Gordonia prachuapensis sp. nov. and Gordonia sesuvii sp. nov., two novel actinobacteria isolated from mangrove sediments and leaves of halophyte Sesuvium portulacastrum in Thailand.

A polyphasic approach was used to characterize two novel actinobacterial strains, designated PKS22-38T and LSe1-13T, which were isolated from mangrove soils and leaves of halophyte Sesuvium portulacastrum (L.), respectively. Phylogenetic analyses based on 16S rRNA gene sequences showed that they belonged to the genus Gordonia and were most closely related to three validly published species with similarities ranging from 98.6 to 98.1 %. The genomic DNA G+C contents of strains PKS22-38T and LSe1-13T were 67.3 and 67.2 mol%, respectively. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between the two strains were 93.3 and 54.9 %, respectively, revealing that they are independent species. Meanwhile, the ANI and dDDH values between the two novel strains and closely related type strains were below 80.5 and 24.0 %, respectively. Strains PKS22-38T and LSe1-13T contained C16 : 0, C18 : 1 ω9c and C18 : 0 10-methyl (TBSA) as the major fatty acids and diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylinositol as the main phospholipids. The predominant menaquinone was MK-9(H2). Based on phenotypic, chemotaxonomic, phylogenetic and genomic data, strains PKS22-38T and LSe1-13T are considered to represent two novel species within the genus Gordonia, for which the names Gordonia prachuapensis sp. nov. and Gordonia sesuvii sp. nov. are proposed, with strain PKS22-38T (=TBRC 17540T=NBRC 116256T) and strain LSe1-13T (=TBRC 17706T=NBRC 116396T) as the type strains, respectively.

Gordonia tangerina sp. nov., isolated from seawater.

A Gram-stain-positive, aerobic bacterium, designated GW1C4-4T, was isolated from the seawater sample from the tidal zone of Guanyinshan Coast, Xiamen, Fujian Province, PR China. The strain was reddish-orange, rod-shaped and non-motile. Cells of strain GW1C4-4T were oxidase-negative and catalase-positive. The strain could grow at 10-42 °C (optimum, 32-35 °C), pH 5-9 (optimum, pH 6) and with 0-10 % NaCl (w/v; optimum, 1 %). Phylogenetic analysis based on the 16S rRNA sequences indicated that strain GW1C4-4T belonged to the genus Gordonia, having the highest similarity to Gordonia mangrovi HNM0687T (98.5 %), followed by Gordonia bronchialis DSM 43247T (98.4 %). The G+C DNA content was 66.5 mol %. Average nucleotide identity and digital DNA-DNA hybridization values between strain GW1C4-4T and G. mangrovi HNM0687T were 85.8 and 30.0 %, respectively. The principal fatty acids of strain GW1C4-4T were C16 : 0, C18 : 0 10-methyl (TBSA) and summed feature 3 (C16 : 1 ω7c/C16 : 1 ω6c). MK-9 (H2) was the sole respiratory quinone. The polar lipids included diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and an unidentified lipid. Based on its phylogenetic, phenotypic, chemotaxonomic and genomic characteristics, it is proposed that strain GW1C4-4T represents a novel species within the genus Gordonia, for which the name Gordonia tangerina sp. nov. is proposed. The type strain is GW1C4-4T (=MCCC 1A18727T=KCTC 49729T).

Gordonia jinghuaiqii sp. nov. and Gordonia zhaorongruii sp. nov., isolated from Tibetan Plateau wildlife.

Four mesophilic and Gram-stain-positive strains (zg-686T/zg-691 and HY186T/HY189) isolated from Tibetan Plateau wildlife (PR China) belong to the genus Gordonia according to 16S rRNA gene and genomic sequence-based phylogenetic/genomic results. They have a DNA G+C content range of 67.4-68.3 mol% and low DNA relatedness (19.2-27.6 %) with all available genomes in the genus Gordonia. Strains zg-686T/zg-691 and HY186T/HY189 had C18 : 1ω9c, C18 : 0 10-methyl, C16 : 1 ω7c/C16 : 1ω6c and C16 : 0 as major cellular fatty acids. The polar lipids detected in strains zg-686T and HY186T included diphosphatidylglycerol, phosphatidylethanolamine, phosphatidyl inositol mannoside and phosphatidylinositol. The respiratory quinones comprised MK8(H2) (10.8 %) and MK9(H2) (89.2 %) for strain zg-686T, and MK6 (7.7 %), MK8(H2) (8.4 %), MK8(H4) (3.1 %) and MK9(H2) (80.8 %) for strain HY186T. Optimal growth conditions were pH 7.0, 35-37 °C and 0.5-1.5 % NaCl (w/v) for strains pair zg-686T/zg-691, and pH 7.0, 28 °C and 1.5 % (w/v) NaCl for strains pair HY186T/HY189. Based on these genotypic and phenotypic results, these four strains could be classified as two different novel species in the genus Gordonia, for which the names Gordonia jinghuaiqii sp. nov. and Gordonia zhaorongruii sp. nov. are proposed. The type strains are zg-686T (=GDMCC 1.1715T =JCM 33890T) and HY186T (=CGMCC 4.7607T =JCM 33466T), respectively.

