Microbial community dynamics and cycling of plutonium and iron in a seasonally stratified and radiologically contaminated pond

Plutonium (Pu) cycling and mobility in the environment can be impacted by the iron cycle and microbial community dynamics. We investigated the spatial and temporal changes of the microbiome in an iron (Fe)-rich, plutonium-contaminated, monomictic reservoir (Pond B, Savannah River Site, South Carolina, USA). The microbial community composition varied with depth during seasonal thermal stratification and was strongly correlated with redox. During stratification, Fe(II) oxidizers (e.g., Ferrovum, Rhodoferax, Chlorobium) were most abundant in the hypoxic/anoxic zones, while Fe(III) reducers (e.g., Geothrix, Geobacter) dominated the deep, anoxic zone. Sulfate reducers and methanogens were present in the anoxic layer, likely contributing to iron and plutonium cycling. Multinomial regression of predicted functions/pathways identified metabolisms highly associated with stratification (within the top 5%), including iron reduction, methanogenesis, C1 compound utilization, fermentation, and aromatic compound degradation. Two sediment cores collected at the Inlet and Outlet of the pond were dominated by putative fermenters and organic matter (OM) degraders. Overall, microbiome analyses revealed the potential for three microbial impacts on the plutonium and iron biogeochemical cycles: (1) plutonium bioaccumulation throughout the water column, (2) Pu-Fe-OM-aggregate formation by Fe(II) oxidizers under microaerophilic/aerobic conditions, and (3) Pu-Fe-OM-aggregate or sediment reductive dissolution and organic matter degradation in the deep, anoxic waters.

Using custom-built primers and nanopore sequencing to evaluate CO-utilizer bacterial and archaeal populations linked to bioH2 production

The microbial community composition of five distinct thermophilic hot springs was effectively described in this work, using broad-coverage nanopore sequencing (ONT MinION sequencer). By examining environmental samples from the same source, but from locations with different temperatures, bioinformatic analysis revealed dramatic changes in microbial diversity and archaeal abundance. More specifically, no archaeal presence was reported with universal bacterial primers, whereas a significant archaea presence and also a wider variety of bacterial species were reported. These results revealed the significance of primer preference for microbiomes in extreme environments. Bioinformatic analysis was performed by aligning the reads to 16S microbial databases for identification using three different alignment methods, Epi2Me (Fastq 16S workflow), Kraken, and an in-house BLAST tool, including comparison at the genus and species levels. As a result, this approach to data analysis had a significant impact on the genera identified, and thus, it is recommended that use of multiple analysis tools to support findings on taxonomic identification using the 16S region until more precise bioinformatics tools become available. This study presents the first compilation of the ONT-based inventory of the hydrogen producers in the designated hot springs in Türkiye.

Laboratory-Controlled Experiments Reveal Microbial Community Shifts during Sediment Resuspension Events

In freshwater ecosystems, dynamic hydraulic events (floods or dam maintenance) lead to sediment resuspension and mixing with waters of different composition. Microbial communities living in the sediments play a major role in these leaching events, contributing to organic matter degradation and the release of trace elements. However, the dynamics of community diversity are seldom studied in the context of ecological studies. Therefore, we carried out laboratory-induced leaching experiments, using sediments from the Villerest dam reservoir (Villerest, France). To assess whole microbial community diversity, we sequenced the archaeal and bacterial 16S rRNA genes using Illumina MiSeq. Our results suggest that the degree of dissolved oxygen found in the water during these resuspension episodes influenced community dynamics, with anoxic waters leading to drastic shifts in sedimentary communities compared to oxic waters. Furthermore, the release of microbial cells from sediments to the water column were more favorable to water colonization when events were caused by oxic waters. Most of the bacteria found in the sediments were chemoorganotrophs and most of the archaea were methanogens. Methylotrophic, as well as archaeal, and bacterial chemoorganotrophs were detected in the leachate samples. These results also show that organic matter degradation occurred, likely participating in carbonate dissolution and the release of trace elements during freshwater resuspension events.

Soil microorganisms facilitated the electrode-driven trichloroethene dechlorination to ethene by Dehalococcoides species in a bioelectrochemical system

Bioelectrochemical dechlorination using organohalide-respiring bacteria (ORBs) is a promising technique for remediating contaminated groundwater. Generally, a longer enrichment period is required for selecting the ORB consortia to achieve bioelectrochemical dechlorination. However, the full dechloriantion is difficult to be achieved due to the absence of functional species (e.g. Dehalococcoides) in previously used enrich cultures. To overcome these challenges, bioelectrochemical dechlorination using a culture enriched with the pre-augmented Dehalococcoides was performed for the first time in this study. A two-chamber bioelectrochemical system (BES) inoculated with a pure Dehalococcoides culture and paddy soil with an applied voltage of -0.3 V (versus a standard hydrogen electrode) as the sole electron donor was used to achieve dechlorination. The ethene formation rate was 10-100 times higher than that in previous studies, indicating that inoculating the system with a pure Dehalococcoides culture and soil microorganisms gave effective full dechlorination performance. Microbial community analysis and bioelectrochemical analysis indicated that Desulfosporosinus species may have facilitated dechlorination through syntrophic interactions with Dehalococcoides. The results indicated that adding Dehalococcoides cells before operating a bioelectrochemical system is an effective way of achieving full dechlorination.

Link between characteristics of Fe(III) oxides and critical role in enhancing anaerobic methanogenic degradation of complex organic compounds

Fe(III) oxides have been investigated to accelerate anaerobic methanogenic degradation of complex organic compounds. However, the critical role linked to the characteristics of different types of Fe(III) oxides is still unclear. Study presented here performed a side-by-side comparison of four types of Fe(III) oxides including Fe(III)-citrate, ferrihydrite, hematite and magnetite to evaluate their effectiveness in methanogenic degradation of phenol. Results showed that, amorphous Fe(III)-citrate group showed the fastest phenol degradation and Fe²⁺ release among all the groups, followed by poorly crystalline ferrihydrite. Although Fe(III)-citrate group also showed the fastest methane production rate, the efficiency of electron recovery in methane production was only 58-78%, which was evidently lower than that in both crystalline hematite (86-89%) and magnetite (93-97%) groups. Methane production rate with non-conductive ferrihydrite was nearly same as that with conductive magnetite, both of which were significantly higher than that with semi-conductive hematite. X-ray Diffraction (XRD) and X-ray photoelectron spectroscopy (XPS) analysis showed that sludge collected from hematite and magnetite group still respectively presented a relatively intact characteristic spectra involved in hematite and magnetite. Differently, the characteristic spectra involved in ferrihydrite was not evident in sludge collected from ferrihydrite group, whereas the characteristic spectra involved in magnetite was detected. Microbial community analysis showed that, both Fe(III)-citrate and ferrihydrite specially enriched Fe(III)-reducing bacteria capable of degrading phenol into fatty acids (Trichococcus and Caloramator) via dissimilatory Fe(III) reduction. Fe(III)-citrate also stimulated the growth of Syntrophus capable of degrading phenol/benzoate into acetate and proceeding direct interspecies electron transfer (DIET). In magnetite and hematite group, the abundance of Enterococcus species evidently increased, and they might proceed DIET with Methanothrix species in syntrophic conversion of fatty acids into methane.

