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1.
Int J Syst Evol Microbiol ; 70(10): 5488-5496, 2020 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-32886593

RESUMO

A novel Gram-stain-negative, non-motile, strictly aerobic, rod-shaped bacterium was isolated from deep-sea hydrothermal sulfide in the northwest Indian Ocean Ridge and designated as strain IOP_32T. Strain IOP_32T could grow at 4-40 °C (optimum, 37 °C), pH 5-9 (optimum, pH 7-8) and salinity of 0-12 % NaCl (w/v; optimum, 2-3 %). The 16S rRNA gene sequence of strain IOP_32T is most similar to Bizionia fulviae EM7T, Bizionia berychis RA3-3-1T, Bizionia paragorgiae KMM 6029T and Oceanihabitans sediminis S9_10T with 95.5-95.3 % similarity. The phylogenomic analysis indicated that strain IOP_32T forms a distinct lineage with Flaviramulus ichthyoenteri Th78T within the family Flavobacteriaceae. The average nucleotide identity, average amino acid identity and percentage of conserved protein values between strain IOP_32T and the type strains of close genera were 72.3-78.5 %, 67.4-76.9 % and 56.3-61.6 %, respectively. The major cellular fatty acid was anteiso-C15 : 0. The respiratory quinone was MK-6. The polar lipids were mainly composed of phosphatidylethanolamine, an unidentified aminophospholipid and five unidentified polar lipids. Strain IOP_32T is significantly different from related genera, which is reflected by the wide adaptability to temperature and salinity levels, the composition of phospholipids and fatty acids, and the results of phylogenetic analyses. The phenotypic properties and phylogenetic data suggest that the lineage represents a novel genus and species within the family Flavobacteriaceae, for which the name Wocania indica gen. sp. nov. is proposed, with the type strain IOP_32T (=MCCC 1A14017 T=KCTC 62660 T). We also propose the reclassification of Flaviramulus ichthyoenteri as Wocania ichthyoenteri comb. nov. (Th78T=DSM 26285T=JCM 18634T=KCTC 32142T).


Assuntos
Flavobacteriaceae/classificação , Fontes Hidrotermais/microbiologia , Filogenia , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Flavobacteriaceae/isolamento & purificação , Oceano Índico , Fosfolipídeos/química , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Vitamina K 2/análogos & derivados , Vitamina K 2/química
2.
Proc Natl Acad Sci U S A ; 117(34): 20453-20461, 2020 08 25.
Artigo em Inglês | MEDLINE | ID: mdl-32817473

RESUMO

Subseafloor mixing of high-temperature hot-spring fluids with cold seawater creates intermediate-temperature diffuse fluids that are replete with potential chemical energy. This energy can be harnessed by a chemosynthetic biosphere that permeates hydrothermal regions on Earth. Shifts in the abundance of redox-reactive species in diffuse fluids are often interpreted to reflect the direct influence of subseafloor microbial activity on fluid geochemical budgets. Here, we examine hydrothermal fluids venting at 44 to 149 °C at the Piccard hydrothermal field that span the canonical 122 °C limit to life, and thus provide a rare opportunity to study the transition between habitable and uninhabitable environments. In contrast with previous studies, we show that hydrocarbons are contributed by biomass pyrolysis, while abiotic sulfate (SO4 2-) reduction produces large depletions in H2 The latter process consumes energy that could otherwise support key metabolic strategies employed by the subseafloor biosphere. Available Gibbs free energy is reduced by 71 to 86% across the habitable temperature range for both hydrogenotrophic SO4 2- reduction to hydrogen sulfide (H2S) and carbon dioxide (CO2) reduction to methane (CH4). The abiotic H2 sink we identify has implications for the productivity of subseafloor microbial ecosystems and is an important process to consider within models of H2 production and consumption in young oceanic crust.


Assuntos
Fontes Hidrotermais/química , Temperatura Alta , Hidrogênio/química , Fontes Hidrotermais/microbiologia , Oxirredução , Água do Mar/química
3.
Appl Environ Microbiol ; 86(21)2020 10 15.
Artigo em Inglês | MEDLINE | ID: mdl-32859597

