Genus Comamonas Research Articles

Comamonas halotolerans sp. nov., isolated from the faecal sample of a zoo animal, Naemorhedus caudatus.

Strain NoAHT (=KACC 23135T=JCM 35999T), a novel Gram-negative, motile bacterium with a rod-shaped morphology, was isolated from the zoo animal faecal samples, specifically the long-tailed goral species Naemorhedus caudatus. The novel bacterial strain grew optimally in a nutrient broth medium under the following conditions: 1-2% (w/v) NaCl, pH 7-8 and 30 °C. The strain NoAHT exhibited high tolerance to NaCl, with the ability to tolerate up to 7% (w/v) NaCl. Based on phylogenetic analyses using 16S rRNA gene sequencing, strain NoAHT was found to have the closest relatedness to Comamonas jiangduensis YW1T (98.5%), Comamonas aquatica ATCC 11330T (97.9%), Comamonas resistens KCTC 82561T (97.9%), Comamonas fluminis CJ34T (97.7%) and Comamonas suwonensis EJ-4T (97.6%). The genome size and genomic DNA G+C content of strain NoAHT were 4.05 Mbp and 55.9 mol%, respectively. A whole-genome-level comparison of strain NoAHT with C. jiangduensis YWT, Comamonas kerstersii LMG 3475T, C. aquatica NBRC 14918T, Comamonas terrigena NBRC 12685T and C. fluminis CJ34T revealed the following orthologous average nucleotide identity values: 80.1, 79.0, 78.6, 76.3 and 75.2%, respectively. The major polar lipids of strain NoAHT were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. Considering our findings in chemotaxonomic, genotypic and phenotypic characteristics, strain NoAHT is identified as a novel species within the genus Comamonas, for which the name Comamonas halotolerans sp. nov. is proposed.

Influence of terrestrial and marine air mass on the constituents and intermixing of bioaerosols over a coastal atmosphere

Abstract. Coastal environments provide an ideal setting for investigating the intermixing processes between terrestrial and marine aerosols. In this study, fine particulate matter (PM2.5) samples categorized into terrestrial, marine, and mixed air masses were collected from a coastal location in northern China. The chemical and biological constituents, including water-soluble ions (WSIs), metallic elements, and bacterial and fungal aerosols, were investigated from January to March 2018, encompassing both the winter heating and spring dust seasons. Terrestrial air masses constituted 59.94 % of the total air masses throughout the sampling period, with a significant increase during severe haze pollution (up to 90 %). These air masses exhibited a higher concentration of PM2.5 (240 µg m−3) and carried more water-soluble ions and metal elements. The terrestrial air mass also contained a larger number of animal parasites or symbionts, as well as human pathogens from anthropogenic emissions, such as Staphylococcus, Deinococcus, Sphingomonas, Lactobacillus, Cladosporium, and Malassezia. Conversely, a significant quantity of saprophytic bacteria such as hydrocarbon-degrading and gut bacteria from the genera Comamonas, Streptococcus, Novosphingobium, and Aerococcus and the saprophytic fungus Aspergillus were the most abundant species in the marine air mass samples. The mixed air mass elucidates the intermixing process of terrestrial and marine sources, a result of microorganisms originating from both anthropogenic and terrestrial emissions, which includes pathogenic microorganisms from hospitals and sewage treatment plants, and a multitude of soil bacteria. A stronger correlation was noted between microorganisms and continental elements in both terrestrial and mixed air mass samples, specifically K+, Mg2+, and Ca2+ derived from soil dust. Marine air masses exhibited a significant correlation with sea salt ions, specifically Na+. In the mixed air mass sample, a fusion of marine and terrestrial microorganisms is characterized by alterations in the ratio of pathogenic to saprophytic microorganisms when compared to samples derived from either terrestrial or marine sources. This study on the constituents and amalgamation of bioaerosols over the coastal atmosphere encompassing distinct air masses is crucial to understand the transport, intermixing processes, and health implications of terrestrial and marine air masses.

