Microbial communities acclimate to recurring changes in soil redox potential status

Rapidly fluctuating environmental conditions can significantly stress organisms, particularly when fluctuations cross thresholds of normal physiological tolerance. Redox potential fluctuations are common in humid tropical soils, and microbial community acclimation or avoidance strategies for survival will in turn shape microbial community diversity and biogeochemistry. To assess the extent to which indigenous bacterial and archaeal communities are adapted to changing in redox potential, soils were incubated under static anoxic, static oxic or fluctuating redox potential conditions, and the standing (DNA‐based) and active (RNA‐based) communities and biogeochemistry were determined. Fluctuating redox potential conditions permitted simultaneous CO₂ respiration, methanogenesis, N₂O production and iron reduction. Exposure to static anaerobic conditions significantly changed community composition, while 4‐day redox potential fluctuations did not. Using RNA : DNA ratios as a measure of activity, 285 taxa were more active under fluctuating than static conditions, compared with three taxa that were more active under static compared with fluctuating conditions. These data suggest an indigenous microbial community adapted to fluctuating redox potential.     

Comparison of Methods for Isolation of Anaerobic Bacteria from Clinical Specimens

Five different anaerobic culture methods and several different media were compared for their ability to recover anaerobes from clinical specimens. Specimens were obtained from patients with documented infections, avoiding contamination with normal flora, and immediately placed in an anaerobic transporter. Each specimen was cultured by all methods and on all the various media. The comparative data indicate that anaerobic jars (GasPak and evacuation-replacement types) are just as effective in the recovery of clinically significant anaerobes as the more complex roll-tube and chamber methods employing prereduced media. Liquid media were disappointing as a "back-up" system but chopped-meat glucose was superior to two thioglycolate formulations. Growth of all anaerobes was poorer on selective media, but these media were very helpful in the workup of specimens containing mixed growth of anaerobic and facultative organisms. A variety of different anaerobes was isolated, but no very fastidious or extremely oxygen-sensitive organisms were recovered. This suggests that such organisms may not play a significant role in causing clinical infections.     

Targeted genomic detection of biosynthetic pathways: anaerobic production of hopanoid biomarkers by a common sedimentary microbe

The lipid biomarker principle requires that preservable molecules (molecular fossils) carry specific taxonomic, metabolic, or environmental information. Historically, an empirical approach was used to link specific taxa with the compounds they produce. The lipids extracted from numerous, but randomly cultured species provided the basis for the interpretation of biomarkers in both modern environments and in the geological record. Now, with the rapid sequencing of hundreds of microbial genomes, a more focused genomic approach can be taken to test phylogenetic patterns and hypotheses about the origins of biomarkers. Candidate organisms can be selected for study on the basis of genes that encode proteins fundamental to the synthesis of biomarker compounds. Hopanoids, a class of pentacyclic triterpenoid lipid biomarkers, provide an illustrative example. For many years, interpretations of biomarker data were made with the assumption that hopanoids are produced only by aerobic organisms. However, the recent discovery of ¹³C‐depleted hopanoids in environments undergoing anaerobic methane oxidation and in enrichment cultures of anammox planctomycetes indicates that some hopanoids are produced anaerobically. To further examine the potential distribution of hopanoid biosynthesis by anaerobes, we searched publicly available genomic databases for the presence of squalene‐hopene cyclase genes in known obligate or facultative anaerobes. Here we present evidence that Geobacter sulfurreducens, Geobacter metallireducens, and Magnetospirillum magnetotacticum, all bacteria common in anoxic environments, have the appropriate genes for hopanoid biosynthesis. We further show that these data accurately predict that G. sulfurreducens does produce a variety of complex hopanoids under strictly anaerobic conditions in pure culture.     

严格厌氧菌铁氧还蛋白的研究进展

铁氧还蛋白(ferredoxin,Fd)是一类含有铁硫簇的小分子蛋白质,广泛存在于自然界中,参与生物体内的呼吸、发酵、固氮、二氧化碳固定和制氢等生理过程.Fd对于严格厌氧的细菌尤为重要,是因为这类细菌的能量代谢高度依赖于低氧化还原电势的生物组分,而Fd能够利用铁硫中心灵活调节其氧还电势,适应低电势需求.本文选取厌氧细菌...     

