Novel Francisella-like endosymbiont and Anaplasma species from Amblyomma nodosum hosted by the anteater Tamandua Mexicana in Mexico.

The microbiome represents a complex network among the various members of the community of microorganisms that are associated with a host. The composition of the bacterial community is essential to supplement multiple metabolic pathways that the host lacks, particularly in organisms with blood-sucking habits such as ticks. On the other hand, some endosymbionts showed some competence with potentially pathogenic microorganisms. Francisella-like endosymbionts (FLEs) encompass a group of gamma-proteobacterias that are closely related to Francisella tularensis, but are usually apathogenic, which brings nutrients like vitamin B and other cofactors to the tick. It has been postulated that the main route of transmission of FLE is vertical; however, evidence has accumulated regarding the possible mechanism of horizontal transmission. Despite growing interest in knowledge of endosymbionts in the Neotropical region, the efforts related to the establishment of their inventory for tick communities are concentrated in South and Central America, with an important gap in knowledge in Mesoamerican countries such as Mexico. For this reason, the aim of this work was to evaluate the presence and diversity of endosymbionts in the highly host-specialized tick Amblyomma nodosum collected from the anteater Tamandua mexicana in Mexico. We analysed 36 A. nodosum for the presence of DNA of endosymbiont (Coxiella and Francisella) and pathogenic (Anaplasma, Borrelia, Ehrlichia and Rickettsia) bacteria. The presence of a member of the genus Francisella and Candidatus Anaplasma brasiliensis was demonstrated. Our findings provide information on the composition of A. nodosum's microbiome, increasing the inventory of bacterial species associated with this hard tick on the American continent.

Steel slag amendment impacts on soil microbial communities and activities of rice (Oryza sativa L.).

With the increase in iron/steel production, the higher volume of by-products (slag) generated necessitates its efficient recycling. Because the Linz-Donawitz (LD) slag is rich in silicon (Si) and other fertilizer components, we aim to evaluate the impact of the LD slag amendment on soil quality (by measuring soil physicochemical and biological properties), plant nutrient uptake, and strengthens correlations between nutrient uptake and soil bacterial communities. We used 16 S rRNA illumine sequencing to study soil bacterial community and APIZYM assay to study soil enzymes involved in C, N, and P cycling. The LD slag was applied at 2 Mg ha-1 to Japonica and Indica rice cultivated under flooded conditions. The LD slag amendment significantly improved soil pH, plant photosynthesis, soil nutrient availability, and the crop yield, irrespective of cultivars. It significantly increased N, P, and Si uptake of rice straw. The slag amendment enhanced soil microbial biomass, soil enzyme activities and enriched certain bacterial taxa featuring copiotrophic lifestyles and having the potential role for ecosystem services provided to the benefit of the plant. The study evidenced that the short-term LD slag amendment in rice cropping systems is useful to improve soil physicochemical and biological status, and the crop yield.

Teredinibacter waterburyi sp. nov., a marine, cellulolytic endosymbiotic bacterium isolated from the gills of the wood-boring mollusc Bankia setacea (Bivalvia: Teredinidae) and emended description of the genus Teredinibacter.

A cellulolytic, aerobic, gammaproteobacterium, designated strain Bs02T, was isolated from the gills of a marine wood-boring mollusc, Bankia setacea (Bivalvia: Teredinidae). The cells are Gram-stain-negative, slightly curved motile rods (2-5×0.4-0.6 µm) that bear a single polar flagellum and are capable of heterotrophic growth in a simple mineral medium supplemented with cellulose as a sole source of carbon and energy. Cellulose, carboxymethylcellulose, xylan, cellobiose and a variety of sugars also support growth. Strain Bs02T requires combined nitrogen for growth. Temperature, pH and salinity optima (range) for growth were 20 °C (range, 10-30 °C), 8.0 (pH 6.5-8.5) and 0.5 M NaCl (range, 0.0-0.8 M), respectively when grown on 0.5 % (w/v) galactose. Strain Bs02T does not require magnesium and calcium ion concentrations reflecting the proportions found in seawater. The genome size is approximately 4.03 Mbp and the DNA G+C content of the genome is 47.8 mol%. Phylogenetic analyses based on 16S rRNA gene sequences, and on conserved protein-coding sequences, show that strain Bs02T forms a well-supported clade with Teredinibacter turnerae. Average nucleotide identity and percentage of conserved proteins differentiate strain Bs02T from Teredinibacter turnerae at threshold values exceeding those proposed to distinguish bacterial species but not genera. These results indicate that strain Bs02T represents a novel species in the previously monotypic genus Teredinibacter for which the name Teredinibacter waterburyi sp. nov. is proposed. The strain has been deposited under accession numbers ATCC TSD-120T and KCTC 62963T.

