Marinitoga okinawensis sp. nov., a novel thermophilic and anaerobic heterotroph isolated from a deep-sea hydrothermal field, Southern Okinawa Trough

Marinitoga aeolica sp. nov., a novel thermophilic anaerobic heterotroph isolated from a shallow hydrothermal field of Panarea Island in the Aeolian archipelago, Italy

A novel thermophilic strain, designated BP5-C20AT, was isolated from the shallow hydrothermal field of the Panarea island in the Aeolian archipelago close to Sicily, Italy. Cells are motile rods surrounded with a 'toga', Gram-stain-negative and display a straight to curved morphology during the exponential phase. Strain BP5-C20AT is thermophilic (optimum 55 °C), moderately acidophilic (optimum pH 5.6) and halotolerant (optimum 25 g l-1 NaCl). It can use yeast extract, peptone and tryptone. It uses the following carbohydrates: cellobiose, fructose, glucose, maltose, starch, sucrose and xylan. Elemental sulphur is used as an electron acceptor and reduced to hydrogen sulphide. The predominant cellular fatty acid is C16 : 0. Phylogenetic analysis showed that strain BP5-C20AT shared 97.3 % 16S rRNA gene sequence identity with the closest related species Marinitoga lauensis LG1T. The complete genome of strain BP5-C20AT is 2.44 Mb in size with a G+C content of 27.3 mol%. The dDDH and ANI values between the genomes of strains BP5-C20AT and M. lauensis LG1T are 31.0 and 85.70% respectively. Finally, from its physiological, metabolic and genomic characteristics, strain BP5-C20AT (=DSM 112332T=JCM 39183 T) is proposed as representative of a novel species of the genus Marinitoga named Marinitoga aeolica sp. nov. and belonging to the order Petrotogales, in the phylum Thermotogota.

Plasmid pMO1 from Marinitoga okinawensis, first non-cryptic plasmid reported within Thermotogota

Mobile genetic elements (MGEs), such as viruses and plasmids, drive the evolution and adaptation of their cellular hosts from all three domains of life. This includes microorganisms thriving in the most extreme environments, like deep-sea hydrothermal vents. However, our knowledge about MGEs still remains relatively sparse in these abyssal ecosystems. Here we report the isolation, sequencing, assembly, and functional annotation of pMO1, a 28.2 kbp plasmid associated with the reference strain Marinitoga okinawensis. Carrying restriction/modification and chemotaxis protein-encoding genes, pMO1 likely affects its host's phenotype and represents the first non-cryptic plasmid described among the phylum Thermotogota.

Vestiges of Adaptation to the Mesophilic Environment in the Genome of Tepiditoga spiralis gen. nov., sp. nov

A novel anaerobic heterotrophic strain, designated strain sy52^T, was isolated from a hydrothermal chimney at Suiyo Seamount in the Pacific Ocean. A 16S rRNA gene analysis revealed that the strain belonged to the family Petrotogaceae in the phylum Thermotogae. The strain was mesophilic with optimum growth at 48°C and the phylum primarily comprised hyperthermophiles and thermophiles. Strain sy52^T possessed unique genomic characteristics, such as an extremely low G+C content and 6 copies of rRNA operons. Genomic analyses of strain sy52^T revealed that amino acid usage in the predicted proteins resulted from adjustments to mesophilic environments. Genomic features also indicated independent adaptions to the mesophilic environment of strain sy52^T and Mesotoga species, which belong to the mesophilic lineage in the phylum Thermotogae. Based on phenotypic and phylogenetic evidence, strain sy52^T is considered to represent a novel genus and species in the family Petrotogaceae with the proposed name Tepiditoga spiralis gen. nov., sp. nov.

