Cross-protection and cross-feeding between Enterobacter and Comamonas promoting their coexistence and cadmium tolerance in Oryza sativa L.

Metabolic cross-feeding is a pervasive interaction between bacteria to acquire novel phenotypes. However, our current understanding of the survival mechanism for cross-feeding in cocultured bacterial biofilms under heavy-metal conditions remains limited. Herein, we found that Comamonas sp. A23 produces L-phenylalanine to activate the L-phenylalanine degradation pathway in Enterobacter sp. A11, enhancing biofilm formation and cadmium [Cd(II)] immobilization in A11. The genes responsible for L-phenylalanine-degradation (paaK) and cell attachment and aggregation (csgAD) are essential for biofilm formation and Cd(II) immobilization in A11 induced by L-phenylalanine. The augmentation of A11 biofilms, in turn, protects A23 under Cd(II) and H2O2 stresses. The plant-based experiments demonstrate that the induction of two rice Cd(II) transporters, OsCOPT4 and OsBCP1, by A11 and A23 enhances rice resistance against Cd(II) and H2O2 stresses. Overall, our findings unveil the mutual dependence between bacteria and rice on L-phenylalanine cross-feeding for survival under abiotic stress.

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.

Comamonas fluminis sp. nov., isolated from the Han River, Republic of Korea.

A Gram-stain-negative, aerobic and motile bacterial strain, designated CJ34T, was isolated from Han River water in the Republic of Korea. Strain CJ34T grew optimally on tryptic soy agar at 30 °C and pH 7.0 in the absence of NaCl. Results of phylogenetic analysis based on 16S rRNA gene sequence showed that strain CJ34T belonged to the genus Comamonas within the family Comamonadaceae and was most closely related to Comamonas testosteroni ATCC 11996T and Comamonas thiooxydans DSM 17888T (both 98.63 % similarity). The average nucleotide identity values between strain CJ34T and two closely related type strains C. testosteroni ATCC 11996T and C. thiooxydans DSM 17888T were 82.77 and 82.73 %, respectively. The major isoprenoid quinone of strain CJ34T was ubiquinone Q-8. The major cellular fatty acids of strain CJ34T were C16 : 0, C16 : 1 ω6c and/or C16 : 1 ω7c and C18 : 1 ω6c and/or C18 : 1 ω7c. The predominant polar lipids of strain CJ34T were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and an unidentified aminophospholipid. Whole genome sequencing revealed that strain CJ34T had a genome of 4.9 Mbp and the G+C content of the genomic DNA was 59.73 mol%. On the basis of the results of this polyphasic taxonomy study, strain CJ34T represents a novel species in the genus Comamonas, for which the name Comamonas fluminis sp. nov. is proposed. The type strain is CJ34T (=KACC 22237T=JCM 34454T).

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.

Bacterial Metabolism Affects the C. elegans Response to Cancer Chemotherapeutics.

The human microbiota greatly affects physiology and disease; however, the contribution of bacteria to the response to chemotherapeutic drugs remains poorly understood. Caenorhabditis elegans and its bacterial diet provide a powerful system to study host-bacteria interactions. Here, we use this system to study how bacteria affect the C. elegans response to chemotherapeutics. We find that different bacterial species can increase the response to one drug yet decrease the effect of another. We perform genetic screens in two bacterial species using three chemotherapeutic drugs: 5-fluorouracil (5-FU), 5-fluoro-2'-deoxyuridine (FUDR), and camptothecin (CPT). We find numerous bacterial nucleotide metabolism genes that affect drug efficacy in C. elegans. Surprisingly, we find that 5-FU and FUDR act through bacterial ribonucleotide metabolism to elicit their cytotoxic effects in C. elegans rather than by thymineless death or DNA damage. Our study provides a blueprint for characterizing the role of bacteria in the host response to chemotherapeutics.

Improved efficiency of asymmetric hydrolysis of 3-substituted glutaric acid diamides with an engineered amidase.

