Protein signatures to identify the different genera within the Xanthomonadaceae family

The Xanthomonadaceae family comprises the genera Xanthomonas and Xylella, which include plant pathogenic species that affect economically important crops. The family also includes the plant growth-promoting bacteria Pseudomonas geniculata and Stenotrophomonas rhizophila, and some other species with biotechnological, medical, and environmental relevance. Previous work identified molecular signatures that helped to understand the evolutionary placement of this family within gamma-proteobacteria. In the present study, we investigated whether insertions identified in highly conserved proteins may also be used as molecular markers for taxonomic classification and identification of members within the Xanthomonadaceae family. Four housekeeping proteins (DNA repair and replication-related and protein translation enzymes) were selected. The insertions allowed discriminating phytopathogenic and plant growth-promoting groups within this family, and also amino acid sequences of these insertions allowed distinguishing different genera and, eventually, species as well as pathovars. Moreover, insertions in the proteins MutS and DNA polymerase III (subunit alpha) are conserved in Xylella fastidiosa, but signatures in DNA ligase NAD-dependent and Valyl tRNA synthetase distinguish particular subspecies within the genus. The genus Stenotrophomonas and Pseudomonas geniculata could be distinguishable based on the insertions in MutS, DNA polymerase III (subunit alpha), and Valyl tRNA synthetase, although insertion in DNA ligase NAD-dependent discriminates these bacteria at the species level. All these insertions differentiate species and pathovars within Xanthomonas. Thus, the insertions presented support evolutionary demarcation within Xanthomonadaceae and provide tools for the fast identification in the field of these bacteria with agricultural, environmental, and economic relevance.

Antimicrobial susceptibility pattern of Stenotrophomonas species isolated from Mexico

BACKGROUND

Stenotrophomonas species are multi-resistant bacteria with ability to cause opportunistic infections.

OBJECTIVE

We isolated 45 Stenotrophomonas species from soil, sewage and the clinic with the aim of investigating their susceptibility to commonly used antimicrobial agents.

METHODOLOGY

The identities of isolates were confirmed with 16S rRNA gene sequence and MALDI-TOF analysis. Anti-microbial resistance, biofilm production and clonal diversity were also evaluated. The minimum inhibitory concentration technique as described by Clinical & Laboratory Standards Institute: CLSI Guidelines (CLSI) was employed for the evaluation of isolate susceptibility to antibiotics.

RESULT

Forty-five Stenotrophomonas species which include 36 environmental strains and 9 clinical strains of S. maltophilia were considered in this study. 32 (88.9 %) environmental strains were identified to be S. maltophilia, 2 (5.6 %) were Stenotrophomonas nitritireducens, and 2 (5.6 %) cluster as Stenotrophomonas spp. Stenotrophomonas isolates were resistant to at least six of the antibiotics tested, including Trimethoprim/Sulfamethoxazole (SXT).

CONCLUSION

Environmental isolates from this study were resistant to SXT which is commonly used for the treatment of S. maltophilia infections. This informs the need for good public hygiene as the environment could be a reservoir of multi-resistant bacteria. It also buttresses the importance of surveillance study in the management of bacterial resistance.

Insights of organic fertilizer micro flora of bovine manure and their useful potentials in sustainable agriculture

Exploration of diverse environmental samples for plant growth-promoting microbes to fulfill the increasing demand for sustainable agriculture resulted in increased use of bacterial biofertilizer. We aimed for the isolation of plant growth-promoting as well as antibiotic sensitive bacteria from bovine manure samples. The basic theme of our study is to highlight potentials of bacteria in manure and the unchecked risk associated with the application of manure i.e. introducing antibiotic-resistant microbial flora, as fertilizer. Fifty-two, morphologically distinct isolates; from eight different manure samples, were subjected to plant growth-promoting parametric tests along with antibiotic resistance. Thirteen antibiotic sensitive bacterial strains with potentials of plant growth promotion further characterized by 16S rRNA ribotyping and the identified genera were Stenotrophomonas, Achromobacter, Pseudomonas, and Brevibacillus. Successful radish seeds germination under sterile in-vitro conditions showed the potential of selected bacterial isolates as plant growth-promoting bacteria. The results of this study confirmed plant growth-promoting characteristics of bovine manures' bacterial strains along with an alarming antibiotic resistance load which comprises 75% of bacterial isolated population. Our study showed distinct results of un-explored manure bacterial isolates for plant growth promotion and flagged ways associated with unchecked manure application in agriculture soil through high load of antibiotic resistant bacteria.

Diversity and hydrocarbon-degrading potential of epiphytic microbial communities on Platanus x acerifolia leaves in an urban area

Plants and their associated bacteria have been suggested to play a role in air pollution mitigation, especially in urban areas. Particularly, epiphytic bacteria might be able to degrade atmospheric hydrocarbons. However, phyllospheric bacterial communities are highly variable depending on several factors, e.g. tree species, leaf age and physiology, environmental conditions. In this work, bacterial communities hosted by urban Platanus x acerifolia leaves were taxonomically characterized using high throughput sequencing of 16S rRNA gene, and their temporal and spatial variability was assessed by comparing samples collected from different locations in the city of Milan (Italy) and in different months. The diversity of alkane hydroxylase (alkB) phylotypes harboured by phyllospheric bacteria associated to urban Platanus trees was also evaluated. Results revealed that temporal changes, which are related to seasonality, acted as a stronger driver both on Platanus phyllospheric community structure and on alkB phylotype diversity than sampling location. Biodiversity of bacterial communities decreased along the growing season, leading to a strong dominance by the genus Stenotrophomonas. On the contrary, diversity of hydrocarbon-degrading populations increased over the months, although it resulted lower than that reported for other habitats. It was therefore hypothesized that atmospheric hydrocarbons might play a key role in the selection of phyllospheric populations in urban areas.

