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PubMed2003

Identification of a novel alpha-proteobacterium causing bacteraemia in an immunocompetent patient.

An 89-year male with pyrexia and suspected bacteremia was admitted to hospital, where a Gram-negative rod was identified from blood culture. The organism was difficult to identify phenotypically and the resulting sequencing of a 559 bp section of the 16S rRNA gene did not have a high homology score (>97.0%) with any deposited GenBank accession numbers and hence was not able to be assigned to a species within any genus. Given that the isolate was a member of the alpha subclass of the Proteobacteria but did not fall into any of the known genera with more than 93.7% homology (Brucella, Rhizobium, Ochrobactrum, Agrobacterium), we believe this isolate to represent a novel alpha-proteobacterium, which was the cause of bacteraemia in this patient.

Aged↗

PubMed2003

Detection methods for the expression of the dissimilatory copper-containing nitrite reductase gene (DnirK) in environmental samples.

In situ assays, based on monoclonal antibodies (mAbs), were developed to study the microbial expression of the bacterial dissimilatory copper-containing nitrite reductase gene (DnirK), one of the key enzymes involved in denitrification, in different ecosystems. With a combination of an anti-DnirK mAb and phylogenetic oligonucleotide probes, it is possible to bring structural and functional aspects of microbial communities together. To perform a double labelling, yielding a high signal strength for both the oligonucleotide and the antibody, cells have to be labelled with the oligonucleotide first followed by immunostaining. When the labelling sequence was changed, the accessibility for the oligonucleotide was reduced if high amounts of DnirK were expressed. Using flow cytometry, it was possible to sort bacterial cells, which were stained by the antibody, from nonlabelled cells. This technique provides means for a detailed analysis of populations, which express DnirK genes in the environment, including structural aspects of a community and detailed promoter studies. Using the immunostaining approach, it was possible to identify bacteria, which have the DnirK system expressed, in samples from a wastewater sewage treatment plant as well as in samples from the rhizosphere of wheat roots. Furthermore, expression studies using an Ochrobactrum anthropi strain were carried out to investigate the correlation between N(2)O production rates and DnirK expression in batch cultures, which had been shifted from aerobic to anaerobic conditions. As expected, expression of DnirK was the highest during periods with the greatest synthesis rates for N(2)O. However, the amount of expressed enzyme was not reduced in the cells, although the N(2)O production rates dropped in the cultures 12 h after the shift from aerobic to anaerobic conditions.

Antibodies, Monoclonal↗

PubMed2003

Genes for an alkaline D-stereospecific endopeptidase and its homolog are located in tandem on Bacillus cereus genome.

Alkaline D-peptidase (Adp) from Bacillus cereus DF4-B is a D-stereospecific endopeptidase acting on oligopeptides composed of D-phenylalanine and the primary structure deduced from its gene, adp, shows a similarity with D-stereospecific hydrolases from Ochrobactrum anthropi strains. We have isolated DNA fragments covering the flanking region of adp from DF4-B genome and found an additional gene, adp2, located upstream of adp. The deduced amino acid sequence of Adp2 showed 96% and 85% identity with those of Adp from B. cereus strains AH559 and DF4-B, respectively. The recombinant Adp2 expressed in Escherichia coli was purified to homogeneity and characterized. It had hydrolyzing activity toward (D-Phe)3, (D-Phe)4, and (D-Phe)6 but did not act on (L-Phe)4, D-Phe-NH2, and L-Phe-NH2, some characteristics that are closely related to those of Adp from strain DF4-B. These results indicate that highly homologous genes encoding D-stereospecific endopeptidases are arranged in a tandem manner on the genomic DNA of B. cereus DF4-B.

3' Flanking Region↗

PubMed1992

Structural similarity of D-aminopeptidase to carboxypeptidase DD and beta-lactamases.

