Abundance and diversity of iron reducing bacteria communities in the sediments of a heavily polluted freshwater lake

Iron reduction mediated by Fe(III)-reducing bacteria (FeRB) occurs in aqueous environments and plays an essential role in removing contaminates in polluted freshwater lakes. Two model FeRB species, Shewanella and Geobacter, have been intensively studied because of their functions in bioremediation, iron reduction, and bioelectricity production. However, the abundance and community diversity of Shewanella and Geobacter in eutrophic freshwater lakes remain largely unknown. In this work, the distribution, abundance and biodiversity of Shewanella, Geobacter and other FeRB in the sediments of a heavily polluted lake, Chaohu Lake, China, across four successive seasons were investigated. Shewanella, Geobacter, and other FeRB were found to be widely distributed in the sediment of this heavily eutrophic lake. Geobacter was abundant with at least one order of magnitude more than Shewanella in cold seasons. Three Shewanella-related operational taxonomic units were detected and sixty one Geobacter-related operational taxonomic units were grouped into three phylogenetic clades. Thiobacillus, Desulfuromonas and Geobacter were identified as the main members of FeRB in the lake sediments. Interestingly, nutrients like carbon, nitrogen, and phosphorus were found to be the key factors governing the abundance and diversity of FeRB. Total FeRB, as well as Geobacter and Shewanella, were more abundant in the heavily eutrophic zone than those in the lightly eutrophic zone. The abundance and diversity of FeRB in the sediments of freshwater lakes were highly related with the degree of eutrophication, which imply that FeRB might have a great potential in alleviating the eutrophication and contamination in aqueous environments.

Electrode plate-culture methods for colony isolation of exoelectrogens from anode microbiomes

Exoelectrogens play central roles in microbial fuel cells and other bioelectrochemical systems (BESs), yet their physiological diversity remains largely elusive due to the lack of efficient methods for the isolation from naturally occurring microbiomes. The present study developed an electrode plate-culture (EPC) method that facilitates selective colony formation by exoelectrogens and used it for isolating them from an exoelectrogenic microbiome enriched from paddy-field soil. In an EPC device, the surface of solidified agarose medium was spread with a suspension of a microbiome and covered with a transparent fluorine doped tin oxide (FTO) electrode (poised at 0 V vs. the standard hydrogen electrode) that served as the sole electron acceptor. The medium contained acetate as the major growth substrate and Coomassie Brilliant Blue as a dye for visualizing colonies under FTO. It was shown that colonies successfully appeared under FTO in association with current generation. Analyses of 16S rRNA gene sequences of colonies indicated that they were affiliated with genera Citrobacter, Geobacter and others. Among them, Citrobacter and Geobacter isolates were found to be exoelectrogenic in pure-culture BESs. These results demonstrate the utility of the EPC method for colony isolation of exoelectrogens.

Sodium chloride concentration determines exoelectrogens in anode biofilms occurring from mangrove-grown brackish sediment

Single-chamber microbial fuel cells (MFCs) were inoculated with mangrove-grown brackish sediment (MBS) and continuously supplied with an acetate medium containing different concentrations of NaCl (0-1.8M). Different from MFCs inoculated with paddy-field soil (high power outputs were observed between 0.05 and 0.1M), power outputs from MBS-MFCs were high at NaCl concentrations from 0 to 0.6M. Amplicon-sequence analyses of anode biofilms suggest that different exoelectrogens occurred from MBS depending on NaCl concentrations; Geobacter occurred abundantly below 0.1M, whereas Desulfuromonas was abundant from 0.3M to 0.6M. These results suggest that NaCl concentration is the major determinant of exoelectrogens that occur in anode biofilms from MBS. It is also suggested that MBS is a potent source of microbes for MFCs to be operated in a wide range of NaCl concentrations.

Size effects of potato waste on its treatment by microbial fuel cell

The performance of microbial fuel cell (MFC) in treating potato cubes with different sizes (the edge size of 3, 5 and 7 mm) was investigated. Current density was found lower as the size of potato cubes increased, even if the differences in their removal were less apparent. At the end of MFC operation for 81 days, both total and soluble chemical oxygen demand reached nearly identical values, irrespective of the potato sizes; and citrate and isobutyrate were two major organic acids remaining in the solutions. Bacterial community analysis using polymerase chain reaction, denaturing gradient gel electrophoresis and sequencing indicated that bacterial species on the anode and in the anodic solution were similar and did not change obviously with potato sizes, and that, in similarity with previous studies on potato-processing wastewater treatment, Proteobacteria and Firmicutes were two dominating phyla. Geobacter was found richer on the anode than in the anodic solutions.

