Dense Community of Hyperthermophilic Sulfur-Dependent Heterotrophs in a Geothermally Heated Shallow Submarine Biotope near Kodakara-Jima Island, Kagoshima, Japan

Mapping the microbial diversity associated with different geochemical regimes in the shallow-water hydrothermal vents of the Aeolian archipelago, Italy

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.

Evolutionary dynamics of the prokaryotic adaptive immunity system CRISPR-Cas in an explicit ecological context

A stochastic, agent-based mathematical model of the coevolution of the archaeal and bacterial adaptive immunity system, CRISPR-Cas, and lytic viruses shows that CRISPR-Cas immunity can stabilize the virus-host coexistence rather than leading to the extinction of the virus. In the model, CRISPR-Cas immunity does not specifically promote viral diversity, presumably because the selection pressure on each single proto-spacer is too weak. However, the overall virus diversity in the presence of CRISPR-Cas grows due to the increase of the host and, accordingly, the virus population size. Above a threshold value of total viral diversity, which is proportional to the viral mutation rate and population size, the CRISPR-Cas system becomes ineffective and is lost due to the associated fitness cost. Our previous modeling study has suggested that the ubiquity of CRISPR-Cas in hyperthermophiles, which contrasts its comparative low prevalence in mesophiles, is due to lower rates of mutation fixation in thermal habitats. The present findings offer a complementary, simpler perspective on this contrast through the larger population sizes of mesophiles compared to hyperthermophiles, because of which CRISPR-Cas can become ineffective in mesophiles. The efficacy of CRISPR-Cas sharply increases with the number of proto-spacers per viral genome, potentially explaining the low information content of the proto-spacer-associated motif (PAM) that is required for spacer acquisition by CRISPR-Cas because a higher specificity would restrict the number of spacers available to CRISPR-Cas, thus hampering immunity. The very existence of the PAM might reflect the tradeoff between the requirement of diverse spacers for efficient immunity and avoidance of autoimmunity.

Sources of organic nitrogen at the serpentinite-hosted Lost City hydrothermal field

The reaction of ultramafic rocks with water during serpentinization at moderate temperatures results in alkaline fluids with high concentrations of reduced chemical compounds such as hydrogen and methane. Such environments provide unique habitats for microbial communities capable of utilizing these reduced compounds in present-day and, possibly, early Earth environments. However, these systems present challenges to microbial communities as well, particularly due to high fluid pH and possibly the availability of essential nutrients such as nitrogen. Here we investigate the source and cycling of organic nitrogen at an oceanic serpentinizing environment, the Lost City hydrothermal field (30°N, Mid-Atlantic Ridge). Total hydrolizable amino acid (THAA) concentrations in the fluids range from 736 to 2300 nm and constitute a large fraction of the dissolved organic carbon (2.5-15.1%). The amino acid distributions, and the relative concentrations of these compounds across the hydrothermal field, indicate they most likely derived from chemolithoautotrophic production. Previous studies have identified the presence of numerous nitrogen fixation genes in the fluids and the chimneys. Organic nitrogen in actively venting chimneys has δ(15) N values as low as 0.1‰ which is compatible with biological nitrogen fixation. Total hydrolizable amino acids in the chimneys are enriched in (13) C by 2-7‰ compared to bulk organic matter. The distribution and absolute δ(13) C(THAA) values are compatible with a chemolithoautotrophic source, an attribution also supported by molar organic C/N ratios in most active chimneys (4.1-5.5) which are similar to those expected for microbial communities. In total, these data indicate nitrogen is readily available to microbial communities at Lost City.

Precambrian lunar volcanic protolife

Five representative terrestrial analogs of lunar craters are detailed relevant to Precambrian fumarolic activity. Fumarolic fluids contain the ingredients for protolife. Energy sources to derive formaldehyde, amino acids and related compounds could be by flow charging, charge separation and volcanic shock. With no photodecomposition in shadow, most fumarolic fluids at 40 K would persist over geologically long time periods. Relatively abundant tungsten would permit creation of critical enzymes, Fischer-Tropsch reactions could form polycyclic aromatic hydrocarbons and soluble volcanic polyphosphates would enable assembly of nucleic acids. Fumarolic stimuli factors are described. Orbital and lander sensors specific to protolife exploration including combined Raman/laser-induced breakdown spectrocsopy are evaluated.