Gordonia mangrovi sp. nov., a novel actinobacterium isolated from mangrove soil in Hainan.

A novel actinobacterium, designated strain HNM0687T, was isolated from mangrove soil samples collected from Hainan Province, PR China and its polyphasic taxonomy was studied. Based on the results of 16S rRNA gene sequence analysis, strain HNM0687T was closely related to Gordonia bronchialis NBRC 16047T (98.7 %), Gordonia rhizosphera NBRC 16068T (98.2 %), Gordonia oryzae RS15-1ST (97.9 %), Gordonia polyisoprenivorans NBRC 16320T (97.7 %) and Gordonia sediminis AMA 120T (97.7 %). Genome-based comparisons revealed a clear distinction in average nucleotide identity values between strain HNM0687T and its closely related strains (74.4-78.3 %). Strain HNM0687T contained meso-diaminopimelic acid, arabinose and galactose in whole-cell hydrolysates. Mycolic acid was present. The menaquinones of strain HNM0687T were MK-9(H2) and MK-7(H2). The phospholipids of the isolate were composed of diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylinositol. The major fatty acids were C16 : 0, C16 : 1 ω7c/C16 : 1 ω6c, C18 : 010-methyl (TBSA), C18 : 0 and C18 : 1 ω9c. Based on its genotypic, chemotaxonomic and phenotypic characteristics, it is concluded that strain HNM0687T represents a novel species of the genus Gordonia for which the name Gordonia mangrovi sp. nov. is proposed. The type strain is HNM0687T (=CCTCC AA 2019074 T=KCTC 49383 T).

Gordonia crocea sp. nov. and Gordonia spumicola sp. nov. isolated from sludge of a wastewater treatment plant.

Two novel actinobacteria, designated NBRC 107696T and NBRC 107697T, were isolated from sludge samples from a wastewater treatment plant and their taxonomic positions were investigated by a polyphasic approach. The cells of the strains were aerobic, rod-shaped, non-motile and non-endospore-forming. The strains contained glutamic acid, alanine and meso-diaminopimelic acid in the peptidoglycan. Galactose and arabinose were detected as cell-wall sugars. The predominant menaquinone was identified as MK-9(H2) and the major fatty acids were C16  :  0, C18 : 1ω9c and C16 : 1ω7c. The DNA G+C contents of NBRC 107696T and NBRC 107697T were 68.07 and 68.99 mol%, respectively. Phylogenetic analyses based on 16S rRNA gene sequence comparisons revealed that NBRC 107696T and NBRC 107697T were a clade with members of the genus Gordonia. The highest 16S rRNA gene sequence similarity values were obtained with Gordonia araii IFM 10211T (98.9 %) for NBRC 107697T, and Gordonia malaquae IMMIB WWCC-22T, Gordonia neofelifaecis AD-6T and Gordonia humi CC-12301T (98.1 %) for NBRC 107696T, respectively. The digital DNA-DNA relatedness data coupled with the combination of genotypic and phenotypic data indicated that the two strains are representatives of two novel separate species. The names proposed to accommodate these two strains are Gordonia spumicola sp. nov. and Gordonia crocea sp. nov., and the type strains are NBRC 107696T (=IFM 10067T=TBRC 11239T) and NBRC 107697T (=IFM 10881T=TBRC 11240T), respectively.

Gordonia insulae sp. nov., isolated from an island soil.

