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1.
Anke Meyerdierks Michael Kube Ivaylo Kostadinov Hanno Teeling Frank Oliver Glöckner Richard Reinhardt Rudolf Amann 《Environmental microbiology》2010,12(2):422-439
Microbial consortia mediating the anaerobic oxidation of methane with sulfate are composed of methanotrophic Archaea (ANME) and Bacteria related to sulfate‐reducing Deltaproteobacteria. Cultured representatives are not available for any of the three ANME clades. Therefore, a metagenomic approach was applied to assess the genetic potential of ANME‐1 archaea. In total, 3.4 Mbp sequence information was generated based on metagenomic fosmid libraries constructed directly from a methanotrophic microbial mat in the Black Sea. These sequence data represent, in 30 contigs, about 82–90% of a composite ANME‐1 genome. The dataset supports the hypothesis of a reversal of the methanogenesis pathway. Indications for an assimilatory, but not for a dissimilatory sulfate reduction pathway in ANME‐1, were found. Draft genome and expression analyses are consistent with acetate and formate as putative electron shuttles. Moreover, the dataset points towards downstream electron‐accepting redox components different from the ones known from methanogenic archaea. Whereas catalytic subunits of [NiFe]‐hydrogenases are lacking in the dataset, genes for an [FeFe]‐hydrogenase homologue were identified, not yet described to be present in methanogenic archaea. Clustered genes annotated as secreted multiheme c‐type cytochromes were identified, which have not yet been correlated with methanogenesis‐related steps. The genes were shown to be expressed, suggesting direct electron transfer as an additional possible mode to shuttle electrons from ANME‐1 to the bacterial sulfate‐reducing partner. 相似文献
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Dos Santos AB de Madrid MP Stams AJ van Lier JB Cervantes FJ 《Biotechnology progress》2005,21(4):1140-1145
The reduction of the azo dye model compounds Reactive Red 2 (RR2) and Reactive Orange 14 (RO14) by mesophilic (30 degrees C) and thermophilic (55 degrees C) anaerobic consortia was studied in batch assays. The contribution of fermentative and methanogenic microorganisms in both temperatures was evaluated in the presence of the fermentative substrate glucose and the methanogenic substrates acetate, H2/CO2, methanol, and formate. Additionally, the effect of the redox mediator riboflavin on electron shuttling was assessed. We concluded that the application of thermophilic anaerobic treatment is an interesting option for the reductive decolorization of azo dyes compared to mesophilic conditions. The use of high temperature may decrease or even take the place of the need for continuous redox mediator dosage in bioreactors, contrarily to the evident effect of those compounds on dye reduction under mesophilic conditions. Both fermenters and methanogens may play an important role during reductive decolorization of dyes, in which mediators are important not only for allowing the different microbes to participate more effectively in this complex reductive biochemistry but also for assisting in the competition for electrons between dyes and other organic and inorganic electron acceptors. 相似文献
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Gladden JM Allgaier M Miller CS Hazen TC VanderGheynst JS Hugenholtz P Simmons BA Singer SW 《Applied and environmental microbiology》2011,77(16):5804-5812
Industrial-scale biofuel production requires robust enzymatic cocktails to produce fermentable sugars from lignocellulosic biomass. Thermophilic bacterial consortia are a potential source of cellulases and hemicellulases adapted to harsher reaction conditions than commercial fungal enzymes. Compost-derived microbial consortia were adapted to switchgrass at 60°C to develop thermophilic biomass-degrading consortia for detailed studies. Microbial community analysis using small-subunit rRNA gene amplicon pyrosequencing and short-read metagenomic sequencing demonstrated that thermophilic adaptation to switchgrass resulted in low-diversity bacterial consortia with a high abundance of bacteria related to thermophilic paenibacilli, Rhodothermus marinus, and Thermus thermophilus. At lower abundance, thermophilic Chloroflexi and an uncultivated lineage of the Gemmatimonadetes phylum were observed. Supernatants isolated from these consortia had high levels of xylanase and endoglucanase activities. Compared to commercial enzyme preparations, the endoglucanase enzymes had a higher thermotolerance and were more stable in the presence of 1-ethyl-3-methylimidazolium acetate ([C2mim][OAc]), an ionic liquid used for biomass pretreatment. The supernatants were used to saccharify [C2mim][OAc]-pretreated switchgrass at elevated temperatures (up to 80°C), demonstrating that these consortia are an excellent source of enzymes for the development of enzymatic cocktails tailored to more extreme reaction conditions. 相似文献