Comamonas endophytica sp. nov., a novel indole acetic acid producing endophyte isolated from bamboo in China.

Two novel indole acetic acid-producing strains, 5MLIRT and D4N7, were isolated from Indosasa shibataeoides in Yongzhou, Hunan province, and Phyllostachys edulis in Hangzhou, Zhejiang province, respectively. Based on their 16S rRNA sequences, strains 5MLIRT and D4N7 were closely related to Comamonas antarcticus 16-35-5T (98.4 % sequence similarity), and the results of 92-core gene phylogenetic trees showed that strains 5MLIRT and D4N7 formed a phylogenetic lineage within the clade comprising Comamonas species. The complete genome size of strain 5MLIRT was 4.49 Mb including two plasmids, and the DNA G+C content was 66.5 mol%. The draft genome of strain D4N7 was 4.26 Mb with 66.7 mol% G+C content. The average nucleotide identity and digital DNA-DNA hybridization values among strain 5MLIRT and species in the genus Comamonas were all below the species delineation threshold. The colonies of strain 5MLIRT and D4N7 were circular with regular margins, convex, pale yellow and 1.0-2.0 mm in diameter when incubated at 30 °C for 3 days. Strains 5MLIRT and D4N7 grew optimally at 30 °C, pH 7.0 and 1.0 % NaCl. The respiratory isoprenoid quinone was ubiquinone-8. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. Polyphasic analyses indicated that strains 5MLIRT and D4N7 could be distinguished from related validly named Comamonas species and represent a novel species of the genus Comamonas, for which the name Comamonas endophytica sp. nov. is proposed. The type strain is 5MLIRT (=ACCC 62069T=GDMCC 1.2958T=JCM 35331T).

Comamonas resistens sp. nov. and Pseudomonas triclosanedens sp. nov., two members of the phylum Pseudomonadota isolated from the wastewater treatment system of a pharmaceutical factory.

Five strains of two novel species were isolated from the wastewater treatment systems of a pharmaceutical factory located in Zhejiang province, PR China. Strains ZM22T and Y6 were identified as belonging to a potential novel species of the genus Comamonas, whereas strains ZM23T, ZM24 and ZM25 were identified as belonging to a novel species of the genus Pseudomonas. These strains were characterized by polyphasic approaches including 16S rRNA gene analysis, multi-locus sequence analysis, average nucleotide identity (ANI), in silico DNA-DNA hybridization (isDDH), physiological and biochemical tests, as well as chemotaxonomic analysis. Genome-based phylogenetic analysis further confirmed that strains ZM22T and Y6 form a distinct clade closely related to Comamonas testosteroni ATCC 11996T and Comamonas thiooxydans DSM 17888T. Strains ZM23T, ZM24 and ZM25 were grouped as a separate clade closely related to Pseudomonas nitroreducens DSM 14399T and Pseudomonas nicosulfuronedens LAM1902T. The orthoANI and isDDH results indicated that strains ZM22T and Y6 belong to the same species. In addition, genomic DNA fingerprinting demonstrated that these strains do not originate from a single clone. The same results were observed for strains ZM23T, ZM24 and ZM25. Strains ZM22T and Y6 were resistant to multiple antibiotics, whereas strains ZM23T, ZM24 and ZM25 were able to degrade an emerging pollutant, triclosan. The phylogenetic, physiological and biochemical characteristics, as well as chemotaxonomy, allowed these strains to be distinguished from their genus, and we therefore propose the names Comamonas resistens sp. nov. (type strain ZM22=MCCC 1K08496T=KCTC 82561T) and Pseudomonas triclosanedens sp. nov. (type strain ZM23T=MCCC 1K08497T=JCM 36056T), respectively.