The gene for D-aminopeptidase (dap) has been isolated from the bacterium Ochrobactrum anthropi SCRC C1-38 [Asano, Y., Nakazawa, A., Kato, Y., & Kondo, K. (1989) J. Biol. Chem. 264, 14233-14239] and its nucleotide sequence determined. An expression plasmid pC138DP (4.5 kb) was constructed by placing the gene downstream of the lac promoter of pUC19. The amount of the enzyme in the cell-free extract of Escherichia coli JM109/pC138DP was elevated to 288,000 units/L of culture, which is about 3600-fold over that of O. anthropi SCRC C1-38. The enzyme comprised about 30% of the total extractable cellular protein. The gene consisted of an open reading frame of 1560 nucleotides which specifies a protein of Mr 57,257. The deduced amino acid sequence of the enzyme showed that it is related to carboxypeptidase DD, beta-lactamases, and penicillin-binding proteins. Seven mutants of the enzyme were generated by site-specific mutagenesis to explore the roles of the residues of interest, around the sequence Ser61-Xaa-Xaa-Lys64, where Xaa is any amino acid, since the identical sequences also appear in the penicillin-recognizing peptide hydrolases with Ser at the active sites. The mutant enzymes expressed in E. coli were purified to homogeneity and kinetically characterized. Replacements of the site at Ser61 and Lys64 yielded mutants showing significantly reduced Vmax values, while most of the Km values remained unchanged. Changes at Cys60, which is adjacent to the likely active center Ser61, to Ser and Gly resulted in the production of enzyme less sensitive to PCMB, with almost unaltered Vmax/Km values. The enzyme appears to be a serine peptidase rather than a thiol one. The inhibition by PCMB in the wild-type enzyme may have been caused by a formation of a mercaptide bond between Cys 60 and PCMB. Considering that D-aminopeptidase, carboxypeptidase DD (a penicillin-binding protein), and beta-lactamase have a common feature in recognizing peptides containing D-amino acid and that the former two catalyze transpeptidation reactions with substrates containing D-alanyl-D-alanine moieties, we propose that the enzyme is a new member of the "penicillin-recognizing enzymes". We showed that the enzyme is actually inhibited by beta-lactam compounds, such as 6-APA, 7-ACA, benzylpenicillin, and ampicillin, although they are not the substrate for the enzyme. The relationship between the primary structures and the reactions catalyzed by D-aminopeptidase and other serine hydrolases beta-lactamases and carboxypeptidase DD is discussed.(ABSTRACT TRUNCATED AT 400 WORDS)

Alcaligenes↗

PubMed2001

Resistance to antibiotics and biocides among non-fermenting Gram-negative bacteria.

OBJECTIVE: To investigate the antibiotic and biocide susceptibilities of clinical isolates of rarely encountered Gram-negative, non-fermenting bacteria. METHODS: Thirty Gram-negative non-fermenting bacterial strains were isolated from blood cultures of oncology patients. These were studied for their resistance to 11 antibiotics. Their susceptibilities to seven biocides used in hospitals were also examined. RESULTS: Isolates of Stenotrophomonas maltophilia and Ochrobactrum anthropi were generally resistant to at least five of the antibiotics, whereas isolates of Comamonas acidivorans, Flavobacterium oryzihabitans, Aeromonas hydrophila, Sphingobacterium spiritivorum, Acinetobacter junii and Acinetobacter lwoffi were generally sensitive to at least nine of the antibiotics. Trovafloxacin and trimethoprim-sulfamethoxazole were the most effective antibacterial agents tested, with 0% and 7%, respectively, of isolates being resistant, whereas 63% of isolates were resistant to aztreonam. Some isolates, sensitive to meropenem and/or ceftazidime in vitro, possessed very high MBC/MIC ratios for these beta-lactams. Two out of three biocides used in hospital pharmacies showed lethal activity towards all strains tested when used at less than one-third of their recommended in-use concentration. Proceine 40 failed to give a 5 log reduction in bacterial cell number for the isolates tested when used at its "in-use" concentration. A concentration of > 500 mg/L chlorhexidine was required to achieve a 5 log reduction for the same isolates. CONCLUSIONS: We have examined the antibiotic susceptibilities of non-fermenting Gram-negative bacterial strains isolated from immunocompromised patients. Despite being sensitive to certain antibiotics in vitro, some isolates were still able to cause serious bacteremia. We have also reported for the first time the susceptibilities of non-fermenting Gram-negative bacteria to common biocides used in hospital infection control, and have shown that some strains are able to persist at the "in-use" concentration of particular biocides. It is therefore important to study further this particular group of organisms, and, in particular, to examine whether there exists a link between resistance to antibiotics and resistance to biocides.