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Juli L. Sherwood James N. Petersen Rodney S. Skeen 《Biotechnology and bioengineering》1999,64(3):342-348
Fed‐batch experiments were performed to determine the carbon tetrachloride (CT)‐degrading ability of three denitrifying consortia cultured from sites not contaminated with CT. A mathematical model was used to quantify the rates of CT transformation by the consortia under both acetate‐limiting and nitrate‐limiting conditions. A rate constant for CT transformation on a cellular protein basis and the fraction of degraded CT transformed to chloroform (CF) were determined for each consortium by optimizing the model to fit the experimental data. The parameters for these experiments were statistically compared to those obtained for previous experiments with a denitrifying consortium cultured from an aquifer soil sample from the US Department of Energy Hanford site in southeastern Washington state. Results of F‐test analysis indicated the rate of CT transformation and the production of CF both were functions of the limiting nutrient. Under nitrate‐limited conditions, the rate constant for CT transformation for all four consortia was about 30 L/gmol/min and approximately 50% of the CT transformed was converted to CF. When acetate was the limiting nutrient, the rate constant for CT transformation was approximately 8 L/gmol/min and the CF yield decreased to about 25%. These results imply the ability to degrade CT may be inherent to some denitrifying organisms, regardless of previous exposure to CT. © 1999 John Wiley & Sons, Inc. Biotechnol Bioeng 64: 342–348, 1999. 相似文献
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Andrius Jasilionis Algirdas Kaupinis Marija Ger Mindaugas Valius Donaldas Chitavichius Nomeda Kuisiene 《Central European Journal of Biology》2012,7(4):587-595
Peptidase family U32 is one of the few whose catalytic type and structure has not yet been described. It is generally accepted that U32 peptidases represent putative collagenases and contribute to the pathogenicity of some bacteria. Meanwhile, U32 peptidases are also found in nonpathogenic bacteria including thermophiles and hyperthermophiles. Here we report cloning of the U32.002 peptidase gene from thermophilic Geobacillus thermoleovorans DSM 15325 and demonstrate expression and characterization of the recombinant protein. It has been determined that U32.002 peptidase is constitutively expressed in the cells of thermophilic G. thermoleovorans DSM 15325. The recombinant oligomeric enzyme showed its activity only against heat-treated collagen. It was unable to degrade albumin, casein, elastin, gelatine and keratin. In contrast to this, the monomeric recombinant protein showed no activity at all. This paper is the first report about the thermophilic U32 peptidase. As the thermophilic bacteria are non-pathogenic, the role of constitutively expressed extracellular collagenolytic U32 peptidase in these bacteria is unclear. 相似文献
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The effect of temperature on granulation and microbial interaction of anaerobic sludges grown in thermophilic upflow anaerobic sludge bed (UASB) reactors was investigated at two different temperatures, 55°C (Run 1) and 65°C (Run 2). Each run consisted of two phases. Phase 1 was conducted by feeding acetate for a period of 200 days. In Phase 2, both reactors were fed a mixture of acetate and sucrose for a further 100 days. During Phase 1, no granulation occurred in the sludge of either run. Microscopic observation revealed that the predominant methanogen was Methanothrix in Run 1, whereas Methanobacterium-like bacteria existed to a significant extent in Run 2. The acetate-utilizing methanogenic activity of both sludges increased with increasing test temperature in the range 55–65°C. Since the acetate-grown sludges exhibited far higher H2-utilizing methanogenic activity than acetate-utilizing methanogenic activity, it is suggested that a syntrophic association of acetate-oxidizing bacteria with hydrogenotrophic methanogens was responsible for a considerable portion of the overall acetate elimination in thermophilic anaerobic sludge. During Phase 2, granules coated with either filamentous bacteria or cocci-type bacteria (both presumably acid-forming bacteria) were successfully established in Run 1 and Run 2, respectively. Since the acetate-utilizing methanogenic activities of the granular sludges were four to five times higher than those of the acetate-grown sludges (Phase 1), the co-existence of these coating bacteria appeared to contribute to the enclosing of acetate consumers inside granules.
