Remarkable impact of PAHs and TPHs on the richness and diversity of bacterial species in surface soils exposed to long-term hydrocarbon pollution

Nowadays, because of substantial use of petroleum-derived fuels the number and extension of hydrocarbon polluted terrestrial ecosystems is in growth worldwide. In remediation of aforementioned sites bioremediation still tends to be an innovative, environmentally attractive technology. Although huge amount of information is available concerning the hydrocarbon degradation potential of cultivable hydrocarbonoclastic bacteria little is known about the in situ long-term effects of petroleum derived compounds on the structure of soil microbiota. Therefore, in this study our aim was to determine the longterm impact of total petroleum hydrocarbons (TPHs), volatile petroleum hydrocarbons (VPHs), total alkyl benzenes (TABs) as well as of polycyclic aromatic hydrocarbons (PAHs) on the structure of bacterial communities of four different contaminated soil samples. Our results indicated that a very high amount of TPH affected positively the diversity of hydrocarbonoclastic bacteria. This finding was supported by the occurrence of representatives of the a-, b-, c-Proteobacteria, Actinobacteria, Flavobacteriia and Bacilli classes. High concentration of VPHs and TABs contributed to the predominance of actinobacterial isolates. In PAH impacted samples the concentration of PAHs negatively correlated with the diversity of bacterial species. Heavily PAH polluted soil samples were mainly inhabited by the representatives of the b-, c- Proteobacteria (overwhelming dominance of Pseudomonas sp.) and Actinobacteria

Zoogloea oleivorans sp. nov., a floc-forming, petroleum hydrocarbon-degrading bacterium isolated from biofilm

A floc-forming, Gram-stain-negative, petroleum hydrocarbon-degrading bacterial strain, designated BucT, was isolated from a petroleum hydrocarbon-contaminated site in Hungary. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain BucT formed a distinct phyletic lineage within the genus Zoogloea. Its closest relative was found to be Zoogloea caeni EMB43T (97.2% 16S rRNA gene sequence similarity) followed by Zoogloea oryzae A-7T (95.9 %), Zoogloea ramigera ATCC 19544T (95.5 %) and Zoogloea resiniphila DhA-35T (95.4 %). The level of DNA–DNA relatedness between strain BucT and Z. caeni EMB43T was 31.6 %. Cells of strain BucT are facultatively aerobic, rod-shaped, and motile by means of a polar flagellum. The strain grew at temperatures of 5–35 6C (optimum 25–28 6C), and at pH 6.0–9.0 (optimum 6.5–7.5). The predominant fatty acids were C16 : 0, C10 : 0 3-OH, C12 : 0 and summed feature 3 (C16 : 1v7c and/or iso-C15 : 0 2-OH). The major respiratory quinone was ubiquinone-8 (Q-8) and the predominant polar lipid was phosphatidylethanolamine. The genomic DNA G+C content was 63.2 mol%. On the basis of the chemotaxonomic, molecular and phenotypic data, isolate BucT is considered to represent a novel species of the genus Zoogloea, for which the name Zoogloea oleivorans sp. nov. is proposed. The type strain is BucT (5DSM 28387T5NCAIM B 02570T)

Transcriptome-Stable Isotope Probing Provides Targeted Functional and Taxonomic Insights Into Microaerobic Pollutant-Degrading Aquifer Microbiota

While most studies using RNA-stable isotope probing (SIP) to date have focused on ribosomal RNA, the detection of 13C-labeled mRNA has rarely been demonstrated. This approach could alleviate some of the major caveats of current non-target environmental “omics.” Here, we demonstrate the feasibility of total RNA-SIP in an experiment where hydrocarbon-degrading microbes from a BTEX-contaminated aquifer were studied in microcosms with 13C-labeled toluene under microoxic conditions. From the total sequencing reads (∼30 mio. reads per density-resolved RNA fraction), an average of 1.2% of reads per sample were identified as non-rRNA, including mRNA. Members of the Rhodocyclaceae (including those related to Quatrionicoccus spp.) were most abundant and enriched in 13C-rRNA, while well-known aerobic degraders such as Pseudomonas spp. remained unlabeled. Transcripts related to cell motility, secondary metabolite formation and xenobiotics degradation were highly labeled with 13C. mRNA of phenol hydroxylase genes were highly labeled and abundant, while other transcripts of toluene-activation were not detected. Clear labeling of catechol 2,3-dioxygenase transcripts supported previous findings that some of these extradiol dioxygenases were adapted to low oxygen concentrations. We introduce a novel combination of total RNA-SIP with calculation of transcript-specific enrichment factors (EFs) in 13C-RNA, enabling a targeted approach to process-relevant gene expression in complex microbiomes

Stable isotope probing of hypoxic toluene degradation at the Siklós aquifer reveals prominent role of Rhodocyclaceae