Anti-Bacterial Agents↗

PubMed2002

Diversity of chromium-resistant and -reducing bacteria in a chromium-contaminated activated sludge.

AIMS: This study attempts to establish a relationship between the Cr(VI) resistance of the culturable microbial community and the Cr(VI) resistance and Cr(VI)-reducing ability of representative strains of each population, in order to assess whether these are exclusive characteristics of one microbial group or abilities shared among many groups. METHODS AND RESULTS: A group of 48 Cr(VI)-resistant isolates, with different colony types, was isolated from chromium-contaminated activated sludge. Sodium dodecyl sulphate-polyacrylamide gel electrophoresis protein patterns and fatty acid methyl ester analysis identified six populations, representing 54% of the isolated bacteria, as belonging to the genera Acinetobacter and Ochrobactrum. The remaining populations included strains identified as species of the beta-Proteobacteria and high G + C Gram-positive bacteria. The Cr(VI) resistance and reduction ability of the strains were tested. All but two isolates grew in the presence of 1 mmol l(-1) Cr(VI). During enrichment, all isolates were able to survive to 2 mmol l(-1) Cr(VI) and complete Cr(VI) reduction was achieved. Representative strains of each population were able to partially reduce (5.4-39.1%) the Cr(VI) present in the growth medium. CONCLUSIONS: Most of the identified isolates have never been reported to be Cr(VI)-resistant and/or Cr(VI)-reducing strains. The mechanisms of Cr(VI) resistance and reduction may differ from group to group; therefore, it is evident that both Cr(VI) resistance and reduction are shared abilities and not an exclusive characteristic of a single group, possibly reflecting horizontal genetic transfer resulting from selective pressure in this contaminated environment. SIGNIFICANCE AND IMPACT OF THE STUDY: To our knowledge, this is the first study of a microbial community under chronic chromate stress and, as the success of microbial-based metal remediation technologies requires a better understanding of the microbial community and the population response to metal stress, it may contribute to the implementation of a strategy of bioremediation of chromate-contaminated environments.

Bacteria↗

PubMed2002

Monoassociation of SCID mice with Helicobacter muridarum, but not four other enterics, provokes IBD upon receipt of T cells.

BACKGROUND & AIMS: Recently, a number of animal models for different aspects of inflammatory bowel disease (IBD) have been developed. The aim of this study was to use one of these to determine whether particular, ostensibly innocuous, intestinal bacteria could provoke or exacerbate IBD. METHODS: Conventionally reared C.B17 SCID mice were compared with germ-free and gnotobiotic mice, monoassociated with 1 of 5 intestinal bacteria, after transfer of CD45RB(high) CD4(+) T cells from conventionally reared congenic BALB/c mice. Recipient mice were monitored over 7-12 weeks for clinical signs of IBD, and tissues were analyzed by histology/flow cytometry for abnormal inflammation and CD4(+) T cell outgrowth. RESULTS: Neither germ-free mice nor mice monoassociated with segmented filamentous bacteria, Ochrobactrum anthropi, a nonpathogenic mutant of Listeria monocytogenes, or Morganella morganii developed any signs of IBD. In contrast, mice monoassociated with Helicobacter muridarum displayed an accelerated development of IBD in 5-6 weeks compared with 8-12 weeks observed in conventionally reared mice. The outgrowth of CD4(+) T cells in spleen and large intestine of H. muridarum monoassociated mice, as well as in conventionally reared mice was significantly higher than that in the other monoassociated mice. CONCLUSIONS: Among the intestinal bacteria tested, H. muridarum can serve as a provocateur of IBD in this model.

