both deep-sea and shallow-water environments. The symbionts are primary producers that gain energy from the oxidation of reduced compounds, such as sulfide and methane, to fix carbon dioxide or methane into biomass to feed their hosts. This review outlines how the symbiotic partners have adapted to living together. We first focus on the phylogenetic and metabolic diversity of these symbioses and then highlight selected research directions that could advance our understanding of the processes that shaped the evolutionary and ecological success of these associations. Expected final online publication date for the Annual Review of Microbiology, Volume 75 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- E Maggie Sogin
- Max Planck Institute for Marine Microbiology, 28359, Bremen, Germany; ,
| | - Manuel Kleiner
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina 27607, USA
| | - Christian Borowski
- Max Planck Institute for Marine Microbiology, 28359, Bremen, Germany; , .,MARUM-Center for Marine Environmental Sciences, University of Bremen, 28359, Bremen, Germany
| | | | - Nicole Dubilier
- Max Planck Institute for Marine Microbiology, 28359, Bremen, Germany; , .,MARUM-Center for Marine Environmental Sciences, University of Bremen, 28359, Bremen, Germany
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20
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Osvatic JT, Wilkins LGE, Leibrecht L, Leray M, Zauner S, Polzin J, Camacho Y, Gros O, van Gils JA, Eisen JA, Petersen JM, Yuen B. Global biogeography of chemosynthetic symbionts reveals both localized and globally distributed symbiont groups. Proc Natl Acad Sci U S A 2021; 118:e2104378118. [PMID: 34272286 PMCID: PMC8307296 DOI: 10.1073/pnas.2104378118] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In the ocean, most hosts acquire their symbionts from the environment. Due to the immense spatial scales involved, our understanding of the biogeography of hosts and symbionts in marine systems is patchy, although this knowledge is essential for understanding fundamental aspects of symbiosis such as host-symbiont specificity and evolution. Lucinidae is the most species-rich and widely distributed family of marine bivalves hosting autotrophic bacterial endosymbionts. Previous molecular surveys identified location-specific symbiont types that "promiscuously" form associations with multiple divergent cooccurring host species. This flexibility of host-microbe pairings is thought to underpin their global success, as it allows hosts to form associations with locally adapted symbionts. We used metagenomics to investigate the biodiversity, functional variability, and genetic exchange among the endosymbionts of 12 lucinid host species from across the globe. We report a cosmopolitan symbiont species, Candidatus Thiodiazotropha taylori, associated with multiple lucinid host species. Ca. T. taylori has achieved more success at dispersal and establishing symbioses with lucinids than any other symbiont described thus far. This discovery challenges our understanding of symbiont dispersal and location-specific colonization and suggests both symbiont and host flexibility underpin the ecological and evolutionary success of the lucinid symbiosis.
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Affiliation(s)
- Jay T Osvatic
- Centre for Microbiology and Environmental Systems Science, University of Vienna, 1090 Vienna, Austria
| | - Laetitia G E Wilkins
- Genome and Biomedical Sciences Facility, Genome Center, University of California, Davis, CA 95616
- Department of Symbiosis, Max Planck Institute for Marine Microbiology, 28209 Bremen, Germany
| | - Lukas Leibrecht
- Centre for Microbiology and Environmental Systems Science, University of Vienna, 1090 Vienna, Austria
| | - Matthieu Leray
- Smithsonian Tropical Research Institute, Apartado 0843-03092, Balboa, Republic of Panama
| | - Sarah Zauner
- Centre for Microbiology and Environmental Systems Science, University of Vienna, 1090 Vienna, Austria
| | - Julia Polzin
- Centre for Microbiology and Environmental Systems Science, University of Vienna, 1090 Vienna, Austria
| | - Yolanda Camacho
- Centro de Investigación en Ciencias del Mar y Limnología, Escuela de Biología, Universidad de Costa Rica, San Pedro 11501-2060, Costa Rica
| | - Olivier Gros
- UMR 7205, Institut de Systématique, Évolution, Biodiversité, Equipe Biologie de la Mangrove, Département de Biologie, Université des Antilles, 97159 Pointe-à-Pitre Cedex, Guadeloupe
| | - Jan A van Gils
- Royal Netherlands Institute for Sea Research,1790 AB Den Burg, The Netherlands
| | - Jonathan A Eisen
- Genome and Biomedical Sciences Facility, Genome Center, University of California, Davis, CA 95616
- Department of Evolution and Ecology, University of California, Davis, CA 95616
- Department of Medical Microbiology and Immunology, University of California, Davis, CA 95616
| | - Jillian M Petersen
- Centre for Microbiology and Environmental Systems Science, University of Vienna, 1090 Vienna, Austria;
| | - Benedict Yuen
- Centre for Microbiology and Environmental Systems Science, University of Vienna, 1090 Vienna, Austria;
