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Morris RM, Mino S. The complete genome sequences of Thioglobus autotrophicus strains EF2 and EF3, isolated from an oxycline in Effingham Inlet, British Columbia. Microbiol Resour Announc 2024; 13:e0111823. [PMID: 38334403 DOI: 10.1128/mra.01118-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 01/23/2024] [Indexed: 02/10/2024] Open
Abstract
Here we provide the complete genome sequences of two chemoautotrophic isolates from the Thioglobaceae family of marine gamma-proteobacteria. The genomes were obtained from pure cultures that were initially isolated from Effingham Inlet in 2013 and revived from freezer stocks for whole genome sequencing in 2023.
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Affiliation(s)
- Robert M Morris
- School of Oceanography, University of Washington, Seattle, Washington, USA
| | - Sayaka Mino
- School of Oceanography, University of Washington, Seattle, Washington, USA
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University, Minato-cho, Hakodate, Japan
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2
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Celussi M, Manna V, Banchi E, Fonti V, Bazzaro M, Flander-Putrle V, Klun K, Kralj M, Orel N, Tinta T. Annual recurrence of prokaryotic climax communities in shallow waters of the North Mediterranean. Environ Microbiol 2024; 26:e16595. [PMID: 38418391 DOI: 10.1111/1462-2920.16595] [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: 09/11/2023] [Accepted: 02/02/2024] [Indexed: 03/01/2024]
Abstract
In temperate coastal environments, wide fluctuations of biotic and abiotic factors drive microbiome dynamics. To link recurrent ecological patterns with planktonic microbial communities, we analysed a monthly-sampled 3-year time series of 16S rRNA amplicon sequencing data, alongside environmental variables, collected at two stations in the northern Adriatic Sea. Time series multivariate analyses allowed us to identify three stable, mature communities (climaxes), whose recurrence was mainly driven by changes in photoperiod and temperature. Mixotrophs (e.g., Ca. Nitrosopumilus, SUP05 clade, and Marine Group II) thrived under oligotrophic, low-light conditions, whereas copiotrophs (e.g., NS4 and NS5 clades) bloomed at higher temperatures and substrate availability. The early spring climax was characterised by a more diverse set of amplicon sequence variants, including copiotrophs associated with phytoplankton-derived organic matter degradation, and photo-auto/heterotrophic organisms (e.g., Synechococcus sp., Roseobacter clade), whose rhythmicity was linked to photoperiod lengthening. Through the identification of recurrent climax assemblages, we begin to delineate a typology of ecosystem based on microbiome composition and functionality, allowing for the intercomparison of microbial assemblages among different biomes, a still underachieved goal in the omics era.
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Affiliation(s)
- Mauro Celussi
- National Institute of Oceanography and Applied Geophysics-OGS, Trieste, Italy
- NBFC, National Biodiversity Future Center, Palermo, Italy
| | - Vincenzo Manna
- National Institute of Oceanography and Applied Geophysics-OGS, Trieste, Italy
- NBFC, National Biodiversity Future Center, Palermo, Italy
| | - Elisa Banchi
- National Institute of Oceanography and Applied Geophysics-OGS, Trieste, Italy
- NBFC, National Biodiversity Future Center, Palermo, Italy
| | - Viviana Fonti
- National Institute of Oceanography and Applied Geophysics-OGS, Trieste, Italy
| | - Matteo Bazzaro
- National Institute of Oceanography and Applied Geophysics-OGS, Trieste, Italy
| | | | - Katja Klun
- Marine Biology Station Piran, National Institute of Biology, Piran, Slovenia
| | - Martina Kralj
- National Institute of Oceanography and Applied Geophysics-OGS, Trieste, Italy
| | - Neža Orel
- Marine Biology Station Piran, National Institute of Biology, Piran, Slovenia
| | - Tinkara Tinta
- Marine Biology Station Piran, National Institute of Biology, Piran, Slovenia
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Ricci F, Greening C. Chemosynthesis: a neglected foundation of marine ecology and biogeochemistry. Trends Microbiol 2024:S0966-842X(23)00332-3. [PMID: 38296716 DOI: 10.1016/j.tim.2023.11.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 11/06/2023] [Accepted: 11/28/2023] [Indexed: 02/02/2024]
Abstract
Chemosynthesis is a metabolic process that transfers carbon to the biosphere using reduced compounds. It is well recognised that chemosynthesis occurs in much of the ocean, but it is often thought to be a negligible process compared to photosynthesis. Here we propose that chemosynthesis is the underlying process governing primary production in much of the ocean and suggest that it extends to a much wider range of compounds, microorganisms, and ecosystems than previously thought. In turn, this process has had a central role in controlling marine biogeochemistry, ecology, and carbon budgets across the vast realms of the ocean, from the dawn of life to contemporary times.