Treatment of seafood processing wastewater using upflow microbial fuel cell for power generation and identification of bacterial community in anodic biofilm

Tubular upflow microbial fuel cell (MFC) utilizing sea food processing wastewater was evaluated for wastewater treatment efficiency and power generation. At an organic loading rate (OLR) of 0.6 g d(-1), the MFC accomplished total and soluble chemical oxygen demand (COD) removal of 83 and 95%, respectively. A maximum power density of 105 mW m(-2) (2.21 W m(-3)) was achieved at an OLR of 2.57 g d(-1). The predominant bacterial communities of anode biofilm were identified as RB1A (LC035455), RB1B (LC035456), RB1C (LC035457) and RB1E (LC035458). All the four strains belonged to genera Stenotrophomonas. The results of the study reaffirms that the seafood processing wastewater can be treated in an upflow MFC for simultaneous power generation and wastewater treatment.

Microbiome of Deep Dentinal Caries Lesions in Teeth with Symptomatic Irreversible Pulpitis

This study used a next-generation sequencing approach to identify the bacterial taxa occurring in the advanced front of caries biofilms associated with pulp exposure and irreversible pulpitis. Samples were taken from the deepest layer of dentinal caries lesions associated with pulp exposure in 10 teeth diagnosed with symptomatic irreversible pulpitis. DNA was extracted and the microbiome was characterized on the basis of the V4 hypervariable region of the 16S rRNA gene by using paired-end sequencing on Illumina MiSeq device. Bacterial taxa were mapped to 14 phyla and 101 genera composed by 706 different OTUs. Three phyla accounted for approximately 98% of the sequences: Firmicutes, Actinobacteria and Proteobacteria. These phyla were also the ones with most representatives at the species level. Firmicutes was the most abundant phylum in 9/10 samples. As for genera, Lactobacillus accounted for 42.3% of the sequences, followed by Olsenella (13.7%), Pseudoramibacter (10.7%) and Streptococcus (5.5%). Half of the samples were heavily dominated by Lactobacillus, while in the other half lactobacilli were in very low abundance and the most dominant genera were Pseudoramibacter, Olsenella, Streptococcus, and Stenotrophomonas. High bacterial diversity occurred in deep dentinal caries lesions associated with symptomatic irreversible pulpitis. The microbiome could be classified according to the relative abundance of Lactobacillus. Except for Lactobacillus species, most of the highly prevalent and abundant bacterial taxa identified in this study have been commonly detected in infected root canals. The detected taxa can be regarded as candidate pathogens for irreversible pulpitis and possibly the pioneers in pulp invasion to initiate endodontic infection.

[Identification of bacterial strain ge15 and its controlling effect on ginseng diseases]

Based on previous results of 16S rDNA sequence homologuous and results of physic-biochemical indexes and morphological characteristics in the present work, bacterial strain ge15 isolated from roots of ginseng plants was identified as Stenotrophomonas rhizophila. Confronting incubation results showed that, strain ge15 inhibited the growth of Alternaria panax, Phytophthora cactorum, and Cylindrocapon destructans significantly, and the width of inhibition zone was 13.3, 24.0, 12.0 mm, respectively. Further results showed that the emergence rate and seedling survive rate of ge15 treatment was significantly higher than those of the control, and which was similar to pesticide carbendazol treatment. The ge15 strain has good application potential in ginseng diseases control without contamination.

[Isolation, identification and characterization of an agarase-producing marine bacterial strain Stenotrophomonas sp. NTa]

OBJECTIVE

To identify and characterize a marine bacterial strain producing agarase.

METHODS

The agarase-producing bacterium was isolated from coastal sediments in Xiamen using agar as the sole carbon source. The strain was identified by the analyses of 16S rRNA gene sequence, phenotype and biochemical reactions. Agarase activity was determined by dinitrosalicylic acid method, and the category of agarase was assayed using chromogenic substrate. At last, the characteristics of agarase were determined.

RESULTS

The results of the 16S rRNA phylogenetic, phenotypic and biochemical analyses showed that: the agar-degrading bacterium NTa belonged to the genus Stenotrophomonas sp.. The strain could produce extracellular agarases, including alpha-agarase and beta-agarase. The optimum temperature and pH of strain NTa agarase were 40 degrees C and 7.0, respectively. The enzymatic activity was stable below 30 degrees C. It also showed stability over a pH range between 7.0 and. 0. Ca2+ could activate agarase activity, and Na+, K+ and Mg2+ had no significant influence. However, Ag', Ba2 , Fe2' , Mn2', Cu2', Zn2+ and Fe3' inhibited the enzyme activity. The enzymatic activity of stain NTa agarase was inhibited by EDTA. The agarase had good resistance to some inhibitors, detergents and denaturant.

CONCLUSION

Stenotrophomonas sp. NTa is a new type of agarase-producing strain, which can produce both alpha-agarase and beta-agarase and has potential applications in the production of agaro-oligosaccharide.

