An automated multiplexed turbidometric and data collection system for measuring growth kinetics of anaerobes dependent on gaseous substrates.

Standard methods of monitoring the growth kinetics of anaerobic microorganisms are generally impractical when there is a protracted or indeterminate period of active growth, and when high numbers of samples or replications are required. As part of our studies of the adaptive evolution of a simple anaerobic syntrophic mutualism, requiring the characterization of many isolates and alternative syntrophic pairings, we developed a multiplexed growth monitoring system using a combination of commercially available electronics and custom designed circuitry and materials. This system automatically monitors up to 64 sealed, and as needed pressurized, culture tubes and reports the growth data in real-time through integration with a customized relational database. The utility of this system was demonstrated by resolving minor differences in growth kinetics associated with the adaptive evolution of a simple microbial community comprised of a sulfate reducing bacterium, Desulfovibrio vulgaris, grown in syntrophic association with Methanococcus maripaludis, a hydrogenotrophic methanogen.

When anaerobes encounter oxygen: mechanisms of oxygen toxicity, tolerance and defence.

The defining trait of obligate anaerobes is that oxygen blocks their growth, yet the underlying mechanisms are unclear. A popular hypothesis was that these microorganisms failed to evolve defences to protect themselves from reactive oxygen species (ROS) such as superoxide and hydrogen peroxide, and that this failure is what prevents their expansion to oxic habitats. However, studies reveal that anaerobes actually wield most of the same defences that aerobes possess, and many of them have the capacity to tolerate substantial levels of oxygen. Therefore, to understand the structures and real-world dynamics of microbial communities, investigators have examined how anaerobes such as Bacteroides, Desulfovibrio, Pyrococcus and Clostridium spp. struggle and cope with oxygen. The hypoxic environments in which these organisms dwell - including the mammalian gut, sulfur vents and deep sediments - experience episodic oxygenation. In this Review, we explore the molecular mechanisms by which oxygen impairs anaerobes and the degree to which bacteria protect their metabolic pathways from it. The emergent view of anaerobiosis is that optimal strategies of anaerobic metabolism depend upon radical chemistry and low-potential metal centres. Such catalytic sites are intrinsically vulnerable to direct poisoning by molecular oxygen and ROS. Observations suggest that anaerobes have evolved tactics that either minimize the extent to which oxygen disrupts their metabolism or restore function shortly after the stress has dissipated.

Oral probiotic activities and biosafety of Lactobacillus gasseri HHuMIN D.

BACKGROUND: Lactobacillus spp. have been researched worldwide and are used in probiotics, but due to difficulties with laboratory cultivation of and experimentation on oral microorganisms, there are few reports of Lactobacillus spp. being isolated from the oral cavity and tested against oral pathogens. This research sought to isolate and determine the safety and inhibitory capabilities of a Lactobacillus culture taken from the human body. RESULTS: One organism was isolated, named "L. gasseri HHuMIN D", and evaluated for safety. A 5% dilution of L. gasseri HHuMIN D culture supernatant exhibited 88.8% inhibition against halitosis-producing anaerobic microorganisms and the organism itself exhibited powerful inhibitory effects on the growth of 11 oral bacteria. Hydrogen peroxide production reached 802 µmol/L after 12 h and gradually diminished until 24 h, it efficiently aggregated with P. catoniae and S. sanguinis, and it completely suppressed S. mutans-manufactured artificial dental plaque. L. gasseri HHuMIN D's KB cell adhesion capacity was 4.41 cells per cell, and the cell adhesion of F. nucleatum and S. mutans diminished strongly in protection and displacement assays. CONCLUSION: These results suggest that L. gasseri HHuMIN D is a safe, bioactive, lactobacterial food ingredient, starter culture, and/or probiotic microorganism for human oral health.

Comparison of microbial community structures between mesophilic and thermophilic anaerobic digestion of vegetable waste.

