Cellulose as extracellular polysaccharide of hot spring sulfur-turf bacterial mat

The carbohydrate fraction of a hot spring sulfur-turf bacterial mat was shown to contain cellulose by the examination of neutral sugar composition, methylation analysis, and the identification of free oligosacchrides obtained from an acetolyzate of the desulfurized sulfur-turf mat. This suggested that the sulfur-oxidizing bacteria composing the sulfur-turf were producers of cellulose.     

Sulfur-metabolizing bacterial populations in microbial mats of the Nakabusa hot spring, Japan

At the Nakabusa hot spring, Japan, dense olive-green microbial mats develop in regions where the slightly alkaline, sulfidic effluent has cooled to 65 °C. The microbial community of such mats was analyzed by focusing on the diversity, as well as the in situ distribution and function of bacteria involved in sulfur cycling. Analyses of 16S rRNA and functional genes (aprA, pufM) suggested the importance of three thermophilic bacterial groups: aerobic chemolithotrophic sulfide-oxidizing species of the genus Sulfurihydrogenibium (Aquificae), anaerobic sulfate-reducing species of the genera Thermodesulfobacterium/Thermodesulfatator, and filamentous anoxygenic photosynthetic species of the genus Chloroflexus. A new oligonucleotide probe specific for Sulfurihydrogenibium was designed and optimized for catalyzed reporter deposition fluorescence in situ hybridization (CARD-FISH). In situ hybridizations of thin mat sections showed a heterogeneous vertical distribution of Sulfurihydrogenibium and Chloroflexus. Sulfurihydrogenibium dominated near the mat surface (50% of the total mat biovolume), while Chloroflexus dominated in deeper layers (up to 64% of the total mat biovolume). Physiological experiments monitoring in vitro changes of sulfide concentration indicated slight sulfide production by sulfate-reducing bacteria under anoxic-dark conditions, sulfide consumption by photosynthetic bacteria under anoxic-light conditions and strong sulfide oxidation by chemolithotrophic members of Aquificae under oxic-dark condition. We therefore propose that Sulfurihydrogenibium spp. act as highly efficient scavengers of oxygen from the spring water, thus creating a favorable, anoxic environment for Chloroflexus and Thermodesulfobacterium/Thermodesulfatator in deeper layers.     

Archaeal and bacterial diversity in two hot spring microbial mats from a geothermal region in Romania

The diversity of archaea and bacteria was investigated in two slightly alkaline, mesophilic hot springs from the Western Plain of Romania. Phylogenetic analysis showed a low diversity of Archaea, only three Euryarchaeota taxa being detected: Methanomethylovorans thermophila, Methanomassiliicoccus luminyensis and Methanococcus aeolicus. Twelve major bacterial groups were identified, both springs being dominated by Cyanobacteria, Chloroflexi and Proteobacteria. While at the phylum/class-level the microbial mats share a similar biodiversity; at the species level the geothermal springs investigated seem to be colonized by specific consortia. The dominant taxa were filamentous heterocyst-containing Fischerella, at 45 °C and non-heterocyst Leptolyngbya and Geitlerinema, at 55 °C. Other bacterial taxa (Thauera sp., Methyloversatilis universalis, Pannonibacter phragmitetus, Polymorphum gilvum, Metallibacterium sp. and Spartobacteria) were observed for the first time in association with a geothermal habitat. Based on their bacterial diversity the two mats were clustered together with other similar habitats from Europe and part of Asia, most likely the water temperature playing a major role in the formation of specific microbial communities that colonize the investigated thermal springs.     

Differential microbial communities in hot spring mats from Western Thailand

The microbial communities of freshwater hot spring mats from Boekleung (Western Thailand) were studied. Temperatures ranged from over 50 up to 57°C. Green-, red-, and yellow colored mat layers were analyzed. In order to detect the major components of the microbial communities constituting the mat as well as the microorganisms showing significant metabolic activity, samples were analyzed using DNA- and RNA-based molecular techniques, respectively. Microbial community fingerprints, performed by denaturing gradient gel electrophoresis (DGGE), revealed clear differences among mat layers. Thermophilic phototrophic microorganisms, Cyanobacteria and Chloroflexi, constituted the major groups in these communities (on average 65 and 51% from DNA and RNA analyses, respectively). Other bacteria detected in the mat were Bacteroidetes, members of the Candidate Division OP10, Actinobacteria, and Planctomycetes. Differently colored mat layers showed characteristic bacterial communities and the major components of the metabolically active fraction of these communities have been identified.     