RESUMO

Deep-sea hydrothermal vent communities are dominated by invertebrates, namely, bathymodiolin mussels, siboglinid tubeworms, and provannid snails. Symbiosis is considered key to successful colonization by these sedentary species in such extreme environments. In the PACManus vent fields, snails, tubeworms, and mussels each colonized a niche with distinct geochemical characteristics. To better understand the metabolic potentials and genomic features contributing to host-environment adaptation, we compared the genomes of the symbionts of Bathymodiolus manusensis, Arcovestia ivanovi, and Alviniconcha boucheti sampled at PACManus, and we discuss their environmentally adaptive features. We found that B. manusensis and A. ivanovi are colonized by Gammaproteobacteria from distinct clades, whereas endosymbionts of B. manusensis feature high intraspecific heterogeneity with differing metabolic potentials. A. boucheti harbored three novel Epsilonproteobacteria symbionts, suggesting potential species-level diversity of snail symbionts. Genome comparisons revealed that the relative abundance of gene families related to low-pH homeostasis, metal resistance, oxidative stress resistance, environmental sensing/responses, and chemotaxis and motility was the highest in A. ivanovi's symbiont, followed by symbionts of the vent-mouth-dwelling snail A. boucheti, and was relatively low in the symbiont of the vent-periphery-dwelling mussel B. manusensis, which is consistent with their environmental adaptations and host-symbiont interactions. Gene families classified as encoding host interaction/attachment, virulence factors/toxins, and eukaryotic-like proteins were most abundant in symbionts of mussels and least abundant in those of snails, indicating that these symbionts may differ in their host colonization strategies. Comparison of Epsilonproteobacteria symbionts to nonsymbionts demonstrated that the expanded gene families in symbionts were related to vitamin B12 synthesis, toxin-antitoxin systems, methylation, and lipopolysaccharide biosynthesis, suggesting that these are vital to symbiont establishment and development in Epsilonproteobacteria IMPORTANCE Deep-sea hydrothermal vents are dominated by several invertebrate species. The establishment of symbiosis has long been thought to be the key to successful colonization by these sedentary species in such harsh environments. However, the relationships between symbiotic bacteria and their hosts and their role in environmental adaptations generally remain unclear. In this paper, we show that the distribution of three host species showed characteristic niche partitioning in the Manus Basin, giving us the opportunity to understand how they adapt to their particular habitats. This study also revealed three novel genomes of symbionts from the snails of A. boucheti Combined with a data set on other ectosymbiont and free-living bacteria, genome comparisons for the snail endosymbionts pointed to several genetic traits that may have contributed to the lifestyle shift of Epsilonproteobacteria into the epithelial cells. These findings could increase our understanding of invertebrate-endosymbiont relationships in deep-sea ecosystems.


Assuntos
Adaptação Biológica , Fenômenos Fisiológicos Bacterianos , Gastrópodes/microbiologia , Fontes Hidrotermais/microbiologia , Mytilidae/microbiologia , Poliquetos/microbiologia , Simbiose , Animais , Bactérias/genética , Genoma Bacteriano , Microbiota , Oceano Pacífico , Papua Nova Guiné
4.
PLoS One ; 15(6): e0234175, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32502166

RESUMO

Shallow-sea hydrothermal systems, like their deep-sea and terrestrial counterparts, can serve as relatively accessible portals into the microbial ecology of subsurface environments. In this study, we determined the chemical composition of 47 sediment porewater samples along a transect from a diffuse shallow-sea hydrothermal vent to a non-thermal background area in Paleochori Bay, Milos Island, Greece. These geochemical data were combined with thermodynamic calculations to quantify potential sources of energy that may support in situ chemolithotrophy. The Gibbs energies (ΔGr) of 730 redox reactions involving 23 inorganic H-, O-, C-, N-, S-, Fe-, Mn-, and As-bearing compounds were calculated. Of these reactions, 379 were exergonic at one or more sampling locations. The greatest energy yields were from anaerobic CO oxidation with NO2- (-136 to -162 kJ/mol e-), followed by reactions in which the electron acceptor/donor pairs were O2/CO, NO3-/CO, and NO2-/H2S. When expressed as energy densities (where the concentration of the limiting reactant is taken into account), a different set of redox reactions are the most exergonic: in sediments affected by hydrothermal input, sulfide oxidation with a range of electron acceptors or nitrite reduction with different electron donors provide 85~245 J per kg of sediment, whereas in sediments less affected or unaffected by hydrothermal input, various S0 oxidation reactions and aerobic respiration reactions with several different electron donors are most energy-yielding (80~95 J per kg of sediment). A model that considers seawater mixing with hydrothermal fluids revealed that there is up to ~50 times more energy available for microorganisms that can use S0 or H2S as electron donors and NO2- or O2 as electron acceptors compared to other reactions. In addition to revealing likely metabolic pathways in the near-surface and subsurface mixing zones, thermodynamic calculations like these can help guide novel microbial cultivation efforts to isolate new species.


Assuntos
Metabolismo Energético , Fontes Hidrotermais , Grécia , Fontes Hidrotermais/microbiologia , Ilhas , Termodinâmica
5.
Int J Syst Evol Microbiol ; 70(6): 3899-3904, 2020 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-32496185

RESUMO

A moderately halophilic bacterium, designated strain KX18D6T, was isolated from the tube of the polychaete Paralvinella hessleri collected from a hydrothermal field located in the Okinawa Trough. Strain KX18D6T was Gram-stain-negative, rod-shaped, facultatively anaerobic, motile, oxidase- and catalase-positive, and grew optimally at 30-35 °C, pH 7.0 and in the presence of 3-5 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain KX18D6T grouped with the members of the genus Salinimonas, including Salinimonas chungwhensis BH030046T (97.7 % sequence similarity), Salinimonas lutimaris DPSR-4T (97.2 %) and Salinimonas sediminis N102T (96.4 %). Genome sequencing of strain KX18D6T revealed a genome size of 4.16 Mb and a DNA G+C content of 47.3 mol%. Genomic average nucleotide identity (orthoANI) values of strain KX18D6T with S. chungwhensis DSM 16280T, S. lutimaris KCTC 23464T and S. sediminis N102T were 76.2, 73.1 and 73.2 %, respectively, while the in silico DNA-DNA hybridization (GGDC) values for strain KX18D6T with these strains were 25.3, 17.7 and 18.0 %, respectively. The major fatty acids were summed feature 3 (C16 : 1 ω7c/C16 : 1 ω6c), C16 : 0 and summed feature 8 (C18 : 1 ω7c/C18 : 1 ω6c). The predominant respiratory quinone was ubiquinone 8, and the predominant polar lipids were phosphatidylethanolamine and phosphatidylglycerol. On the basis of comparative analysis of phylogenetic, phylogenomic, phenotypic and chemotaxonomic characteristics, strain KX18D6T (=KCTC 72464T=MCCC 1K03884T) is clearly distinguishable from the type strains of species of the genus Salinimonas and is considered to represent a novel species of the genus Salinimonas, for which the name Salinimonas iocasae sp. nov. is proposed.