Ability of the So-Called Obligate Hydrocarbonoclastic Bacteria to Utilize Nonhydrocarbon Substrates Thus Enhancing Their Activities Despite their Misleading Name.

BACKGROUND: The group of the so-called obligate hydrocarbonoclastic bacteria (OHCB) are marine microorganisms affiliated with the genera Alcanivorax, Cycloclasticus, Oleiphilus and Thalassolituus. This small group plays a major role in oil-bioremediation in marine ecosystems. Marinobacter and Planomicrobium are considered related to this group. The OHCB are claimed to be obligate to hydrocarbon nutrition. This study argues against this claim. RESULTS: Four Alcanivorax species, three Marinobacter species and Planomicrobium okeanokoites from the Arabian/Persian Gulf proved to be not obligate to hydrocarbon nutrition. Although the eight strains grew on crude oil, n-octadecane and phenanthrene as sole carbon substrates, their growth was weaker than on certain nonhydrocarbon, organic compounds viz. peptone, glutamic acid, pyruvic acid, sucrose, mannose and others. Glucose and lactose failed to support the growth of seven of the eight tested strains. Mannose was utilized by five and sucrose by six strains. The well-known intermediate metabolite; pyruvic acid was utilized by all the eight strains, and lactic acid by five strains. In batch cultures, all the tested species consumed higher proportions of peptone than of n-alkanes and phenanthrene. When peptone and crude oil were provided together into the medium, the OHCB started to consume peptone first, and the enriched bacterial populations consumed oil effectively. Added nonhydrocarbon substrates biostimulated oil-consumption by all OHCB species. CONCLUSION: The tested OHCB species are not obligate hydrocarbon-utilizers. This provides them with the merit of survival, should their marine ecosystems become oil- or hydrocarbon-free. The fact that conventional, organic substrates biostimulated hydrocarbon-consumption by the tested bacterial species confirms the facultative nature of those organisms and is interesting from the practical point of view.

Bacteria associated with moon jellyfish during bloom and post-bloom periods in the Gulf of Trieste (northern Adriatic).

Jellyfish are a prominent component of the plankton community. They frequently form conspicuous blooms which may interfere with different human enterprises. Among the aspects that remain understudied are jellyfish associations with microorganisms having potentially important implications for organic matter cycling. To the best of our knowledge, this study is the first to investigate the bacterial community associated with live moon jellyfish (Aurelia solida, Scyohozoa) in the Adriatic Sea. Using 16S rRNA clone libraries and culture-based methods, we have analyzed the bacterial community composition of different body parts: the exumbrella surface, oral arms, and gastric cavity, and investigated possible differences in medusa-associated bacterial community structure at the time of the jellyfish population peak, and during the senescent phase at the end of bloom. Microbiota associated with moon jellyfish was different from ambient seawater bacterial assemblage and varied between different body parts. Betaproteobacteria (Burkholderia, Cupriavidus and Achromobacter) dominated community in the gastral cavity of medusa, while Alphaproteobacteria (Phaeobacter, Ruegeria) and Gammaproteobacteria (Stenotrophomonas, Alteromonas, Pseudoalteromonas and Vibrio) prevailed on 'outer' body parts. Bacterial community structure changed during senescent phase, at the end of the jellyfish bloom, showing an increased abundance of Gammaproteobacteria, exclusively Vibrio. The results of cultured bacterial isolates showed the dominance of Gammaproeteobacteria, especially Vibrio and Pseudoalteromonas in all body parts. Our results suggest that jellyfish associated bacterial community might have an important role for the host, and that anthropogenic pollution in the Gulf of Trieste might affect their community structure.