The availability of oxygen is often a limiting factor for the degradation of aromatic hydrocarbons in subsurface environments. However, while both aerobic and anaerobic degraders have been intensively studied, degradation betwixt, under micro- or hypoxic conditions has rarely been addressed. It is speculated that in environments with limited, but sustained oxygen supply, such as in the vicinity of groundwater monitoring wells, hypoxic degradation may take place. A large diversity of subfamily I.2.C extradiol dioxygenase genes has been previously detected in a BTEX-contaminated aquifer in Hungary. Older literature suggests that such catabolic potentials could be associated to hypoxic degradation. Bacterial communities dominated by members of the Rhodocyclaceae were found, but the majority of the detected C23O genotypes could not be affiliated to any known bacterial degrader lineages. To address this, a stable isotope probing (SIP) incubation of site sediments with 13C7-toluene was performed under microoxic conditions. A combination of 16S rRNA gene amplicon sequencing and T-RFLP fingerprinting of C23O genes from SIP gradient fractions revealed the central role of degraders within the Rhodocyclaceae in hypoxic toluene degradation. The main assimilators of 13C were identified as members of the genera Quatrionicoccus and Zoogloea, and a yet uncultured group of the Rhodocyclaceae

Talajmikrobiológiai paraméterek változása szántóként és rétként hasznosított réti szolonyec talajokban

Összefoglalás A hazánk területének megközelítően 10%-át fedő szikes talajokban zajló talajkémiai folyamatok részletes vizsgálatával ellentétben, a talajmikrobiológiai folyamatokról és állapotokról kevesebb ismerettel rendelkezünk. Munkánkban ezért egy réti szolonyec talaj kémiai, fizikai és mikrobiológiai tulajdonságait vizsgáltuk szántó és rét hasznosítású területen. Munkánk célja a rét és szántó művelési ág talajkémiai, -fizikai és - mikrobiológiai tulajdonságainak megállapítása, a kémiai és mikrobiológiai tulajdonságok közötti kapcsolatok feltárása réti szolonyec talajon, ahol a korábbi vizsgálatok elsősorban a talajkémiai változásokra koncentráltak. A szántó és rét művelési ág talaja egyes kémiai és mikrobiológiai paraméterekben szignifikánsan különbözött egymástól. A talaj mikrobiológiai aktivitása, a talajban élő mikrobák mennyisége egyaránt nagyobb volt a rétként hasznosított területen. Eredményeink felhívják a figyelmet a minél hosszabb ideig tartó növényborítás biztosításának fontosságára a talaj szervesanyag-tartalmának megőrzésében, növelésében, és az ehhez szorosan kapcsolódó aktívabb talajéletfenntartásában. A művelési ág hatása olyan erőteljes a talaj vizsgált mikrobiológiai változóira, hogy azok statisztikailag elkülönítették a szántó és rét művelési ágakat annak ellenére, hogy a korábbi mintavételi terület két-két, a területekre jellemző mikrobiális biomassza szén szélsőértéket mutató pontjaiból vettük a talajmintákat. Ugyanakkor a vizsgált kémiai, fizikai változók csoportja még nem igazolta a két művelési ág talajmintáinak statisztikai különbségét. Eredményeink tehát igazolják, hogy a talajok mikrobiológiai paraméterei gyorsabban jelezhetik a talajokban bekövetkező, esetleges negatív változásokat, mint a kémiai és/vagy fizikai paraméterek

Sphingobacterium hungaricum sp. nov. a novel species on the borderline of the genus Sphingobacterium

A Gram-reaction-negative bacterial strain, designated Kb22 T , was isolated from agricultural soil and characterised using a polyphasic approach to determine its taxonomic position. On the basis of 16S rRNA gene sequence analysis, the strain shows highest similarity (94.39%) with Sphingobacterium nematocida M-SX103 T . The highest ANI (71.83%) value was found with Sphingobacterium composti T5-12 T , and the highest AAI (66.65%) value was found with Sphingobacterium olei HAL-9 T . Cells are aerobic, non-motile rods. The isolate was found to be positive for catalase and oxidase tests. The assembled genome of strain Kb22 T has a total length of 4,06 Mb, the DNA G+C content is 38.1 mol%. The only isoprenoid quinone is menaquinone 7 (MK-7). The major fatty acids are iso-C 15:0 (28.4%), summed feature 3 (C 16:1 ω 7 c and/or iso-C 15:0 2-OH) (25.7%) and iso-C 17:0 3-OH (19.7%). Based on phenotypic characteristics and phylogenetic analysis, it is concluded that strain Kb22 T is a member of the genus Sphingobacterium and represents a novel species, for which the name Sphingobacterium hungaricum sp. nov. is proposed. The type strain of the species is strain Kb22 T (=LMG 31574 = NCAIM B.02638