Diverticulosis is not associated with altered gut microbiota nor is it predictive of future diverticulitis: a population-based colonoscopy study

Background The etiopathogenesis of diverticular disease is unknown. Objective To compare the fecal and mucosa-associated microbiota between participants with and without diverticulosis and participants who later developed diverticulitis versus those that did not from a population-based study. Methods The PopCol study, conducted in Stockholm, Sweden, invited a random sample of 3556 adults to participate, of which 745 underwent colonoscopy. Overall, 130 participants (17.5%) had diverticulosis. 16S rRNA gene sequencing was conducted on available sigmoid biopsy samples from 529 and fecal samples from 251 individuals. We identified individuals who subsequently developed acute diverticulitis up to 13 years after sample collection. In a case-control design matching for gender, age (+/−5 years), smoking and antibiotic exposure, we compared taxonomic composition, richness and diversity of the microbiota between participants with or without diverticulosis, and between participants who later developed acute diverticulitis versus those who did not. Results No differences in microbiota richness or diversity were observed between participants with or without diverticulosis, nor for those who developed diverticulitis compared with those who did not. No bacterial taxa were significantly different between participants with diverticulosis compared with those without diverticulosis. Individuals who later developed acute diverticulitis (2.8%) had a higher abundance of genus Comamonas than those who did not (p = .027). Conclusions In a population-based cohort study the only significant difference was that those who later develop diverticulitis had more abundance of genus Comamonas. The significance of Comamonas is unclear, suggesting a limited role for the gut microbiota in the etiopathogenesis of diverticular disease.

Milk kefir alters fecal microbiota impacting gut and brain health in mice.

Kefir is a fermented beverage made of a symbiotic microbial community that stands out for health benefits. Although its microbial profile is still little explored, its effects on modulation of gut microbiota and production of short-chain fatty acids (SCFAs) seems to act by improving brain health. This work aimed to analyze the microbiota profile of milk kefir and its effect on metabolism, oxidative stress, and in the microbiota-gut-brain axis in a murine model. The experimental design was carried out using C57BL-6 mice (n = 20) subdivided into groups that received 0.1mL water or 0.1mL (10% w/v) kefir. The kefir proceeded to maturation for 48h, and then it was orally administered, via gavage, to the animals for 4weeks. Physicochemical, microbiological, antioxidant analyzes, and microbial profiling of milk kefir beverage were performed as well as growth parameters, food intake, serum markers, oxidative stress, antioxidant enzymes, SCFAs, and metabarcoding were analyzed in the mice. Milk kefir had 76.64 ± 0.42% of free radical scavenging and the microbiota composed primarily by the genus Comamonas. Moreover, kefir increased catalase and superoxide dismutase (colon), and SCFAs in feces (butyrate), and in the brain (butyrate and propionate). Kefir reduced triglycerides, uric acid, and affected the microbiome of animals increasing fecal butyrate-producing bacteria (Lachnospiraceae and Lachnoclostridium). Our results on the brain and fecal SCFAs and the antioxidant effect found were associated with the change in the gut microbiota caused by kefir, which indicates that kefir positively influences the gut-microbiota-brain axis and contributes to the preservation of gut and brain health. KEY POINTS: • Milk kefir modulates fecal microbiota and SCFA production in brain and colon. • Kefir treatment increases the abundance of SCFA-producing bacteria. • Milk kefir increases antioxidant enzymes and influences the metabolism of mice.

Genome-based analyses of the genus Acidovorax: proposal of the two novel genera Paracidovorax gen. nov., Paenacidovorax gen. nov. and the reclassification of Acidovorax antarcticus as Comamonas antarctica comb. nov. and emended description of the genus Acidovorax.

