Stable-isotope probing combined with amplicon sequencing and metagenomics identifies key bacterial benzene degraders under microaerobic conditions.

The primary aim of the present study was to reveal the major differences between benzene-degrading bacterial communities evolve under aerobic versus microaerobic conditions and to reveal the diversity of those bacteria, which can relatively quickly degrade benzene even under microaerobic conditions. For this, parallel aerobic and microaerobic microcosms were set up by using groundwater sediment of a BTEX-contaminated site and C labelled benzene. The evolved total bacterial communities were first investigated by 16S rRNA gene Illumina amplicon sequencing, followed by a density gradient fractionation of DNA and a separate investigation of "heavy" and "light" DNA fractions.

Bacterial community composition of Hungarian salt-affected soils under different land uses.

Salinization and sodification are serious and worldwide growing threats to healthy soil functions. Although plants developed a plethora of traits to cope with high salinity, soil bacteria are also essential players of the adaptation process. However, there is still lack of knowledge on how other biotic and abiotic factors, such as land use or different soil properties, affect the bacterial community structure of these soils.

sp. nov., a novel aromatic hydrocarbon-degrading bacterium isolated from a xylene-degrading enrichment culture.

A Gram-stain-negative strain, designated as D2M1 was isolated from xylene-degrading enrichment culture and characterized using a polyphasic approach to determine its taxonomic position. The 16S rRNA gene sequence analysis revealed that strain D2M1 belongs to the genus , with the highest 16S rRNA gene similarity to DSM 64 (99.93 %), followed by DSM 23535 (98.

Combined Omics Approach Reveals Key Differences between Aerobic and Microaerobic Xylene-Degrading Enrichment Bacterial Communities: ─A Hitherto Unknown Player Emerges from the Microbial Dark Matter.

Among monoaromatic hydrocarbons, xylenes, especially the and isomers, are the least biodegradable compounds in oxygen-limited subsurface environments. Although much knowledge has been gained regarding the anaerobic degradation of xylene isomers in the past 2 decades, the diversity of those bacteria which are able to degrade them under microaerobic conditions is still unknown. To overcome this limitation, aerobic and microaerobic xylene-degrading enrichment cultures were established using groundwater taken from a xylene-contaminated site, and the associated bacterial communities were investigated using a polyphasic approach.

Selective enrichment, identification, and isolation of diclofenac, ibuprofen, and carbamazepine degrading bacteria from a groundwater biofilm.

Diclofenac, ibuprofen, and carbamazepine are three of the most widely detected and most concerning pharmaceutical residues in aquatic ecosystems. The aim of this study was to identify bacteria that may be involved in their degradation from a bacterial biofilm. Selective enrichment cultures in mineral salt solution containing pharmaceutical compounds as sole source of carbon and energy were set up, and population dynamics were monitored using shotgun metagenome sequencing.

Glyphosate versus glyphosate based ionic liquids: Effect of cation on glyphosate biodegradation, soxA and phnJ genes abundance and microbial populations changes during soil bioaugmentation.

The applicability of herbicidal ionic liquids (HILs) as an alternative form of herbicides is currently evaluated. Yet, the available research is lacking information on the behaviour of herbicidal ionic liquids upon addition to the environment, i.e.

Isolation of sp. nov from a hydrocarbon-contaminated groundwater capable of degrading benzene-, toluene-, - and -xylene under microaerobic conditions.

Members of the genus are known to be widespread in hydrocarbon contaminated environments because of their remarkable ability to degrade a variety of petroleum hydrocarbons, including BTEX (benzene, toluene, ethylbenzene and xylene) compounds. During an enrichment investigation which aimed to study microaerobic xylene degradation in a legacy petroleum hydrocarbon-contaminated groundwater, a novel Gram-stain-negative, aerobic, motile and rod-shaped bacterial strain, designated as MAP12 was isolated. It was capable of degrading benzene, toluene, - and - xylene effectively under both aerobic and microaerobic conditions.

Microaerobic enrichment of benzene-degrading bacteria and description of Ideonella benzenivorans sp. nov., capable of degrading benzene, toluene and ethylbenzene under microaerobic conditions.

In the present study, the bacterial community structure of enrichment cultures degrading benzene under microaerobic conditions was investigated through culturing and 16S rRNA gene Illumina amplicon sequencing. Enrichments were dominated by members of the genus Rhodoferax followed by Pseudomonas and Acidovorax. Additionally, a pale amber-coloured, motile, Gram-stain-negative bacterium, designated B7 was isolated from the microaerobic benzene-degrading enrichment cultures and characterized using a polyphasic approach to determine its taxonomic position.

Nocardioides carbamazepini sp. nov., an ibuprofen degrader isolated from a biofilm bacterial community enriched on carbamazepine.

From the metagenome of a carbamazepine amended selective enrichment culture the genome of a new to science bacterial species affiliating with the genus Nocardioides was reconstructed. From the same enrichment an aerobic actinobacterium, strain CBZ_1, sharing 99.4% whole-genome sequence similarity with the reconstructed Nocardioides sp.

Flavobacterium hungaricum sp. nov. a novel soil inhabitant, cellulolytic bacterium isolated from plough field.

A Gram-negative bacterial strain, named Kb82, was isolated from agricultural soil and a polyphasic approach was used for characterisation and to determine its taxonomic position. Based on 16S rRNA gene sequence analysis, the highest similarity was found with Flavobacterium artemisiae SYP-B1015 (98.2%).

sp. nov., a novel aromatic hydrocarbon-degrading bacterium isolated from benzene-, and xylene-degrading enrichment cultures, and emended description of the genus .