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Affiliation(s)
- Francesco Ricci
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; Securing Antarctica's Environmental Future, Monash University, Clayton, VIC 3800, Australia.
| | - Chris Greening
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; Securing Antarctica's Environmental Future, Monash University, Clayton, VIC 3800, Australia; Centre to Impact AMR, Monash University, Melbourne, Victoria, Australia.
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4
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Namsaraev Z, Kozlova A, Tuzov F, Krylova A, Izotova A, Makarov I, Bezgreshnov A, Melnikova A, Trofimova A, Kuzmin D, Patrushev M, Toshchakov S. Biogeographic Analysis Suggests Two Types of Planktonic Prokaryote Communities in the Barents Sea. BIOLOGY 2023; 12:1310. [PMID: 37887020 PMCID: PMC10604488 DOI: 10.3390/biology12101310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 09/22/2023] [Accepted: 09/22/2023] [Indexed: 10/28/2023]
Abstract
The Barents Sea is one of the most rapidly changing Arctic regions, with an unprecedented sea ice decline and increase in water temperature and salinity. We have studied the diversity of prokaryotic communities using 16S metabarcoding in the western and northeastern parts of the Barents Sea along the Kola Section and the section from Novaya Zemlya to Franz Joseph Land. The hypothesis-independent clustering method revealed the existence of two distinct types of communities. The most common prokaryotic taxa were shared between two types of communities, but their relative abundance was different. It was found that the geographic location of the sampling sites explained more than 30% of the difference between communities, while no statistically significant correlation between environmental parameters and community composition was found. The representatives of the Psychrobacter, Sulfitobacter and Polaribacter genera were dominant in samples from both types of communities. The first type of community was also dominated by members of Halomonas, Pseudoalteromonas, Planococcaceae and an unclassified representative of the Alteromonadaceae family. The second type of community also had a significant proportion of Nitrincolaceae, SAR92, SAR11 Clade I, NS9, Cryomorphaceae and SUP05 representatives. The origin of these communities can be explained by the influence of environmental factors or by the different origins of water masses. This research highlights the importance of studying biogeographic patterns in the Barents Sea in comparison with those in the North Atlantic and Arctic Ocean prokaryote communities.
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Affiliation(s)
- Zorigto Namsaraev
- Kurchatov Centre for Genome Research, National Research Centre “Kurchatov Institute”, 123182 Moscow, Russia
- Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia
| | - Aleksandra Kozlova
- Kurchatov Centre for Genome Research, National Research Centre “Kurchatov Institute”, 123182 Moscow, Russia
| | - Fedor Tuzov
- Department of Oceanology, Faculty of Geography, Lomonosov Moscow State University, 119991 Moscow, Russia
- All-Russian Research Institute for Civil Defense and Emergencies, 121352 Moscow, Russia
| | - Anastasia Krylova
- Kurchatov Centre for Genome Research, National Research Centre “Kurchatov Institute”, 123182 Moscow, Russia
| | - Anna Izotova
- Kurchatov Centre for Genome Research, National Research Centre “Kurchatov Institute”, 123182 Moscow, Russia
| | | | - Andrei Bezgreshnov
- Arctic and Antarctic Research Institute, 199397 Saint Petersburg, Russia
| | - Anna Melnikova
- Kurchatov Centre for Genome Research, National Research Centre “Kurchatov Institute”, 123182 Moscow, Russia
| | - Anna Trofimova
- Department of Geography and Hydrometeorology, Higher School of Natural Sciences and Technologies, Northern (Arctic) Federal University, 163002 Arkhangelsk, Russia
| | - Denis Kuzmin
- Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia
| | - Maksim Patrushev
- Kurchatov Centre for Genome Research, National Research Centre “Kurchatov Institute”, 123182 Moscow, Russia
| | - Stepan Toshchakov
- Kurchatov Centre for Genome Research, National Research Centre “Kurchatov Institute”, 123182 Moscow, Russia