A mycolic acid-containing actinobacterium designated strain MMS17-SY073T was isolated from island soil. The isolate showed best growth at 25 °C, pH 6, and 0 % (w/v) NaCl. The phylogenetic analysis based on 16S rRNA gene sequences indicated that strain MMS17-SY073T belongs to the genus Gordonia, and is mostly related to the type strains of Gordonia soli (98.5 % sequence similarity), Gordonia polyisoprenivorans (98.1%), and Gordonia hankookensis (97.8%). The genome-based comparisons showed a clear distinction between the strain and the two neighbouring species, G. soli and G. polyisoprenivorans, with the average nucleotide identities (ANI) of 75.8 and 76.3 %, respectively. Notably, the genome of strain MMS17-SY073T was the largest in total stretch and gene counts among the complete genomes of Gordonia, and contained a number of biosynthetic gene clusters for secondary metabolites, in particular those for non-ribosomal peptide synthetases. The major polar lipids were diphosphatidyl glycerol (DPG), phosphatidyl glycerol (PG), phosphatidyl ethanolamine (PE), phosphatidyl inositol (PI) and phosphatidyl inositol mannoside (PIM). The isoprenoid quinone was MK-9(H2), and the main fatty acids were C16 : 0 (30.2%) and 10-methyl-C18 : 0 (33.7%). The whole cell hydrolysates contained galactose, arabinose, and meso-diaminopimelic acid. The DNA G+C content was 67.4 mol%. Based on phenotypic, chemotaxonomic and genetic analysis, strain MMS17-SY073T should be classified as a new species of the genus Gordonia, for which the name Gordonia insulae sp. nov. is proposed (type strain=MMS17-SY073T=KCTC 49257T=JCM 33277T).

Analysis of genome sequence and trehalose lipid production peculiarities of the thermotolerant Gordonia strain.

Gordoniae are one of the most promising hydrocarbon-oxidizing actinobacteria. Here we present the genome sequence analysis of thermotolerant strain Gordonia sp. 1D isolated from oil-refinery soil. It is capable of alkane consumption and biosurfactant production at temperatures of up to 50°C. Gordonia sp. 1D demonstrates maximum biosurfactant production when grown on hexadecane, and at 40°C it was slightly higher than at 27°C: 35 and 39 mN/m, respectively. For the first time, it was experimentally confirmed that the carbohydrate component of extracellular biosurfactants produced by strain 1D is trehalose. In addition, genes for the production of trehalose lipid biosurfactants were identified. The genetic determinants for two different pathways for trehalose synthesis were found. The strain carries genes otsA and otsB involved in de novo trehalose biosynthesis. Moreover, the genes treY and treZ responsible for trehalose biosynthesis from maltooligosaccharides and starch or glycogen were identified.

Gordonia oryzae sp. nov., isolated from rice plant stems (Oryza sativa L.).

A novel endophytic actinomycete, designated strain RS15-1ST, was isolated from surface-sterilized stems of Oryza sativa L. collected from Sisaket province, Thailand. The colony of strain was strong orange, catalase-positive and oxidase-negative. Growth occurred at a temperature range of 17-37 °C, at pH 4.0-9.0 and in the presence of 0-13 % (w/v) NaCl. Phylogenetic analyses based on the 16S rRNA sequences showed that strain RS15-1ST belonged to the genus Gordonia and was closely related to Gordonia polyisoprenivorans DSM 44302T (98.8 %) and Gordonia rhizosphera DSM 44383T (98.4 %). The major cellular fatty acids were C16 : 0, C18 : 0 10-methyl (tbsa), C16 : 1ω7c/C16 : 1ω6c and C18 : 1ω9c. The menaquinones were MK-9(H2) and MK-8(H2). Strain RS15-1ST contained meso-diaminopimelic acid, arabinose, galactose, mannose and ribose in whole-cell hydrolysates. The polar lipids of the strain were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol mannosides, an unidentified polar lipid and two unidentified phospholipids. The DNA G+C content was 66.3 mol%. In silico DNA-DNA hybridization of strain RS15-1ST showed 48.3 and 20.5 % relatedness to its closest neighbours, Gordonia polyisoprenivorans DSM 44302T and Gordonia rhizosphera DSM 44383T, respectively. Based on data of genotypic, phenotypic, phylogenetic and chemotaxonomic analysis, strain RS15-1ST represents a novel species of the genus Gordonia, for which the name Gordonia oryzae sp. nov. is proposed. The type strain is RS15-1ST (=TBRC 8485T=NBRC 113446T).