The anaerobic digestion performance correlates with the functional microbial community. Mesophilic and thermophilic digestions of vegetable waste were conducted, and dynamics of the microbial community were investigated. The mesophilic and thermophilic collapsed stages occurred at organic loading rates of 1.5 and 2.0 g VS/(L d) due to the accumulation of volatile fatty acids with final concentrations of 2276 and 6476 mg/L, respectively. A high concentration of volatile fatty acids caused the severe inhibition of methanogens, which finally led to the imbalance between acetogenesis and methanogenesis. The mesophilic digestion exhibited a higher microbial diversity and richness than the thermophilic digestion. Syntrophic acetate-oxidizing coupled with hydrogenotrophic methanogenesis was the dominant pathway in the thermophilic stable system, and acetoclastic methanogenesis in the mesophilic stable system. The dominant acidogens, syntrophus, and methanogens were unclassified_f__Anaerolineaceae (8.68%), Candidatus_Cloacamonas (19.70%), Methanosaeta (6.10%), and Methanosarcina (4.08%) in the mesophilic stable stage, and Anaerobaculum (12.59%), Syntrophaceticus (4.84%), Methanosarcina (30.58%), and Methanothermobacter (3.17%) in thermophilic stable stage. Spirochaetae and Thermotogae phyla were the characteristic microorganisms in the mesophilic and thermophilic collapsed stages, respectively. These findings provided valuable information for the deep understanding of the difference of the microbial community and methane-producing mechanism between mesophilic and thermophilic digestion of vegetable waste.

An inexpensive anaerobic chamber for the genetic manipulation of strictly anaerobic bacteria.

Strictly anaerobic bacteria are important to both human health and industrial usage. These bacteria are sensitive to oxygen, therefore, it is preferable to manipulate these microbes in an anaerobic chamber. However, commercial anaerobic chambers (CACs) are expensive, making them less accessible to scientists with a limited budget, especially to those in developing countries. The high price of commercial chambers has hindered, at least partially, the progress of research on anaerobes in developing countries. In the research presented here, we developed an inexpensive and reliable anaerobic chamber and successfully achieved routine maintenance of eleven strictly anaerobic bacterial strains. Furthermore, genetic manipulation examples have been set for both Clostridioidesdifficile 630 and Clostridiumbeijerinckii NCIMB 8052 strains to validate that the chamber could applied to advanced genetic engineering of strictly anaerobes. C. difficile and C. beijerinckii were both genetically manipulated in this chamber, showing it's utility for the genetic engineering of anaerobes. Most importantly, the anaerobic chamber was 76% - 88% less expensive than a CACs and has similar functionality with regards to the cultivation and manipulation of strictly anaerobic bacteria. The anaerobic chamber described in this study will promote the research of anaerobes in developing counties and scientists who have limited research budgets.

Effects of biotin on promoting anammox bacterial activity.

Anaerobic ammonium oxidation (anammox) bacteria significantly improve the efficiency and reduce cost of nitrogen removal in wastewater treatment plants. However, their slow growth and vulnerable activity limit the application of anammox technology. In this paper, the enhancement of biotin on the nitrogen removal activity of anammox bacteria in short-term batch experiments was studied. We found that biotin played a significant role in promoting anammox activity within a biotin concentration range of 0.1-1.5 mg/L. At a biotin concentration of 1.0 mg/L, the total nitrogen removal rate (NRR) increased by 112%, extracellular polymeric substance (EPS) secretion and heme production significantly improved, and anammox bacterial biomass increased to maximum levels. Moreover, the predominant genus of anammox bacteria was Candidatus Brocadia.

Inhibitory effect of LL-37 and human lactoferricin on growth and biofilm formation of anaerobes associated with oral diseases.

