Biochemical characterization of the L1-like metallo-β-lactamase from Stenotrophomonas lactitubi

L1-like metallo-β-lactamases (MBLs) exhibit diversity and are highly conserved. Although the presence of the blaL1-like gene is known, the biochemical characteristics are unclear. This study aimed to characterize an L1-like MBL from Stenotrophomonas lactitubi. It showed 70.9-99.7% similarity to 50 L1-like amino acid sequences. The characteristic kinetic parameter was its high hydrolyzing efficiency for ampicillin and nitrocefin. Furthermore, L1-like from S. lactitubi was distinctly more susceptible to inhibition by EDTA than that to inhibition by 2,6-pyridinedicarboxylic acid.

The type VI secretion system of Stenotrophomonas rhizophila CFBP13503 limits the transmission of Xanthomonas campestris pv. campestris 8004 from radish seeds to seedlings

Stenotrophomonas rhizophila CFBP13503 is a seedborne commensal bacterial strain, which is efficiently transmitted to seedlings and can outcompete the phytopathogenic bacterium Xanthomonas campestris pv. campestris (Xcc8004). The type VI secretion system (T6SS), an interference contact-dependent mechanism, is a critical component of interbacterial competition. The involvement of the T6SS of S. rhizophila CFBP13503 in the inhibition of Xcc8004 growth and seed-to-seedling transmission was assessed. The T6SS cluster of S. rhizophila CFBP13503 and nine putative effectors were identified. Deletion of two T6SS structural genes, hcp and tssB, abolished the competitive advantage of S. rhizophila against Xcc8004 in vitro. The population sizes of these two bacterial species were monitored in seedlings after inoculation of radish seeds with mixtures of Xcc8004 and either S. rhizophila wild-type (wt) strain or isogenic hcp mutant. A significant decrease in the population size of Xcc8004 was observed during confrontation with the S. rhizophila wt in comparison with T6SS-deletion mutants in germinated seeds and seedlings. We found that the T6SS distribution among 835 genomes of the Stenotrophomonas genus is scarce. In contrast, in all available S. rhizophila genomes, T6SS clusters are widespread and mainly belong to the T6SS group i4. In conclusion, the T6SS of S. rhizophila CFBP13503 is involved in the antibiosis against Xcc8004 and reduces seedling transmission of Xcc8004 in radish. The distribution of this T6SS cluster in the S. rhizophila complex could make it possible to exploit these strains as biocontrol agents against X. campestris pv. campestris.

StenM_174: A Novel Podophage That Infects a Wide Range of Stenotrophomonas spp. and Suggests a New Subfamily in the Family Autographiviridae

Stenotrophomonas maltophilia was discovered as a soil bacterium associated with the rhizosphere. Later, S. maltophilia was found to be a multidrug-resistant hospital-associated pathogen. Lytic bacteriophages are prospective antimicrobials; therefore, there is a need for the isolation and characterization of new Stenotrophomonas phages. The phage StenM_174 was isolated from litter at a poultry farm using a clinical strain of S. maltophilia as the host. StenM_174 reproduced in a wide range of clinical and environmental strains of Stenotrophomonas, mainly S. maltophilia, and it had a podovirus morphotype. The length of the genomic sequence of StenM_174 was 42,956 bp, and it contained 52 putative genes. All genes were unidirectional, and 31 of them encoded proteins with predicted functions, while the remaining 21 were identified as hypothetical ones. Two tail spike proteins of StenM_174 were predicted using AlphaFold2 structural modeling. A comparative analysis of the genome shows that the Stenotrophomonas phage StenM_174, along with the phages Ponderosa, Pepon, Ptah, and TS-10, can be members of the new putative genus Ponderosavirus in the Autographiviridae family. In addition, the analyzed data suggest a new subfamily within this family.

Identification and characterization of a versatile keratinase, KerZJ, from Stenotrophomonas sp. LMY

Keratinases have drawn increasing attention in recent decades owing to their catalytic versatility and broad applications from agriculture to medicine. In the present study, we isolated a highly keratinolytic and fibrinolytic bacterium from the campus soil and named it Stenotrophomonas sp. LMY based on genetic information. To identify the potential keratinase genes, the genome sequence of the strain was obtained and analyzed. Sequence alignment and comparison revealed that the protein 1_737 (KerZJ) had the highest sequence homology to a reported keratinase KerBL. We recombinantly expressed KerZJ in Escherichia coli Origami™ (DE) pLysS and purified it to homogeneity. KerZJ showed the highest activity at 40 °C and pH 9.0, and metal ions exhibited no significant effects on its activity. Although reducing agents would break the disulfide bonds in KerZJ and reduce its activity, KerZJ still exhibited the ability to hydrolyze feather keratin in the presence of β-ME. KerZJ could efficiently digest human prion proteins. In addition, KerZJ showed fibrinolytic activity on fibrin plates and effectively eliminated blood clots in a thrombosis mouse model without side effects. Our results suggest that KerZJ is a versatile keratinase with significant potential for keratin treatment, decontamination of prions, and fibrinolytic therapy.

Isolation, characterization, and genome analysis of novel bacteriophage - Stenotrophomonas phageCM1

A common environmental bacteria called Stenotrophomonas maltophilia has become an organism responsible for significant nosocomial infection, mortality in immunocompromised patients, and significantly increasing morbidity and is challenging to treat due to the antibiotic resistance activity of the organism. and bacteriophage therapy is one of the promising treatments against the organism. In this research, we isolated, identified, and characterized Stenotrophomonas phage CM1 against S. maltophilia. Stenotrophomonas phage CM1 head was measured to have a diameter of around 224.25 nm and a tail length of about 159 nm. The phage was found to have noticeable elongated tail spikes around 125 nm in length, the Myoviridae family of viruses, which is categorized under the order Caudovirales. The ideal pH for growth was around 7, demonstrated good thermal stability when incubated at 37-60 °C for 30 min or 60 min, and phage infectivity decreased marginally after 30 min of incubation at 1-5% chloroform concentration. Phage was 3,19,518 base pairs long and had an averaged G + C composition of 43.9 %; 559 open-reading frames (ORFs) were found in the bacteriophage genome, in which 508 of them are hypothetical proteins, 22 of them are other known proteins, 29 of them are tRNAs, and one of them is restriction enzyme. A phylogenetic tree was reconstructed, demonstrating that CM1 shares a close evolutionary relationship with other Stenotrophomonas phages.

