Isolation and characterization of a thermophilic, acetate-utilizing methanogenic bacterium

Abstract A thermophilic acetate-decarboxylating methanogenic bacterium was isolated from a laboratory-scale 60°C sludge digestor. Cells form straight filaments with flat to blunted ends normally consisting of 2–3 cells held together by a sheath-like outer cell wall. The organism uses acetate, H₂-CO₂ and formate for methanogenesis and growth. With acetate as the sole methanogenic substrate, almost all of the radioactivity from methyl-labelled acetate appeared as methane. Acetate was converted to methane in equimolar amounts with a doubling time of 3 days.     

The first methane-oxidizing bacterium from the upper mixing layer of the deep ocean:Methylomonas pelagica sp. nov.

Methane enrichment of twenty-three 100-ml portions of seawater from three stations in the Sargasso Sea yielded the same obligate type I methanotroph. It is pigmented white, requires NaCl, grows well in seawater with either methane or methanol, but not on other C₁ compounds nor on C–C bonded organic matter, and it uses either ammonia or nitrate but not dinitrogen as a nitrogen source. Formaldehyde is produced in marked amounts from methanol. Growth occurs at 20° and 30°C but not at 10°C and is inhibited in natural sunlight. Representative isolates from each hydrographic station assimilate one-carbon units via the ribulose monophosphate pathway for formaldehyde fixation, and have a DNA base composition of 49 mol% guanine plus cytosine. The type strain, NCMB 2265, has been namedMethylomonas pelagica sp. nov. This upper ocean methanotroph may obtain its C₁ substrates in situ from particles of algal debris that become anoxic, ferment, and accumulate in the thermocline to form a false benthos.     

Isolation and characterization of a marine methanogenic bacterium from the biofilm of a shiphull in Los Angeles harbor

A marine mesophilic, irregular coccoid methanogen, which shows close resemblance toMethanococcus sp., was isolated from the biofilm of shiphulls docked in Los Angeles harbor. Hydrogen plus carbon dioxide or formate served as substrates for methanogenesis in a mineral salt medium. The isolate did not use acetate and methanol as sole source of carbon and energy. The organism had an optimal pH range of 6.8–7.0 and a temperature optimum of 37°C. Elevated levels of sodium chloride were required for optimum growth. Optimum levels of total sulfide and magnesium chloride for growth were 1.0mm and 10mm respectively. The isolate used ammonia as nitrogen source. The concentration of 30mm ammonium chloride supported maximum growth of the isolate.     

Enrichment and characterization of an anammox bacterium from a rotating biological contactor treating ammonium-rich leachate

Anaerobic ammonium oxidation with nitrite to N2 (anammox) is a recently discovered microbial reaction with interesting potential for nitrogen removal from wastewater. We enriched an anammox culture from a rotating disk contactor (near K?lliken, Switzerland) that was used to treat ammonium-rich leachate with low organic carbon content. This enrichment led to a relative population size of 88% anammox bacteria. The microorganism carrying out the anammox reaction was identified by analysis of the 16S rDNA sequence and by fluorescence in situ hybridization (FISH) with 16S-rRNA-targeting probes. The percentage sequence identity between the 16S rDNA sequences of the K?lliken anammox organism and the archetype anammox strain Candidatus Brocadia anammoxidans was 90.9%, but between 98.5 and 98.9% with Candidatus Kuenenia stuttgartiensis, an organism identified in biofilms by molecular methods. The K?lliken culture catalyzed the anaerobic oxidation of ammonium with nitrite in a manner seemingly identical to that of Candidatus B. anammoxidans, but exhibited higher tolerance to phosphate (up to 20 mM) and to nitrite (up to 13 mM) and was active at lower cell densities. Anammox activity was observed only between pH 6.5 and 9, with an optimum at pH 8 and a temperature optimum at 37 degrees C. Hydroxylamine and hydrazine, which are intermediates of the anammox reaction of Candidatus B. anammoxidans, were utilized by the K?lliken organisms, and approximately 15% of the nitrite utilized during autotrophic growth was converted to nitrate. Electron microscopy showed a protein-rich region in the center of the cells surrounded by a doughnut-shaped region containing ribosomes and DNA. This doughnut-shape region was observed with FISH as having a higher fluorescence intensity. Similar to Candidatus B. anammoxidans, the K?lliken anammox organism typically formed homogenous clusters containing up to several hundred cells within an extracellular matrix.     