Thiosocius teredinicola gen. nov., sp. nov., a sulfur-oxidizing chemolithoautotrophic endosymbiont cultivated from the gills of the giant shipworm, Kuphus polythalamius.

A chemolithoautotrophic sulfur-oxidizing, diazotrophic, facultatively heterotrophic, endosymbiotic bacterium, designated as strain 2141T, was isolated from the gills of the giant shipworm Kuphus polythalamius (Teredinidae: Bivalvia). Based on its 16S rRNA sequence, the endosymbiont falls within a clade that includes the as-yet-uncultivated thioautotrophic symbionts of a marine ciliate and hydrothermal vent gastropods, uncultivated marine sediment bacteria, and a free-living sulfur-oxidizing bacterium ODIII6, all of which belong to the Gammaproteobacteria. The endosymbiont is Gram-negative, rod-shaped and has a single polar flagellum when grown in culture. This bacterium can be grown chemolithoautotrophically on a chemically defined medium supplemented with either hydrogen sulfide, thiosulfate, tetrathionate or elemental sulfur. The closed-circular genome has a DNA G+C content of 60.1 mol% and is 4.79 Mbp in size with a large nitrogenase cluster spanning nearly 40 kbp. The diazotrophic capability was confirmed by growing the strain on chemolithoautotrophic thiosulfate-based medium without a combined source of fixed nitrogen. The bacterium is also capable of heterotrophic growth on organic acids such as acetate and propionate. The pH, temperature and salinity optima for chemolithoautotrophic growth on thiosulfate were found to be 8.5, 34 °C and 0.2 M NaCl, respectively. To our knowledge, this is the first report of pure culture of a thioautotrophic animal symbiont. The type strain of Thiosocius teredinicola is PMS-2141T.STBD.0c.01aT (=DSM 108030T).

The selective pressures on the microbial community in a metal-contaminated aquifer.

In many environments, toxic compounds restrict which microorganisms persist. However, in complex mixtures of inhibitory compounds, it is challenging to determine which specific compounds cause changes in abundance and prevent some microorganisms from growing. We focused on a contaminated aquifer in Oak Ridge, Tennessee, USA that has large gradients of pH and widely varying concentrations of uranium, nitrate, and many other inorganic ions. In the most contaminated wells, the microbial community is enriched in the Rhodanobacter genus. Rhodanobacter abundance is positively correlated with low pH and high concentrations of uranium and 13 other ions and we sought to determine which of these ions are selective pressures that favor the growth of Rhodanobacter over other taxa. Of these ions, low pH and high UO22+, Mn2+, Al3+, Cd2+, Zn2+, Co2+, and Ni2+ are both (a) selectively inhibitory of a Pseudomonas isolate from an uncontaminated well vs. a Rhodanobacter isolate from a contaminated well, and (b) reach toxic concentrations (for the Pseudomonas isolate) in the Rhodanobacter-dominated wells. We used mixtures of ions to simulate the groundwater conditions in the most contaminated wells and verified that few isolates aside from Rhodanobacter can tolerate these eight ions. These results clarify which ions are likely causal factors that impact the microbial community at this field site and are not merely correlated with taxonomic shifts. Furthermore, our general high-throughput approach can be applied to other environments, isolates, and conditions to systematically help identify selective pressures on microbial communities.

Co-culture development and bioformulation efficacy of psychrotrophic PGPRs to promote growth and development of Pea (Pisum sativum) plant.