Diversity of blaL1-like genes in Stenotrophomonas species: insights from genome analysis of publicly available genome sequences

L1 metallo-β-lactamases produced by Stenotrophomonas maltophilia exhibit high diversity. Here, we characterized the genomes of Stenotrophomonas species harboring blaL1-like genes using publicly available genome sequences. Our findings provide evidence that Stenotrophomonas species with blaL1-like genes constitute a complex comprising many species with high genetic diversity, and similarities between blaL1-like genes are lower than those of the genome. This suggests that the diversity of blaL1-like is attributable to species diversity in Stenotrophomonas species harboring blaL1-like and the rapid evolutionary changes in blaL1-like genes.

The mechanism of Se(IV) multisystem resistance in Stenotrophomonas sp. EGS12 and its prospect in selenium-contaminated environment remediation

Human activities have led to elevated levels of selenium (Se) in the environment, which poses a threat to ecosystems and human health. Stenotrophomonas sp. EGS12 (EGS12) has been identified as a potential candidate for the bioremediation of repair selenium-contaminated environment because of its ability to efficiently reduce Se(IV) to form selenium nanospheres (SeNPs). To better understand the molecular mechanism of EGS12 in response to Se(IV) stress, a combination of transmission electron microscopy (TEM), genome sequencing techniques, metabolomics and transcriptomics were employed. The results indicated that under 2 mM Se(IV) stress, 132 differential metabolites (DEMs) were identified, and they were significantly enriched in metabolic pathways such as glutathione metabolism and amino acid metabolism. Under the Se(IV) stress of 2 mM, 662 differential genes (DEGs) involved in heavy metal transport, stress response, and toxin synthesis were identified in EGS12. These findings suggest that EGS12 may respond to Se(IV) stress by engaging various mechanisms such as forming biofilms, repairing damaged cell walls/cell membranes, reducing Se(IV) translocation into cells, increasing Se(IV) efflux, multiplying Se(IV) reduction pathways and expelling SeNPs through cell lysis and vesicular transport. The study also discusses the potential of EGS12 to repair Se contamination alone and co-repair with Se-tolerant plants (e.g. Cardamine enshiensis). Our work provides new insights into microbial tolerance to heavy metals and offers valuable information for bio-remediation techniques on Se(IV) contamination.

Transcriptome Profiling of Stenotrophomonas sp. Strain WZN-1 Reveals Mechanisms of 2,2',4,4'-Tetrabromodiphenyl Ether (BDE-47) Biotransformation

The brominated flame retardant 2,2',4,4'-tetrabromodiphenyl ether (BDE-47) is extensively used, stable, and difficult to degrade in the environment. The existence of BDE-47 could pose a certain risk to the environment and human health. However, the biotransformation mechanisms of BDE-47 by microorganisms remain unclear. In this study, aerobic degradation of BDE-47 by Stenotrophomonas sp. strain WZN-1 and transcriptome analysis were carried out. BDE-47 degradation by Stenotrophomonas sp. strain WZN-1 was mainly through the biological action of intracellular enzymes via the route of debromination and hydroxylation. The results of the transcriptome sequencing indicated the differentially expressed genes were related to transport, metabolism, and stress response. The key processes involved the microbial transmembrane transportation of BDE-47, energy anabolism, synthesis, and metabolism of functional enzymes, stress response, and other biological processes of gene regulation. In particular, bacterial chemotaxis played a potential role in biodegradation of BDE-47 by Stenotrophomonas sp. strain WZN-1. This study provides the first insights into the biotransformation of Stenotrophomonas sp. strain WZN-1 to BED-47 stress and shows potential for application in remediation of polluted environments.

In silico analysis of diversity, specificity and molecular evolution of Stenotrophomonas phages

In this study, we have focused on the lytic phage proteins encoded by the Stenotrophomonas phages. A total of 60 lytic proteins were identified to be encoded by 19 different phages. Those proteins were characterized under eight classes: amidases, muramidases, pectate lyase, peptidases, holins and spanins. The phages encoding these proteins come under the family of Ackermannviridae, Autographiviridae, Myoviridae, Podoviridae and Siphoviridae. All the phages encoding those proteins were found to infect Stenotrophomonas maltophilia. Among the phages, about 50% were found to undergo a lytic lifecycle. The isolated proteins were clustered according to the similarity in the amino acid sequence. These clusters were used to make their phylogenetic tree. The co-occurrence of the amidase, pectate lyase and lipase genes in the phage genome was found using a correlation analysis.

Enhancement of phenol biodegradation: Metabolic division of labor in co-culture of Stenotrophomonas sp. N5 and Advenella sp. B9

The aim of this work is to study the synergistic effect of Stenotrophomonas sp. N5 and Advenella sp. B9 co-culture (COC) on enhancement of phenol biodegradation. These two strains utilizing phenol as sole carbon and energy source were isolated from phenol-containing coking wastewater. The results of biodegradation experiment showed the COC of N5 and B9 has stronger capability to degrade phenol than either of mono-culture (MOC). Growth kinetics studies indicated inhibitory effect of phenol on COC was reduced by the interaction of N5 and B9 in COC. The RNA-Seq results demonstrated that phenol biodegradation was enhanced by metabolic division of labor (DOL) in COC based on the expression of key genes for phenol degradation. GO enrichment analysis of differentially expressed genes (DEGs) indicated DEGs between COC and MOC degradation systems are mainly concentrated in the synthesis of cell components, microbial growth and metabolism, and catalytic activity. The expression of 3 transcriptional factors (LysR, Two-component system response regulator, and TetR families) which can regulate degradation of aromatic compounds, was identified beneficial to phenol degradation.

Frequency and diversity of Stenotrophomonas spp. carrying blaKPC in recreational coastal waters

Stenotrophomonas can survive in a wide range of environments and is considered an opportunistic pathogen. Because of its intrinsic resistance to beta-lactams, this genus is considered irrelevant in studies addressing the environmental spread of antimicrobial resistance genes of medical importance. Consequently, studies on environmental Stenotrophomonas carrying acquired carbapenemase-encoding genes are scarce, though not inexistent. Here, we investigated the frequency and diversity of Stenotrophomonas spp. carrying genes encoding carbapenemases of medical relevance in coastal waters with distinct pollution degrees over one year. Among 319 isolates recovered, 220 (68.9%) showed bla_KPC. The frequency of bla_KPC-positive Stenotrophomonas spp. was not correlated with thermotolerant counts in coastal waters evaluated. All isolates were susceptible to minocycline, levofloxacin, and trimethoprim-sulfamethoxazole. PFGE typing of 101 bla_KPC-positive isolates revealed 55 pulsotypes with 5 subtypes, all of which carried the bla_KPC-2 variant. Interspecies differentiation of pulsotypes' representatives revealed 55 isolates belonging to the S. maltophilia complex (91.7%) and 5 S. acidaminiphila (8.3%). The bla_KPC-2 gene was more frequently harbored on transposable elements found in enterobacteria of clinical origin, especially Tn4401b. Even though beta-lactams are no therapeutic options to treat Stenotrophomonas infections, the occurrence of a highly relevant antimicrobial resistance determinant harbored on mobile genetic elements in a diverse collection of these ubiquitous microorganisms is noteworthy. Therefore, Stenotrophomonas may act as acceptor, stable reservoirs, and potential vectors of antimicrobial resistance in environmental settings, especially aquatic matrices, and should not be neglected.

