An rpoD gene sequence based evaluation of cultured Pseudomonas diversity on different growth media.

The last decade has shown an increased interest in the utilization of bacteria for applications ranging from bioremediation to wastewater purification and promotion of plant growth. In order to extend the current number of micro-organism mediated applications, a continued quest for new agents is required. This study focused on the genus Pseudomonas, which is known to harbour strains with a very diverse set of interesting properties.

Hazenella coriacea gen. nov., sp. nov., isolated from clinical specimens.

A Gram-staining-positive, endospore-forming rod was isolated independently from clinical specimens in New York State, USA, once in 2009 and twice in 2011. The three isolates had identical 16S rRNA gene sequences and, based on their 16S rRNA gene sequence, are most closely related to the type strains of Laceyella sediminis and L. sacchari (94.

Evaluation of oprI and oprL genes as molecular markers for the genus Pseudomonas and their use in studying the biodiversity of a small Belgian River.

A multiplex PCR based on oprI and oprL, coding for the outer membrane lipoprotein I and the peptidoglycan-associated lipoprotein OprL, respectively, was developed for the detection of Pseudomonas strains from a bacterial collection isolated from a small river. To study the diversity of these Pseudomonas isolates, an oprI-oprL gene sequence database of 94 Pseudomonas type strains was constructed. Phylogenetic analysis of the concatenated oprI and oprL gene sequences of the Pseudomonas type strains showed that they were largely congruent with the classification based on the MLSA approach based on 16S rRNA, gyrB, rpoB and rpoD gene sequences of Mulet et al.

Neisseria oralis sp. nov., isolated from healthy gingival plaque and clinical samples.

A polyphasic analysis was undertaken of seven independent isolates of gram-negative cocci collected from pathological clinical samples from New York, Louisiana, Florida and Illinois and healthy subgingival plaque from a patient in Virginia, USA. The 16S rRNA gene sequence similarity among these isolates was 99.7-100 %, and the closest species with a validly published name was Neisseria lactamica (96.

Tardiphaga robiniae gen. nov., sp. nov., a new genus in the family Bradyrhizobiaceae isolated from Robinia pseudoacacia in Flanders (Belgium).

Gram-negative, rod-shaped bacteria were isolated from Robinia pseudoacacia root nodules. On the basis of the 16S rRNA gene phylogeny, they are closely related to Bradyrhizobium, Rhodopseudomonas and Nitrobacter species (97% sequence similarity), belonging to the class Alphaproteobacteria and family Bradyrhizobiaceae. The results of physiological and biochemical tests together with sequence analysis of housekeeping genes (atpD, dnaK, gyrB, recA and rpoB) allowed differentiation of this group from other validly published Bradyrhizobiaceae genera.

Taxonomic revision of the genus Geobacillus: emendation of Geobacillus, G. stearothermophilus, G. jurassicus, G. toebii, G. thermodenitrificans and G. thermoglucosidans (nom. corrig., formerly 'thermoglucosidasius'); transfer of Bacillus thermantarcticus to the genus as G. thermantarcticus comb. nov.; proposal of Caldibacillus debilis gen. nov., comb. nov.; transfer of G. tepidamans to Anoxybacillus as A. tepidamans comb. nov.; and proposal of Anoxybacillus caldiproteolyticus sp. nov.

Sixty-two strains of thermophilic aerobic endospore-forming bacteria were subjected to polyphasic taxonomic study including 16S rRNA gene sequence analysis, polar lipid and fatty acid analysis, phenotypic characterization, and DNA-DNA hybridization experiments. Distinct clusters of the species Geobacillus stearothermophilus, Geobacillus thermodenitrificans, Geobacillus toebii and Geobacillus thermoglucosidasius were formed, allowing their descriptions to be emended, and the distinctiveness of the poorly represented species Geobacillus jurassicus, Geobacillus subterraneus and Geobacillus caldoxylosilyticus was confirmed. It is proposed that the name Geobacillus thermoglucosidasius be corrected to Geobacillus thermoglucosidans nom.

Lysinibacillus macroides sp. nov., nom. rev.

'Bacillus macroides' ATCC 12905(T) ( = DSM 54(T) = LMG 18474(T)), isolated in 1947 from cow dung, was not included in the Approved Lists of Bacterial Names and so it lost standing in bacteriological nomenclature. Reinvestigation of the strain, including DNA-DNA relatedness experiments, revealed that 'Bacillus macroides' is genomically distinct from its closest relatives Lysinibacillus xylanilyticus, Lysinibacillus boronitolerans and Lysinibacillus fusiformis (as determined by 16S rRNA gene sequence analysis, with pairwise similarity values of 99.2, 98.