Gordonia sediminis sp. nov., an actinomycete isolated from mangrove sediment.

The taxonomic position of an actinomycete designated AMA 120T, isolated from mangrove sediment, was clarified by phenotypic, chemotaxonomic and phylogenetic studies. The 16S rRNA gene sequence revealed that strain AMA 120T was most closely related to Gordonia rhizosphera NBRC 16068T (98.9 %), Gordonia polyisoprenivorans NBRC 16320T (98.1 %) and Gordonia bronchialis NBRC 16047T (98.1 %). A fragment of the gyrB gene of strain AMA 120T formed a distinct phyletic line with G. rhizosphera NBRC 16068T (95.4 %). Strain AMA 120T contained meso-diaminopimelic acid, arabinose and galactose as cell-wall components, and MK-9(H2) was the predominant menaquinone. The polar lipid profile for this strain consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol mannoside and two unidentified phospholipids. Mycolic acid was present. The major fatty acids were C16 : 0, C18 : 1ω9c and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c). The DNA-DNA relatedness values between AMA 120T and close species were below 70 %. There was an obvious distinction in the average nucleotide identity distribution between strain AMA 120T and its closely related strains at around 75-92%. The DNA G+C content of strain AMA 120T was 66.6 mol%. These results, coupled with the phenotypic and chemotaxonomic data, indicated that strain AMA 120T represents a novel species of the genus Gordonia, for which the name Gordoniasediminis sp. nov. is proposed. The type strain is AMA 120T (=TBRC 7109T=NBRC 113236T).

Characterization and genomic analysis of highly efficient thermotolerant oil-degrading bacterium Gordonia sp. 1D.

A thermotolerant bacterial strain 1D isolated from refinery oil-contaminated soil was identified as Gordonia sp. based on the analysis of 16S rRNA and gyrB gene sequences. The strain was found to utilize crude oil, diesel fuel, and a wide spectrum of alkanes at temperatures up to 50 °C. Strain 1D is the first representative of Gordonia amicalis capable of utilizing alkanes of chain length up to С36 at a temperature of 45-50 °C. The degree of crude oil degradation by Gordonia sp. 1D at 45 °C was 38% in liquid medium and 40% in soil (with regard to abiotic loss). There are no examples of so effective hydrocarbon-oxidizing thermotolerant Gordonia in the world literature. The 1D genome analysis revealed the presence of two alkane hydroxylase gene clusters, genes of dibenzothiophene cleavage, and the cleavage of salicylate and gentisate - naphthalene metabolism intermediates. The highly efficient thermotolerant strain Gordonia sp. 1D can be used in remediation of oil-contaminated soils in hot climates.

An insight into the ecology, diversity and adaptations of Gordonia species.

The bacterial genus Gordonia encompasses a variety of versatile species that have been isolated from a multitude of environments. Gordonia was described as a genus about 20 years ago, and to date, 39 different species have been identified. Gordonia is recognized for symbiotic associations with multiple hosts, including aquatic (marine and fresh water) biological forms and terrestrial invertebrates. Some Gordonia species isolated from clinical specimens are known to be opportunistic human pathogens causing secondary infections in immunocompromised and immunosuppressive individuals. They are also predominant in mangrove ecosystems and terrestrial sites. Members of the genus Gordonia are ecologically adaptable and show marked variations in their properties and products. They generate diverse bioactive compounds and produce a variety of extracellular enzymes. In addition, production of surface active compounds and carotenoid pigments allows this group of microorganisms to grow under different conditions. Several isolates from water and soil have been implicated in bioremediation of different environments and plant associated species have been explored for agricultural applications. This review highlights the prevalence of the members of this versatile genus in diverse environments, details its associations with living forms, summarizes the biotechnologically relevant products that can be obtained and discusses the salient genomic features that allow this Actinomycete to survive in different ecological niches.

Gordonia phthalatica sp. nov., a di-n-butyl phthalate-degrading bacterium isolated from activated sludge.