Microorganisms from deep-sea hydrothermal vents

With a rich variety of chemical energy sources and steep physical and chemical gradients, hydrothermal vent systems offer a range of habitats to support microbial life. Cultivation-dependent and independent studies have led to an emerging view that diverse microorganisms in deep-sea hydrothermal vents live their chemolithoautotrophic, heterotrophic, or mixotrophic life with versatile metabolic strategies. Biogeochemical processes are mediated by microorganisms, and notably, processes involving or coupling the carbon, sulfur, hydrogen, nitrogen, and metal cycles in these unique ecosystems. Here, we review the taxonomic and physiological diversity of microbial prokaryotic life from cosmopolitan to endemic taxa and emphasize their significant roles in the biogeochemical processes in deep-sea hydrothermal vents. According to the physiology of the targeted taxa and their needs inferred from meta-omics data, the media for selective cultivation can be designed with a wide range of physicochemical conditions such as temperature, pH, hydrostatic pressure, electron donors and acceptors, carbon sources, nitrogen sources, and growth factors. The application of novel cultivation techniques with real-time monitoring of microbial diversity and metabolic substrates and products are also recommended.

Supplementary Information

The online version contains supplementary material available at 10.1007/s42995-020-00086-4.

Effect of Cultivation Parameters on Fermentation and Hydrogen Production in the Phylum Thermotogae

The phylum Thermotogae is composed of a single class (Thermotogae), 4 orders (Thermotogales, Kosmotogales, Petrotogales, Mesoaciditogales), 5 families (Thermatogaceae, Fervidobacteriaceae, Kosmotogaceae, Petrotogaceae, Mesoaciditogaceae), and 13 genera. They have been isolated from extremely hot environments whose characteristics are reflected in the metabolic and phenotypic properties of the Thermotogae species. The metabolic versatility of Thermotogae members leads to a pool of high value-added products with application potentials in many industry fields. The low risk of contamination associated with their extreme culture conditions has made most species of the phylum attractive candidates in biotechnological processes. Almost all members of the phylum, especially those in the order Thermotogales, can produce bio-hydrogen from a variety of simple and complex sugars with yields close to the theoretical Thauer limit of 4 mol H₂/mol consumed glucose. Acetate, lactate, and L-alanine are the major organic end products. Thermotagae fermentation processes are influenced by various factors, such as hydrogen partial pressure, agitation, gas sparging, culture/headspace ratio, inoculum, pH, temperature, nitrogen sources, sulfur sources, inorganic compounds, metal ions, etc. Optimization of these parameters will help to fully unleash the biotechnological potentials of Thermotogae and promote their applications in industry. This article gives an overview of how these operational parameters could impact Thermotogae fermentation in terms of sugar consumption, hydrogen yields, and organic acids production.

Draft Genome Sequences of Two Marinitoga camini Isolates Producing Bacterioviruses

Here, we present the draft genome sequences of two thermophilic Marinitoga strain members of the Thermotogales order, Marinitoga camini DV1155 and Marinitoga camini DV1197. These strains were isolated from deep-sea hydrothermal vents of the Mid-Atlantic Ridge.

Marinitoga arctica sp. nov., a thermophilic, anaerobic heterotroph isolated from a Mid-Ocean Ridge vent field

A thermophilic, anaerobic, heterotrophic bacterium, designated 2PyrY55-1T, was isolated from the wall of an active hydrothermal white-smoker chimney in the Soria Moria vent field (71° N) at the Mohns Ridge in the Norwegian-Greenland Sea. Cells of the strain were Gram-negative, motile rods that possessed a polar flagellum and a sheath-like outer structure ('toga'). Growth was observed at 45-70 °C (optimum 65 °C), at pH 5.0-7.5 (optimum pH 5.5) and in 1.5-5.5 % (w/v) NaCl (optimum 2.5 %). The strain grew on pyruvate, complex proteinaceous substrates and various sugars. Cystine and elemental sulfur were used as electron acceptors, and sulfide was then produced. The G+C content of the genomic DNA was 27 mol% (Tm method). Cellular fatty acids included C16 : 0, C14 : 0, C16 : 1ω7c and/or iso-C15 : 0 2-OH, C16 : 1ω9c, C18 : 1ω9c, C18 : 0, C18 : 1ω7c and C12 : 0. Phylogenetic analyses of the 16S rRNA gene showed that the strain belonged to the genus Marinitoga in the family Petrotogaceae. Based on the phylogenetic and chemotaxonomic data, strain 2PyrY55-1T (=DSM 29778T=JCM 30566T) is the type strain of a novel species of the genus Marinitoga, for which the name Marinitoga arctica sp. nov. is proposed.