Comparative Genomics of Stenotrophomonas maltophilia and Stenotrophomonas rhizophila Revealed Characteristic Features of Both Species

Although Stenotrophomonas maltophilia strains are efficient biocontrol agents, their field applications have raised concerns due to their possible threat to human health. The non-pathogenic Stenotrophomonas rhizophila species, which is closely related to S. maltophilia, has been proposed as an alternative. However, knowledge regarding the genetics of S. rhizophila is limited. Thus, the aim of the study was to define any genetic differences between the species and to characterise their ability to promote the growth of plant hosts as well as to enhance phytoremediation efficiency. We compared 37 strains that belong to both species using the tools of comparative genomics and identified 96 genetic features that are unique to S. maltophilia (e.g., chitin-binding protein, mechanosensitive channels of small conductance and KGG repeat-containing stress-induced protein) and 59 that are unique to S. rhizophila (e.g., glucosylglycerol-phosphate synthase, cold shock protein with the DUF1294 domain, and pteridine-dependent dioxygenase-like protein). The strains from both species have a high potential for biocontrol, which is mainly related to the production of keratinases (KerSMD and KerSMF), proteinases and chitinases. Plant growth promotion traits are attributed to the biosynthesis of siderophores, spermidine, osmoprotectants such as trehalose and glucosylglycerol, which is unique to S. rhizophila. In eight out of 37 analysed strains, the genes that are required to degrade protocatechuate were present. While our results show genetic differences between the two species, they had a similar growth promotion potential. Considering the information above, S. rhizophila constitutes a promising alternative for S. maltophilia for use in agricultural biotechnology.

Urban and agricultural soils in Southern California are a reservoir of carbapenem-resistant bacteria

Carbapenems are last‐resort β‐lactam antibiotics used in healthcare facilities to treat multidrug‐resistant infections. Thus, most studies on identifying and characterizing carbapenem‐resistant bacteria (CRB) have focused on clinical settings. Relatively, little is still known about the distribution and characteristics of CRBs in the environment, and the role of soil as a potential reservoir of CRB in the United States remains unknown. Here, we have surveyed 11 soil samples from 9 different urban or agricultural locations in the Los Angeles–Southern California area to determine the prevalence and characteristics of CRB in these soils. All samples tested contained CRB with a frequency of <10 to 1.3 × 10⁴ cfu per gram of soil, with most agricultural soil samples having a much higher relative frequency of CRB than urban soil samples. Identification and characterization of 40 CRB from these soil samples revealed that most of them were members of the genera Cupriavidus, Pseudomonas, and Stenotrophomonas. Other less prevalent genera identified among our isolated CRB, especially from agricultural soils, included the genera Enterococcus, Bradyrhizobium, Achromobacter, and Planomicrobium. Interestingly, all of these carbapenem‐resistant isolates were also intermediate or resistant to at least 1 noncarbapenem antibiotic. Further characterization of our isolated CRB revealed that 11 Stenotrophomonas, 3 Pseudomonas, 1 Enterococcus, and 1 Bradyrhizobium isolates were carbapenemase producers. Our findings show for the first time that both urban and agricultural soils in Southern California are an underappreciated reservoir of bacteria resistant to carbapenems and other antibiotics, including carbapenemase‐producing CRB.

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.

Isolation and characterization of amoxicillin-resistant bacteria and amoxicillin-induced alteration in its protein profiling and RNA yield

Amoxicillin-resistant bacteria were isolated using selective enrichment procedure. The morphological, biochemical and molecular characterization based on 16S rRNA gene sequencing and phylogenetic analysis of the bacterial strain WA5 confirmed that the strain belongs to the genus Stenotrophomonas. The bacteria were named as Stenotrophomonas sp. strain WA5 (MK110499). Substantial growth was seen in M9 minimal media supplemented with 5 mg L^-1 of amoxicillin as a sole source of carbon and energy. RNA yield was also observed to be decreased in the presence of amoxicillin. Amoxicillin (5 mg L^-1)-induced alteration is seen on bacterial protein profile and unique polypeptide bands were seen to be induced in the presence of amoxicillin, the bands were subjected to trypsin digestion, and LC-MS/MS analysis showed that the bands belong to the family of DNA-dependent RNA polymerase subunit β (rpoC). Plasmid DNA isolation indicated the presence of antibiotic-resistant genes being harboured by the plasmid.

Effects of α-pinene on the pinewood nematode (Bursaphelenchus xylophilus) and its symbiotic bacteria

The pinewood nematode (PWN), Bursaphelenchus xylophilus, is an important plant-parasitic nematode that can cause severe mortality of pine trees. This PWN-induced harm to plants may be closely related to the abundance and diversity of the symbiotic microorganisms of the parasitic nematode. In this study, nematodes were divided into untreated and antibiotic-treated groups. Nematodes were treated by fumigation with different amounts of α-pinene, and the resultant mortality rates were analyzed statistically. Concentrations of symbiotic bacteria were calculated as colony-forming units per nematode. High-throughput sequencing was used to investigate the bacterial community structure. The results showed that the mortality of nematodes increased slightly with an increasing concentration of α-pinene, and nematodes untreated with antibiotics were more sensitive to α-pinene than those treated with antibiotics. The highest abundance of symbiotic bacteria was obtained via medium and low levels of α-pinene, but for which community diversity was the lowest (Shannon and Simpson indexes). The proportion of Pseudomonas spp. in the symbiotic bacteria of nematodes without antibiotics was relatively high (more than 70%), while that of Stenotrophomonas spp. was low (6%–20%). However, the proportion of Stenotrophomonas spp. was larger than that of Pseudomonas spp in the symbiotic bacteria associated with the antibiotic-treated nematodes. Pseudomonas sp. increased after pinene treatment, whereas Stenotrophomonas spp. decreased. These results indicate that although α-pinene has low toxicity to PWNs over a short time period, α-pinene ultimately influences the abundance and community diversity of the symbiotic bacteria of these nematodes; this influence may potentially disturb the development and reproduction of nematodes in the process of infecting pine trees.