Prokaryote diversity and virus abundance in shallow hydrothermal vents of the Mediterranean Sea (Panarea Island) and the Pacific Ocean (north Sulawesi-Indonesia)

Despite their ubiquitous distribution in tectonically active coastal zones, shallow water hydrothermal vents have been less investigated than deep-sea vents. In the present study, we investigated the role of viral control and fluid emissions on prokaryote abundance, diversity, and community structure (total Archaea, total Bacteria, and sulphate-reducing bacteria) in waters and sediments surrounding the caldera of four different shallow-water hydrothermal vents (three located in the Mediterranean Sea and one in the Pacific Ocean). All vents, independent of their location, generally displayed a significant decrease of benthic prokaryote abundance, as well as its viable fraction, with increasing distance from the vent. Prokaryote assemblages were always dominated by Bacteria. Benthic Archaea accounted for 23-33% of total prokaryote abundance in the Mediterranean Sea and from 13 to 29% in the Pacific Ocean, whereas in the water column they accounted for 25-38%. The highest benthic bacterial ribotype richness was observed in close proximity of the vents (i.e., at 10-cm distance from the emissions), indicating that vent fluids might influence bacterial diversity in surrounding sediments. Virioplankton and viriobenthos abundances were low compared to other marine systems, suggesting that temperature and physical-chemical conditions might influence viral survival in these vent systems. We thus hypothesize that the high bacterial diversity observed in close proximity of the vents is related with the highly variable vent emissions, which could favor the coexistence of several prokaryotic species.

Temporal changes in fluid chemistry and energy profiles in the vulcano island hydrothermal system

In June 2003, the geochemical composition of geothermal fluids was determined at 9 sites in the Vulcano hydrothermal system, including sediment seeps, geothermal wells, and submarine vents. Compositional data were combined with standard state reaction properties to determine the overall Gibbs free energy (DeltaG(r) ) for 120 potential lithotrophic and heterotrophic reactions. Lithotrophic reactions in the H-O-N-S-C-Fe system were considered, and exergonic reactions yielded up to 120 kJ per mole of electrons transferred. The potential for heterotrophy was characterized by energy yields from the complete oxidation of 6 carboxylic acids- formic, acetic, propanoic, lactic, pyruvic, and succinic-with the following redox pairs: O(2)/H(2)O, SO(4) (2)/H(2)S, NO(3) ()/NH(4) (+), S(0)/H(2)S, and Fe(3)O(4)/Fe(2+). Heterotrophic reactions yielded 6-111 kJ/mol e(). Energy yields from both lithotrophic and heterotrophic reactions were highly dependent on the terminal electron acceptor (TEA); reactions with O(2) yielded the most energy, followed by those with NO(3) (), Fe(III), SO(4) (2), and S(0). When only reactions with complete TEA reduction were included, the exergonic lithotrophic reactions followed a similar electron tower. Spatial variability in DeltaG(r) was significant for iron redox reactions, owing largely to the wide range in Fe(2+) and H(+) concentrations. Energy yields were compared to those obtained for samples collected in June 2001. The temporal variations in geochemical composition and energy yields observed in the Vulcano hydrothermal system between 2001 and 2003 were moderate. The largest differences in DeltaG(r) over the 2 years were from iron redox reactions, due to temporal changes in the Fe(2+) and H(+) concentrations. The observed variations in fluid composition across the Vulcano hydrothermal system have the potential to influence not only microbial diversity but also the metabolic strategies of the resident microbial communities.

Culture-dependent and -independent characterization of microbial communities associated with a shallow submarine hydrothermal system occurring within a coral reef off Taketomi Island, Japan

Microbial communities in a shallow submarine hydrothermal system near Taketomi Island, Japan, were investigated using cultivation-based and molecular techniques. The main hydrothermal activity occurred in a craterlike basin (depth, approximately 23 m) on the coral reef seafloor. The vent fluid (maximum temperature, >52 degrees C) contained 175 microM H2S and gas bubbles mainly composed of CH4 (69%) and N2 (29%). A liquid serial dilution cultivation technique targeting a variety of metabolism types quantified each population in the vent fluid and in a white microbial mat located near the vent. The most abundant microorganisms cultivated from both the fluid and the mat were autotrophic sulfur oxidizers, including mesophilic Thiomicrospira spp. and thermophilic Sulfurivirga caldicuralii. Methane oxidizers were the second most abundant organisms in the fluid; one novel type I methanotroph exhibited optimum growth at 37 degrees C, and another novel type I methanotroph exhibited optimum growth at 45 degrees C. The number of hydrogen oxidizers cultivated only from the mat was less than the number of sulfur and methane oxidizers, although a novel mesophilic hydrogen-oxidizing member of the Epsilonproteobacteria was isolated. Various mesophilic to hyperthermophilic heterotrophs, including sulfate-reducing Desulfovibrio spp., iron-reducing Deferribacter sp., and sulfur-reducing Thermococcus spp., were also cultivated. Culture-independent 16S rRNA gene clone analysis of the vent fluid and mat revealed highly diverse archaeal communities. In the bacterial community, S. caldicuralii was identified as the predominant phylotype in the fluid (clonal frequency, 25%). Both bacterial clone libraries indicated that there were bacterial communities involved in sulfur, hydrogen, and methane oxidation and sulfate reduction. Our results indicate that there are unique microbial communities that are sustained by active chemosynthetic primary production rather than by photosynthetic production in a shallow hydrothermal system where sunlight is abundant.