A Continuous Culture System for Assessing Microbial Activities in the Piezosphere

Continuous culture under elevated pressures is an important technique for expanding the exploration of microbial growth and survival in extreme environments associated with the deep biosphere. Here we present a benchtop stirred continuous culture bioreactor capable of withstanding temperatures ranging from 25 to 120°C and pressures as high as 69 MPa. The system is configured to allow the employment of media enriched in dissolved gases, under oxic or anoxic conditions, while permitting periodic sampling of the incubated organisms with minimal physical/chemical disturbance inside the reactor. In a pilot experiment, the fermentative growth of the thermopiezophilic bacterium Marinitoga piezophila was investigated continuously for 382 h at 65°C and at pressures ranging from 0.1 to 40 MPa while the medium flow rate was varied from 2 to 0.025 ml/min. The enhanced growth observed at 30 and 40 MPa and 0.025 ml/min supports the pressure preferences of M. piezophila when grown fermentatively. This assay successfully demonstrates the capabilities of the bioreactor for continuous culturing at a variety of dilution rates, pressures, and temperatures. We anticipate that this technology will accelerate our understanding of the physiological and metabolic status of microorganisms under temperature, pressure, and energy regimes resembling those of the Earth's piezosphere.

Petrotoga japonica sp. nov., a thermophilic, fermentative bacterium isolated from Yabase Oilfield in Japan

A gram-negative, motile, fermentative, thermophilic bacterium, designated AR80(T), was isolated from a high-temperature oil reservoir in Yabase Oilfield in Akita, Japan. Cells were rod-shaped, motile by means of polar flagella, and formed circular, convex, white colonies. The strain grew at 40-65 °C (optimum 60 °C), 0.5-9 % (w/v) NaCl (optimum 0.5-1 %), pH 6-9 (optimum pH 7.5), and elemental sulfur or thiosulfate serves as terminal electron acceptor. Phylogenetic analysis of 16S rRNA gene sequences indicated that strain AR80(T) belonged to the genus Petrotoga and shared approximately 94.5 % sequence similarity with the type species of this genus. The G + C content of genomic DNA was 32.4 mol% while the value of DNA-DNA hybridization between the closest relative species Petrotoga miotherma and AR80(T) was 58.1 %. The major cellular fatty acids of strain AR80(T) consisted of 18:1 w9c, 16:0, and 16:1 w9c. Based on genetic and phenotypic properties, strain AR80(T) was different with other identified Petrotoga species and represents as a novel species, for which the name Petrotoga japonica sp. nov. is proposed. The type strain is AR80(T) (=NBRC 108752(T) = KCTC 15103(T) = HUT 8122(T)).

Reconstruction of ancestral 16S rRNA reveals mutation bias in the evolution of optimal growth temperature in the Thermotogae phylum

Optimal growth temperature is a complex trait involving many cellular components, and its physiology is not yet fully understood. Evolution of continuous characters, such as optimal growth temperature, is often modeled as a one-dimensional random walk, but such a model may be an oversimplification given the complex processes underlying the evolution of continuous characters. Recent articles have used ancestral sequence reconstruction to infer the optimal growth temperature of ancient organisms from the guanine and cytosine content of the stem regions of ribosomal RNA, allowing inferences about the evolution of optimal growth temperature. Here, we investigate the optimal growth temperature of the bacterial phylum Thermotogae. Ancestral sequence reconstruction using a nonhomogeneous model was used to reconstruct the stem guanine and cytosine content of 16S rRNA sequences. We compare this sequence reconstruction method with other ancestral character reconstruction methods, and show that sequence reconstruction generates smaller confidence intervals and different ancestral values than other reconstruction methods. Unbiased random walk simulation indicates that the lower temperature members of the Thermotogales have been under directional selection; however, when a simulation is performed that takes possible mutations into account, it is the high temperature lineages that are, in fact, under directional selection. We find that the evolution of Thermotogales optimal growth temperatures is best fit by a biased random walk model. These findings suggest that it may be easier to evolve from a high optimal growth temperature to a lower one than vice versa.