Stenotrophomonas-Like Bacteria Are Widespread Symbionts in Cone Snail Venom Ducts

Cone snails are biomedically important sources of peptide drugs, but it is not known whether snail-associated bacteria affect venom chemistry. To begin to answer this question, we performed 16S rRNA gene amplicon sequencing of eight cone snail species, comparing their microbiomes with each other and with those from a variety of other marine invertebrates. We show that the cone snail microbiome is distinct from those in other marine invertebrates and conserved in specimens from around the world, including the Philippines, Guam, California, and Florida. We found that all venom ducts examined contain diverse 16S rRNA gene sequences bearing closest similarity to Stenotrophomonas bacteria. These sequences represent specific symbionts that live in the lumen of the venom duct, where bioactive venom peptides are synthesized.IMPORTANCE In animals, symbiotic bacteria contribute critically to metabolism. Cone snails are renowned for the production of venoms that are used as medicines and as probes for biological study. In principle, symbiotic bacterial metabolism could either degrade or synthesize active venom components, and previous publications show that bacteria do indeed contribute small molecules to some venoms. Therefore, understanding symbiosis in cone snails will contribute to further drug discovery efforts. Here, we describe an unexpected, specific symbiosis between bacteria and cone snails from around the world.

Isolation and identification of 3-bromocarbazole-degrading bacteria

In this study, a bacterial strain, CH-1, capable of degrading 3-bromocarbazole (3-BCZ) was isolated from a polluted soil. Based on its physio-biochemical characteristics and 16S rRNA genes, strain CH-1 was identified as a Stenotrophomonas sp. Strain CH-1 was able to degrade 70% of 50 mg/L 3-BCZ within 8 d at pH 7.0 and 30°C in mineral salt medium (MSM). During the process, the main intermediate metabolite was identified as (2E, 4Z)-6-(2-amino-5-bromophenyl)-2-hydroxy-6-oxhexa-2, 4-dienoic by gas (2E, 4Z)-6-(2-amino-5-bromophenyl)-2-hydroxy-6-oxhexa-2,4-dienoic via gas chromatograph-mass spectrometry (GC-MS) analysis. The metabolite disappeared after 14 d, suggesting that the metabolite can also be degraded by strain CH-1. 3-BCZ is a new persistent organic pollutant. This is the first report of the biodegradation of 3-BCZ. The results indicated that strain CH-1 may be a promising bacterial candidate for the bioremediation of environments polluted with polyhalogenated carbazoles (PHCs).

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.

The plant is crucial: specific composition and function of the phyllosphere microbiome of indoor ornamentals

The plant microbiome is a key determinant of plant health. Less is known about the phyllosphere microbiota and its driving factors in built environments. To study the variability of the microbiome in relation to plant genotype and climate under different controlled conditions, we investigated 14 phylogenetically diverse plant species grown in the greenhouses of the Botanical Garden in Graz (Austria). All investigated plants showed specific bacterial abundances of up to 10(6) CFU cm(-2) on their leaves. Bacterial diversity (H('): 2.4-7.9) and number of putative OTUs (461-2013) were strongly plant species dependent. Statistical analysis showed a significantly higher correlation of community composition to plant genotype in comparison to the ambient climatic variables. In addition to the microbiome structure, we studied the antagonistic potential towards the foliar pathogen Botrytis cinerea as functional indicator. A high proportion of isolates (up to 58%) were able to inhibit pathogen growth by production of volatile organic compounds (VOCs). Data of structure and function were linked: frequently isolated VOCs producers (e.g. Bacillus and Stenotrophomonas) were highly present in phyllosphere communities, which were dominated by members of Firmicutes This study indicates that indoor ornamentals feature a distinct, stable microbiota on leaves irrespective of the indoor climate.

Characterization of cadmium-resistant bacteria and their potential for reducing accumulation of cadmium in rice grains

Cadmium (Cd) pollution is a serious widespread environmental problem that not only destroys the microbial ecology of soil and decreases crop production, but also poses a serious risk to human health. Many methods have been used for the remediation of Cd pollution but none of these is totally satisfactory. Microbial remediation strategies have attracted increasing interest since they are environmentally friendly and cost-effective. In the present study, three Cd-resistant bacteria were isolated and evaluated for potential application in Cd bioremediation. Based on their morphological, physiological and biochemical characteristics, together with 16S rDNA gene sequence analyses, bacteria were identified as Stenotrophomonas acidaminiphila (2#), Pseudomonas aeruginosa (9#) and Delftia tsuruhatensis (12#). Pseudomonas aeruginosa showed very high tolerance to metals, especially Cd (2200mg/L), Zn (1800mg/L) and Pb (1200mg/L), and is thought to be a multi-metal-resistant bacterium. Pseudomonas aeruginosa was also sensitive to 13 different antibiotics. The effects of the bacterial strains on the growth of rice plants and their ability to reduce Cd accumulation from Cd-contaminated soils in pot experiments were also evaluated. For Oryza sativa L. A grown in contaminated soil (3mg/kg Cd), the accumulation of Cd was decreased by 31.2 and 25.5% in brown rice and polished rice, respectively, by strain 9#; Pseudomonas aeruginosa was more effective in reducing Cd accumulation in rice grains than a mixture of strains. For Oryza sativa L. B, a mixture of strains acting synergistically was more effective than a single strain in reducing Cd accumulation; treatment with mixed strains (strains+3mg/kg Cd) resulted in 41.3, 35.9, and 32.6% reductions in Cd accumulation in unhulled rice, brown rice and polished rice, respectively. Although different results were obtained for two rice varieties, it can still be concluded that Cd-resistant bacteria are suitable for reducing Cd accumulation in rice grains and show potential for bioremediation of Cd-contaminated soils.