AIMS: To improve the efficiency of asymmetric hydrolysis of 3-(4-chlorophenyl) glutaric acid diamide (CGD) using a recombinant Comamonas sp. KNK3-7 amidase (CoAM) produced in Escherichia coli. METHODS AND RESULTS: The CoAM gene was cloned, sequenced and found to comprise 1512 bp, encoding a polypeptide of 54 054 Da. CoAM-transformed E. coli were able to perform R-selective hydrolysis of CGD; however, complete conversion of 166·2 mmol l(-1) CGD in 28 h could not be obtained. We attempted to optimize the reactivity of CoAM by mutating single amino acids in the substrate-binding domain. Notably, the methionine-substituted L146M mutant enzyme showed increased reactivity, completing the conversion of 166·2 mmol l(-1) CGD in just 4 h. The Km value for L146M was lower than that of CoAM. CONCLUSIONS: We succeeded in creating the L146M mutant of CoAM with increased substrate affinity and found that this was the best mutant for the hydrolysis of CGD. SIGNIFICANCE AND IMPACT OF THE STUDY: Increasing the efficiency of hydrolysis of 3-substituted glutaric acid diamides is useful to improve the synthesis of optically active 3-substituted gamma-aminobutyric acid. This is the first report of efficient hydrolysis of CGD using amidase mutant-producing E. coli cells.

Comamonas humi sp. nov., isolated from soil.

A bacterial strain, designated GAU11(T), was isolated from soil in Japan. Cells of the strain were Gram-stain-negative, aerobic, non-motile rods. The 16S rRNA gene sequence of strain GAU11(T) showed high similarity to those of Comamonas zonglianii BF-3(T) (98.8 %), Pseudacidovorax intermedius CC21(T) (96.4 %), Acidovorax caeni R-24608(T) (96.2 %), Alicycliphilus denitrificans K601(T) (96.2 %), Pseudorhodoferax soli TBEA3(T) (95.9 %) and Comamonas terrigena LMG 1253(T) (95.9 %). Strain GAU11(T) contained ubiquinone 8 as the sole ubiquinone and diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol as major polar lipids. Its major cellular fatty acids were C16 : 0, C18 : 1ω7c and summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH). The DNA G+C content of strain GAU11(T) was 68.2 mol%. The DNA-DNA relatedness between strain GAU11(T) and C. zonglianii DSM 22523(T) was 52 or 68 % (reciprocal value). Phenotypic characterization indicated that strain GAU11(T) represents a member of the genus Comamonas, but at the same time distinguished it from C. zonglianii DSM 22523(T). From polyphasic characterization, this strain should be classified as representing a novel species of the genus Comamonas, for which the name Comamonas humi sp. nov. (type strain GAU11(T) = JCM 19903(T) = DSM 28451(T)) is proposed.

Comamonas guangdongensis sp. nov., isolated from subterranean forest sediment, and emended description of the genus Comamonas.

A facultatively anaerobic bacterium, strain CY01(T), isolated from subterranean forest sediment collected from Guangdong Province, China, was investigated using a polyphasic taxonomic approach. The cells were short rods, Gram-negative, non-sporulating and motile. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain CY01(T) showed highest sequence similarities to Comamonas thiooxydans S23(T) (98.0 %), Comamonas testosteroni JCM 5832(T) (97.9 %), Comamonas koreensis KCTC 12005(T) (97.7 %) and Comamonas odontotermitis LMG 23579(T) (97.0 %). The major respiratory quinone was ubiquinone-8. The major cellular fatty acids were summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c), C16 : 0 and summed feature 8 (C18 : 1ω6c and/or C18 : 1ω7c). Based on the phylogenetic analysis, DNA-DNA hybridization, whole-cell fatty acid composition as well as biochemical characteristics, strain CY01(T) was clearly distinguishable from all recognized species of the genus Comamonas and should be classified as a representative of a novel species of the genus, for which the name Comamonas guangdongensis sp. nov. is proposed. The type strain is CY01(T) ( = CCTCC AB 2011133(T) = KACC 16241(T)).

Comamonas jiangduensis sp. nov., a biosurfactant-producing bacterium isolated from agricultural soil.