Mesoaciditoga lauensis gen. nov., sp. nov., a moderately thermoacidophilic member of the order Thermotogales from a deep-sea hydrothermal vent

A novel moderately thermophilic, heterotrophic bacterium was isolated from a deep-sea hydrothermal vent deposit from the Mariner field along the Eastern Lau Spreading Center of the south-western Pacific Ocean. Cells were short motile rods (about 0.4×0.8 µm) that occurred singly or in pairs and were surrounded by a sheath-like membrane or 'toga'. The cells grew between 45 and 65 °C (optimum 57-60 °C) and at pH 4.1-6.0 (optimum pH 5.5-5.7) and grew optimally at 3 % (w/v) NaCl. The isolate grew on a range of carbon and proteinaceous substrates and reduced sulfur. The G+C content of the DNA was about 45 mol%. Phylogenetic analysis of the 16S rRNA gene sequence placed the new isolate as a deeply diverging lineage within the order Thermotogales. Based on the physiological, morphological and phylogenetic data, the isolate represents a novel species of a new genus with the proposed name Mesoaciditoga lauensis gen. nov., sp. nov. The type strain of Mesoaciditoga lauensis is cd-1655R(T) ( = DSM 25116(T) = OCM 1212(T)).

Isolation and characterization of a thermophilic, obligately anaerobic and heterotrophic marine Chloroflexi bacterium from a Chloroflexi-dominated microbial community associated with a Japanese shallow hydrothermal system, and proposal for Thermomarinilinea lacunofontalis gen. nov., sp. nov

A novel marine thermophilic and heterotrophic Anaerolineae bacterium in the phylum Chloroflexi, strain SW7^T, was isolated from an in situ colonization system deployed in the main hydrothermal vent of the Taketomi submarine hot spring field located on the southern part of Yaeyama Archipelago, Japan. The microbial community associated with the hydrothermal vent was predominated by thermophilic heterotrophs such as Thermococcaceae and Anaerolineae, and the next dominant population was thermophilic sulfur oxidizers. Both aerobic and anaerobic hydrogenotrophs including methanogens were detected as minor populations. During the culture-dependent viable count analysis in this study, an Anaerolineae strain SW7^T was isolated from an enrichment culture at a high dilution rate. Strain SW7^T was an obligately anaerobic heterotroph that grew with fermentation and had non-motile thin rods 3.5–16.5 μm in length and 0.2 μm in width constituting multicellular filaments. Growth was observed between 37–65°C (optimum 60°C), pH 5.5–7.3 (optimum pH 6.0), and 0.5–3.5% (w/v) NaCl concentration (optimum 1.0%). Based on the physiological and phylogenetic features of a new isolate, we propose a new species representing a novel genus Thermomarinilinea: the type strain of Thermomarinilinea lacunofontalis sp. nov., is SW7^T (=JCM15506^T=KCTC5908^T).

Complete genome sequence of the thermophilic, piezophilic, heterotrophic bacterium Marinitoga piezophila KA3

Marinitoga piezophila KA3 is a thermophilic, anaerobic, chemoorganotrophic, sulfur-reducing bacterium isolated from the Grandbonum deep-sea hydrothermal vent site at the East Pacific Rise (13°N, 2,630-m depth). The genome of M. piezophila KA3 comprises a 2,231,407-bp circular chromosome and a 13,386-bp circular plasmid. This genome was sequenced within Department of Energy Joint Genome Institute CSP 2010.

