Long-term patterns of hydrocarbon biodegradation and bacterial community composition in epipelagic and mesopelagic zones of an Arctic fjord.

Oil spill attenuation in Arctic marine environments depends on oil-degrading bacteria. However, the seasonally harsh conditions in the Arctic such as nutrient limitations and sub-zero temperatures limit the activity even for bacteria capable of hydrocarbon metabolism at low temperatures. Here, we investigated whether the variance between epipelagic (seasonal temperature and inorganic nutrient variations) and mesopelagic zone (stable environmental conditions) could limit the growth of oil-degrading bacteria and lead to lower oil biodegradation rates in the epipelagic than in the mesopelagic zone. Therefore, we deployed absorbents coated with three oil types in a SW-Greenland fjord system at 10-20 m (epipelagic) and 615-650 m (mesopelagic) water depth for one year. During this period we monitored the development and succession of the bacterial biofilms colonizing the oil films by 16S rRNA gene amplicon quantification and sequencing, and the progression of oil biodegradation by gas chromatography - mass spectrometry oil fingerprinting analysis. The removal of hydrocarbons was significantly different, with several polycyclic aromatic hydrocarbons showing longer half-life times in the epipelagic than in the mesopelagic zone. Bacterial community composition and density (16S rRNA genes/ cm2) significantly differed between the two zones, with total bacteria reaching to log-fold higher densities (16S rRNA genes/cm2) in the mesopelagic than epipelagic oil-coated absorbents. Consequently, the environmental conditions in the epipelagic zone limited oil biodegradation performance by limiting bacterial growth.

Spatial separation of ribosomes and DNA in Asgard archaeal cells.

The origin of the eukaryotic cell is a major open question in biology. Asgard archaea are the closest known prokaryotic relatives of eukaryotes, and their genomes encode various eukaryotic signature proteins, indicating some elements of cellular complexity prior to the emergence of the first eukaryotic cell. Yet, microscopic evidence to demonstrate the cellular structure of uncultivated Asgard archaea in the environment is thus far lacking. We used primer-free sequencing to retrieve 715 almost full-length Loki- and Heimdallarchaeota 16S rRNA sequences and designed novel oligonucleotide probes to visualize their cells in marine sediments (Aarhus Bay, Denmark) using catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH). Super-resolution microscopy revealed 1-2 µm large, coccoid cells, sometimes occurring as aggregates. Remarkably, the DNA staining was spatially separated from ribosome-originated FISH signals by 50-280 nm. This suggests that the genomic material is condensed and spatially distinct in a particular location and could indicate compartmentalization or membrane invagination in Asgard archaeal cells.

Biodegradation of water-accommodated aromatic oil compounds in Arctic seawater at 0 °C.

Oil spills in Arctic marine environments are expected to increase concurrently with the expansion of shipping routes and petroleum exploitation into previously inaccessible ice-dominated regions. Most research on oil biodegradation focusses on the bulk oil, but the fate of the water-accommodated fraction (WAF), mainly composed of toxic aromatic compounds, is largely underexplored. To evaluate the bacterial degradation capacity of such dissolved aromatics in Greenlandic seawater, microcosms consisting of 0 °C seawater polluted with WAF were investigated over a 3-month period. With a half-life (t1/2) of 26 days, m-xylene was the fastest degraded compound, as measured by gas chromatography - mass spectrometry. Substantial slower degradation was observed for ethylbenzene, naphthalenes, phenanthrene, acenaphthylene, acenaphthene and fluorenes with t1/2 of 40-105 days. Colwellia, identified by 16S rRNA gene sequencing, was the main potential degrader of m-xylene. This genus occupied up to 47 % of the bacterial community until day 10 in the microcosms. Cycloclasticus and Zhongshania aliphaticivorans, potentially utilizing one-to three-ringed aromatics, replaced Colwellia between day 10 and 96 and occupied up to 6 % and 23 % of the community, respectively. Although most of the WAF can ultimately be eliminated in microcosms, our results suggest that the restoration of an oil-impacted Arctic environment may be slow as most analysed compounds had t1/2 of over 2-3 months and the detrimental effects of a spill towards the marine ecosystem likely persist during this time.

Constraints on CaCO3 precipitation in superabsorbent polymer by aerobic bacteria.