This study was conducted to evaluate the antimicrobial potential of the antimicrobial peptides (AMP) LL-37 and human Lactoferricin (LfcinH) on the planktonic growth and biofilm formation of oral pathogenic anaerobes related to caries and periodontitis. Multi-species bacterial suspensions of either facultative anaerobic bacteria (FAB: Streptococcus mutans, Streptococcus sanguinis, Actinomyces naeslundii) or obligate anaerobic bacteria (OAB: Veillonella parvula, Parvimonas micra, Fusobacterium nucleatum) were incubated with different concentrations of AMP solutions for 8 h. Planktonic growth was registered with an ATP-based cell viability assay for FAB and via plate counting for OAB. Biofilms were grown on ZrO2 discs for 4 days in a mixture of the multi-species bacterial suspensions and AMP solutions. Biofilm mass was quantified using a microtiter plate biofilm assay with crystal violet staining. An overall planktonic growth inhibition and biofilm mass reduction of FAB and OAB was registered for LL-37 and LfcinH. Significant inhibitory threshold concentrations of LL-37 were observed in all experiments (p < 0.0001). No significant threshold was observed for LfcinH. Biofilm mass of OAB was barely reduced by LfcinH. The complete mechanisms of the AMPs are not fully understood yet. While LL-37 shows promising features as potential therapeutic for biofilm-associated oral diseases, LfcinH seems unsuitable for this particular indication. For clinical AMP use, further investigations will be necessary.

Enzyme systems of thermophilic anaerobic bacteria for lignocellulosic biomass conversion.

Economic production of lignocellulose degrading enzymes for biofuel industries is of considerable interest to the biotechnology community. While these enzymes are widely distributed in fungi, their industrial production from other sources, particularly by thermophilic anaerobic bacteria (growth Topt ≥ 60 °C), is an emerging field. Thermophilic anaerobic bacteria produce a large number of lignocellulolytic enzymes having unique structural features and employ different schemes for biomass degradation, which can be classified into four systems namely; 'free enzyme system', 'cell anchored enzymes', 'complex cellulosome system', and 'multifunctional multimodular enzyme system'. Such enzymes exhibit high specific activity and have a natural ability to withstand harsh bioprocessing conditions. However, achieving a higher production of these thermostable enzymes at current bioprocessing targets is challenging. In this review, the research opportunities for these distinct enzyme systems in the biofuel industry and the associated technological challenges are discussed. The current status of research findings is highlighted along with a detailed description of the categorization of the different enzyme production schemes. It is anticipated that high temperature-based bioprocessing will become an integral part of sustainable bioenergy production in the near future.

Characterization of medical relevant anaerobic microorganisms by isothermal microcalorimetry.

Detection of anaerobe bacteria by culture methods requires appropriate media, special growth conditions, additional detection techniques and it typically takes several days. Therefore, anaerobes are often missed in patient specimens under routine culture conditions. Microcalorimetry may provide a simple and accurate real-time method for faster and better detection of anaerobes. An isothermal calorimeter which detect minimal changes of temperature over time was used for the calorimetric experiments. In order to find optimal growth conditions, seven reference or clinical strains of medical relevant anaerobe bacteria were tested under different circumstances. First, the strains were tested with different growth media. After determining the optimal medium for each strain, the gas phase was modified by adding 3 mL or 4 mL medium, to evaluate growth under conditions with less oxygen. Cooked Meat Medium was best supporting growth of the tested strains, including Cutibacterium acnes, Fusobacterium nucleatum, Finegoldia magna, Parvimonas micra, Bacteroides fragilis and Actinomyces odontolyticus, followed by thioglycolate. The best medium to detect Clostridioides difficile was H-Medium. All tested strains showed better growth in 4 mL medium than in 3 mL. The detection time ranged between 10 and 72 h. Our results demonstrated that the sensitivity and the detection time of anaerobe bacteria can be improved by isothermal calorimetry with optimization of growth conditions. Therefore, calorimetric detection, a practical, quick and easy-to-do method, has the potential to replace current microbiological methods.

Clinical utility of anaerobic culture of cerebrospinal fluid.