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21
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Jensen S, Frank JA, Arntzen MØ, Duperron S, Vaaje-Kolstad G, Hovland M. Endozoicomonadaceae symbiont in gills of Acesta clam encodes genes for essential nutrients and polysaccharide degradation. FEMS Microbiol Ecol 2021; 97:6275716. [PMID: 33988698 PMCID: PMC8755941 DOI: 10.1093/femsec/fiab070] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 05/12/2021] [Indexed: 01/29/2023] Open
Abstract
Gammaproteobacteria from the family Endozoicomonadaceae have emerged as widespread associates of dense marine animal communities. Their abundance in coral reefs involves symbiotic relationships and possibly host nutrition. We explored functions encoded in the genome of an uncultured Endozoicomonadaceae 'Candidatus Acestibacter aggregatus' that lives inside gill cells of large Acesta excavata clams in deep-water coral reefs off mid-Norway. The dominance and deep branching lineage of this symbiont was confirmed using 16S rRNA gene sequencing and phylogenomic analysis from shotgun sequencing data. The 4.5 Mb genome binned in this study has a low GC content of 35% and is enriched in transposon and chaperone gene annotations indicating ongoing adaptation. Genes encoding functions potentially involved with the symbiosis include ankyrins, repeat in toxins, secretion and nutritional systems. Complete pathways were identified for the synthesis of eleven amino acids and six B-vitamins. A minimal chitinolytic machinery was indicated from a glycosyl hydrolase GH18 and a lytic polysaccharide monooxygenase LPMO10. Expression of the latter was confirmed using proteomics. Signal peptides for secretion were identified for six polysaccharide degrading enzymes, ten proteases and three lipases. Our results suggest a nutritional symbiosis fuelled by enzymatic products from extracellular degradation processes.
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Affiliation(s)
- Sigmund Jensen
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, PO Box 5003, 1432 Ås, Norway
| | - Jeremy A Frank
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, PO Box 5003, 1432 Ås, Norway
| | - Magnus Ø Arntzen
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, PO Box 5003, 1432 Ås, Norway
| | - Sébastien Duperron
- UMR 7245 Muséum National d'Histoire Naturelle/CNRS Molécules de Communication et Adaptation des Micro-organismes and Institut Universitaire de France, CP39, 12 rue Buffon, F-75231 Paris Cedex 05, France
| | - Gustav Vaaje-Kolstad
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, PO Box 5003, 1432 Ås, Norway
| | - Martin Hovland
- Department of Biology, University of Bergen, PO Box 7803, 5020 Bergen, Norway.,Centre for Geobiology, University of Bergen, PO Box 7803, 5020 Bergen, Norway
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22
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O'Brien PA, Andreakis N, Tan S, Miller DJ, Webster NS, Zhang G, Bourne DG. Testing cophylogeny between coral reef invertebrates and their bacterial and archaeal symbionts. Mol Ecol 2021; 30:3768-3782. [PMID: 34060182 DOI: 10.1111/mec.16006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 05/16/2021] [Accepted: 05/24/2021] [Indexed: 12/25/2022]
Abstract
Marine invertebrates harbour a complex suite of bacterial and archaeal symbionts, a subset of which are probably linked to host health and homeostasis. Within a complex microbiome it can be difficult to tease apart beneficial or parasitic symbionts from nonessential commensal or transient microorganisms; however, one approach is to detect strong cophylogenetic patterns between microbial lineages and their respective hosts. We employed the Procrustean approach to cophylogeny (PACo) on 16S rRNA gene derived microbial community profiles paired with COI, 18S rRNA and ITS1 host phylogenies. Second, we undertook a network analysis to identify groups of microbes that were co-occurring within our host species. Across 12 coral, 10 octocoral and five sponge species, each host group and their core microbiota (50% prevalence within host species replicates) had a significant fit to the cophylogenetic model. Independent assessment of each microbial genus and family found that bacteria and archaea affiliated to Endozoicomonadaceae, Spirochaetaceae and Nitrosopumilaceae have the strongest cophylogenetic signals. Further, local Moran's I measure of spatial autocorrelation identified 14 ASVs, including Endozoicomonadaceae and Spirochaetaceae, whose distributions were significantly clustered by host phylogeny. Four co-occurring subnetworks were identified, each of which was dominant in a different host group. Endozoicomonadaceae and Spirochaetaceae ASVs were abundant among the subnetworks, particularly one subnetwork that was exclusively comprised of these two bacterial families and dominated the octocoral microbiota. Our results disentangle key microbial interactions that occur within complex microbiomes and reveal long-standing, essential microbial symbioses in coral reef invertebrates.