A phthalate esters-degrading bacterial strain, designated QH-11T, was isolated from an activated sludge wastewater treatment plant in Beijing, PR China. The cells were aerobic, Gram-stain-positive, non-motile, catalase-positive, oxidase-negative, short rods and formed white colonies on trypticase soy agar. This isolate contained meso-diaminopimelic acid as the diagnostic diamino acid and whole-cell hydrolysates contained arabinose and ribose. Diphosphatidylglycerol and phosphatidylethanolamine were the predominant polar lipids. According to the results of full-length of 16S rRNA gene sequence analysis, QH-11T represented a member of the genus Gordonia and showed the highest sequence similarity to Gordonia hydrophobica DSM 44015T (99.2 %), but was distinguishable by a low level of DNA-DNA relatedness (37.8 %). Genome-based comparisons indicated a clear distinction from the top ten most similar type strains (16S rRNA gene sequence) with pairwise average nucleotide identities (ANI) between 74.6 and 83.4 %. The predominant respiratory quinone was MK-9(H2), the mycolic acids present had 56 to 62 carbon atoms, and the major fatty acids were C16 : 0 (33.3 %), C17 : 1ω8c (23.4 %) and C18 : 1ω9c (17.9 %). The DNA G+C content was 68.0 mol%. On the basis of the results of DNA-DNA hybridization, ANI and physiological and biochemical tests, it is proposed that QH-11T represents a novel species of the genus Gordonia, for which the name Gordonia phthalatica sp. nov. is proposed. The type strain is QH-11T (CICC 24107T =KCTC 39933T).

Identification and characterisation of isoprene-degrading bacteria in an estuarine environment.

Approximately one-third of volatile organic compounds (VOCs) emitted to the atmosphere consists of isoprene, originating from the terrestrial and marine biosphere, with a profound effect on atmospheric chemistry. However, isoprene provides an abundant and largely unexplored source of carbon and energy for microbes. The potential for isoprene degradation in marine and estuarine samples from the Colne Estuary, UK, was investigated using DNA-Stable Isotope Probing (DNA-SIP). Analysis at two timepoints showed the development of communities dominated by Actinobacteria including members of the genera Mycobacterium, Rhodococcus, Microbacterium and Gordonia. Representative isolates, capable of growth on isoprene as sole carbon and energy source, were obtained from marine and estuarine locations, and isoprene-degrading strains of Gordonia and Mycobacterium were characterised physiologically and their genomes were sequenced. Genes predicted to be required for isoprene metabolism, including four-component isoprene monooxygenases (IsoMO), were identified and compared with previously characterised examples. Transcriptional and activity assays of strains growing on isoprene or alternative carbon sources showed that growth on isoprene is an inducible trait requiring a specific IsoMO. This study is the first to identify active isoprene degraders in estuarine and marine environments using DNA-SIP and to characterise marine isoprene-degrading bacteria at the physiological and molecular level.

Removal Capacities of Polycyclic Aromatic Hydrocarbons (PAHs) by a Newly Isolated Strain from Oilfield Produced Water.

The polycyclic aromatic hydrocarbon (PAH)-degrading strain Q8 was isolated from oilfield produced water. According to the analysis of a biochemical test, 16S rRNA gene, house-keeping genes and DNA-DNA hybridization, strain Q8 was assigned to a novel species of the genus Gordonia. The strain could not only grow in mineral salt medium (MM) and utilize naphthalene and pyrene as its sole carbon source, but also degraded mixed naphthalene, phenanthrene, anthracene and pyrene. The degradation ratio of these four PAHs reached 100%, 95.4%, 73.8% and 53.4% respectively after being degraded by Q8 for seven days. A comparative experiment found that the PAHs degradation efficiency of Q8 is higher than that of Gordonia alkaliphila and Gordonia paraffinivorans, which have the capacities to remove PAHs. Fourier transform infrared spectra, saturate, aromatic, resin and asphaltene (SARA) and gas chromatography-mass spectrometry (GC-MS) analysis of crude oil degraded by Q8 were also studied. The results showed that Q8 could utilize n-alkanes and PAHs in crude oil. The relative proportions of the naphthalene series, phenanthrene series, thiophene series, fluorene series, chrysene series, C21-triaromatic steroid, pyrene, and benz(a)pyrene were reduced after being degraded by Q8. Gordonia sp. nov. Q8 had the capacity to remediate water and soil environments contaminated by PAHs or crude oil, and provided a feasible way for the bioremediation of PAHs and oil pollution.

Gordonia hongkongensis sp. nov., isolated from blood culture and peritoneal dialysis effluent of patients in Hong Kong.

