Draft Genome Sequence of Desulfosporosinus fructosivorans Strain 63.6FT, Isolated from Marine Sediment in the Baltic Sea.

Desulfosporosinus fructosivorans strain 63.6FT is a strictly anaerobic, spore-forming, sulfate-reducing bacterium isolated from marine sediment in the Baltic Sea. Here, we report the draft genome sequence of D. fructosivorans 63.6FT.

Draft Genome Sequences of Six Vibrio diazotrophicus Strains Isolated from Deep Subsurface Sediments of the Baltic Sea.

We present here the draft genome sequences of six Vibrio diazotrophicus strains, which were isolated from deep subseafloor sediments of the Baltic Sea. The genomic sequences contained several virulence and antibiotic resistance genes. These genome sequences provide insights into the genetic composition and evolution of the genus Vibrio in marine environments.

Marinisporobacter balticus gen. nov., sp. nov., Desulfosporosinus nitroreducens sp. nov. and Desulfosporosinus fructosivorans sp. nov., new spore-forming bacteria isolated from subsurface sediments of the Baltic Sea.

Four novel Gram-stain-positive, endospore-forming bacteria of the order Clostridiales were isolated from subsurface sediments sampled during International Ocean Discovery Program Expedition 347 to the Baltic Sea. One strain (59.4MT) grew as an obligate heterotroph by aerobic respiration and anaerobically by fermentation. Optimum growth was observed with 0.5 % NaCl at 25 °C and pH 7.0-7.3. Analysis of 16S rRNA gene sequences of 59.4MT revealed Alkaliphilus transvaalensis (92.3 % identity), Candidatus Geosporobacter ferrireducens (92.2 %), Geosporobacter subterraneus (91.9 %) and Alkaliphilus peptidifermentans (91.7 %) to be the closest relatives. On the basis of the results of phenotypic and genotypic analyses, we propose that strain 59.4MT represents a novel species within a novel genus, Marinisporobacter balticus gen. nov., sp. nov., with the type strain 59.4MT (=DSM 102940T=JCM 31103T). Three other strains, 59.4F, 59.4BT and 63.6FT, were affiliated with the genus Desulfosporosinus and grew as strictly anaerobic sulfate reducers. These strains additionally used thiosulfate, elemental sulfur, sulfite and DMSO as electron acceptors and hydrogen as an electron donor. Strains 59.4F and 59.4BT had identical 16S rRNA gene sequences, which were most similar to those of Desulfosporosinus lacus (97.8 %), Desulfosporosinus hippei (97.3 %) and Desulfosporosinus orientis (97.3 %). Strain 63.6FT was closely related to D. lacus (97.7 %), Desulfosporosinus meridiei (96.6 %) and D. hippei (96.5 %). The similarity of 16S rRNA gene sequences of strains 59.4BT and 63.6FT was 96.6 %. We propose the new names Desulfosporosinus nitroreducens sp. nov., incorporating strain 59.4F (=DSM 101562=JCM 31104) and the type strain 59.4BT (=DSM 101608T=JCM 31105T), and Desulfosporosinus fructosivorans sp. nov., with the type strain 63.6FT (=DSM 101609T=JCM 31106T).

Labilibaculum manganireducens gen. nov., sp. nov. and Labilibaculum filiforme sp. nov., Novel Bacteroidetes Isolated from Subsurface Sediments of the Baltic Sea.