Anaerobic meningitis is a rare serious clinical condition which mainly affects vulnerable populations and patients with predisposing factors such as head trauma, prior neurosurgical procedures or implantable medical devices such as ventriculoperitoneal shunts or ventricular drains. In this study we retrieved data from aerobic and anaerobic cultures of cerebrospinal (CSF) or ventricular fluid ordered over a 5 year period at our institution. A total of 8868 aerobic and 594 anaerobic cultures were performed from 2013 to 2017. 24/594 (4%) anaerobic cultures from 14 patients were positive for anaerobes. Only 3 of those patients were diagnosed clinically with anaerobic meningitis, each with predisposing factors, while anaerobes (Cutibacterium acnes and Clostridium perfringens) recovered from the remaining 21 patients were regarded as contaminants. 129/8868 (1.45%) aerobic CSF cultures were positive for anaerobes. 120/129 (93%) cultures recovered C. acnes while non-C. acnes anaerobes were recovered in the remaining 9 cultures and were deemed to be contaminants. In the majority of situations, recovery of C. acnes from CSF or ventricular fluid was regarded as contamination. Our cohort included 18 patients with a ventriculoperitoneal shunt or ventricular drain, 17 of whom had C. acnes recovered from either aerobic or anaerobic culture, and 10 were treated with targeted antibiotics and surgical replacement of the shunt or drain. Anaerobic culture of the CSF or ventricular fluid aided in identification of two patients with anaerobic meningitis and an additional two patients with shunt infection. Anaerobe culture of CSF is important in identification of anaerobic meningitis, as growth of anaerobes other than C. acnes is rare from aerobic CSF culture.

Improvement of a disk diffusion method for antibiotic susceptibility testing of anaerobic bacteria. French recommendations revisited for 2020.

The disk diffusion test is very popular but for anaerobes the main pitfalls arise from the significant variation of diameters for an individual MIC and the weak correlation observed between the MIC's values and diameters zone that generates many major and very major errors. AIMS OF THE STUDY: without any change in the methodology and revisiting only new diameter breakpoints, we try to improve the previous French recommendations and therefore decrease number of errors by introducing recent EUCAST concepts such as ECOFF and ATU Zone. METHOD: MIC determination by agar dilution was done on 100 anaerobes against 6 antibiotics. Clinical categorization was based on EUCAST Breakpoints. Disk-diffusion method was realized on the same Brucella blood agar incubated in an anaerobic chamber. 550 categorizations by both methods could be done as amoxicillin was not tested on the 50 B. fragilis group. As anaerobic infections are severe and treated by antibiotics at higher dosage, we focus on resistance breakpoint to avoid mainly very major errors (VME). Distribution of inhibition zones for each MIC allow us to fix the zone diameter breakpoints. These results were matched to a large data on distribution of zone diameters for each antibiotic collected from two French hospitals from 1990 to 2005. As example for metronidazole and the B. fragilis group, we calculated the cut-off diameter (15 mm) from a wild type population, at a time when there was no resistance to this antibiotic and observed that it was identical to the diameter breakpoint for susceptibility. RESULTS: For an individual value of MIC, the distribution of diameters is wider for anaerobes especially for clindamycin and metronidazole. Using a 15 mm breakpoint for these two antibiotics limits dramatically the number of very major errors but slowly increases the number of major errors that could be overcome by MIC determination if inhibition zone is less than 15 mm. ATU zones (Area of technical uncertainty) were introduced for amoxicillin-clavulanate (17-20 mm), piperacillin-tazobactam (17-20 mm), imipenem (18-23 mm). Categorization inside the ATU requires MIC determination. Finally, out of 550 determinations, VME were observed in 1.45% of cases, an acceptable rate. CONCLUSION: in combination with introduction of ATU zones disk diffusion method allows to detect resistant strains with little MIC determinations and very major errors.

Microbial community dynamics during anaerobic co-digestion of corn stover and swine manure at different solid content, carbon to nitrogen ratio and effluent volumetric percentages.