A novel biosurfactant-producing strain, designated YW1(T), was isolated from agricultural soil. Its taxonomic position was investigated using a polyphasic approach. The cells were short rods, Gram-negative, non-sporulating and motile. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain YW1(T) was a member of the genus Comamonas, and showed highest sequence similarities to Comamonas aquatica LMG 2370(T) (98.5%), Comamonas kerstersii LMG 3475(T) (97.7%) and Comamonas terrigena LMG 1253(T) (97.7%). Furthermore, DNA-DNA hybridization experiments against these three strains gave results that were clearly lower than 70% DNA-DNA similarity, and consequently confirmed that this new strain does not belong to a previously described species of the genus Comamonas. The major respiratory quinone was ubiquinone-8. The major fatty acids (>5%) were C16:0 (30.1%), summed feature 3 (C16:1ω6c and/or C16:1ω7c; 25.4%), summed feature 8 (C18:1ω6c and/or C18:1ω7c; 15.3%), C17:0 cyclo (7.4%) and C14:0 (5.8%). The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, unknown phospholipids and unknown lipids. Based on the phylogenetic analysis, DNA-DNA hybridization, whole-cell fatty acid composition as well as biochemical characteristics, strain YW1(T) was clearly distinguishable from all species of the genus Comamonas with validly published names and should be classified as a representative of a novel species of the genus Comamonas, for which the name Comamonas jiangduensis sp. nov. is proposed. The type strain is YW1(T) (=CCTCC AB 2012033(T)=KACC 16697(T)).

[The cnr-like operon in strain Comamonas sp. encoding resistance to cobalt and nickel].

Plasmid pBS501 was detected in the strain Comamonas sp. BS501. This plasmid specifies high level of induced resistance (5 mM) to cobalt/nickel both in the host strain and in related strains C. testosteroni B-1241 and C. acidovorans B-1251. Hybridization analysis revealed a homology of pBS501 restriction fragments with the only well-characterized operon cnrXYHCBAT that resides in plasmid pMOL28 from Cupriavidus metallidurans CH34. Essential differences in the structural organization of the cobalt/nickel resistance determinant were found between plasmid pBS501 and the cnr-operon.

Comamonas granuli sp. nov., isolated from granules used in a wastewater treatment plant.

A Gram-negative, motile, rod-shaped, non-spore-forming bacterial strain, designated as Ko03(T), was isolated from microbial granules, and was characterized, using a polyphasic approach, in order to determine its taxonomic position. The isolate was positive for catalase and oxidase, but negative for gelatinase and beta-galactosidase. Phylogenetic analyses using the 16S rRNA gene sequence showed that the strain formed a monophyletic branch towards the periphery of the evolutionary radiation occupied by the genus Comamonas, its closest neighbors being Comamonas koreensis KCTC 12005(T) (95.9% sequence similarity), Comamonas nitrativorans DSM 13191(T) (95.7%), and Comamonas odontotermitis LMG 23579(T) (95.7%). Strain Ko03(T) had a genomic DNA G+C content of 68.4 mol% and the predominant respiratory quinone was Q-8. The major fatty acids were C(16:1) omega7c (44.7%), C(16:0) (28.1%), C(18:1) (16.1%), and C(10:0) 3-OH (3.5%). These chemo-taxonomic results supported the affiliation of strain Ko03(T) to the genus Comamonas. However, low 16S rRNA gene sequence similarity values and distinguishing phenotypic characteristics allowed genotypic and phenotypic differentiation of strain Ko03(T) from recognized Comamonas species. On the basis of its phenotypic properties and phylogenetic distinctiveness, strain Ko03(T) represents a novel species of the genus Comamonas, for which the name Comamonas granuli sp. nov. is proposed. The type strain is Ko03(T) (=KCTC 12199(T)=NBRC 101663(T)).

Comamonas composti sp. nov., isolated from food waste compost.

A bacterial strain designated YY287(T), isolated from food waste compost, was investigated by polyphasic taxonomic approach. The cells were rod-shaped, Gram-negative, non-pigmented, non-spore-forming and non-fermentative. Phylogenetic analyses using the 16S rRNA gene sequence showed that the strain formed a monophyletic branch towards the periphery of the evolutionary radiation occupied by the genus Comamonas; its closest neighbours were the type strains Comamonas testosteroni DSM 50244(T) (96.5%), Comamonas terrigena DSM 7099(T) (95.4%), Comamonas odontotermitis Dant 3-8(T) (95.2%) and Comamonas koreensis KCTC 12005(T) (94.6%). Strain YY287(T) was clearly distinguished from all of these strains using phylogenetic analysis, DNA-DNA hybridization, fatty acid composition data and a range of physiological and biochemical characteristics. The major fatty acids were 16:0 (33%), 18:1omega7c (13%) and summed feature 3 (16:1omega7c and/or 15:0 iso 2-OH; 41%). The DNA G+C content of the genomic DNA was 62.8 mol%. It is evident from the genotypic and phenotypic data that strain YY287(T) represents a novel species in the genus Comamonas, for which the name Comamonas composti sp. nov. is proposed. The type strain is YY287(T) (=BCRC 17659(T)=LMG 24008(T)).