A halophilic thermotolerant Bacillus isolated from a marine hot spring able to produce a new exopolysaccharide

A halophilic, thermotolerant Bacillus strain (B3-15), isolated from water of a shallow, marine hot spring at Vulcano Island (Eolian Islands, Italy), produced an exocellular polysaccharide at 165 mg l^–1. It grew on kerosene as sole carbon source and was resistant to Cd²⁺, Zn²⁺, As²⁺ and Hg²⁺. From 16S rDNA analysis, strain B3-15 was related to B. licheniformis. The exopolysaccharide was a tetrasaccharide repeating unit essentially constituted by sugars having a manno-pyranosidic configuration.     

Biogeochemical processes in the algal-bacterial mats of the Urinskii alkaline hot spring

The structure and production characteristics of microbial communities from the Urinskii alkaline hot spring (Buryat Republic, Russia) have been investigated. A distinctive characteristic of this hot spring is the lack of sulfide in the issuing water. The water temperature near the spring vents ranged from 69 to 38.5°C and pH values ranged from 8.8 to 9.2. The total mineralization of water was less than 0.1 g/liter. Temperature has a profound effect on the species composition and biogeochemical processes occurring in the algal-bacterial mats of the Urinskii hot spring. The maximum diversity of the phototrophic community was observed at the temperatures 40 and 46°C. A total of 12 species of cyanobacteria, 4 species of diatoms, and one species of thermophilic anoxygenic phototrophic bacteria, Chloroflexus aurantiacus, have been isolated from mat samples. At temperatures above 40°C, the filamentous cyanobacterium Phormidium laminosum was predominant; its cell number and biomass concentration comprised 95.1 and 63.9%, respectively. At lower temperatures, the biomass concentrations of the cyanobacterium Oscillatoria limosa and diatoms increased (50.2 and 36.4%, respectively). The cyanobacterium Mastigocladus laminosus, which is normally found in neutral or slightly acidic hydrothermal systems, was detected in microbial communities. As the diatom concentration increases, so does the dry matter concentration in mats, while the content of organic matter decreases. The concentrations of proteins and carbohydrates reached their maximum levels at 45–50°C. The maximum average rate of oxygenic photosynthesis [2.1 g C/(m² day)], chlorophyll a content (343.4 mg/m²), and cell number of phototrophic microorganisms were observed at temperatures from 45 to 50°C. The peak mass of bacterial mats (56.75 g/m²) occurred at a temperature of 65–60°C. The maximum biomass concentration of phototrophs (414.63 × 10^?6 g/ml) and the peak rate of anoxygenic photosynthesis [0.42 g C/(m² day)] were observed at a temperature of 35–40°C.     

Biogeochemical processes in the algal-bacterial mats of the Urinskii alkaline hot spring

The structure and production characteristics of microbial communities from the Urinskii alkaline hot spring (Buryat Republic, Russia) have been investigated. A distinctive characteristic of this hot spring is the lack of sulfide in the issuing water. The water temperature near the spring vents ranged from 69 to 38.5 degrees C and pH values ranged from 8.8 to 9.2. The total mineralization of water was less than 0.1 g/liter. Temperature has a profound effect on the species composition and biogeochemical processes occurring in the algal-bacterial mats of the Urinskii hot spring. The maximum diversity of the phototrophic community was observed at the temperatures 40 and 46 degrees C. A total of 12 species of cyanobacteria, 4 species of diatoms, and one species of thermophilic anoxygenic phototrophic bacteria, Chloroflexus aurantiacus, have been isolated from mat samples. At temperatures above 40 degrees C, the filamentous cyanobacterium Phormidium laminosum was predominant; its cell number and biomass concentration were 95.1 and 63.9%, respectively. At lower temperatures, the biomass concentrations of the cyanobacterium Oscillatoria limosa and diatoms increased (50.2 and 36.4%, respectively). The cyanobacterium Mastigocladus laminosus, which is normally found in neutral or slightly acidic hydrothermal systems, was detected in microbial communities. As the diatom concentration increases, so does the dry matter concentration in mats, while the content of organic matter decreases. The concentrations of proteins and carbohydrates reached their maximum levels at 45-50 degrees C. The maximum average rate of oxygenic photosynthesis (2.1 g C/m2 day), chlorophyll a content (343.4 mg/m2), and cell number of phototrophic microorganisms were observed at temperatures from 45 to 50 degrees C. The peak mass of bacterial mats (56.75 g/m2) occurred at a temperature of 65-60 degrees C. The maximum biomass concentration of phototrophs (414.63 x 10(-6) g/ml) and the peak rate of anoxygenic photosynthesis [0.42 g C/(m2 day)] were observed at a temperature of 35-40 degrees C.     

