Occurrence of Nitrate Reductase and Molybdopterin in Xanthomonas maltophilia

Temperature Sensitivity and Composition of Nitrate-Reducing Microbiomes from a Full-Scale Woodchip Bioreactor Treating Agricultural Drainage Water

Denitrifying woodchip bioreactors (WBR), which aim to reduce nitrate (NO3-) pollution from agricultural drainage water, are less efficient when cold temperatures slow down the microbial transformation processes. Conducting bioaugmentation could potentially increase the NO3- removal efficiency during these specific periods. First, it is necessary to investigate denitrifying microbial populations in these facilities and understand their temperature responses. We hypothesized that seasonal changes and subsequent adaptations of microbial populations would allow for enrichment of cold-adapted denitrifying bacterial populations with potential use for bioaugmentation. Woodchip material was sampled from an operating WBR during spring, fall, and winter and used for enrichments of denitrifiers that were characterized by studies of metagenomics and temperature dependence of NO3- depletion. The successful enrichment of psychrotolerant denitrifiers was supported by the differences in temperature response, with the apparent domination of the phylum Proteobacteria and the genus Pseudomonas. The enrichments were found to have different microbiomes' composition and they mainly differed with native woodchip microbiomes by a lower abundance of the genus Flavobacterium. Overall, the performance and composition of the enriched denitrifying population from the WBR microbiome indicated a potential for efficient NO3- removal at cold temperatures that could be stimulated by the addition of selected cold-adapted denitrifying bacteria.

Stenotrophomonas maltophilia Differential Gene Expression in Synthetic Cystic Fibrosis Sputum Reveals Shared and Cystic Fibrosis Strain-Specific Responses to the Sputum Environment

Stenotrophomonas maltophilia is a Gram-negative opportunistic pathogen that can infect the lungs of people with cystic fibrosis (CF). The highly viscous mucus in the CF lung, expectorated as sputum, serves as the primary nutrient source for microbes colonizing this site and induces virulence-associated phenotypes and gene expression in several CF pathogens. Here, we characterized the transcriptional responses of three S. maltophilia strains during exposure to synthetic CF sputum medium (SCFM2) to gain insight into how this organism interacts with the host in the CF lung. These efforts led to the identification of 881 transcripts differentially expressed by all three strains, many of which reflect the metabolic pathways used by S. maltophilia in sputum, as well as altered stress responses. The latter correlated with increased resistance to peroxide exposure after pregrowth in SCFM2 for two of the strains. We also compared the SCFM2 transcriptomes of two S. maltophilia CF isolates to that of the acute infection strain, S. maltophilia K279a, allowing us to identify CF isolate-specific signatures in differential gene expression. The expression of genes from the accessory genomes was also differentially altered in response to SCFM2. Finally, a number of biofilm-associated genes were differentially induced in SCFM2, particularly in K279a, which corresponded to increased aggregation and biofilm formation in this strain relative to both CF strains. Collectively, this work details the response of S. maltophilia to an environment that mimics important aspects of the CF lung, identifying potential survival strategies and metabolic pathways used by S. maltophilia during infections.IMPORTANCE Stenotrophomonas maltophilia is an important infecting bacterium in the airways of people with cystic fibrosis (CF). However, compared to the other CF pathogens, S. maltophilia has been relatively understudied. The significance of our research is to provide insight into the global transcriptomic changes of S. maltophilia in response to a medium that was designed to mimic important aspects of the CF lung. This study elucidates the overall metabolic changes that occur when S. maltophilia encounters the CF lung and generates a road map of candidate genes to test using in vitro and in vivo models of CF.

Modules of co-occurrence in the cyanobacterial pan-genome reveal functional associations between groups of ortholog genes

Cyanobacteria are a monophyletic phylogenetic group of global importance and have received considerable attention as potential host organisms for the renewable synthesis of chemical bulk products from atmospheric CO₂. The cyanobacterial phylum exhibits enormous metabolic diversity with respect to morphology, lifestyle and habitat. As yet, however, research has mostly focused on few model strains and cyanobacterial diversity is insufficiently understood. In this respect, the increasing availability of fully sequenced bacterial genomes opens new and unprecedented opportunities to investigate the genetic inventory of organisms in the context of their pan-genome. Here, we seek understand cyanobacterial diversity using a comparative genome analysis of 77 fully sequenced and assembled cyanobacterial genomes. We use phylogenetic profiling to analyze the co-occurrence of clusters of likely ortholog genes (CLOGs) and reveal novel functional associations between CLOGs that are not captured by co-localization of genes. Going beyond pair-wise co-occurrences, we propose a network approach that allows us to identify modules of co-occurring CLOGs. The extracted modules exhibit a high degree of functional coherence and reveal known as well as previously unknown functional associations. We argue that the high functional coherence observed for the modules is a consequence of the similar-yet-diverse nature of cyanobacteria. Our approach highlights the importance of a multi-strain analysis to understand gene functions and environmental adaptations, with implications beyond the cyanobacterial phylum. The analysis is augmented with a simple toolbox that facilitates further analysis to investigate the co-occurrence neighborhood of specific CLOGs of interest.