Enrichment and isolation of a nitropropanol-metabolizing bacterium from the rumen.

A bacterium capable of metabolizing nitropropanol, nitropropionate, and nitrate has been isolated from a mixed ruminal population enriched for enhanced rates of nitropropanol metabolism. The numbers of nitropropanol-metabolizing bacteria in mixed populations increased > 10,000-fold during enrichment; the rates of nitropropanol metabolism increased 8-fold. Hydrogen and phytone were important nutrients for nitropropanol metabolism.     

A sulfate-reducing bacterium from the oxic layer of a microbial mat from Solar Lake (Sinai), Desulfovibrio oxyclinae sp. nov.

In an investigation on the oxygen tolerance of sulfate-reducing bacteria, a strain was isolated from a 10⁷-fold dilution of the upper 3-mm layer of a hypersaline cyanobacterial mat (transferred from Solar Lake, Sinai). The isolate, designated P1B, appeared to be well-adapted to the varying concentrations of oxygen and sulfide that occur in this environment. In the presence of oxygen strain P1B respired aerobically with the highest rates [260 nmol O₂ min^–1 (mg protein)^–1] found so far among marine sulfate-reducing bacteria. Besides H₂ and lactate, even sulfide or sulfite could be oxidized with oxygen. The sulfur compounds were completely oxidized to sulfate. Under anoxic conditions, it grew with sulfate, sulfite, or thiosulfate as the electron acceptor using H₂, lactate, pyruvate, ethanol, propanol, or butanol as the electron donor. Furthermore, in the absence of electron donors the isolate grew by disproportionation of sulfite or thiosulfate to sulfate and sulfide. The highest respiration rates with oxygen were obtained with H₂ at low oxygen concentrations. Aerobic growth of homogeneous suspensions was not obtained. Additions of 1% oxygen to the gas phase of a continuous culture resulted in the formation of cell clumps wherein the cells remained viable for at least 200 h. It is concluded that strain P1B is oxygen-tolerant but does not carry out sulfate reduction in the presence of oxygen under the conditions tested. Analysis of the 16S rDNA sequence indicated that strain P1B belongs to the genus Desulfovibrio, with Desulfovibrio halophilus as its closest relative. Based on physiological properties strain P1B could not be assigned to this species. Therefore, a new species, Desulfovibrio oxyclinae, is proposed. Received: 7 August 1996 / Accepted: 29 January 1997     

Structural and chemical characterization of the S layer of a Pseudomonas-like bacterium.

Sections and freeze-fractured preparations showed an S layer on the surface of Pseudomonas-like strain EU2. Polyacrylamide gel electrophoresis of cell envelopes extracted with 1% sodium dodecyl sulfate (SDS) at room temperature showed three proteins (45K, 55K, and 110K). The 55K protein was identified as the S-layer protein. Incubation in 1.5 M guanidine hydrochloride removed the S layer from cell envelopes and dissociated the structure into subunits. The soluble 55K protein reassembled into planar sheets upon removal of the guanidine hydrochloride by dialysis. Electron microscopy and image processing indicated that these sheets had p4 symmetry in projection with a lattice constant of 13.2 +/- 0.1 nm (corresponding to 9.3 nm between adjacent fourfold axes). In some instances these reassemblies appeared to form small three-dimensional crystals which gave particularly clear views of the structure in projection because of the superimposition of information from a number of layers. A model is proposed with molecules having rounded lobes connected by a narrower linker region and joining at the lobes to form the fourfold axes of the array. The pattern superficially resembles those of other bacterial S layers, such as those of Aeromonas salmonicida, Aeromonas hydrophila, and Azotobacter vinelandii. Extraction of cell envelopes with 1% SDS at 50 degrees C released the 110K protein from the envelopes and removed an amorphous backing layer from the S layer. The 45K protein displayed heat-modifiable migration in SDS-polyacrylamide gel electrophoresis and was insoluble in SDS at 50 degrees C or in high concentrations of guanidine hydrochloride, suggesting that it was associated with the peptidoglycan.     