Assuntos
Alteromonadaceae/classificação , Fontes Hidrotermais/microbiologia , Filogenia , Alteromonadaceae/isolamento & purificação , Animais , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Sedimentos Geológicos/microbiologia , Hibridização de Ácido Nucleico , Oceano Pacífico , Fosfolipídeos/química , Poliquetos , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Ubiquinona/química
6.
Mar Genomics ; 52: 100733, 2020 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-32571576

RESUMO

Crassaminicella sp. strain SY095 is an anaerobic mesophilic marine bacterium that was recently isolated from a deep-sea hydrothermal vent on the Southwest Indian Ridge. Here, we present the complete genome sequence of strain SY095. The genome consists of a chromosome of 3,046,753 bp (G + C content of 30.81%) and a plasmid of 36,627 bp (G + C content of 31.29%), encodes 2966 protein, 135 tRNA genes, and 34 rRNA genes. Numerous genes are related to peptide transport, amino acid metabolism, motility, and sporulation. This agrees with the observation that strain SY095 is a spore-forming, motile, and chemoheterotrophic bacterium. Further, the genome harbors multiple prophages that carry all the genes necessary for viral particle synthesis. Some prophages carry additional genes that may be involved in the regulation of sporulation. This is the first reported genome of a bacterium from the genus Crassaminicella, providing insights into the microbial adaptation strategies to the deep-sea hydrothermal vent environment.


Assuntos
Clostridiaceae/genética , Genoma Bacteriano , Fontes Hidrotermais/microbiologia , Anaerobiose , Clostridiaceae/metabolismo , Oceano Índico , Sequenciamento Completo do Genoma
7.
Int J Syst Evol Microbiol ; 70(5): 3139-3144, 2020 May.
Artigo em Inglês | MEDLINE | ID: mdl-32375934

RESUMO

A Gram-stain-positive, non-flagellated, non-gliding, coccoid bacterial strain, designated JLT9T, was isolated from the shallow-sea hydrothermal system off Kueishantao Island, Taiwan, ROC. Strain JLT9T was aerobic, chemoheterotrophic and grew optimally at 35 °C, at pH 6.0 and in the presence of 2.5 % (w/v) NaCl. Strain JLT9T exhibited highest 16S rRNA gene sequence similarity to Serinicoccus marinus DSM 15273T (98.83 %). Phylogenetic trees based on 16S rRNA gene sequences revealed that strain JLT9T belonged to the genus Serinicoccus, clustering with Serinicoccus marinus JC1078T, Serinicoccus profundi MCCC 1A05965T, Serinicoccus sediminis GP-T3-3T and Serinicoccus chungangensis CAU9536T. The digital DNA-DNA genome hybridization values between strain JLT9T and the closest related strain S. marinus DSM 15273T was 34.30 %. The DNA G+C content was 72.43 mol%. The dominant fatty acids were identified as iso-C15 : 0 (41.4 %) and iso-C16 : 0 (24.7 %). The polar lipids of strain JLT9T comprised diphosphatidylglycerol, phosphatidylcholine, phosphatidylglycerol, three unidentified glycolipid and an unidentified phospholipid. The predominant isoprenoid quinone was MK-8 (H4). The cell wall contained ornithine and serine, and no diaminopimelic acid. On the basis of phylogenetic data and several distinct phenotypic characteristics, strain JLT9T represents a novel species of the genus Serinicoccus, for which the name Serinicoccus hydrothermalis sp. nov. is proposed. The type strain is JLT9T (=CGMCC 1.15779T=JCM 31502T).


Assuntos
Actinomycetales/classificação , Fontes Hidrotermais/microbiologia , Filogenia , Água do Mar/microbiologia , Actinomycetales/isolamento & purificação , Técnicas de Tipagem Bacteriana , Composição de Bases , Parede Celular/química , DNA Bacteriano/genética , Ácido Diaminopimélico/química , Ácidos Graxos/química , Glicolipídeos/química , Ilhas , Hibridização de Ácido Nucleico , Peptidoglicano/química , Fosfolipídeos/química , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Taiwan , Vitamina K 2/análogos & derivados , Vitamina K 2/química
8.
mBio ; 11(2)2020 04 21.
Artigo em Inglês | MEDLINE | ID: mdl-32317322