Geobacter, Anaeromyxobacter and Anaerolineae populations are enriched on anodes of root exudate-driven microbial fuel cells in rice field soil

Plant-based sediment microbial fuel cells (PMFCs) couple the oxidation of root exudates in living rice plants to current production. We analysed the composition of the microbial community on anodes from PMFC with natural rice field soil as substratum for rice by analysing 16S rRNA as an indicator of microbial activity and diversity. Terminal restriction fragment length polymorphism (TRFLP) analysis indicated that the active bacterial community on anodes from PMFCs differed strongly compared with controls. Moreover, clones related to Deltaproteobacteria and Chloroflexi were highly abundant (49% and 21%, respectively) on PMFCs anodes. Geobacter (19%), Anaeromyxobacter (15%) and Anaerolineae (17%) populations were predominant on anodes with natural rice field soil and differed strongly from those previously detected with potting soil. In open circuit (OC) control PMFCs, not allowing electron transfer, Deltaproteobacteria (33%), Betaproteobacteria (20%), Chloroflexi (12%), Alphaproteobacteria (10%) and Firmicutes (10%) were detected. The presence of an electron accepting anode also had a strong influence on methanogenic archaea. Hydrogenotrophic methanogens were more active on PMFC (21%) than on OC controls (10%), whereas acetoclastic Methanosaetaceae were more active on OC controls (31%) compared with PMFCs (9%). In conclusion, electron accepting anodes and rice root exudates selected for distinct potential anode-reducing microbial populations in rice soil inoculated PMFC.

Long-term nitrogen fertilization of paddy soil shifts iron-reducing microbial community revealed by RNA-(13)C-acetate probing coupled with pyrosequencing

Iron reduction is an important biogeochemical process in paddy soils, yet little is known about the microbial coupling between nitrogen and iron reduction. Here, we investigated the shift of acetate-metabolizing iron-reducers under long-term nitrogen fertilization using (13)C-acetate-based ribosomal RNA (rRNA)-stable isotope probing (SIP) and pyrosequencing in an incubation experiment, and the shift of putative iron-reducers in original field samples were investigated by 16S rRNA gene-based pyrosequencing. During SIP incubations, in the presence of iron(III) oxyhydroxides, more iron(II) formation and less methane production were detected in nitrogen-fertilized (N) compared with non-fertilized (NF) soil. In (13)C-rRNA from microcosms amended with ferrihydrite (FER), Geobacter spp. were the important active iron-reducers in both soils, and labeled to a greater extent in N (31% of the bacterial classified sequences) than NF soils (11%). Pyrosequencing of the total 16S rRNA transcripts from microcosms at the whole community level further revealed hitherto unknown metabolisms of potential FER reduction by microorganisms including Pseudomonas and Solibacillus spp. in N soil, Dechloromonas, Clostridium, Bacillus and Solibacillus spp. in NF soil. Goethite (GOE) amendment stimulated Geobacter spp. to a lesser extent in both soils compared with FER treatment. Pseudomonas spp. in the N soil and Clostridium spp. in the NF soil may also be involved in GOE reduction. Pyrosequencing results from field samples showed that Geobacter spp. were the most abundant putative iron-reducers in both soils, and significantly stimulated by long-term nitrogen fertilization. Overall, for the first time, we demonstrate that long-term nitrogen fertilization promotes iron(III) reduction and modulates iron-reducing bacterial community in paddy soils.

Evidence of Geobacter-associated phage in a uranium-contaminated aquifer

Geobacter species may be important agents in the bioremediation of organic and metal contaminants in the subsurface, but as yet unknown factors limit the in situ growth of subsurface Geobacter well below rates predicted by analysis of gene expression or in silico metabolic modeling. Analysis of the genomes of five different Geobacter species recovered from contaminated subsurface sites indicated that each of the isolates had been infected with phage. Geobacter-associated phage sequences were also detected by metagenomic and proteomic analysis of samples from a uranium-contaminated aquifer undergoing in situ bioremediation, and phage particles were detected by microscopic analysis in groundwater collected from sediment enrichment cultures. Transcript abundance for genes from the Geobacter-associated phage structural proteins, tail tube Gp19 and baseplate J, increased in the groundwater in response to the growth of Geobacter species when acetate was added, and then declined as the number of Geobacter decreased. Western blot analysis of a Geobacter-associated tail tube protein Gp19 in the groundwater demonstrated that its abundance tracked with the abundance of Geobacter species. These results suggest that the enhanced growth of Geobacter species in the subsurface associated with in situ uranium bioremediation increased the abundance and activity of Geobacter-associated phage and show that future studies should focus on how these phages might be influencing the ecology of this site.

