Multiple factors drive the abundance and diversity of the diazotrophic community in typical farmland soils of China.

Biological nitrogen fixation plays an important role in nitrogen cycling by transferring atmospheric N2 to plant-available N in the soil. However, the diazotrophic activity and distribution in different types of soils remain to be further explored. In this study, 152 upland soils were sampled to examine the diazotrophic abundance, nitrogenase activity, diversity and community composition by quantitative polymerase chain reaction, acetylene reduction assay and the MiSeq sequencing of nifH genes, respectively. The results showed that diazotrophic abundance and nitrogenase activity varied among the three soil types. The diazotrophic community was mainly dominated by Bradyrhizobium, Azospirillum, Myxobacter, Desulfovibrio and Methylobacterium. The symbiotic diazotroph Bradyrhizobium was widely distributed among soils, while the distribution of free-living diazotrophs showed large variation and was greatly affected by multiple factors. Crop type and soil properties directly affected the diazotrophic ɑ-diversity, while soil properties, climatic factors and spatial distance together influenced the diazotrophic community. Network structures were completely different among all three types of soils, with most complex interactions observed in the Red soil. These findings suggest that diazotrophs have various activities and distributions in the three soil types, which played different roles in nitrogen input in agricultural soil in China, being driven by multiple environmental factors.

Induction and inhibition of oral malodor.

Volatile sulfur compounds (VSCs) such as hydrogen sulfide (H2 S) and methyl mercaptan (CH3 SH) are the main components of oral malodor, and are produced as the end products of the proteolytic processes of oral microorganisms. The main pathway of proteolysis is the metabolism of sulfur-containing amino acids by gram-negative anaerobic bacteria. Gram-positive bacteria may promote VSC production by gram-negative anaerobes by cleaving sugar chains from glycoproteins and thus providing proteins. A large variety of bacteria within the oral microbiota are thought to be involved in the complex phenomenon of halitosis. Oral microbiota associated with a lack of oral malodor, oral microbiota associated with severe and H2 S-dominant oral malodor, and oral microbiota associated with severe and CH3 SH-dominant oral malodor have been distinguished through molecular approaches using the 16S rRNA gene. Pathological halitosis may primarily be addressed through treatment of causative diseases. In all cases, plaque control is the basis of oral malodor control, and dentifrices, mouthwashes, and functional foods play a supplementary role in addition to brushing. Recently, the use of natural ingredients in products tends to be favored due to the increase in antibiotic-resistant strains and the side effects of some chemical ingredients. In addition, probiotics and vaccines are expected to offer new strategies for improving the oral conditions through mechanisms other than antibacterial agents.

Abditibacterium utsteinense sp. nov., the first cultivated member of candidate phylum FBP, isolated from ice-free Antarctic soil samples.

Most bacterial lineages are known only by molecular sequence data from environmental surveys and represent the uncultivated majority. One of these lineages, candidate phylum FBP, is widespread in extreme environments on Earth, ranging from polar and desert ecosystems to wastewater and contaminated mine sites. Here we report on the characterization of strain LMG 29911T, the first cultivated representative of the FBP lineage. The strain was isolated from a terrestrial surface sample from Utsteinen, Sør Rondane Mountains, East Antarctica and is a Gram-negative, aerobic, oligotrophic chemoheterotrophic bacterium. It displays growth in a very narrow pH range, use of only a limited number of carbon sources, but also a metabolism optimized for survival in low-nutrient habitats. Remarkably, phenotypic and genome analysis indicated an extreme resistance against antibiotics and toxic compounds. We propose the names Abditibacterium utsteinense for this bacterium and Abditibacteriota for the former candidate phylum FBP. Furthermore, inter- and intra-phylum relationships indicate Armatimonadetes, a neighboring lineage to the Abditibacteriota, to be a superphylum.

Agricultural anaerobic digestion power plants in Ireland and Germany: policy and practice.