RESUMO

Cold seeps and hydrothermal vents deliver large amounts of methane and other gaseous alkanes into marine surface sediments. Consortia of archaea and partner bacteria thrive on the oxidation of these alkanes and its coupling to sulfate reduction. The inherently slow growth of the involved organisms and the lack of pure cultures have impeded the understanding of the molecular mechanisms of archaeal alkane degradation. Here, using hydrothermal sediments of the Guaymas Basin (Gulf of California) and ethane as the substrate, we cultured microbial consortia of a novel anaerobic ethane oxidizer, "Candidatus Ethanoperedens thermophilum" (GoM-Arc1 clade), and its partner bacterium "Candidatus Desulfofervidus auxilii," previously known from methane-oxidizing consortia. The sulfate reduction activity of the culture doubled within one week, indicating a much faster growth than in any other alkane-oxidizing archaea described before. The dominance of a single archaeal phylotype in this culture allowed retrieval of a closed genome of "Ca. Ethanoperedens," a sister genus of the recently reported ethane oxidizer "Candidatus Argoarchaeum." The metagenome-assembled genome of "Ca. Ethanoperedens" encoded a complete methanogenesis pathway including a methyl-coenzyme M reductase (MCR) that is highly divergent from those of methanogens and methanotrophs. Combined substrate and metabolite analysis showed ethane as the sole growth substrate and production of ethyl-coenzyme M as the activation product. Stable isotope probing demonstrated that the enzymatic mechanism of ethane oxidation in "Ca. Ethanoperedens" is fully reversible; thus, its enzymatic machinery has potential for the biotechnological development of microbial ethane production from carbon dioxide.IMPORTANCE In the seabed, gaseous alkanes are oxidized by syntrophic microbial consortia that thereby reduce fluxes of these compounds into the water column. Because of the immense quantities of seabed alkane fluxes, these consortia are key catalysts of the global carbon cycle. Due to their obligate syntrophic lifestyle, the physiology of alkane-degrading archaea remains poorly understood. We have now cultivated a thermophilic, relatively fast-growing ethane oxidizer in partnership with a sulfate-reducing bacterium known to aid in methane oxidation and have retrieved the first complete genome of a short-chain alkane-degrading archaeon. This will greatly enhance the understanding of nonmethane alkane activation by noncanonical methyl-coenzyme M reductase enzymes and provide insights into additional metabolic steps and the mechanisms underlying syntrophic partnerships. Ultimately, this knowledge could lead to the biotechnological development of alkanogenic microorganisms to support the carbon neutrality of industrial processes.


Assuntos
Anaerobiose , Archaea/metabolismo , Etano/metabolismo , Archaea/classificação , Archaea/genética , Bactérias/classificação , Bactérias/genética , Bactérias/metabolismo , Biomarcadores , Metabolismo Energético , Genoma Arqueal , Genômica/métodos , Sedimentos Geológicos/microbiologia , Fontes Hidrotermais/microbiologia , Redes e Vias Metabólicas , Tipagem Molecular , Oxirredução , Filogenia , RNA Ribossômico 16S/genética
9.
Arch Microbiol ; 202(6): 1477-1488, 2020 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-32193579

RESUMO

Shallow hydrothermal systems are extreme environments. The sediments and fluids emitted from the vents present unusual physical and chemical conditions compared to other marine areas, which promotes unique biodiversity that has been of great interest for biotechnology for some years. In this work, a bioprospective study was carried out to evaluate the capacity of bacteria associated with shallow hydrothermal vents to produce biofilm-inhibiting compounds. Degradation assays of N-acyl homoserine lactone (AHL) autoinducers (C6HSL) involved in the quorum sensing process were carried out on 161 strains of bacteria isolated from three shallow hydrothermal systems located in Baja California Sur (BCS), Mexico. The biosensor Chromobacterium violaceum CV026 was used. Twenty-three strains showed activity, and organic extracts were obtained with ethyl acetate. The potential of the extracts to inhibit the formation of biofilms was tested against two human pathogenic strains (Pseudomonas aeruginosa PAO1 and Aeromonas caviae ScH3), a shrimp pathogen (Vibrio parahaemolyticus M8), and two marine strains identified as producing biofilms on submerged surfaces (Virgibacillus sp C29 and Vibrio alginolyticus C96). The results showed that Vibrio alginolyticus and Brevibacillus thermoruber, as well as some thermotolerant strains (mostly Bacillus), produce compounds that inhibit bacterial biofilms (B. licheniformis, B. paralicheniformis, B. firmus, B. oceanizedimenis, B. aerius and B. sonorensis).


Assuntos
Antibacterianos/metabolismo , Antibiose/fisiologia , Biofilmes/crescimento & desenvolvimento , Chromobacterium/metabolismo , Fontes Hidrotermais/microbiologia , 4-Butirolactona/análogos & derivados , 4-Butirolactona/metabolismo , Aeromonas caviae/efeitos dos fármacos , Bacillus/efeitos dos fármacos , Brevibacillus/efeitos dos fármacos , Chromobacterium/isolamento & purificação , Chromobacterium/fisiologia , México , Pseudomonas aeruginosa/efeitos dos fármacos , Percepção de Quorum/fisiologia , Vibrio alginolyticus/efeitos dos fármacos
10.
Appl Environ Microbiol ; 86(8)2020 04 01.
Artigo em Inglês | MEDLINE | ID: mdl-32033949