Correspondence to: S. Uemura 相似文献
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A dialysis cultivation system was used to enrich slow-growing moderately thermophilic anaerobic bacteria at high cell densities. Bicarbonate buffered mineral salts medium with 5 mM glutamate as the sole carbon and energy source was used and the incubation temperature was 55 degrees C. The reactor inoculum originated from anaerobic methanogenic granular sludge bed reactors. The microbial population was monitored over a period of 2 years using the most probable number (MPN) technique. In the reactor glutamate was readily degraded to ammonium, methane, and carbon dioxide. Cell numbers of glutamate-degrading organisms increased 400-fold over the first year. In medium supplemented with bromoethane sulfonic acid (BES, an inhibitor of methanogenesis), tenfold lower cell numbers were counted, indicating the syntrophic nature of glutamate degradation. After 2 years of reactor operation the predominant organisms were isolated and characterized. Methanobacterium thermoautotrophicum (strain R43) and a Methanosaeta thermophila strain (strain A) were the predominant hydrogenotrophic and acetoclastic methanogens, respectively. The numbers in which the organisms were present in the reactor after 24 months of incubation were 8.6 x 10(9) and 3.8 x 10(7) mL(-1) sludge, respectively. The most predominant glutamate-degrading organism (8.6 x 10(7) mL(-1) sludge), strain Z, was identified as a new species, Caloramator coolhaasii. It converted glutamate to hydrogen, acetate, some propionate, ammonium, and carbon dioxide. Growth of this syntrophic organism on glutamate was strongly enhanced by the presence of methanogens. 相似文献
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Spatial variations of methanotrophic consortia at cold methane seeps: implications from a high-resolution molecular and isotopic approach 总被引:2,自引:0,他引:2
Anaerobic methane‐oxidizing microbial communities in sediments at cold methane seeps are important factors in controlling methane emission to the ocean and atmosphere. Here, we investigated the distribution and carbon isotopic signature of specific biomarkers derived from anaerobic methanotrophic archaea (ANME groups) and sulphate‐reducing bacteria (SRB) responsible for the anaerobic oxidation of methane (AOM) at different cold seep provinces of Hydrate Ridge, Cascadia margin. The special focus was on their relation to in situ cell abundances and methane turnover. In general, maxima in biomarker abundances and minima in carbon isotope signatures correlated with maxima in AOM and sulphate reduction as well as with consortium biomass. We found ANME‐2a/DSS aggregates associated with high abundances of sn‐2,3‐di‐O‐isoprenoidal glycerol ethers (archaeol, sn‐2‐hydroxyarchaeol) and specific bacterial fatty acids (C16:1ω5c, cyC17:0ω5,6) as well as with high methane fluxes (Beggiatoa site). The low to medium flux site (Calyptogena field) was dominated by ANME‐2c/DSS aggregates and contained less of both compound classes but more of AOM‐related glycerol dialkyl glycerol tetraethers (GDGTs). ANME‐1 archaea dominated deeper sediment horizons at the Calyptogena field where sn‐1,2‐di‐O‐alkyl glycerol ethers (DAGEs), archaeol, methyl‐branched fatty acids (ai‐C15:0, i‐C16:0, ai‐C17:0), and diagnostic GDGTs were prevailing. AOM‐specific bacterial and archaeal biomarkers in these sediment strata generally revealed very similar δ13C‐values of around ?100. In ANME‐2‐dominated sediment sections, archaeal biomarkers were even more 13C‐depleted (down to ?120), whereas bacterial biomarkers were found to be likewise 13C‐depleted as in ANME‐1‐dominated sediment layers (δ13C: ?100). The zero flux site (Acharax field), containing only a few numbers of ANME‐2/DSS aggregates, however, provided no specific biomarker pattern. Deeper sediment sections (below 20 cm sediment depth) from Beggiatoa covered areas which included solid layers of methane gas hydrates contained ANME‐2/DSS typical biomarkers showing subsurface peaks combined with negative shifts in carbon isotopic compositions. The maxima were detected just above the hydrate layers, indicating that methane stored in the hydrates may be available for the microbial community. The observed variations in biomarker abundances and 13C‐depletions are indicative of multiple environmental and physiological factors selecting for different AOM consortia (ANME‐2a/DSS, ANME‐2c/DSS, ANME‐1) along horizontal and vertical gradients of cold seep settings. 相似文献