Microbial communities in deep subsurface sediments are challenged by the decrease in amount and quality of organic substrates with depth. In sediments of the Baltic Sea, they might additionally have to cope with an increase in salinity from ions that have diffused downward from the overlying water during the last 9000 years. Here, we report the isolation and characterization of four novel bacteria of the Bacteroidetes from depths of 14-52 m below seafloor (mbsf) of Baltic Sea sediments sampled during International Ocean Discovery Program (IODP) Expedition 347. Based on physiological, chemotaxonomic and genotypic characterization, we propose that the four strains represent two new species within a new genus in the family Marinifilaceae, with the proposed names Labilibaculum manganireducens gen. nov., sp. nov. (type strain 59.10-2MT) and Labilibaculum filiforme sp. nov. (type strains 59.16BT) with additional strains of this species (59.10-1M and 60.6M). The draft genomes of the two type strains had sizes of 5.2 and 5.3 Mb and reflected the major physiological capabilities. The strains showed gliding motility, were psychrotolerant, neutrophilic and halotolerant. Growth by fermentation of mono- and disaccharides as well as pyruvate, lactate and glycerol was observed. During glucose fermentation, small amounts of electron equivalents were transferred to Fe(III) by all strains, while one of the strains also reduced Mn(IV). Thereby, the four strains broaden the phylogenetic range of prokaryotes known to reduce metals to the group of Bacteroidetes. Halotolerance and metal reduction might both be beneficial for survival in deep subsurface sediments of the Baltic Sea.

Virus Dynamics Are Influenced by Season, Tides and Advective Transport in Intertidal, Permeable Sediments.

Sandy surface sediments of tidal flats exhibit high microbial activity due to the fast and deep-reaching transport of oxygen and nutrients by porewater advection. On the other hand during low tide, limited transport results in nutrient and oxygen depletion concomitant to the accumulation of microbial metabolites. This study represents the first attempt to use flow-through reactors to investigate virus production, virus transport and the impact of tides and season in permeable sediments. The reactors were filled with intertidal sands of two sites (North beach site and backbarrier sand flat of Spiekeroog island in the German Wadden Sea) to best simulate advective porewater transport through the sediments. Virus and cell release along with oxygen consumption were measured in the effluents of reactors during continuous flow of water through the sediments as well as in tidal simulation experiments where alternating cycles with and without water flow (each for 6 h) were operated. The results showed net rates of virus production (0.3-13.2 × 106 viruses cm-3 h-1) and prokaryotic cell production (0.3-10.0 × 105 cells cm-3 h-1) as well as oxygen consumption rates (56-737 µmol l-1 h-1) to be linearly correlated reflecting differences in activity, season and location of the sediments. Calculations show that total virus turnover was fast with 2 to 4 days, whereas virus-mediated cell turnover was calculated to range between 5-13 or 33-91 days depending on the assumed burst sizes (number of viruses released upon cell lysis) of 14 or 100 viruses, respectively. During the experiments, the homogenized sediments in the reactors became vertically structured with decreasing microbial activities and increasing impact of viruses on prokaryotic mortality with depth. Tidal simulation clearly showed a strong accumulation of viruses and cells in the top sections of the reactors when the flow was halted indicating a consistently high virus production during low tide. In conclusion, cell lysis products due to virus production may fuel microbial communities in the absence of advection-driven nutrient input, but are eventually washed off the surface sediment during high tide and being transported into deeper sediment layers or into the water column together with the produced viruses.

Genome sequence of Shimia str. SK013, a representative of the Roseobacter group isolated from marine sediment.