The methane production and the microbial community dynamics of thermophilic anaerobic co-digestion (AD) of corn stover, swine manure and effluent were conducted at total solid (TS) content of 5%, 10% and 15%, the carbon to nitrogen ratio (C/N) of 20, 30 and 40 and the effluent volumetric percentage (EVP) of 20%, 40% and 60%. For batches with 5% TS, the highest methane yield of 238.5-283.1 mL g-1 volatile solid (VS) and the specific methane productivity of 138.5-152.2 mL g-1 initial VS were obtained at the C/N ratios of 20 and 30. For the mixtures with 10% and 15% TS, the highest methane yield was 341.9 mL g-1 VS and 351.2 mL g-1 VS, respectively, when the C/N ratio of 20% and 60% EVP conditions were maintained. Co-digestion of swine manure with corn stover caused an obvious shift in microbial population, in which the archaeal population changed from 0.3% to 2.8% and the bacterial community changed from 97.2% to 99.7%. The experimental batches with the highest relative abundance of the archaeal population (2.00% of total microbial population for 5% TS, 1.74% for 10% TS and 2.76% for 15% TS) had the highest rate of methanogenesis subsequently enhancing methane production (283.08 mL g-1 VS for 5% TS, 341.91 mL g-1 VS for 10% TS and 351.23 mL g-1 VS for 15% TS). The results of microbiome analysis enabled understanding the key populations in biomethane generation.

Disruption of Cross-Feeding Inhibits Pathogen Growth in the Sputa of Patients with Cystic Fibrosis.

A critical limitation in the management of chronic polymicrobial infections is the lack of correlation between antibiotic susceptibility testing (AST) and patient responses to therapy. Underlying this disconnect is our inability to accurately recapitulate the in vivo environment and complex polymicrobial communities in vitro However, emerging evidence suggests that, if modeled and tested accurately, interspecies relationships can be exploited by conventional antibiotics predicted to be ineffective by standard AST. As an example, under conditions where Pseudomonas aeruginosa relies on cocolonizing organisms for nutrients (i.e., cross-feeding), multidrug-resistant P. aeruginosa may be indirectly targeted by inhibiting the growth of its metabolic partners. While this has been shown in vitro using synthetic bacterial communities, the efficacy of a "weakest-link" approach to controlling host-associated polymicrobial infections has not yet been demonstrated. To test whether cross-feeding inhibition can be leveraged in clinically relevant contexts, we collected sputa from cystic fibrosis (CF) subjects and used enrichment culturing to isolate both P. aeruginosa and anaerobic bacteria from each sample. Predictably, both subpopulations showed various antibiotic susceptibilities when grown independently. However, when P. aeruginosa was cultured and treated under cooperative conditions in which it was dependent on anaerobic bacteria for nutrients, the growth of both the pathogen and the anaerobe was constrained despite their intrinsic antibiotic resistance profiles. These data demonstrate that the control of complex polymicrobial infections may be achieved by exploiting obligate or facultative interspecies relationships. Toward this end, in vitro susceptibility testing should evolve to more accurately reflect in vivo growth environments and microbial interactions found within them.IMPORTANCE Antibiotic efficacy achieved in vitro correlates poorly with clinical outcomes after treatment of chronic polymicrobial diseases; if a pathogen demonstrates susceptibility to a given antibiotic in the lab, that compound is often ineffective when administered clinically. Conversely, if a pathogen is resistant in vitro, patient treatment with that same compound can elicit a positive response. This discordance suggests that the in vivo growth environment impacts pathogen antibiotic susceptibility. Indeed, here we demonstrate that interspecies relationships among microbiotas in the sputa of cystic fibrosis patients can be targeted to indirectly inhibit the growth of Pseudomonas aeruginosa The therapeutic implication is that control of chronic lung infections may be achieved by exploiting obligate or facultative relationships among airway bacterial community members. This strategy is particularly relevant for pathogens harboring intrinsic multidrug resistance and is broadly applicable to chronic polymicrobial airway, wound, and intra-abdominal infections.

Microbiological profile of chronic osteomyelitis with special reference to anaerobic osteomyelitis in a tertiary care hospital of coastal Karnataka.