Animals↗

PubMed1997

Nuclear magnetic resonance timecourse studies of glyphosate metabolism by microbial soil isolates.

1. Triple Resonance Isotope EDited nmr spectroscopy (TRIED) has been developed to detect and examine minute levels of glyphosate metabolites in microbial soil isolates. Using stable isotopic labelling (13C and 15N), TRIED allows the simultaneous detection of multiple metabolites in crude matrices at submicrogram levels. An improvement over earlier techniques where milligrams are needed, TRIED can detect 500 ng of triply labelled compound in a crude sample (1:14,000 mass ratio) in just hours. 2. TRIED is used here to compare the kinetics and metabolic pathways of glyphosate metabolism by two strains of Ochrobactrum anthropi, LBAA and S5. Both LBAA and S5 appear to metabolize glyphosate primarily via the aminomethylphosphonate (AMPA) pathway, since no detectable levels of glycine or sarcosine are observed in the media or lysates of either microbe. The formation of N-methylAMPA is common to the metabolism of both microorganisms, but N-acetylAMPA is observed only in LBAA. N-methylacetamide is detected predominantly in media and lysates of S5, although some evidence also points to the formation of this metabolite in LBAA. 3. Results are consistent with conventional radioactive tracer studies. TRIED nmr provides more specific structural information complementary to radiolabel methods. Both nmr and radioactivity studies show S5 glyphosate metabolism to be much slower than that of LBAA.

Animals↗

PubMed1999

Crystallization and preliminary X-ray analysis of a new L-aminopeptidase-D-amidase/D-esterase activated by a Gly-Ser peptide bond hydrolysis.

Ochrobactrum anthropi possesses an L-aminopeptidase (DmpA) also able to act as a D-amidase/D-esterase. DmpA (40 kDa) is activated by auto-catalyzed protein splicing liberating an alpha-amino group presumably used as a general base in the catalytic mechanism. Two crystal forms were obtained at 294 K in 13-16% PEG 2000 mono-methylether at pH 9.0, adding either 0.2 M magnesium chloride or 1 M lithium chloride. Crystals of the first form belong to the space group C2221 and diffract to 3.0 A resolution, whereas crystals of the second form belong to the space group P21212 and diffract to 2.3 A resolution. Initial screening for heavy-atom derivatives on form II crystals, has led to a well substituted Hg derivative.

Aminopeptidases↗

PubMed1996

Hemicellulose-degrading bacteria and yeasts from the termite gut.

Termites play a major role in the recycling of photosynthetically fixed carbon. With the aid of their symbiotic intestinal flora, they are able to degrade extensively wood constituents such as cellulose and hemicellulose. Nevertheless, the microbial species involved in the degradation of hemicelluloses are poorly defined. The purpose of this paper was to examine the microflora involved in hemicellulose degradation. Different aerobic and facultatively anaerobic bacteria and yeasts were isolated using xylan, arabinogalactan and carboxymethylcellulose as substrates. Gram-positive isolates belonged to the genera Bacillus, Paenibacillus, Streptomyces or the actinobacteria group, while the Gram-negative strains were assigned to the genera Pseudomonas, Acinetobacter, Ochrobactrum, and to genera belonging to the family Enterobacteriaceae. The spectrum and activity of xylan- and arabinogalactan-hydrolysing glycosidases of these new isolates, together with additional bacterial strains originally obtained from enrichments with aromatic compounds were determined.

Animals↗

PubMed1996

Specificity of six gene sequences for the detection of the genus Brucella by DNA amplification.