Geobacter soli sp. nov., a dissimilatory Fe(III)-reducing bacterium isolated from forest soil

A novel Fe(III)-reducing bacterium, designated GSS01(T), was isolated from a forest soil sample using a liquid medium containing acetate and ferrihydrite as electron donor and electron acceptor, respectively. Cells of strain GSS01(T) were strictly anaerobic, Gram-stain-negative, motile, non-spore-forming and slightly curved rod-shaped. Growth occurred at 16-40 °C and optimally at 30 °C. The DNA G+C content was 60.9 mol%. The major respiratory quinone was MK-8. The major fatty acids were C(16:0), C(18:0) and C(16:1)ω7c/C(16:1)ω6c. Strain GSS01(T) was able to grow with ferrihydrite, Fe(III) citrate, Mn(IV), sulfur, nitrate or anthraquinone-2,6-disulfonate, but not with fumarate, as sole electron acceptor when acetate was the sole electron donor. The isolate was able to utilize acetate, ethanol, glucose, lactate, butyrate, pyruvate, benzoate, benzaldehyde, m-cresol and phenol but not toluene, p-cresol, propionate, malate or succinate as sole electron donor when ferrihydrite was the sole electron acceptor. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain GSS01(T) was most closely related to Geobacter sulfurreducens PCA(T) (98.3% sequence similarity) and exhibited low similarities (94.9-91.8%) to the type strains of other species of the genus Geobacter. The DNA-DNA relatedness between strain GSS01(T) and G. sulfurreducens PCA(T) was 41.4 ± 1.1%. On the basis of phylogenetic analysis, phenotypic characterization and physiological tests, strain GSS01(T) is believed to represent a novel species of the genus Geobacter, and the name Geobacter soli sp. nov. is proposed. The type strain is GSS01(T) ( =KCTC 4545(T) =MCCC 1K00269(T)).

Reactor performance in terms of COD and nitrogen removal and bacterial community structure of a three-stage rotating bioelectrochemical contactor

Integrating microbial fuel cell (MFC) into rotating biological contactor (RBC) creates an opportunity for enhanced removal of COD and nitrogen coupled with energy generation from wastewater. In this study, a three-stage rotating bioelectrochemical contactor (referred to as RBC-MFC unit) integrating MFC with RBC technology was constructed for simultaneous removal of carbonaceous and nitrogenous compounds and electricity generation from a synthetic medium containing acetate and ammonium. The performance of the RBC-MFC unit was compared to a control reactor (referred to as RBC unit) that was operated under the same conditions but without current generation (i.e. open-circuit mode). The effect of hydraulic loading rate (HLR) and COD/N ratio on the performance of the two units was investigated. At low (3.05 gCOD g⁻¹N) and high COD/N ratio (6.64 gCOD g⁻¹N), both units achieved almost similar COD and ammonia-nitrogen removal. However, the RBC-MFC unit achieved significantly higher denitrification and nitrogen removal compared to the RBC unit indicating improved denitrification at the cathode due to current flow. The average voltage under 1000 Ω external resistance ranged between 0.03 and 0.30 V and between 0.02 and 0.21 V for stages 1 and 2 of the RBC-MFC unit. Pyrosequencing analysis of bacterial 16S rRNA gene revealed high bacterial diversity at the anode and cathode of both units. Genera that play a role in nitrification (Nitrospira; Nitrosomonas), denitrification (Comamonas; Thauera) and electricity generation (Geobacter) were identified at the electrodes. Geobacter was only detected on the anode of the RBC-MFC unit. Nitrifiers and denitrifiers were more abundant in the RBC-MFC unit compared to the RBC unit and were largely present on the cathode of both units suggesting that most of the nitrogen removal occurred at the cathode.

Harvesting electricity with Geobacter bremensis isolated from compost

Electrochemically active (EA) biofilms were formed on metallic dimensionally stable anode-type electrode (DSA), embedded in garden compost and polarized at +0.50 V/SCE. Analysis of 16S rRNA gene libraries revealed that biofilms were heavily enriched in Deltaproteobacteria in comparison to control biofilms formed on non-polarized electrodes, which were preferentially composed of Gammaproteobacteria and Firmicutes. Among Deltaproteobacteria, sequences affiliated with Pelobacter and Geobacter genera were identified. A bacterial consortium was cultivated, in which 25 isolates were identified as Geobacter bremensis. Pure cultures of 4 different G. bremensis isolates gave higher current densities (1400 mA/m² on DSA, 2490 mA/m² on graphite) than the original multi-species biofilms (in average 300 mA/m² on DSA) and the G. bremensis DSM type strain (100–300 A/m² on DSA; 2485 mA/m² on graphite). FISH analysis confirmed that G. bremensis represented a minor fraction in the original EA biofilm, in which species related to Pelobacter genus were predominant. The Pelobacter type strain did not show EA capacity, which can explain the lower performance of the multi-species biofilms. These results stressed the great interest of extracting and culturing pure EA strains from wild EA biofilms to improve the current density provided by microbial anodes.