Methanogenesis from acetate: Physiology of a thermophilic, acetate-utilizing methanogenic bacterium

Abstract The biosynthesis of K88, K99 and F41 fibrillae by enterotoxigenic Escherichia coli strains was shown to be dependent on the growth phase of the cultures. An increase in adhesin production was observed, during exponential growth reaching its maximum at the end of this phase; thereafter adhesin production was arrested.
A simple and rapid purification procedure was developed for adhesins isolated from exponentially growing cells.     

Immobilization of the methanogenic bacterium Methanosarcina barkeri

Whole cells of the methanogen Methanosarcina barkeri were immobilized in an alginate network which was crosslinked with Ca²⁺ ions. The rates of methanol conversion to methane of entrapped cells were found to be in the same range as the corresponding rates of free cells. Furthermore, immobilized cells were active for a longer period than free cells. The particle size of the spherical alginate beads (1.2 mm-3.7 mm ?) and thus diffusion had no obvious influence on the turnover of methanol. The half-value period for methanol conversion activity determined in a buffer medium was approximately 4 days at 37°C for entrapped cells. The apparent K_m value K for such cells was nearly 140mM and the V_max value was about 1.2 μmol methanol/min/mg entrapped protein. Therefore the high rates of methanol degradation measured, e.g., 0.5 μmol methanol/min/mg entrapped protein, indicated that the immobilization technique preserved the cellular functions of this methanogenic bacterium.     

Evidence for a plasmid in a methanogenic bacterium.

Among 15 strains of methanogens, one plasmid, pMP1, was identified in the new coccoid isolate PL-12/M. It could not be detected in the cleared lysate, but it was detected in the viscous pellet. The plasmid had a molecular weight of ca. 4.6 x 10(6). A restriction enzyme cleavage map of the cloned plasmid was derived.     

Enrichment of lignocellulose-degrading microbial communities from natural and engineered methanogenic environments

The aim of this study was to develop an effective bioaugmentation concept for anaerobic digesters treating lignocellulosic biomass such as straw. For that purpose, lignocellulose-degrading methanogenic communities were enriched on wheat straw from cow and goat rumen fluid as well as from a biogas reactor acclimated to lignocellulosic biomass (sorghum as mono-substrate). The bacterial communities of the enriched cultures and the different inocula were examined by 454 amplicon sequencing of 16S rRNA genes while the methanogenic archaeal communities were analyzed by terminal restriction fragment length polymorphism (T-RFLP) fingerprinting of the mcrA gene. Bacteroidetes was the most abundant phylum in all samples. Within the Bacteroidetes phylum, Bacteroidaceae was the most abundant family in the rumen-derived enrichment cultures, whereas Porphyromonadaceae was the predominant one in the reactor-derived culture. Additionally, the enrichment procedure increased the relative abundance of Ruminococcaceae (phylum: Firmicutes) in all cultures. T-RFLP profiles of the mcrA gene amplicons highlighted that the ruminal methanogenic communities were composed of hydrogenotrophic methanogens dominated by the order Methanobacteriales regardless of the host species. The methanogenic communities changed significantly during the enrichment procedure, but still the strict hydrogenotrophic Methanobacteriales and Methanomicrobiales were the predominant orders in the enrichment cultures. The bioaugmentation potential of the enriched methanogenic cultures will be evaluated in further studies.

