Succession of Deferribacteres and Epsilonproteobacteria through a nitrate-treated high-temperature oil production facility.

Members of Epsilonproteobacteria and Deferribacteres have been implied in nitrate-induced souring control in high-temperature oil production facilities. Here we report on their diversity and abundance in the injection and production part of a nitrate-treated, off-shore oil facility (Halfdan, Denmark) and aimed to assess their potential in souring control. Nitrate addition to deoxygenated seawater shifted the low-biomass seawater community dominated by Gammaproteobacteria closely affiliated with the genus Colwellia to a high-biomass community with significantly higher species richness. Epsilonproteobacteria accounted for less than 1% of the total bacterial community in the nitrate-amended injection water and were most likely outcompeted by putative nitrate-reducing, methylotrophic Gammaproteobacteria of the genus Methylophaga. Reservoir passage and recovery of the oil resulted in a significant change in the bacterial community. Members of the thermophilic Deferribacteres were the second major fraction of the bacterial community in the production water (~30% of the total bacterial community). They were not found in the injection water and were therefore assumed to be indigenous to the reservoir. Additional diversity analysis and targeted quantification of periplasmic nitrate reductase (napA) genes indicated that most resident Deferribacteres possessed the functional potential to contribute to nitrate reduction in the system. In sum, the dominance of nitrate-reducing Deferribacteres and the low relative abundance of Epsilonproteobacteria throughout the production facility suggested that the Deferribacteres play a major role in nitrate-induced souring control at high temperatures.

Microbial growth studies in biodiesel blends.

Introduction of biofuels to the fuel matrix poses new questions and challenges. The present study investigates the microbiological stability of biodiesel blends in small scale microcosms. The study presents results from incubations of diesel-biodiesel blends with contaminated inoculation water collected from diesel storage tanks to ensure the presence of relevant fuel degrading bacteria. DAPI and qPCR analyses has subsequently shown an increased bacterial growth and activity in the microcosms containing biodiesel blends as the carbon source compared to those microcosms where neat fossil diesel made up the carbon source. Several anaerobic microorganisms have been identified after incubation. Presence of methanogens, sulfate-reducing bacteria and nitrate reducing bacteria has furthermore been confirmed by chemical analyses, supplemented by observations of methane formation in biodiesel incubations. The findings will contribute to the knowledge base for a safer introduction of biodiesel in the fuel matrix by employment of proper house-keeping and monitoring methods.

Microbial community associated with glucose-induced enhanced biological phosphorus removal.

The microbial community associated with enhanced biological phosphorus removal with glucose as the main carbon source at 11 degrees C was investigated using microscopy and molecular fingerprinting techniques. The study lasted 77 days and comprised two stages-Stage 1 when the mixture of glucose, yeast and dried milk was the organic carbon source and Stage 2 when glucose was the single carbon source. Rhodocyclus-related polyphosphate accumulating organisms, alpha-Proteobacteria and Bacteroidetes constituted 42% in Stage 1 and 45% in Stage 2, 21% in Stage 1 and 16% in Stage 2, and 10% in Stage 1 and 7% in Stage 2 of the total bacteria, respectively. The Trichococcus genus from the low GC Gram-positive bacteria was possibly responsible for lactic acid production from glucose. The microbial community was gradually changing throughout the experiment and appeared to stabilize towards the end of the experiment. Periods of suboptimal phosphorus removal could have been caused by competition among different microbial communities for carbon substrate.

Uncultured archaea in deep marine subsurface sediments: have we caught them all?

Deep marine subsurface sediments represent a novel archaeal biosphere with unknown physiology; the sedimentary subsurface harbors numerous novel phylogenetic lineages of archaea that are at present uncultured. Archaeal 16S rRNA analyses of deep subsurface sediments demonstrate their global occurrence and wide habitat range, including deep subsurface sediments, methane seeps and organic-rich coastal sediments. These subsurface archaeal lineages were discovered by PCR of extracted environmental DNA; their detection ultimately depends on the specificity of the archaeal PCR 16S rRNA primers. Surprisingly high mismatch frequencies for some archaeal PCR primers result in amplification bias against the corresponding archaeal lineages; this review presents some examples. Obviously, most archaeal 16S rRNA PCR primers were developed either before the discovery of these deep subsurface archaeal lineages, or without taking their sequence variants into account. PCR surveys with multiple primer combinations, revision and updates of primers whenever possible, and increasing use of PCR-independent methods in molecular microbial ecology will contribute to a more comprehensive view of subsurface archaeal communities.