Obligately phototrophic Chloroflexus: primary production in anaerobic hot spring microbial mats

Microbial mats which lack cyanobacteria occur at 50° to 65° C in the sulfide-containing Mammoth Springs of Yellowstone National Park. The principal organisms within these mats are filamentous bacteria which resemble Chloroflexus aurantiacus. The incorporation of [¹⁴C]-HCO ₃ ^- into mat material depended upon both light and sulfide, and was not inhibited when complete natural light was replaced with far-red and infra-red radiation. [¹⁴C]-acetate was incorporated in a light-dependent reaction which was stimulated by, but did not require, sulfide. In situ experiments with microelectrodes demonstrated net sulfide uptake by the mat in the light, and net sulfide production by the mat in the dark, suggesting the operation of a sulfur cycle.Filamentous phototrophic bacteria isolated from the mat were incapable of sustained growth in the presence of O₂.Simultaneous exposure of cultures to light and O₂ caused degradation of bacteriochlorophyll c. The stimulation of light-dependent [¹⁴C]-HCO ₃ ^- -uptake by sulfide was more pronounced in these isolates than in strains of Chloroflexus aurantiacus.     

Phylogenetic characterization of microbial mats and streamers from a Japanese alkaline hot spring with a thermal gradient

Dense microbial mats and streamers of various colors developed in an alkaline-hot spring water at 48-76 degrees C and ~0.077 mm sulfide in Nakabusa, Japan. The microbial community structures with a thermal gradient were compared by denaturing gradient gel electrophoresis (DGGE) analysis of the PCR-amplified 16S ribosomal RNA gene fragments. The sequence analysis revealed that a predominant cyanobacterial DGGE band phylogenetically related to Synechococcus elongatus was detected only from green mats at 48 degrees C. Four DGGE bands were detected commonly from green mats at 48 degrees C, orange mats at 58 degrees C and brown mats at 60 degrees C. The sequence analysis revealed that these were phylogenetically related to Chloroflexaceae group, Rhodothermus group, a candidate division OP10, and an unclassified bacterium. On the other hand, Aquificae-, Thermodesulfobacteria-, Thermus group-, and Crenarchaeota-like sequences were detected as a predominant component of DGGE profiling from the streamers only at temperatures over 66 degrees C, but no phototrophic bacterial bands were detected. Thus, the microbial community structure above 60 degrees C was drastically different from that at the lower temperatures. After the addition of hydrogen into in vitro gray streamers with in situ spring water, sulfide production markedly occurred in the presence of ambient sulfate at 66 degrees C. This result suggests that in situ sulfide is partly produced by Thermodesulfobacteria-like sulfate-reducing bacteria in the streamers.     

Thermodesulfovibrio hydrogeniphilus sp. nov., a new thermophilic sulphate-reducing bacterium isolated from a Tunisian hot spring

A new thermophilic sulphate-reducing bacterium (strain Hbr5^T) was enriched and isolated from a terrestrial Tunisian hot spring. It was a non-spore-forming Gram-negative curved or vibrio-shaped bacterium. It appeared singly or in long chains and was actively motile by a polar flagellum. It possessed c-type cytochromes and desulfofuscidin. Growth occurred between 50 and 70 °C, with an optimum of 65 °C at pH 7.1. In the presence of sulphate as a terminal electron acceptor, this strain readily used H₂ but formate only poorly. It could use sulphate, thiosulphate, sulphite or arsenate as electron acceptors. Its DNA G+C content was 36.1 mol%. Based on phenotypic, genomic, and phylogenetic characteristics, strain Hbr5^T (=DSM 18151^T, =JCM 13991^T) is proposed to be assigned to a novel species of genus Thermodesulfovibrio, T. hydrogeniphilus sp. nov.     

Community ecology of hot spring cyanobacterial mats: predominant populations and their functional potential

Phototrophic microbial mat communities from 60 °C and 65 °C regions in the effluent channels of Mushroom and Octopus Springs (Yellowstone National Park, WY, USA) were investigated by shotgun metagenomic sequencing. Analyses of assembled metagenomic sequences resolved six dominant chlorophototrophic populations and permitted the discovery and characterization of undescribed but predominant community members and their physiological potential. Linkage of phylogenetic marker genes and functional genes showed novel chlorophototrophic bacteria belonging to uncharacterized lineages within the order Chlorobiales and within the Kingdom Chloroflexi. The latter is the first chlorophototrophic member of Kingdom Chloroflexi that lies outside the monophyletic group of chlorophototrophs of the Order Chloroflexales. Direct comparison of unassembled metagenomic sequences to genomes of representative isolates showed extensive genetic diversity, genomic rearrangements and novel physiological potential in native populations as compared with genomic references. Synechococcus spp. metagenomic sequences showed a high degree of synteny with the reference genomes of Synechococcus spp. strains A and B′, but synteny declined with decreasing sequence relatedness to these references. There was evidence of horizontal gene transfer among native populations, but the frequency of these events was inversely proportional to phylogenetic relatedness.     