DNA extracted from all Brucella species, reference and vaccine strains were amplified by PCR using primers specific for the genes encoding a 31-kDa Brucella protein, the heat shock proteins (DnaJ, DnaK, HtrA and GroEL) and 16S RNA. No difference was found between Brucella species and biovars with all primer pairs used, even after restriction enzyme analysis of the amplified fragments. The specificity of the amplified products was confirmed by hybridization with a digoxigenin 3'-labelled specific probe and by PCR using 98 non-Brucella micro-organisms' DNA. Only Ochrobactrum anthropi and Phyllobacterium spp. yielded a PCR product by using 31-kDa DnaK, DnaJ, GroEL and 16S RNA primers. After hybridization and restriction analysis, 16S RNA fragments of 3301 and 3331 O. anthropi strains showed a total similarity to those from Brucella. A similar result was shown with DnaJ fragments obtained with 3301 strain of O. anthropi after EcoRI digestion.

Blotting, Southern↗

PubMed2006

Differential inductions of TNF-alpha and IGTP, IIGP by structurally diverse classic and non-classic lipopolysaccharides.

The innate immune system recognizes microbes by characteristic molecules like the Gram-negative lipopolysaccharide (LPS). Lipid A (the LPS bioactive moiety) signals through toll-like receptors (TLRs) to induce pro-inflammatory molecules and small GTPases of the p47 family involved in intracellular pathogen control. We tested TNF-alpha and p47-GTPase induction in macrophages using classical LPSs [lipid As with glucosamine backbones, ester- and amide-linked C14:0(3-OH) and C12 to C16 in acyloxyacyl groups] of wild type and mutant Escherichia coli and Yersinia species and non-classical LPSs [lipid As with diaminoglucose, ester-linked 3-OH-fatty acids and C28:0(27-OH) and C23:0(29-OH) in acyloxyacyl groups] of plant endosymbionts (Rhizobium), intracellular pathogens (Brucella and Legionella) and phylogenetically related opportunistic bacteria (Ochrobactrum). Classical but not non-classical LPSs efficiently induced TNF-alpha, IIGP and IGTP p47-GTPase expression. Remarkably, the acyloxyacyl groups in classical LPSs necessary to efficiently induce TNF-alpha were not necessary to induce p47-GTPases, suggesting that different aspects of lipid A are involved in this differential induction. This was confirmed by using PPDM2, a non-endotoxic lipid A-structurally related synthetic glycolipid. Despite their different bioactivity, all types of LPSs signalled through TLR-4 and not through TLR-2. However, whereas TNF-alpha induction was myeloid differentiation factor 88 (MyD88)-dependent, that of p47-GTPases occurred via a MyD88-independent pathway. These observations show that different aspects of the LPS pathogen-associated molecular pattern may be triggering different signalling pathways linked to the same TLR. They also reinforce the hypothesis that non-classical lipid As act as virulence factors by favouring the escape from the innate immune system.

Animals↗

PubMed2006

Cloning, expression and characterization of immunogenic aminopeptidase N from Brucella melitensis.

A 97-kDa purified aminopeptidase N (PepN) of Brucella melitensis was previously identified to be immunogenic in humans. The B. melitensis pepN gene was cloned, expressed in Escherichia coli and purified by affinity chromatography. The recombinant PepN (rPepN) exhibited the same biochemical properties, specificity and susceptibility to inhibitors as the native PepN. rPepN was evaluated as a diagnostic antigen in an indirect enzyme-linked immunosorbent assay (ELISA) using sera from patients with acute and chronic brucellosis. The specificity of the ELISA was determined with sera from healthy donors. The ELISA had a cutoff value of 0.156 with 100% specificity and 100% sensitivity. Higher sensitivity was obtained using rPepN compared with crude extract from B. melitensis. Anti-PepN sera did not exhibit serological cross-reaction to crude extracts from Rhizobium tropici, Ochrobactrum anthropi, Yersinia enterocolitica 09 or E. coli O157H7.