Colombian Andean thermal springs: reservoir of thermophilic anaerobic bacteria producing hydrolytic enzymes

Anaerobic cultivable microbial communities in thermal springs producing hydrolytic enzymes were studied. Thermal water samples from seven thermal springs located in the Andean volcanic belt, in the eastern and central mountain ranges of the Colombian Andes were used as inocula for the growth and isolation of thermophilic microorganisms using substrates such as starch, gelatin, xylan, cellulose, Tween 80, olive oil, peptone and casamino acids. These springs differed in temperature (50-70 °C) and pH (6.5-7.5). The predominant ion in eastern mountain range thermal springs was sulphate, whereas that in central mountain range springs was bicarbonate. A total of 40 anaerobic thermophilic bacterial strains that belonged to the genera Thermoanaerobacter, Caloramator, Anoxybacillus, Caloranaerobacter, Desulfomicrobium, Geotoga, Hydrogenophilus, Desulfacinum and Thermoanaerobacterium were isolated. To investigate the metabolic potential of these isolates, selected strains were analysed for enzymatic activities to identify strains than can produce hydrolytic enzymes. We demonstrated that these thermal springs contained diverse microbial populations of anaerobic thermophilic comprising different metabolic groups of bacteria including strains belonging to the genera Thermoanaerobacter, Caloramator, Anoxybacillus, Caloranaerobacter, Desulfomicrobium, Geotoga, Hydrogenophilus, Desulfacinum and Thermoanaerobacterium with amylases, proteases, lipases, esterases, xylanases and pectinases; therefore, the strains represent a promising source of enzymes with biotechnological potential.

Complete Genome Sequence of Caloramator sp. Strain E03, a Novel Ethanologenic, Thermophilic, Obligately Anaerobic Bacterium

Here, we report the complete genome sequence of Caloramator sp. strain E03, an anaerobic thermophile that was isolated from a hot spring within the Rabbit Creek area of Yellowstone National Park. The assembly contains a single 2,984,770-bp contig with a G+C content of 31.3% and is predicted to encode 2,678 proteins.

Genus-Wide Assessment of Lignocellulose Utilization in the Extremely Thermophilic Genus Caldicellulosiruptor by Genomic, Pangenomic, and Metagenomic Analyses

Metagenomic data from Obsidian Pool (Yellowstone National Park, USA) and 13 genome sequences were used to reassess genus-wide biodiversity for the extremely thermophilic Caldicellulosiruptor The updated core genome contains 1,401 ortholog groups (average genome size for 13 species = 2,516 genes). The pangenome, which remains open with a revised total of 3,493 ortholog groups, encodes a variety of multidomain glycoside hydrolases (GHs). These include three cellulases with GH48 domains that are colocated in the glucan degradation locus (GDL) and are specific determinants for microcrystalline cellulose utilization. Three recently sequenced species, Caldicellulosiruptor sp. strain Rt8.B8 (renamed here Caldicellulosiruptor morganii), Thermoanaerobacter cellulolyticus strain NA10 (renamed here Caldicellulosiruptor naganoensis), and Caldicellulosiruptor sp. strain Wai35.B1 (renamed here Caldicellulosiruptor danielii), degraded Avicel and lignocellulose (switchgrass). C. morganii was more efficient than Caldicellulosiruptor bescii in this regard and differed from the other 12 species examined, both based on genome content and organization and in the specific domain features of conserved GHs. Metagenomic analysis of lignocellulose-enriched samples from Obsidian Pool revealed limited new information on genus biodiversity. Enrichments yielded genomic signatures closely related to that of Caldicellulosiruptor obsidiansis, but there was also evidence for other thermophilic fermentative anaerobes (Caldanaerobacter, Fervidobacterium, Caloramator, and Clostridium). One enrichment, containing 89.8% Caldicellulosiruptor and 9.7% Caloramator, had a capacity for switchgrass solubilization comparable to that of C. bescii These results refine the known biodiversity of Caldicellulosiruptor and indicate that microcrystalline cellulose degradation at temperatures above 70°C, based on current information, is limited to certain members of this genus that produce GH48 domain-containing enzymes.IMPORTANCE The genus Caldicellulosiruptor contains the most thermophilic bacteria capable of lignocellulose deconstruction, which are promising candidates for consolidated bioprocessing for the production of biofuels and bio-based chemicals. The focus here is on the extant capability of this genus for plant biomass degradation and the extent to which this can be inferred from the core and pangenomes, based on analysis of 13 species and metagenomic sequence information from environmental samples. Key to microcrystalline hydrolysis is the content of the glucan degradation locus (GDL), a set of genes encoding glycoside hydrolases (GHs), several of which have GH48 and family 3 carbohydrate binding module domains, that function as primary cellulases. Resolving the relationship between the GDL and lignocellulose degradation will inform efforts to identify more prolific members of the genus and to develop metabolic engineering strategies to improve this characteristic.

Temporal dynamics and metabolic correlation between lactate-producing and hydrogen-producing bacteria in sugarcane vinasse dark fermentation: The key role of lactate

This study aimed to better understand the role of different microbial groups and the determining fermentation pathways in a biohydrogen (bioH₂)-producing reactor fed with sugarcane vinasse by using next-generation sequencing and principal component analysis (PCA). Both microbial structure and dynamics were characterized. The highest bioH₂ production levels were associated with the Thermoanaerobacterium genus, whilst lactate-producing bacteria comprised the dominant genera (e.g. Lactobacillus and Leuconostoc) within the reactor at both stable and unstable bioH₂-producing periods. PCA further revealed that the fermentation of lactate played a dual role in the reactor, as both bioH₂-producing (acetate+lactate→butyrate+bioH₂) and non-bioH₂-producing (lactate→propionate+acetate) routes could be observed. Overall, the results suggested that lactate is the primary alternative carbon source in vinasse-fed systems subjected to carbohydrate-shortage conditions.