Microbially induced CaCO3 precipitation (MICP) can give concrete self-healing properties. MICP agents are typically bacterial endospores which are coated into shelled granules, infused into expanded clay, or embedded into superabsorbent polymer (SAP). When small cracks appear in the cured concrete, the encapsulation is broken and the metabolic CO2 production from the germinated bacteria causes healing of the cracks by precipitation of CaCO3. Such systems are being tested empirically at large scales, but survival of endospores through preparation and application, as well as germination and growth kinetics of the germinated vegetative cells, remains poorly resolved. We encapsulated endospores of Bacillus subtilis and Bacillus alkalinitrilicus in crosslinked acrylamide-based SAP and quantified their germination, growth, and, in the case of B. alkalinitrilicus, CaCO3 precipitation potential. The endospores survived crosslinking and desiccation inside the polymer matrix. Microcalorimetry and microscopy showed that ~ 80% of the encapsulated endospores of both strains readily germinated after rehydration of freeze-dried SAP. Germinated cells grew into dense colonies of cells inside the SAP, and those of B. alkalinitrilicus calcified with up to 0.3 g CaCO3 produced per g desiccated SAP when incubated aerobically. Measurements by planar optodes indicated that the precipitation rates were inherently oxygen limited due to diffusional constraints, rather than limited by electron donor or Ca2+ availability. Such oxygen limitation will limit MICP in all water-saturated and oxygen-dependent systems, and MICP agents based on anaerobic bacteria, e.g., nitrate reducers, should be developed to broaden the applicability of bioactive self-healing concretes to wet and waterlogged environments.

Optical Sensing of pH and O2 in the Evaluation of Bioactive Self-Healing Cement.

Leakage from cementitious structures with a retaining function can have devastating environmental consequences. Leaks can originate from cracks within the hardened cementitious material that is supposed to seal the structure off from the surrounding environment. Bioactive self-healing concretes containing bacteria capable of microbially inducing CaCO3 precipitation have been suggested to mitigate the healing of such cracks before leaking occurs. An important parameter determining the biocompatibility of concretes and cements is the pH environment. Therefore, a novel ratiometric pH optode imaging system based on an inexpensive single-lens reflex (SLR) camera was used to characterize the pH of porewater within cracks of submerged hydrated oil and gas well cement. This enabled the imaging of pH with a spatial distribution in high resolution (50 µm per pixel) and a gradient of 1.4 pH units per 1 mm. The effect of fly ash substitution and hydration time on the pH of the cement surface was evaluated by this approach. The results show that pH is significantly reduced from pH >11 to below 10 with increasing fly ash content as well as hydration time. The assessment of bioactivity in the cement was evaluated by introducing superabsorbent polymers with encapsulated Bacillus alkalinitrilicus endospores into the cracks. The bacterial activity was measured using oxygen optodes, which showed the highest bacterial activity with increasing amounts of fly ash substitution in the cement, correlating with the decrease in the pH. Overall, our results demonstrate that the pH of well cements can be reliably measured and modified to sustain the microbial activity.

Glacial Runoff Promotes Deep Burial of Sulfur Cycling-Associated Microorganisms in Marine Sediments.

Marine fjords with active glacier outlets are hot spots for organic matter burial in the sediments and subsequent microbial mineralization. Here, we investigated controls on microbial community assembly in sub-arctic glacier-influenced (GI) and non-glacier-influenced (NGI) marine sediments in the Godthåbsfjord region, south-western Greenland. We used a correlative approach integrating 16S rRNA gene and dissimilatory sulfite reductase (dsrB) amplicon sequence data over six meters of depth with biogeochemistry, sulfur-cycling activities, and sediment ages. GI sediments were characterized by comparably high sedimentation rates and had "young" sediment ages of <500 years even at 6 m sediment depth. In contrast, NGI stations reached ages of approximately 10,000 years at these depths. Sediment age-depth relationships, sulfate reduction rates (SRR), and C/N ratios were strongly correlated with differences in microbial community composition between GI and NGI sediments, indicating that age and diagenetic state were key drivers of microbial community assembly in subsurface sediments. Similar bacterial and archaeal communities were present in the surface sediments of all stations, whereas only in GI sediments were many surface taxa also abundant through the whole sediment core. The relative abundance of these taxa, including diverse Desulfobacteraceae members, correlated positively with SRRs, indicating their active contributions to sulfur-cycling processes. In contrast, other surface community members, such as Desulfatiglans, Atribacteria, and Chloroflexi, survived the slow sediment burial at NGI stations and dominated in the deepest sediment layers. These taxa are typical for the energy-limited marine deep biosphere and their relative abundances correlated positively with sediment age. In conclusion, our data suggests that high rates of sediment accumulation caused by glacier runoff and associated changes in biogeochemistry, promote persistence of sulfur-cycling activity and burial of a larger fraction of the surface microbial community into the deep subsurface.