Cyanobacteria are photoautotrophic prokaryotes of global importance and offer great potential as host organisms for the renewable synthesis of chemical bulk products, including biofuels, from atmospheric CO₂. As yet, however, research has mostly focussed on a small number of model strains and the genetic inventory of the cyanobacterial phylum is still insufficiently understood. The rapidly increasing availability of fully sequenced cyanobacterial genomes opens new and unprecendented possibilities to study the diversity of cyanobacterial strain in the context of the cyanobacterial pan-genome. Here, we seek to understand the genetic inventory of individual cyanobacterial strains based on the hypothesis that genes that are functionally related also co-occur within the genomes of different strains. We confirm this hypothesis by in depth analysis of co-occurrence that goes beyond pair-wise co-occurrences. We show that co-occurrence does not imply co-localization on the genome. Our work provides a novel approach to infer gene function and highlights the importance of a multi-strain analysis, with implications beyond the analysis of the cyanobacterial phylum.

Identification of Electrode Respiring, Hydrocarbonoclastic Bacterial Strain Stenotrophomonas maltophilia MK2 Highlights the Untapped Potential for Environmental Bioremediation

Electrode respiring bacteria (ERB) possess a great potential for many biotechnological applications such as microbial electrochemical remediation systems (MERS) because of their exoelectrogenic capabilities to degrade xenobiotic pollutants. Very few ERB have been isolated from MERS, those exhibited a bioremediation potential toward organic contaminants. Here we report once such bacterial strain, Stenotrophomonas maltophilia MK2, a facultative anaerobic bacterium isolated from a hydrocarbon fed MERS, showed a potent hydrocarbonoclastic behavior under aerobic and anaerobic environments. Distinct properties of the strain MK2 were anaerobic fermentation of the amino acids, electrode respiration, anaerobic nitrate reduction and the ability to metabolize n-alkane components (C8–C36) of petroleum hydrocarbons (PH) including the biomarkers, pristine and phytane. The characteristic of diazoic dye decolorization was used as a criterion for pre-screening the possible electrochemically active microbial candidates. Bioelectricity generation with concomitant dye decolorization in MERS showed that the strain is electrochemically active. In acetate fed microbial fuel cells (MFCs), maximum current density of 273 ± 8 mA/m² (1000 Ω) was produced (power density 113 ± 7 mW/m²) by strain MK2 with a coulombic efficiency of 34.8%. Further, the presence of possible alkane hydroxylase genes (alkB and rubA) in the strain MK2 indicated that the genes involved in hydrocarbon degradation are of diverse origin. Such observations demonstrated the potential of facultative hydrocarbon degradation in contaminated environments. Identification of such a novel petrochemical hydrocarbon degrading ERB is likely to offer a new route to the sustainable bioremedial process of source zone contamination with simultaneous energy generation through MERS.

Denitrification by cystic fibrosis pathogens - Stenotrophomonas maltophilia is dormant in sputum

OBJECTIVE

Chronic Pseudomonas aeruginosa lung infection is the most severe complication for cystic fibrosis (CF) patients. Infected endobronchial mucus of CF patients contains anaerobic zones mainly due to the respiratory burst of polymorphonuclear leukocytes. We have recently demonstrated ongoing denitrification in sputum from patients infected with P. aeruginosa. Therefore we aimed to investigate, whether the pathogenicity of several known CF pathogens is correlated to their ability to perform denitrification.

METHODS

We measured denitrification with N(2)O microsensors in concert with anaerobic growth measurements by absorbance changes and colony counting in isolates from 32 CF patients chronically infected with the highly pathogenic bacteria P. aeruginosa, Achromobacter xylosoxidans, Burkholderia multivorans or the less pathogenic bacterium Stenotrophomonas maltophilia. Consumption of NO(3)(-) and NO(2)(-) was estimated by the Griess Assay. All isolates were assayed during 2 days of incubation in anaerobic LB broth with NO(3)(-) or NO(2)(-). PNA FISH staining of 16S rRNA was used to estimate the amount of ribosomes per bacterial cells and thereby the in situ growth rate of S. maltophilia in sputum.