RESUMO

The Lost City hydrothermal field on the Mid-Atlantic Ridge supports dense microbial life on the lofty calcium carbonate chimney structures. The vent field is fueled by chemical reactions between the ultramafic rock under the chimneys and ambient seawater. These serpentinization reactions provide reducing power (as hydrogen gas) and organic compounds that can serve as microbial food; the most abundant of these are methane and formate. Previous studies have characterized the interior of the chimneys as a single-species biofilm inhabited by the Lost City Methanosarcinales, but they also indicated that this methanogen is unable to metabolize formate. The new metagenomic results presented here indicate that carbon cycling in these Lost City chimney biofilms could depend on the metabolism of formate by Chloroflexi populations. Additionally, we present evidence for metabolically diverse, formate-utilizing Sulfurovum populations and new genomic and phylogenetic insights into the unique Lost City Methanosarcinales IMPORTANCE Primitive forms of life may have originated around hydrothermal vents at the bottom of the ancient ocean. The Lost City hydrothermal vent field, fueled by just rock and water, provides an analog for not only primitive ecosystems but also potential extraterrestrial rock-powered ecosystems. The microscopic life covering the towering chimney structures at the Lost City has been previously documented, yet little is known about the carbon cycling in this ecosystem. These results provide a better understanding of how carbon from the deep subsurface can fuel rich microbial ecosystems on the seafloor.


Assuntos
Chloroflexi/genética , Formiatos/metabolismo , Genoma Bacteriano , Oceano Atlântico , Carbono/metabolismo , Chloroflexi/metabolismo , Fontes Hidrotermais/microbiologia
11.
Int J Syst Evol Microbiol ; 70(4): 2554-2559, 2020 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-32101515

RESUMO

An orange-pigmented, short-rod-shaped, aerobic and non-motile bacterial strain, designated TK008T, was isolated from the shallow-sea hydrothermal systems off Kueishantao Island in Taiwan, China, and it was studied by using a polyphasic taxonomic approach. Cells were Gram-stain-negative, and catalase- and oxidase-positive. Strain TK008T exhibited highest 16S rRNA gene sequence similarity of 97.1 % to Paracoccus pacificus F14T. The phylogenetic trees based on 16S rRNA gene sequences showed that strain TK008T was a member of the genus Paracoccus. Digital DNA-DNA hybridization values between strain TK008T and two closely related species (Paracoccus zhejiangensis and Paracoccus tegillarcae) were 20.6 and 20.9 %. The average nucleotide identity values of strain TK008T compared with P. zhejiangensis and P. tegillarcae were 75.2 and 74.6 % respectively. The major isoprenoid quinone was ubiquinone-10. The predominant fatty acids (>10 %) were summed feature 8 (C18 : 1ω6c and/or C18 : 1ω7c). The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, three unidentified phospholipids, two unidentified lipids and an unidentified glycolipid. The DNA G+C content of strain TK008T from genomic sequence data was 62.54 mol%. On the basis of polyphasic analysis, strain TK008T represents a novel species, for which the name Paracoccus aurantiacus sp. nov. is proposed. The type strain is TK008T (=CGMCC 1.13898T=JCM 33630T).


Assuntos
Fontes Hidrotermais/microbiologia , Paracoccus/classificação , Filogenia , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Glicolipídeos/química , Ilhas , Hibridização de Ácido Nucleico , Paracoccus/isolamento & purificação , Fosfolipídeos/química , Pigmentação , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Taiwan , Ubiquinona/análogos & derivados , Ubiquinona/química
12.
Appl Environ Microbiol ; 86(8)2020 04 01.
Artigo em Inglês | MEDLINE | ID: mdl-32060020

RESUMO

The deep-sea hydrothermal vent shrimp Rimicaris exoculata largely depends on a dense epibiotic chemoautotrophic bacterial community within its enlarged cephalothoracic chamber. However, our understanding of shrimp-bacterium interactions is limited. In this report, we focused on the deltaproteobacterial epibiont of R. exoculata from the relatively unexplored South Mid-Atlantic Ridge. A nearly complete genome of a Deltaproteobacteria epibiont was binned from the assembled metagenome. Whole-genome phylogenetic analysis reveals that it is affiliated with the genus Desulfobulbus, representing a potential novel species for which the name "Candidatus Desulfobulbus rimicarensis" is proposed. Genomic and transcriptomic analyses reveal that this bacterium utilizes the Wood-Ljungdahl pathway for carbon assimilation and harvests energy via sulfur disproportionation, which is significantly different from other shrimp epibionts. Additionally, this epibiont has putative nitrogen fixation activity, but it is extremely active in directly taking up ammonia and urea from the host or vent environments. Moreover, the epibiont could be distinguished from its free-living relatives by various features, such as the lack of chemotaxis and motility traits, a dramatic reduction in biosynthesis genes for capsular and extracellular polysaccharides, enrichment of genes required for carbon fixation and sulfur metabolism, and resistance to environmental toxins. Our study highlights the unique role and symbiotic adaptation of Deltaproteobacteria in deep-sea hydrothermal vent shrimps.IMPORTANCE The shrimp Rimicaris exoculata represents the dominant faunal biomass at many deep-sea hydrothermal vent ecosystems along the Mid-Atlantic Ridge. This organism harbors dense bacterial epibiont communities in its enlarged cephalothoracic chamber that play an important nutritional role. Deltaproteobacteria are ubiquitous in epibiotic communities of R. exoculata, and their functional roles as epibionts are based solely on the presence of functional genes. Here, we describe "Candidatus Desulfobulbus rimicarensis," an uncultivated deltaproteobacterial epibiont. Compared to campylobacterial and gammaproteobacterial epibionts of R. exoculata, this bacterium possessed unique metabolic pathways, such as the Wood-Ljungdahl pathway, as well as sulfur disproportionation and nitrogen fixation pathways. Furthermore, this epibiont can be distinguished from closely related free-living Desulfobulbus strains by its reduced genetic content and potential loss of functions, suggesting unique adaptations to the shrimp host. This study is a genomic and transcriptomic analysis of a deltaproteobacterial epibiont and largely expands the understanding of its metabolism and adaptation to the R. exoculata host.