Two Gram-reaction-negative strains, designated as B13 and MA2-2, were isolated from two different aromatic hydrocarbon-degrading enrichment cultures and characterized using a polyphasic approach to determine their taxonomic position. The two strains had identical 16S rRNA gene sequences and were most closely related to E9 (97.36 %) and SA-279 (96.

Development of a bacterial consortium from Variovorax paradoxus and Pseudomonas veronii isolates applicable in the removal of BTEX.

In this study, we report on the development of a novel bacterial consortium, consisting of Variovorax paradoxus and Pseudomonas veronii isolates, applicable in the biodegradation of all six BTEX compounds (benzene, toluene, ethylbenzene, o-, m- and p-xylene) and the bioremediation of contaminated sites. The co-cultivability of the selected bacterial isolates was determined in nutrient-rich medium, as well as in BTEX amended mineral salts solution using Terminal Restriction Fragment Length Polymorphism (T-RFLP) and CFU determinations. BTEX biodegradation capacity of the two-strain consortium was assessed in mineral salts solution, where a series of BTEX depletions and supplementations occurred, as well as in a real, BTEX polluted environmental sample (contaminated groundwater) in the presence of the autochthonous bacterial community.

Evaluating the aerobic xylene-degrading potential of the intrinsic microbial community of a legacy BTEX-contaminated aquifer by enrichment culturing coupled with multi-omics analysis: uncovering the role of Hydrogenophaga strains in xylene degradation.

To develop effective bioremediation strategies, it is always important to explore autochthonous microbial community diversity using substrate-specific enrichment. The primary objective of this present study was to reveal the diversity of aerobic xylene-degrading bacteria at a legacy BTEX-contaminated site where xylene is the predominant contaminant, as well as to identify potential indigenous strains that could effectively degrade xylenes, in order to better understand the underlying facts about xylene degradation using a multi-omics approach. Henceforward, parallel aerobic microcosms were set up using different xylene isomers as the sole carbon source to investigate evolved bacterial communities using both culture-dependent and independent methods.

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

A Gram-reaction-negative bacterial strain, designated Kb22, was isolated from agricultural soil and characterized 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 %) to M-SX103.

Potential of Variovorax paradoxus isolate BFB1_13 for bioremediation of BTEX contaminated sites.

Here, we report and discuss the applicability of Variovorax paradoxus strain BFB1_13 in the bioremediation of BTEX contaminated sites. Strain BFB1_13 was capable of degrading all the six BTEX-compounds under both aerobic (O conc. 8 mg l) and micro-aerobic/oxygen-limited (O conc.

Sphingobacterium pedocola sp. nov. a novel halotolerant bacterium isolated from agricultural soil.

A Gram-reaction-negative halotolerant bacterial strain, designated Ka21, 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, highest similarity was found with Sphingobacterium alkalisoli Y3L14 (96.72%).

sp. nov., isolated from hydrocarbon-polluted groundwater from an oil refinery in Hungary.

A Gram-stain-negative, aerobic, non-spore-forming, rod-shaped bacterial strain (UP-52) was isolated from hydrocarbon-polluted groundwater located near an oil refinery in Tiszaujvaros, Hungary. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the isolate belongs to the genus in the family . Its closely related species are (98.

sp. nov., a cellulolytic bacterium isolated from agricultural soil.

A novel Gram-reaction-negative bacterial strain, designated Ka43, 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 (97.1 %) to E50.

sp. nov., isolated from a -xylene-degrading enrichment culture, capable of degrading benzene, - and -xylene.

A benzene, - and -xylene-degrading Gram-stain-negative, aerobic, yellow-pigmented bacterium, designated as D2P1, was isolated from a -xylene-degrading enrichment culture. Phylogenetic analyses based on 16S rRNA genes showed that D2P1 shares a distinct phyletic lineage within the genus and shows highest 16S rRNA gene sequence similarity to NBRC 102512 (99.2 %) and NBRC 102513 (98.

Saccharibacteria as Organic Carbon Sinks in Hydrocarbon-Fueled Communities.

Organisms of the candidate phylum Saccharibacteria have frequently been detected as active members of hydrocarbon degrading communities, yet their actual role in hydrocarbon degradation remained unclear. Here, we analyzed three enrichment cultures of hydrocarbon-amended groundwater samples using genome-resolved metagenomics to unravel the metabolic potential of indigenous Saccharibacteria. Community profiling based on ribosomal proteins revealed high variation in the enrichment cultures suggesting little reproducibility although identical cultivation conditions were applied.

sp. nov., isolated from marine plastic debris from Zakynthos Island, Greece.

A Gram-negative, dark orange-pigmented, aerobic, non-spore-forming, coccoid-shaped bacterium designated as ZS-1/3 was isolated from a floating plastic litter (polypropylene straw) sample, collected from shallow seawater near the public beach of Laganas on Zakynthos island, Greece. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the isolate is affiliated with the genus in the family . Its closest relatives are (98.

Planktonic and Benthic Bacterial Communities of the Largest Central European Shallow Lake, Lake Balaton and Its Main Inflow Zala River.

Lake Balaton is the largest European shallow lake, which underwent cultural eutrophication in the '70-80s. Therefore, strict pollution control measures were introduced and the water quality has become meso-eutrophic since the millennium. Due to the touristic significance and change in trophic levels of the lake, numerous ecological studies were carried out, but none of them was focused on both benthic and planktonic microbial communities at the same time.

Availability of Nitrite and Nitrate as Electron Acceptors Modulates Anaerobic Toluene-Degrading Communities in Aquifer Sediments.

Microorganisms are essential in the degradation of environmental pollutants. Aromatic hydrocarbons, e.g.