The functional potential and active populations of the pit mud microbiome for the production of Chinese strong-flavour liquor

The popular distilled Chinese strong‐flavour liquor (CSFL) is produced by solid fermentation in the ground pit. Microbes inhabiting in the pit mud (PM) on the walls of the fermentation pit are responsible for the production of caproic acid (CA) that determines the quality of CSFL to a large degree. However, little is known about the active microbial populations and metabolic potential of the PM microbiome. Here, we investigated the overall metabolic features of the PM microbiome and its active microbial components by combining metagenomics and MiSeq‐sequencing analyses of the 16S rRNA genes from DNA and RNA (cDNA). Results showed that prokaryotes were predominant populations in the PM microbiome, accounting for 95.3% of total metagenomic reads, while eukaryotic abundance was only 1.8%. The dominant prokaryotic phyla were Firmicutes, Euryarchaeota, Bacteroidetes, Actinobacteria and Proteobacteria, accounting for 48.0%, 19.0%, 13.5%, 2.5% and 2.1% of total metagenomic reads respectively. Most genes encoding putative metabolic pathways responsible for the putative CA production via chain elongation pathway were detected. This indicated that the PM microbiome owned functional potential for synthesizing CA from ethanol or lactate. Some key genes encoding enzymes involved in hydrogenotrophic and acetoclastic methanogenesis pathways were detected in the PM metagenome, suggesting the possible occurrence of interspecies hydrogen transfer between CA‐producing bacteria and methanogens. The 16S rDNA and 16S rRNA profiles showed that the Clostridial cluster IV, Lactobacillus, Caloramator, Clostridium, Sedimentibacter, Bacteroides and Porphyromonas were active populations in situ, in which Clostridial cluster IV and Clostridium were likely involved in the CA production. This study improved our understandings on the active populations and metabolic pathways of the PM microbiome involved in the CA synthesis in the CSFL fermentation.

Biohydrogen production from xylose by fresh and digested activated sludge at 37, 55 and 70 °C

Two heat-treated inocula, fresh and digested activated sludge from the same municipal wastewater treatment plant, were compared for their H₂ production via dark fermentation at mesophilic (37 °C), thermophilic (55 °C) and hyperthermophilic (70 °C) conditions using xylose as the substrate. At both 37 and 55 °C, the fresh activated sludge yielded more H₂ than the digested sludge, whereas at 70 °C, neither of the inocula produced H₂ effectively. A maximum yield of 1.85 mol H₂ per mol of xylose consumed was obtained at 55 °C. H₂ production was linked to acetate and butyrate production, and there was a linear correlation (R² = 0.96) between the butyrate and H₂ yield for the fresh activated sludge inoculum at 55 °C. Approximately 2.4 mol H₂ per mol of butyrate produced were obtained against a theoretical maximum of 2.0, suggesting that H₂ was produced via the acetate pathway prior to switching to the butyrate pathway due to the increased H₂ partial pressure. Clostridia sp. were the prevalent species at both 37 and 55 °C, irrespectively of the inoculum type. Although the two inocula originated from the same plant, different thermophilic microorganisms were detected at 55 °C. Thermoanaerobacter sp., detected only in the fresh activated sludge cultures, may have contributed to the high H₂ yield obtained with such an inoculum.

Draft Genome Sequence of the 1,2-Dichloroethane-Utilizing Micrococcus sp. Strain NDB3Y10, Isolated from an Australian Bore Well Producing Coal Seam Gas

Micrococcus luteus strain NDB3Y10, which utilizes 1,2-dichloroethane as a carbon source, was isolated from a bore well that produces coal seam gas. The draft genome size of the strain was 2.49 Mb with a G+C content of 72.97%. Genes involved in the metabolism of halogenated substrates, including halogenated hydrocarbons, were identified.

Draft Genome Sequence of Microbacterium sp. TNHR37B Isolated from a Heated Aquifer Bore Well of the Great Artesian Basin, Australia

Microbacterium sp. strain TNHR37B was isolated from a geothermal bore well sample (50°C) collected from a region of coal seam gas extraction activities. The 3.5-Mb genome with a G+C content of 69.9% contained unique genes, and a low similarity value for average nucleotide identity using BLAST was observed with the available 73 Microbacterium sp. genomes.

Bacterial DNA Extraction Using Individual Enzymes and Phenol/Chloroform Separation

Marmur (4) developed one of the first detailed comprehensive methods for purifying bacterial DNA. This procedure is now outdated, and can be difficult to follow for those with limited experience in molecular biology. Here, we provide a modernized, simplified protocol for extracting bacterial DNA and discuss how this can be incorporated into microbiology laboratory courses for biology majors.

Orenia metallireducens sp. nov. Strain Z6, a Novel Metal-Reducing Member of the Phylum Firmicutes from the Deep Subsurface

A novel halophilic and metal-reducing bacterium, Orenia metallireducens strain Z6, was isolated from briny groundwater extracted from a 2.02 km-deep borehole in the Illinois Basin, IL. This organism shared 96% 16S rRNA gene similarity with Orenia marismortui but demonstrated physiological properties previously unknown for this genus. In addition to exhibiting a fermentative metabolism typical of the genus Orenia, strain Z6 reduces various metal oxides [Fe(III), Mn(IV), Co(III), and Cr(VI)], using H₂ as the electron donor. Strain Z6 actively reduced ferrihydrite over broad ranges of pH (6 to 9.6), salinity (0.4 to 3.5 M NaCl), and temperature (20 to 60°C). At pH 6.5, strain Z6 also reduced more crystalline iron oxides, such as lepidocrocite (γ-FeOOH), goethite (α-FeOOH), and hematite (α-Fe₂O₃). Analysis of X-ray absorption fine structure (XAFS) following Fe(III) reduction by strain Z6 revealed spectra from ferrous secondary mineral phases consistent with the precipitation of vivianite [Fe₃(PO₄)₂] and siderite (FeCO₃). The draft genome assembled for strain Z6 is 3.47 Mb in size and contains 3,269 protein-coding genes. Unlike the well-understood iron-reducing Shewanella and Geobacter species, this organism lacks the c-type cytochromes for typical Fe(III) reduction. Strain Z6 represents the first bacterial species in the genus Orenia (order Halanaerobiales) reported to reduce ferric iron minerals and other metal oxides. This microbe expands both the phylogenetic and physiological scopes of iron-reducing microorganisms known to inhabit the deep subsurface and suggests new mechanisms for microbial iron reduction. These distinctions from other Orenia spp. support the designation of strain Z6 as a new species, Orenia metallireducens sp. nov.