Assuntos
Adaptação Biológica , Decápodes/microbiologia , Deltaproteobacteria/isolamento & purificação , Genoma Bacteriano , Fontes Hidrotermais/microbiologia , Simbiose , Animais , Oceano Atlântico , Deltaproteobacteria/classificação , Deltaproteobacteria/genética , Deltaproteobacteria/fisiologia , Traços de História de Vida , Filogenia
13.
Int J Mol Sci ; 21(1)2020 Jan 06.
Artigo em Inglês | MEDLINE | ID: mdl-31935923

RESUMO

The hyperthermo-piezophilic archaeon Palaeococcus pacificus DY20341T, isolated from East Pacific hydrothermal sediments, can utilize elemental sulfur as a terminal acceptor to simulate growth. To gain insight into sulfur metabolism, we performed a genomic and transcriptional analysis of Pa. pacificus DY20341T with/without elemental sulfur as an electron acceptor. In the 2001 protein-coding sequences of the genome, transcriptomic analysis showed that 108 genes increased (by up to 75.1 fold) and 336 genes decreased (by up to 13.9 fold) in the presence of elemental sulfur. Palaeococcus pacificus cultured with elemental sulfur promoted the following: the induction of membrane-bound hydrogenase (MBX), NADH:polysulfide oxidoreductase (NPSOR), NAD(P)H sulfur oxidoreductase (Nsr), sulfide dehydrogenase (SuDH), connected to the sulfur-reducing process, the upregulation of iron and nickel/cobalt transfer, iron-sulfur cluster-carrying proteins (NBP35), and some iron-sulfur cluster-containing proteins (SipA, SAM, CobQ, etc.). The accumulation of metal ions might further impact on regulators, e.g., SurR and TrmB. For growth in proteinous media without elemental sulfur, cells promoted flagelin, peptide/amino acids transporters, and maltose/sugar transporters to upregulate protein and starch/sugar utilization processes and riboflavin and thiamin biosynthesis. This indicates how strain DY20341T can adapt to different living conditions with/without elemental sulfur in the hydrothermal fields.


Assuntos
Adaptação Fisiológica , Fontes Hidrotermais/microbiologia , Enxofre/metabolismo , Thermococcaceae/metabolismo , Transcriptoma , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Hidrogenase/genética , Hidrogenase/metabolismo , Proteínas com Ferro-Enxofre/genética , Proteínas com Ferro-Enxofre/metabolismo , Oceanos e Mares , Thermococcaceae/genética
15.
ISME J ; 14(1): 135-150, 2020 01.
Artigo em Inglês | MEDLINE | ID: mdl-31595051

RESUMO

Deep-sea hydrothermal vents and methane seeps are often densely populated by animals that host chemosynthetic symbiotic bacteria, but the molecular mechanisms of such host-symbiont relationship remain largely unclear. We characterized the symbiont genome of the seep-living siboglinid Paraescarpia echinospica and compared seven siboglinid-symbiont genomes. Our comparative analyses indicate that seep-living siboglinid endosymbionts have more virulence traits for establishing infections and modulating host-bacterium interaction than the vent-dwelling species, and have a high potential to resist environmental hazards. Metatranscriptome and metaproteome analyses of the Paraescarpia holobiont reveal that the symbiont is highly versatile in its energy use and efficient in carbon fixation. There is close cooperation within the holobiont in production and supply of nutrients, and the symbiont may be able to obtain nutrients from host cells using virulence factors. Moreover, the symbiont is speculated to have evolved strategies to mediate host protective immunity, resulting in weak expression of host innate immunity genes in the trophosome. Overall, our results reveal the interdependence of the tubeworm holobiont through mutual nutrient supply, a pathogen-type regulatory mechanism, and host-symbiont cooperation in energy utilization and nutrient production, which is a key adaptation allowing the tubeworm to thrive in deep-sea chemosynthetic environments.


