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.

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.

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 phosphorivorans sp. nov., isolated from a wastewater bioreactor with phosphorus removal.

Two Gram-stain-positive, non-endospore-forming actinobacteria (Ca8(T)and Ca14) were isolated from a bioreactor with extensive phosphorus removal. Based on 16S rRNA gene sequence similarity comparisons, strains Ca8(T) and Ca14 were shown to belong to the genus Gordonia and were most closely related to Gordonia hirsuta DSM 44140(T) (98.0 % sequence similarity) and Gordonia hydrophobica DSM 44015(T) (97.2 %). In comparison with the sequences of the type strains of all other species of the genus Gordonia tested, similarities were below 97 %. The quinone systems of the strains were determined to consist predominantly of MK-9H(2). The polar lipid profile for both organisms consisted of diphosphatidylglycerol, phosphatidylglycerol, phospatidylethanolamine, phosphatidylinositol and phosphatidylinositol mannoside. Whole-organism hydrolysates contained meso-diaminopimelic acid as the diamino acid of the peptidoglycan; mycolic acids were detected as well. These chemotaxonomic traits and the major fatty acids, which were C(16 : 1)cis-9, C(16 : 0) and C(18 : 1) and tuberculostearic acid strongly supported the grouping of strains Ca8(T) and Ca14 into the genus Gordonia. The two strains showed a DNA-DNA similarity of 96 %. DNA-DNA hybridizations of strain Ca8(T) with G. hirsuta DSM 44140(T) and G. hydrophobica DSM 44015(T) resulted in values of 26.3 and 25.0 %, respectively. These results and those of the physiological and biochemical tests allowed a clear phenotypic differentiation of strains Ca8(T) and Ca14 from the most closely related species of the genus Gordonia. It is concluded that strains Ca8(T) and Ca14 represent a novel species, for which the name Gordonia phosphorivorans sp. nov. is proposed, with the type strain Ca8(T) (= DSM 45630(T) = CCUG 61533(T) = CCM 7957(T) = LMG 26648(T)).

Molecular detection and phylogenetic characterization of Gordonia species in heavily oil-contaminated soils.

This study was undertaken to assess genetic diversity among Gordonia species present in heavily oil-contaminated sites using both a culture-dependent and a culture-independent (PCR-denaturing gradient gel electrophoresis (DGGE)) approach. Soil samples for this purpose were collected from 8 different heavily (crude) oil-contaminated industrial park sites located around Kaohsiung County, Taiwan. Using Gordonia-specific PCR-DGGE, a significant increase in Gordonia species diversity was noted in 1% heavily oil-enriched soil. A total of 67 strains were scored and identified as Gordonia after genus-specific PCR amplification and sequencing. BOX-PCR fingerprinting of culturable Gordonia showed wide strain diversity. A total of 33 different strains were identified from most of the sampling sites. Based on gyrB gene sequence analysis, all Gordonia strains could be segregated into five major clusters. Gordonia amicalis was the predominant species in all oil-amended soil samples. Isolates sharing <98.5% gyrB gene sequence similarities with Gordonia type strains represent indigenous novel Gordonia species. Variations in phenotypic characteristics further confirm the presence of a wide range of species and strain diversity among Gordonia isolates. Based on the genotypic and phenotypic details obtained here, we conclude that heavily oil-contaminated soil supports diverse indigenous Gordonia strains.

Degradation of car engine base oil by Rhodococcus sp. NDKK48 and Gordonia sp. NDKY76A.

Two microorganisms (NDKK48 and NDKY76A) that degrade long-chain cyclic alkanes (c-alkanes) were isolated from soil samples. Strains NDKK48 and NDKY76A were identified as Rhodococcus sp. and Gordonia sp., respectively. Both strains used not only normal alkane (n-alkane) but also c-alkane as a sole carbon and energy source, and the strains degraded more than 27% of car engine base oil (1% addition).

Biodegradation of Maya crude oil fractions by bacterial strains and a defined mixed culture isolated from Cyperus laxus rhizosphere soil in a contaminated site.

Ten bacterial strains were isolated by enrichment culture, using as carbon sources either aliphatics or an aromatic-polar mixture. Oxygen uptake rate was used as a criterion to determine culture transfer timing at each enrichment stage. Biodegradation of aliphatics (10,000 mg L(-1)) and an aromatic-polar mixture (5000 mg L(-1), 2:1) was evaluated for each of the bacterial strains and for a defined culture made up with a standardized mixture of the isolated strains. Degradation of total hydrocarbons (10,000 mg L(-1)) was also determined for the defined mixed culture. Five bacterial strains were able to degrade more than 50% of the aliphatic fraction. The most extensive biodegradation (74%) was obtained with strain Bs 9A, while strains Ps 2AP and UAM 10AP were able to degrade up to 15% of the aromatic-polar mixture. The defined mixed culture degraded 47% of the aliphatics and 6% of the aromatic-polar mixture. The defined mixed culture was able to degrade about 40% of the aliphatic fraction and 26% of the aromatic fraction when grown in the presence of total hydrocarbons, while these microorganisms did not consume the polar hydrocarbons fraction. The proposed strategy that combines enrichment culture together with oxygen uptake rate allowed the isolation of bacterial strains that are able to degrade specific hydrocarbons fractions at high consumption rates.