The Polyextremophilic Bacterium Clostridium paradoxum Attains Piezophilic Traits by Modulating Its Energy Metabolism and Cell Membrane Composition.

In polyextremophiles, i.e., microorganisms growing preferentially under multiple extremes, synergistic effects may allow growth when application of the same extremes alone would not. High hydrostatic pressure (HP) is rarely considered in studies of polyextremophiles, and its role in potentially enhancing tolerance to other extremes remains unclear. Here, we investigated the HP-temperature response in Clostridium paradoxum, a haloalkaliphilic moderately thermophilic endospore-forming bacterium, in the range of 50 to 70°C and 0.1 to 30 MPa. At ambient pressure, growth limits were extended from the previously reported 63°C to 70°C, defining C. paradoxum as an actual thermophile. Concomitant application of high HP and temperature compared to standard conditions (i.e., ambient pressure and 50°C) remarkably enhanced growth, with an optimum growth rate observed at 22 MPa and 60°C. HP distinctively defined C. paradoxum physiology, as at 22 MPa biomass, production increased by 75% and the release of fermentation products per cell decreased by >50% compared to ambient pressure. This metabolic modulation was apparently linked to an energy-preserving mechanism triggered by HP, involving a shift toward pyruvate as the preferred energy and carbon source. High HPs decreased cell damage, as determined by Syto9 and propidium iodide staining, despite no organic solute being accumulated intracellularly. A distinct reduction in carbon chain length of phospholipid fatty acids (PLFAs) and an increase in the amount of branched-chain PLFAs occurred at high HP. Our results describe a multifaceted, cause-and-effect relationship between HP and cell metabolism, stressing the importance of applying HP to define the boundaries for life under polyextreme conditions.IMPORTANCE Hydrostatic pressure (HP) is a fundamental parameter influencing biochemical reactions and cell physiology; however, it is less frequently applied than other factors, such as pH, temperature, and salinity, when studying polyextremophilic microorganisms. In particular, how HP affects microbial tolerance to other and multiple extremes remains unclear. Here, we show that under polyextreme conditions of high pH and temperature, Clostridium paradoxum demonstrates a moderately piezophilic nature as cultures grow to highest cell densities and most efficiently at a specific combination of temperature and HP. Our results highlight the importance of considering HP when exploring microbial physiology under extreme conditions and thus have implications for defining the limits for microbial life in nature and for optimizing industrial bioprocesses occurring under multiple extremes.

In situ biodegradation, photooxidation and dissolution of petroleum compounds in Arctic seawater and sea ice.

In pristine sea ice-covered Arctic waters the potential of natural attenuation of oil spills has yet to be uncovered, but increasing shipping and oil exploitation may bring along unprecedented risks of oil spills. We deployed adsorbents coated with thin oil films for up to 2.5 month in ice-covered seawater and sea ice in Godthaab Fjord, SW Greenland, to simulate and investigate in situ biodegradation and photooxidation of dispersed oil. GC-MS-based chemometric methods for oil fingerprinting were used to identify characteristic signatures for dissolution, biodegradation and photooxidation. In sub-zero temperature seawater, fast degradation of n-alkanes was observed with estimated half-life times of ∼7 days. PCR amplicon sequencing and qPCR quantification of bacterial genes showed that a biofilm with a diverse microbial community colonised the oil films, yet a population related to the psychrophilic hydrocarbonoclastic gammaproteobacterium Oleispira antarctica seemed to play a key role in n-alkane degradation. Although Oleispira populations were also present in sea ice, we found that biofilms in sea ice had 25 to 100 times lower bacterial densities than in seawater, which explained the non-detectable n-alkane degradation in sea ice. Fingerprinting revealed that photooxidation, but not biodegradation, transformed polycyclic aromatic compounds through 50 cm-thick sea ice and in the upper water column with removal rates up to ∼1% per day. Overall, our results showed a fast biodegradation of n-alkanes in sea ice-covered seawater, but suggested that oils spills will expose the Arctic ecosystem to bio-recalcitrant PACs over prolonged periods of time.