Unique ecophysiology among U(VI)-reducing bacteria as revealed by evaluation of oxygen metabolism in Anaeromyxobacter dehalogenans strain 2CP-C

Anaeromyxobacter spp. respire soluble hexavalent uranium, U(VI), leading to the formation of insoluble U(IV), and are present at the uranium-contaminated Oak Ridge Integrated Field Research Challenge (IFC) site. Pilot-scale in situ bioreduction of U(VI) has been accomplished in area 3 of the Oak Ridge IFC site following biostimulation, but the susceptibility of the reduced material to oxidants (i.e., oxygen) compromises long-term U immobilization. Following oxygen intrusion, attached Anaeromyxobacter dehalogenans cells increased approximately 5-fold from 2.2x10(7)+/-8.6x10(6) to 1.0x10(8)+/-2.2x10(7) cells per g of sediment collected from well FW101-2. In the same samples, the numbers of cells of Geobacter lovleyi, a population native to area 3 and also capable of U(VI) reduction, decreased or did not change. A. dehalogenans cells captured via groundwater sampling (i.e., not attached to sediment) were present in much lower numbers (<1.3x10(4)+/-1.1x10(4) cells per liter) than sediment-associated cells, suggesting that A. dehalogenans cells occur predominantly in association with soil particles. Laboratory studies confirmed aerobic growth of A. dehalogenans strain 2CP-C at initial oxygen partial pressures (pO2) at and below 0.18 atm. A negative linear correlation [micro=(-0.09xpO2)+0.051; R2=0.923] was observed between the instantaneous specific growth rate micro and pO2, indicating that this organism should be classified as a microaerophile. Quantification of cells during aerobic growth revealed that the fraction of electrons released in electron donor oxidation and used for biomass production (fs) decreased from 0.52 at a pO2 of 0.02 atm to 0.19 at a pO2 of 0.18 atm. Hence, the apparent fraction of electrons utilized for energy generation (i.e., oxygen reduction) (fe) increased from 0.48 to 0.81 with increasing pO2, suggesting that oxygen is consumed in a nonrespiratory process at a high pO2. The ability to tolerate high oxygen concentrations, perform microaerophilic oxygen respiration, and preferentially associate with soil particles represents an ecophysiology that distinguishes A. dehalogenans from other known U(VI)-reducing bacteria in area 3, and these features may play roles for stabilizing immobilized radionuclides in situ.

Improvement of the anodic bioelectrocatalytic activity of mixed culture biofilms by a simple consecutive electrochemical selection procedure

In this paper we demonstrate that the anodic, bioelectrocatalytic performance of wastewater inoculum based, mixed culture microbial biofilms can be considerably improved by using a consecutive, purely electrochemical selection and biofilm acclimatization procedure. The procedure may represent an alternative to a repetitive mechanical biofilm removal, re-suspension and electrochemically facilitated biofilm formation. By using the proposed technique, the bioelectrocatalytic current density was increased from the primary to the secondary biofilm from 250 microAcm(-2) to about 500 microAcm(-2); and the power density of respective microbial fuel cells could be increased from 686 mWm(-2) to 1487 mWm(-2). The electrochemical characterization of the biofilms reveals a strong similarity to Geobacter sulfurreducens biofilms, which may indicate a dominating role of this bacterium in the biofilms.

[Isolation of functional bacteria guided by PCR-DGGE technology from high temperature petroleum reservoirs]

It is a brand-new method to isolate functional bacteria from high temperature petroleum reservoirs according to the sequence information obtained from PCR-DGGE patterns. Three-set primers of 16S rDNA high variable region, V3, V8, V9, were compared. The results showed that more microbial diversity information could be obtained from the PCR product of V9 region. Sequence analysis indicated that the dominant bacteria in the petroleum reservoir had high sequence similarity with bacteria from alpha, beta, gamma-Proteobacterias and Bacilli from the GenBank database. According to the sequences information, multi-cultivation technology including enrichment cultivation, special cultivation and direct cultivation methods were employed, and finally, five strains (three strains by traditional methods) were isolated from oil-water samples. Among them, three thermophilic hydrocarbon-degrading bacteria, which belonged to Bacillus sp., Geobacillus sp. and Petrobacter sp., respectively, could grow well under 55 degrees C in obligate anaerobic condition. The crude oil could be utilized by these strains with the degradation rate of 56.5%, 70.01% and 31.78% respectively along with the viscosity reduction rate of 40%, 54.55% and 29.09%, meanwhile the solidify points of crude oil were reduced by 3.7, 5.2 and 3.1 degrees C. Therefore, the combination of sequence information from PCR-DGGE and altering cultivation conditions is an available novel method to isolate more functional microorganisms which could be utilized for microbial enhanced oil recovery.