Lipopolysaccharides of three classes of supersensitive mutants of Salmonella typhimurium

Abstract Cresyl violet acetate was found to be an appropriate redox-indicator dye in anaerobic culture media with low redox potentials. Low redox potentials ( E '_h−250 to −300 mV) in media were obtained by addition of dithiothreitol (DTT). DTT and cresyl violet acetate in media did not influence the total number of anaerobes cultured from human feces.     

Rumen methanogens: a review

The Methanogens are a diverse group of organisms found in anaerobic environments such as anaerobic sludge digester, wet wood of trees, sewage, rumen, black mud, black sea sediments, etc which utilize carbon dioxide and hydrogen and produce methane. They are nutritionally fastidious anaerobes with the redox potential below −300 mV and usually grow at pH range of 6.0–8.0 [1]. Substrates utilized for growth and methane production include hydrogen, formate, methanol, methylamine, acetate, etc. They metabolize only restricted range of substrates and are poorly characterized with respect to other metabolic, biochemical and molecular properties.     

Production and properties of reaginic antibodies in rabbits infected with Clonorchis sinensis or Schistosoma japonicum

The production of reaginic antibodies detected by homologous passive cutaneous anaphylaxis (PCA) was demonstrated in all rabbits experimentally infected with either Clonorchis sinensis or Schistosoma japonicum. The antibodies appeared in the sera as early as 3 weeks after exposure and persisted with relatively high titers for at least 7 weeks in some animals. The antisera of rabbits infected with C. sinensis were found to be cross reactive against heterologous trematode antigens, although PCA titers were less than 3% of the titer by the homologous antigen; no cross reaction was observed between S. japonicum antiserum and the heterologous antigens. PCA activity of the antisera was completely destroyed in some samples by heat treatment at 56 C for 2 hr, but partially in the others even after heating for 6 hr. However, the physicochemical properties of these antibodies were analogous to human IgE; the PCA activity was eluted with 0.035 M phosphate buffer from a DEAE-cellulose column and recovered in the ascending portion of the IgG peak by Sephadex G-200 gel filtration. PCA activity was found in a β region in preparative agar electrophoresis.     

Host factors predisposing to anaerobic infections

Abstract Factors that predispose to infection in general, of course, may predispose to infection with anaerobes. Included in this category are diabetes mellitus, neutropenia, hypogammaglobulinaemia, malignancy, splenectomy, collagen vascular disease, cytotoxic drug therapy, corticosteroid therapy and other immunosuppression. However, even with these situations there may be certain, more specific, associations: anaerobic cholecystitis and anaerobic osteomyelitis in diabetics, neutropenic colitis, and the increased incidence of local anaerobic infections associated with carcinoma of the lung, colon and uterus. Conditions that lead to decreased redox potential more specifically predispose to infection with anaerobes. Included in this category are obstruction and stasis, tissue anoxia, tissue destruction, vascular insufficiency, prior aerobic infection, burns, foreign body implantation, and calcium salts in a wound (in association with fractures). Other specific clinical situations that predispose to anaerobic infections include leukaemia; oral, gastrointestinal, and female pelvic surgery; trauma at other sites; childbirth; aspiration pneumonia; human and animal bites; and therapy with agents with poor activity against anaerobes (e.g. aminoglycosides, quinolones). AIDS patients appear to be predisposed to severe periodontal disease and its complications.     

Anaerobic Bacteriology in 75 Cases of Thoracic Empyema in Sofia,Bulgaria

The aim of this study was to evaluate the prevalence of anaerobes in patients with thoracic empyema over a period of 30 months and to assess the susceptibility of the isolates to penicillin, clindamycin and metronidazole. Seventy-nine pleural fluid specimens were obtained from 75 adult patients with empyema. Anaerobic isolates were identified by Crystal anaerobes identification system and routine methods. Susceptibility testing was conducted using broth microdilution method and limited agar dilution test. Anaerobic bacteria were found in 50 (66.7%) of the patients and included 96 isolates representing 16 genera. The predominant Gram-positive anaerobes were Peptostreptococcus species (19 isolates) and Streptococcus intermedius (10), and the commonest Gram-negative species were Fusobacterium nuleatum (13),Fusobacterium necrophorum (6) and Prevotella inermedia (3). From two to four anaerobes per specimen were present in 57.4% of the specimens yielding anaerobic bacteria. The susceptibility of the Gram-negative anaerobic isolates to penicillin and that of the Gram-positive anaerobes to clindamyin and metronidazole were unpredictable. The variable resistance patterns among anaerobes and the predominance of mixed anaerobic infections highlight the role of the anaerobic dignostics in case of serious pleuropulmonary diseases.     