Biosynthesis of gold and silver nanoparticles using a novel marine strain of Stenotrophomonas

The present study aims at exploiting marine microbial diversity for biosynthesis of metal nanoparticles and also investigates role of microbial proteins in the process of bio-mineralization of gold and silver. This is the first report for concurrent production of gold and silver nanoparticles (AuNPs and AgNPs) by extracellular secretion of a novel strain of Stenotrophomonas, isolated from Indian marine origin. This novel strain has faster rate kinetics for AgNPs synthesis than any other organism reported earlier. The nanoparticles were further characterized using UV-vis spectrophotometer, TEM, DLS and EDAX confirming their size ranging from 10-50 nm and 40-60 nm in dimensions for AuNPs and AgNPs, respectively. TEM analysis indicated formation of multi-shaped nanoparticles with heterogeneous size distribution in both the cases. Finally, the SDS-PAGE analysis of extracellular media supernatant suggested a potential involvement of certain low molecular weight secretory proteins in AuNPs and AgNPs biosynthesis.

Degradative potential of Stenotrophomonas strain HPC383 having genes homologous to dmp operon

A strain, Stenotrophomonas HPC383 is isolated from effluent treatment plant treating wastewater from pesticide industry; degrades various aromatic compounds (cresols, phenol, catechol, 4methyl-catechol and hydroquinone) and crude oil, as determined through HPLC and GC analysis. Culture HPC383 could degrade (%) various compounds (1 mM) from a mixture: phenol - 99, p-cresol - 100, 4-methylcatechol - 96 and hydroquinone - 43 within 48 h of incubation, whereas it took 7 days to degrade 94% of 0.5% crude oil. Gene locus dmpN, to identify phenol degrading capacity was determined by PCR followed by southern analysis. The sequenced DNA fragment exhibited 99% sequence similarity to phenol hydroxylase gene from Arthrobacter sp. W1 (FJ610336). Amino acid sequence analysis of phenol hydroxylase reveals it to belong to high-Ks (affinity constant) group. Application of HPC383 in bioremediation of aquatic and terrestrial sites contaminated with petrochemical has been suggested.

[Isolation and identification of a polyhydroxyalkanoate producing strain]

OBJECTIVE

We screened and isolated polyhydroxyalkanoate producing bacteria.

METHODS

The strains were isolated from sludge from a beer brewery and screened by Sudan black B staining method. The isolated strains were identified according to their morphological features, physiological and biochemical analysis as well as 16S rRNA gene sequence analysis. The product extracted with hot chloroform from the isolated strain HG-B-1 was confirmed by Fourier transform infrared spectra.

RESULTS

We isolated a bacterium, HG-B-1, from sludge collected from a beer brewery in Guangdong province, China. The yield of polyhydroxyalkanoates was 23.4% (w/w) based on dried weight of the bacterium cells when HG-B-1 grew in a medium containing saccharose. We analyzed 16S rRNA nucleotide sequence, and ascertained the phylogenetic position of the strain.

CONCLUSION

Strain HG-B-1 with PHAs biosynthesis ability was identified as Stenotrophomonas maltophlia.

Evaluation of genetic and functional diversity of Stenotrophomonas isolates from diverse effluent treatment plants

In this study, the samples were collected from nine ETPs and soil contaminated with petroleum products. The genetic diversity of 30 Stenotrophomonas isolates was demonstrated by phylogenetic analysis of their 16S rRNA gene nucleotide sequences, and randomly amplified polymorphic DNA (RAPD) analysis supplemented with in silico signature and restriction enzyme (REs--AluI, BfaI, DpnII, HaeIII, RsaI and Tru9I) digestion analyses. Genetic diversity based on nucleotide sequence data revealed distinct clusters. Functional diversity was analysed on the basis of the abilities of these isolates to degrade phenol, p-cresol, catechol, 4-methylcatechol and hydroquinone. Based on the environmental, genetic and functional diversities, a consortium of mixed defined microbes has been proposed for bioremediation programs.

Stenotrophomonas daejeonensis sp. nov., isolated from sewage

A Gram-stain-negative, motile, aerobic bacterial strain, designated MJ03(T), was isolated from sewage and was characterized taxonomically by using a polyphasic approach. Comparative 16S rRNA gene sequence analysis showed that strain MJ03(T) belongs to the family Xanthomonadaceae, class Gammaproteobacteria, and was related most closely to Stenotrophomonas acidaminiphila AMX 19(T) (97.9  % sequence similarity), Stenotrophomonas humi R-32729(T) (97.1  %), Stenotrophomonas nitritireducens L2(T) (96.9  %), Stenotrophomonas maltophila ATCC 13637(T) (96.8  %) and Stenotrophomonas terrae R-32768(T) (96.7  %). The G+C content of the genomic DNA of strain MJ03(T) was 64.7 mol%. The detection of a quinone system with ubiquinone Q-8 as the predominant component and a fatty acid profile with iso-C₁₅:₀, iso-C₁₁:₀, iso-C₁₄:₀, iso-C₁₇:₁ω9c, iso-C₁₁:₀ 3-OH and iso-C₁₃:₀ 3-OH as major components supported the affiliation of strain MJ03(T) to the genus Stenotrophomonas. However, levels of DNA-DNA relatedness between strain MJ03(T) and the type strains of five closely related species of the genus Stenotrophomonas ranged from 11 to 34  %, showing clearly that the isolate represents a novel genospecies. Strain MJ03(T) could be differentiated clearly from its phylogenetic neighbours on the basis of several phenotypic, genotypic and chemotaxonomic features. Therefore, strain MJ03(T) is considered to represent a novel species of the genus Stenotrophomonas, for which the name Stenotrophomonas daejeonensis sp. nov. is proposed. The type strain is MJ03(T) (=KCTC 22451(T) =JCM 16244(T)).