The genus Acidovorax is a genetically heterogeneous species clustering that comprises many environmental and plant-pathogenic taxa. To better understand the evolutionary relationships among the Acidovorax species, 22 available genome sequences of type strains including the genera Acidovorax and Comamonas were used to conduct the genome-based analyses. Three well-supported monophyletic clusters of the Acidovorax species were determined based on the phylogenomic tree reconstructed using core genes, while they were not grouped in the 16S rRNA gene-based phylogenetic tree. The species arrangements of the genus Acidovorax were further confirmed by the comparisons of the digital DNA-DNA hybridization and average nucleotide identity (ANI) values. The ANI, average amino acid identity, and the percentage of conserved proteins values among the inter-clusters were approximately 83, 81, and 61%, respectively, and thus were proposed as practical thresholds for genus delineation. Besides, Acidovorax antarcticus was much closer to members of the genus Comamonas rather than those of the genus Acidovorax based on the genome-based analysis. Taken together, we propose the division of the current genus Acidovorax into the emended genus Acidovorax and the two novel genera Paracidovorax gen. nov., Paenacidovorax gen. nov. and the transfer of Acidovorax antarcticus into the genus Comamonas as Comamonas antarctica comb. nov.

The Emergence of the Genus Comamonas as Important Opportunistic Pathogens.

Comamonas spp. are non-fermenting Gram-negative bacilli. They were first discovered in 1894, and since then, twenty-four species have been characterized. The natural habitat of these bacteria is soil, wastewater/sludge, fresh water such as ponds and rivers, and the animal intestinal microbiome. They were also isolated from industrial settings, such as activated sludge and polluted soil, and from the hospital environment and clinical samples, such as urine, pus, blood, feces, and kidney. Comamonas spp. are associated with environmental bioremediation and are considered an important environmental bacterium rather than a human pathogen. However, in the 1980s, they became a concern when several human infections associated with these species were reported. Here, the Comamonas genus was examined in terms of its members, identification techniques, and pathogenicity. Seventy-seven infection cases associated with these microorganisms that have been discussed in the literature were identified and investigated in this project. All relevant information regarding year of infection, country of origin, patient information such as age, sex, underlying medical conditions if any, type of infection caused by the Comamonas species, antibiotic susceptibility testing, treatment, and outcomes for the patient were extracted from case reports. The findings suggest that even though Comamonas spp. are thought of as being of low virulence, they have caused harmful health conditions in many healthy individuals and even death in patients with underlying conditions. Antimicrobial treatment of infections associated with these species, in general, was not very difficult; however, it can become an issue in the future because some strains are already resistant to different classes of antibiotics. Therefore, these pathogens should be considered of such importance that they should be included in the hospital screening programs.

Indole metabolism by phenol-stimulated activated sludges: Performance, microbial communities and network analysis

Indole and phenol often coexist in the coking wastewater, while the effects of phenol on microbial communities of indole metabolism were less explored. In this study, the microbial interactions within activated sludge microbial communities stimulated by indole (group A) or by indole and phenol (group B) were systematically investigated in sequencing batch reactors (SBRs). The results showed that the removal of indole was increased by adding phenol. By using high-throughput sequencing technology, it was found that α-diversity was reduced in both groups. According to the relative abundance analysis, the indole-degrading genus Comamonas was the core genus in both groups (33.94% and 61.40%). But another indole-degrading genus Pseudomonas was only enriched in group A with 12.22% relative abundance. Meanwhile, common aromatic degrading genus Dyella and Thermomonas were enriched only in group B. It was found that the relative abundance of cytochrome P450 and styrene degradation enzymes were increased in group B by PICRUSt analysis. Based on the phylogenetic molecular ecological networks (pMENs), module hub OTU_1149 (Burkholderia) was only detected in group B, and the positive interactions between the key functional genus Burkholderia and other bacteria were increased. This study provides new insights into our understanding of indole metabolism communities stimulated by phenol, which would provide useful information for practical coking wastewater treatment.