Shimia strain SK013 is an aerobic, Gram-negative, rod shaped alphaproteobacterium affiliated with the Roseobacter group within the family Rhodobacteraceae. The strain was isolated from surface sediment (0-1 cm) of the Skagerrak at 114 m below sea level. The 4,049,808 bp genome of Shimia str. SK013 comprises 3,981 protein-coding genes and 47 RNA genes. It contains one chromosome and no extrachromosomal elements. The genome analysis revealed the presence of genes for a dimethylsulfoniopropionate lyase, demethylase and the trimethylamine methyltransferase (mttB) as well as genes for nitrate, nitrite and dimethyl sulfoxide reduction. This indicates that Shimia str. SK013 is able to switch from aerobic to anaerobic metabolism and thus is capable of aerobic and anaerobic sulfur cycling at the seafloor. Among the ability to convert other sulfur compounds it has the genetic capacity to produce climatically active dimethyl sulfide. Growth on glutamate as a sole carbon source results in formation of cell-connecting filaments, a putative phenotypic adaptation of the surface-associated strain to the environmental conditions at the seafloor. Genome analysis revealed the presence of a flagellum (fla1) and a type IV pilus biogenesis, which is speculated to be a prerequisite for biofilm formation. This is also related to genes responsible for signalling such as N-acyl homoserine lactones, as well as quip-genes responsible for quorum quenching and antibiotic biosynthesis. Pairwise similarities of 16S rRNA genes (98.56 % sequence similarity to the next relative S. haliotis) and the in silico DNA-DNA hybridization (21.20 % sequence similarity to S. haliotis) indicated Shimia str. SK013 to be considered as a new species. The genome analysis of Shimia str. SK013 offered first insights into specific physiological and phenotypic adaptation mechanisms of Roseobacter-affiliated bacteria to the benthic environment.

Significance of archaeal nitrification in hypoxic waters of the Baltic Sea.

Ammonia-oxidizing archaea (AOA) of the phylum Thaumarchaeota are widespread, and their abundance in many terrestrial and aquatic ecosystems suggests a prominent role in nitrification. AOA also occur in high numbers in oxygen-deficient marine environments, such as the pelagic redox gradients of the central Baltic Sea; however, data on archaeal nitrification rates are scarce and little is known about the factors, for example sulfide, that regulate nitrification in this system. In the present work, we assessed the contribution of AOA to ammonia oxidation rates in Baltic deep basins and elucidated the impact of sulfide on this process. Rate measurements with (15)N-labeled ammonium, CO(2) dark fixation measurements and quantification of AOA by catalyzed reporter deposition-fluorescence in situ hybridization revealed that among the three investigated sites the highest potential nitrification rates (122-884 nmol l(-1)per day) were measured within gradients of decreasing oxygen, where thaumarchaeotal abundance was maximal (2.5-6.9 × 10(5) cells per ml) and CO(2) fixation elevated. In the presence of the archaeal-specific inhibitor GC(7), nitrification was reduced by 86-100%, confirming the assumed dominance of AOA in this process. In samples spiked with sulfide at concentrations similar to those of in situ conditions, nitrification activity was inhibited but persisted at reduced rates. This result together with the substantial nitrification potential detected in sulfidic waters suggests the tolerance of AOA to periodic mixing of anoxic and sulfidic waters. It begs the question of whether the globally distributed Thaumarchaeota respond similarly in other stratified water columns or whether the observed robustness against sulfide is a specific feature of the thaumarchaeotal subcluster present in the Baltic Deeps.

Hydrogen, acetate, and lactate as electron donors for microbial manganese reduction in a manganese-rich coastal marine sediment.

The role of hydrogen, acetate, and lactate as electron donors for microbial manganese reduction was investigated in manganese-rich marine sediment from Gullmar Fjord (Sweden). Here, manganese reduction accounted for 50% of the anaerobic carbon oxidation at 0-15 cm sediment depth. In anoxic incubations from 0 to 5 cm depth, where manganese reduction dominated completely as terminal electron-accepting process, the combined contribution of acetate and lactate as electron donors for manganese reducers corresponded to < » of the electron flow. The concentrations, ¹4C-radiotracer turnover rates, and contributions to carbon oxidation of acetate and lactate associated with manganese reduction were similar to those found in deeper horizons dominated by concomitant iron and sulfate reduction and sulfate reduction alone, respectively. By contrast, hydrogen concentrations increased considerably with sediment depth, indicating thermodynamic control of the competition between the electron-accepting processes, and hydrogen may have contributed substantially to the > 75% of the electron flow that did not involve acetate and lactate. Alternatively, the oxidation of more complex organic substrates could be involved. Our study provides the first direct evidence of substrate utilization by a natural manganese-reducing community and indicates similar mechanisms of thermodynamic control and competition for electron donors as known from sediments dominated by iron reduction, sulfate reduction, or methanogenesis.