The process of anaerobic digestion (AD) is valued as a carbon-neutral energy source, while simultaneously treating organic waste, making it safer for disposal or use as a fertilizer on agricultural land. The AD process in many European nations, such as Germany, has grown from use of small, localized digesters to the operation of large-scale treatment facilities, which contribute significantly to national renewable energy quotas. However, these large AD plants are costly to run and demand intensive farming of energy crops for feedstock. Current policy in Germany has transitioned to support funding for smaller digesters, while also limiting the use of energy crops. AD within Ireland, as a new technology, is affected by ambiguous governmental policies concerning waste and energy. A clear governmental strategy supporting on-site AD processing of agricultural waste will significantly reduce Ireland's carbon footprint, improve the safety and bioavailability of agricultural waste, and provide an indigenous renewable energy source. © 2016 Society of Chemical Industry.

Optimization of a bioremediation system of soluble uranium based on the biostimulation of an indigenous bacterial community.

High concentrations of uranium(VI) in the Witwatersrand Basin, South Africa from mining leachate is a serious environmental concern. Treatment systems are often ineffective. Therefore, optimization of a bioremediation system that facilitates the bioreduction of U(VI) based on biostimulation of indigenous bacterial communities can be a viable alternative. Tolerance of the indigenous bacteria to high concentrations of U and the amount of citric acid required for U removal was optimized. Two bioreactor studies which showed effective U(VI) removal more than 99 % from low (0.0037 mg L(-1)) and high (10 mg L(-1)) concentrations of U to below the limit allowed by South African National Standards for drinking water (0.0015 mg L(-1)). The second bioreactor was able to successfully adapt even with increasing levels of U(VI) feed water up to 10 mg L(-1), provided that enough electron donor was available. Molecular biology analyses identified Desulfovibrio sp. and Geobacter sp. among known species, which are known to reduce U(VI). The mineralogical analysis determined that part of the uranium precipitated intracellularly, which meant that the remaining U(VI) was precipitated as U(IV) oxides and TEM-EDS also confirmed this analysis. This was predicted with the geochemical model from the chemical data, which demonstrated that the treated drainage was supersaturated with respect to uraninite > U4O9 > U3O8 > UO2(am). Therefore, the tolerance of the indigenous bacterial community could be optimized to remediate up to 10 mg L(-1), and the system can thus be upscaled and employed for remediation of U(VI) impacted sites.

Anaerobic codigestion of sewage sludge and glycerol, focusing on process kinetics, microbial dynamics and sludge dewaterability.

Anaerobic codigestion (AcoD) is a proven option to significantly boost biogas production while utilizing existing digesters and infrastructure. The aim of the present research was to conduct an exhaustive study regarding anaerobic codigestion of mixed sewage sludge and crude glycerol considering impacts on organic load, hydraulic load, process performance and microbial community. The methane potential of crude glycerol varied from 370 mL CH4·g(-1) VS to 483 mL CH4·g(-1) VS for different samples tested. The half maximal inhibitory concentration of crude glycerol was 1.01 g VS L(-1), and the primary mechanism of inhibition was through overload from rapid fermentation rather than the presence of toxic compounds in the crude glycerol. In continuous operation over 200 days, feeding glycerol at up to 2% v/v, increased organic load by up to 70% and resulted in a 50% increase in methane production. Glycerol dosing resulted in no change in apparent dewaterability, with both codigestion and control reactors returning values of 22%-24%. Members of the phylum Thermotogae emerged as a niche population during AcoD of sewage sludge and glycerol; however there was no gross change in microbial community structure and only minimal changes in diversity. AcoD did not result in synergisms between sewage sludge and crude glycerol. Actually, at dose rate up to 2% v/v glycerol dosing is still an effective strategy to increase the organic loading rate of continuous anaerobic digesters with minimal impact of the hydraulic retention time. Nonetheless, the dose rate must be managed to: (i) prevent process inhibition and (ii) ensure sufficient degradation time to produce a stable biosolids product.

Kosmotoga pacifica sp. nov., a thermophilic chemoorganoheterotrophic bacterium isolated from an East Pacific hydrothermal sediment.