Comamonas odontotermitis sp. nov., isolated from the gut of the termite Odontotermes formosanus.

A bacterial strain, designated Dant 3-8(T), isolated from the gut of the termite Odontotermes formosanus, was investigated by a polyphasic taxonomic approach. The cells were rod-shaped, Gram-negative, non-pigmented, non-spore-forming and non-fermentative. Phylogenetic analyses using the 16S rRNA gene sequence showed that the strain formed a monophyletic branch towards the periphery of the evolutionary radiation occupied by the genus Comamonas, its closest neighbours being Comamonas testosteroni DSM 50244(T) (96.4 % sequence similarity), Comamonas koreensis KCTC 12005(T) (96.0 %) and Comamonas terrigena DSM 7099(T) (96.2 %). Strain Dant 3-8(T) was clearly distinguished from all of these strains by using phylogenetic analysis, DNA-DNA hybridization, whole-cell protein profiles, fatty acid composition data and a range of physiological and biochemical characteristics. It is evident from the genotypic and phenotypic data that Dant 3-8(T) represents a novel species in the genus Comamonas, for which the name Comamonas odontotermitis sp. nov. is proposed. The type strain is Dant 3-8(T) (=BCRC 17576(T)=LMG 23579(T)).

4-Chlorobenzoate uptake in Comamonas sp. strain DJ-12 is mediated by a tripartite ATP-independent periplasmic transporter.

The fcb gene cluster involved in the hydrolytic dehalogenation of 4-chlorobenzoate is organized in the order fcbB-fcbA-fcbT1-fcbT2-fcbT3-fcbC in Comamonas sp. strain DJ-12. The genes are operonic and inducible with 4-chloro-, 4-iodo-, and 4-bromobenzoate. The fcbT1, fcbT2, and fcbT3 genes encode a transporter in the secondary TRAP (tripartite ATP-independent periplasmic) family. An fcbT1T2T3 knockout mutant shows a much slower growth rate on 4-chlorobenzoate compared to the wild type. 4-Chlorobenzoate is transported into the wild-type strain five times faster than into the fcbT1T2T3 knockout mutant. Transport of 4-chlorobenzoate shows significant inhibition by 4-bromo-, 4-iodo-, and 4-fluorobenzoate and mild inhibition by 3-chlorobenzoate, 2-chlorobenzoate, 4-hydroxybenzoate, 3-hydroxybenzoate, and benzoate. Uptake of 4-chlorobenzoate is significantly inhibited by ionophores which collapse the proton motive force.

Emended description of the species Lampropedia hyalina.

Three Lampropedia hyalina strains from different habitats were compared by phenotypic, chemotaxonomic and molecular characteristics. All strains form coccoid cells and have been reported to grow as square tablets of eight to 64 cells. However, two of these strains (ATCC 11041T and ATCC 43383) have apparently lost this ability, and the third strain may temporarily lose this capacity under certain cultivation conditions. The three strains showed only minor differences in metabolic characteristics: the main significant physiological difference was the ability to accumulate polyphosphate under alternating anaerobic-aerobic conditions found for DSM 15336. The three strains showed high similarity in fatty acid composition and only slight differences in the G + C content (63-67 mol%) and DNA-DNA reassociation (90-95 % relatedness). Comparative 16S rRNA gene sequence analyses on these three strains and three Lampropedia hyalina 16S rRNA gene sequences deposited at NCBI showed that they are all very similar (> 98.8 %) and that they form a distinct group among the 'Betaproteobacteria', showing between 94.6 and 93 % 16S rRNA gene similarity to members of various genera such as Acidovorax, Aquaspirillum, Brachymonas, Comamonas, Delftia and Xenophilus. Fluorescent in situ hybridization with oligonucleotide probes targeting betaproteobacteria on the 16S rRNA and 23S rRNA gene level further supported the conclusion that all investigated strains are members of the 'Betaproteobacteria'. Two oligonucleotide probes were designed and successfully applied for culture-independent identification of Lampropedia hyalina by means of fluorescent in situ hybridization.