Chemoautotrophic growth of ammonia-oxidizing Thaumarchaeota enriched from a pelagic redox gradient in the Baltic Sea.

Ammonia-oxidizing archaea (AOA) are an important component of the planktonic community in aquatic habitats, linking nitrogen and carbon cycles through nitrification and carbon fixation. Therefore, measurements of these processes in culture-based experiments can provide insights into their contributions to energy conservation and biomass production by specific AOA. In this study, by enriching AOA from a brackish, oxygen-depleted water-column in the Landsort Deep, central Baltic Sea, we were able to investigate ammonium oxidation, chemoautotrophy, and growth in seawater batch experiments. The highly enriched culture consisted of up to 97% archaea, with maximal archaeal numbers of 2.9 × 10(7) cells mL(-1). Phylogenetic analysis of the 16S rRNA and ammonia monooxygenase subunit A (amoA) gene sequences revealed an affiliation with assemblages from low-salinity and freshwater habitats, with Candidatus Nitrosoarchaeum limnia as the closest relative. Growth correlated significantly with nitrite production, ammonium consumption, and CO2 fixation, which occurred at a ratio of 10 atoms N oxidized per 1 atom C fixed. According to the carbon balance, AOA biomass production can be entirely explained by chemoautotrophy. The cellular carbon content was estimated to be 9 fg C per cell. Single-cell-based (13)C and (15)N labeling experiments and analysis by nano-scale secondary ion mass spectrometry provided further evidence that cellular carbon was derived from bicarbonate and that ammonium was taken up by the cells. Our study therefore revealed that growth by an AOA belonging to the genus Nitrosoarchaeum can be sustained largely by chemoautotrophy.

Identification of acetate-oxidizing bacteria in a coastal marine surface sediment by RNA-stable isotope probing in anoxic slurries and intact cores.

We investigated the terminal electron-accepting pathways and the acetate-oxidizing bacteria in surface sediment (0-5 mm depth) of Aarhus Bay, Denmark, in anoxic slurry and intact core incubations. In the intact cores, oxygen, nitrate, oxides of manganese and iron, and sulfate were all available and likely all used as electron acceptors by the microbial community, whereas microbial iron and sulfate reduction dominated in the slurries. The availability of electron acceptors clearly affected which organisms were labeled by 16S rRNA-stable isotope probing (SIP). Members of the Oceanospirillaceae were identified as (13) C-acetate oxidizers in both types of incubations, but bacteria related to Colwellia and Arcobacter oxidized acetate in the intact core, while members of the Desulfuromonadales and Acidithiobacillaceae did so in the slurry incubation. Desulfuromonadales sequences also dominated 16S rRNA gene clone libraries from the highest positive dilution of the acetate-oxidizing most probable number cultures with manganese and iron oxides. Thus, members of Desulfuromonadales are likely important for acetate oxidation coupled to iron and manganese reduction in situ, while the identified Gammaproteobacteria and affiliates of Arcobacter may utilize oxygen, nitrate and manganese oxides. Our study further highlights some of the biases that are associated with the use of RNA-SIP as well as slurry and intact core incubations.

Three manganese oxide-rich marine sediments harbor similar communities of acetate-oxidizing manganese-reducing bacteria.