Numerous microbes reside in the rhizosphere having plant growth promoting activity, and enhancing the property by increasing plant yield. Plant growth promoting rhizobacteria (PGPR) has gradually increased in agriculture and offers an attractive way to replace chemical fertilizers, pesticides and supplements. Soil was collected from the rhizosphere of an agricultural farm and the psychrotrophic bacterial strains STA3 (KY888133) and RM2 (KY888134) were successfully isolated, and screened on the basis of phosphate solubilization. Further characterization was carried out by morphological, biochemical, and 16S rDNA characterization methods. The unique nature of psychrotrophic Pentoea ananatis and a suitable combination with Pseudomonas fluorescens regarding plant growth promotion activity has not been studied before to our knowledge. An assessment of various parameters of plant growth promoting activity, such as IAA, phosphate solubilization, bio-control activity, HCN and siderophore production, has been carried out. Both strains were found to be positive in various parameters except HCN and Biocontrol activity, which were positive only for the strain RM2. Also, shelf life and their efficacy was determined before and after formulation. A great consistency was observed in all the cultures, even after 70 days of storage under bio-formulation at room temperature, while in the case of the co-culture CPP-2, the cfu ml-1 was greater, followed by RM2 and STA3. Moreover, the growth indices of the pea plant were found to be better in the co-culture CPP-2 compared with individual strains, followed by RM2 and STA3. Thus, the study suggests that the co-culture CPP-2 has a great potential for plant growth promotion as compared with individual strains followed by RM2 and STA3.

Rhodanobacter ginsengiterrae sp. nov., an antagonistic bacterium against root rot fungal pathogen Fusarium solani, isolated from ginseng rhizospheric soil.

A novel bacterium, designated DCY112T, was isolated from the rhizospheric soil of a ginseng-cultivated field in Gochang-gun, Republic of Korea. Based on 16S rRNA gene sequence analysis, this isolate was assigned to the genus Rhodanobacter and is closely related to Rhodanobacter soli DCY45T (98.0%) and R. umsongensis GR24-2T (98.0%). Strain DCY112T is Gram-negative, catalase- and oxidase-positive, aerobic, non-motile, rod-shaped, and produces yellow-pigmented colonies on R2A medium. Q-8 was the predominant respiratory quinone. The major cellular fatty acids were iso-C15:0, iso-C17:0, and summed feature 9 (iso-C17:1 ω9c and/or 10-methyl-C16:0). The major polar lipids were phosphatidylglycerol (PG), phosphatidylethanolamine (PE), an unknown amino lipid (AL1), and an unidentified polar lipid (L3). The genomic DNA G + C content was 65.2 mol%. DNA-DNA homology values between strain DCY112T and related strains were lower than 55%. The low DNA relatedness data in combination with phenotypic and genotypic tests indicated that strain DCY112T could not be assigned to a recognized species. Strain DCY112T showed antagonistic activity against the fungal pathogen Fusarium solani (KACC 44891T), which causes ginseng root rot. The results of this study support that strain DCY112T is a novel species belonging to the genus Rhodanobacter, for which the name Rhodanobacter ginsengiterrae is proposed. The type strain is DCY112T (= KCTC 62018T = JCM 32167T).

Impact of plant growth-promoting rhizobacteria on root colonization potential and life cycle of Rhizophagus irregularis following co-entrapment into alginate beads.

AIMS: This study aimed at evaluating the impact of seven plant growth-promoting rhizobacteria (PGPR) on root colonization and life cycle of Rhizophagus irregularis MUCL 41833 when co-entrapped in alginate beads. METHODS AND RESULTS: Two in vitro experiments were conducted. The first consisted of the immobilization of R. irregularis and seven PGPR isolates into alginate beads to assess the effect of the bacteria on the pre-symbiotic growth of the fungus. In the second experiment, the best performing PGPR from experiment 1 was tested for its ability to promote the symbiotic development of the AMF in potato plantlets from three cultivars. Results showed that only one isolate identified as Pseudomonas plecoglossicida (R-67094) promoted germ tube elongation and hyphal branching of germinated spores during the pre-symbiotic phase of the fungus. This PGPR further promoted the symbiotic development of the AMF in potato plants. CONCLUSIONS: The co-entrapment of Ps. plecoglossicida R-67094 and R. irregularis MUCL 41833 in alginate beads improved root colonization by the AMF and its further life cycle under the experimental conditions. SIGNIFICANCE AND IMPACT OF THE STUDY: Co-entrapment of suitable AMF-PGPR combinations within alginate beads may represent an innovative technology that can be fine-tuned for the development of efficient consortia-based bioformulations.