Two bacterial strains, HKU50T and HKU46, were isolated in Hong Kong from the blood culture and the peritoneal dialysis effluent of two patients. The strains are Gram-stain-positive, acid-fast, non-motile, non-sporulating bacilli. They grow on Columbia agar with 5 % defibrinated sheep blood and brain-heart infusion agar under aerobic conditions with 5 % CO2 at 37 °C as pink-to-orange, non-haemolytic colonies. The strains are catalase-positive and oxidase-negative, and have a unique biochemical profile distinguishable from other closely related species. DNA sequencing revealed that both isolates possessed multiple intra-genomic 16S rRNA gene copies (99.8-100 % sequence identities to Gordonia lacunae NRRL B-24551T and Gordonia terrae NRRL B-16283T). Phylogenetic analysis of the 16S rRNA gene, secA1 and gyrB showed that the two isolates formed a distinct branch within the genus Gordonia and were most closely related to G. lacunae and G. terrae. DNA-DNA hybridization demonstrated ≤53.7 % and ≤49.4 % DNA relatedness between the two isolates and G. lacunae, and between the two isolates and G. terrae, respectively. Hierarchical cluster analysis of MALDI-TOF MS main spectrum profiles showed that strains HKU50T and HKU46 were closely related to each other, but were distinct from G. lacunae, G. terrae, or any other species of the genus Gordonia in the Bruker database. The chemotaxonomic traits of the two strains were highly similar, and the major fatty acids were summed feature 4 (iso-C15 : 0 2-OH/C16 : 1trans-9), C16 : 0, C18 : 1cis-9, and tuberculostearic acid. A novel species named Gordonia hongkongensis sp. nov. is proposed to accommodate strains HKU50T and HKU46, with strain HKU50T (=CCOS 955T=CIP 111027T=NBRC 111234T=NCCP 16210T) as the type strain.

Dibenzothiophene desulfurization capability and evolutionary divergence of newly isolated bacteria.

Metabolically microorganisms are diverse, and they are capable of transforming almost every known group of chemical compounds present in coal and oil in various forms. In this milieu, one of the important microbial metabolic processes is the biodesulfurization [cleavage of carbon-sulfur (C-S) bond] of thiophenic compounds, such as dibenzothiophene (DBT), which is the most abundant form of organic sulfur present in fossil fuels. In the current study, ten newly isolated bacterial isolates, designated as species of genera Gordonia, Amycolatopsis, Microbacterium and Mycobacterium, were enriched from different samples in the presence of DBT as a sole source of organic sulfur. The HPLC analysis of the DBT grown cultures indicated the consumption of DBT and accumulation of 2-hydroxybiphenyl (2-HBP). Detection of 2-HBP, a marker metabolite of 4S (sulfoxide-sulfone-sulfinate-sulfate) pathway, suggested that the newly isolated strains harbored metabolic activity for DBT desulfurization through the cleavage of C-S bond. The maximum 2-HBP formation rate was 3.5 µmol/g dry cell weight (DCW)/h. The phylogenetic analysis of the new isolates showed that they had diverse distribution within the phylogenetic tree and formed distinct clusters, suggesting that they might represent strains of already reported species or they were altogether new species. Estimates of evolutionary divergence showed high level of nucleotide divergence between the isolates within the same genus. The new isolates were able to use a range of heterocyclic sulfur compounds, thus making them suitable candidates for a robust biodesulfurization system for fossil fuels.

Bacteriophages of wastewater foaming-associated filamentous Gordonia reduce host levels in raw activated sludge.

Filamentous bacteria are a normal and necessary component of the activated sludge wastewater treatment process, but the overgrowth of filamentous bacteria results in foaming and bulking associated disruptions. Bacteriophages, or phages, were investigated for their potential to reduce the titer of foaming bacteria in a mixed-microbial activated sludge matrix. Foaming-associated filamentous bacteria were isolated from activated sludge of a commercial wastewater treatment plan and identified as Gordonia species by 16S rDNA sequencing. Four representative phages were isolated that target G. malaquae and two un-named Gordonia species isolates. Electron microscopy revealed the phages to be siphophages with long tails. Three of the phages--GordTnk2, Gmala1, and GordDuk1--had very similar ~76 kb genomes, with >93% DNA identity. These genomes shared limited synteny with Rhodococcus equi phage ReqiDocB7 and Gordonia phage GTE7. In contrast, the genome of phage Gsput1 was smaller (43 kb) and was not similar enough to any known phage to be placed within an established phage type. Application of these four phages at MOIs of 5-15 significantly reduced Gordonia host levels in a wastewater sludge model by approximately 10-fold as compared to non-phage treated reactors. Phage control was observed for nine days after treatment.

