Comparative Bioremediation of Tetradecane, Cyclohexanone and Cyclohexane by Filamentous Fungi from Polluted Habitats in Kazakhstan.

Studying the fates of oil components and their interactions with ecological systems is essential for developing comprehensive management strategies and enhancing restoration following oil spill incidents. The potential expansion of Kazakhstan's role in the global oil market necessitates the existence of land-specific studies that contribute to the field of bioremediation. In this study, a set of experiments was designed to assess the growth and biodegradation capacities of eight fungal strains sourced from Kazakhstan soil when exposed to the hydrocarbon substrates from which they were initially isolated. The strains were identified as Aspergillus sp. SBUG-M1743, Penicillium javanicum SBUG-M1744, SBUG-M1770, Trichoderma harzianum SBUG-M1750 and Fusarium oxysporum SBUG-1746, SBUG-M1748, SBUG-M1768 and SBUG-M1769 using the internal transcribed spacer (ITS) region. Furthermore, microscopic and macroscopic evaluations agreed with the sequence-based identification. Aspergillus sp. SBUG-M1743 and P. javanicum SBUG-M1744 displayed remarkable biodegradation capabilities in the presence of tetradecane with up to a 9-fold biomass increase in the static cultures. T. harzianum SBUG-M1750 exhibited poor growth, which was a consequence of its low efficiency of tetradecane degradation. Monocarboxylic acids were the main degradation products by SBUG-M1743, SBUG-M1744, SBUG-M1750, and SBUG-M1770 indicating the monoterminal degradation pathway through ß-oxidation, while the additional detection of dicarboxylic acid in SBUG-M1768 and SBUG-M1769 cultures was indicative of the fungus' ability to undertake both monoterminal and diterminal degradation pathways. F. oxysporum SBUG-M1746 and SBUG-M1748 in the presence of cyclohexanone showed a doubling of the biomass with the ability to degrade the substrate almost completely in shake cultures. F. oxysporum SBUG-M1746 was also able to degrade cyclohexane completely and excreted all possible metabolites of the degradation pathway. Understanding the degradation potential of these fungal isolates to different hydrocarbon substrates will help in developing effective bioremediation strategies tailored to local conditions.

Bacterial crude oil and polyaromatic hydrocarbon degraders from Kazakh oil fields as barley growth support.

Bacterial strains of the genera Arthrobacter, Bacillus, Dietzia, Kocuria, and Micrococcus were isolated from oil-contaminated soils of the Balgimbaev, Dossor, and Zaburunye oil fields in Kazakhstan. They were selected from 1376 isolated strains based on their unique ability to use crude oil and polyaromatic hydrocarbons (PAHs) as sole source of carbon and energy in growth experiments. The isolated strains degraded a wide range of aliphatic and aromatic components from crude oil to generate a total of 170 acid metabolites. Eight metabolites were detected during the degradation of anthracene and of phenanthrene, two of which led to the description of a new degradation pathway. The selected bacterial strains Arthrobacter bussei/agilis SBUG 2290, Bacillus atrophaeus SBUG 2291, Bacillus subtilis SBUG 2285, Dietzia kunjamensis SBUG 2289, Kocuria rosea SBUG 2287, Kocuria polaris SBUG 2288, and Micrococcus luteus SBUG 2286 promoted the growth of barley shoots and roots in oil-contaminated soil, demonstrating the enormous potential of isolatable and cultivable soil bacteria in soil remediation. KEY POINTS: • Special powerful bacterial strains as potential crude oil and PAH degraders. • Growth on crude oil or PAHs as sole source of carbon and energy. • Bacterial support of barley growth as resource for soil remediation.

Characterization of the Mycoremediation of n-Alkanes and Branched-Chain Alkanes by Filamentous Fungi from Oil-Polluted Soil Samples in Kazakhstan.

For decades, researchers have focused on containing terrestrial oil pollution. The heterogeneity of soils, with immense microbial diversity, inspires them to transform pollutants and find cost-effective bioremediation methods. In this study, the mycoremediation potentials of five filamentous fungi isolated from polluted soils in Kazakhstan were investigated for their degradability of n-alkanes and branched-chain alkanes as sole carbon and energy sources. Dry weight estimation and gas chromatography-mass spectrometry (GC-MS) monitored the growth and the changes in the metabolic profile during degradation, respectively. Penicillium javanicum SBUG-M1741 and SBUG-M1742 oxidized medium-chain alkanes almost completely through mono- and di-terminal degradation. Pristane degradation by P. javanicum SBUG-M1741 was >95%, while its degradation with Purpureocillium lilacinum SBUG-M1751 was >90%. P. lilacinum SBUG-M1751 also exhibited the visible degradation potential of tetradecane and phytane, whereby in the transformation of phytane, both the mono- and di-terminal degradation pathways as well as α- and ß-oxidation steps could be described. Scedosporium boydii SBUG-M1749 used both mono- and di-terminal degradation pathways for n-alkanes, but with poor growth. Degradation of pristane by Fusarium oxysporum SBUG-M1747 followed the di-terminal oxidation mechanism, resulting in one dicarboxylic acid. These findings highlight the role of filamentous fungi in containing oil pollution and suggest possible degradation pathways.

The soil microbial food web revisited: Predatory myxobacteria as keystone taxa?