Using algae bacteria consortia to effectively treat coking wastewater: Performance, microbial community, and mechanism

Coking wastewater is widely generated and poses a significant threat to the environment. Adopting algae bacteria consortia is promising and viable for coking wastewater treatment. In this study, the performance of activated sludge, non-aerated and aerated algae-bacteria consortia (ABC) for treating coking wastewater was investigated and compared. Aerated ABC showed maximum 87.16 ± 1.12% COD removal rates while non-aerated ABC could remove 78.62 ± 0.56% COD. TIN removal rates of aerated ABC and non-aerated ABC were 72.50 ± 0.78% and 80.99 ± 1.26%, respectively. Algae addition could increase the removal performance due to the material exchange between algae and bacteria. Aerated ABC had a larger particle size (119–225 μm) and good settling performance. Genus Comamonas, nitrogen removal bacteria, was predominant in two ABC reactors (average 62% and 60%, respectively) treating low coking wastewater. By comparison, genus Planococcus, denitrifying bacteria, became predominant in aerated algae-bacteria with a higher concentration of coking wastewater. Both genus Comamonas and Planococcus were detected with the benzene ring cleavage reaction function genes. The nitrogen removal pathway showed that nitrogen was removed by ammonia detoxification and nitrate dissimilation. The findings of this study would contribute to the application of ABC in coking wastewater treatment with reduce aeration energy input.

Unraveling the bacterial diversity of Cangar Hot Spring, Indonesia by Next Generation Sequencing of 16S rRNA gene

Abstract. Geraldi A, Tay CC, Ni’matuzahroh, Fatimah, Hanafi WNW. 2021. Unraveling the bacterial diversity of Cangar Hot Spring, Indonesia by Next Generation Sequencing of 16S rRNA gene. Biodiversitas 22: 4060-4066. This study is the first attempt at using the Next Generation Sequencing (NGS) method with 16S rRNA to understand the bacterial community structure in an Indonesian hot spring. This study aims to unravel the bacterial diversity of the Cangar Hot Spring as one of the most explored natural hot springs in East Java, Indonesia. We found Proteobacteria and Bacteroidetes as the two most abundant phyla. We discovered the first occurrence of genera Cloacibacterium and Methylobacillus in the hot spring ecosystem, which was the most dominant genera at Cangar Hot Spring. We also found several potential bacteria for bioindustry and bioremediation, such as Acinetobacter junii and Pseudomonas alcaligenes. Besides that, we also observed opportunistic pathogens from genera Comamonas and Vogesella. This study result will provide valuable information for further bioprospecting of bacteria with commercial potential and the development of health and safety measures in the Cangar Hot Spring, among others. Hopefully, this report would encourage the use of NGS technology for studying other hot springs in Indonesia.

Analyses of deodorization performance of mixotrophic biotrickling filter reactor using different industrial and agricultural wastes as packing material

In this study, to efficiently remove malodorous gas and reduce secondary pollution under mixotrophic conditions, pine bark, coal cinder, straw and mobile bed biofilm reactor (MBBR) fillers were used as packing materials in a biological trickling filter (BTF) to simultaneously treat high-concentration H2S and NH3. The results showed that the removal rate of BTF-A filled with pine bark was the highest, which was 86.31% and 94.06% under the H2S and NH3 loading rates of 53.59 g/m³·h while the empty bed residence time (EBRT) was 40.5 s. The theoretical maximum load was obtained by fitting the kinetic curve, and the value were 90.09 g H2S m-³·h−1 and 172.41 g NH3 m-³·h−1. Meanwhile, after treating with 720 ppm of NH3, the average concentration of NO3- in the BTF circulating fluid was only 127.58 mg/L, indicating the better performance of secondary pollutants control. Microbiological analysis showed that Dokdonella, Micropruina, Candidatus_Alysiosphaera, Nakamurella and Thiobacillus possessed high abundance at the genus level, and their entire percentage in four BTF reactors were 62.87%, 46.32%, 47.98%, and 57.35% respectively. It is worthwhile that the genera Comamonas and Trichococcus with heterotrophic nitrification and aerobic denitrification capabilities and proportion of 3.66%, 1.45%, 5.43%, and 3.23% were observed in four reactors.

Exopolysaccharides From Lactobacillus paracasei Isolated From Kefir as Potential Bioactive Compounds for Microbiota Modulation.