Stratified communities of active Archaea in deep marine subsurface sediments.

Archaeal 16S rRNA was extracted from samples of deep marine subsurface sediments from Peru Margin site 1227, Ocean Drilling Program leg 201. The amounts of archaeal 16S rRNA in each extract were quantified by serial dilution and reverse transcription (RT)-PCR. The results indicated a 1,000-fold variation in rRNA content with depth in the sediment, with the highest concentrations found near the sediment surface and in the sulfate-methane transition zone (SMTZ). The phylogenetic composition of the active archaeal population revealed by cloning and sequencing of RT-PCR products changed with depth. Several phylotypes affiliated with marine benthic group B (MBGB) dominated clone libraries from the upper part of the SMTZ and were detected only in this layer. Members of the miscellaneous crenarchaeotal group (MCG) dominated clone libraries from the other layers. These results demonstrate that archaeal communities change in activity and community composition over short distances in geochemically distinct zones of deep subseafloor sediments and that these changes are traceable in the rRNA pool. It was shown for the first time that members of both the MCG and MBGB Archaea are more active in the SMTZ than in layers above and below. This indicates that they benefit either directly or indirectly from the anaerobic oxidation of methane. They also appear to be ecophysiologically flexible, as they have been retrieved from a wide range of marine sediments of various geochemical properties.

Antimicrobial properties of Dead Sea black mineral mud.

BACKGROUND: The unique, black, hypersaline mud mined from the Dead Sea shores is extensively used in mud packs, masks, and topical body and facial treatments in spas surrounding the lake, and in cosmetic preparations marketed worldwide, but little is known about its antimicrobiological properties. METHODS: We performed detailed microbial and chemical analysis of Dead Sea mineral mud compounded in dermatological and cosmetic preparations. RESULTS: Using conventional bacteriological media (with or without salt augmentation), we found surprisingly low numbers of colony-forming microorganisms in the mud. The highest counts (up to 20,000 colonies per gram, mostly consisting of endospore-forming bacteria) were obtained on sheep blood agar. Test microorganisms (i.e. Escherichia coli, Staphylococcus aureus, Propionibacterium acnes, Candida albicans) rapidly lost their viability when added to the mud. Zones of growth inhibition were observed around discs of Dead Sea mud placed on agar plates inoculated with Candida or with Propionibacterium, but not with Staphylococcus or Escherichia. The effect was also found when the mud was sterilized by gamma irradiation. Using (35)S-labeled sulfate as a tracer, bacterial dissimilatory sulfate reduction could be demonstrated at a low rate (0.13 +/- 0.03 nmol/cm(3).d). CONCLUSION: The antibacterial properties of Dead Sea mud are probably owing to chemical and/or physical phenomena. Possible modes of antimicrobial action of the mud in relation to its therapeutic properties are discussed.

Heterotrophic Archaea dominate sedimentary subsurface ecosystems off Peru.

Studies of deeply buried, sedimentary microbial communities and associated biogeochemical processes during Ocean Drilling Program Leg 201 showed elevated prokaryotic cell numbers in sediment layers where methane is consumed anaerobically at the expense of sulfate. Here, we show that extractable archaeal rRNA, selecting only for active community members in these ecosystems, is dominated by sequences of uncultivated Archaea affiliated with the Marine Benthic Group B and the Miscellaneous Crenarchaeotal Group, whereas known methanotrophic Archaea are not detectable. Carbon flow reconstructions based on stable isotopic compositions of whole archaeal cells, intact archaeal membrane lipids, and other sedimentary carbon pools indicate that these Archaea assimilate sedimentary organic compounds other than methane even though methanotrophy accounts for a major fraction of carbon cycled in these ecosystems. Oxidation of methane by members of Marine Benthic Group B and the Miscellaneous Crenarchaeotal Group without assimilation of methane-carbon provides a plausible explanation. Maintenance energies of these subsurface communities appear to be orders of magnitude lower than minimum values known from laboratory observations, and ecosystem-level carbon budgets suggest that community turnover times are on the order of 100-2,000 years. Our study provides clues about the metabolic functionality of two cosmopolitan groups of uncultured Archaea.