Biodegradation of p-nitrophenol and 4-chlorophenol by Stenotrophomonas sp

A bacterium named LZ-1 capable of utilizing high concentrations of p-nitrophenol (PNP) (up to 500 mg L(-1)) as the sole source of carbon, nitrogen and energy was isolated from an activated sludge. Based on the results of phenotypic features and phylogenetic similarity of 16S rRNA gene sequences, strain LZ-1 was identified as a Stenotrophomonas sp. Other p-substituted phenols such as 4-chlorophenol (4-CP) were also degraded by strain LZ-1, and both PNP and 4-CP were degraded via the hydroquinone pathway exclusively. Strain LZ-1 could degrade PNP and 4-CP simultaneously and the degradation of PNP was greatly accelerated due to the increased biomass supported by 4-CP. An indigenous plasmid was found to be responsible for phenols degradation. In soil samples, 100 mg kg(-1) of PNP and 4-CP in mixtures were removed by strain LZ-1 (10(6) cells g(-1)) within 14 and 16 days respectively, and degradation activity was maintained over a wide range of temperatures (4-35 degrees C). Therefore, strain LZ-1 can potentially be used in bioremediation of phenolic compounds either individually or as a mixture in the environment.

Occurrence and antagonistic potential of Stenotrophomonas strains isolated from deep-sea invertebrates

Stenotrophomonas maltophilia is known to be of significance as opportunistic pathogen as well as a source of biocontrol and bioremediation activities. S. maltophilia strains have been isolated from rhizospheres, soil, clinical material, aquatic habitats, but little is known about Stenotrophomonas strains recovered from marine environments. During a survey of the biodiversity of Pseudomonas-like bacteria associated with deep-sea invertebrates six Stenotrophomonas strains were isolated from sponge, sea urchin, and ophiura specimens collected from differing Pacific areas, including the Philippine Sea, the Fiji Sea and the Bering Sea. 16S rRNA gene sequence analysis confirmed an assignment of marine isolates to the genus Stenotrophomonas as it placed four strains into the S. maltophilia CIP 60.77T cluster and two related to the S. rhizophila DSM 14405T. Together with a number of common characteristics typical of S. maltophilia and S. rhizophila marine isolates exhibited differences in pigmentation, a NaCl tolerance, a range of temperatures, which supported their growth, substrate utilization pattern, and antibiotics resistance. Strains displayed hemolytic and remarkable inhibitory activity against a number of fungal cultures and Gram-positive microorganisms, but very weak or none against Candida albicans. This is the first report on isolation, taxonomic characterization and antimicrobial activity of Stenotrophomonas strains isolated from deep-sea invertebrates.

Isolation and characterization of diuron-degrading bacteria from lotic surface water

The bacterial community structure of a diuron-degrading enrichment culture from lotic surface water samples was analyzed and the diuron-degrading strains were selected using a series of techniques combining temporal temperature gradient gel electrophoresis (TTGE) of 16 S rDNA gene V1-V3 variable regions, isolation of strains on agar plates, colony hybridization methods, and biodegradation assays. The TTGE fingerprints revealed that diuron had a strong impact on bacterial community structure and highlighted both diuron-sensitive and diuron-adapted bacterial strains. Two bacterial strains, designated IB78 and IB93 and identified as belonging to Pseudomonas sp. and Stenotrophomonas sp., were isolated and shown to degrade diuron in pure resting cells in a first-order kinetic reaction during the first 24 h of incubation with no 3,4-DCA detected. The percentages of degradation varied from 25% to 60% for IB78 and 20% to 65% for IB93 and for a diuron concentration range from 20 mg/L to 2 mg/L, respectively. It is interesting to note that diuron was less degraded by single isolates than by mixed resting cells, thereby underlining a cumulative effect between these two strains. To the best of our knowledge, this is the first report of diuron-degrading strains isolated from lotic surface water.

Stenotrophomonas terrae sp. nov. and Stenotrophomonas humi sp. nov., two nitrate-reducing bacteria isolated from soil

Three Gram-negative, rod-shaped, non-spore-forming, nitrate-reducing isolates (R-32746, R-32768T and R-32729T) were obtained from soil. Analysis of repetitive sequence-based PCR showed that the three isolates represented two different strains. 16S rRNA gene sequence analysis and DNA–DNA hybridization placed them within the genus Stenotrophomonas and revealed that they were genotypically different from each other and from all recognized Stenotrophomonas species. Analysis of the fatty acid composition and physiological and biochemical tests allowed differentiation from their closest phylogenetic neighbours. They are therefore considered to represent two novel species, for which the names Stenotrophomonas terrae sp. nov. and Stenotrophomonas humi sp. nov. are proposed, with strains R-32768T (=LMG 23958T=DSM 18941T) and R-32729T (=LMG 23959T=DSM 18929T), respectively, as the type strains.