Multidrug Resistance in Quinolone-Resistant Gram-Negative Bacteria Isolated from Hospital Effluent and the Municipal Wastewater Treatment Plant.

This study is aimed to assess if hospital effluents represent an important supplier of multidrug-resistant (MDR) Gram-negative bacteria that, being discharged in the municipal collector, may be disseminated in the environment and bypassed in water quality control systems. From a set of 101 non-Escherichia coli Gram-negative bacteria with reduced susceptibility to quinolones, was selected a group of isolates comprised by those with the highest indices of MDR (defined as nonsusceptibility to at least one agent in six or more antimicrobial categories, MDR ≥6) or resistance to meropenem or ceftazidime (n = 25). The isolates were identified and characterized for antibiotic resistance phenotype, plasmid-mediated quinolone resistance (PMQR) genes, and other genetic elements and conjugative capacity. The isolates with highest MDR indices were mainly from hospital effluent and comprised ubiquitous bacterial groups of the class Gammaproteobacteria, of the genera Aeromonas, Acinetobacter, Citrobacter, Enterobacter, Klebsiella, and Pseudomonas, and of the class Flavobacteriia, of the genera Chryseobacterium and Myroides. In this group of 25 strains, 19 identified as Gammaproteobacteria harbored at least one PMQR gene (aac(6')-Ib-cr, qnrB, qnrS, or oqxAB) or a class 1 integron gene cassette encoding aminoglycoside, sulfonamide, or carbapenem resistance. Most of the E. coli J53 transconjugants with acquired antibiotic resistance resulted from conjugation with Enterobacteriaceae. These transconjugants demonstrated acquired resistance to a maximum of five classes of antibiotics, one or more PMQR genes and/or a class 1 integron gene cassette. This study shows that ubiquitous bacteria, other than those monitored in water quality controls, are important vectors of antibiotic resistance and can be disseminated from hospital effluent to aquatic environments. This information is relevant to support management options aiming at the control of this public health problem.

Microbial community successional patterns in beach sands impacted by the Deepwater Horizon oil spill.

Although petroleum hydrocarbons discharged from the Deepwater Horizon (DWH) blowout were shown to have a pronounced impact on indigenous microbial communities in the Gulf of Mexico, effects on nearshore or coastal ecosystems remain understudied. This study investigated the successional patterns of functional and taxonomic diversity for over 1 year after the DWH oil was deposited on Pensacola Beach sands (FL, USA), using metagenomic and 16S rRNA gene amplicon techniques. Gamma- and Alphaproteobacteria were enriched in oiled sediments, in corroboration of previous studies. In contrast to previous studies, we observed an increase in the functional diversity of the community in response to oil contamination and a functional transition from generalist populations within 4 months after oil came ashore to specialists a year later, when oil was undetectable. At the latter time point, a typical beach community had reestablished that showed little to no evidence of oil hydrocarbon degradation potential, was enriched in archaeal taxa known to be sensitive to xenobiotics, but differed significantly from the community before the oil spill. Further, a clear succession pattern was observed, where early responders to oil contamination, likely degrading aliphatic hydrocarbons, were replaced after 3 months by populations capable of aromatic hydrocarbon decomposition. Collectively, our results advance the understanding of how natural benthic microbial communities respond to crude oil perturbation, supporting the specialization-disturbance hypothesis; that is, the expectation that disturbance favors generalists, while providing (microbial) indicator species and genes for the chemical evolution of oil hydrocarbons during degradation and weathering.