IMPORTANCE

A novel iron-reducing species, Orenia metallireducens sp. nov., strain Z6, was isolated from groundwater collected from a geological formation located 2.02 km below land surface in the Illinois Basin, USA. Phylogenetic, physiologic, and genomic analyses of strain Z6 found it to have unique properties for iron reducers, including (i) active microbial iron-reducing capacity under broad ranges of temperatures (20 to 60°C), pHs (6 to 9.6), and salinities (0.4 to 3.5 M NaCl), (ii) lack of c-type cytochromes typically affiliated with iron reduction in Geobacter and Shewanella species, and (iii) being the only member of the Halanaerobiales capable of reducing crystalline goethite and hematite. This study expands the scope of phylogenetic affiliations, metabolic capacities, and catalytic mechanisms for iron-reducing microbes.

Characterization and Adaptation of Anaerobic Sludge Microbial Communities Exposed to Tetrabromobisphenol A

The increasing occurrence of tetrabromobisphenol A (TBBPA) in the environment is raising questions about its potential ecological and human health impacts. TBBPA is microbially transformed under anaerobic conditions to bisphenol A (BPA). However, little is known about which taxa degrade TBBPA and the adaptation of microbial communities exposed to TBBPA. The objectives of this study were to characterize the effect of TBBPA on microbial community structure during the start-up phase of a bench-scale anaerobic sludge reactor, and identify taxa that may be associated with TBBPA degradation. TBBPA degradation was monitored using LC/MS-MS, and the microbial community was characterized using Ion Torrent sequencing and qPCR. TBBPA was nearly completely transformed to BPA via reductive debromination in 55 days. Anaerobic reactor performance was not negatively affected by the presence of TBBPA and the bulk of the microbial community did not experience significant shifts. Several taxa showed a positive response to TBBPA, suggesting they may be associated with TBBPA degradation. Some of these taxa had been previously identified as dehalogenating bacteria including Dehalococcoides, Desulfovibrio, Propionibacterium, and Methylosinus species, but most had not previously been identified as having dehalogenating capacities. This study is the first to provide in-depth information on the microbial dynamics of anaerobic microbial communities exposed to TBBPA.

A molecular phylogenetic framework for Bacillus subtilis using genome sequences and its application to Bacillus subtilis subspecies stecoris strain D7XPN1, an isolate from a commercial food-waste degrading bioreactor

A thermophilic, heterotrophic and facultatively anaerobic bacterium designated strain D7XPN1 was isolated from Baku BakuKing™, a commercial food-waste degrading bioreactor (composter). The strain grew optimally at 45 °C (growth range between 24 and 50 °C) and pH 7 (growth pH range between pH 5 and 9) in Luria Broth supplemented with 0.3 % glucose. Strain D7XPN1 tolerated up to 7 % NaCl and showed amylolytic and xylanolytic activities. 16S rRNA gene analysis placed strain D7XPN1 in the cluster represented by Bacillus subtilis and the genome analysis of the 4.1 Mb genome sequence determined using RAST (Rapid Annotation using Subsystem Technology) indicated a total of 5116 genomic features were present of which 2320 features could be grouped into several subsystem categories. Of these, 615 features were related to carbohydrate metabolism which included a range of enzymes with potential in the biodegradation of food wastes, a property consistent with the ecological habitat of the isolate. ANIb (Average Nucleotide Identity based on BLAST) analysis with 49 Bacillus subtilis genomes indicated that it was distantly related to the three currently taxonomically validated B. subtilis subspecies namely B. subtilis subsp. subtilis (95.6 %), B. subtilis subsp. spizizenii (93 %) and B. subtilis subsp. inaquosorum (92 %) and based on our current knowledge warranted that it be included as a separate cluster together with strain JS which it was closely related (98.69 %). The close relationship of strains D7XPN1 and JS is also supported from our results from electronic DNA–DNA Hybridization (e-DDH) studies. Furthermore, our additional in-depth phylogenomic analyses using three different datasets unequivocally supported the creation of a fourth B. subtilis subspecies to include strains D7XPN1 and JS for which we propose strain D7XPN1^T (=KCTC 33554^T, JCM 30051^T) as the type strain, and designate it as B. subtilis subsp. stecoris.

Draft Genome Sequence of Caloramator mitchellensis, a Thermoanaerobe Isolated from the Waters of the Great Artesian Basin

The genome sequence of Caloramator mitchellensis strain VF08, a rod-shaped, heterotrophic, strictly anaerobic bacterium isolated from the free-flowing waters of a Great Artesian Basin (GAB) bore well located in Mitchell, an outback Queensland town in Australia, is reported here. The analysis of the 2.42-Mb genome sequence indicates that the attributes of the genome are consistent with its physiological and phenotypic traits.

High organic loading rate on thermophilic hydrogen production and metagenomic study at an anaerobic packed-bed reactor treating a residual liquid stream of a Brazilian biorefinery

This study evaluated the influence of a high organic loading rate (OLR) on thermophilic hydrogen production at an up-flow anaerobic packed-bed reactor (APBR) treating a residual liquid stream of a Brazilian biorefinery. The APBR, filled with low-density polyethylene, was operated at an OLR of 84.2 kg-COD m(-3) d(-1). This value was determined in a previous study. The maximum values of hydrogen production and yield were 5,252.6 mL-H2 d(-1) and 3.7 mol-H2 mol(-1)(total carbohydrates), respectively. However, whereas the OLR remained constant, the specific organic load rate (sOLR) decreased throughout operation from 1.38 to 0.72 g-Total carbohydratesg-VS(-1) h(-1), this decrease negatively affected hydrogen production. A sOLR of 0.98 g-Total carbohydratesg-VS(-1) h(-1) was optimal for hydrogen production. The microbial community was studied using 454-pyrosequencing analysis. Organisms belonging to the genera Caloramator, Clostridium, Megasphaera, Oxobacter, Thermoanaerobacterium, and Thermohydrogenium were detected in samples taken from the reactor at operation days 30 and 60, suggesting that these organisms contribute to hydrogen production.