Evolution of temperature optimum in Thermotogaceae and the prediction of trait values of uncultured organisms

Quantitative characterization of the mode and rate of phenotypic evolution is rarely applied to prokaryotes. Here, we present an analysis of temperature optimum (T_opt) evolution in the thermophilic family Thermotogaceae, which has a large number of cultured representatives. We use log-rate-interval analysis to show that T_opt evolution in Thermotogaceae is consistent with a Brownian motion (BM) evolutionary model. The properties of the BM model are used to a establish confidence intervals on the unknown phenotypic trait value of an uncultured organism, given its distance to a close relative with known trait value. Cross-validation by bootstrapping indicates that the predictions are robust.

Marinitoga litoralis sp. nov., a thermophilic, heterotrophic bacterium isolated from a coastal thermal spring on Île Saint-Paul, Southern Indian Ocean

A novel thermophilic, anaerobic and organotrophic bacterium, designated strain MC3T, was isolated from a coastal thermal spring on Île Saint-Paul in the Southern Indian Ocean. Cells of strain MC3T were motile rods, 0.8–1.0 μm wide and 1.0–2.4 μm long during exponential phase and up to 7.0 μm long during stationary phase. Strain MC3T was an anaerobic organotroph able to use diverse organic compounds. It was also able to reduce sulfur to sulfide. Growth was observed at temperatures ranging from 45 to 70 °C (optimum at 60 °C), between pH 5.5 and 7.5 (optimum at pH 6) and from 8 to 46 g NaCl l−1 (optimum at 26 g l−1). The total G+C content of the genomic DNA was 26.2 mol%. Phylogenetic analysis based on 16S rRNA gene sequence comparisons indicated that strain MC3T was affiliated with the genus Marinitoga within the order Thermotogales. It shared 94.4–95.7 % 16S rRNA gene sequence similarity with strains of other Marinitoga species; Marinitoga hydrogenitolerans was found to be the most closely related organism. Based on the data from the phylogenetic analysis and the physiological properties of the novel isolate, strain MC3T should be classified as a representative of a novel species, for which the name Marinitoga litoralis sp. nov. is proposed; the type strain is MC3T (=DSM 21709T =JCM 15581T).

Oceanotoga teriensis gen. nov., sp. nov., a thermophilic bacterium isolated from offshore oil-producing wells

A novel, moderately thermophilic, chemo-organotrophic bacterium was isolated from formation fluid samples from an offshore oil-production well head at Bombay High (Western India). Cells were rod-shaped with a sheath-like outer structure ('toga'); the cells appeared singly, in pairs or in short chains. Cells grew at 25-70 °C (optimum 55-58 °C), pH 5.5-9.0 (optimum pH 7.3-7.8) and 0-12  % (w/v) NaCl (optimum 4.0-4.5  %). The isolate was able to grow on various carbohydrates or complex proteinaceous substances. The isolate reduced thiosulfate and elemental sulfur. The major end products of glucose fermentation were acetate, H₂ and CO₂. The DNA G+C content of the genomic DNA was 26.8 mol%. Phylogenetic analysis of the 16S rRNA gene placed the strain within the order Thermotogales in the bacterial domain. On the basis of 16S rRNA gene sequence comparisons and in combination with morphological and physiological characteristics, the isolate represents a novel species of new genus, for which the name Oceanotoga teriensis gen. nov., sp. nov. is proposed. The type strain of the type species is OCT74(T) (=JCM 15580(T)=LMG 24865(T)).