Sporosarcina newyorkensis sp. nov. from clinical specimens and raw cow's milk.

Twelve independent isolates of a gram-positive, endospore-forming rod were recovered from clinical specimens in New York State, USA, and from raw milk in Flanders, Belgium. The 16S rRNA gene sequences for all isolates were identical. The closest species with a validly published name, based on 16S rRNA gene sequence, is Sporosarcina koreensis (97.

Emended descriptions of Bacillus sporothermodurans and Bacillus oleronius with the inclusion of dairy farm isolates of both species.

Bacillus sporothermodurans is an industrially important micro-organism because of its ability to produce endospores which resist ultra-high temperature (UHT) and industrial sterilization processes. It was described by Pettersson et al. (1996) [Pettersson, B.

Influence of storage conditions on the growth of Pseudomonas species in refrigerated raw milk.

The refrigerated storage of raw milk throughout the dairy chain prior to heat treatment creates selective conditions for growth of psychrotolerant bacteria. These bacteria, mainly belonging to the genus Pseudomonas, are capable of producing thermoresistant extracellular proteases and lipases, which can cause spoilage and structural defects in pasteurized and ultra-high-temperature-treated milk (products). To map the influence of refrigerated storage on the growth of these pseudomonads, milk samples were taken after the first milking turn and incubated laboratory scale at temperatures simulating optimal and suboptimal preprocessing storage conditions.

Bacillus thermolactis sp. nov., isolated from dairy farms, and emended description of Bacillus thermoamylovorans.

A polyphasic taxonomic study was performed on 22 thermotolerant, aerobic, endospore-forming bacteria from dairy environments. Seventeen isolates were retrieved from raw milk, one from a filter cloth and four from grass, straw or milking equipment. These latter four isolates (R-6546, R-7499, R-7764 and R-7440) were identified as Bacillus thermoamylovorans based on DNA-DNA hybridizations (values above 70 % with Bacillus thermoamylovorans LMG 18084(T)) but showed discrepancies in characteristics with the original species description, so an emended description of this species is given.

Emended descriptions of Geobacillus thermoleovorans and Geobacillus thermocatenulatus.

Nineteen thermophilic, aerobic, endospore-forming bacterial strains were subjected to 16S rRNA gene sequence analysis. Eight of these strains had been received as cultures of Geobacillus kaustophilus, G. lituanicus, G.

Identification of a gene coding for a deglycosylating enzyme in Hypocrea jecorina.

An enzyme with mannosyl glycoprotein endo-N-acetyl-beta-D-glucosaminidase (ENGase)-type activity was partially purified from the extracellular medium of the mould Hypocrea jecorina (Trichoderma reesei). Internal peptides were generated and used to identify the gene in the T. reesei genome.

Toxinogenic and spoilage potential of aerobic spore-formers isolated from raw milk.

The harmful effects on the quality and safety of dairy products caused by aerobic spore-forming isolates obtained from raw milk were characterized. Quantitative assessment showed strains of Bacillus subtilis, the Bacillus cereus group, Paenibacillus polymyxa and Bacillus amyloliquefaciens to be strongly proteolytic, along with Bacillus licheniformis, Bacillus pumilus and Lysinibacillus fusiformis to a lesser extent. Lipolytic activity could be demonstrated in strains of B.

Heterogeneity of heat-resistant proteases from milk Pseudomonas species.

Pseudomonas fragi, Pseudomonas lundensis and members of the Pseudomonas fluorescens group may spoil Ultra High Temperature (UHT) treated milk and dairy products, due to the production of heat-stable proteases in the cold chain of raw milk. Since the aprX gene codes for a heat-resistant protease in P. fluorescens, the presence of this gene has also been investigated in other members of the genus.

Comparative analysis of the diversity of aerobic spore-forming bacteria in raw milk from organic and conventional dairy farms.

Bacterial contamination of raw milk can originate from different sources: air, milking equipment, feed, soil, faeces and grass. It is hypothesized that differences in feeding and housing strategies of cows may influence the microbial quality of milk. This assumption was investigated through comparison of the aerobic spore-forming flora in milk from organic and conventional dairy farms.