Assuntos
Bactérias/genética , Bactérias/metabolismo , Poliquetos/microbiologia , Simbiose , Animais , Bactérias/patogenicidade , Ciclo do Carbono , Perfilação da Expressão Gênica , Genômica , Fontes Hidrotermais/microbiologia , Imunidade Inata/genética , Poliquetos/genética , Poliquetos/imunologia , Poliquetos/metabolismo , Proteômica , Simbiose/genética
16.
Microb Ecol ; 79(1): 38-49, 2020 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-31079197

RESUMO

To study the role of exoelectrogens within the trophic network of deep-sea hydrothermal vents, we performed successive subcultures of a hyperthermophilic community from a hydrothermal chimney sample on a mix of electron donors in a microbial fuel cell system. Electrode (the electron acceptor) was swapped every week to enable fresh development from spent media as inoculum. The MFC at 80 °C yielded maximum current production increasing from 159 to 247 mA m-2 over the subcultures. The experiments demonstrated direct production of electric current from acetate, pyruvate, and H2 and indirect production from yeast extract and peptone through the production of H2 and acetate from fermentation. The microorganisms found in on-electrode communities were mainly affiliated to exoelectrogenic Archaeoglobales and Thermococcales species, whereas in liquid media, the communities were mainly affiliated to fermentative Bacillales and Thermococcales species. The work shows interactions between fermentative microorganisms degrading complex organic matter into fermentation products that are then used by exoelectrogenic microorganisms oxidizing these reduced compounds while respiring on a conductive support. The results confirmed that with carbon cycling, the syntrophic relations between fermentative microorganisms and exoelectrogens could enable some microbes to survive as biofilm in extremely unstable conditions. Graphical Abstract Schematic representation of cross-feeding between fermentative and exoelectrogenic microbes on the surface of the conductive support. B, Bacillus/Geobacillus spp.; Tc, Thermococcales; Gg, Geoglobus spp.; Py, pyruvate; Ac, acetate.


Assuntos
Archaea/química , Archaea/fisiologia , Fontes Hidrotermais/microbiologia , Acetatos/metabolismo , Archaea/classificação , Archaea/genética , Biofilmes , Eletricidade , Eletrodos/microbiologia , Fermentação , Hidrogênio/metabolismo , Oxirredução , Ácido Pirúvico/metabolismo
17.
Environ Microbiol ; 22(1): 329-342, 2020 01.
Artigo em Inglês | MEDLINE | ID: mdl-31691434

RESUMO

Thermoprofundales (Marine Benthic Group D archaea, MBG-D) is a newly proposed archaeal order and widely distributed in global marine sediment, and the members in the order may play a vital role in carbon cycling. However, the lack of pure cultures of these oeganisms has hampered the recognition of their catabolic roles. Here, by constructing high-quality metagenome-assembled genomes (MAGs) of two new subgroups of Thermoprofundales from hydrothermal sediment and predicting their catabolic pathways, we here provide genomic evidences that Thermoprofundales are capable of degrading aromatics via the phenylacetic acid (PAA) pathway. Then, the gene sequences of phenylacetyl-CoA ligase (PCL), a key enzyme for the PAA pathway, were searched in reference genomes. The widespread distribution of PCL genes among 14.9% of archaea and 75.9% of Thermoprofundales further supports the importance of the PAA pathway in archaea, particularly in Thermoprofundales where no ring-cleavage dioxygenases were found. Two PCLs from Thermoprofundales MAGs, PCLM8-3 and PCLM10-15 , were able to convert PAA to phenylacetyl-CoA (PA-CoA) in vitro, demonstrating the involvement of Thermoprofundales in aromatics degradation through PAA via CoA activation. Their acid tolerance (pH 5-7), high-optimum temperatures (60°C and 80°C), thermostability (stable at 60°C and 50°C for 48 h) and broad substrate spectra imply that Thermoprofundales are capable of transforming aromatics under extreme conditions. Together with the evidence of in situ transcriptional activities for most genes related to the aromatics pathway in Thermoprofundales, these genomic, and biochemical evidences highlight the essential role of this ubiquitous and abundant archaeal order in the carbon cycle of marine sediments.


Assuntos
Archaea/metabolismo , Sedimentos Geológicos/microbiologia , Fenilacetatos/metabolismo , Hidrocarbonetos Policíclicos Aromáticos/metabolismo , Acetilcoenzima A/genética , Archaea/classificação , Archaea/genética , Ciclo do Carbono , Coenzima A Ligases/genética , Genômica , Fontes Hidrotermais/microbiologia , Metagenoma
18.
Int J Syst Evol Microbiol ; 70(1): 234-239, 2020 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-31613743

RESUMO

A new mesophilic bacterium, designated strain 13-15AT, was isolated from the deep-sea water from the Carlsberg Ridge, northwestern Indian Ocean. Cells were short rods and motile with a single polar flagellum. Growth was observed in the presence of 85-1700 mM NaCl (optimum 680 mM), at 10-45 °C (optimum, 28 °C) and pH 5.0-9.0 (optimum, pH 7.0). The isolate was an obligate chemolithoautotroph capable of growth using thiosulfate, sulfide, elemental sulfur or tetrathionate as the sole energy source, carbon dioxide as the sole carbon source, and molecular oxygen as the sole electron acceptor. Molecular hydrogen did not support growth. The major fatty acids were C16 : 1 (45.0 %), C18 : 1 (22.5 %) and C16 : 0 (20.1 %). The G+C content of the genomic DNA was 41.6 mol%. The results of phylogenetic analysis based on 16S rRNA gene sequences showed that the novel isolate belonged to the genus Thiomicrorhabdus and was most closely related to Thiomicrorhabdus hydrogeniphila MAS2T (94.8 % sequence similarity). On the basis of the taxonomic data obtained in this study, strain 13-15AT represents a novel species of the genus Thiomicrorhabdus, for which the name Thiomicrorhabdus indica sp. nov. is proposed, with the type strain 13-15AT (=MCCC 1A13986T=KCTC 15750T).