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Gene expression and extracellular matrix ultrastructure of a mineralizing chondrocyte cell culture system 总被引:4,自引:3,他引:4
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Conditions were defined for promoting cell growth, hypertrophy, and extracellular matrix mineralization of a culture system derived from embryonic chick vertebral chondrocytes. Ascorbic acid supplementation by itself led to the hypertrophic phenotype as assessed by respective 10- and 15-fold increases in alkaline phosphatase enzyme activity and type X synthesis. Maximal extracellular matrix mineralization was obtained, however, when cultures were grown in a nutrient-enriched medium supplemented with both ascorbic acid and 20 mM beta-glycerophosphate. Temporal studies over a 3-wk period showed a 3-4-fold increase in DNA accompanied by a nearly constant DNA to protein ratio. In this period, total collagen increased from 3 to 20% of the cell layer protein; total calcium and phosphorus contents increased 15-20-fold. Proteoglycan synthesis was maximal until day 12 but thereafter showed a fourfold decrease. In contrast, total collagen synthesis showed a greater than 10-fold increase until day 18, a result suggesting that collagen synthesis was replacing proteoglycan synthesis during cellular hypertrophy. Separate analysis of individual collagen types demonstrated a low level of type I collagen synthesis throughout the 21-d time course. Collagen types II and X synthesis increased during the first 2 wk of culture; thereafter, collagen type II synthesis decreased while collagen type X synthesis continued to rise. Type IX synthesis remained at undetectable levels throughout the time course. The levels of collagen types I, II, IX, and X mRNA and the large proteoglycan core protein mRNA paralleled their levels of synthesis, data indicating pretranslational control of synthesis. Ultrastructural examination revealed cellular and extracellular morphology similar to that for a developing hypertrophic phenotype in vivo. Chondrocytes in lacunae were surrounded by a well-formed extracellular matrix of randomly distributed collagen type II fibrils (approximately 20-nm diam) and extensive proteoglycan. Numerous vesicular structures could be detected. Cultures mineralized reproducibly and crystals were located in extracellular matrices, principally associated with collagen fibrils. There was no clear evidence of mineral association with extracellular vesicles. The mineral was composed of calcium and phosphorus on electron probe microanalysis and was identified as a very poorly crystalline hydroxyapatite on electron diffraction. In summary, these data suggest that this culture system consists of chondrocytes which undergo differentiation in vitro as assessed by their elevated levels of alkaline phosphatase and type X collagen and their ultrastructural appearance.(ABSTRACT TRUNCATED AT 400 WORDS) 相似文献