Draft Genome Sequence of Anoxybacillus Strain BCO1, Isolated from a Thermophilic Microbial Mat Colonizing the Outflow of a Bore Well of the Great Artesian Basin of Australia

Anoxybacillus strain BCO1, isolated from a thermophilic (50°C) microbial mat colonizing an outflow of a Great Artesian bore well of Australia, possessed a genome of ~2.8 Mb, with a G+C content of 41.7 mol%, and encoded 3,205 genes.

Community analysis of plant biomass-degrading microorganisms from Obsidian Pool, Yellowstone National Park

The conversion of lignocellulosic biomass into biofuels can potentially be improved by employing robust microorganisms and enzymes that efficiently deconstruct plant polysaccharides at elevated temperatures. Many of the geothermal features of Yellowstone National Park (YNP) are surrounded by vegetation providing a source of allochthonic material to support heterotrophic microbial communities adapted to utilize plant biomass as a primary carbon and energy source. In this study, a well-known hot spring environment, Obsidian Pool (OBP), was examined for potential biomass-active microorganisms using cultivation-independent and enrichment techniques. Analysis of 33,684 archaeal and 43,784 bacterial quality-filtered 16S rRNA gene pyrosequences revealed that archaeal diversity in the main pool was higher than bacterial; however, in the vegetated area, overall bacterial diversity was significantly higher. Of notable interest was a flooded depression adjacent to OBP supporting a stand of Juncus tweedyi, a heat-tolerant rush commonly found growing near geothermal features in YNP. The microbial community from heated sediments surrounding the plants was enriched in members of the Firmicutes including potentially (hemi)cellulolytic bacteria from the genera Clostridium, Anaerobacter, Caloramator, Caldicellulosiruptor, and Thermoanaerobacter. Enrichment cultures containing model and real biomass substrates were established at a wide range of temperatures (55-85 °C). Microbial activity was observed up to 80 °C on all substrates including Avicel, xylan, switchgrass, and Populus sp. Independent of substrate, Caloramator was enriched at lower (<65 °C) temperatures while highly active cellulolytic bacteria Caldicellulosiruptor were dominant at high (>65 °C) temperatures.

Draft Genome Sequence of Paenibacillus Strain P1XP2, a Polysaccharide-Degrading, Thermophilic, Facultative Anaerobic Bacterium Isolated from a Commercial Bioreactor Degrading Food Waste

The analysis of the ~5.8-Mb draft genome sequence of a moderately thermophilic, heterotrophic, facultative anaerobic bacterium, Paenibacillus strain P1XP2, identified genes for enzymes with the potential for degrading complex food wastes, a property consistent with the ecological habitat of the isolate.

Draft Genome Sequence of Bacillus subtilis Strain D7XPN1, Isolated from Commercial Bioreactor-Degrading Food Waste

The analysis of the 4.1-Mb draft genome sequence of a moderately thermophilic, heterotrophic, and facultatively anaerobic bacterium, Bacillus subtilis strain D7XPN1, identified genes for a range of enzymes with potential in the biodegradation of food waste, a property consistent with the ecological habitat of the isolate.

Draft Genome Sequence of Fervidicella metallireducens Strain AeBT, an Iron-Reducing Thermoanaerobe from the Great Artesian Basin

The genome sequence of Fervidicella metallireducens strain AeB^T, a curved, heterotrophic, thermoanaerobic, and iron-reducing bacterium isolated from a gray microbial mat colonizing the free-flowing waters of a Great Artesian Basin (GAB) bore well located in outback Queensland, Australia, is reported here. The analysis of the 2.9-Mb sequence indicates that the attributes of the genome are consistent with its physiological and phenotypic traits.

Caloramator quimbayensis sp. nov., an anaerobic, moderately thermophilic bacterium isolated from a terrestrial hot spring

An anaerobic, moderately thermophilic, terminal-spore-forming bacterium, designated strain USBA AT, was isolated from a terrestrial hot spring located at an altitude of 2683 m in the Andean region of Colombia (04° 50′ 14.0″ N 75° 32′ 53.4″ W). Cells of strain USBA AT were Gram-stain-positive, straight to slightly curved rods (0.9×2.5 µm), that were arranged singly or in pairs, and were motile by means of flagella. Growth occurred at 37–55 °C and pH 6.0–8.0, with a doubling time of 2 h under the optimal conditions (50 °C and pH 7.0). Glucose fermentation in strain USBA AT required yeast extract or peptone (each at 0.2 %, w/v). The novel strain fermented sugars, amino acids, Casamino acids, propanol, propionate, starch and dextrin, but no growth was observed on galactose, lactose, xylose, histidine, serine, threonine, benzoate, butyrate, lactate, pyruvate, succinate, methanol, ethanol, glycerol, casein, gelatin or xylan. The end products of glucose fermentation were formate, acetate, ethanol and lactate. Strain USBA AT did not grow autotrophically (with CO2 as carbon source and H2 as electron donor) and did not reduce thiosulfate, sulfate, elemental sulfur, sulfite, vanadium (V) or Fe (III) citrate. Growth of strain USBA AT was inhibited by ampicillin, chloramphenicol, kanamycin, penicillin and streptomycin (each at 10 µg ml−1). The predominant fatty acids were iso-C15 : 0, C16 : 0 and iso-C17 : 0 and the genomic DNA G+C content was 32.6 mol%. 16S rRNA gene sequence analysis indicated that strain USBA AT belonged in the phylum Firmicutes and that its closest relative was Caloramator viterbiensis JW/MS-VS5T (95.0 % sequence similarity). A DNA–DNA relatedness value of only 30 % was recorded in hybridization experiments between strain USBA AT and Caloramator viterbiensis DSM 13723T. Based on the phenotypic, chemotaxonomic and phylogenetic evidence and the results of the DNA–DNA hybridization experiments, strain USBA AT represents a novel species of the genus Caloramator , for which the name Caloramator quimbayensis sp. nov. is proposed. The type strain is USBA AT ( = CMPUJ U833T  = DSM 22093T).