Aromatic compound degradation by iron reducing bacteria isolated from irrigated tropical paddy soils

Forty-six candidate phenol/benzoate degrading-iron reducing bacteria were isolated from long-term irrigated tropical paddy soils by enrichment procedures. Pure cultures and some prepared mixed cultures were examined for ferric oxide reduction and phenol/benzoate degradation. All the isolates were iron reducers, but only 56.5% could couple iron reduction to phenol and/or benzoate degradation, as evidenced by depletion of phenol and benzoate after one week incubation. Analysis of degradative capability using Biolog MT plates revealed that most of them could degrade other aromatic compounds such as ferulic acid, vanillic acid, and hydroxybenzoate. Mixed-cultures and soil samples displayed greater capacity for aromatic degradation and iron reduction than pure bacterial isolates, suggesting that these reactions may be coupled via a consortia-based mechanism in paddy soils.

Detection and quantification of Geobacter lovleyi strain SZ: implications for bioremediation at tetrachloroethene- and uranium-impacted sites

Geobacter lovleyi strain SZ reduces hexavalent uranium, U(VI), to U(IV) and is the first member of the metal-reducing Geobacter group capable of using tetrachloroethene (PCE) as a growth-supporting electron acceptor. Direct and nested PCR with specific 16S rRNA gene-targeted primer pairs distinguished strain SZ from other known chlorinated ethene-dechlorinating bacteria and closely related Geobacter isolates, including its closest cultured relative, G. thiogenes. Detection limits for direct and nested PCR were approximately 1 x 10(6) and 1 x 10(4) 16S rRNA gene copies per mul of template DNA, respectively. A quantitative real-time PCR (qPCR) approach increased the sensitivity to as few as 30 16S rRNA gene copies per mul of template DNA but was less specific. Melting curve analysis and comparison of the shapes of amplification plots identified false-positive signals and distinguished strain SZ from G. thiogenes when analyzed separately. These indicators were less reliable when target (strain SZ) DNA and nontarget (G. thiogenes) DNA with high sequence similarity were mixed, indicating that the development of qPCR protocols should not only evaluate specificity but also explore the effects of nontarget DNA on the accuracy of quantification. Application of specific tools detected strain SZ-like amplicons in PCE-dechlorinating consortia, including the bioaugmentation consortium KB-1, and two chlorinated ethene-impacted groundwater samples. Strain SZ-like amplicons were also detected in 13 of 22 groundwater samples following biostimulation at the uranium- and chlorinated solvent-contaminated Integrated Field-Scale Subsurface Research Challenge (IFC) site in Oak Ridge, TN. The numbers of strain SZ-like cells increased from below detection to 2.3 x 10(7) +/- 0.1 x 10(7) per liter groundwater, suggesting that strain SZ-like organisms contribute to contaminant transformation. The G. lovleyi strain SZ-specific tools will be useful for monitoring bioremediation efforts at uranium- and/or chlorinated solvent-impacted sites such as the Oak Ridge IFC site.

Comparison of anode bacterial communities and performance in microbial fuel cells with different electron donors

Microbial fuel cells (MFCs) harness the electrochemical activity of certain microbes for the production of electricity from reduced compounds. Characterizations of MFC anode biofilms have collectively shown very diverse microbial communities, raising ecological questions about competition and community succession within these anode-reducing communities. Three sets of triplicate, two-chamber MFCs inoculated with anaerobic sludge and differing in energy sources (acetate, lactate, and glucose) were operated to explore these questions. Based on 16S rDNA-targeted denaturing gradient gel electrophoresis (DGGE), all anode communities contained sequences closely affiliated with Geobacter sulfurreducens (>99% similarity) and an uncultured bacterium clone in the Bacteroidetes class (99% similarity). Various other Geobacter-like sequences were also enriched in most of the anode biofilms. While the anode communities in replicate reactors for each substrate generally converged to a reproducible community, there were some variations in the relative distribution of these putative anode-reducing Geobacter-like strains. Firmicutes were found only in glucose-fed MFCs, presumably serving the roles of converting complex carbon into simple molecules and scavenging oxygen. The maximum current density in these systems was negatively correlated with internal resistance variations among replicate reactors and, likely, was only minimally affected by anode community differences in these two-chamber MFCs with high internal resistance.

[Characterization of thermophilic strain SY-14 with capability to lyse bacterial cells]

One spore-forming thermophilic bacterial strain SY-14, isolated from sewage sludge compost, showed significant capability to lyse bacterial cells. The strain was identified as Geobacillus sp. based on morphological characteristics and homology identification of 16S rDNA sequence. The optimal temperature and pH for growth were about 60 degrees C and pH 6.0-7.0 respectively. The culture supernatant of SY-14 showed lytic activity against both intact and thermal inactivated bacterial cells, and the cell lysis percentages at 6 hours were 70% and 85% respectively. The lytic activity of the culture supernatant decreased significantly after heat treatment, which inferred the lytic activity mainly derived from extracellular lytic enzymes of SY-14. The lytic activity of the culture supernatants of SY-14 increased significantly during the log phase in the batch culture process, and then decreased quickly after the maximum activity was reached. The culture supernatant of SY-14 showed lytic activity against all the five tested Gram-negative strains and some tested Gram-positive strains.