Trophic interactions are crucial for carbon cycling in food webs. Traditionally, eukaryotic micropredators are considered the major micropredators of bacteria in soils, although bacteria like myxobacteria and Bdellovibrio are also known bacterivores. Until recently, it was impossible to assess the abundance of prokaryotes and eukaryotes in soil food webs simultaneously. Using metatranscriptomic three-domain community profiling we identified pro- and eukaryotic micropredators in 11 European mineral and organic soils from different climes. Myxobacteria comprised 1.5-9.7% of all obtained SSU rRNA transcripts and more than 60% of all identified potential bacterivores in most soils. The name-giving and well-characterized predatory bacteria affiliated with the Myxococcaceae were barely present, while Haliangiaceae and Polyangiaceae dominated. In predation assays, representatives of the latter showed prey spectra as broad as the Myxococcaceae. 18S rRNA transcripts from eukaryotic micropredators, like amoeba and nematodes, were generally less abundant than myxobacterial 16S rRNA transcripts, especially in mineral soils. Although SSU rRNA does not directly reflect organismic abundance, our findings indicate that myxobacteria could be keystone taxa in the soil microbial food web, with potential impact on prokaryotic community composition. Further, they suggest an overlooked, yet ecologically relevant food web module, independent of eukaryotic micropredators and subject to separate environmental and evolutionary pressures.

Moniliella spathulata, an oil-degrading yeast, which promotes growth of barley in oil-polluted soil.

The yeast strain Moniliella spathulata SBUG-Y 2180 was isolated from oil-contaminated soil at the Tengiz oil field in the Atyrau region of Kazakhstan on the basis of its unique ability to use crude oil and its components as the sole carbon and energy source. This yeast used a large number of hydrocarbons as substrates (more than 150), including n-alkanes with chain lengths ranging from C10 to C32, monomethyl- and monoethyl-substituted alkanes (C9-C23), and n-alkylcyclo alkanes with alkyl chain lengths from 3 to 24 carbon atoms as well as substituted monoaromatic and diaromatic hydrocarbons. Metabolism of this huge range of hydrocarbon substrates produced a very large number of aliphatic, alicyclic, and aromatic acids. Fifty-one of these were identified by GC/MS analyses. This is the first report of the degradation and formation of such a large number of compounds by a yeast. Inoculation of barley seeds with M. spathulata SBUG-Y 2180 had a positive effect on shoot and root development of plants grown in oil-contaminated sand, pointing toward potential applications of the yeast in bioremediation of polluted soils. KEY POINTS: • Moniliella spathulata an oil-degrading yeast • Increase of the growth of barley.

Diversity and degradative capabilities of bacteria and fungi isolated from oil-contaminated and hydrocarbon-polluted soils in Kazakhstan.

Bacteria and fungi were isolated from eight different soil samples from different regions in Kazakhstan contaminated with oil or salt or aromatic compounds. For the isolation of the organisms, we used, on the one hand, typical hydrocarbons such as the well utilizable aliphatic alkane tetradecane, the hardly degradable multiple-branched alkane pristane, and the biaromatic compound biphenyl as enrichment substrates. On the other hand, we also used oxygenated derivatives of alicyclic and monoaromatic hydrocarbons, such as cyclohexanone and p-tert-amylphenol, which are known as problematic pollutants. Seventy-nine bacterial and fungal strains were isolated, and 32 of them that were clearly able to metabolize some of these substrates, as tested by HPLC-UV/Vis and GC-MS analyses, were characterized taxonomically by DNA sequencing. Sixty-two percent of the 32 isolated strains from 14 different genera belong to well-described hydrocarbon degraders like some Rhodococci as well as Acinetobacter, Pseudomonas, Fusarium, Candida, and Yarrowia species. However, species of the bacterial genus Curtobacterium, the yeast genera Lodderomyces and Pseudozyma, as well as the filamentous fungal genera Purpureocillium and Sarocladium, which have rarely been described as hydrocarbon degrading, were isolated and shown to be efficient tetradecane degraders, mostly via monoterminal oxidation. Pristane was exclusively degraded by Rhodococcus isolates. Candida parapsilosis, Fusarium oxysporum, Fusarium solani, and Rhodotorula mucilaginosa degraded cyclohexanone, and in doing so accumulate ε-caprolactone or hexanedioic acid as metabolites. Biphenyl was transformed by Pseudomonas/Stenotrophomonas isolates. When p-tert-amylphenol was used as growth substrate, none of the isolated strains were able to use it.

From oil spills to barley growth - oil-degrading soil bacteria and their promoting effects.

Heavy contamination of soils by crude oil is omnipresent in areas of oil recovery and exploitation. Bioremediation by indigenous plants in cooperation with hydrocarbon degrading microorganisms is an economically and ecologically feasible means to reclaim contaminated soils. To study the effects of indigenous soil bacteria capable of utilizing oil hydrocarbons on biomass production of plants growing in oil-contaminated soils eight bacterial strains were isolated from contaminated soils in Kazakhstan and characterized for their abilities to degrade oil components. Four of them, identified as species of Gordonia and Rhodococcus turned out to be effective degraders. They produced a variety of organic acids from oil components, of which 59 were identified and 7 of them are hitherto unknown acidic oil metabolites. One of them, Rhodococcus erythropolis SBUG 2054, utilized more than 140 oil components. Inoculating barley seeds together with different combinations of these bacterial strains restored normal growth of the plants on contaminated soils, demonstrating the power of this approach for bioremediation. Furthermore, we suggest that the plant promoting effect of these bacteria is not only due to the elimination of toxic oil hydrocarbons but possibly also to the accumulation of a variety of organic acids which modulate the barley's rhizosphere environment.

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.