RESULTS

Supplemental NO(3)(-) caused increased production of N(2)O by P. aeruginosa, A. xylosoxidans and B. multivorans and increased growth for all pathogens. Growth was, however, lowest for S. maltophilia. NO(3)(-) was metabolized by all pathogens, but only P. aeruginosa was able to remove NO(2)(-). S. maltophilia had limited growth in sputum as seen by the weak PNA FISH staining.

CONCLUSIONS

All four pathogens were able to grow anaerobically by NO(3)(-) reduction. Denitrification as demonstrated by N(2)O production was, however, not found in S. maltophilia isolates. The ability to perform denitrification may contribute to the pathogenicity of the infectious isolates since complete denitrification promotes faster anaerobic growth. The inability of S. maltophilia to proliferate by denitrification and therefore grow in the anaerobic CF sputum may explain its low pathogenicity in CF patients.

Purification of Two Nitrate Reductases from Xanthomonas maltophilia Grown in Aerobic Cultures

Xanthomonas maltophilia ATCC 17666 is an obligate aerobe that accumulates nitrite when grown on nitrate. Spectra of membranes from nitrate-grown cells exhibited b-type cytochrome peaks and A(615-630) indicative of d-type cytochrome but no absorption peaks corresponding to c-type cytochromes. The nitrate reductase (NR) activity was located in the membrane fraction. Triton X-100-extracted reduced methyl viologen-NRs were purified on DE-52, hydroxylapatite, and Sephacryl S-300 columns to specific activities of 52 to 67 mumol of nitrite formed per min per mg of protein. The cytochrome-containing NR(I) separated on sodium dodecyl sulfate-polyacrylamide gel electrophoresis into a 135-kDa alpha-subunit, a 64-kDa beta-subunit, and a 23-kDa gamma-subunit with relative band intensities indicative of a 1:1:1 alpha/beta/gamma subunit ratio and a M(r) of 222,000. The electronic spectrum of dithionite-reduced purified NR displayed peaks at 425, 528, and 558 nm, indicative of the presence of a cytochrome b, an interpretation consistent with the pyridine hemochrome spectrum formed. The cytochrome b of the NR was reduced under anaerobic conditions by menadiol and oxidized by nitrate with the production of nitrite. This NR contained 0.96 Mo, 12.5 nonheme iron, and 1 heme per 222 kDa: molybdopterin was detected with the Neurospora crassa nit-1 assay. A smaller reduced methyl viologen-NR (169 kDa), present in various concentrations in the Triton X-100 preparations, lacked a cytochrome spectrum and did not oxidize menadiol. The characteristics of the NRs and the absence of c-type cytochromes provide insights into why X. maltophilia accumulates nitrite.

The complete genome, comparative and functional analysis of Stenotrophomonas maltophilia reveals an organism heavily shielded by drug resistance determinants

BACKGROUND

Stenotrophomonas maltophilia is a nosocomial opportunistic pathogen of the Xanthomonadaceae. The organism has been isolated from both clinical and soil environments in addition to the sputum of cystic fibrosis patients and the immunocompromised. Whilst relatively distant phylogenetically, the closest sequenced relatives of S. maltophilia are the plant pathogenic xanthomonads.

RESULTS

The genome of the bacteremia-associated isolate S. maltophilia K279a is 4,851,126 bp and of high G+C content. The sequence reveals an organism with a remarkable capacity for drug and heavy metal resistance. In addition to a number of genes conferring resistance to antimicrobial drugs of different classes via alternative mechanisms, nine resistance-nodulation-division (RND)-type putative antimicrobial efflux systems are present. Functional genomic analysis confirms a role in drug resistance for several of the novel RND efflux pumps. S. maltophilia possesses potentially mobile regions of DNA and encodes a number of pili and fimbriae likely to be involved in adhesion and biofilm formation that may also contribute to increased antimicrobial drug resistance.

CONCLUSION

The panoply of antimicrobial drug resistance genes and mobile genetic elements found suggests that the organism can act as a reservoir of antimicrobial drug resistance determinants in a clinical environment, which is an issue of considerable concern.

Effect of environmental factors on biofilm formation by clinical Stenotrophomonas maltophilia isolates

The influence of environmental factors (temperature, aerobiosis-anaerobiosis, static-dynamic conditions, pH) was determined on biofilm formation by 51 S. maltophilia clinical isolates. The strains produced more biofilm at 32 degrees C than at 37 or 18 degrees C. Aerobic and 6% CO2 atmosphere yielded comparable biofilm amounts, higher than under anaerobic conditions. Biofilm production was not affected by static vs. agitated culture conditions. Biofilm production at pH 7.5 and 8.5 was comparable but significantly higher than at pH 5.5. The capacity of individual strains to form biofilm and thus contribute to the severity of some diseases is influenced by host traits and environmental conditions at the site of infection, and play an important role in the pathogenesis of biomaterial-related disease caused by S. maltophilia.