A novel strictly anaerobic thermophilic heterotrophic bacterium, strain SLHLJ1(T), was isolated from a Pacific hydrothermal sediment. Cells were Gram-negative coccobacilli (approximately 1.0 × 0.6 µm) with a toga. It grew at temperatures between 33 and 78 °C (optimum 70 °C). Elemental sulphur and L-cystine stimulated its growth. It contained C16:0, C16:1 ω11c, C18:0 and C18:1 ω9c as major fatty acids (>5%), 3 phospholipids and 2 glycolipids as polar lipids. Its DNA G+C content was 43.7 mol%. Phylogenetic analyses based on 16S rRNA gene sequences placed strain SLHLJ1(T) within the family Thermotogaceae. The novel isolate was most closely related to Kosmotoga arenicorallina (97.93 % 16S rRNA gene sequence similarity), K. olearia (92.43%) and K. shengliensis (92.17 %). On the basis of phenotypic, chemotaxonomic and phylogenetic comparisons with its closest relatives, we propose its assignment to a novel species of the genus Kosmotoga. The name Kosmotoga pacifica sp. nov. is proposed with strain SLHLJ1(T) (=DSM 26965(T) = JCM 19180(T) = UBOCC 3254(T)) as the type species.

Microbial community structure and dynamics in two-stage vs single-stage thermophilic anaerobic digestion of mixed swine slurry and market bio-waste.

The microbial community of a thermophilic two-stage process was monitored during two-months operation and compared to a conventional single-stage process. Qualitative and quantitative microbial dynamics were analysed by Denaturing Gradient Gel Electrophoresis (DGGE) and real-time PCR techniques, respectively. The bacterial community was dominated by heat-shock resistant, spore-forming clostridia in the two-stage process, whereas a more diverse and dynamic community (Firmicutes, Bacteroidetes, Synergistes) was observed in the single-stage process. A significant evolution of bacterial community occurred over time in the acidogenic phase of the two-phase process with the selection of few dominant species associated to stable hydrogen production. The archaeal community, dominated by the acetoclastic Methanosarcinales in both methanogen reactors, showed a significant diversity change in the single-stage process after a period of adaptation to the feeding conditions, compared to a constant stability in the methanogenic reactor of the two-stage process. The more diverse and dynamic bacterial and archaeal community of single-stage process compared to the two-stage process accounted for the best degradation activity, and consequently the best performance, in this reactor. The microbiological perspective proved a useful tool for a better understanding and comparison of anaerobic digestion processes.

Biological sulfate reduction in the acidogenic phase of anaerobic digestion under dissimilatory Fe (III)--reducing conditions.

In this study, a novel approach was developed for sulfate - containing wastewater treatment via dosing Fe2O3 in a two - stage anaerobic reactor (A1, S1). The addition of Fe2O3 in its second stage i.e. acidogenic sulfate-reducing reactor (S1) resulted in microbial reduction of Fe (III), which significantly enhanced the biological sulfate reduction. In reactor S1, increasing influent sulfate concentration to 1400 mg/L resulted in a higher COD removal (27.3%) and sulfate reduction (57.9%). In the reference reactor without using Fe2O3 (S2), the COD and sulfate removal were 15.6% and 29%, respectively. The combined performance of the two-stage anaerobic reactor (A1, S1) also showed a higher COD removal of 74.2%. Denaturing gradient gel electrophoresis (DGGE) and phylogenetic analysis showed that the dominant bacteria with high similarity to IRB species as well as sulfate reducer Desulfovibrio and acidogenic bacteria (AB) were enriched in S1. Quantitative Polymerase Chain Reaction (qPCR) analysis presented a higher proportion of sulfate reducer Desulfovibrio marrakechensis and Fe (III) reducer Iron-reducing bacteria HN54 in S1.

Occurrence and fate of volatile siloxanes in a municipal wastewater treatment plant of Beijing, China.

The occurrence and fate of four cyclic and two linear volatile siloxanes were studied in a municipal Wastewater Treatment Plant (WWTP), Beijing City, China. Aqueous and sludge samples were analyzed by solid-phase microextraction (SPME) coupled with gas chromatography-mass spectrometry (GC-MS). In the studied WWTP, four cyclic analogs (D3-D6) had significantly higher concentrations and frequencies than the two linear analogs [Octamethyltrisiloxane (L3) and Decamethyltetrasiloxane (L4)], with inputs into the WWTP ranging from 78.2 to 387.7 kg/year. Removal efficiencies of volatile cyclic siloxanes in two parallel secondary treatment processes ranged from 59.3 to 92.7%. For volatile cyclic siloxanes, relative fractions of mass loss by adsorption to sludge ranged from 8.3 to 53.0%, and their adsorption capacities were significantly affected by the dissolved organic matter. Besides adsorption, they were eliminated mainly in anaerobic units (44.4-84.3%). Through in vitro biodegradation experiments, we concluded that in the anaerobic compartments, Hexamethylcyclotrisiloxane (D3) and Dodecamethylcyclohexasiloxane (D6) were eliminated mostly by volatilization, while Octamethylcyclotetrasiloxane (D4) and Decamethylcyclopentasiloxane (D5) may be eliminated by both volatilization and degradation. Furthermore, microbe catalysis hydrolysis was identified as one of the main degradation pathways for D4 and D5 in anaerobic compartments.