Microbiota coexists in true symbiosis with the host playing pivotal roles as a key element for well-being and health. Exopolysaccharides from lactic acid bacteria are an alternative as novel potential prebiotics that increase microbiota diversity. Considering this, the aim of the present work was to evaluate the capacity of the EPS produced by two L. paracasei strains isolated from kefir grains, to be metabolized in vitro by fecal microbiota producing short chain fatty acids. For this purpose, fecal samples from healthy children were inoculated in a basal medium with EPS and incubated in anaerobiosis at 37°C for 24, 48, and 72 h. DGGE profiles and the production of SCFA after fermentation were analyzed. Additionally, three selected samples were sequenced by mass sequencing analysis using Ion Torrent PGM. EPS produced by L. paracasei CIDCA 8339 (EPS8339) and CIDCA 83124 (EPS83124) are metabolized by fecal microbiota producing a significant increase in SCFA. EPS8339 fermentation led to an increment of propionate and butyrate, while fermentation of EPS83124 increased butyrate levels. Both EPS led to a profile of SCFA different from the ones obtained with inulin or glucose fermentation. DGGE profiles of 72 h fermentation demonstrated that both EPS showed a different band profile when compared to the controls; EPS profiles grouped in a cluster that have only 65% similarity with glucose or inulin profiles. Mass sequencing analysis demonstrated that the fermentation of EPS8339 leads to an increase in the proportion of the genera Victivallis, Acidaminococcus and Comamonas and a significant drop in the proportion of enterobacteria. In the same direction, the fermentation of EPS83124 also resulted in a marked reduction of Enterobacteriaceae with a significant increase in the genus Comamonas. It was observed that the changes in fecal microbiota and SCFA profile exerted by both polymers are different probably due to differences in their structural characteristics. It can be concluded that EPS synthesized by both L. paracasei strains, could be potentially used as bioactive compound that modify the microbiota increasing the production of propionic and butyric acid, two metabolites highly associated with beneficial effects both at the gastrointestinal and extra-intestinal level.

Comamonas flocculans sp. nov., a Floc-Forming Bacterium Isolated from Livestock Wastewater.

A Gram-negative, aerobic, non-motile, rod-shaped, floc-forming, and non-spore-forming bacterium, designated as NLF-7-7T, was isolated from the biofilm of a sample collected from a livestock wastewater treatment plant in Nonsan, Republic of Korea. Strain NLF-7-7T, forms a visible floc and grows in the flocculated state. Cells of strain NLF-7-7T grew optimally at pH 6.5 and 30°C and in the presence of 0.5% (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain NLF-7-7T belonged to the family Comamonadaceae, and was most closely related to Comamonas badia DSM 17552T (95.8% similarity) and Comamonas nitrativorans 23310T (94.0% similarity). The phylogenetic and phenotypic data indicate strain NLF-7-7T is clearly distinguished from the Comamonas lineage. The major cellular fatty acids were C10:0 3OH, C16:0, and summed feature 3 (C16:1 ω6c/C16:1 ω7c). The respiratory quinone was Q-8. The polar lipids were composed of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, and an unidentified aminolipid. The DNA G+C content of strain NLF-7-7 was 68.0mol%. Based on the phenotypic, chemotaxonomic, and phylogenetic properties, strain NLF-7-7T represents a novel species of the genus Comamonas, for which the name Comamonas flocculans sp. nov. is proposed. The type strain is C. flocculans NLF-7-7T (=KCTC 62943T). The GenBank/EMBL/DDBJ accession number for the 16S rRNA gene sequence of Comamonas flocculans NLF-7-7T is MN527436. The whole-genome shotgun BioProject Number is PRJNA555370 with the Accession Number CP042344.