Kosmotoga olearia gen. nov., sp. nov., a thermophilic, anaerobic heterotroph isolated from an oil production fluid

A novel thermophilic, heterotrophic bacterium, strain TBF 19.5.1(T), was isolated from oil production fluid at the Troll B oil platform in the North Sea. Cells of strain TBF 19.5.1(T) were non-motile rods with a sheath-like structure, or toga. The strain was Gram-negative and grew at 20-80 degrees C (optimum 65 degrees C), pH 5.5-8.0 (optimum pH 6.8) and NaCl concentrations of 10-60 g l(-1) (optimum 25-30 g l(-1)). For a member of the order Thermotogales, the novel isolate is capable of unprecedented growth at low temperatures, with an optimal doubling time of 175 min (specific growth rate 0.24 h(-1)) and a final optical density of >1.4 when grown on pyruvate at 37 degrees C. Various carbohydrates, proteinaceous compounds and pyruvate served as growth substrates. Thiosulfate, but not elemental sulfur, enhanced growth of the isolate. Sulfate also enhanced growth, but sulfide was not produced. The strain grew in the presence of up to approximately 15 % oxygen, but only if cysteine was included in the medium. Growth of the isolate was inhibited by acetate, lactate and propionate, while butanol and malate prevented growth. The major fermentation products formed on maltose were hydrogen, carbon dioxide and acetic acid, with traces of ethanol and propionic acid. The G+C content of the genomic DNA was 42.5 mol%. Phylogenetic analyses of the 16S and 23S rRNA gene sequences as well as 29 protein-coding ORFs placed the strain within the bacterial order Thermotogales. Based on the phylogenetic analyses and the possession of a variety of physiological characteristics not previously found in any species of this order, it is proposed that the strain represents a novel species of a new genus within the family Thermotogaceae, order Thermotogales. The name Kosmotoga olearia gen. nov., sp. nov. is proposed. The type strain of Kosmotoga olearia is TBF 19.5.1(T) (=DSM 21960(T) =ATCC BAA-1733(T)).

Comparison of microbial communities associated with phase-separation-induced hydrothermal fluids at the Yonaguni Knoll IV hydrothermal field, the Southern Okinawa Trough

Microbial communities associated with a variety of hydrothermal emissions at the Yonaguni Knoll IV hydrothermal field, the southernmost Okinawa Trough, were analyzed by culture-dependent and -independent techniques. In this hydrothermal field, dozens of vent sites hosting physically and chemically distinct hydrothermal fluids were observed. Variability in the gas content and formation in the hydrothermal fluids was observed and could be controlled by the potential subseafloor phase-separation and -partition processes. The hydrogen concentration in the hydrothermal fluids was also variable (0.8-3.6 mmol kg(-1)) among the chimney sites, but was unusually high as compared with those in other Okinawa Trough hydrothermal fields. Despite the physical and chemical variabilities of the hydrothermal fluids, the microbial communities were relatively similar among the habitats. Based on both culture-dependent and -independent analyses of the microbial community structures, members of Thermococcales, Methanococcales and Desulfurococcales likely represent the predominant archaeal components, while members of Nautiliaceae and Thioreductoraceae are considered to dominate the bacterial population. Most of the abundant microbial components appear to be chemolithotrophs sustained by hydrogen oxidation. The relatively consistent microbial communities found in this study could have been because of the sufficient input of hydrogen from the hydrothermal fluids rather than other chemical properties.

Diversity of thermophilic anaerobes

Thermophilic anaerobes are Archaea and Bacteria that grow optimally at temperatures of 50 degrees C or higher and do not require the use of O(2) as a terminal electron acceptor for growth. The prokaryotes with this type of physiology are studied for a variety of reasons, including (a) to understand how life can thrive under extreme conditions, (b) for their biotechnological potential, and (c) because anaerobic thermophiles are thought to share characteristics with the early evolutionary life forms on Earth. Over 300 species of thermophilic anaerobes have been described; most have been isolated from thermal environments, but some are from mesobiotic environments, and others are from environments with temperatures below 0 degrees C. In this overview, the authors outline the phylogenetic and physiological diversity of thermophilic anaerobes as currently known. The purpose of this overview is to convey the incredible diversity and breadth of metabolism within this subset of anaerobic microorganisms.