Contrasting community composition of endospores and vegetative Firmicutes in a marine sediment suggests both endogenous and exogenous sources of endospore accumulation.

Bacterial endospores are highly abundant in marine sediments, but their taxonomic identity and ecology is largely unknown. We selectively extracted DNA from endospores and vegetative cells and sequenced 16S rRNA genes to characterize the composition of the endospore and vegetative Firmicutes communities in the sediment and water column of Aarhus Bay (Denmark). The endospore community in the sediment was dominated by the families Bacillaceae, Lachnospiraceae, Clostridiaceae and Ruminoccocaceae. These families were also represented in the vegetative community in the sediment and the endospore community in the water column. OTUs of high relative abundance in the endospore community were also represented in the vegetative Firmicutes community. Other OTUs were exclusively found in the endospore communities. This suggests that endospores accumulate in marine sediments due to passive deposition from the water column and sporulation of vegetative cells in the sediment. Some OTUs were detected in the endospore community of the water column and the vegetative community the sediment indicating that endospores deposited from the water column may germinate upon burial/deposition in the sediment. We provide novel insight into the composition of endospore communities in marine sediments and highlight their role in microbial dispersal and as a seed bank in subsurface sediments.

The marine sulfate reducer Desulfobacterium autotrophicum HRM2 can switch between low and high apparent half-saturation constants for dissimilatory sulfate reduction.

Studies of the kinetics of dissimilatory sulfate reduction in marine sediment have shown that a mixture of marine sulfate-reducing bacteria (SRB) can reduce sulfate with both a high and low apparent sulfate half-saturation constant (Km). However, all marine pure cultures investigated have shown only low-sulfate affinity sulfate reduction kinetics. It remains unknown whether marine high sulfate-affinity sulfate reduction is catalyzed by unknown SRB or whether known SRB possess unrecognized high-affinity sulfate reduction systems. We used 35S-sulfate incubation experiments to show that cultures of Desulfobacterium autotrophicum HMR2 will switch from low-affinity to high-affinity sulfate reduction when sulfate concentrations fall below 500 µM. The mean Km was 150 µM at high sulfate concentrations and 8 µM at low sulfate concentrations. The high-affinity Km value is comparable to values found in SRB inhabiting freshwater sediments and D. autotrophicum cultures could deplete sulfate to below our detection limit of 25 nM. The switch in Km value was accompanied by a change in the expression of genes encoding membrane-bound transport proteins putatively involved in sulfate uptake in D. autotrophicum. Our results demonstrate that a marine sulfate reducer can efficiently reduce sulfate at both high and low sulfate concentrations, possibly by activation of different sulfate transporters in the membrane.

Description of Endozoicomonas ascidiicola sp. nov., isolated from Scandinavian ascidians.

Two gram-negative, facultative anaerobic, chemoorganoheterotrophic, motile and rod-shaped bacteria, strains AVMART05(T) and KASP37, were isolated from ascidians (Tunicata, Ascidiaceae) of the genus Ascidiella collected at Gullmarsfjord, Sweden. The strains are the first cultured representatives of an ascidian-specific lineage within the genus Endozoicomonas (Gammaproteobacteria, Oceanospirillales, Hahellaceae). Both strains feature three distinct 16S rRNA gene paralogs, with identities of 98.9-99.1% (AVMART05(T)) and 97.7-98.8% (KASP37) between paralogs. The strains are closely related to Endozoicomonas atrinae and Endozoicomonas elysicola, with which they share 97.3-98.0% 16S rRNA gene sequence identity. Digital DNA-DNA hybridization, average nucleotide identity, and tetra-nucleotide correlation analysis indicate that both strains belong to a single species distinct from their closest relatives. Both strains feature similar DNA G+C contents of 46.70mol% (AVMART05(T)) and 44.64mol% (KASP37). The fatty acid patterns of AVMART05(T) and KASP37 are most similar to those of Endozoicomonas euniceicola and Endozoicomonas gorgoniicola. Based on the polyphasic approach, we propose the species Endozoicomonas ascidiicola sp. nov. to accommodate the newly isolated strains. E. ascidiicola sp. nov. is represented by the type strain AVMART05(T) (=DSM 100913(T)=LMG 29095(T)) and strain KASP37 (=DSM 100914=LMG 29096).