Microaerophilic biodegradation of raw textile effluent by synergistic activity of bacterial community DR4

Treatment of raw textile effluent (RTE) is very difficult, due to its inherent heterogeneous, low-biodegradable and toxic compositions. Pure and mixed microbial cultures have limited metabolic capabilities in effective mineralization of complex RTE. Therefore, in this study a novel bacterial community DR4 was enriched directly into a complex RTE consisting of 27 different dyes using textile dye polluted soil as an inoculum. The rigorous enrichment process resulted in acclimatization of a taxonomically distinct bacterial population, with an abundance of the genus Comamonas in the bacterial community DR4 as compared to the abundance of Pseudomonas in the RTE respectively, as revealed by high-throughput 16S rRNA gene (V3–V4 region) sequencing. Microaerophilic treatment of RTE by enriched bacterial community DR4, in the presence of optimized electron donor (sucrose) and nitrogen source (yeast extract) resulted in 88% of American Dye Manufacturer's Institute (ADMI) removal and 98% of Chemical oxygen demand (COD) reduction within 32 h at 37 °C. In silico prediction of the functional genes within bacterial community DR4 was made by Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) analysis. The PICRUSt analysis revealed high abundance of xenobiotic degradation and metabolism genes. The predicted functional genes and textile dye degradation pathways were further validated using Ultraviolet–visible spectroscopy (UV–Vis), Fourier transform infrared (FTIR) spectroscopy and High Resolution Liquid Chromatography coupled with Mass Spectrometry (HR-LCMS) based characterization of textile dye degradation metabolites. The activity of azoreductases in the cell-free extracts (CFE) of the enriched bacterial community DR4 was induced by 1.83–7.81 folds in the presence of representative textile dyes as compared to uninduced samples, which confirmed their role in textile effluent decolourization. The degradation of four representative azo dyes present in RTE such as Disperse orange 30, Reactive red 152, Direct blue 2 and Acid brown 15 depicted symmetric degradation of azo bonds by bacterial community DR4.

Metataxonomic analyses reveal differences in aquifer bacterial community as a function of creosote contamination and its potential for contaminant remediation

Metataxonomic approach was used to describe the bacterial community from a creosote-contaminated aquifer and to access the potential for in situ bioremediation of the polycyclic aromatic hydrocarbons (PAHs) by biostimulation. In general, the wells with higher PAH contamination had lower richness and diversity than others, using the Shannon and Simpson indices. By the principal coordinate analysis (PCoA) it was possible to observe the clustering of the bacterial community of most wells in response of the presence of PAH contamination. The significance analysis using edgeR package of the R program showed variation in the abundance of some Operational Taxonomic Units (OTUs) of contaminated wells compared to uncontaminated ones. Taxons enriched in the contaminated wells were correlated positively (p < 0.05) with the hydrocarbons, according to redundancy analysis (RDA). All these enriched taxa have been characterized as PAH degrading agents, such as the genus Comamonas, Geobacter, Hydrocarboniphaga, Anaerolinea and Desulfomonile. Additionally, it was possible to predict, with the PICRUSt program, a greater proportion of pathways and genes related to the degradation of PAHs in the wells with higher contamination levels. We conclude that the contaminants promoted the enrichment of several groups of degrading bacteria in the area, which strengthens the feasibility of applying biostimulation as an aquifer remediation strategy.

Bacterial Community Analysis on the Skin of Odorrana grahami and Proposal of Comamonas aquatica subsp. aquatica subsp. nov. and Comamonas aquatica subsp. rana subsp. nov.

Several studies indicated that Odorrana grahami (O. grahami) skin contains abundant antimicrobial peptides, and the skin was recognized as hostile habitat for microorganisms. In this study, the microbial community was evaluated by 16S rRNA gene sequencing, and two associated bacterial isolates were obtained and characterized from the skin of O. grahami. Sixteen bacterial genera were identified from the O. grahami skin by uncultured clone sequences. The dominant groups were Comamonas, Bacillus and Morganella, and the genus Comamonas was the most abundant group (41.7% of the total) of the community. Fortunately, strains CW-25T and CW-518 belonging to genus Comamonas were isolated by plating dilutions. The polyphasic taxonomy results indicated that strain CW-25T was a member of Comamonas aquatica, it showed much higher antimicrobials resistance than the closest C. aquatica strains of LMG 2370T, LMG5937 and LMG 6112 isolated from freshwater. Based on the polyphasic taxonomic studies and antimicrobials resistance characteristics, two subspecies of Comamonas aquatica subsp. aquatica nov. and Comamonas aquatica subsp. rana nov. were proposed. The super-antimicrobial resistance endows the strains of Comamonas aquatica subsp. rana inhabit the O. grahami skin, and the primary defense of O. grahami might be composed by the antimicrobial peptides and the native bacteria.