Sulphur isotope fractionation during the reduction of elemental sulphur and thiosulphate by Dethiosulfovibrio spp.

Stable sulphur isotope fractionation was investigated during reduction of thiosulphate and elemental sulphur at 28°C by growing batch cultures of the sulphur- and thiosulphate-reducing bacteria Dethiosulfovibrio marinus (type strain DSM 12537) and Dethiosulfovibrio russensis (type strain DSM 12538), using citrate as carbon and energy source. The cell-specific thiosulphate reduction rate in the growth phase was 7.4±3.9 fmol cell(-1) d(-1). The hydrogen sulphide produced was enriched in (32)S by 10.3±1 ‰ compared with total thiosulphate sulphur, close to previous experimental results observed for other sulphate- and non-sulphate-reducing bacteria. Elemental sulphur reduction yields sulphur isotope enrichment factors between-1.3 and-5.2 ‰ for D. russensis and-1.7 and-5.1 ‰ for D. marinus. The smaller fractionation effects are observed in the exponential growth phase (cellular rates between 5 and 70 fmol S° cell(-1) d(-1)) and enhanced discrimination under conditions of citrate depletion and cell lysis (cellular rates between 0.3 and 3 fmol S° cell(-1) d(-1)).

Influence of ferric iron on complete dechlorination of trichloroethylene (TCE) to ethene: Fe(III) reduction does not always inhibit complete dechlorination.

The effects of Fe(III) reduction on TCE, cis-DCE, and VC dechlorination were studied in both contaminated aquifer material and enrichment cultures. The results from sediment batch experiments demonstrated that Fe(III) reduction did not inhibit complete dechlorination. TCE was reduced concurrently with Fe(III) in the first 40 days of the incubations. While all incubations (plus and minus Fe(III)) generated approximately the same mass of ethene within the experimental time frame, Fe(III) speciation (ferrihydrite versus Fe(III)-NTA) had an impact on daughter product distribution and dechlorination kinetics. 16S rRNA gene clone library sequencing identified Dehalococcoides and Geobacteraceae as dominant populations, which included G. lovleyi like organisms. Quantitative PCR targeting 16S rRNA genes and Reductive Dehalogenase genes (tceA, bvcA, vcrA) indicated that Dehalococcoides and Geobacteraceae were enriched concurrently in the TCE-degrading, Fe(III)-reducing sediments. Enrichment cultures demonstrated that soluble Fe(III) had a greater impact on cis-DCE and VC reduction than solid-phase Fe(III). Geobacteraceae and Dehalococcoides were also coenriched in the liquid cultures, and the Dehalococcoides abundance in the presence of Fe(III) was not significantly different from those in the cultures without Fe(III). Hydrogen reached steady-state concentrations most amenable to complete dechlorination very quickly when Fe(III) was present in the culture, suggesting that Fe(III) reduction may actually help dechlorination. This was contrasted to hydrogen levels in nitrate-amended enrichments, in which hydrogen concentration was too low for any chlororespiration.

Effect of an essential oil-containing mouth rinse on VSC-producing bacteria on the tongue.

The objective of the present study was to investigate the inhibitory effect of a commercially available essential oil-containing mouth rinse 12 hours after a single rinse and two weeks of twice daily rinsing, on volatile sulphur compounds (VSC) producing bacteria on the tongue. The study was a randomized, double-blind, controlled crossover design. Thirty-six healthy subjects, aged 20-48 years, volunteered to participate in the study. Subjects were randomly assigned to rinse twice daily with either an essential oil-containing mouth rinse (Cool Mint Listerine Antiseptic) or a negative control rinse. Bacteria samples were taken from the dorsum of the tongue at baseline, after the first rinse and two weeks later. They were plated on OOPS medium to enumerate the VSC-producing bacteria. Intergroup comparisons of log10 transformed colony-forming units of the samples were made using analysis of covariance. Each comparison was performed at a 5% significance level. The mean VSC-producing bacteria in subjects using the essential oil mouth rinse were significantly lower than those using the control rinse twice daily. In healthy subjects, rinsing with an essential oil-containing mouth rinse can have a significant effect on VSC-producing bacteria on the tongue and may be useful for controlling intrinsic oral malodor over prolonged periods.