Caloramator boliviensis sp. nov., a thermophilic, ethanol-producing bacterium isolated from a hot spring

A novel moderately thermophilic, anaerobic, ethanol-producing bacterial strain, 45BT, was isolated from a mixed sediment water sample collected from a hot spring at Potosi, Bolivia. The cells were straight to slightly curved rods approximately 2.5 µm long and 0.5 µm wide. The strain was Gram-stain-variable, spore-forming and monotrichously flagellated. Growth of the strain was observed at 45–65 °C and pH 5.5–8.0, with optima of 60 °C and pH 6.5. The substrates utilized by strain 45BT were xylose, cellobiose, glucose, arabinose, sucrose, lactose, maltose, fructose, galactose, mannose, glycerol, xylan, carboxymethylcellulose and yeast extract. The main fermentation product from xylose and cellobiose was ethanol (0.70 and 0.45 g ethanol per gram of consumed sugar, respectively). Acetate, lactate, propionate, carbon dioxide and hydrogen were also produced in minor quantities. 1,3-Propanediol was produced when glycerol-containing medium was supplemented with yeast extract. The major cellular fatty acids were anteiso-C15 : 0, C16 : 0, iso-C16 : 0, C15 : 1, iso-C14 : 0, C13 : 0 and C14 : 0. The polar lipids diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, an aminoglycolipid and 15 other unidentified lipids were predominant. The DNA G+C content of strain 45BT was 32.6 mol%. Phylogenetic analysis based on 16S rRNA gene sequence similarity revealed that strain 45BT is located within the Gram-type positive Bacillus – Clostridium branch of the phylogenetic tree. On the basis of morphological and physiological properties and phylogenetic analysis, strain 45BT represents a novel species, for which the name Caloramator boliviensis sp. nov. is proposed; the type strain is 45BT ( = DSM 22065T = CCUG 57396T).

Alkalitalea saponilacus gen. nov., sp. nov., an obligately anaerobic, alkaliphilic, xylanolytic bacterium from a meromictic soda lake

A Gram-positive, obligately anaerobic, motile, slender, flexible rod, designated SC/BZ-SP2(T), was isolated from mixed alkaline water and sediment of Soap Lake, Washington State, USA. Strain SC/BZ-SP2(T) formed salmon to pink colonies and was alkaliphilic. The isolate grew at pH(35 °C) 7.5-10.5 (optimum pH(35 °C) 9.7), at 8-40 °C (optimum 35-37 °C) and with 0.35-1.38 M Na(+) (optimum 0.44-0.69 M Na(+)). The isolate utilized L-arabinose, D-ribose, D-xylose, D-fructose, D-mannose, D-galactose, cellobiose, maltose, sucrose, trehalose, sorbitol, xylan, malate and yeast extract as carbon and energy sources; best growth was observed with L-arabinose, cellobiose, maltose and trehalose. The major fermentation products from beechwood xylan were propionate and acetate. The dominant fatty acids were iso-C(15:0), anteiso-C(15:0), iso-C(17:0) 3-OH, C(17:0) 3-OH and C(15:0) 3-OH. The cell-wall sugars were ribose, xylose, galactose and glucose. Thiosulfate and sulfite could be reduced to sulfide. The genomic DNA G+C content was 39.5 ± 0.9 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain SC/BZ-SP2(T) belonged to the family Marinilabiliaceae of the order Bacteroidales, class Bacteroidia. The most closely related strains were Alkaliflexus imshenetskii Z-7010(T) (91.8% 16S rRNA gene sequence similarity), Marinilabilia salmonicolor Cy s1(T) (91.0%) and Anaerophaga thermohalophila Fru22(T) (90.4%). On the basis of phenotypic, chemotaxonomic and phylogenetic features, strain SC/BZ-SP2(T) represents a novel species in a new genus of the family Marinilabiliaceae, for which the name Alkalitalea saponilacus gen. nov., sp. nov. is proposed. The type strain of Alkalitalea saponilacus is SC/BZ-SP2(T) (=ATCC BAA-2172(T) =DSM 24412(T)).

Desulfotomaculum varum sp. nov., a moderately thermophilic sulfate-reducing bacterium isolated from a microbial mat colonizing a Great Artesian Basin bore well runoff channel

A strictly anaerobic moderately thermophilic bacterium, designated strain RH04-3^T (T = type strain), was isolated from a red colored microbial mat that colonizes a Great Artesian Basin (GAB) bore well (Registered Number 17263) runoff channel at 66 °C. The cells of strain RH04-3^T were straight to slightly curved, sporulating, Gram-positive rods (2.0–5.0 × 1.0 μm) that grew optimally at 50 °C (temperature growth range between 37 and 55 °C) and at pH 7 (pH growth range of 5.0 and 8.5). Growth was inhibited by NaCl concentrations ≥1.5% (w/v), and by chloramphenicol, streptomycin, tetracycline, penicillin and ampicillin. The strain utilized fructose, mannose, glycerol, lactate, pyruvate and H₂ in the presence of sulfate, and fermented pyruvate in the absence of sulfate. Strain RH04-3^T reduced sulfate, sulfite, thiosulfate and elemental sulfur, but not nitrate, nitrite, iron(III), arsenate(V), vanadium(V) or cobalt(III) as terminal electron acceptors. The G + C content of DNA was 52.4 ± 0.8 mol % as determined by the thermal denaturation (Tm) method. 16S rRNA sequence analysis indicated that strain RH04-3^T was a member of the genus Desulfotomaculum and was most closely related to Desulfotomaculum putei (similarity value of 95.2%) and Desulfotomaculum hydrothermale (similarity value of 93.6%). On the basis of phylogenetic and phenotypic characteristics, strain RH04-3^T is considered to represent a novel species of the genus Desulfotomaculum, for which the name Desulfotomaculum varum sp. nov. is proposed. The type strain RH04-3^T = JCM 16158^T = KCTC 5794^T.