Detection of DNA from a range of bacterial species in the knee joints of dogs with inflammatory knee arthritis and associated degenerative anterior cruciate ligament rupture

Mixtures of bacterial nucleic acids can often be detected in synovial joints affected with arthritis. We investigated the potential role of such mixtures of bacterial nucleic acids in the pathogenesis of arthritis in a naturally occurring canine model. Dogs with a common inflammatory knee arthritis in which associated pathological degenerative anterior cruciate ligament (ACL) rupture often develops were studied. Synovial biopsies were obtained from 43 dogs with the naturally occurring ACL rupture arthropathy, 12 dogs with normal knees and intact ACL, and 16 dogs with normal knees and experimentally induced ACL rupture. Using PCR, specimens were tested for Borrelia burgdorferi OspA and p66 gene sequences. Broad-ranging 16S rRNA primers were also used; 'panbacterial' PCR products were cloned and multiple clones were sequenced for bacterial identification. Synovium was also studied histologically. The presence of bacterial DNA within the synovium was significantly associated with the naturally occurring ACL rupture arthropathy (p<0.05); knee joints from 37% of these dogs were PCR-positive. Mixtures of bacterial DNA were common and often included environmental bacteria; predominant organisms included Borrelia burgdorferi and Stenotrophomonas maltophilia. DNA from environmental bacteria was only found in dogs with the naturally occurring ACL rupture arthopathy; joints from 33% of affected dogs contained such bacterial DNA. Synovial inflammation developed in dogs with both naturally occurring and experimentally induced ACL rupture, when compared with intact ACL controls (p<0.01). These results indicate that mixtures of DNA derived from environmental bacteria are commonly found in the knee joint of a naturally occurring canine arthropathy, often in association with a recognized joint pathogen. Our results also suggest that knee instability alone is not responsible for this finding and have led us to hypothesize that mixtures of bacterial DNA are an important causative factor in the pathogenesis of inflammatory arthritis in this canine model.

Stenotrophomonas dokdonensis sp. nov., isolated from soil

A Gram-negative, rod-shaped, Stenotrophomonas-like bacterial strain, DS-16(T), was isolated from soil from Dokdo, Korea, and subjected to a polyphasic taxonomic study. Strain DS-16(T) grew optimally at pH 6.0-7.0 and 30 degrees C in the presence of 0.5 % (w/v) NaCl. It contained Q-8 as the predominant ubiquinone and iso-C(16 : 0), iso-C(15 : 0) and iso-C(17 : 1)omega9c as the major fatty acids. The DNA G + C content was 65.1 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain DS-16(T) joined the cluster comprising Stenotrophomonas species. The levels of 16S rRNA gene sequence similarity between strain DS-16(T) and the type strains of Stenotrophomonas species ranged from 95.5 to 97.5 %. DNA-DNA relatedness data and differential phenotypic properties, together with the phylogenetic distinctiveness of strain DS-16(T), demonstrated that this novel strain differs from Stenotrophomonas species with validly published names. On the basis of phenotypic, phylogenetic and genetic data, strain DS-16(T) (=KCTC 12543(T) = CIP 108839(T)) should be classified in the genus Stenotrophomonas as a member of a novel species, for which the name Stenotrophomonas dokdonensis sp. nov. is proposed.

[Isolation, identification and phylogenetic analysis of a pathogenic bacterium in channel catfish]

A pathogenic bacterium (CCF00024) was isolated from the kidney and liver of the diseased channel catfish with acute epidemic disease. Artificial infection proved that the bacterium was the pathogen of the disease. Its morphological, physiological, biochemical characteristics and 16S rDNA sequence analysis were studied. The isolated strain is an aerobic, non-fermentative bacterium. The bacteria are gram negative, rods, with polar multi-flagella; Oxidase-negative, methyl-red-negative, lysine decarboxylase-positive, DNAase-positive, urease-positive, lipase-positive and protease-positive. The bacteria can't utilize most of sugars with production of acid, except maltose and mannose. A phylogenetic tree was constructed by comparing the 16S rDNA sequence of the isolated strain (GenBank accession number AY970826) with other relative bacteria species in the RDP and GenBank databases. In the phylogenetic tree CCF00024, Stenotrophomonas maltophilia 13637T, Stenotrophomonas maltophilia MG958T, and Stenotrophomonas maltophilia M5-1 constitute a branch. The similarity value between strain CCF00024 and those 5 strains Stenotrophomonas maltophilia are 99.4%-99.6%. According to morphological, physiological, biochemical characteristics and phylogenetic analysis, the isolated strain (CCF00024) is identified as Stenotrophomonas maltophilia.

Degradation of Low-Ethoxylated Nonylphenols by a Stenotrophomonas Strain and Development of New Phylogenetic Probes for Stenotrophomonas spp. Detection

An aerobic bacterium (BCc6), isolated from nonylphenol polyethoxylates (NPEOs)-contaminated sludge, was shown to be capable of degrading low-ethoxylated NPEO mixtures. Sequencing of 16S rRNA gene (rDNA) showed that it clustered with Stenotrophomonas nitritireducens. Fluorescent in situ hybridization (FISH), performed on BCc6 strain and on the previously isolated Stenotrophomonas BCaL2, also involved in NPEO degradation but clustering with S. maltophilia, showed that strain BCc6 did not hybridize with the S. maltophilia-specific probe, and neither of the two strains hybridized with probes targeted to the Gammaproteobacteria site, rDNA analyses performed on the two strains evidenced two new polymorphisms, the first one at the 23S rRNA Gammaproteobacteria site, characterizing the known members of the Stenotrophomonas genus, and the other one at the 16S rRNA level, characteristic of S. nitritireducens. Two new FISH probes were designed accordingly, tested on control bacterial cultures, and employed for in situ monitoring of Stenotrophomonas representatives.