Dissimilatory manganese reduction dominates anaerobic carbon oxidation in marine sediments with high manganese oxide concentrations, but the microorganisms responsible for this process are largely unknown. In this study, the acetate-utilizing manganese-reducing microbiota in geographically well-separated, manganese oxide-rich sediments from Gullmar Fjord (Sweden), Skagerrak (Norway) and Ulleung Basin (Korea) were analyzed by 16S rRNA-stable isotope probing (SIP). Manganese reduction was the prevailing terminal electron-accepting process in anoxic incubations of surface sediments, and even the addition of acetate stimulated neither iron nor sulfate reduction. The three geographically distinct sediments harbored surprisingly similar communities of acetate-utilizing manganese-reducing bacteria: 16S rRNA of members of the genera Colwellia and Arcobacter and of novel genera within the Oceanospirillaceae and Alteromonadales were detected in heavy RNA-SIP fractions from these three sediments. Most probable number (MPN) analysis yielded up to 10(6) acetate-utilizing manganese-reducing cells cm(-3) in Gullmar Fjord sediment. A 16S rRNA gene clone library that was established from the highest MPN dilutions was dominated by sequences of Colwellia and Arcobacter species and members of the Oceanospirillaceae, supporting the obtained RNA-SIP results. In conclusion, these findings strongly suggest that (i) acetate-dependent manganese reduction in manganese oxide-rich sediments is catalyzed by members of taxa (Arcobacter, Colwellia and Oceanospirillaceae) previously not known to possess this physiological function, (ii) similar acetate-utilizing manganese reducers thrive in geographically distinct regions and (iii) the identified manganese reducers differ greatly from the extensively explored iron reducers in marine sediments.

Thermophilic anaerobes in Arctic marine sediments induced to mineralize complex organic matter at high temperature.

Marine sediments harbour diverse populations of dormant thermophilic bacterial spores that become active in sediment incubation experiments at much higher than in situ temperature. This response was investigated in the presence of natural complex organic matter in sediments of two Arctic fjords, as well as with the addition of freeze-dried Spirulina or individual high-molecular-weight polysaccharides. During 50 degrees C incubation experiments, Arctic thermophiles catalysed extensive mineralization of the organic matter via extracellular enzymatic hydrolysis, fermentation and sulfate reduction. This high temperature-induced food chain mirrors sediment microbial processes occurring at cold in situ temperatures (near 0 degrees C), yet it is catalysed by a completely different set of microorganisms. Using sulfate reduction rates (SRR) as a proxy for organic matter mineralization showed that differences in organic matter reactivity determined the extent of the thermophilic response. Fjord sediments with higher in situ SRR also supported higher SRR at 50 degrees C. Amendment with Spirulina significantly increased volatile fatty acids production and SRR relative to unamended sediment in 50 degrees C incubations. Spirulina amendment also revealed temporally distinct sulfate reduction phases, consistent with 16S rRNA clone library detection of multiple thermophilic Desulfotomaculum spp. enriched at 50 degrees C. Incubations with four different fluorescently labelled polysaccharides at 4 degrees C and 50 degrees C showed that the thermophilic population in Arctic sediments produce a different suite of polymer-hydrolysing enzymes than those used in situ by the cold-adapted microbial community. Over time, dormant marine microorganisms like these are buried in marine sediments and might eventually encounter warmer conditions that favour their activation. Distinct enzymatic capacities for organic polymer degradation could allow specific heterotrophic populations like these to play a role in sustaining microbial metabolism in the deep, warm, marine biosphere.

A constant flux of diverse thermophilic bacteria into the cold Arctic seabed.

Microorganisms have been repeatedly discovered in environments that do not support their metabolic activity. Identifying and quantifying these misplaced organisms can reveal dispersal mechanisms that shape natural microbial diversity. Using endospore germination experiments, we estimated a stable supply of thermophilic bacteria into permanently cold Arctic marine sediment at a rate exceeding 10(8) spores per square meter per year. These metabolically and phylogenetically diverse Firmicutes show no detectable activity at cold in situ temperatures but rapidly mineralize organic matter by hydrolysis, fermentation, and sulfate reduction upon induction at 50 degrees C. The closest relatives to these bacteria come from warm subsurface petroleum reservoir and ocean crust ecosystems, suggesting that seabed fluid flow from these environments is delivering thermophiles to the cold ocean. These transport pathways may broadly influence microbial community composition in the marine environment.