Assessment of the Microbial Constituents of the Home Environment of Individuals with Cystic Fibrosis (CF) and Their Association with Lower Airways Infections

Introduction

Cystic fibrosis (CF) airways are colonized by a polymicrobial community of organisms, termed the CF microbiota. We sought to define the microbial constituents of the home environment of individuals with CF and determine if it may serve as a latent reservoir for infection.

Methods

Six patients with newly identified CF pathogens were included. An investigator collected repeat sputum and multiple environmental samples from their homes. Bacteria were cultured under both aerobic and anaerobic conditions. Morphologically distinct colonies were selected, purified and identified to the genus and species level through 16S rRNA gene sequencing. When concordant organisms were identified in sputum and environment, pulsed-field gel electrophoresis (PFGE) was performed to determine relatedness. Culture-independent bacterial profiling of each sample was carried out by Illumina sequencing of the V3 region of the 16s RNA gene.

Results

New respiratory pathogens prompting investigation included: Mycobacterium abscessus(2), Stenotrophomonas maltophilia(3), Pseudomonas aeruginosa(3), Pseudomonas fluorescens(1), Nocardia spp.(1), and Achromobacter xylosoxidans(1). A median 25 organisms/patient were cultured from sputum. A median 125 organisms/home were cultured from environmental sites. Several organisms commonly found in the CF lung microbiome were identified within the home environments of these patients. Concordant species included members of the following genera: Brevibacterium(1), Microbacterium(1), Staphylococcus(3), Stenotrophomonas(2), Streptococcus(2), Sphingomonas(1), and Pseudomonas(4). PFGE confirmed related strains (one episode each of Sphinogomonas and P. aeruginosa) from the environment and airways were identified in two patients. Culture-independent assessment confirmed that many organisms were not identified using culture-dependent techniques.

Conclusions

Members of the CF microbiota can be found as constituents of the home environment in individuals with CF. While the majority of isolates from the home environment were not genetically related to those isolated from the lower airways of individuals with CF suggesting alternate sources of infection were more common, a few genetically related isolates were indeed identified. As such, the home environment may rarely serve as either the source of infection or a persistent reservoir for re-infection after clearance.     

Antarctic strict anaerobic microbiota from <Emphasis Type="Italic">Deschampsia antarctica</Emphasis> vascular plants rhizosphere reveals high ecology and biotechnology relevance

The Antarctic soil microbial community has a crucial role in the growth and stabilization of higher organisms, such as vascular plants. Analysis of the soil microbiota composition in that extreme environmental condition is crucial to understand the ecological importance and biotechnological potential. We evaluated the efficiency of isolation and abundance of strict anaerobes in the vascular plant Deschampsia antarctica rhizosphere collected in the Antarctic’s Admiralty Bay and associated biodiversity to metabolic perspective and enzymatic activity. Using anaerobic cultivation methods, we identified and isolated a range of microbial taxa whose abundance was associated with Plant Growth-Promoting Bacteria (PGPB) and presences were exclusively endemic to the Antarctic continent. Firmicutes was the most abundant phylum (73 %), with the genus Clostridium found as the most isolated taxa. Here, we describe two soil treatments (oxygen gradient and heat shock) and 27 physicochemical culture conditions were able to increase the diversity of anaerobic bacteria isolates. Heat shock treatment allowed to isolate a high percentage of new species (63.63 %), as well as isolation of species with high enzymatic activity (80.77 %), which would have potential industry application. Our findings contribute to the understanding of the role of anaerobic microbes regarding ecology, evolutionary, and biotechnological features essential to the Antarctic ecosystem.     

The role of auxiliary oxidants in the maintenance of a balanced redox poise for photosynthesis in bacteria

Carotenoid absorbance changes were used to monitor the development of membrane potential in intact cell suspensions of Rhodopseudomonas capsulata strain N22. Low concentrations of phenazine methosulphate almost completely inhibited the generation of membrane potential in the light by anaerobic cells. The light-dependent reactions were restored by addition of either trimethylamine N-oxide, dimethylsulphoxide, nitrous oxide, or oxygen. In Rhodopseudomonas capsulata strain N22 DNAR⁺ addition of nitrate was also effective. The inhibition by phenazine methosulphate and restoration by auxiliary oxidant were observed in the presence of sufficient rotenone to block NADH dehydrogenase or with low concentrations of uncoupling agent to dissipate the membrane potential under dark, anaerobic conditions. It is suggested that in intact cells of these organisms there are mechanisms which operate to maintain the electron-transport chain at an optimal redox poise for efficient photosynthesis. Phenazine methosulphate perturbs the optimal redox poise by hastening equilibrium of the photosynthetic electron-transport chain with low-potential couples in the cell. The addition of auxiliary oxidants restores the optimal redox poise. This suggests a role in photosynthesis for the pathways of respiratory electron flow to nitrate, nitrous oxide, trimethylamine N-oxide/dimethylsulphoxide and oxygen.     