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Barosa B, Ferrillo A, Selci M, Giardina M, Bastianoni A, Correggia M, di Iorio L, Bernardi G, Cascone M, Capuozzo R, Intoccia M, Price R, Vetriani C, Cordone A, Giovannelli D. Mapping the microbial diversity associated with different geochemical regimes in the shallow-water hydrothermal vents of the Aeolian archipelago, Italy. Front Microbiol 2023; 14:1134114. [PMID: 37637107 PMCID: PMC10452888 DOI: 10.3389/fmicb.2023.1134114] [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: 12/29/2022] [Accepted: 07/25/2023] [Indexed: 08/29/2023] Open
Abstract
Shallow-water hydrothermal vents are unique marine environments ubiquitous along the coast of volcanically active regions of the planet. In contrast to their deep-sea counterparts, primary production at shallow-water vents relies on both photoautotrophy and chemoautotrophy. Such processes are supported by a range of geochemical regimes driven by different geological settings. The Aeolian archipelago, located in the southern Tyrrhenian sea, is characterized by intense hydrothermal activity and harbors some of the best sampled shallow-water vents of the Mediterranean Sea. Despite this, the correlation between microbial diversity, geochemical regimes and geological settings of the different volcanic islands of the archipelago is largely unknown. Here, we report the microbial diversity associated with six distinct shallow-water hydrothermal vents of the Aeolian Islands using a combination of 16S rRNA amplicon sequencing along with physicochemical and geochemical measurements. Samples were collected from biofilms, fluids and sediments from shallow vents on the islands of Lipari, Panarea, Salina, and Vulcano. Two new shallow vent locations are described here for the first time. Our results show the presence of diverse microbial communities consistent in their composition with the local geochemical regimes. The shallow water vents of the Aeolian Islands harbor highly diverse microbial community and should be included in future conservation efforts.
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Affiliation(s)
- Bernardo Barosa
- Department of Biology, University of Naples “Federico II”, Naples, Italy
| | | | - Matteo Selci
- Department of Biology, University of Naples “Federico II”, Naples, Italy
| | - Marco Giardina
- Department of Biology, University of Naples “Federico II”, Naples, Italy
| | - Alessia Bastianoni
- Department of Biology, University of Naples “Federico II”, Naples, Italy
| | - Monica Correggia
- Department of Biology, University of Naples “Federico II”, Naples, Italy
| | - Luciano di Iorio
- Department of Biology, University of Naples “Federico II”, Naples, Italy
| | | | - Martina Cascone
- Department of Biology, University of Naples “Federico II”, Naples, Italy
| | - Rosaria Capuozzo
- Department of Biology, University of Naples “Federico II”, Naples, Italy
| | - Michele Intoccia
- Department of Biology, University of Naples “Federico II”, Naples, Italy
| | - Roy Price
- School of Marine and Atmospheric Sciences, Stony Brook, NY, United States
| | - Costantino Vetriani
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, United States
- Department of Marine and Coastal Science, Rutgers University, New Brunswick, NJ, United States
| | - Angelina Cordone
- Department of Biology, University of Naples “Federico II”, Naples, Italy
| | - Donato Giovannelli
- Department of Biology, University of Naples “Federico II”, Naples, Italy
- Department of Marine and Coastal Science, Rutgers University, New Brunswick, NJ, United States
- Istituto per le Risorse Biologiche e Biotecnologiche Marine, Consiglio Nazionale Delle Ricerche, CNR-IRBIM, Ancona, Italy
- Earth-Life Science Institute, Tokyo Institute of Technology, Ookayama, Tokyo, Japan
- Marine Chemistry and Geochemistry Department–Woods Hole Oceanographic Institution, Woods Hole, MA, United States
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Structure-Function Covariation of Phycospheric Microorganisms Associated with the Typical Cross-Regional Harmful Macroalgal Bloom. Appl Environ Microbiol 2023; 89:e0181522. [PMID: 36533927 PMCID: PMC9888261 DOI: 10.1128/aem.01815-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Unravelling the structure-function variation of phycospheric microorganisms and its ecological correlation with harmful macroalgal blooms (HMBs) is a challenging research topic that remains unclear in the natural dynamic process of HMBs. During the world's largest green tide bloom, causative macroalgae Ulva prolifera experienced dramatic changes in growth state and environmental conditions, providing ideal scenarios for this investment. Here, we assess the phycospheric physicochemical characteristics, the algal host's