Brucella melitensis↗

PubMed1993

Phylogenetic analysis of the family Rhizobiaceae and related bacteria by sequencing of 16S rRNA gene using PCR and DNA sequencer.

The 16S rRNA gene sequences of 19 strains covering 97% of the molecules were determined for the members of the family Rhizobiaceae and related bacteria by PCR and DNA sequencer. The three biovars of Agrobacterium were located separately, whereas Agrobacterium rubi clustered with A. tumefaciens. Phylogenetic locations for the species of the genera Rhizobium, Sinorhizobium, Agrobacterium, Phylobacterium, Mycoplana (M. dimorpha), Ochrobactrum, Brucella and Rochalimaea (a rickettsia) were intermingled with each other with the similarity values higher than 92%. The family Rhizobiaceae should be redefined including the above-mentioned genera despite the ability for plant association and nitrogen fixation. Bradyrhizobium japonicum and Mycoplana bullata were far remote from the other species and should be excluded from this family.

Base Sequence↗

PubMed1997

Localization and characterization of a specific linear epitope of the Brucella DnaK protein.

We have previously produced and characterized four monoclonal antibodies to the Brucella DnaK protein which were derived from mice infected with B. melitensis or immunized with the B. melitensis cell wall fraction. By use of a recombinant DNA technique, we have localized a linear epitope, recognized by two of these monoclonal antibodies (V78/07B01/G11 and V78/09D04/D08), in the last 21 amino acids of the C-terminal region of the Brucella DnaK protein. The C-terminal region has been reported to be the most variable region among DnaK proteins. The two other monoclonal antibodies (A53/09G03/D02 and A53/01C10/A10) failed to react with the recombinant clones and might recognize discontinuous epitopes of the Brucella DnaK protein. The four monoclonal antibodies reacted with all recognized Brucella species and biovars in immunoblotting after SDS-PAGE. Monoclonal antibodies V78/07B01/G11 and V78/09D04/D08 did not react with reported cross-reacting bacteria nor with bacteria of the alpha-2 subdivision of the class Proteobacteria for which a close genetic relationship with Brucella spp. has been reported. However, monoclonal antibodies A53/09G03/D02 and A53/01C10/A10 reacted with Phyllobacterium rubiacearum and/or Ochrobactrum anthropi, both bacteria of the alpha-2 subdivision of the class Proteobacteria. The Brucella genus DnaK specific epitopes could be of importance for diagnostic purposes.

Adenosine Triphosphatases↗

PubMed2006

Recurrent outbreaks of root mat in cucumber and tomato are associated with a monomorphic, cucumopine, Ri-plasmid harboured by various Alphaproteobacteria.

Recurrent outbreaks of root mat have occurred in the UK and France in cucumber and tomato. Root mat is caused by bacterial strains harbouring a Ri-plasmid (pRi). Fifteen root mat-associated (RMA) cucumopine pRi were analysed by PCR-restriction fragment length polymorphism (RFLP) and Southern blotting. These pRi were harboured by Agrobacterium biovar 1 strains isolated during a 1970s outbreak of root mat in UK soil grown cucumber, and also by Agrobacterium biovar 1, Ochrobactrum, Rhizobium and Sinorhizobium isolated during outbreaks of root mat in cucumber and tomato grown hydroponically in the UK and France since 1993. PCR-RFLP analysis of the T-DNA and virD2 regions showed sequence homology between all cucumopine pRi, indicating that these pRi are monomorphic, and thus this pRi remained in the UK without inducing symptoms for some 15 years between outbreaks in the 1970s and 1990s. Cucumopine pRi were also shown to possess the virE2 substitute GALLS gene by Southern blotting. Two other pRi, harboured by Agrobacterium isolated from a recent root mat outbreak in one tomato crop, were also shown to possess the GALLS gene but were shown not to be cucumopine pRi by PCR-RFLP.

Alphaproteobacteria↗

PubMed2005

A DmpA-homologous protein from Pseudomonas sp. is a dipeptidase specific for beta-alanyl dipeptides.