Isolation and characterization of Thermanaerothrix daxensis gen. nov., sp. nov., a thermophilic anaerobic bacterium pertaining to the phylum "Chloroflexi", isolated from a deep hot aquifer in the Aquitaine Basin.

A new strictly anaerobic thermophilic multicellular filamentous bacterium (0.2-0.3µm×>100µm), designated GNS-1(T), was isolated from a deep hot aquifer in France. It was non-motile, and stained Gram-negative. Optimal growth was observed at 65°C, pH 7.0, and 2gL(-1) of NaCl. Strain GNS-1(T) was chemoorganotrophic fermenting ribose, glucose, galactose, arabinose, fructose, mannose, maltose, sucrose, xylose, raffinose, pyruvate, and xylan. Yeast extract was required for growth. The end products of glucose fermentation were lactate, acetate, CO(2), and H(2). The G+C content of the DNA was 57.6mol%. Its closest phylogenetic relative was Bellilinea caldifistulae with 92.5% similarity. Based on phylogenetic, genotypic and phenotypic characteristics, strain GNS-1(T) (DSM 23592(T), JCM 16980(T)) is proposed to be assigned to a novel species of a novel genus within the class Anaerolineae (subphylum I), phylum "Chloroflexi", Thermanaerothrix daxensis gen. nov., sp. nov. The GenBank accession number is HM596746.

Stereospecific microbial production of isoflavanones from isoflavones and isoflavone glucosides.

A Gram-negative anaerobic microorganism, MRG-1, isolated from human intestine showed high activities of deglycosylation and reduction of daidzin, based on rapid TLC analysis. A rod-shaped strain MRG-1 was identified as a new species showing 91.0% homology to Coprobacillus species, based on 16S rRNA sequence analysis. The strain MRG-1 showed ß-glucosidase activity toward daidzin and genistin, and daidzein and genistein were produced, respectively. However, the strain MRG-1 did not react with flavone glycosides, flavanone glycosides, and isoflavone C-glucoside. Besides, MRG-1 showed stereoselective reductase activity to isoflavone, daidzein, genistein, 7-hydroxyisoflavone, and formononetin, resulting in the formation of corresponding R-isoflavanone enantiomers. The new isoflavanones of 7-hydroxyisoflavanone and dihydroformononetin were characterized by NMR, and the absolute configurations of the enantiomers were determined with CD spectroscopy. The kinetic study of the anaerobic biotransformation showed both activities were exceptionally fast compared to the reported conversion by other anaerobic bacteria.

Increased d-lactic Acid intestinal bacteria in patients with chronic fatigue syndrome.

Patients with chronic fatigue syndrome (CFS) are affected by symptoms of cognitive dysfunction and neurological impairment, the cause of which has yet to be elucidated. However, these symptoms are strikingly similar to those of patients presented with D-lactic acidosis. A significant increase of Gram positive facultative anaerobic faecal microorganisms in 108 CFS patients as compared to 177 control subjects (p<0.01) is presented in this report. The viable count of D-lactic acid producing Enterococcus and Streptococcus spp. in the faecal samples from the CFS group (3.5 x 10(7) cfu/L and 9.8 x 10(7) cfu/L respectively) were significantly higher than those for the control group (5.0 x 10(6) cfu/L and 8.9 x 10(4) cfu/L respectively). Analysis of exometabolic profiles of Enterococcus faecalis and Streptococcus sanguinis, representatives of Enterococcus and Streptococcus spp. respectively, by NMR and HPLC showed that these organisms produced significantly more lactic acid (p<0.01) from (13)C-labeled glucose, than the Gram negative Escherichia coli. Further, both E. faecalis and S. sanguinis secrete more D-lactic acid than E. coli. This study suggests a probable link between intestinal colonization of Gram positive facultative anaerobic D-lactic acid bacteria and symptom expressions in a subgroup of patients with CFS. Given the fact that this might explain not only neurocognitive dysfunction in CFS patients but also mitochondrial dysfunction, these findings may have important clinical implications.