Characterization of cadmium-resistant bacteria for its potential in promoting plant growth and cadmium accumulation in Sesbania bispinosa root

The cadmium (Cd) resistant bacteria were isolated from soils of Damanganga river, Vapi, and identified 11 potential Cd resistant bacteria based on 16S rDNA sequences. The Cd resistant bacteria belonged to four different genera: Providencia spp., Morganella sp., Stenotrophomonas sp., and Bacillus spp. The assessment of plant growth-promoting (PGP) parameters revealed that the Cd tolerant bacteria showed one or more PGP properties. Further, a pot experiment was conducted to elucidate the effects of Cd resistant bacteria on the plant growth and the uptake of Cd by Sesbania bispinosa. The bacterized seedlings recorded 36.0-74.8% and 21.2-32.9% higher root and shoot lengths, respectively, in Cd amended soil compared with control. The Cd mobilization in the root of S. bispinosa by microbial inoculants ranged from 0.02 ± 0.01 to 1.11 ± 0.06 ppm. The enhanced concentrations of Cd accumulation in S. bispinosa roots correspond to the effect of the bacterial strains on metal mobilization in soil. The present observations showed that the Cd resistant strains protect the plants against the inhibitory effects of Cd, probably due to the production of PGP properties. The present results provided a new insight into the phytoremediation of Cd contaminated soil.

Identification of arsenic resistant endophytic bacteria from Pteris vittata roots and characterization for arsenic remediation application

Mitigation of arsenic (As) pollution is a topical environmental issue of high R&D priority. The present investigation was carried out to isolate As resistant endophytes from the roots of Indian ecotype Pteris vittata and characterize their As transformation and tolerance ability, plant growth promoting characteristics and their role to facilitate As uptake by the plant. A total of 8 root endophytes were isolated from plants grown in As amended soil (25 mg As kg(-1)). These isolates were studied for minimum inhibitory concentration (MIC), arsenite As(III) - arsenate As(V) transformation ability, plant growth promoting (PGP) characteristics through siderophore, indole acetic acid (IAA) production, phosphatase, ACC deaminase activity, and presence of arsenite oxidase (aox) and arsenite transporter (arsB) genes. On the basis of 16S rDNA sequence analysis, these isolates belong to Proteobacteria, Firmicutes and Bacteroidetes families under the genera Bacillus, Enterobacter, Stenotrophomonas and Rhizobium. All isolates were found As tolerant, of which one isolates showed highest tolerance up to 1000 mg L(-1) concentration in SLP medium. Five isolates were IAA positive with highest IAA production up to 60 mg/L and two isolates exhibited siderophore activity. Phosphatase activity was shown by only one isolate while ACC deaminase activity was absent in all the isolates. The As transformation study by silver nitrate test showed that only two strains had dual characteristics of As(III) oxidation and As (V) reduction, four strains exhibited either of the characteristics while other two didn't confirmed any of the two characteristics. Presence of aox gene was detected in two strains and arsB gene in six isolates. The strain with highest As tolerance also showed highest IAA production and occurrence of arsB gene. Present investigation may open up further scope of utilizing these endophytes for up gradation of phytoextraction process.

Isolation and characterization of a hydrocarbonoclastic bacterial enrichment from total petroleum hydrocarbon contaminated sediments: potential candidates for bioaugmentation in bio-based processes

Seven hydrocarbonoclastic new bacterial isolates were isolated from dredged sediments of a river estuary in Italy. The sediments were contaminated by shipyard activities since decades, mainly ascribable to the exploitation of diesel oil as the fuel for recreational and commercial navigation of watercrafts. The bacterial isolates were able to utilize diesel oil as sole carbon source. Their metabolic capacities were evaluated by GC-MS analysis, with reference to the depletion of both the normal and branched alkanes, the nC18 fatty acid methyl ester and the unresolved complex mixture of organic compounds. They were taxonomically identified as different species of Stenotrophomonas and Pseudomonas spp. by the combination of amplified ribosomal DNA restriction analysis (ARDRA) and repetitive sequence-based PCR (REP-PCR) analysis. The metabolic activities of interest were analyzed both in relation to the single bacterial strains and to the combination of the latter as a multibacterial species system. After 6 days of incubation in mineral medium with diesel oil as sole carbon source, the Stenotrophomonas sp. M1 strain depleted 43-46 % of Cn-alkane from C28 up to C30, 70 % of the nC18 fatty acid methyl ester and the 46 % of the unresolved complex mixture of organic compounds. On the other hand, the Pseudomonas sp. NM1 strain depleted the 76 % of the nC18 fatty acid methyl ester, the 50 % of the unresolved complex mixture of organic compounds. The bacterial multispecies system was able to completely deplete Cn-alkane from C28 up to C30 and to deplete the 95 % of the unresolved complex mixture of organic compounds. The isolates, either as single strains and as a bacterial multispecies system, were proposed as candidates for bioaugmentation in bio-based processes for the decontamination of dredged sediments.

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.

Biodegradation of C.I. Acid Red 1 by indigenous bacteria Stenotrophomonas sp. BHUSSp X2 isolated from dye contaminated soil

A significant proportion of xenobiotic recalcitrant azo dyes are being released in environment during carpet dyeing. The bacterial strain Stenotrophomonas sp. BHUSSp X2 was isolated from dye contaminated soil of carpet industry, Bhadohi, India. The isolated bacterial strain was identified morphologically, biochemically, and on the basis of 16S rRNA gene sequence. The isolate decolorized 97 % of C.I. Acid Red 1 (Acid RED G) at the concentration of 200 mg/l within 6 h under optimum static conditions (temperature -35 °C, pH 8, and initial cell concentration 7 × 10(7) cell/ml). Drastic reduction in dye degradation rate was observed beyond initial dye concentration from 500 mg/l (90 %), and it reaches to 25 % at 1000 mg/l under same set of conditions. The analysis related to decolorization and degradation was done using UV-Vis spectrophotometer, HPLC, and FTIR, whereas the GC-MS technique was utilized for the identification of degradation products. Phytotoxicity analysis revealed that degradation products are less toxic as compared to the original dye.

Cadmium-tolerant bacteria induce metal stress tolerance in cereals

Cadmium usually hampers plant growth, but bacterial inoculation may improve stress tolerance in plants to Cd by involving various mechanisms. The objective was to characterize and identify bacteria that improve plant growth under Cd stress and reduce Cd uptake. Cadmium-tolerant bacteria were isolated from rhizosphere soil, which was irrigated with tannery effluent, and six strains were selected as highly tolerant to Cd, showing minimum inhibitory concentration as 500 mg L(-1) or 4.45 mmol L(-1). These strains were identified by 16S rRNA gene analysis and functional analysis in regard to plant growth promotion characteristics. To determine their effect on cereal growth under Cd stress, seeds were inoculated with these strains individually and grown in soil contaminated with three Cd levels (0, 40 and 80 mg kg(-1)). Biomass production, relative water content (RWC), electrolyte leakage (ELL) and tissue Cd concentration were measured. Biomass of both cereals was inhibited strongly when exposed to Cd; however, bacterial inoculation significantly reduced the suppressive effect of Cd on cereal growth and physiology. The bacterial isolates belonged to the genera Klebsiella, Stenotrophomonas, Bacillus and Serratia. Maize was more sensitive than wheat to Cd. Klebsiella sp. strain CIK-502 had the most pronounced effects in promoting maize and wheat growth and lowering Cd uptake under Cd stress.