biology, the phycospheric bacterial constitutive patterns, and the functional potential during the U. prolifera green tide. Our results indicated that (i) variation in the phycosphere nutrient structure was closely related to the growth state of U. prolifera; (ii) stochastic processes govern phycospheric bacterial assembly, and the contribution of deterministic processes to assembly varied among phycospheric seawater bacteria and epiphytic bacteria; (iii) phycospheric seawater bacteria and epiphytic bacteria exhibited significant heterogeneity variation patterns in community composition, structure, and metabolic potential; and (iv) phycospheric bacteria with carbon or nitrogen metabolic functions potentially influenced the nutrient utilization of U. prolifera. Furthermore, the keystone genera play a decisive role in the structure-function covariation of phycospheric bacterial communities. Our study reveals complex interactions and linkages among environment-algae-bacterial communities which existed in the macroalgal phycosphere and highlights the fact that phycospheric microorganisms are closely related to the fate of the HMBs represented by the green tide. IMPORTANCE Harmful macroalgal blooms represented by green tides have become a worldwide marine ecological problem. Unraveling the structure-function variation of phycospheric microorganisms and their ecological correlation with HMBs is challenging. This issue is still unclear in the natural dynamics of HMBs. Here, we revealed the complex interactions and linkages among environment-algae-bacterial communities in the phycosphere of the green macroalgae Ulva prolifera, which causes the world's largest green tides. Our study provides new ideas to increase our understanding of the variation patterns of macroalgal phycospheric bacterial communities and the formation mechanisms and ecological effects of green tides and highlights the importance of phycospheric microorganisms as a robust tool to help understand the fate of HMBs.
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Osman EO, Vohsen SA, Girard F, Cruz R, Glickman O, Bullock LM, Anderson KE, Weinnig AM, Cordes EE, Fisher CR, Baums IB. Capacity of deep-sea corals to obtain nutrition from cold seeps aligned with microbiome reorganization. GLOBAL CHANGE BIOLOGY 2023; 29:189-205. [PMID: 36271605 PMCID: PMC10092215 DOI: 10.1111/gcb.16447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Revised: 09/08/2022] [Accepted: 09/16/2022] [Indexed: 06/16/2023]
Abstract
Cold seeps in the deep sea harbor various animals that have adapted to utilize seepage chemicals with the aid of chemosynthetic microbes that serve as primary producers. Corals are among the animals that live near seep habitats and yet, there is a lack of evidence that corals gain benefits and/or incur costs from cold seeps. Here, we focused on Callogorgia delta and Paramuricea sp. type B3 that live near and far from visual signs of currently active seepage at five sites in the deep Gulf of Mexico. We tested whether these corals rely on chemosynthetically-derived food in seep habitats and how the proximity to cold seeps may influence; (i) coral colony traits (i.e., health status, growth rate, regrowth after sampling, and branch loss) and associated epifauna, (ii) associated microbiome, and (iii) host transcriptomes. Stable isotope data showed that many coral colonies utilized chemosynthetically derived food, but the feeding strategy differed by coral species. The microbiome composition of C. delta, unlike Paramuricea sp., varied significantly between seep and non-seep colonies and both coral species were associated with various sulfur-oxidizing bacteria (SUP05). Interestingly, the relative abundances of SUP05 varied among seep and non-seep colonies and were strongly correlated with carbon and nitrogen stable isotope values. In contrast, the proximity to cold seeps did not have a measurable effect on gene expression, colony traits, or associated epifauna in coral species. Our work provides the first evidence that some corals may gain benefits from living near cold seeps with apparently limited costs to the colonies. Cold seeps provide not only hard substrate but also food to cold-water corals. Furthermore, restructuring of the microbiome communities (particularly SUP05) is likely the key adaptive process to aid corals in utilizing seepage-derived carbon. This highlights that those deep-sea corals may upregulate particular microbial symbiont communities to cope with environmental gradients.