Thermaerobacter litoralis sp. nov., a strictly aerobic and thermophilic bacterium isolated from a coastal hydrothermal field

A novel thermophilic bacterium, strain KW1(T), was isolated from a coastal hydrothermal field on the Satsuma Peninsula, Kagoshima Prefecture, Japan. The variably Gram-stained cells were motile rods with flagella, did not form spores and proliferated at 52-78 degrees C (optimum, 70 degrees C), pH 5-8 (optimum, pH 7) and 0-4.5 % NaCl (optimum, 1.0 %). The novel isolate was a strictly aerobic heterotroph that utilized complex proteinaceous substrates as well as a variety of carboxylic acids and amino acids. The G+C content of the genomic DNA was 70.8 mol%. Analysis of 16S rRNA gene sequences indicated that strain KW1(T) is closely related to Thermaerobacter subterraneus C21(T) (98.4 % sequence similarity). However, the DNA-DNA hybridization value for strain KW1(T) and T. subterraneus ATCC BAA-137(T) was below 46 %. On the basis of the molecular and physiological traits of strain KW1(T), it represents a novel species of the genus Thermaerobacter, for which the name Thermaerobacter litoralis sp. nov. is proposed. The type strain is KW1(T) (=JCM 13210(T)=DSM 17372(T)).

Natural chaperonin of the hyperthermophilic archaeum, Thermococcus strain KS-1: a hetero-oligomeric chaperonin with variable subunit composition

To study the difference in expression of the chaperonin alpha- and beta-subunits in Thermococcus strain KS-1 (T. KS-1), we measured their intracellular contents at various growth temperatures using subunit-specific antibodies. The beta-subunit was significantly more abundant with increasing temperature (maximum at 93 degrees C), whereas the alpha-subunit was not. Native PAGE with Western blot analysis indicated that the natural chaperonins in the crude extracts of T. KS-1 cells grown between 65 degrees C and 95 degrees C migrate as single bands with different mobility. The recombinant alpha- and beta-subunit homo-oligomers migrated differently from each other and from natural chaperonins. Immunoprecipitation also showed that the natural chaperonin was the hetero-oligomer. These results indicate that chaperonin in T. KS-1 formed a hetero-oligomer with variable subunit composition, and that the beta-subunit may be adapted to a higher temperature than the alpha-subunit. T. KS-1 probably changes its chaperonin subunit composition to acclimatize to the ambient temperature.

Distribution and physiological characteristics of hyperthermophiles in the Kubiki oil reservoir in Niigata, Japan

The distribution of culturable hyperthermophiles was studied in relation to environmental conditions in the Kubiki oil reservoir in Japan, where the temperature was between 50 and 58 degrees C. Dominant hyperthermophilic cocci and rods were isolated and shown to belong to the genera Thermococcus and Thermotoga, respectively, by 16S rDNA analyses. Using the most-probable-number method, we found that hyperthermophilic cocci were widely distributed in several unconnected fault blocks in the Kubiki oil reservoir. In 1996 to 1997, their populations in the production waters from oil wells were 9.2 x 10(3) to 4.6 x 10(4) cells/ml, or 10 to 42% of total cocci. On the other hand, hyperthermophilic rods were found in only one fault block of the reservoir with populations less than 10 cells/ml. Dominant Thermococcus and Thermotoga spp. grew at reservoir temperatures and utilized amino acids and sugars, respectively, as sole carbon sources. While organic carbon was plentiful in the environment, these hyperthermophiles were unable to grow in the formation water due to lack of essential nutrients. Concentrations of some organic and inorganic substances differed among fault blocks, indicating that the movement of formation water between fault blocks was restricted. This finding suggests that the supply of nutrients via fluid current is limited in this subterranean environment and that the organisms are starved in the oil reservoir. Under starved conditions at 50 degrees C, culturable cells of Thermococcus sp. remained around the initial cell density for about 200 days, while those of Thermotoga sp. decreased exponentially to 0. 01% of the initial cell density after incubation for the same period. The difference in survivability between these two hyperthermophiles seems to reflect their populations in the fault blocks. These results indicate that hyperthermophilic cocci and rods adapt to the subterranean environment of the Kubiki oil reservoir by developing an ability to survive under starved conditions.