Oxygen metabolism,oxidative stress and acid-base physiology of dental plaque biofilms

Dental plaque is a natural biofilm which has been a focus of attention for many years because of its known roles in caries and periodontal diseases. Acid production by plaque bacteria leads to the erosion of tooth mineral in caries, and the cariogenicity of plaque is related to population levels of acid-tolerant organisms such as mutants streptococci. However, the biofilm character of plaque allows for survival of a diverse flora, including less acid-tolerant organisms, some of which can produce ammonia from arginine or urea to counter acidification. Plaque is often considered to be relatively anaerobic. However, evidence is presented here that both supragingival and subgingival plaque have active oxygen metabolism and that plaque bacteria, including anaerobes, have developed defenses against oxidative stress. Even in subgingival plaque associated with periodontitis, measured residual oxygen levels are sufficient to allow for oxygen metabolism by organisms considered to be extremely anaerobic such asTreponema denticola, which metabolizes oxygen by means of NADH oxidases and produces the protective enzymes superoxide dismutase and NADH peroxidase. The finding that plaque bacteria produce a variety of protective enzymes is a good indicator that oxidative stress is a part of their everyday life. The biofilm character of plaque allows for population diversity and coexistence of aerobes, anaerobes and microaerophiles. Overall, agents that affect oxidative metabolism offer possibilities for reducing the pathogenic activities of plaque.     

Suppurative Thyroiditis: An Unusual Case Caused by Actinomyces naeslundi

A case of suppurative thyroiditis due to A.naeslundi is recorded. The clinical features (including the difficulty in establishing a clinical diagnosis) have been noted. This is the first instance of A.naeslundi being considered the etiological agent of actinomycosis of the thyroid. It is also the first report incriminating A.naeslundi as a pathogen, since up to now it was considered only a saprophyte.The etiological role of A.naeslundi in this case of suppurative thyroiditis is strongly supported by the following findings:1. A.naeslundi was isolated without the presence of other pathogenic micro-organisms.2. A sulphur granule was demonstrated in the caseous pus after incision of the abscess.3. There was a favourable response to specific antibiotic therapy.     

Studies on the cloacal flora of three species of free-living British reptile

Cloacal swabs from seven free-living Grass snakes ( Nutrix natrix ), six adders ( Vipera berus ) and 17 slow-worms ( Anguis fragilis ) were cultured for aerobic and anaerobic bacteria. The number of species isolated was 18, 16 and 29, respectively, and the most prevalent organisms were entero-cocci (Grass snakes) and Escherichia coli (adders and slow-worms). There were surprisingly few anaerobes. Bacteria with zoonotic potential included Arizona (Salmonella) arizonae from four slow-worms and Yersinia pseudotuberculosis from an adder.     

Anaerobic methane oxidation potential and bacteria in freshwater lakes: Seasonal changes and the influence of trophic status

Nitrite-dependent anaerobic methane oxidation (n-damo), mainly carried out by n-damo bacteria, is an important pathway for mitigating methane emission from freshwater lakes. Although n-damo bacteria have been detected in a variety of freshwater lakes, their potential and distribution, and associated environmental factors, remain unclear. Therefore, the current study investigated the potential and distribution of anaerobic methanotrophs in sediments from Erhai Lake and Dianchi Lake, two adjacent freshwater lakes in the Yunnan Plateau with different trophic status. Both lakes showed active anaerobic methane oxidation potential and harbored a high density of n-damo bacteria. Based on the n-damo pmoA gene, sediment n-damo bacterial communities mainly consisted of Candidatus Methylomirabils oxyfera and Candidatus Methylomirabils sinica, as well as novel n-damo organisms. Sediment anaerobic methane oxidation potential and the n-damo bacterial community showed notable differences among seasons and between lakes. The environmental variables associated with lake trophic status (e.g. total nitrogen, ammonia nitrogen, nitrate nitrogen, and total organic carbon) might have significant impacts on the anaerobic methane oxidation potential, as well as the abundance and community structure of n-damo bacteria. Therefore, trophic status could determine the n-damo process in freshwater lake sediment.     