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Affiliation(s)
- Eslam O. Osman
- Department of BiologyThe Pennsylvania State UniversityState CollegePennsylvaniaUSA
- Marine Biology LabZoology Department, Faculty of ScienceAl‐Azhar UniversityCairoEgypt
- Red Sea Research Center (RSRC)King Abdullah University of Science and Technology (KAUST)ThuwalSaudi Arabia
| | - Samuel A. Vohsen
- Department of BiologyThe Pennsylvania State UniversityState CollegePennsylvaniaUSA
| | - Fanny Girard
- Department of BiologyThe Pennsylvania State UniversityState CollegePennsylvaniaUSA
- Monterey Bay Aquarium Research InstituteMoss LandingCAUSA
| | - Rafaelina Cruz
- Department of BiologyThe Pennsylvania State UniversityState CollegePennsylvaniaUSA
| | - Orli Glickman
- Department of BiologyThe Pennsylvania State UniversityState CollegePennsylvaniaUSA
| | - Lena M. Bullock
- Department of BiologyThe Pennsylvania State UniversityState CollegePennsylvaniaUSA
| | - Kaitlin E. Anderson
- Department of BiologyThe Pennsylvania State UniversityState CollegePennsylvaniaUSA
| | | | | | - Charles R. Fisher
- Department of BiologyThe Pennsylvania State UniversityState CollegePennsylvaniaUSA
| | - Iliana B. Baums
- Department of BiologyThe Pennsylvania State UniversityState CollegePennsylvaniaUSA
- Helmholtz Institute for Functional Marine Biodiversity (HIFMB)AmmerländerHeerstraße 231, 26129 OldenburgGermany
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He Y, Zeng X, Xu F, Shao Z. Diversity of Mixotrophic Neutrophilic Thiosulfate- and Iron-Oxidizing Bacteria from Deep-Sea Hydrothermal Vents. Microorganisms 2022; 11:microorganisms11010100. [PMID: 36677390 PMCID: PMC9861301 DOI: 10.3390/microorganisms11010100] [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: 11/11/2022] [Revised: 12/22/2022] [Accepted: 12/22/2022] [Indexed: 01/04/2023] Open
Abstract
At deep-sea hydrothermal vents, sulfur oxidation and iron oxidation are of the highest importance to microbial metabolisms, which are thought to contribute mainly in chemolithoautotrophic groups. In this study, 17 mixotrophic neutrophilic thiosulfate- and iron-oxidizing bacteria were isolated from hydrothermal fields on the Carlsberg Ridge in the Indian Ocean, nine to the γ-proteobacteria (Halomonas (4), Pseudomonas (2), Marinobacter (2), and Rheinheimera (1)), seven to the α-proteobacteria (Thalassospira, Qipengyuania, Salipiger, Seohaeicola, Martelella, Citromicrobium, and Aurantimonas), and one to the Actinobacteria (Agromyces), as determined by their 16S rRNA and genome sequences. The physiological characterization of these isolates revealed wide versatility in electron donors (Fe(II) and Mn(II), or thiosulfate) and a variety of lifestyles as lithotrophic or heterotrophic, microaerobic, or anaerobic. As a representative strain, Pseudomonas sp. IOP_13 showed its autotrophic gowth from 105 cells/ml to 107 cells/ml;carbon dioxide fixation capacity with the δ13CVPDB in the biomass increased from -27.42‱ to 3460.06‱; the thiosulfate-oxidizing ability with produced SO42- increased from 60 mg/L to 287 mg/L; and the iron-oxidizing ability with Fe(II) decreased from 10 mM to 5.2 mM. In addition, iron-oxide crust formed outside the cells. Gene coding for energy metabolism involved in possible iron, manganese, and sulfur oxidation, and denitrification was identified by their genome analysis. This study sheds light on the function of the mixotrophic microbial community in the iron/manganese/sulfur cycles and the carbon fixation of the hydrothermal fields.