Stenotrophomonas koreensis sp. nov., isolated from compost in South Korea

A Gram-negative, rod-shaped, non-spore-forming bacterium (TR6-01T) was isolated from compost near Daejeon city in South Korea. On the basis of 16S rRNA gene sequence similarity, strain TR6-01T was shown to belong to the class Gammaproteobacteria, related to Stenotrophomonas acidaminiphila (97.1 %) and Stenotrophomonas maltophilia (96.9 %); the phylogenetic distance from any other established species within the genus Stenotrophomonas was less than 97.0 %. Phenotypic and chemotaxonomic data (major ubiquinone Q-8; fatty acid profile) supported the affiliation of strain TR6-01T to the genus Stenotrophomonas. The results of DNA-DNA hybridization and physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain TR6-01T from the five Stenotrophomonas species with validly published names. TR6-01T therefore represents a novel species, for which the name Stenotrophomonas koreensis sp. nov. is proposed, with the type strain TR6-01T (= KCTC 12211T = JCM 13256T).

Stenotrophomonas africana Drancourt et al. 1997 is a later synonym of Stenotrophomonas maltophilia (Hugh 1981) Palleroni and Bradbury 1993

Type and reference strains of Stenotrophomonas maltophilia and Stenotrophomonas africana were compared with each other and with the type strains of other Stenotrophomonas species, using SDS-PAGE of whole-cell proteins, DNA–DNA hybridization and extensive biochemical characterization. S. maltophilia LMG 958T and S. africana LMG 22072T had very similar whole-cell-protein patterns and were also biochemically very similar. A DNA–DNA binding level of 70 % between both type strains confirmed that S. africana and S. maltophilia represent the same taxon. It is concluded that S. africana is a later synonym of S. maltophilia.

Identification of genomic groups in the genusStenotrophomonasusinggyrBRFLP analysis

Stenotrophomonas maltophilia isolates have been recovered from various clinical samples, including the respiratory tract of cystic fibrosis (CF) patients, but this organism is also widespread in nature. Previously it has been shown that there is a considerable genomic diversity within S. maltophilia. The aims of our study were to determine the taxonomic resolution of restriction fragment length polymorphism (RFLP) analysis of the polymerase chain reaction-amplified gyrB gene for the genus Stenotrophomonas. Subsequently, we wanted to use this technique to screen a set of S. maltophilia isolates (with emphasis on a specific subset, isolates recovered from CF patients), to assess the genomic diversity within this group. In this study we investigated 191 Stenotrophomonas sp. isolates (including 40 isolates recovered from CF patients) by means of gyrB RFLP. The taxonomic resolution of gyrB RFLP, and hence its potential as an identification tool, was confirmed by comparison with results from published and novel DNA-DNA hybridisation experiments. Our data also indicate that the majority of CF isolates grouped in two clusters. This may indicate that isolates from specific genomic groups have an increased potential for colonisation of the respiratory tract of CF patients.

Conservation of the response regulator gene gacA in Pseudomonas species

The response regulator gene gacA influences the production of several secondary metabolites in both pathogenic and beneficial Pseudomonas spp. In this study, we developed primers and a probe for the gacA gene of Pseudomonas species and sequenced a 425 bp fragment of gacA from ten Pseudomonas strains isolated from different plant-associated environments. Polymerase chain reaction analysis and Southern hybridization showed that gacA is highly conserved within the genus Pseudomonas: multiple strains of different Pseudomonas species all responded positively to the probe, whereas no response was obtained from 18 other strains representing 14 species that belong to eight different genera of Gram-negative bacteria other than Pseudomonas. Furthermore, from a total of approximately 550 indigenous bacterial isolates obtained from the rhizosphere of wheat, all isolates that hybridized with the gacA probe were classified as Pseudomonas spp. by group-specific primers. Isolates that did not respond with the gacA probe and primers were identified as bacterial genera other than Pseudomonas, including Stenotrophomonas, Cryseomonas and Comamonas spp. These results indicate that gacA can be used as a complementary genetic marker for detection of Pseudomonas spp. in environmental samples. Phylogenetic relationships inferred from the newly sequenced gacA fragments and the sequences of gacA homologues present in the databases, showed six distinct clusters that correspond to the following bacterial families: Pseudomonaceae, Enterobacteriaceae, Alteromonadaceae, Vibrionaceae, Burkholderia and Xanthomonas. Within the Pseudomonadaceae and Enterobacteriaceae, polymorphisms within gacA and its homologues allowed identification of six and five subclusters respectively. Comparison of the gacA gene and GacA protein-based trees with the tree inferred from 16S rDNA sequences yielded a similar overall clustering. These results suggest that gacA and its homologues may provide complementary markers for phylogenetic studies of Pseudomonas spp. and Gram-negative bacteria other than Pseudomonas.