Chronic osteomyelitis is a relapsing, persistent, low-grade inflammation of bone caused by various infectious agents. The present study, conducted over a two-year period, on specimens received from cases of chronic osteomyelitis was, to determine the frequency of isolation of aerobic and anaerobic bacteria and to analyse their antimicrobial susceptibility pattern. Specimens were processed for Gram stain, aerobic and anaerobic culture, and were identified according to standard techniques. Significant growth was observed in 102/204 specimens, in which aerobic growth was observed in 62 (60.8%) and anaerobic in 40 (39.2%). Resistance to metronidazole and clindamycin was observed in 6.7% and 30% of the anaerobic isolates, respectively. None of these were resistant to meropenem. A significant proportion of anaerobic isolates were found to be resistant to commonly used empirical drugs, such as clindamycin, thus necessitating a need for routine anaerobic susceptibility testing.

Biotreatment of high-salinity wastewater: current methods and future directions.

Saline wastewaters are usually generated by various industries, including the chemical, pharmaceutical, agricultural, and aquacultural industries. The discharge of untreated high-salinity wastewater may cause serious environmental pollution and damage the aquatic, terrestrial, and wetland ecosystems. For many countries, the treatment of saline wastewater has become an important task. Generally, saline wastewaters are treated through physical and chemical methods. However, these traditional techniques are associated with higher treatment costs and the generation of byproducts. In contrast, biotreatment techniques are environmentally friendly and inexpensive. This review highlights the sources and environmental concerns of high-salinity wastewater and illustrates the latest problems and solutions to the use of biological approaches for treating saline wastewater. Although high salinity may inhibit the effectiveness of aerobic and anaerobic biological wastewater treatment methods, such strategies as selecting salt-adapted microorganisms capable of degrading pollutants with tolerance to high salinity and optimizing operating conditions can be effective. This mini-review may serve as a reference for future efforts to treat high-salinity wastewater.

Improved Isolation of Uncultured Anaerobic Bacteria using Medium Prepared with Separate Sterilization of Agar and Phosphate.

We previously demonstrated that a simple modification in the preparation of agar media, i.e., autoclaving phosphate and agar separately (termed the "PS protocol"), improved the culturability of aerobic microorganisms by reducing the generation of reactive oxygen species. We herein investigated the effects of the PS protocol on the cultivation of anaerobic microorganisms using sludge from a wastewater treatment system as a microbial source. The application of the PS protocol increased colony numbers and the frequency of phylogenetically novel isolates under aerobic, nitrate reduction, and fermentation conditions. The PS protocol is useful for isolating both aerobic and anaerobic microorganisms.

Impact of Simulated Martian Conditions on (Facultatively) Anaerobic Bacterial Strains from Different Mars Analogue Sites.

Five bacterial (facultatively) anaerobic strains, namely Buttiauxella sp. MASE-IM-9, Clostridium sp. MASE-IM-4, Halanaerobium sp. MASE-BB-1, Trichococcus sp. MASE-IM-5, and Yersinia intermedia MASE-LG-1 isolated from different extreme natural environments were subjected to Mars relevant environmental stress factors in the laboratory under controlled conditions. These stress factors encompassed low water activity, oxidizing compounds, and ionizing radiation. Stress tests were performed under permanently anoxic conditions. The survival rate after addition of sodium perchlorate (Na-perchlorate) was found to be species-specific. The inter-comparison of the five microorganisms revealed that Clostridium sp. MASE-IM-4 was the most sensitive strain (D10-value (15 min, NaClO4) = 0.6 M). The most tolerant microorganism was Trichococcus sp. MASE-IM-5 with a calculated D10-value (15 min, NaClO4) of 1.9 M. Cultivation in the presence of Na-perchlorate in Martian relevant concentrations up to 1 wt% led to the observation of chains of cells in all strains. Exposure to Na-perchlorate led to a lowering of the survival rate after desiccation. Consecutive exposure to desiccating conditions and ionizing radiation led to additive effects. Moreover, in a desiccated state, an enhanced radiation tolerance could be observed for the strains Clostridium sp. MASE-IM-4 and Trichococcus sp. MASE-IM-5. These data show that anaerobic microorganisms from Mars analogue environments can resist a variety of Martian-simulated stresses either individually or in combination. However, responses were species-specific and some Mars-simulated extremes killed certain organisms. Thus, although Martian stresses would be expected to act differentially on microorganisms, none of the expected extremes tested here and found on Mars prevent the growth of anaerobic microorganisms.