Stenotrophomonas comparative genomics reveals genes and functions that differentiate beneficial and pathogenic bacteria

BACKGROUND

In recent years, the number of human infections caused by opportunistic pathogens has increased dramatically. Plant rhizospheres are one of the most typical natural reservoirs for these pathogens but they also represent a great source for beneficial microbes with potential for biotechnological applications. However, understanding the natural variation and possible differences between pathogens and beneficials is the main challenge in furthering these possibilities. The genus Stenotrophomonas contains representatives found to be associated with human and plant host.

RESULTS

We used comparative genomics as well as transcriptomic and physiological approaches to detect significant borders between the Stenotrophomonas strains: the multi-drug resistant pathogenic S. maltophilia and the plant-associated strains S. maltophilia R551-3 and S. rhizophila DSM14405T (both are biocontrol agents). We found an overall high degree of sequence similarity between the genomes of all three strains. Despite the notable similarity in potential factors responsible for host invasion and antibiotic resistance, other factors including several crucial virulence factors and heat shock proteins were absent in the plant-associated DSM14405T. Instead, S. rhizophila DSM14405T possessed unique genes for the synthesis and transport of the plant-protective spermidine, plant cell-wall degrading enzymes, and high salinity tolerance. Moreover, the presence or absence of bacterial growth at 37°C was identified as a very simple method in differentiating between pathogenic and non-pathogenic isolates. DSM14405T is not able to grow at this human-relevant temperature, most likely in great part due to the absence of heat shock genes and perhaps also because of the up-regulation at increased temperatures of several genes involved in a suicide mechanism.

CONCLUSIONS

While this study is important for understanding the mechanisms behind the emerging pattern of infectious diseases, it is, to our knowledge, the first of its kind to assess the risk of beneficial strains for biotechnological applications. We identified certain traits typical of pathogens such as growth at the human body temperature together with the production of heat shock proteins as opposed to a temperature-regulated suicide system that is harnessed by beneficials.

[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.

Microcystin-degrading activity of an indigenous bacterial strain Stenotrophomonas acidaminiphila MC-LTH2 isolated from Lake Taihu

Microcystin-LR (MC-LR) and microcystin-RR (MC-RR) produced by harmful cyanobacterial blooms (HCBs) pose substantial threats to the ecosystem and public health due to their potential hepatotoxicity. Degradation of microcystins (MCs) by indigenous bacteria represents a promising method for removing MCs from fresh water without harming the aquatic environment, but only a few microcystin (MC)-degrading bacteria have been isolated and had their mechanisms reported. This study aimed to isolate indigenous bacteria from Lake Taihu, and investigate the capability and mechanism of MC degradation by these bacteria. During a Microcystis bloom, an indigenous MC-degrading bacterium designated MC-LTH2 was successfully isolated from Lake Taihu, and identified as Stenotrophomonas acidaminiphila based on phylogenetic analysis. In the presence of MC-LR together with MC-RR, the strain MC-LTH2 was capable of totally degrading both simultaneously in 8 days, at rates of 3.0 mg/(L⋅d) and 5.6 mg/(L⋅d), respectively. The degradation rates of MCs were dependent on temperature, pH, and initial MC concentration. Adda (3-amino-9-methoxy-2, 6, 8-trimethyl-10-phenyldeca-4, 6-dienoic acid) was detected as an intermediate degradation product of MCs using high performance liquid chromatography coupled with time-of-flight mass spectrometry (HPLC-TOF-MS). To the best of our knowledge, this is the first report of Stenotrophomonas acidaminiphila capable of degrading two MC analogues and other compounds containing Adda residue completely under various conditions, although the mlrA gene in the strain was not detected. These results indicate the Stenotrophomonas acidaminiphila strain MC-LTH2 possesses a significant potential to be used in bioremediation of water bodies contaminated by MC-LR and MC-RR, and is potentially involved in the degradation of MCs during the disappearance of the HCBs in Lake Taihu.

Simultaneous Cr(VI) reduction and phenol degradation using Stenotrophomonas sp. isolated from tannery effluent contaminated soil

This study presents simultaneous hexavalent chromium (Cr(VI)) reduction and phenol degradation using Stenotrophomonas sp., isolated from tannery effluent contaminated soil. Phenol was used as the sole carbon and energy source for Cr(VI) reduction. The optimization of different operating parameters was done using Placket-Burman design (PBD) and Box-Behnken design (BBD). The significant operating variables identified by PBD were initial Cr(VI) and phenol concentration, pH, temperature, and reaction time. These variables were optimized by a three-level BBD and the optimum initial Cr(VI) concentration, initial phenol concentration, pH, temperature, and reaction time obtained were 16.59 mg/l, 200.05 mg/l, 7.38, 31.96 °C and 4.07 days, respectively. Under the optimum conditions, 81.27 % Cr(VI) reduction and 100 % phenol degradation were observed experimentally. The results concluded that the Stenotrophomonas sp. could be used to decontaminate the effluents containing Cr(VI) and phenol effectively.

Antibiotic resistance of bacteria isolated from the internal organs of edible snow crabs

Antibiotic resistance and microbiota within edible snow crabs are important for the Chionoecetes (snow crab) fishing industry. We investigated these parameters using culture methods and antibiotic susceptibility tests with six internal organs from three species of Chionoecetes. Each sample revealed many unexpected microbial species within Chionoecetes internal organs. On the basis of 16S rRNA sequence analysis of 381 isolates, the most abundant genera identified in Chionoecetes opilio were Acinetobacter spp. (24%), Bacillus spp. (4%), Pseudomonas spp. (34%), Stenotrophomonas spp. (28%), and Agreia spp. (11%). In Chionoecetes sp. crabs, Acinetobacter spp. (23%), Bacillus spp. (12%), and Psychrobacter spp. (20%) were most prevalent, while Agreia spp. (11%), Bacillus spp. (31%), Microbacterium spp. (10%), Rhodococcus spp. (12%), and Agrococcus spp. (6%) were most abundant in C. japonicus. Our antibiotic resistance test found resistance to all nine antibiotics tested in 19, 14, and two of the isolates from C. opilio, Chionoecetes sp., and, C. japonicus respectively. Our results are the first to show that microbes with antibiotic resistance are widely distributed throughout the internal organs of natural snow crabs.