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Affiliation(s)
- Paul A O'Brien
- College of Science and Engineering, James Cook University, Townsville, Qld, Australia.,Australian Institute of Marine Science, Townsville, Qld, Australia.,AIMS@JCU, Townsville, Qld, Australia.,ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Qld, Australia
| | - Nikos Andreakis
- College of Science and Engineering, James Cook University, Townsville, Qld, Australia
| | - Shangjin Tan
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, China.,State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
| | - David J Miller
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Qld, Australia.,Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, Qld, Australia.,College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, Qld, Australia
| | - Nicole S Webster
- Australian Institute of Marine Science, Townsville, Qld, Australia.,AIMS@JCU, Townsville, Qld, Australia.,Australian Centre for Ecogenomics, University of Queensland, Brisbane, Qld, Australia
| | - Guojie Zhang
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, China.,Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark.,State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| | - David G Bourne
- College of Science and Engineering, James Cook University, Townsville, Qld, Australia.,Australian Institute of Marine Science, Townsville, Qld, Australia.,AIMS@JCU, Townsville, Qld, Australia
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23
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Metagenomes, Metatranscriptomes, and Metagenome-Assembled Genomes from Chesapeake and Delaware Bay (USA) Water Samples. Microbiol Resour Announc 2021; 10:e0026221. [PMID: 34042480 PMCID: PMC8201625 DOI: 10.1128/mra.00262-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Here, we present 36 metagenomes, 59 metatranscriptomes, and 373 metagenome-assembled genomes (MAGs) from Chesapeake and Delaware Bay water samples. This data set will be useful for studying microbial biogeochemical cycling in estuaries.
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24
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Lim SJ, Davis B, Gill D, Swetenburg J, Anderson LC, Engel AS, Campbell BJ. Gill microbiome structure and function in the chemosymbiotic coastal lucinid Stewartia floridana. FEMS Microbiol Ecol 2021; 97:6168404. [PMID: 33705534 DOI: 10.1093/femsec/fiab042] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 03/09/2021] [Indexed: 11/14/2022] Open
Abstract
Lucinid bivalves harbor environmentally acquired, chemosynthetic, gammaproteobacterial gill endosymbionts. Lucinid gill microbiomes, which may contain other gammaproteobacterial and/or spirochete taxa, remain under-sampled. To understand inter-host variability of the lucinid gill microbiome, specifically in the bacterial communities, we analyzed the microbiome content of Stewartia floridana collected from Florida. Sampled gills contained a monospecific gammaproteobacterial endosymbiont expressing lithoautotrophic, mixotrophic, diazotrophic and C1 compound oxidation-related functions previously characterized in similar lucinid species. Another low-abundance Spirochaeta-like species in ∼72% of the sampled gills was most closely related to Spirochaeta-like species in another lucinid Phacoides pectinatus and formed a clade with known marine Spirochaeta symbionts. The spirochete expressed genes were involved in heterotrophy and the transport of sugars, amino acids, peptides and other substrates. Few muscular and neurofilament genes from the host and none from the gammaproteobacterial and spirochete symbionts were differentially expressed among quadrats predominantly covered with seagrass species or 80% bare sand. Our results suggest that spirochetes are facultatively associated with S. floridana, with potential scavenging and nutrient cycling roles. Expressed stress- and defense-related functions in the host and symbionts also suggest species-species communications, which highlight the need for further study of the interactions among lucinid hosts, their microbiomes and their environment.