Inhibition of anaerobic ammonium oxidation (anammox) bacteria by addition of high and low concentrations of chloramphenicol and comparison of attached- and suspended-growth.

Inhibition of anammox activities was tested with two ranges of chloramphenicol (CAP) concentration (5, 10, 20, 50, and 100 mg L-1) and (100, 500, and 1000 µg L-1). In a short-term study, strong inhibition of activity was dependent of CAP concentration in both attached-growth (SBR-A) and suspended-growth (SBR-S) systems. The activities of attached-growth cultures at all CAP concentrations were reversible after 1 day, while activities for suspended-growth cultures were only gradually reversible dependent on the CAP concentrations. In long-term studies with daily additions of 6 mg L-1 CAP, the anammox activity on day 41 in SBR-A had decreased to 18% baseline (SAA reduced from 0.528 to 0.096 mg N mg-1 VSS d-1). More rapid reduction of anammox activity was observed in SBR-S, down to 17% baseline after only 27 days (SAA decreased from 0.576 to 0.096 mg N mg-1 VSS d-1). Inhibition was irreversible in both SBR-S and SBR-A after the long-term study. With lower CAP additions (100-1000 µg L-1), the activities in both reactors were stable during daily CAP addition for two weeks. Attached-growth cultures tended to be more tolerant of CAP addition than suspended-growth cultures. Both un-competitive and non-competitive models could be used to compare anammox activities with the higher CAP concentrations. The SAAmax [fx] (the maximum specific anammox activity) and hKi (the inhibition constant) of SBR-A were 0.48 mg N mg-1 VSS d-1 and 98.3 mg L-1, respectively. The SAAmax[fx] and Ki of SBR-S were 1.25 mg N mg-1 VSS d-1and 71.1 mg L-1, respectively.

Comparative analysis of the effects of five soil fumigants on the abundance of denitrifying microbes and changes in bacterial community composition.

Soil fumigation is currently the most effective method for controlling soil-borne pests and diseases in high-value crops. To better understand the effect of chloropicrin (CP), dazomet (DZ), dimethyl disulfide (DMDS), allyl isothiocyanate (AITC) and 1,3-dichloropropene (1,3-D) fumigants on soil microorganisms, this study monitored changes in the diversity and community composition of soil bacteria involved in denitrification using real-time PCR and high-throughput gene sequencing techniques. These five fumigants significantly decreased the bacterial population size in some phyla including Proteobacteria, Chloroflexi and Acidobacteria, and increased the bacterial population size in other phyla such as Firmicutes, Gemmatimonadetes, Actinobacteria, Verrucomicrobia, Saccharibacteria and Parcubacteria. Although bacterial diversity declined after CP fumigation, it was briefly stimulated by the other four fumigants. Meanwhile, all five fumigants temporarily decreased populations of denitrifying bacteria containing the napA, narG, nirS or nirK enzyme-encoding genes. Denitrifiers bearing the cnorB, qnorB or nosZ genes were relatively stable following DZ and DMDS fumigation. However, cnorB and nosZ decreased initially following CP, AITC and 1,3-D fumigation. Simultaneously, the abundance of qnorB significantly increased in AITC and 1,3-D fumigated soils. These results showed that soil fumigation significantly shifted the abundance and community structure of denitrifying bacteria. This study will help to predict the response of different phyla of denitrifying bacteria to soil fumigation.

Intracellular offspring released from SFB filaments are flagellated.

The gut commensal segmented filamentous bacterium (SFB) attaches to the ileal epithelium and potently stimulates the host immune system. Using transmission electron microscopy (TEM), we show that mouse and rat SFB are flagellated above the concave tip at the unicellular intracellular offspring (IO) stage and that flagellation occurs prior to full IO differentiation and release of IOs from SFB filaments. This finding adds a missing link to the SFB life cycle.