Geobacter pickeringii sp. nov., Geobacter argillaceus sp. nov. and Pelosinus fermentans gen. nov., sp. nov., isolated from subsurface kaolin lenses

The goal of this project was to isolate representative Fe(III)-reducing bacteria from kaolin clays that may influence iron mineralogy in kaolin. Two novel dissimilatory Fe(III)-reducing bacteria, strains G12(T) and G13(T), were isolated from sedimentary kaolin strata in Georgia (USA). Cells of strains G12(T) and G13(T) were motile, non-spore-forming regular rods, 1-2 mum long and 0.6 mum in diameter. Cells had one lateral flagellum. Phylogenetic analyses using the 16S rRNA gene sequence of the novel strains demonstrated their affiliation to the genus Geobacter. Strain G12(T) was most closely related to Geobacter pelophilus (94.7 %) and Geobacter chapellei (94.1 %). Strain G13(T) was most closely related to Geobacter grbiciae (95.3 %) and Geobacter metallireducens (95.1 %). Based on phylogenetic analyses and phenotypic differences between the novel isolates and other closely related species of the genus Geobacter, the isolates are proposed as representing two novel species, Geobacter argillaceus sp. nov. (type strain G12(T)=ATCC BAA-1139(T)=JCM 12999(T)) and Geobacter pickeringii sp. nov. (type strain G13(T)=ATCC BAA-1140(T)=DSM 17153(T)=JCM 13000(T)). Another isolate, strain R7(T), was derived from a primary kaolin deposit in Russia. The cells of strain R7(T) were motile, spore-forming, slightly curved rods, 0.6 x 2.0-6.0 microm in size and with up to six peritrichous flagella. Strain R7(T) was capable of reducing Fe(III) only in the presence of a fermentable substrate. 16S rRNA gene sequence analysis demonstrated that this isolate is unique, showing less than 92 % similarity to bacteria of the Sporomusa-Pectinatus-Selenomomas phyletic group, including 'Anaerospora hongkongensis' (90.2 %), Acetonema longum (90.6 %), Dendrosporobacter quercicolus (90.9 %) and Anaerosinus glycerini (91.5 %). On the basis of phylogenetic analysis and physiological tests, strain R7(T) is proposed to represent a novel genus and species, Pelosinus fermentans gen. nov., sp. nov. (type strain R7(T)=DSM 17108(T)=ATCC BAA-1133(T)), in the Sporomusa-Pectinatus-Selenomonas group.

[Geoalkalibacter ferrihydriticus gen. nov., sp. nov., the first alkaliphilic representative of the family Geobacteraceae, isolated from a soda lake]

Investigation of iron reduction in bottom sediments of alkaline soda lakes resulted in the isolation of a new obligately anaerobic iron-reducing bacterium, strain Z-0531, from Lake Khadyn (Tuva Republic, Russia) sediment samples. The cells of strain Z-0531 are short (1.0-1.5 by 0.3-0.5 microm), motile, non-spore-forming, gram-negative rods. The isolate is an obligate alkaliphile, developing in the pH range of 7.8-10.0, with an optimum at pH 8.6. It does not require NaCl but grows at NaCl concentrations of 0-50 g/1l. It can oxidize acetate with such electron acceptors as amorphous Fe(llI) hydroxide (AFH), EDTA-Fe(III), anthraquinone-2,6-disulfonate (quinone), Mn(IV), and S(0). On media with EDTA-Fe(III), the isolate can oxidize, apart from acetate, ethanol, pyruvate, oxalate, arginine, tartrate, lactate, propionate, and serine. H2 is not utilized. The reduced products formed during growth with AFH are siderite or magnetite, depending on the growth conditions. The isolate is incapable of fermenting sugars, peptides, and amino acids. Yeast extract or vitamins are required as growth factors. The organism is capable of dinitrogen fixation and harbors the nifH gene. The DNA G+C content is 55.3 mol %. 16S rRNA analysis places strain Z-0531 into the family Geobacteraceae. Its closest relative (93% similarity) is Desulfuromonas palmitatis. Based on phenotypic distinctions and phylogenetic position, it is proposed that strain Z-0531 be assigned to the new genus and species Geoalkalibacter ferrihydriticus gen. nov., sp. nov.