Saccharide breakdown and fermentation by the honey bee gut microbiome.

The honey bee, the world's most important agricultural pollinator, relies exclusively on plant-derived foods for nutrition. Nectar and pollen collected by honey bees are processed and matured within the nest through the activities of honey bee-derived microbes and enzymes. In order to better understand the contribution of the microbial community to food processing in the honey bee, we generated a metatranscriptome of the honey bee gut microbiome. The function of the microbial community in the honey bee, as revealed by metatranscriptome sequencing, resembles that of other animal guts and food-processing environments. We identified three major bacterial classes that are active in the gut (γ-Proteobacteria, Bacilli and Actinobacteria), all of which are predicted to participate in the breakdown of complex macromolecules (e.g. polysaccharides and polypeptides), the fermentation of component parts of these macromolecules, and the generation of various fermentation products, such as short-chain fatty acids and alcohol. The ability of the microbial community to metabolize these carbon-rich food sources was confirmed through the use of community-level physiological profiling. Collectively, these findings suggest that the gut microflora of the honey bee harbours bacterial members with unique roles, which ultimately can contribute to the processing of plant-derived food for colonies.

Perspicuibacter marinus gen. nov., sp. nov., a semi-transparent bacterium isolated from surface seawater, and description of Arenicellaceae fam. nov. and Arenicellales ord. nov.

A Gram-stain-negative, non-motile, mesophilic, aerobic, rod-shaped bacterium, strain 2-9(T), was isolated from surface seawater at Muroto city, Kochi prefecture, Japan. The strain was transparent on 1/5 strength marine broth plate but became easily visible when the plate was supplemented with pyruvate. Phylogenetic analyses based on the 16S rRNA gene sequence showed that the strain fell within the class Gammaproteobacteria and was most closely related to the genus Arenicella (92.7-93.0 % 16S rRNA gene sequence similarities to type strains of species of this genus) of an unclassified order within this class. The DNA G+C content of strain 2-9(T) was 41.7 mol%. The major fatty acids were C18 : 1ω7c (37.6 %), C16 : 1ω7c and/or iso-C15 : 0 2-OH (summed feature 3; 19.1 %), C18 : 0 (10.8 %), C16 : 0 (10.2 %) and an unidentified fatty acid with an equivalent chain-length value of 11.799 (9.5 %). The major polar lipids were phosphatidylglycerol, phosphatidylethanolamine and three unidentified lipids. Ubiquinone-8 (Q-8) was detected as the sole isoprenoid quinone. From these taxonomic data, it is proposed that strain 2-9(T) represents a novel species of a new genus, Perspicuibacter marinus gen. nov., sp. nov. The type strain of the type species is 2-9(T) ( = NBRC 110144(T) = KCTC 42196(T)). A new family, Arenicellaceae fam. nov. (type genus Arenicella), and order, Arenicellales ord. nov., of the class Gammaproteobacteria are proposed to accommodate the novel taxon.

'Candidatus Competibacter'-lineage genomes retrieved from metagenomes reveal functional metabolic diversity.

The glycogen-accumulating organism (GAO) 'Candidatus Competibacter' (Competibacter) uses aerobically stored glycogen to enable anaerobic carbon uptake, which is subsequently stored as polyhydroxyalkanoates (PHAs). This biphasic metabolism is key for the Competibacter to survive under the cyclic anaerobic-'feast': aerobic-'famine' regime of enhanced biological phosphorus removal (EBPR) wastewater treatment systems. As they do not contribute to phosphorus (P) removal, but compete for resources with the polyphosphate-accumulating organisms (PAO), thought responsible for P removal, their proliferation theoretically reduces the EBPR capacity. In this study, two complete genomes from Competibacter were obtained from laboratory-scale enrichment reactors through metagenomics. Phylogenetic analysis identified the two genomes, 'Candidatus Competibacter denitrificans' and 'Candidatus Contendobacter odensis', as being affiliated with Competibacter-lineage subgroups 1 and 5, respectively. Both have genes for glycogen and PHA cycling and for the metabolism of volatile fatty acids. Marked differences were found in their potential for the Embden-Meyerhof-Parnas and Entner-Doudoroff glycolytic pathways, as well as for denitrification, nitrogen fixation, fermentation, trehalose synthesis and utilisation of glucose and lactate. Genetic comparison of P metabolism pathways with sequenced PAOs revealed the absence of the Pit phosphate transporter in the Competibacter-lineage genomes--identifying a key metabolic difference with the PAO physiology. These genomes are the first from any GAO organism and provide new insights into the complex interaction and niche competition between PAOs and GAOs in EBPR systems.