Diversity of transconjugants that acquired plasmid pJP4 or pEMT1 after inoculation of a donor strain in the A- and B-horizon of an agricultural soil and description of Burkholderia hospita sp. nov. and Burkholderia terricola sp. nov

We examined the diversity of transconjugants that acquired the catabolic plasmids pJP4 or pEMT1, which encode degradation of 2,4-dichlorophenoxyacetic acid (2,4-D), in microcosms with agricultural soil inoculated with a donor strain (Dejonghe, W., Goris, J., El Fantroussi, S., Höfte, M., De Vos, P., Verstraete, W., and Top, E. M. Appl. Environ. Microbiol. 2000, p. 3297-3304). Using repetitive element PCR fingerprinting, eight different rep-clusters and six separate isolates could be discriminated among 95 transconjugants tested. Representative isolates were identified using 16S rDNA sequencing, cellular fatty acid analysis, whole-cell protein analysis and/or DNA-DNA hybridisations. Plasmids pJP4 and pEMT1 appeared to have a similar transfer and expression range, and were preferably acquired and expressed in soil by indigenous representatives of Ralstonia and Burkholderia. Two rep-clusters were shown to represent novel Burkholderia species, for which the names Burkholderia hospita sp. nov. and Burkholderia terricola sp. nov. are proposed. When easily degradable carbon sources were added together with the plasmid-bearing donor strain, also a significant proportion of Stenotrophomonas maltophilia isolates were found. The transconjugant collections isolated from A- (0-30 cm depth) and B-horizon (30-60 cm depth) soil were similar, except for B. terricola transconjugants, which were only isolated from the B-horizon.

Microbiota of periapical lesions refractory to endodontic therapy

The periapical microbiota of 36 teeth with refractory apical periodontitis was investigated. None of the teeth had responded to conventional endodontic or long-term (> 6 months), calcium-hydroxide treatment. Eight patients had received antibiotics systemically. After anaerobic culture, a total of 148 microbial strains were detected among 67 microbial species. One of the 36 lesions was culture-negative. Approximately half (51.0%) of the bacterial strains were anaerobic. Gram-positive species constituted 79.5% of the flora. Facultative organisms, such as Staphylococcus, Enterococcus, Enterobacter, Pseudomonas, Stenotrophomonas, Sphingomonas, Bacillus, or Candida species were recovered from 27 of the lesions (75%). Sulfur granules were found in 9 lesions (25%). In these granules Actinomyces israelii, A. viscosus, A. naeslundii, and A. meyeri were identified. Other bacterial species, both gram-positive and gram-negative, were detected in the granules as well. Two sulfur granules did not contain Actinomyces. Scanning electron microscopy demonstrated rod- and spirochete-like cells in the granules, and transmission electron microscopy revealed organisms with copious amounts of extracellular material. Outer membrane vesicles were also seen. Some of the granules were calcified. This study demonstrated a wide variety of microorganisms, particularly gram-positive ones, in the periapical lesions of teeth with refractory apical periodontitis.

Microscale biosensor for measurement of volatile fatty acids in anoxic environments

A microscale biosensor for acetate, propionate, isobutyrate, and lactate is described. The sensor is based on the bacterial respiration of low-molecular-weight, negatively charged species with a concomitant reduction of NO(-)(3) to N(2)O. A culture of denitrifying bacteria deficient in N(2)O reductase was immobilized in front of the tip of an electrochemical N(2)O microsensor. The bacteria were separated from the outside environment by an ion-permeable membrane and supplied with nutrients (except for electron donors) from a medium reservoir behind the N(2)O sensor. The signal of the sensor, which corresponded to the rate of N(2)O production, was proportional to the supply of the electron donor to the bacterial mass. The selectivity for volatile fatty acids compared to other organic compounds was increased by selectively enhancing the transport of negatively charged compounds into the sensor by electrophoretic migration (electrophoretic sensitivity control). The sensor was susceptible to interference from O(2), N(2)O, NO(2)(-), H(2)S, and NO(-)(3). Interference from NO(-)(3) was low and could be quantified and accounted for. The detection limit was equivalent to about 1 microM acetate, and the 90% response time was 30 to 90 s. The response of the sensor was not affected by changes in pH between 5.5 and 9 and was also unaffected by changes in salinity in the range of 2 to 32 per thousand. The functioning of the sensor over a temperature span of 7 to 30 degrees C was investigated. The concentration range for a linear response was increased five times by increasing the temperature from 7 to 19.5 degrees C. The life span of the biosensor varied between 1 and 3 weeks after manufacturing.

Stenotrophomonas acidaminiphila sp. nov., a strictly aerobic bacterium isolated from an upflow anaerobic sludge blanket (UASB) reactor

Two of several strictly aerobic, mesophilic bacteria isolated from a lab-scale upflow anaerobic sludge blanket (UASB) reactor treating a petrochemical wastewater, strains AMX 17 and AMX 19T, were subjected to detailed taxonomic study. Cells were gram-negative, motile, non-sporulating, straight to curved rods with a polar flagellum. The isolates exhibited phenotypic traits of members of the genus Stenotrophomonas, including cellular fatty acid composition and the limited range of substrates that could be used. Sugars and many amino acids were utilized. Antibiotic susceptibility and physiological characteristics were determined. The DNA base composition was 66.9 mol% G+C. Phylogenetic analysis revealed that the nearest relatives were Stenotrophomonas maltophilia LMG 11114, Stenotrophomonas nitritireducens DSM 12575T and Pseudomonas pictorum ATCC 23328T (similarity of 98.1-98.8%). Xanthomonas species, S. maltophilia LMG 958T and Stenotrophomonas africana CIP 104854T showed high 16S rRNA sequence similarities (96.4-97.3%). The high similarity found in cellular fatty acid profiles and identical partial 16S rRNA sequences (500 bp) for strains AMX 17 and AMX 19T indicate that they belong to the same species. DNA-DNA hybridizations revealed respectively 26.7, 31, 65.8 and 43.6% homology between isolate AMX 19T and S. africana CIP 104854T, S. maltophilia CIP 60.77T, S. nitritireducens DSM 12575T and P. pictorum ATCC 23328T. These results allow the proposal of strain AMX 19T (= DSM 13117T = ATCC 700916T = CIP 106456T) as representative of a novel species of the genus Stenotrophomonas, with the name Stenotrophomonas acidaminiphila sp. nov.