Detailed investigation of the microbial community in foaming activated sludge reveals novel foam formers.

Foaming of activated sludge (AS) causes adverse impacts on wastewater treatment operation and hygiene. In this study, we investigated the microbial communities of foam, foaming AS and non-foaming AS in a sewage treatment plant via deep-sequencing of the taxonomic marker genes 16S rRNA and mycobacterial rpoB and a metagenomic approach. In addition to Actinobacteria, many genera (e.g., Clostridium XI, Arcobacter, Flavobacterium) were more abundant in the foam than in the AS. On the other hand, deep-sequencing of rpoB did not detect any obligate pathogenic mycobacteria in the foam. We found that unknown factors other than the abundance of Gordonia sp. could determine the foaming process, because abundance of the same species was stable before and after a foaming event over six months. More interestingly, although the dominant Gordonia foam former was the closest with G. amarae, it was identified as an undescribed Gordonia species by referring to the 16S rRNA gene, gyrB and, most convincingly, the reconstructed draft genome from metagenomic reads. Our results, based on metagenomics and deep sequencing, reveal that foams are derived from diverse taxa, which expands previous understanding and provides new insight into the underlying complications of the foaming phenomenon in AS.

Enrichment of aliphatic, alicyclic and aromatic acids by oil-degrading bacteria isolated from the rhizosphere of plants growing in oil-contaminated soil from Kazakhstan.

Three microbial strains were isolated from the rhizosphere of alfalfa (Medicago sativa), grass mixture (Festuca rubra, 75 %; Lolium perenne, 20 %; Poa pratensis, 10 %), and rape (Brassica napus) on the basis of their high capacity to use crude oil as the sole carbon and energy source. These isolates used an unusually wide spectrum of hydrocarbons as substrates (more than 80), including n-alkanes with chain lengths ranging from C12 to C32, monomethyl- and monoethyl-substituted alkanes (C12-C23), n-alkylcyclo alkanes with alkyl chain lengths from 4 to 18 carbon atoms, as well as substituted monoaromatic and diaromatic hydrocarbons. These three strains were identified as Gordonia rubripertincta and Rhodococcus sp. SBUG 1968. During their transformation of this wide range of hydrocarbon substrates, a very large number of aliphatic, alicyclic, and aromatic acids was detected, 44 of them were identified by GC/MS analyses, and 4 of them are described as metabolites for the first time. Inoculation of plant seeds with these highly potent bacteria had a beneficial effect on shoot and root development of plants which were grown on oil-contaminated sand.

Gordonia iterans sp. nov., isolated from a patient with pneumonia.

A second novel clinical actinobacterial strain, designated IFM 10348(T), was isolated from the sputum of the same Japanese patient with bacterial pneumonia from whom the type strain of Gordonia araii had been isolated. The strains differed in phylogenetic position and drug-resistance profiles. The taxonomic position of strain IFM 10348(T) was clarified by phenotypic, chemotaxonomic and phylogenetic studies. Phylogenetic analyses based on 16S rRNA gene sequences clearly demonstrated that strain IFM 10348(T) occupied a distinct clade within the genus Gordonia and was related closely to Gordonia malaquae DSM 45064(T) and Gordonia hirsuta DSM 44140(T) (97.3 and 97.1% similarities, respectively). Strain IFM 10348(T) was also clearly differentiated from G. malaquae DSM 45064(T) and G. hirsuta DSM 44140(T) based on gyrB and secA1 gene sequence similarity values. Strain IFM 10348(T) had MK-9(H2) as the predominant menaquonine, contained meso-diaminopimelic acid, arabinose, galactose and glucosamine as cell-wall components, and contained C18:1ω9c, summed feature 3 (C16:1ω7c and/or C16:1ω6c) and C16:0 as the major cellular fatty acids. Mycolic acids were present. The DNA G+C content of strain IFM 10348(T) was 68.0 mol%. DNA-DNA relatedness data coupled with the combination of genotypic and phenotypic data indicated that strain IFM 10348(T) represents a novel species of the genus Gordonia, for which the name Gordonia iterans sp. nov. is proposed. The type strain is IFM 10348(T) ( = CCTCC M2011245(T) = NCCB 100436(T)).