Assuntos
Fontes Hidrotermais/microbiologia , Filogenia , Piscirickettsiaceae/classificação , Água do Mar/microbiologia , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Oceano Índico , Oxirredução , Piscirickettsiaceae/isolamento & purificação , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Enxofre , Tiossulfatos
19.
PLoS One ; 14(12): e0226616, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31887170

RESUMO

This paper reports the diversity of fungi associated with substrates collected at a shallow hydrothermal vent field at Kueishan Island, Taiwan, using both culture-based and metabarcoding methods. Culture of fungi from yellow sediment (with visible sulfur granules), black sediment (no visible sulfur granules), the vent crab Xenograpsus testudinatus, seawater and, animal egg samples resulted in a total of 94 isolates. Species identification based on the internal transcribed spacer regions of the rDNA revealed that the yellow sediment samples had the highest species richness with 25 species, followed by the black sediment (23) and the crab (13). The Ascomycota was dominant over the Basidiomycota; the dominant orders were Agaricales, Capnodiales, Eurotiales, Hypocreales, Pleosporales, Polyporales and Xylariales. Hortaea werneckii was the only common fungus isolated from the crab, seawater, yellow and black sediment samples. The metabarcoding analysis amplifying a small fragment of the rDNA (from 18S to 5.8S) recovered 7-27 species from the black sediment and 12-27 species from the yellow sediment samples and all species belonged to the Ascomycota and the Basidiomycota. In the yellow sediments, the dominant order was Pleosporales and this order was also dominant in the black sediment together with Sporidiobolales. Based on the results from both methods, 54 and 49 species were found in the black and yellow sediments, respectively. Overall, a higher proportion of Ascomycota (~70%) over Basidiomycota was recovered in the yellow sediment and the two phyla were equally abundant in the black sediment. The top five dominant fungal orders in descending order based on species richness were Pleosporales>Eurotiales>Polyporales>Hypocreales>Capnodiales in the black sediment samples, and Polyporales>Pleosporales>Eurotiales>Capnodiales>Hypocreales in the yellow sediment samples. This study is the first to observe a high diversity of fungi associated with various substrates at a marine shallow water hydrothermal vent ecosystem. While some fungi found in this study were terrestrial species and their airborne spores might have been deposited into the marine sediment, several pathogenic fungi of animals, including Acremonium spp., Aspergillus spp., Fusarium spp., Malassezia spp., Hortaea werneckii, Parengyodontium album, and Westerdykella dispersa, were recovered suggesting that these fungi may be able to cause diseases of marine animals.


Assuntos
Biodiversidade , Técnicas de Cultura/métodos , Código de Barras de DNA Taxonômico/métodos , Fungos/isolamento & purificação , Fontes Hidrotermais/microbiologia , Ascomicetos/isolamento & purificação , Basidiomycota/isolamento & purificação , Fungos/genética , Fungos/patogenicidade , Sedimentos Geológicos/microbiologia , Taiwan
20.
Artigo em Inglês | MEDLINE | ID: mdl-31750261

RESUMO

The Bacillus cereus group is frequently isolated from soil, plants, food, and other environments. In this study, we report the first isolation and characterization of a B. cereus group member, Bacillus wiedmannii SR52, from the hydrothermal field in the Iheya Ridge of Okinawa Trough. SR52 was isolated from the gills of shrimp Alvinocaris longirostris, an invertebrate species found abundantly in the ecosystems of the hydrothermal vents, and is most closely related to B. wiedmannii FSL W8-0169. SR52 is aerobic, motile, and able to form endospores. SR52 can grow in NaCl concentrations up to 9%. SR52 has a circular chromosome of 5,448,361 bp and a plasmid of 137,592 bp, encoding 5,709 and 189 genes, respectively. The chromosome contains 297 putative virulence genes, including those encoding enterotoxins and hemolysins. Fourteen rRNA operons, 107 tRNAs, and 5 sRNAs are present in the chromosome, and 7 tRNAs are present in the plasmid. SR52 possesses 13 genomic islands (GIs), all on the chromosome. Comparing to FSL W8-0169, SR52 exhibits several streaking features in its genome, notably an exceedingly large number of non-coding RNAs and GIs. In vivo studies showed that following intramuscular injection into fish, SR52 was able to disseminate in tissues and cause mortality; when inoculated into mice, SR52 induced acute mortality and disseminated transiently in tissues. In vitro studies showed that SR52 possessed hemolytic activity, and the extracellular product of SR52 exhibited a strong cytotoxic effect. These results provided the first insight into the cytotoxicity and genomic feature of B. wiedmannii from the deep-sea hydrothermal environment.


Assuntos
Bacillus/genética , Genoma Bacteriano , Genômica , Fontes Hidrotermais/microbiologia , Animais , Bacillus/isolamento & purificação , Microbiologia Ambiental , Feminino , Peixes/microbiologia , Genômica/métodos , Japão , Camundongos , Filogenia , RNA Ribossômico 16S/genética , Virulência/genética , Sequenciamento Completo do Genoma
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