Uncultured Desulfobacteraceae and Crenarchaeotal group C3 incorporate 13C-acetate in coastal marine sediment.

Stable isotope probing (SIP) of deoxyribonucleic acid (DNA) was used to identify microbes incorporating (13) C-labeled acetate in sulfate-reducing sediment from Aarhus Bay, Denmark. Sediment was incubated in medium containing 10 mM sulfate and different (13) C-acetate (10, 1, 0.1 mM) concentrations. The resultant changes in microbial community composition were monitored in total and SIP-fractionated DNA during long-term incubations. Chemical analyses demonstrated metabolic activity in all sediment slurries, with sulfate-reducing activity largely determined by initial acetate concentrations. Sequencing of 16S rRNA gene PCR amplicons showed that the incubations shifted the bacterial but not the archaeal community composition. After 3 months of incubation, only sediment slurries incubated with 10 mM (13) C-acetate showed detectable (13) C-DNA labeling. Based on 16S rRNA and dsrB gene PCR amplicon sequencing, the (13) C-labeled DNA pool was dominated by a single type of sulfate reducer representing a novel genus in the family Desulfobacteraceae. In addition, members of the uncultivated Crenarchaeotal group C3 were enriched in the (13) C-labeled DNA. Our results were reproducible across biological replicate experiments and provide new information about the identities of uncultured acetate-consuming bacteria and archaea in marine sediments.

Phylogenetic and environmental diversity of DsrAB-type dissimilatory (bi)sulfite reductases.

The energy metabolism of essential microbial guilds in the biogeochemical sulfur cycle is based on a DsrAB-type dissimilatory (bi)sulfite reductase that either catalyzes the reduction of sulfite to sulfide during anaerobic respiration of sulfate, sulfite and organosulfonates, or acts in reverse during sulfur oxidation. Common use of dsrAB as a functional marker showed that dsrAB richness in many environments is dominated by novel sequence variants and collectively represents an extensive, largely uncharted sequence assemblage. Here, we established a comprehensive, manually curated dsrAB/DsrAB database and used it to categorize the known dsrAB diversity, reanalyze the evolutionary history of dsrAB and evaluate the coverage of published dsrAB-targeted primers. Based on a DsrAB consensus phylogeny, we introduce an operational classification system for environmental dsrAB sequences that integrates established taxonomic groups with operational taxonomic units (OTUs) at multiple phylogenetic levels, ranging from DsrAB enzyme families that reflect reductive or oxidative DsrAB types of bacterial or archaeal origin, superclusters, uncultured family-level lineages to species-level OTUs. Environmental dsrAB sequences constituted at least 13 stable family-level lineages without any cultivated representatives, suggesting that major taxa of sulfite/sulfate-reducing microorganisms have not yet been identified. Three of these uncultured lineages occur mainly in marine environments, while specific habitat preferences are not evident for members of the other 10 uncultured lineages. In summary, our publically available dsrAB/DsrAB database, the phylogenetic framework, the multilevel classification system and a set of recommended primers provide a necessary foundation for large-scale dsrAB ecology studies with next-generation sequencing methods.

Survival of prokaryotes in a polluted waste dump during remediation by alkaline hydrolysis.

A combination of culture-dependent and culture-independent techniques was used to characterize bacterial and archaeal communities in a highly polluted waste dump and to assess the effect of remediation by alkaline hydrolysis on these communities. This waste dump (Breakwater 42), located in Denmark, contains approximately 100 different toxic compounds including large amounts of organophosphorous pesticides such as parathions. The alkaline hydrolysis (12 months at pH >12) decimated bacterial and archaeal abundances, as estimated by 16S rRNA gene-based qPCR, from 2.1 × 10(4) and 2.9 × 10(3) gene copies per gram wet soil respectively to below the detection limit of the qPCR assay. Clone libraries constructed from PCR-amplified 16S rRNA gene fragments showed a significant reduction in bacterial diversity as a result of the alkaline hydrolysis, with preferential survival of Betaproteobacteria, which increased in relative abundance from 0 to 48 %. Many of the bacterial clone sequences and the 27 isolates were related to known xenobiotic degraders. An archaeal clone library from a non-hydrolyzed sample showed the presence of three main clusters, two representing methanogens and one representing marine aerobic ammonia oxidizers. Isolation of alkalitolerant bacterial pure cultures from the hydrolyzed soil confirmed that although alkaline hydrolysis severely reduces microbial community diversity and size certain bacteria survive a prolonged alkaline hydrolysis process. Some of the isolates from the hydrolyzed soil were capable of growing at high pH (pH 10.0) in synthetic media indicating that they could become active in in situ biodegradation upon hydrolysis.