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Affiliation(s)
- Shen Jean Lim
- Department of Biological Sciences, Clemson University, Clemson, SC 29634, USA
| | - Brenton Davis
- Department of Biological Sciences, Clemson University, Clemson, SC 29634, USA
| | - Danielle Gill
- Department of Biological Sciences, Clemson University, Clemson, SC 29634, USA
| | - John Swetenburg
- Department of Biological Sciences, Clemson University, Clemson, SC 29634, USA
| | - Laurie C Anderson
- Department of Geology and Geological Engineering, South Dakota School of Mines & Technology, Rapid City, SD 57701, USA
| | - Annette Summers Engel
- Department of Earth and Planetary Sciences, University of Tennessee Knoxville, Knoxville, TN 37920, USA
| | - Barbara J Campbell
- Department of Biological Sciences, Clemson University, Clemson, SC 29634, USA
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25
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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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26
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Cutting out the middle clam: lucinid endosymbiotic bacteria are also associated with seagrass roots worldwide. ISME JOURNAL 2020; 14:2901-2905. [PMID: 32929207 DOI: 10.1038/s41396-020-00771-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Revised: 08/18/2020] [Accepted: 09/02/2020] [Indexed: 11/09/2022]
Abstract
Seagrasses and lucinid bivalves inhabit highly reduced sediments with elevated sulphide concentrations. Lucinids house symbiotic bacteria (Ca. Thiodiazotropha) capable of oxidising sediment sulphide, and their presence in sediments has been proposed to promote seagrass growth by decreasing otherwise phytotoxic sulphide levels. However, vast and productive seagrass meadows are present in ecosystems where lucinids do not occur. Hence, we hypothesised that seagrasses themselves host these sulphur-oxidising Ca. Thiodiazotropha that could aid their survival when lucinids are absent. We analysed newly generated and publicly available 16S rRNA gene sequences from seagrass roots and sediments across 14 seagrass species and 10 countries and found that persistent and colonising seagrasses across the world harbour sulphur-oxidising Ca. Thiodiazotropha, regardless of the presence of lucinids. We used fluorescence in situ hybridisation to visually confirm the presence of Ca. Thiodiazotropha on roots of Halophila ovalis, a colonising seagrass species with wide geographical, water depth range, and sedimentary sulphide concentrations. We provide the first evidence that Ca. Thiodiazotropha are commonly present on seagrass roots, providing another mechanism for seagrasses to alleviate sulphide stress globally.
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27
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Mizutani Y, Mori T, Miyazaki T, Fukuzaki S, Tanaka R. Microbial community analysis in the gills of abalones suggested possible dominance of epsilonproteobacterium in Haliotis gigantea. PeerJ 2020; 8:e9326. [PMID: 32655989 PMCID: PMC7333650 DOI: 10.7717/peerj.9326] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Accepted: 05/18/2020] [Indexed: 02/01/2023] Open
Abstract
Gills are important organs for aquatic invertebrates because they harbor chemosynthetic bacteria, which fix inorganic carbon and/or nitrogen and provide their hosts with organic compounds. Nevertheless, in contrast to the intensive researches related to the gut microbiota, much is still needed to further understand the microbiota within the gills of invertebrates. Using abalones as a model, we investigated the community structure of microbes associated with the gills of these invertebrates using next-generation sequencing. Molecular identification of representative bacterial sequences was performed using cloning, nested PCR and fluorescence in situ hybridization (FISH) analysis with specific primers or probes. We examined three abalone species, namely Haliotis gigantea, H. discus and H. diversicolor using seawater and stones as controls. Microbiome analysis suggested that the gills of all three abalones had the unclassified Spirochaetaceae (one OTU, 15.7 ± 0.04%) and Mycoplasma sp. (one OTU, 9.1 ± 0.03%) as the core microbes. In most libraries from the gills of H. gigantea, however, a previously unknown epsilonproteobacterium species (one OTU) was considered as the dominant bacterium, which accounted for 62.2% of the relative abundance. The epsilonproteobacterium was only detected in the gills of H. diversicolor at 0.2% and not in H. discus suggesting that it may be unique to H. gigantea. Phylogenetic analysis performed using a near full-length 16S rRNA gene placed the uncultured epsilonproteobacterium species at the root of the family Helicobacteraceae. Interestingly, the uncultured epsilonproteobacterium was commonly detected from gill tissue rather than from the gut and foot tissues using a nested PCR assay with uncultured epsilonproteobacterium-specific primers. FISH analysis with the uncultured epsilonproteobacterium-specific probe revealed that probe-reactive cells in H. gigantea had a coccus-like morphology and formed microcolonies on gill tissue. This is the first report to show that epsilonproteobacterium has the potential to be a dominant species in the gills of the coastal gastropod, H. gigantea.