Distribution of cultivated and uncultivated cyanobacteria and Chloroflexus-like bacteria in hot spring microbial mats

Oligodeoxynucleotide hybridization probes were developed to complement specific regions of the small subunit (SSU) rRNA sequences of cultivated and uncultivated cyanobacteria and Chloroflexus-like bacteria, which inhabit hot spring microbial mats. The probes were used to investigate the natural distribution of SSU rRNAs from these species in mats of Yellowstone hot springs of different temperatures and pHs as well as changes in SSU rRNA distribution resulting from 1-week in situ shifts in temperature, pH, and light intensity. Synechococcus lividus Y-7c-s SSU rRNA was detected only in the mat of a slightly acid spring, from which it may have been initially isolated, or when samples from a more alkaline spring were incubated in the more acid spring. Chloroflexus aurantiacus Y-400-fl SSU rRNA was detected only in a high-temperature mat sample from the alkaline Octopus Spring or when lower-temperature samples from this mat were incubated at the high-temperature site. SSU rRNAs of uncultivated species were more widely distributed. Temperature distributions and responses to in situ temperature shifts suggested that some of the uncultivated cyanobacteria might be adapted to high-, moderate-, and low-temperature ranges whereas an uncultivated Chloroflexus-like bacterium appears to have broad temperature tolerance. SSU rRNAs of all uncultivated species inhabiting a 48 to 51 degrees C Octopus Spring mat site were most abundant in the upper 1 mm and were not detected below a 2.5-to 3.5-mm depth, a finding consistent with their possible phototrophic nature. However, the effects of light intensity reduction on these SSU rRNAs were variable, indicating the difficulty of demonstrating a phototrophic phenotype in light reduction experiments.     

Bacterial and archaeal diversity in two hot spring microbial mats from the geothermal region of Tengchong, China

We investigated the bacterial and archaeal diversity in two hot spring microbial mats from the geothermal region of Tengchong in the Yunnan Province, China, using direct molecular analyses. The Langpu (LP) laminated mat was found by the side of a boiling pool with temperature of 60-65?°C and a pH of 8.5, while the Tengchong (TC) streamer mat consisted of white streamers in a slightly acidic (pH 6.5) hot pool outflow with a temperature of 72?°C. Four 16S rRNA gene clone libraries were constructed and restriction enzyme analysis of the inserts was used to identify unique sequences and clone frequencies. From almost 200 clones screened, 55 unique sequences were retrieved. Phylogenetic analysis showed that the LP mat consisted of a diverse bacterial population [Cyanobacteria, Chloroflexi, Chlorobia, Nitrospirae, 'Deinococcus-Thermus', Proteobacteria (alpha, beta and delta subdivisions), Firmicutes, Bacteroidetes and Actinobacteria], while the archaeal population was dominated by methanogenic Euryarchaeota and Crenarchaeota. In contrast, the TC streamer mat consisted of a bacterial population dominated by Aquificae, while the archaeal population also contained Korarchaeota as well as Crenarchaeota and methanogenic Euryarchaeota. These mats harboured clone sequences affiliated to unidentified lineages, suggesting that they are a potential source for discovering novel bacteria and archaea.     

Streptomyces calidiresistens sp. nov., isolated from a hot spring sediment

A Streptomyces-like actinomycete strain, designated as YIM 78087^T, was isolated from a sediment sample collected from Hehua hot spring in Tengchong, Yunnan province, south-west China. The taxonomic position of strain YIM 78087^T was investigated by a polyphasic approach. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain YIM 78087^T belongs to the genus Streptomyces and is closely related to Streptomyces fimbriatus DSM 40942^T, Streptomyces marinus DSM 41968^T and Streptomyces qinglanensis DSM 42035^T (97.18, 97.05 and 97.1 % similarity, respectively). Combined with the low values of DNA–DNA hybridization between strain YIM 78087^T and its closest neighbours, these analyses indicated that this new isolate represents a different genomic species in the genus Streptomyces. The predominant menaquinones of strain YIM 78087^T were identified as MK-9 (H₄) and MK-9 (H₆). The major fatty acids were identified as anteiso-C_15:0 (28.4 %), anteiso-C_17:0 (23.0 %) and iso-C_16:0 (15.1 %). The whole-cell hydrolysates found to contain glucose, mannose and ribose. The DNA G+C content was determined to be 73.0 mol%. Based on the comparative analysis of phenotypic and genotypic characteristics, it is proposed that strain YIM 78087^T represents a novel species of the genus Streptomyces, for which the name Streptomyces calidiresistens sp. nov., is proposed. The type strain is YIM 78087^T (=BCRC 16955^T=DSM 42108^T=JCM 19629^T).     