Methanotrophic bacteria in oilsands tailings ponds of northern Alberta.

We investigated methanotrophic bacteria in slightly alkaline surface water (pH 7.4-8.7) of oilsands tailings ponds in Fort McMurray, Canada. These large lakes (up to 10 km(2)) contain water, silt, clay and residual hydrocarbons that are not recovered in oilsands mining. They are primarily anoxic and produce methane but have an aerobic surface layer. Aerobic methane oxidation was measured in the surface water at rates up to 152 nmol CH4 ml(-1) water d(-1). Microbial diversity was investigated via pyrotag sequencing of amplified 16S rRNA genes, as well as by analysis of methanotroph-specific pmoA genes using both pyrosequencing and microarray analysis. The predominantly detected methanotroph in surface waters at all sampling times was an uncultured species related to the gammaproteobacterial genus Methylocaldum, although a few other methanotrophs were also detected, including Methylomonas spp. Active species were identified via (13)CH4 stable isotope probing (SIP) of DNA, combined with pyrotag sequencing and shotgun metagenomic sequencing of heavy (13)C-DNA. The SIP-PCR results demonstrated that the Methylocaldum and Methylomonas spp. actively consumed methane in fresh tailings pond water. Metagenomic analysis of DNA from the heavy SIP fraction verified the PCR-based results and identified additional pmoA genes not detected via PCR. The metagenome indicated that the overall methylotrophic community possessed known pathways for formaldehyde oxidation, carbon fixation and detoxification of nitrogenous compounds but appeared to possess only particulate methane monooxygenase not soluble methane monooxygenase.

Jellyfish modulate bacterial dynamic and community structure.

Jellyfish blooms have increased in coastal areas around the world and the outbreaks have become longer and more frequent over the past few decades. The Mediterranean Sea is among the heavily affected regions and the common bloom-forming taxa are scyphozoans Aurelia aurita s.l., Pelagia noctiluca, and Rhizostoma pulmo. Jellyfish have few natural predators, therefore their carcasses at the termination of a bloom represent an organic-rich substrate that supports rapid bacterial growth, and may have a large impact on the surrounding environment. The focus of this study was to explore whether jellyfish substrate have an impact on bacterial community phylotype selection. We conducted in situ jellyfish-enrichment experiment with three different jellyfish species. Bacterial dynamic together with nutrients were monitored to assess decaying jellyfish-bacteria dynamics. Our results show that jellyfish biomass is characterized by protein rich organic matter, which is highly bioavailable to 'jellyfish-associated' and 'free-living' bacteria, and triggers rapid shifts in bacterial population dynamics and composition. Based on 16S rRNA clone libraries and denaturing gradient gel electrophoresis (DGGE) analysis, we observed a rapid shift in community composition from unculturable Alphaproteobacteria to culturable species of Gammaproteobacteria and Flavobacteria. The results of sequence analyses of bacterial isolates and of total bacterial community determined by culture independent genetic analysis showed the dominance of the Pseudoalteromonadaceae and the Vibrionaceae families. Elevated levels of dissolved proteins, dissolved organic and inorganic nutrient release, bacterial abundance and carbon production as well as ammonium concentrations characterized the degradation process. The biochemical composition of jellyfish species may influence changes in the amount of accumulated dissolved organic and inorganic nutrients. Our results can contribute insights into possible changes in bacterial population dynamics and nutrient pathways following jellyfish blooms which have important implications for ecology of coastal waters.