Endospores of thermophilic bacteria as tracers of microbial dispersal by ocean currents.

Microbial biogeography is influenced by the combined effects of passive dispersal and environmental selection, but the contribution of either factor can be difficult to discern. As thermophilic bacteria cannot grow in the cold seabed, their inactive spores are not subject to environmental selection. We therefore conducted a global experimental survey using thermophilic endospores that are passively deposited by sedimentation to the cold seafloor as tracers to study the effect of dispersal by ocean currents on the biogeography of marine microorganisms. Our analysis of 81 different marine sediments from around the world identified 146 species-level 16S rRNA phylotypes of endospore-forming, thermophilic Firmicutes. Phylotypes showed various patterns of spatial distribution in the world oceans and were dispersal-limited to different degrees. Co-occurrence of several phylotypes in locations separated by great distances (west of Svalbard, the Baltic Sea and the Gulf of California) demonstrated a widespread but not ubiquitous distribution. In contrast, Arctic regions with water masses that are relatively isolated from global ocean circulation (Baffin Bay and east of Svalbard) were characterized by low phylotype richness and different compositions of phylotypes. The observed distribution pattern of thermophilic endospores in marine sediments suggests that the impact of passive dispersal on marine microbial biogeography is controlled by the connectivity of local water masses to ocean circulation.

Complete genome sequence of Desulfocapsa sulfexigens, a marine deltaproteobacterium specialized in disproportionating inorganic sulfur compounds.

Desulfocapsa sulfexigens SB164P1 (DSM 10523) belongs to the deltaproteobacterial family Desulfobulbaceae and is one of two validly described members of its genus. This strain was selected for genome sequencing, because it is the first marine bacterium reported to thrive on the disproportionation of elemental sulfur, a process with a unresolved enzymatic pathway in which elemental sulfur serves both as electron donor and electron acceptor. Furthermore, in contrast to its phylogenetically closest relatives, which are dissimilatory sulfate-reducers, D. sulfexigens is unable to grow by sulfate reduction and appears metabolically specialized in growing by disproportionating elemental sulfur, sulfite or thiosulfate with CO2 as the sole carbon source. The genome of D. sulfexigens contains the set of genes that is required for nitrogen fixation. In an acetylene assay it could be shown that the strain reduces acetylene to ethylene, which is indicative for N-fixation. The circular chromosome of D. sulfexigens SB164P1 comprises 3,986,761 bp and harbors 3,551 protein-coding genes of which 78% have a predicted function based on auto-annotation. The chromosome furthermore encodes 46 tRNA genes and 3 rRNA operons.

Dispersal of thermophilic Desulfotomaculum endospores into Baltic Sea sediments over thousands of years.

Patterns of microbial biogeography result from a combination of dispersal, speciation and extinction, yet individual contributions exerted by each of these mechanisms are difficult to isolate and distinguish. The influx of endospores of thermophilic microorganisms to cold marine sediments offers a natural model for investigating passive dispersal in the ocean. We investigated the activity, diversity and abundance of thermophilic endospore-forming sulfate-reducing bacteria (SRB) in Aarhus Bay by incubating pasteurized sediment between 28 and 85 °C, and by subsequent molecular diversity analyses of 16S rRNA and of the dissimilatory (bi)sulfite reductase (dsrAB) genes within the endospore-forming SRB genus Desulfotomaculum. The thermophilic Desulfotomaculum community in Aarhus Bay sediments consisted of at least 23 species-level 16S rRNA sequence phylotypes. In two cases, pairs of identical 16S rRNA and dsrAB sequences in Arctic surface sediment 3000 km away showed that the same phylotypes are present in both locations. Radiotracer-enhanced most probable number analysis revealed that the abundance of endospores of thermophilic SRB in Aarhus Bay sediment was ca. 10(4) per cm(3) at the surface and decreased exponentially to 10(0) per cm(3) at 6.5 m depth, corresponding to 4500 years of sediment age. Thus, a half-life of ca. 300 years was estimated for the thermophilic SRB endospores deposited in Aarhus Bay sediments. These endospores were similarly detected in the overlying water column, indicative of passive dispersal in water masses preceding sedimentation. The sources of these thermophiles remain enigmatic, but at least one source may be common to both Aarhus Bay and Arctic sediments.