A silicified bird from Quaternary hot spring deposits

The first avian fossil recovered from high-temperature hot spring deposits is a three-dimensional external body mould of an American coot (Fulica americana) from Holocene sinters of Yellowstone National Park, Wyoming, USA. Silica encrustation of the carcass, feathers and colonizing microbial communities occurred within days of death and before substantial soft tissue degradation, allowing preservation of gross body morphology, which is usually lost under other fossilization regimes. We hypothesize that the increased rate and extent of opal-A deposition, facilitated by either passive or active microbial mediation following carcass colonization, is required for exceptional preservation of relatively large, fleshy carcasses or soft-bodied organisms by mineral precipitate mould formation. We suggest physico-chemical parameters conducive to similar preservation in other vertebrate specimens, plus distinctive sinter macrofabric markers of hot spring subenvironments where these parameters are met.     

Distribution of cultivated and uncultivated cyanobacteria and Chloroflexus-like bacteria in hot spring microbial mats.

Oligodeoxynucleotide hybridization probes were developed to complement specific regions of the small subunit (SSU) rRNA sequences of cultivated and uncultivated cyanobacteria and Chloroflexus-like bacteria, which inhabit hot spring microbial mats. The probes were used to investigate the natural distribution of SSU rRNAs from these species in mats of Yellowstone hot springs of different temperatures and pHs as well as changes in SSU rRNA distribution resulting from 1-week in situ shifts in temperature, pH, and light intensity. Synechococcus lividus Y-7c-s SSU rRNA was detected only in the mat of a slightly acid spring, from which it may have been initially isolated, or when samples from a more alkaline spring were incubated in the more acid spring. Chloroflexus aurantiacus Y-400-fl SSU rRNA was detected only in a high-temperature mat sample from the alkaline Octopus Spring or when lower-temperature samples from this mat were incubated at the high-temperature site. SSU rRNAs of uncultivated species were more widely distributed. Temperature distributions and responses to in situ temperature shifts suggested that some of the uncultivated cyanobacteria might be adapted to high-, moderate-, and low-temperature ranges whereas an uncultivated Chloroflexus-like bacterium appears to have broad temperature tolerance. SSU rRNAs of all uncultivated species inhabiting a 48 to 51 degrees C Octopus Spring mat site were most abundant in the upper 1 mm and were not detected below a 2.5-to 3.5-mm depth, a finding consistent with their possible phototrophic nature. However, the effects of light intensity reduction on these SSU rRNAs were variable, indicating the difficulty of demonstrating a phototrophic phenotype in light reduction experiments.     

Phototrophs in high-iron-concentration microbial mats: physiological ecology of phototrophs in an iron-depositing hot spring

At Chocolate Pots Hot Springs in Yellowstone National Park the source waters have a pH near neutral, contain high concentrations of reduced iron, and lack sulfide. An iron formation that is associated with cyanobacterial mats is actively deposited. The uptake of [(14)C]bicarbonate was used to assess the impact of ferrous iron on photosynthesis in this environment. Photoautotrophy in some of the mats was stimulated by ferrous iron (1.0 mM). Microelectrodes were used to determine the impact of photosynthetic activity on the oxygen content and the pH in the mat and sediment microenvironments. Photosynthesis increased the oxygen concentration to 200% of air saturation levels in the top millimeter of the mats. The oxygen concentration decreased with depth and in the dark. Light-dependent increases in pH were observed. The penetration of light in the mats and in the sediments was determined. Visible radiation was rapidly attenuated in the top 2 mm of the iron-rich mats. Near-infrared radiation penetrated deeper. Iron was totally oxidized in the top few millimeters, but reduced iron was detected at greater depths. By increasing the pH and the oxygen concentration in the surface sediments, the cyanobacteria could potentially increase the rate of iron oxidation in situ. This high-iron-content hot spring provides a suitable model for studying the interactions of microbial photosynthesis and iron deposition and the role of photosynthesis in microbial iron cycling. This model may help clarify the potential role of photosynthesis in the deposition of Precambrian banded iron formations.