Acetate, lactate, propionate, and isobutyrate as electron donors for iron and sulfate reduction in Arctic marine sediments, Svalbard.

The contribution of volatile fatty acids (VFA) as e(-)-donors for anaerobic terminal oxidation of organic carbon through iron and sulfate reduction was studied in Arctic fjord sediment. Dissolved inorganic carbon, Fe(2+), VFA concentrations, and sulfate reduction were monitored in slurries from the oxidized (0-2 cm) and the reduced (5-9 cm) zone. In the 0-2 cm layer, 2/3 of the mineralization could be attributed to sulfate reduction and 1/3 to iron reduction. In the 5-9 cm layer, sulfate reduction was the sole mineralization process. Acetate and lactate turnover rates were measured by radiotracer. Inhibition of sulfate reduction with selenate resulted in the accumulation of acetate, propionate, and isobutyrate. The acetate turnover rates determined by radiotracer and accumulation after inhibition were similar. VFA turnover accounted for 21% and 52% of the mineralization through sulfate reduction in the 0-2 and 5-9 cm layer, respectively. Acetate and lactate turnover in the inhibited 0-2 cm slurry was attributed to iron reduction and accounted for 10% and 2% of the iron reduction. Therefore, 88% and 79% of the iron and sulfate reduction in the 0-2 cm layer, respectively, must be fueled by alternative e(-)-donors. The accumulation of VFA in the selenate-inhibited 0-2 cm slurry did not enhance iron reduction, indicating that iron reducers were not limited by VFA availability.

Desulfuromonas svalbardensis sp. nov. and Desulfuromusa ferrireducens sp. nov., psychrophilic, Fe(III)-reducing bacteria isolated from Arctic sediments, Svalbard.

Two psychrophilic, Gram-negative, rod-shaped, motile bacteria (strains 112T and 102T) that conserved energy from dissimilatory Fe(III) reduction concomitant with acetate oxidation were isolated from permanently cold Arctic marine sediments. Both strains grew at temperatures down to -2 degrees C, with respective temperature optima of 14 degrees C and 14-17 degrees C for strains 112T and 102T. The isolated strains reduced Fe(III) using common fermentation products such as acetate, lactate, propionate, formate or hydrogen as electron donors, and they also grew with fumarate as the sole substrate. As alternatives to Fe(III), they reduced fumarate, S0 and Mn(IV). Based on 16S rRNA gene sequence similarity, strain 112T was most closely related to Desulfuromonas acetoxidans (97.0 %) and Desulfuromonas thiophila NZ27T (95.5 %), and strain 102T to Malonomonas rubra Gra Mal 1T (96.3 %) and Desulfuromusa succinoxidans GylacT (95.9 %) within the Deltaproteobacteria. Strains 112T and 102T therefore represent novel species, for which the names Desulfuromonas svalbardensis sp. nov. (type strain 112T=DSM 16958T=JCM 12927T) and Desulfuromusa ferrireducens sp. nov. (type strain 102T=DSM 16956T=JCM 12926T) are proposed.

Desulfovibrio frigidus sp. nov. and Desulfovibrio ferrireducens sp. nov., psychrotolerant bacteria isolated from Arctic fjord sediments (Svalbard) with the ability to reduce Fe(III).