Responses of the Anaerobic Bacterial Community to Addition of Organic C in Chromium(VI)- and Iron(III)-Amended Microcosms

Chromium (VI) is toxic to microorganisms and can inhibit the biodegradation of organic pollutants in contaminated soils. We used microcosms amended with either glucose or protein (to drive bacterial community change) and Fe(III) (to stimulate iron-reducing bacteria) to study the effect of various concentrations of Cr(VI) on anaerobic bacterial communities. Microcosms were destructively sampled based on microbial activity (measured as evolution of CO₂) and analyzed for the following: (i) dominant bacterial community by PCR-denaturing gradient gel electrophoresis (DGGE) of the 16S rRNA gene; (ii) culturable Cr-resistant bacteria; and (iii) enrichment of iron-reducing bacteria of the Geobacteraceae family by real-time PCR. The addition of organic C stimulated the activities of anaerobic communities. Cr(VI) amendment resulted in lower rates of CO₂ production in glucose microcosms and a slow mineralization phase in protein-amended microcosms. Glucose and protein amendments selected for different bacterial communities. This selection was modified by the addition of Cr(VI), since some DGGE bands were intensified and new bands appeared in Cr(VI)-amended microcosms. A second dose of Cr(VI), added after the onset of activity, had a strong inhibitory effect when higher levels of Cr were added, indicating that the developing Cr-resistant communities had a relatively low tolerance threshold. Most of the isolated Cr-resistant bacteria were closely related to previously studied Cr-resistant anaerobes, such as Pantoea, Pseudomonas, and Enterobacter species. Geobacteraceae were not enriched during the incubation. The studied Cr(VI)-contaminated soil contained a viable anaerobic bacterial community; however, Cr(VI) altered its composition, which could affect the soil biodegradation potential.     

Retrospective Analysis of Anaerobic Bacterial Findings at a University Hospital in Rosario,Argentina from 1995 to 1997

Even though considerable progress has been made during recent years in anaerobic bacteriology, processing of anaerobes is, for small laboratories, a challenge. In order to evaluate all steps of anaerobic processing, we retrospectively analysed indications for anaerobic culture, the proportion of specimens yielding anaerobes on group and genus level and the distribution according to site of infection. We recovered anaerobes in 41 of 143 specimens. Twenty-five specimens with a positive finding for anaerobes were processed on clinicians' request and 16 were tested on the microbiologist's initiative. Anaerobes were mostly recovered from soft tissue infections, blood culture and intra-abdominal specimens. The most frequently isolated genera were Clostridium and Porphyromonas. Our results suggest the necessity of discussion between microbiologists and clinicians in order to analyse procedures, provide guidelines and consider the advantage and limitations of anaerobic bacteriology.     

Positive correlation between the levels of natural killer cells and the in vivo resistance to syngeneic tumor transplants as influenced by various routes of administration of Corynebacterium parvum bacteria.

Depending on the route of administration, heat-killed Corynebacterium parvum (C. parvum) bacteria caused an increase or decrease of natural killer (NK)-cell activity in mice. We used a syngeneic tumor with known susceptibility to NK lysis in vitro. The tumor was administered to mice whose NK levels had been increased or decreased by previous inoculations of C. parvum bacteria. A positive correlation between changes in NK-cell activity as measured in vitro and changes in tumor resistance as measured in vivo was observed. Additional evidence was provided in support of the view that NK cells may play an important role in resistance to tumor growth. The route of administration of C. parvum was considered important for protection against tumor growth.     

Regulation of cyclic photophosphorylation in Rhodospirillum rubrum by the redox state of nicotinamide-adenine dinucleotide

We have investigated the effect of the redox state of added NAD on the rates of anaerobic cyclic photophosphorylation which are supported by membrane vesicles isolated from Rhodospirillum rubrum. As the redox potential of NAD was lowered, the activity decreased according to a typical potentiometric titration. The Nernst plot showed an apparent midpoint potential (E′_o) of ?350 mV and had a slope which corresponded to a two-electron transition. Besides, an almost identical potentiometric relationship was found to exist between the extent of light-elicited ATP formation in anaerobic suspensions of intact R. rubrum cells and the redox potential of intracellular NAD. These results suggest that physiological photophosphorylation in R. rubrum requires the oxidized form of a membrane-bound constituent (E′_o = ?350 mV) whose redox state is controlled by the redox state of cytoplasmic NAD.