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Affiliation(s)
- Yukino Mizutani
- Graduate School of Bioresources, Mie University, Tsu, Mie, Japan
| | - Tetsushi Mori
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Koganei, Tokyo, Japan
| | - Taeko Miyazaki
- Graduate School of Bioresources, Mie University, Tsu, Mie, Japan
| | - Satoshi Fukuzaki
- Graduate School of Bioresources, Mie University, Tsu, Mie, Japan
| | - Reiji Tanaka
- Graduate School of Bioresources, Mie University, Tsu, Mie, Japan
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28
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Yuen B, Polzin J, Petersen JM. Organ transcriptomes of the lucinid clam Loripes orbiculatus (Poli, 1791) provide insights into their specialised roles in the biology of a chemosymbiotic bivalve. BMC Genomics 2019; 20:820. [PMID: 31699041 PMCID: PMC6836662 DOI: 10.1186/s12864-019-6177-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 10/03/2019] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND The lucinid clam Loripes orbiculatus lives in a nutritional symbiosis with sulphur-oxidizing bacteria housed in its gills. Although our understanding of the lucinid endosymbiont physiology and metabolism has made significant progress, relatively little is known about how the host regulates the symbiosis at the genetic and molecular levels. We generated transcriptomes from four L. orbiculatus organs (gills, foot, visceral mass, and mantle) for differential expression analyses, to better understand this clam's physiological adaptations to a chemosymbiotic lifestyle, and how it regulates nutritional and immune interactions with its symbionts. RESULTS The transcriptome profile of the symbiont-housing gill suggests the regulation of apoptosis and innate immunity are important processes in this organ. We also identified many transcripts encoding ion transporters from the solute carrier family that possibly allow metabolite exchange between host and symbiont. Despite the clam holobiont's clear reliance on chemosynthesis, the clam's visceral mass, which contains the digestive tract, is characterised by enzymes involved in digestion, carbohydrate recognition and metabolism, suggesting that L. orbiculatus has a mixotrophic diet. The foot transcriptome is dominated by the biosynthesis of glycoproteins for the construction of mucus tubes, and receptors that mediate the detection of chemical cues in the environment. CONCLUSIONS The transcriptome profiles of gills, mantle, foot and visceral mass provide insights into the molecular basis underlying the functional specialisation of bivalve organs adapted to a chemosymbiotic lifestyle.
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Affiliation(s)
- Benedict Yuen
- Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria.
| | - Julia Polzin
- Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
| | - Jillian M Petersen
- Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
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29
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Extensive Thioautotrophic Gill Endosymbiont Diversity within a Single Ctena orbiculata (Bivalvia: Lucinidae) Population and Implications for Defining Host-Symbiont Specificity and Species Recognition. mSystems 2019; 4:4/4/e00280-19. [PMID: 31455638 PMCID: PMC6712303 DOI: 10.1128/msystems.00280-19] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Seagrass-dwelling members of the bivalve family Lucinidae harbor environmentally acquired gill endosymbionts. According to previous studies, lucinid symbionts potentially represent multiple strains from a single thioautotrophic gammaproteobacterium species. This study utilized genomic- and transcriptomic-level data to resolve symbiont taxonomic, genetic, and functional diversity from Ctena orbiculata endosymbiont populations inhabiting carbonate-rich sediment at Sugarloaf Key, FL (USA). The sediment had mixed seagrass and calcareous green alga coverage and also was colonized by at least five other lucinid species. Four coexisting, thioautotrophic endosymbiont operational taxonomic units (OTUs), likely representing four strains from two different bacterial species, were identified from C. orbiculata Three of these OTUs also occurred at high relative abundances in the other sympatric lucinid species. Interspecies genetic differences averaged about 5% lower at both pairwise average nucleotide identity and amino acid identity than interstrain differences. Despite these genetic differences, C. orbiculata endosymbionts shared a high number of metabolic functions, including highly expressed thioautotrophy-related genes and a moderately to weakly expressed conserved one-carbon (C1) oxidation gene cluster previously undescribed in lucinid symbionts. Few symbiont- and host-related genes, including those encoding symbiotic sulfurtransferase, host respiratory functions, and host sulfide oxidation functions, were differentially expressed between seagrass- and alga-covered sediment locations. In contrast to previous studies, the identification of multiple endosymbiont taxa within and across C. orbiculata individuals, which were also shared with other sympatric lucinid species, suggests that neither host nor endosymbiont displays strict taxonomic specificity. This necessitates further investigations into the nature and extent of specificity of lucinid hosts and their symbionts.IMPORTANCE Symbiont diversity and host/symbiont functions have been comprehensively profiled for only a few lucinid species. In this work, unprecedented thioautotrophic gill endosymbiont taxonomic diversity was characterized within a Ctena orbiculata population associated with both seagrass- and alga-covered sediments. Endosymbiont metabolisms included known chemosynthetic functions and an additional conserved, previously uncharacterized C1 oxidation pathway. Lucinid-symbiont associations were not species specific because this C. orbiculata population hosted multiple endosymbiont strains and species, and other sympatric lucinid species shared overlapping symbiont 16S rRNA gene diversity profiles with C. orbiculata Our results suggest that lucinid-symbiont association patterns within some host species could be more taxonomically diverse than previously thought. As such, this study highlights the importance of holistic analyses, at the population, community, and even ecosystem levels, in understanding host-microbe association patterns.
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