Draft genome sequence of Caloramator australicus strain RC3T, a thermoanaerobe from the Great Artesian Basin of Australia

Caloramator australicus strain RC3(T) (JCM 15081(T) = KCTC 5601(T)) is the type strain of a newly identified thermophilic species, which was isolated from red microbial mats that thrive at 66°C in the runoff channel of a Great Artesian Basin bore (New Lorne bore, registered number 17263) in outback Queensland, Australia. The ability of the C. australicus strain to use metals as terminal electron acceptors has led to concerns that it could colonize and enhance corrosion of the metal casing of Great Artesian Basin bore well pipes and that this could subsequently lead to bore failure and loss of water availability for the community which is so reliant on it. The genome of the C. australicus strain has been sequenced, and annotation of the ~2.65-Mb sequence indicates that the attributes are consistent with physiological and phenotypic traits.

Tistlia consotensis gen. nov., sp. nov., an aerobic, chemoheterotrophic, free-living, nitrogen-fixing alphaproteobacterium, isolated from a Colombian saline spring

A Gram-negative, aerobic, mesophilic, non-spore-forming, chemotrophic, chlorophyll-lacking, nitrogen-fixing bacterium, designated strain USBA 355T, was isolated from the saline spring ‘Salado de Consotá’ situated in the Colombian Andes. The non-flagellated cells of strain USBA 355T were straight to slightly curved rods (0.6–0.7 × 3.0–3.5 μm). Growth occurred optimally at 30 °C (growth temperature range between 20 and 40 °C), at pH 6.5–6.7 (pH growth range between 5.0 and 8.0) and at 0.5 % NaCl (w/v) (range between 0 and 4 %). The major quinone present was Q-10 and the predominant fatty acids identified were C19 : 0 cyclo ω8c, C18 : 1 ω7c and C18 : 0. The G+C content of the chromosomal DNA was 71±1 mol%. 16S rRNA gene sequence analysis indicated that strain USBA 355T formed a distant phylogenetic line of descent with members of the genus Thalassobaculum, family Rhodospirillaceae, class Alphaproteobacteria (90 % gene sequence similarity). Comparison of the phylogenetic, chemotaxonomic and physiological features of strain USBA 355T with all other members of the family Rhodospirillaceae suggested that it represents a novel genus and species for which the name Tistlia consotensis gen. nov., sp. nov. is proposed. The type strain of the type species is USBA 355T (=JCM 15529T=KCTC 22406T).

Thermovenabulum gondwanense sp. nov., a thermophilic anaerobic Fe(III)-reducing bacterium isolated from microbial mats thriving in a Great Artesian Basin bore runoff channel

A strictly anaerobic, thermophilic bacterium, designated strain R270T, was isolated from microbial mats thriving in the thermal waters (66 °C) of a Great Artesian Basin bore (registered no. 17263) runoff channel. Cells of strain R270T were straight to slightly curved rods (3.50–6.00×0.75–1.00 μm) that stained Gram-positive, but possessed a Gram-negative cell-wall ultrastructure. Strain R270T grew optimally in tryptone-yeast extract-Casamino acids medium at 65 °C (growth temperature range between 50 and 70 °C) and at pH 7.0 (growth pH range between 6.0 and 9.0). In the presence of 0.02 and 0.10 % yeast extract, pyruvate and Casamino acids were the only substrates fermented from a wide spectrum of substrates tested. Fe(III), Mn(IV), thiosulfate and elemental sulfur were used as electron acceptors in the presence 0.2 % yeast extract, but not sulfate, sulfite, nitrate, nitrite or fumarate. Growth of strain R270T increased in the presence of Fe(III), which was reduced in the presence of peptone, tryptone, Casamino acids, amyl media, starch, pyruvate, H2 and CO2, but not in the presence of acetate, lactate, propionate, formate, benzoate, glycerol or ethanol. Growth and Fe(III) reduction were inhibited by chloramphenicol, streptomycin, tetracycline, penicillin, ampicillin and 2 % NaCl (w/v). The DNA G+C content of strain R270T was 41±1 mol% (T m) and phylogenetic analysis of the 16S rRNA gene indicated that this isolate was closely related to Thermovenabulum ferriorganovorum DSM 14006T (similarity value of 96.1 %) within the family ‘Thermoanaerobacteraceae’, class ‘Clostridia’, phylum ‘Firmicutes’. On the basis of the phylogenetic distance separating the two, together with differences in a number of key phenotypic characteristics, strain R270T represents a novel species of the genus Thermovenabulum, for which the name Thermovenabulum gondwanense sp. nov. is proposed; the type strain is R270T (=KCTC 5616T=DSM 21133T).

Desulfosoma caldarium gen. nov., sp. nov., a thermophilic sulfate-reducing bacterium from a terrestrial hot spring

A thermophilic, sulfate-reducing bacterium, designated strain USBA-053(T), was isolated from a terrestrial hot spring located at a height of 2500 m in the Colombian Andes (5° 45' 33.29″ N 73° 6' 49.89″ W), Colombia. Cells of strain USBA-053(T) were oval- to rod-shaped, Gram-negative and motile by means of a single polar flagellum. The strain grew autotrophically with H(2) as the electron donor and heterotrophically on formate, propionate, butyrate, valerate, isovalerate, lactate, pyruvate, ethanol, glycerol, serine and hexadecanoic acid in the presence of sulfate as the terminal electron acceptor. The main end products from lactate degradation, in the presence of sulfate, were acetate, CO(2) and H(2)S. Strain USBA-053(T) fermented pyruvate in the absence of sulfate and grew optimally at 57 °C (growth temperature ranged from 50 °C to 62 °C) and pH 6.8 (growth pH ranged from 5.7 to 7.7). The novel strain was slightly halophilic and grew in NaCl concentrations ranging from 5 to 30 g l(-1), with an optimum at 25 g l(-1) NaCl. Sulfate, thiosulfate and sulfite were used as electron acceptors, but not elemental sulfur, nitrate or nitrite. The G+C content of the genomic DNA was 56±1 mol%. 16S rRNA gene sequence analysis indicated that strain USBA-053(T) was a member of the class Deltaproteobacteria, with Desulfacinum hydrothermale MT-96(T) as the closest relative (93 % gene sequence similarity). On the basis of physiological characteristics and phylogenetic analysis, it is suggested that strain USBA-053(T) represents a new genus and novel species for which the name Desulfosoma caldarium gen. nov., sp. nov. is proposed. The type strain of the type species is USBA-053(T) ( = KCTC 5670(T) = DSM 22027(T)).