Filamentous bacteria transport electrons over centimetre distances.

Oxygen consumption in marine sediments is often coupled to the oxidation of sulphide generated by degradation of organic matter in deeper, oxygen-free layers. Geochemical observations have shown that this coupling can be mediated by electric currents carried by unidentified electron transporters across centimetre-wide zones. Here we present evidence that the native conductors are long, filamentous bacteria. They abounded in sediment zones with electric currents and along their length they contained strings with distinct properties in accordance with a function as electron transporters. Living, electrical cables add a new dimension to the understanding of interactions in nature and may find use in technology development.

Description of Citricoccus nitrophenolicus sp. nov., a para-nitrophenol degrading actinobacterium isolated from a wastewater treatment plant and emended description of the genus Citricoccus Altenburger et al. 2002.

A novel actinobacterium, designated PNP1(T), was isolated from a wastewater treatment plant at a pesticide factory by selective enrichment with para-nitrophenol. The strictly aerobic strain PNP1(T) grew with para-nitrophenol as the sole carbon and energy source. Metabolism of para-nitrophenol resulted in the stoichiometric release of nitrite. When incubated with both para-nitrophenol and acetate, para-nitrophenol was degraded and utilized as growth substrate prior to acetate. When grown on acetate (in the absence of ammonium) both nitrite and nitrate served as nitrogen sources, nitrate being quantitatively reduced to nitrite which accumulated in cultures during aerobic growth. Cells were coccoid and stained Gram-positive, were non-motile and did not form endospores. Colonies of strain PNP1(T) on agar medium were bright yellow, circular and smooth. The dominant menaquinone was MK-8(H(2)) (54%) and the major cellular fatty acid was anteiso C15:0 (75%). Strain PNP1(T) grew optimally at 27°C, at pH 8-8.5, at salinities 3% (w/v) NaCl, yet exhibited a substantial halotolerance with growth occurring at salinities up to 17% (w/v) NaCl. In addition to para-nitrophenol, a range of sugars, short chain fatty acids and alcohols served as electron donors for growth. The DNA G + C mol% was 68%. The genotypic and phenotypic properties suggest that strain PNP1(T) represents a novel species of the actinobacterial genus Citricoccus for which the name Citricoccus nitrophenolicus is proposed. It is the first member of this genus that has been reported to hydrolyze and grow on para-nitrophenol. The type strain is PNP1(T) (=DSM 23311(T) = CCUG 59571(T)).

Marinimicrobium haloxylanilyticum sp. nov., a new moderately halophilic, polysaccharide-degrading bacterium isolated from Great Salt Lake, Utah.

A new moderately halophilic, strictly aerobic, Gram-negative bacterium, strain SX15(T), was isolated from hypersaline surface sediment of the southern arm of Great Salt Lake (Utah, USA). The strain grew on a number of carbohydrates and carbohydrate polymers such as xylan, starch, carboxymethyl cellulose and galactomannan. The strain grew at salinities ranging from 2 to 22% NaCl (w/v). Optimal growth occurred in the presence of 7-11% NaCl (w/v) at a temperature of 35°C and a pH of 6.7-8.2. Major whole-cell fatty acids were C16:0 (30.5%), C18:0 (14.8%), C18:1ω7c (13.1%) and C12:0 (7.8%). The G+C content of the DNA was 60 ± 0.5 mol%. By 16S rRNA gene sequence analysis, strain SX15(T) was shown to be affiliated to members of the gammaproteobacterial genus Marinimicrobium with pair wise identity values of 92.9-94.6%. The pheno- and genotypic properties suggest that strain SX15(T) represents a novel species of the genus Marinimicrobium for which the name Marinimicrobium haloxylanilyticum is proposed. The type strain is SX15(T) (= DSM 23100(T) = CCUG 59572(T)).