Evaluation of the VITEK 2 system for the identification and susceptibility testing of three species of nonfermenting gram-negative rods frequently isolated from clinical samples

VITEK 2 is a new automatic system for the identification and susceptibility testing of the most clinically important bacteria. In the present study 198 clinical isolates, including Pseudomonas aeruginosa (n = 146), Acinetobacter baumannii (n = 25), and Stenotrophomonas maltophilia (n = 27) were evaluated. Reference susceptibility testing of cefepime, cefotaxime, ceftazidime, ciprofloxacin, gentamicin, imipenem, meropenem, piperacillin, tobramycin, levofloxacin (only for P. aeruginosa), co-trimoxazole (only for S. maltophilia), and ampicillin-sulbactam and tetracycline (only for A. baumannii) was performed by microdilution (NCCLS guidelines). The VITEK 2 system correctly identified 91.6, 100, and 76% of P. aeruginosa, S. maltophilia, and A. baumannii isolates, respectively, within 3 h. The respective percentages of essential agreement (to within 1 twofold dilution) for P. aeruginosa and A. baumannii were 89.0 and 88.0% (cefepime), 91.1 and 100% (cefotaxime), 95.2 and 96.0% (ceftazidime), 98.6 and 100% (ciprofloxacin), 88.4 and 100% (gentamicin), 87.0 and 92.0% (imipenem), 85.0 and 88.0% (meropenem), 84.2 and 96.0% (piperacillin), and 97.3 and 80% (tobramycin). The essential agreement for levofloxacin against P. aeruginosa was 86.3%. The percentages of essential agreement for ampicillin-sulbactam and tetracycline against A. baumannii were 88.0 and 100%, respectively. Very major errors for P. aeruginosa (resistant by the reference method, susceptible with the VITEK 2 system [resistant to susceptible]) were noted for cefepime (0.7%), cefotaxime (0.7%), gentamicin (0.7%), imipenem (1.4%), levofloxacin (2.7%), and piperacillin (2.7%) and, for one strain of A. baumannii, for imipenem. Major errors (susceptible to resistant) were noted only for P. aeruginosa and cefepime (2.0%), ceftazidime (0.7%), and piperacillin (3.4%). Minor errors ranged from 0.0% for piperacillin to 22.6% for cefotaxime against P. aeruginosa and from 0.0% for piperacillin and ciprofloxacin to 20.0% for cefepime against A. baumannii. The VITEK 2 system provided co-trimoxazole MICs only for S. maltophilia; no very major or major errors were obtained for co-trimoxazole against this species. It is concluded that the VITEK 2 system allows the rapid identification of S. maltophilia and most P. aeruginosa and A. baumannii isolates. The VITEK 2 system can perform reliable susceptibility testing of many of the antimicrobial agents used against P. aeruginosa and A. baumannii. It would be desirable if new versions of the VITEK 2 software were able to determine MICs and the corresponding clinical categories of agents active against S. maltophilia.

Outbreak of Stenotrophomonas maltophilia bacteremia in allogenic bone marrow transplant patients: role of severe neutropenia and mucositis

From March 1997 through November 1997, 8 allogenic bone marrow transplant (BMT) patients developed Stenotrophomonas maltophilia bacteremia on the hematology service at UCLA Medical Center (Los Angeles). Five of these patients had undergone transplantation during the same hospitalization that S. maltophilia bacteremia was detected (case patients). Compared with 7 concurrently hospitalized allogenic BMT patients (control patients), the 5 case patients were more likely to have been hospitalized in room A (P=.045), to have severe neutropenia on the culture date (P=.028), to have a longer duration of severe neutropenia (P=.05), to have severe mucositis (P=. 028), and to have received total parenteral nutrition (P=.028). Pulsed-field gel electrophoresis revealed that 2 of 3 isolates from case patients hospitalized in room A were identical. In allogenic BMT patients, severe neutropenia and severe mucositis may promote infection with S. maltophilia by impairing host defenses.

Characterization of N2O-producing Xanthomonas-like isolates from biofilters as Stenotrophomonas nitritireducens sp. nov., Luteimonas mephitis gen. nov., sp. nov. and Pseudoxanthomonas broegbernensis gen. nov., sp. nov

A group of yellow-pigmented isolates from ammonia-supplied biofilters showed an unusual denitrification reaction. All strains reduced nitrite but not nitrate without production of nitrogen (N2). The only product found was nitrous oxide (N2O). The strains were divided into two clusters and one separate strain by their fatty acid profiles, which were similar to the fatty acid profiles of the genera Xanthomonas and Stenotrophomonas. Analyses of the 165 rDNA sequences showed that these clusters and the separate strain form three independent lines within the Xanthomonas branch of the Proteobacteria. The evolutionary distances of the isolates to members of the related genera Xanthomonas, Stenotrophomonas and Xylella calculated by the 16S rDNA sequences led to the proposal of two new genera and three new species, Stenotrophomonas nitritireducens sp. nov., Luteimonas mephitis gen. nov., sp. nov. and Pseudoxanthomonas broegbernensis gen. nov., sp. nov. The type strains are Stenotrophomonas nitritireducens L2T (= DSM 12575T), Luteimonas mephitis B1953/27.1T (= DSM 12574T) and Pseudoxanthomonas broegbernensis B1616/1T (= DSM 12573T).