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Aims: This study aimed at isolating thermophilic bacteria that utilize cheap carbon substrates for the economically feasible production of poly(3‐hydroxybutyrate), poly(3HB), at elevated temperatures. Methods and Results: Thermophilic bacteria were enriched from an aerobic organic waste treatment plant in Germany, and from hot springs in Egypt. Using the viable colony staining method for hydrophobic cellular inclusions with Nile red in mineral salts medium (MSM) containing different carbon sources, six Gram‐negative bacteria were isolated. Under the cultivation conditions used in this study, strains MW9, MW11, MW12, MW13 and MW14 formed stable star‐shaped cell‐aggregates (SSCAs) during growth; only strain MW10 consisted of free‐living rod‐shaped cells. The phylogenetic relationships of the strains as derived from 16S rRNA gene sequence comparisons revealed them as members of the Alphaproteobacteria. The 16S rRNA gene sequences of the isolates were very similar (>99% similarity) and exhibited similarities ranging from 93 to 99% with the most closely related species that were Chelatococcus daeguensis, Chelatococcus sambhunathii , Chelatococcus asaccharovorans, Bosea minatitlanensis, Bosea thiooxidans and Methylobacterium lusitanum. Strains MW9, MW10, MW13 and MW14 grew optimally in MSM with glucose, whereas strains MW11 and MW12 preferred glycerol as sole carbon source for growth and poly(3HB) accumulation. The highest cell density and highest poly(3HB) content attained were 4·8 g l?l (cell dry weight) and 73% (w/w), respectively. Cells of all strains grew at temperatures between 37 and 55°C with the optimum growth at 50°C. Conclusions: New PHA‐accumulating thermophilic bacterial strains were isolated and characterized to produce poly(3HB) from glucose or glycerol in MSM at 50°C. SSCAs formation was reported during growth. Significance and Impact of the Study: To the best of our knowledge, this is the first report on the formation of SSCAs by PHA‐accumulating bacteria and also by thermophilic bacteria. PHA‐producing thermophiles can significantly reduce the costs of fermentative PHA production. 相似文献
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Bacillus coagulans tolerance to 1‐ethyl‐3‐methylimidazolium‐based ionic liquids in aqueous and solid‐state thermophilic culture
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Christopher W. Simmons Amitha P. Reddy Jean S. VanderGheynst Blake A. Simmons Steven W. Singer 《Biotechnology progress》2014,30(2):311-316
The use of ionic liquids (ILs) to disrupt the recalcitrant structure of lignocellulose and make polysaccharides accessible to hydrolytic enzymes is an emerging technology for biomass pretreatment in lignocellulosic biofuel production. Despite efforts to reclaim and recycle IL from pretreated biomass, residual IL can be inhibitory to microorganisms used for downstream fermentation. As a result, pathways for IL tolerance are needed to improve the activity of fermentative organisms in the presence of IL. In this study, microbial communities from compost were cultured under high‐solids and thermophilic conditions in the presence of 1‐ethyl‐3‐methylimidazolium‐based ILs to enrich for IL‐tolerant microorganisms. A strain of Bacillus coagulans isolated from an IL‐tolerant community was grown in liquid and solid‐state culture in the presence of the ILs 1‐ethyl‐3‐methylimidazolium acetate ([C2mim][OAc]) or 1‐ethyl‐3‐methylimidazolium chloride ([C2mim][Cl]) to gauge IL tolerance. Viability and respiration varied with the concentration of IL applied and the type of IL used. B. coagulans maintained growth and respiration in the presence of 4 wt% IL, a concentration similar to that present on IL‐pretreated biomass. In the presence of both [C2mim][OAc] and [C2mim][Cl] in liquid culture, B. coagulans grew at a rate approximately half that observed in the absence of IL. However, in solid‐state culture, the bacteria were significantly more tolerant to [C2mim][Cl] compared with [C2mim][OAc]. B. coagulans tolerance to IL under industrially relevant conditions makes it a promising bacterium for understanding mechanisms of IL tolerance and discovering IL tolerance pathways for use in other microorganisms, particularly those used in bioconversion of IL‐pretreated plant biomass. © 2013 American Institute of Chemical Engineers Biotechnol. Prog., 30:311–316, 2014 相似文献