Isolation and characterization of an endosulfan-degrading strain, Stenotrophomonas sp. LD-6, and its potential in soil bioremediation

Aerobic bacteria degrading endosulfan were isolated from contaminated sludge. One of the isolates, LD-6, was identified as Stenotrophomonas sp. The bacterium could utilize endosulfan as the sole source of carbon and sulfur. 100 mg/l endosulfan was completely degraded within 10 days, and endosulfan diol and endosulfan ether were detected as major metabolites with a slight decrease in culture pH. The results indicated that Stenotrophomonas. sp. LD-6 might degrade endosulfan by a non-oxidative pathway. Biodegradation of both isomers was relatively better at a temperature range of 25-35 degrees C, with a maximum at 30 degrees C. In addition, cell crude extract of strain LD-6 could metabolize endosulfan rapidly, and degradative enzymes were intracellular distributed and constitutively expressed. Besides, application of the strain was found to promote the removal of endosulfan in soil. This study might help with the future research in better understanding of the biodegradation.

Arsenic-resistant bacteria solubilized arsenic in the growth media and increased growth of arsenic hyperaccumulator Pteris vittata L

The role of arsenic-resistant bacteria (ARB) in arsenic solubilization from growth media and growth enhancement of arsenic-hyperaccumulator Pteris vittata L. was examined. Seven ARB (tolerant to 10 mM arsenate) were isolated from the P. vittata rhizosphere and identified by 16S rRNA sequencing as Pseudomonas sp., Comamonas sp. and Stenotrophomonas sp. During 7-d hydroponic experiments, these bacteria effectively solubilized arsenic from the growth media spiked with insoluble FeAsO₄ and AlAsO₄ minerals (from < 5 μg L⁻¹ to 5.04-7.37 mg L⁻¹ As) and enhanced plant arsenic uptake (from 18.1-21.9 to 35.3-236 mg kg⁻¹ As in the fronds). Production of (1) pyochelin-type siderophores by ARB (fluorescent under ultraviolet illumination and characterized with thin layer chromatography) and (2) root exudate (dissolved organic C) by P. vittata may be responsible for As solubilization. Increase in P. vittata root biomass from 1.5-2.2 to 3.4-4.2 g/plant dw by ARB and by arsenic was associated with arsenic-induced plant P uptake. Arsenic resistant bacteria may have potential to enhance phytoremediation of arsenic-contaminated soils by P. vittata.

[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.

Genetic engineering of Stenotrophomonas strain YC-1 to possess a broader substrate range for organophosphates

In this work, Stenotrophomonas sp. strain YC-1, a native soil bacterium that produces methyl parathion hydrolase (MPH), was genetically engineered to possess a broader substrate range for organophosphates (OPs). A surface anchor system derived from the truncated ice nucleation protein (INPNC) from Pseudomonas syringae was used to target organophosphorus hydrolase (OPH) onto the cell surface of strain YC-1, reducing the potential substrate uptake limitation. The surface localization of INPNC-OPH was verified by cell fractionation, Western blot, proteinase accessibility, and immunofluorescence microscopy. No growth inhibition was observed for the engineered strain, and suspended cultures retained almost 100% activity over a period of 2 weeks. Concomitant expression of OPH in strain YC-1 resulted in a recombinant strain capable of simultaneously degrading diethyl and dimethyl OPs. A mixture of six OP pesticides (0.2 mM each) could be degraded completely within 5 h. The broader substrate specificity in combination with the rapid degradation rate makes this engineered strain a promising candidate for in situ remediation of OP-contaminated sites.

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)).

Isolation of a methyl parathion-degrading strain Stenotrophomonas sp. SMSP-1 and cloning of the ophc2 gene

A rod-shaped, gram-negative bacterium Stenotrophomonas sp. SMSP-1 was isolated from the sludge of a wastewater treating system of a pesticide manufacturer. Strain SMSP-1 could hydrolyze methyl parathion to p-nitrophenol (PNP) and dimethyl phosphorothioate but could not degrade PNP further. Strain SMSP-1 was able to hydrolyze other organophosphate pesticides, including fenitrothion, ethyl parathion, fenthion, and phoxim, but not chlorpyrifos. A 4395-bp DNA fragment, including an organophosphorus hydrolase encoding gene ophc2, was cloned from the chromosome of strain SMSP-1 using the shotgun technique. Its sequence analysis showed that ophc2 was associated with a typical mobile element ISPpu12 consisting of tnpA (encoding a transposase), lspA (encoding a lipoprotein signal peptidase), and orf1 (encoding a CDF family heavy metal/H(+) antiporter). The ophc2 gene was effectively expressed in E. coli. This is the second report of cloning the ophc2 gene and the first report of this gene from the genus of Stenotrophomonas.

Simultaneous degradation of organophosphates and 4-substituted phenols by Stenotrophomonas species LZ-1 with surface-displayed organophosphorus hydrolase

Organophosphorous hydrolase (OPH) was expressed onto the surface of a Stenotrophomonas species (LZ-1), capable of simultaneously degrading 4-substituted phenols, using the N- and C-terminal domains of ice nucleation protein (INPNC) as an anchoring motif for the first time. The engineered strain LZ-1 could degrade p-nitrophenyl-substituted organophosphates as well as their hydrolytic product, PNP, rapidly. Especially, addition of 4-CP (below 0.8 mM) significantly accelerated the complete degradation of above organophosphates (47.1, 34.0, and 40% reduction of time of paraoxon, parathion, and methyl-parathion, respectively) through the accelerated degradation of PNP due to enhanced cell growth supported by 4-CP as the carbon source. OPH could be surface-displayed at a high level without inhibition of cell growth and OPH activity in the presence of 4-CP. In soil samples, strain LZ-1 could also remove these compounds successfully. Functional display of heterologous proteins on the surface of indigenous bacteria could provide a promising technology for effective bioremediation of sites contaminated with mixed organic pollutants.

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.

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.