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Keller-Costa T, Kozma L, Silva SG, Toscan R, Gonçalves J, Lago-Lestón A, Kyrpides NC, Nunes da Rocha U, Costa R. Metagenomics-resolved genomics provides novel insights into chitin turnover, metabolic specialization, and niche partitioning in the octocoral microbiome. MICROBIOME 2022; 10:151. [PMID: 36138466 PMCID: PMC9502895 DOI: 10.1186/s40168-022-01343-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 08/03/2022] [Indexed: 05/31/2023]
Abstract
BACKGROUND The role of bacterial symbionts that populate octocorals (Cnidaria, Octocorallia) is still poorly understood. To shed light on their metabolic capacities, we examined 66 high-quality metagenome-assembled genomes (MAGs) spanning 30 prokaryotic species, retrieved from microbial metagenomes of three octocoral species and seawater. RESULTS Symbionts of healthy octocorals were affiliated with the taxa Endozoicomonadaceae, Candidatus Thioglobaceae, Metamycoplasmataceae, unclassified Pseudomonadales, Rhodobacteraceae, unclassified Alphaproteobacteria and Ca. Rhabdochlamydiaceae. Phylogenomics inference revealed that the Endozoicomonadaceae symbionts uncovered here represent two species of a novel genus unique to temperate octocorals, here denoted Ca. Gorgonimonas eunicellae and Ca. Gorgonimonas leptogorgiae. Their genomes revealed metabolic capacities to thrive under suboxic conditions and high gene copy numbers of serine-threonine protein kinases, type 3-secretion system, type-4 pili, and ankyrin-repeat proteins, suggesting excellent capabilities to colonize, aggregate, and persist inside their host. Contrarily, MAGs obtained from seawater frequently lacked symbiosis-related genes. All Endozoicomonadaceae symbionts harbored endo-chitinase and chitin-binging protein-encoding genes, indicating that they can hydrolyze the most abundant polysaccharide in the oceans. Other symbionts, including Metamycoplasmataceae and Ca. Thioglobaceae, may assimilate the smaller chitin oligosaccharides resulting from chitin breakdown and engage in chitin deacetylation, respectively, suggesting possibilities for substrate cross-feeding and a role for the coral microbiome in overall chitin turnover. We also observed sharp differences in secondary metabolite production potential between symbiotic lineages. Specific Proteobacteria taxa may specialize in chemical defense and guard other symbionts, including Endozoicomonadaceae, which lack such capacity. CONCLUSION This is the first study to recover MAGs from dominant symbionts of octocorals, including those of so-far unculturable Endozoicomonadaceae, Ca. Thioglobaceae and Metamycoplasmataceae symbionts. We identify a thus-far unanticipated, global role for Endozoicomonadaceae symbionts of corals in the processing of chitin, the most abundant natural polysaccharide in the oceans and major component of the natural zoo- and phytoplankton feed of octocorals. We conclude that niche partitioning, metabolic specialization, and adaptation to low oxygen conditions among prokaryotic symbionts likely contribute to the plasticity and adaptability of the octocoral holobiont in changing marine environments. These findings bear implications not only for our understanding of symbiotic relationships in the marine realm but also for the functioning of benthic ecosystems at large. Video Abstract.
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Affiliation(s)
- Tina Keller-Costa
- Institute for Bioengineering and Biosciences, Instituto Superior Técnico, University of Lisbon, Lisbon, Portugal
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, Instituto Superior Técnico, University of Lisbon, Lisbon, Portugal
| | - Lydia Kozma
- Institute for Bioengineering and Biosciences, Instituto Superior Técnico, University of Lisbon, Lisbon, Portugal
- École Polytechnique Fédérale de Lausanne, Écublens, Switzerland
| | - Sandra G. Silva
- Institute for Bioengineering and Biosciences, Instituto Superior Técnico, University of Lisbon, Lisbon, Portugal
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, Instituto Superior Técnico, University of Lisbon, Lisbon, Portugal
| | - Rodolfo Toscan
- Helmholtz Centre for Environmental Research, Leipzig, Germany
| | - Jorge Gonçalves
- Centro de Ciências Do Mar, Universidade Do Algarve, Faro, Portugal
| | - Asunción Lago-Lestón
- Centro de Investigación Científica Y de Educación Superior de Ensenada, Ensenada, Mexico
| | - Nikos C. Kyrpides
- Department of Energy, Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | | | - Rodrigo Costa
- Institute for Bioengineering and Biosciences, Instituto Superior Técnico, University of Lisbon, Lisbon, Portugal
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, Instituto Superior Técnico, University of Lisbon, Lisbon, Portugal
- Centro de Ciências Do Mar, Universidade Do Algarve, Faro, Portugal
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Duncan KT, Elshahed MS, Sundstrom KD, Little SE, Youssef NH. Influence of tick sex and geographic region on the microbiome of Dermacentor variabilis collected from dogs and cats across the United States. Ticks Tick Borne Dis 2022; 13:102002. [PMID: 35810549 DOI: 10.1016/j.ttbdis.2022.102002] [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: 03/14/2022] [Revised: 06/28/2022] [Accepted: 07/02/2022] [Indexed: 11/18/2022]
Abstract