[Metabolism of the thermophilic bacterium Oceanithermus profundus].

The metabolism of the novel facultatively anaerobic thermophilic bacterium Oceanithermus profundus was studied during growth on maltose, acetate, pyruvate, and hydrogen. The utilization of carbohydrates was shown to proceed via the glycolytic pathway. Under microaerobic growth conditions, the metabolism of O. profundus grown on maltose depended on the substrate concentration. At an initial maltose concentration of 1.4 mM, O. profundus carried out oxygen respiration, and in the presence of 3.5 mM maltose, facilitated fermentation occurred, with the formation of acetate and ethanol and limited involvement of oxygen. The use of pyruvate and acetate occurs via the TCA cycle. In cells grown on acetate, the activity of glyoxylate pathway enzymes was revealed. Depending on the energy-yielding process providing for growth (oxygen respiration or nitrate reduction), cells contained cytochromes a and c or b, respectively. The results obtained demonstrate the plasticity of the metabolism of O. profundus, which thus appears to be well-adjusted to the rapidly changing conditions in deep-sea hydrothermal vents.

Toll-like receptor 2-mediated interleukin-8 expression in gingival epithelial cells by the Tannerella forsythia leucine-rich repeat protein BspA.

Tannerella forsythia is a gram-negative anaerobe strongly associated with chronic human periodontitis. This bacterium expresses a cell surface-associated and secreted protein, designated BspA, which has been recognized as an important virulence factor. The BspA protein belongs to the leucine-rich repeat (LRR) and bacterial immunoglobulin-like protein families. BspA is, moreover, a multifunctional protein which interacts with a variety of host cells, including monocytes which appear to respond to BspA through Toll-like receptor (TLR) signaling. Since gingival epithelium forms a barrier against periodontal pathogens, this study was undertaken to determine if gingival epithelial cells respond to BspA challenge and if TLRs play any role in BspA recognition. This study was also directed towards identifying the BspA domains responsible for cellular activation. We provide direct evidence for BspA binding to TLR2 and demonstrate that the release of the chemokine interleukin-8 from human gingival epithelial cells by BspA is TLR2 dependent. Furthermore, the LRR domain of BspA is involved in activation of TLR2, while TLR1 serves as a signaling partner. Thus, our findings suggest that BspA is an important modulator of host innate immune responses through activation of TLR2 in cooperation with TLR1.

Effect of fatty acids on growth of conjugated-linoleic-acids-producing bacteria in rumen.

Microorganisms with high activity of linoleic acid delta12-cis,delta11-trans-isomerase were isolated from the digestive tract of ruminants and characterized. The isolate with the highest isomerase activity was identified as Pseudobutyrivibrio ruminis. The susceptibility of this strain to 3 fatty acids added to the grow medium was determined. A significant inhibition of bacterial growth (during a 3-d period) by linoleic acid (0.1 %) and oleic acid (5 ppm) was observed; no inhibition was found in the presence of stearic acid.

Comparison of antagonistic ability against enteropathogens by G+ and G- anaerobic dominant components of human fecal microbiota.

To confirm if anaerobic G+-components are those responsible for the function of colonization resistance, obligate anaerobic G+- and G- -bacteria from normal dominant microbiota of human feces were isolated from three successive collections and then used in in vitro assays for antagonism against two enteropathogenic bacteria. The production of inhibitory diffusible compounds was determined on supplemented BHI agar and MRS agar media for G- - and G+-bacteria, respectively. Salmonella enterica subsp. enterica serovar Typhimurium and Shigella sonnei were used as indicators. G+-bacteria presented a higher overall antagonistic frequency against both pathogenic bacteria (57 and 64 % for S. enterica serovar Typhimurium and S. sonnei, respectively) when compared to G+-microorganisms but with a quite elevated variation between volunteers (0-100 %) and collection samples (40-72 and 40-80 % for S. enterica sv. Typhimurium and S. sonnei, respectively). On the other hand, only three among 143 G- -isolates tested showed antagonistic activity. The results showed that, at least in vitro, obligate anaerobic G+-components of the dominant human fecal microbiota present a higher potential for antagonism against the enteropathogenic models tested than do G- -bacteria.