Identification of acetate-assimilating microorganisms under methanogenic conditions in anoxic rice field soil by comparative stable isotope probing of RNA

Acetate is the most abundant intermediate of organic matter degradation in anoxic rice field soil and is converted to CH(4) and/or CO(2). Aceticlastic methanogens are the primary microorganisms dissimilating acetate in the absence of sulfate and reducible ferric iron. In contrast, very little is known about bacteria capable of assimilating acetate under methanogenic conditions. Here, we identified active acetate-assimilating microorganisms by using a combined approach of frequent label application at a low concentration and comparative RNA-stable isotope probing with (13)C-labeled and unlabeled acetate. Rice field soil was incubated anaerobically at 25 degrees C for 12 days, during which (13)C-labeled acetate was added at a concentration of 500 muM every 3 days. (13)C-labeled CH(4) and CO(2) were produced from the beginning of the incubation and accounted for about 60% of the supplied acetate (13)C. RNA was extracted from the cells in each sample taken and separated by isopycnic centrifugation according to molecular weight. Bacterial and archaeal populations in each density fraction were screened by reverse transcription-PCR-mediated terminal restriction fragment polymorphism analysis. No differences in the bacterial populations were observed throughout the density fractions of the unlabeled treatment. However, in the heavy fractions of the (13)C treatment, terminal restriction fragments (T-RFs) of 161 bp and 129 bp in length predominated. These T-RFs were identified by cloning and sequencing of 16S rRNA as from a Geobacter sp. and an Anaeromyxobacter sp., respectively. Apparently these bacteria, which are known as dissimilatory iron reducers, were able to assimilate acetate under methanogenic conditions, i.e., when CO(2) was the predominant electron acceptor. We hypothesize that ferric iron minerals with low bioavailability might have served as electron acceptors for Geobacter spp. and Anaeromyxobacter spp. under these conditions.

Internal contamination of air-driven low-speed handpieces and attached prophy angles

BACKGROUND

In an in vitro crossover study, the authors investigated whether the interior of low-speed handpiece/prophy-angle systems becomes contaminated during operation and submersion into Geobacillus stearothermophilus.

METHODS

This study involved two types of handpieces attached to eight brands of prophy angles. The researchers operated angles attached to sterile handpieces for 60 seconds. They then analyzed the inside surfaces of the angle, nosecone and motor. They tested each prophy angle and handpiece 10 times.

RESULTS

In the 160 tests of handpieces contaminated at the prophy cup end, the spores traveled into the motor gears 32 times (20 percent). In the other 160 tests in which the motor gears were contaminated, the test bacterium traveled through the prophy cup in 75 instances (47 percent).

CONCLUSIONS

The in vitro data suggest that low-speed handpiece motors can become contaminated internally during use with prophy angles. Also, internal contaminants appear to have been released from the handpiece.

CLINICAL IMPLICATIONS

The results suggest that low-speed hand-pieces can become contaminated internally during use. Unless low-speed handpieces are sterilized properly between patients, they may become cross-contaminated.

Geobacter lovleyi sp. nov. strain SZ, a novel metal-reducing and tetrachloroethene-dechlorinating bacterium

A bacterial isolate, designated strain SZ, was obtained from noncontaminated creek sediment microcosms based on its ability to derive energy from acetate oxidation coupled to tetrachloroethene (PCE)-to-cis-1,2-dichloroethene (cis-DCE) dechlorination (i.e., chlororespiration). Hydrogen and pyruvate served as alternate electron donors for strain SZ, and the range of electron acceptors included (reduced products are given in brackets) PCE and trichloroethene [cis-DCE], nitrate [ammonium], fumarate [succinate], Fe(III) [Fe(II)], malate [succinate], Mn(IV) [Mn(II)], U(VI) [U(IV)], and elemental sulfur [sulfide]. PCE and soluble Fe(III) (as ferric citrate) were reduced at rates of 56.5 and 164 nmol min(-1) mg of protein(-1), respectively, with acetate as the electron donor. Alternate electron acceptors, such as U(VI) and nitrate, did not inhibit PCE dechlorination and were consumed concomitantly. With PCE, Fe(III) (as ferric citrate), and nitrate as electron acceptors, H(2) was consumed to threshold concentrations of 0.08 +/- 0.03 nM, 0.16 +/- 0.07 nM, and 0.5 +/- 0.06 nM, respectively, and acetate was consumed to 3.0 +/- 2.1 nM, 1.2 +/- 0.5 nM, and 3.6 +/- 0.25 nM, respectively. Apparently, electron acceptor-specific acetate consumption threshold concentrations exist, suggesting that similar to the hydrogen threshold model, the measurement of acetate threshold concentrations offers an additional diagnostic tool to delineate terminal electron-accepting processes in anaerobic subsurface environments. Genetic and phenotypic analyses classify strain SZ as the type strain of the new species, Geobacter lovleyi sp. nov., with Geobacter (formerly Trichlorobacter) thiogenes as the closest relative. Furthermore, the analysis of 16S rRNA gene sequences recovered from PCE-dechlorinating consortia and chloroethene-contaminated subsurface environments suggests that Geobacter lovleyi belongs to a distinct, dechlorinating clade within the metal-reducing Geobacter group. Substrate versatility, consumption of electron donors to low threshold concentrations, and simultaneous reduction of electron acceptors suggest that strain SZ-type organisms have desirable characteristics for bioremediation applications.