     

Enrichment and characterization of ammonia-oxidizing archaea from the open ocean: phylogeny,physiology and stable isotope fractionation

Archaeal genes for ammonia oxidation are widespread in the marine environment, but direct physiological evidence for ammonia oxidation by marine archaea is limited. We report the enrichment and characterization of three strains of pelagic ammonia-oxidizing archaea (AOA) from the North Pacific Ocean that have been maintained in laboratory culture for over 3 years. Phylogenetic analyses indicate the three strains belong to a previously identified clade of water column-associated AOA and possess 16S ribosomal RNA genes and ammonia monooxygenase subunit a (amoA) genes highly similar (98–99% identity) to those recovered in DNA and complementary DNA clone libraries from the open ocean. The strains grow in natural seawater-based liquid medium while stoichiometrically converting ammonia (NH₃) to nitrite (NO₂⁻). Ammonia oxidation by the enrichments is only partially inhibited by allylthiourea at concentrations known to completely inhibit cultivated ammonia-oxidizing bacteria. The three strains were used to determine the nitrogen stable isotope effect (¹⁵ɛ_NH3) during archaeal ammonia oxidation, an important parameter for interpreting stable isotope ratios in the environment. Archaeal ¹⁵ɛ_NH3 ranged from 13‰ to 41‰, within the range of that previously reported for ammonia-oxidizing bacteria. Despite low amino acid identity between the archaeal and bacterial Amo proteins, their functional diversity as captured by ¹⁵ɛ_NH3 is similar.     

A diphytanyl ether analog of phosphatidylserine from a methanogenic bacterium, Methanobrevibacter arboriphilus

Several ninhydrin-positive lipids were found in methanogenic bacteria and the structure of one of them, designated as PNL2 from Methanobrevibacter arboriphilus, was identified as a diphytanyl ether analog of phosphatidylserine. The chromatographic behavior of the lipid on thin-layer plates and on a DEAE-cellulose column was identical to the ester form of phosphatidylserine. The infrared spectra showed the presence of amino, carboxyl, ether, and phosphate groups, and the absence of an ester linkage. The hydrophobic portion of the lipid was identified as diphytanyl glycerol diether on the basis of the mass spectrum of the acetolysis product and gas-liquid chromatography of the iodinated alkyl chain prepared by hydroiodic acid cleavage of PNL2. The fast atom bombardment-ionization and field desorption mass spectrum provided a molecular weight of 819 and several fragment ions consistent with the proposed structure. Hydrofluoric acid hydrolysis resulted in water-soluble products including serine, phosphoserine, and ammonia, which accounted for 95% of hydrolyzed PNL2. The lipid product of the hydrolysis was mainly the diether form of phosphatidic acid. This is the first report on the structural characterization of an amino-containing phospholipid in archaebacteria. Amino lipids have been found in many other methanogenic bacteria.     

Fermentation of methanethiol and dimethylsulfide by a newly isolated methanogenic bacterium

From dilution series in defined mineral medium, a marine iregular coccoid methanogenic bacterium (strain MTP4) was isolated that was able to grow on methanethiol as sole source of energy. The strain also grew on dimethylsulfide, mono-, di-, and trimethylamine, methanol and acetate. On formate the organism produced methane without significant growth. Optimal growth on MT, with doubling times of about 20 h, occurred at 30°C in marine medium. The isolate required p-aminobenzoate and a further not identified vitamin. Strain MTP4 had a high tolerance to hydrogen sulfide but was very sensitive to mechanical forces or addition of detergents such as Triton X-100 or sodium dodecylsulfate. Methanethiol was fermented by strain MTP4 according to the following equation:

一株锰氧化细菌的分离、鉴定及其锰氧化特性

【目的】获得锰氧化细菌,对锰矿周边土壤中生物所参与的锰氧化过程进行初探。【方法】依据细菌是否能氧化Mn(Ⅱ),形成棕褐色锰氧化物进行筛选。利用染料LBB对生成的锰氧化物进行检测。通过考察分离菌株的形态、生理特征和16S r RNA基因、gyr B基因、gyr A基因序列的同源性对分离菌株进行鉴定。分析筛选菌与所在属已知锰氧化菌的亲缘关系。利用LBB显色法检测氧化锰的动态生成,通过扫描电镜-能谱分析和X射线衍射技术分析生物氧化锰的表征。【结果】获得1株锰氧化细菌菌株,命名为CP133,综合形态、生理及分子分析结果,鉴定为蜡样芽孢杆菌(Bacillus cereus),分离菌株与多株分离自海洋及土壤的芽孢类锰氧化菌在进化上具有一定的差异。与其他菌株比较菌株CP133具有较强的锰氧化能力,进入稳定期后可生成紧密结合在菌体周围的无定形态生物氧化锰。【结论】从锰矿周边土壤分离出1株具有较强锰氧化功能的蜡样芽孢杆菌,丰富了土壤芽孢类锰氧化菌的资源,同时也为锰矿周围土壤与锰氧化菌间的生物地球化学循环提供了线索及材料。     

Isolation and characterization of a new hydrogen-utilizing bacterium from the rumen

Abstract A new H2 CO2-utilizing acetogenic bacterium was isolated from the rumen of a mature deer. This is the first report of a spore-forming Gram-negative bacterial species from the rumen. The organism was a strictly anaerobic, motile rod and was able to grow autotrophically on hydrogen and carbon dioxide. Acetate was the major product detected. Glucose, fructose and lactate were also fermented heterotrophically. The optimum pH for growth was 7.0–7.5, and the optimum temperature was 37–42 °C. Yeast extract was required for growth and rumen fluid was highly stimulatory. The DNA base ratio was 52.9 ± 0.5 mol% G + C. On the basis of these characteristics and fermentation products, the isolate was considered to be different from acetogenic bacteria described previously.     

Isolation and characterization of methanogenic bacteria from rice paddies

Abstract Enrichment cultures for H₂-CO₂, methanol- or acetate-utilizing methanogens were prepared from two rice field soil samples. All the cultures except one acetate enrichment showed significant methane production. Pure cultures of Methanobacterium - and Methanosarcina -like organisms were isolated from H₂-CO₂ and methanol enrichment cultures, respectively, and were characterized for various nutritional and growth conditions. The organisms had an optimal pH range of 6.4–6.6 and a temperature optimum of 37°C. The Methanobacterium isolates were able to utilize H₂-CO₂ but no other substrates as sole energy source, while the Methanosarcina isolates were able to utilize methanol, methylamines or H₂-CO₂ as sole energy sources. Both Methanobacterium isolates and one isolate of Methanosarcina were able to use dinitrogen as the sole source of nitrogen for growth. The isolates used several sulfur compounds as sole sources of sulfur.     

Enrichment, isolation and characterization of pentachlorophenol degrading bacterium Acinetobacter sp. ISTPCP-3 from effluent discharge site

Three pentachlorophenol (PCP) degrading bacterial strains were isolated from sediment core of pulp and paper mill effluent discharge site. The strains were continuously enriched in mineral salts medium supplemented with PCP as sole source of carbon and energy. One of the acclimated strains with relatively high PCP degradation capability was selected and characterized in this study. Based on morphology, biochemical tests, 16S rDNA sequence analysis and phylogenetic characteristics, the strains showed greatest similarity with Acinetobacter spp. The strain was identified as Acinetobacter sp. ISTPCP-3. The physiological characteristics and optimum growth conditions of the bacterial strain were investigated. The results of optimum growth temperature revealed that it was a mesophile. The optimum growth temperature for the strain was 30°C. The preferential initial pH for the strain was ranging at 6.5–7.5, the optimum pH was 7. The bacterium was able to tolerate and degrade PCP up to a concentration of 200 mg/l. Increase in PCP concentration had a negative effect on biodegradation rate and PCP concentration above 250 mg/l was inhibitory to its growth. Acinetobacter sp. ISTPCP-3 was able to utilize PCP through an oxidative route with ortho ring-cleavage with the formation of 2,3,5,6-tetrachlorohydroquinone and 2-chloro-1,4-benzenediol, identified using gas chromatograph–mass spectrometric (GC–MS) analysis. The degradation pathway followed by isolated bacterium is different from previously characterized pathway.