As tick-borne diseases continue to increase across North America, current research strives to understand how the tick microbiome may affect pathogen acquisition, maintenance, and transmission. Prior high throughput amplicon-based microbial diversity surveys of the widespread tick Dermacentor variabilis have suggested that life stage, sex, and geographic region may influence the composition of the tick microbiome. Here, adult D. variabilis ticks (n = 145) were collected from dogs and cats from 32 states with specimens originating from all four regions of the United States (West, Midwest, South, and Northeast), and the tick microbiome was examined via V4-16S rRNA gene amplification and Illumina sequencing. A total of 481,246 bacterial sequences were obtained (median 2924 per sample, range 399-11,990). Fifty genera represented the majority (>80%) of the sequences detected, with the genera Allofrancisella and Francisella being the most abundant. Further, 97%, 23%, and 5.5% of the ticks contained sequences belonging to Francisella spp., Rickettsia spp., and Coxiella spp., respectively. No Ehrlichia spp. or Anaplasma spp. were identified. Co-occurrence analysis, by way of correlation coefficients, between the top 50 most abundant genera demonstrated five strong positive and no strong negative correlation relationships. Geographic region had a consistent effect on species richness with ticks from the Northeast having a significantly greater level of richness. Alpha diversity patterns were dependent on tick sex, with males exhibiting higher levels of diversity, and geographical region, with higher level of diversity observed in ticks obtained from the Northeast, but not on tick host. Community structure, or beta diversity, of tick microbiome was impacted by tick sex and geographic location, with microbiomes of ticks from the western US exhibiting a distinct community structure when compared to those from the other three regions (Northeast, South, and Midwest). In total, LEfSe (Linear discriminant analysis Effect Size) identified 18 specific genera driving these observed patterns of diversity and community structure. Collectively, these findings highlight the differences in bacterial diversity of D. variabilis across the US and supports the interpretation that tick sex and geographic region affects microbiome composition across a broad sampling distribution.
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Affiliation(s)
- Kathryn T Duncan
- Department of Pathobiology, College of Veterinary Medicine, Oklahoma State University, Room 250 McElroy Hall, Stillwater, OK 74078, USA.
| | - Mostafa S Elshahed
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Kellee D Sundstrom
- Department of Pathobiology, College of Veterinary Medicine, Oklahoma State University, Room 250 McElroy Hall, Stillwater, OK 74078, USA
| | - Susan E Little
- Department of Pathobiology, College of Veterinary Medicine, Oklahoma State University, Room 250 McElroy Hall, Stillwater, OK 74078, USA
| | - Noha H Youssef
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
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Piontek J, Meeske C, Hassenrück C, Engel A, Jürgens K. Organic matter availability drives the spatial variation in the community composition and activity of Antarctic marine bacterioplankton. Environ Microbiol 2022; 24:4030-4048. [PMID: 35656758 DOI: 10.1111/1462-2920.16087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 05/27/2022] [Indexed: 11/30/2022]
Abstract
Carbon cycling by Antarctic microbial plankton is poorly understood but it plays a major role in CO2 sequestration in the Southern Ocean. We investigated the summer bacterioplankton community in the largely understudied Weddell Sea, applying Illumina amplicon sequencing, measurements of bacterial production and chemical analyses of organic matter. The results revealed that the patchy distribution of productive coastal polynyas and less productive, mostly ice-covered sites was the major driver of the spatial changes in the taxonomic composition and activity of bacterioplankton. Gradients in organic matter availability induced by phytoplankton blooms were reflected in the concentrations and composition of dissolved carbohydrates and proteins. Bacterial production at bloom stations was, on average, 2.7 times higher than at less productive sites. Abundant bloom-responsive lineages were predominately affiliated with ubiquitous marine taxa, including Polaribacter, Yoonia-Loktanella, Sulfitobacter, the SAR92 clade, and Ulvibacter, suggesting a widespread genetic potential for adaptation to sub-zero seawater temperatures. A co-occurrence network analysis showed that dominant taxa at stations with low phytoplankton productivity were highly connected, indicating beneficial interactions. Overall, our study demonstrates that heterotrophic bacterial communities along Weddell Sea ice shelves were primarily constrained by the availability of labile organic matter rather than low seawater temperature. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Judith Piontek
- Leibniz Institute for Baltic Sea Research Warnemünde, Germany
| | | | | | - Anja Engel
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Germany
| | - Klaus Jürgens
- Leibniz Institute for Baltic Sea Research Warnemünde, Germany
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