Comparison of microbial community compositions of injection and production well samples in a long-term water-flooded petroleum reservoir.

Water flooding plays an important role in recovering oil from depleted petroleum reservoirs. Exactly how the microbial communities of production wells are affected by microorganisms introduced with injected water has previously not been adequately studied. Using denaturing gradient gel electrophoresis (DGGE) approach and 16S rRNA gene clone library analysis, the comparison of microbial communities is carried out between one injection water and two production waters collected from a working block of the water-flooded Gudao petroleum reservoir located in the Yellow River Delta. DGGE fingerprints showed that the similarities of the bacterial communities between the injection water and production waters were lower than between the two production waters. It was also observed that the archaeal composition among these three samples showed no significant difference. Analysis of the 16S rRNA gene clone libraries showed that the dominant groups within the injection water were Betaproteobacteria, Gammaproteobacteria and Methanomicrobia, while the dominant groups in the production waters were Gammaproteobacteria and Methanobacteria. Only 2 out of 54 bacterial operational taxonomic units (OTUs) and 5 out of 17 archaeal OTUs in the injection water were detected in the production waters, indicating that most of the microorganisms introduced by the injection water may not survive to be detected in the production waters. Additionally, there were 55.6% and 82.6% unique OTUs in the two production waters respectively, suggesting that each production well has its specific microbial composition, despite both wells being flooded with the same injection water.

Identification of a novel subgroup of uncultured gammaproteobacterial glycogen-accumulating organisms in enhanced biological phosphorus removal sludge.

The presence of glycogen-accumulating organisms (GAO) has been hypothesized to be a cause of deterioration in enhanced biological phosphorus removal (EBPR) processes due to their abilities to out-compete polyphosphate-accumulating organisms (PAO). Based on 16S rRNA gene sequences, new members of uncultured gammaproteobacterial GAO (GB) were identified from sludge samples of a lab-scale sequencing batch reactor used for EBPR. The new GB formed a phylogenetic lineage (GB8) clearly distinct from the previously reported seven GB subgroups. Because the new GB8 members were not targeted by the known fluorescence in situ hybridization (FISH) oligonucleotide probes, a GB8-specific FISH probe (GB429) and a new FISH probe (GB742) targeting all eight GB subgroups were designed, and the phenotypic properties of the new GB8 members were investigated. FISH and microautoradiography approaches showed that GB429-targeted cells (GB8) were large coccobacilli (2-4 µm in size) with the ability to take up acetate under anaerobic conditions, but unable to accumulate polyphosphate under the subsequent aerobic conditions, consistent with in situ phenotypes of GB. FISH analyses on several sludge samples showed that members of GB8 were commonly detected as the majority of GB in lab- and full-scale EBPR processes. In conclusion, this study showed that members of GB8 could be a subgroup of GB with an important role in EBPR deterioration. Designs of FISH probes which hybridize with broader GB subgroups at different hierarchical levels will contribute to studies of the distributions and ecophysiologies of GB in lab- or full-scale EBPR plants.

Deep-sea oil plume enriches indigenous oil-degrading bacteria.

The biological effects and expected fate of the vast amount of oil in the Gulf of Mexico from the Deepwater Horizon blowout are unknown owing to the depth and magnitude of this event. Here, we report that the dispersed hydrocarbon plume stimulated deep-sea indigenous γ-Proteobacteria that are closely related to known petroleum degraders. Hydrocarbon-degrading genes coincided with the concentration of various oil contaminants. Changes in hydrocarbon composition with distance from the source and incubation experiments with environmental isolates demonstrated faster-than-expected hydrocarbon biodegradation rates at 5°C. Based on these results, the potential exists for intrinsic bioremediation of the oil plume in the deep-water column without substantial oxygen drawdown.