The Core- and Pan-Genomic Analyses of the Genus Comamonas: From Environmental Adaptation to Potential Virulence.

Comamonas is often reported to be one of the major members of microbial communities in various natural and engineered environments. Versatile catabolic capabilities of Comamonas have been studied extensively in the last decade. In contrast, little is known about the ecological roles and adaptation of Comamonas to different environments as well as the virulence of potentially pathogenic Comamonas strains. In this study, we provide genomic insights into the potential ecological roles and virulence of Comamonas by analysing the entire gene set (pangenome) and the genes present in all genomes (core genome) using 34 genomes of 11 different Comamonas species. The analyses revealed that the metabolic pathways enabling Comamonas to acquire energy from various nutrient sources are well conserved. Genes for denitrification and ammonification are abundant in Comamonas, suggesting that Comamonas plays an important role in the nitrogen biogeochemical cycle. They also encode sophisticated redox sensory systems and diverse c-di-GMP controlling systems, allowing them to be able to effectively adjust their biofilm lifestyle to changing environments. The virulence factors in Comamonas were found to be highly species-specific. The conserved strategies used by potentially pathogenic Comamonas for surface adherence, motility control, nutrient acquisition and stress tolerance were also revealed.

Evolution of Functional Bacteria in a Polycyclic Aromatic Hydrocarbon (PAH)-Degrading Bioreactor.

In this study a laboratory-scale sequencing batch bioreactor was constructed, using phenanthrene/pyrene as the sole carbon-source, to demonstrate the removal efficiencies of polycyclic aromatic hydrocarbons (PAHs) and the evolution process of a functional bacterial community. The removal rates were: COD, 51.4 to 76.3%; phenanthrene, 63.5 to 92.4%; and pyrene, 65.9 to 90.1%. Quantification analysis indicated that in sludge samples from the phenanthrene/pyrene degradation stage, the contents of 16S rRNA and ring-hydroxylating dioxygenase genes of Gram-positive and Gram-negative bacteria were 10-and 72-, 102- and 1152-, 31- and 905-fold higher, respectively, than those in seed sludge samples. Clone sequencing and evolution analysis showed that genera Comamonas, Pseudomonas, and Mycobacterium were distributed across all samples and were significant PAH-degrading populations, but some genera, such as Polaromonas and Nocardioides, were substantially enriched only when phenanthrene/pyrene was fed. Correspondingly, the functional genes nidA3, phnAc, and ndoC2 were distributed across all samples, whereas nagAc, pdoA2, and pdoA were enriched only when phenanthrene/pyrene was fed.

Complete genome sequencing of Comamonas kerstersii 8943, a causative agent for peritonitis

Because of poor differentiation among the members of genus Comamonas using phenotypic methods, human infections caused by C. kerstersii are sporadically reported in the literature. Here, we represent the first complete genome sequence of C. kerstersii 8943, which caused peritonitis in a patient with continuous ambulatory peritoneal dialysis (CAPD). The complete genome with no gaps was obtained using third-generation Pacific Biosciences (PacBio) RSII sequencing system with single-molecule real-time (SMRT) analysis. Protein-coding genes, rRNAs and tRNAs were predicted. Functional annotations of the genome using different databases revealed several genes related to pathogenicity including antibiotic resistance genes and prophages. Our work demonstrates that whole genome sequencing can enhance the resolution of clinical investigations and our data can be used as a reference genome during the rapid diagnosis of C. kerstersii infections in the future.