Correlations between arsenic in Maine groundwater and microbial populations as determined by fluorescence in situ hybridization

Arsenic is known to cause serious health effects when consumed in drinking water. In the state of Maine, approximately half of the population relies on private groundwater wells for their drinking water. Of those wells, as many as 13% may contain arsenic levels above the current EPA maximum contaminant level of 10 microgl(-1). Microorganisms can potentially contribute to arsenic release into groundwater through several mechanisms. Some can reduce arsenate to arsenite, which is more toxic and may be more mobile. Sulfurospirillum species NP4, which was isolated from well water, respires arsenate and could act in this way. Microorganisms can also act indirectly by reducing bedrock surface coatings, such as iron oxyhydroxides, that adsorb arsenic in the groundwater environment. The genus Geobacter contains many species that are capable of iron reduction that could play a role in the indirect release of arsenic into groundwater. Water samples from Northport, ME and the Branch Lake region of Ellsworth, ME, which both have elevated groundwater arsenic levels, have been probed using fluorescence in situ hybridization (FISH), to determine the percentage of the population that is NP4 and the percentage that are Geobacter species. Geobacter abundance correlates well with the total arsenic concentration indicating that indirect mechanisms could be important in releasing arsenic. NP4 appears to be reducing arsenate since its prevalence correlates well with arsenite, the end product of arsenate respiration.

Geobacter bemidjiensis sp. nov. and Geobacter psychrophilus sp. nov., two novel Fe(III)-reducing subsurface isolates

Fe(III)-reducing isolates were recovered from two aquifers in which Fe(III) reduction is known to be important. Strain BemTwas enriched from subsurface sediments collected in Bemidji, MN, USA, near a site where Fe(III) reduction is important in aromatic hydrocarbon degradation. Strains P11, P35Tand P39 were isolated from the groundwater of an aquifer in Plymouth, MA, USA, in which Fe(III) reduction is important because of long-term inputs of acetate as a highway de-icing agent to the subsurface. All four isolates were Gram-negative, slightly curved rods that grew best in freshwater media. Strains P11, P35Tand P39 exhibited motility via means of monotrichous flagella. Analysis of the 16S rRNA andnifDgenes indicated that all four strains areδ-proteobacteria and members of theGeobactercluster of theGeobacteraceae. Differences in phenotypic and phylogenetic characteristics indicated that the four isolates represent two novel species within the genusGeobacter. All of the isolates coupled the oxidation of acetate to the reduction of Fe(III) [iron(III) citrate, amorphous iron(III) oxide, iron(III) pyrophosphate and iron(III) nitrilotriacetate]. All four strains utilized ethanol, lactate, malate, pyruvate and succinate as electron donors and malate and fumarate as electron acceptors. Strain BemTgrew fastest at 30 °C, whereas strains P11, P35Tand P39 grew equally well at 17, 22 and 30 °C. In addition, strains P11, P35Tand P39 were capable of growth at 4 °C. The namesGeobacter bemidjiensissp. nov. (type strain BemT=ATCC BAA-1014T=DSM 16622T=JCM 12645T) andGeobacter psychrophilussp. nov. (strains P11, P35Tand P39; type strain P35T=ATCC BAA-1013T=DSM 16674T=JCM 12644T) are proposed.

Automated purification and suspension array detection of 16S rRNA from soil and sediment extracts by using tunable surface microparticles

Autonomous, field-deployable molecular detection systems require seamless integration of complex biochemical solutions and physical or mechanical processing steps. In an attempt to simplify the fluidic requirements for integrated biodetection systems, we used tunable surface microparticles both as an rRNA affinity purification resin in a renewable microcolumn sample preparation system and as the sensor surface in a flow cytometer detector. The tunable surface detection limits in both low- and high-salt buffers were 1 ng of total RNA ( approximately 10(4) cell equivalents) in 15-min test tube hybridizations and 10 ng of total RNA ( approximately 10(5) cell equivalents) in hybridizations with the automated system (30-s contact time). RNA fragmentation was essential for achieving tunable surface suspension array specificity. Chaperone probes reduced but did not completely eliminate cross-hybridization, even with probes sharing <50% identity to target sequences. Nonpurified environmental extracts did not irreparably affect our ability to classify color-coded microparticles, but residual environmental constituents significantly quenched the Alexa-532 reporter fluor. Modulating surface charge did not influence the interaction of soluble environmental contaminants with conjugated beads. The automated system greatly reduced the effects of fluorescence quenching, especially in the soil background. The automated system was as efficacious as manual methods for simultaneous sample purification, hybridization, and washing prior to flow cytometry detection. The implications of unexpected target cross-hybridization and fluorescence quenching are discussed relative to the design and implementation of an integrated microbial monitoring system.