Strains 18T, 61T and 77 were isolated from two permanently cold fjord sediments on the west coast of Svalbard. The three psychrotolerant strains, with temperature optima at 20-23 degrees C, were able to grow at the freezing point of sea water, -2 degrees C. The strains oxidized important fermentation products such as hydrogen, formate and lactate with sulfate as the electron acceptor. Sulfate could be replaced by sulfite, thiosulfate or elemental sulfur. Poorly crystalline and soluble Fe(III) compounds were reduced in sulfate-free medium, but no growth occurred under these conditions. In the absence of electron acceptors, fermentative growth was possible. The pH optimum for the strains was around 7.1. The DNA G+C contents were 43.3 and 42.0 mol% for strains 18T and 61T, respectively. Strains 18T, 61T and 77 were most closely related to Desulfovibrio hydrothermalis (95.0-95.7 % 16S rRNA gene sequence similarity). Strains 18T and 77, exhibiting 99.9 % sequence similarity, represent a novel species for which the name Desulfovibrio frigidus sp. nov. is proposed. The type strain is strain 18T (=DSM 17176T = JCM 12924T). Strain 61T was closely related to strains 18T and 77 (97.6 and 97.5 % 16S rRNA gene sequence similarity), but on the basis of DNA-DNA hybridization strain 61T represents a novel species for which the name Desulfovibrio ferrireducens sp. nov. is proposed. The type strain is strain 61T (=DSM 16995T = JCM 12925T).

Desulfotomaculum arcticum sp. nov., a novel spore-forming, moderately thermophilic, sulfate-reducing bacterium isolated from a permanently cold fjord sediment of Svalbard.

Strain 15T is a novel spore-forming, sulfate-reducing bacterium isolated from a permanently cold fjord sediment of Svalbard. Sulfate could be replaced by sulfite or thiosulfate. Hydrogen, formate, lactate, propionate, butyrate, hexanoate, methanol, ethanol, propanol, butanol, pyruvate, malate, succinate, fumarate, proline, alanine and glycine were used as electron donors in the presence of sulfate. Growth occurred with pyruvate as sole substrate. Optimal growth was observed at pH 7.1-7.5 and concentrations of 1-1.5 % NaCl and 0.4 % MgCl2. Strain 15T grew between 26 and 46.5 degrees C and optimal growth occurred at 44 degrees C. Therefore, strain 15T apparently cannot grow at in situ temperatures of Arctic sediments from where it was isolated, and it was proposed that it was present in the sediment in the form of spores. The DNA G+C content was 48.9 mol%. Strain 15T was most closely related to Desulfotomaculum thermosapovorans MLF(T) (93.5 % 16S rRNA gene sequence similarity). Strain 15T represents a novel species, for which the name Desulfotomaculum arcticum sp. nov. is proposed. The type strain is strain 15T (=DSM 17038T = JCM 12923T).

Microscopic examination of distribution and phenotypic properties of phylogenetically diverse Chloroflexaceae-related bacteria in hot spring microbial mats.

We investigated the diversity, distribution, and phenotypes of uncultivated Chloroflexaceae-related bacteria in photosynthetic microbial mats of an alkaline hot spring (Mushroom Spring, Yellowstone National Park). By applying a directed PCR approach, molecular cloning, and sequence analysis of 16S rRNA genes, an unexpectedly large phylogenetic diversity among these bacteria was detected. Oligonucleotide probes were designed to target 16S rRNAs from organisms affiliated with the genus Chloroflexus or with the type C cluster, a group of previously discovered Chloroflexaceae relatives of this mat community. The application of peroxidase-labeled probes in conjunction with tyramide signal amplification enabled the identification of these organisms within the microbial mats by fluorescence in situ hybridization (FISH) and the investigation of their morphology, abundance, and small-scale distribution. FISH was combined with oxygen microelectrode measurements, microscope spectrometry, and microautoradiography to examine their microenvironment, pigmentation, and carbon source usage. Abundant type C-related, filamentous bacteria were found to flourish within the cyanobacterium-dominated, highly oxygenated top layers and to predominate numerically in deeper orange-colored zones of the investigated microbial mats, correlating with the distribution of bacteriochlorophyll a. Chloroflexus sp. filaments were rare at 60 degrees C but were more abundant at 70 degrees C, where they were confined to the upper millimeter of the mat. Both type C organisms and Chloroflexus spp. were observed to assimilate radiolabeled acetate under in situ conditions.