Spatial heterogeneity of bacterial populations along an environmental gradient at a shallow submarine hydrothermal vent near Milos Island (Greece)

The spatial heterogeneity of bacterial populations at a shallow-water hydrothermal vent in the Aegean Sea close to the island of Milos (Greece) was examined at two different times by using acridine orange staining for total cell counts, cultivation-based techniques, and denaturing gradient gel electrophoresis (DGGE) analysis of PCR-amplified 16S rRNA gene fragments. Concurrent with measurements of geochemical parameters, samples were taken along a transect from the center of the vent to the surrounding area. Most-probable-number (MPN) counts of metabolically defined subpopulations generally constituted a minor fraction of the total cell counts; both counting procedures revealed the highest cell numbers in a transition zone from the strongly hydrothermally influenced sediments to normal sedimentary conditions. Total cell counts ranged from 3.2 x 10(5) cells ml(-1) in the water overlying the sediments to 6.4 x 10(8) cells g (wet weight) of sediment(-1). MPN counts of chemolithoautotrophic sulfur-oxidizing bacteria varied between undetectable and 1.4 x 10(6) cells g(-1). MPN counts for sulfate-reducing bacteria and dissimilatory iron-reducing bacteria ranged from 8 to 1.4 x 10(5) cells g(-1) and from undetectable to 1.4 x 10(6) cells g(-1), respectively. DGGE revealed a trend from a diverse range of bacterial populations which were present in approximately equal abundance in the transition zone to a community dominated by few populations close to the center of the vent. Temperature was found to be an important parameter in determining this trend. However, at one sampling time this trend was not discernible, possibly due to storm-induced disturbance of the upper sediment layers.

Purification and characterization of two reversible and ADP-dependent acetyl coenzyme A synthetases from the hyperthermophilic archaeon Pyrococcus furiosus

Pyrococcus furiosus is a strictly anaerobic archaeon (archaebacterium) that grows at temperatures up to 105 degrees C by fermenting carbohydrates and peptides. Cell extracts have been previously shown to contain an unusual acetyl coenzyme A (acetyl-CoA) synthetase (ACS) which catalyzes the formation of acetate and ATP from acetyl-CoA by using ADP and phosphate rather than AMP and PPi. We show here that P. furiosus contains two distinct isoenzymes of ACS, and both have been purified. One, termed ACS I, uses acetyl-CoA and isobutyryl-CoA but not indoleacetyl-CoA or phenylacetyl-CoA as substrates, while the other, ACS II, utilizes all four CoA derivatives. Succinyl-CoA did not serve as a substrate for either enzyme. ACS I and ACS II have similar molecular masses (approximately 140 kDa), and both appear to be heterotetramers (alpha2beta2) of two different subunits of 45 (alpha) and 23 (beta) kDa. They lack metal ions such as Fe2+, Cu2+, Zn2+, and Mg2+ and are stable to oxygen. At 25 degrees C, both enzymes were virtually inactive and exhibited optimal activities above 90 degrees C (at pH 8.0) and at pH 9.0 (at 80 degrees C). The times required to lose 50% of their activity at 80 degrees C were about 18 h for ACS I and 8 h for ACS II. With both enzymes in the acid formation reactions, ADP and phosphate could be replaced by GDP and phosphate but not by CDP and phosphate or by AMP and PPi. The apparent Km values for ADP, GDP, and phosphate were approximately 150, 132, and 396 microM, respectively, for ACS I (using acetyl-CoA) and 61, 236, and 580 microM, respectively, for ACS II (using indoleacetyl-CoA). With ADP and phosphate as substrates, the apparent Km values for acetyl-CoA and isobutyryl-CoA were 25 and 29 microM, respectively, for ACS I and 26 and 12 microM, respectively, for ACS II. With ACS II, the apparent Km value for phenylacetyl-CoA was 4 microM. Both enzymes also catalyzed the reverse reaction, the ATP-dependent formation of the CoA derivatives of acetate (I and II), isobutyrate (I and II), phenylacetate (II only), and indoleacetate (II only). The N-terminal amino acid sequences of the two subunits of ACS I were similar to those of ACS II and to that of a hypothetical 67-kDa protein from Escherichia coli but showed no similarity to mesophilic ACS-type enzymes. To our knowledge, ACS I and II are the first ATP-utilizing enzymes to be purified from a hyperthermophile, and ACS II is the first enzyme of the ACS type to utilize aromatic CoA derivatives.