Caloramator mitchellensis sp. nov., a thermoanaerobe isolated from the geothermal waters of the Great Artesian Basin of Australia, and emended description of the genus Caloramator

A strictly thermophilic anaerobe, designated strain VF08(T), was isolated from a water sample collected from a Great Artesian Basin bore (registered bore number 22981) situated at Mitchell, QLD, Australia. Cells of isolate VF08(T) were slightly curved, non-sporulating rods (1.5-3.5 x 0.4-0.8 μm), which stained Gram-negative but possessed a Gram-positive cell-wall ultrastructure. The strain grew optimally in tryptone-yeast extract-glucose (TYEG) medium at 55 °C (temperature growth range between 37 and 60 °C) and a pH of 7 (pH growth range, 6.0-9.0). Yeast extract or tryptone was required for growth on glucose, fructose, xylose, maltose, sucrose, raffinose, cellobiose, ribose, pyruvate, tryptone, peptone, Casamino acids, amyl media and serine, but could also support growth as the sole carbon source. End products from glucose fermentation were acetate, ethanol, CO₂ and H₂. The strain reduced vanadium(V), but not iron(III), manganese(IV), elemental sulfur, sulfate, thiosulfate, sulfite, nitrate or nitrite in the presence of 0.2  % yeast extract, peptone, tryptone, glucose, sucrose and Casamino acids, but an increase in the growth rate or cell yield was not observed. Growth was inhibited by chloramphenicol, streptomycin, tetracycline, penicillin, ampicillin and ≥ 2  % NaCl (w/v). The G+C content of the DNA was 38.4 ± 0.8 mol% as determined by the thermal denaturation (T(m)) method. 16S rRNA gene sequence analysis revealed that isolate VF08(T) was a member of the genus Caloramator with Caloramator australicus and Caloramator fervidus (formerly Clostridium fervidus) being the closest relatives with similarity values of 85.0 and 86.1  %, respectively, when helix 6 nucleotides were included in the analysis, and 95.2  % and 94  %, respectively, when these nucleotides were masked from the analysis. Further analysis revealed that strain VF08(T) formed an individual cluster (cluster II) within the genus Caloramator and could be distinguished from other species within the genus Caloramator (clusters I, III and IV) on the basis of signature nucleotides and differences in phenotypic traits. These data suggest that strain VF08(T) is a novel species of the genus Caloramator, for which the name Caloramator mitchellensis sp. nov. is proposed. The type strain is VF08(T) (=JCM 15828(T)=KCTC 5735(T)). An emended description of the genus Caloramator is also provided.

Dethiosulfovibrio salsuginis sp. nov., an anaerobic, slightly halophilic bacterium isolated from a saline spring

A mesophilic, strictly anaerobic, slightly halophilic bacterium, designated strain USBA 82T, was isolated from a terrestrial saline spring in the Colombian Andes. The non-spore-forming curved rods (5–7×1.3 μm) with pointed or rounded ends, stained Gram-negative and were motile by means of laterally inserted flagella. The strain grew optimally at 30 °C (growth range 20–40 °C), pH 7.3 (growth range pH 5.5–8.5) and 2 % (w/v) NaCl (growth range 0.1–7 % NaCl). The strain fermented peptides, amino acids and a few organic acids, but growth was not observed on carbohydrates, alcohols or fatty acids. The strain reduced thiosulfate and sulfur to sulfide. Sulfate, sulfite, nitrate and nitrite were not used as electron acceptors. On peptone alone, acetate, succinate, propionate and traces of ethanol were formed, but in the presence of thiosulfate, acetate and succinate were formed. The G+C content of the chromosomal DNA was 52 mol% (T m).16S rRNA gene sequence analysis indicated that strain USBA 82T was affiliated to Dethiosulfovibrio peptidovorans within the phylum Synergistetes with a similarity value of approximately 93 %. Based on the differences between the new strain and the type species of the genus Dethiosulfovibrio, we suggest that strain USBA 82T represents a novel species of the genus for which the name Dethiosulfovibrio salsuginis sp. nov. is proposed. The type strain is USBA 82T (=DSM 21565T=KCTC 5659T).

Fervidicella metallireducens gen. nov., sp. nov., a thermophilic, anaerobic bacterium from geothermal waters

A strictly anaerobic, thermophilic bacterium, designated strain AeB(T), was isolated from microbial mats colonizing a run-off channel formed by free-flowing thermal water from a bore well (registered number 17263) of the Great Artesian Basin, Australia. Cells of strain AeB(T) were slightly curved rods (2.5-6.0x1.0 mum) that stained Gram-negative and formed spherical terminal to subterminal spores. The strain grew optimally in tryptone-yeast extract-Casamino acids medium at 50 degrees C (range 37-55 degrees C) and pH 7 (range pH 5-9). Strain AeB(T) grew poorly on yeast extract (0.2 %) and tryptone (0.2 %) as sole carbon sources, which were obligately required for growth on other energy sources. Growth of strain AeB(T) increased in the presence of various carbohydrates and amino acids, but not organic acids. End products detected from glucose fermentation were ethanol, acetate, CO2 and H2. In the presence of 0.2 % yeast extract, iron(III), manganese(IV), vanadium(V) and cobalt(III) were reduced, but not sulfate, thiosulfate, sulfite, elemental sulfur, nitrate or nitrite. Iron(III) was also reduced in the presence of tryptone, peptone, Casamino acids and amyl media (Research Achievement), but not starch, xylan, chitin, glycerol, ethanol, pyruvate, benzoate, lactate, acetate, propionate, succinate, glycine, serine, lysine, threonine, arginine, glutamate, valine, leucine, histidine, alanine, aspartate, isoleucine or methionine. Growth was inhibited by chloramphenicol, streptomycin, tetracycline, penicillin, ampicillin and NaCl concentrations >2 %. The DNA G+C content was 35.4+/-1 mol%, as determined by the thermal denaturation method. 16S rRNA gene sequence analysis indicated that strain AeB(T) is a member of the family Clostridiaceae, class Clostridia, phylum 'Firmicutes', and is positioned approximately equidistantly between the genera Sarcina, Anaerobacter, Caloramator and Clostridium (16S rRNA gene similarity values of 87.8-90.9 %). On the basis of 16S rRNA gene sequence comparisons and physiological characteristics, strain AeB(T) is considered to represent a novel species in a new genus, for which the name Fervidicella metallireducens gen. nov., sp. nov. is proposed; the type strain is AeB(T) (=JCM 15555(T)=KCTC 5667(T)).