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One‐step enzyme purification and immobilization were developed based on simple adsorption of a family 3 cellulose‐binding module (CBM)‐tagged protein on the external surface of high‐capacity regenerated amorphous cellulose (RAC). An open reading frame (ORF) Cthe0217 encoding a putative phosphoglucose isomerase (PGI, EC 5.3.1.9) from a thermophilic bacterium Clostridium thermocellum was cloned and the recombinant proteins with or without CBM were over‐expressed in Escherichia coli. The rate constant (kcat) and Michaelis–Menten constant (Km) of CBM‐free PGI at 60°C were 2,765 s?1 and 2.89 mM, respectively. PGI was stable at a high protein concentration of 0.1 g/L but deactivated rapidly at low concentrations. Immobilized CBM (iCBM)‐PGI on RAC was extremely stable at ~60°C, nearly independent of its mass concentration in bulk solution, because its local concentration on the solid support was constant. iCBM‐PGI at a low concentration of 0.001 g/L had a half‐life time of 190 h, approximately 80‐fold of that of free PGI. Total turn‐over number of iCBM‐PGI was as high as 1.1 × 109 mole of product per mole of enzyme at 60°C. These results suggest that a combination of low‐cost enzyme immobilization and thermoenzyme led to an ultra‐stable enzyme building block suitable for cell‐free synthetic pathway biotransformation that can implement complicated biochemical reactions in vitro. © 2011 American Institute of Chemical Engineers Biotechnol. Prog., 2011. 相似文献
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DNA can be introduced into the thermophilic cyanobacteriumSynechococcus elongatus by electroporation or conjugation. Its genome can be readily manipulated through integrative transformation or by using promiscuous RSF1010-derived plasmids that can be transferred unaltered betweenEscherichia coli andSynechococcus elongatus. These vectors can therefore be used for in vivo studies of cyanobacterial proteins in both mesophilic and thermophilic cyanobacterial backgrounds. As a preliminary step towards the analysis of structure-function relationships of photosystem I (PSI) from this thermophile, the genes encoding the PSI subunits PsaF, PsaL, and PsaK were inactivated and shown to be non-essential inS. elongatus. In addition, PSI reaction centres were extracted from apsaL ? strain exclusively as monomeric complexes. 相似文献
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Functional and structural diversity in GH62 α‐L‐arabinofuranosidases from the thermophilic fungus Scytalidium thermophilum
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Amrit Pal Kaur Boguslaw P. Nocek Xiaohui Xu Michael J. Lowden Juan Francisco Leyva Peter J. Stogios Hong Cui Rosa Di Leo Justin Powlowski Adrian Tsang Alexei Savchenko 《Microbial biotechnology》2015,8(3):419-433
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An oligonucleotide composed of a contiguous stretch of RNA and DNA residues has been developed to facilitate the correction of single‐base mutations of episomal and chromosomal targets in mammalian cells. The design of the oligonucleotide exploited the highly recombinogenic RNA‐DNA hybrids and featured hairpin capped ends avoiding destruction by cellular helicases or exonucleases. The RNA‐DNA oligonucleotide (RDO) was designed to correct a point mutation in the tyrosinase gene and caused a permanent gene correction in mouse albino melanocytes, determined by clonal analysis at the level of genomic sequence, protein and phenotypic change. Recently, we demonstrated correction of the tyrosinase gene using the same RDO in vivo, as detected by dark pigmentation of several hairs and DOPA staining of hair follicles in the treated skin of albino mice. Such RDOs might hold a promise as a therapeutic method for the treatment of skin diseases. However, the frequency of gene correction varies among different cells, indicating that cellular activities, such as recombination and repair, may be important for gene conversion by RDOs. As this technology becomes more widely utilized in the scientific community, it will be important to understand the mechanism and to optimize the design of RDOs to improve their efficiency and general applicability. 相似文献