Removal of cadmium ions during stationary growth phase by an extremely cadmium-resistant strain of Stenotrophomonas sp

Stenotrophomonas sp. CD02 was isolated from a site that previously had been contaminated with high concentrations of the heavy metals cadmium (3 mg kg(-1)) and chromium (115 mg kg(-1)). This strain was able to grow on complex (Luria Bertani) medium containing high concentrations of cadmium ion (up to 4 mM). Additionally, it could remove up to 80% of the dissolved ions but only after reaching stationary growth phase. Strain CD02 also tolerated high concentrations of other heavy metals such as chromium, zinc, copper, nickel, and lead at levels more than 2 mM. Although strain CD02 can tolerate much higher cadmium concentrations than the three Stenotrophomonas maltophilia strains tested, they all possess resistance to the same range of antibiotics. This suggests that strain CD02 possesses a mechanism that allows it to tolerate and remove cadmium differently from those conferring resistance to antibiotics. Strain CD02 can be a suitable candidate for heavy metal bioremediation in contaminated environment because it is able to tolerate high concentration of heavy metals and remove cadmium aerobically.

Selection for biocontrol bacteria antagonistic toward Rosellinia necatrix by enrichment of competitive avocado root tip colonizers

Biological control of soil-borne pathogens is frequently based on the application of antagonistic microorganisms selected solely for their ability to produce in vitro antifungal factors. The aim of this work was to select bacteria that efficiently colonize the roots of avocado plants and display antagonism towards Rosellinia necatrix, the causal agent of avocado white root rot. A high frequency of antagonistic strains (ten isolates, 24.4%) was obtained using a novel procedure based on the selection of competitive avocado root tip colonizers. Amplification and sequencing of the 16S rRNA gene, in combination with biochemical characterization, showed that eight and two of the selected isolates belonged to the genera Pseudomonas and Stenotrophomonas, respectively. Characterization of antifungal compounds produced by the antagonistic strains showed variable production of exoenzymes and HCN. Only one of these strains, Pseudomonas sp. AVO94, produced a compound that could be related to antifungal antibiotics. All of the ten selected strains showed twitching motility, a cell movement involved in competitive colonization of root tips. Production of N-acyl-homoserine lactones and indole-3-acetic acid was also reported for some of these isolates. Resistance to several bacterial antibiotics was tested, and three strains showing resistance to only one of them were selected for biocontrol assays. The three selected strains persisted in the rhizosphere of avocado plants at levels considered crucial for efficient biocontrol, 10(5)-10(6) colony forming units/g of root; two of them, Pseudomonas putida AVO102 and Pseudomonas pseudoalcaligenes AVO110, demonstrated significant protection of avocado plants against white root rot.

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.

Isolation of bacteria able to grow on both polyethylene glycol (PEG) and polypropylene glycol (PPG) and their PEG/PPG dehydrogenases

Two bacterial consortia growing on a random copolymer of ethylene glycol and propylene glycol units were obtained by enrichment cultures from various microbial samples. Six major strains included in both consortia were purified and identified as Sphingomonads, Pseudomonas sp. and Stenotrophomonas maltophilia. Three of them (Sphingobium sp. strain EK-1, Sphingopyxis macrogoltabida strain EY-1, and Pseudomonas sp. strain PE-2) utilized both PEG and polypropylene glycol (PPG) as a sole carbon source. Four PEG-utilizing bacteria had PEG dehydrogenase (PEG-DH) activity, which was induced by PEG. PCR products from DNA of these bacteria generated with primers designed from a PEG-DH gene (AB196775 for S. macrogoltabida strain 103) indicated the presence of a sequence that is the homologous to the PEG-DH gene (99% identity). On the other hand, five PPG-utilizing bacteria had PPG dehydrogenase (PPG-DH) activity, but the activity was constitutive. PCR of a PPG-DH gene was performed using primers designed from a polyvinyl alcohol dehydrogenase (PVA-DH) gene (AB190288 for Sphingomonas sp. strain 113P3) because a PPG-DH gene has not been cloned yet, but both PPG-DH and PVA-DH were active toward PPG and PVA (Mamoto et al. 2006). PCR products of the five strains did not have similarity to each other or to oxidoreductases including PVA-DH.

Serological cross-reactivity of environmental isolates of Enterobacter, Escherichia, Stenotrophomonas, and Aerococcus with Shigella spp.-specific antisera

Using protocols designed for the isolation of Shigella from environmental freshwater samples from different regions of Bangladesh, 11 bacterial strains giving rise to Shigella-like colonies on selective agar plates and showing serological cross-reaction with Shigella-specific antisera were isolated. Phylogenetic analyses revealed that three of the isolates were most closely related to Escherichia coli, four to Enterobacter sp., two to Stenotrophomonas, and two isolates belonged to the Gram-positive genus Aerococcus. The isolates cross-reacted with six different serotypes of Shigella and were, in each case, highly type-specific. Two of the isolates belonging to the Enterobacter and Escherichia genera gave extremely strong cross-reactivity with Shigella dysenteriae and Shigella boydii antisera, respectively. The Aerococcus isolates gave relatively weak but significant cross-reactions with S. dysenteriae. Western blot analysis revealed that a number of antigens from the isolates cross-react with Shigella spp. The results indicate that important Shigella spp. surface antigens are shared by a number of environmental bacteria, which have implications for the use of serological methods in attempts for the detection and recovery of Shigella from aquatic environments.

Cloning of mpd gene from a chlorpyrifos-degrading bacterium and use of this strain in bioremediation of contaminated soil

An effective chlorpyrifos-degrading bacterium (named strain YC-1) was isolated from the sludge of the wastewater treating system of an organophosphorus pesticides manufacturer. Based on the results of phenotypic features, phylogenetic similarity of 16S rRNA gene sequences and BIOLOG test, strain YC-1 was identified as the genus Stenotrophomonas. The isolate utilized chlorpyrifos as the sole source of carbon and phosphorus for its growth and hydrolyzed chlorpyrifos to 3,5,6-trichloro-2-pyridinol. Parathion, methyl parathion, and fenitrothion also could be degraded by strain YC-1 when provided as the sole source of carbon and phosphorus. The gene encoding the organophosphorus hydrolase was cloned using a PCR cloning strategy based on the known methyl parathion degrading (mpd) gene of Plesiomonas sp. M6. Sequence blast result indicated this gene has 99% similar to mpd. The inoculation of strain YC-1 (10(6) cells g(-1)) to soil treated with 100 mg kg(-1) chlorpyrifos resulted in a higher degradation rate than in noninoculated soils. Theses results highlight the potential of this bacterium to be used in the cleanup of contaminated pesticide waste in the environment.