We have determined the nucleotide sequence of a DNA fragment covering the flanking region of the R-stereoselective amidase gene, ramA, from the Pseudomonas sp. MCI3434 genome and found an additional gene, bapA, coding for a protein showing sequence similarity to DmpA aminopeptidase from Ochrobactrum anthropi LMG7991 (43% identity). The DmpA (called L-aminopeptidase D-Ala-esterase/amidase) hydrolyzes alanine-p-nitroanilide, alaninamide, and alanine methylester with a preference for the D-configuration of the alanine, whereas the enzyme acts as an L-stereoselective aminopeptidase on a tripeptide Ala-(Gly)2, indicating a reverse stereoselectivity [Fanuel L, Goffin C, Cheggour A, Devreese B, Van Driessche G, Joris B, Van Beeumen J & Frère J-M (1999) Biochem J341, 147-155]. A recombinant BapA exhibiting hydrolytic activity toward D-alanine-p-nitroanilide was purified from the cell-free extract of an Escherichia coli transformant overexpressing the bapA gene and characterized. The purified enzyme contained two polypeptides corresponding to residues 1-238 (alpha-peptide) and 239-366 (beta-peptide) of the precursor as observed for DmpA. On gel-filtration chromatography, BapA in the native form appeared to be a tetramer. It had maximal activity at 60 degrees C and pH 9.0-10.0, and was inactivated in the presence of p-chloromercuribenzoate, N-ethylmaleimide, dithiothreitol, Zn2+, Ag+, Cd2+ or Hg2+. The enzyme hydrolyzed D-alanine-p-nitroanilide more efficiently than L-alanine-p-nitroanilide the same as DmpA. Furthermore, BapA was found to hydrolyze peptide bonds of beta-alanyl dipeptides including beta-Ala-L-Ala, beta-Ala-Gly, beta-Ala-L-His (carnosine), beta-Ala-L-Leu, and (beta-Ala)2 with high efficiency compared to D-alanine-p-nitroanilide. Beta-alaninamide was also efficiently hydrolyzed, but the enzyme did not act on the peptides containing proteinogenic amino acids or their D-counterparts for N-terminal residues. Based on its unique substrate specificity, the enzyme should not be called L-aminopeptidase D-Ala-esterase/amidase but beta-Ala-Xaa dipeptidase.

Alanine↗

PubMed2006

Differences in microbial activity and microbial populations of peat associated with suppression of damping-off disease caused by Pythium sylvaticum.

The microbiological characteristics associated with disease-suppressive peats are unclear. We used a bioassay for Pythium sylvaticum-induced damping-off of cress seedlings to identify conducive and suppressive peats. Microbial activity in unconditioned peats was negatively correlated with the counts of P. sylvaticum at the end of the bioassay. Denaturing gradient gel electrophoresis (DGGE) profiling and clone library analyses of small-subunit rRNA gene sequences from two suppressive and two conducive peats differed in the bacterial profiles generated and the diversity of sequence populations. There were also significant differences between bacterial sequence populations from suppressive and conducive peats. The frequencies of a number of microbial groups, including the Rhizobium-Agrobacterium group (specifically sequences similar to those for the genera Ochrobactrum and Zoogloea) and the Acidobacteria, increased specifically in the suppressive peats, although no single bacterial group was associated with disease suppression. Fungal DGGE profiles varied little over the course of the bioassay; however, two bands associated specifically with suppressive samples were detected. Sequences from these bands corresponded to Basidiomycete yeast genera. Although the DGGE profiles were similar, fungal sequence diversity also increased during the bioassay. Sequences highly similar to those of Cryptococcus increased in relative abundance during the bioassay, particularly in the suppressive samples. This study highlights the importance of using complementary approaches to molecular profiling of complex populations and provides the first report that basidiomycetous yeasts may be associated with the suppression of Pythium-induced diseases in peats.

Basidiomycota↗