Silvimonas soli sp. nov., a new member of Chromobacteriaceae isolated from soil in Norrbyskär island, Sweden.

A novel bacterial species is described that was isolated from the soil of Norrbyskär island (Sweden). This Gram-negative, facultatively anaerobic and motile rod, designated 17-6T, was classified in the family Chromobacteriaceae, class Betaproteobacteria, and further characterized by a polyphasic approach. Comparative 16S rRNA gene analysis revealed the potential species novelty of the strain, with Silvimonas terrae (98.20 % similarity) and Silvimonas amylolytica (98.13 %) being its closest type strains. The phylogenetic novelty of the isolate at the level of species was confirmed using phylogenetic analyses based on the whole genome: average nucleotide identity values ranged from 79 to 81 %, average amino acid identity values from 75 to 81 % and percentage of conserved proteins values from 69-81 % with the members of genera Silvimonas and Amantichitinum. On the basis of phenotypic, phylogenetic, functional and genotypic analyses, we propose the isolate as the type strain of a novel species within the genus Silvimonas with the designation Silvimonas soli 17-6T (=DSM 115342T=CCM 9308T).

Genomic analysis of dibenzofuran-degrading Pseudomonas veronii strain Pvy reveals its biodegradative versatility.

Certain industrial chemicals accumulate in the environment due to their recalcitrant properties. Bioremediation uses the capability of some environmental bacteria to break down these chemicals and attenuate the pollution. One such bacterial strain, designated Pvy, was isolated from sediment samples from a lagoon in Romania located near an oil refinery due to its capacity to degrade dibenzofuran (DF). The genome sequence of the Pvy strain was obtained using an Oxford Nanopore MiniION platform. According to the consensus 16S rRNA gene sequence that was compiled from six 16S rRNA gene copies contained in the genome and orthologous average nucleotide identity (OrthoANI) calculation, the Pvy strain was identified as Pseudomonas veronii, which confirmed the identification obtained with the aid of MALDI-TOF mass spectrometry and MALDI BioTyper. The genome was analyzed with respect to enzymes responsible for the overall biodegradative versatility of the strain. The Pvy strain was able to derive carbon from naphthalene (NP) and several aromatic compounds of natural origin, including salicylic, protocatechuic, p-hydroxybenzoic, trans-cinnamic, vanillic, and indoleacetic acids or vanillin, and was shown to degrade but not utilize DF. In total seven loci were found in the Pvy genome, which enables the strain to participate in the degradation of these aromatic compounds. Our experimental data also indicate that the transcription of the NP-dioxygenase α-subunit gene (ndoB), carried by the plasmid of the Pvy strain, is inducible by DF. These features make the Pvy strain a potential candidate for various bioremediation applications.

Bacterial succession in oil-contaminated soil under phytoremediation with poplars.

Petroleum hydrocarbons (PHCs) continue to be among the most common pollutants in soil worldwide. Phytoremediation has become a sustainable way of dealing with PHC contamination. We conducted the off-site phytoremediation of PHC-polluted soil from an oil tanker truck accident, where poplars were used for the phytoremediation of the oil-polluted soil in a boreal climate during a seven-year treatment. The succession of bacterial communities over the entire phytoremediation process was monitored using microbial ecological tools relying on high-throughput 16S rRNA gene sequencing. Upon the successful depletion of PHCs from soil, endophytic communities were analyzed in order to assess the complete plant-associated microbiome after the ecological recovery. The rhizosphere-associated soil exhibited different bacterial dynamics than unplanted soil, but both soils experienced succession of bacteria over time, with diversity being negatively correlated with PHC concentration. In the relatively short growing season in North Europe, seasonal variations in environmental conditions were identified that contributed to the dynamics of bacterial communities. Overall, our study proved that phytoremediation using poplar trees can be used to assist in the removal of PHCs from soils in boreal climate conditions and provides new insight into the succession patterns of bacterial communities associated with these plants.

Bioremediation of chlorophenol-contaminated sawmill soil using pilot-scale bioreactors under consecutive anaerobic-aerobic conditions.

Chlorophenols (CPs), including pentachlorophenol (PCP), are chemicals of concern due to their toxicity and persistence. Here we describe a successful reactor-based remediation of CP-contaminated soil and assess changes in the toxicity patterns and bacterial communities during the remediation. The remediation consisted of separating half of the contaminated soil to be ground (samples M) in order to test whether the grinding expedited the remediation, the other half was left unground (samples P). Both soils were mixed with wastewater treatment sludge to increase their bacterial diversity and facilitate the degradation of CPs, and the resultant mixtures were placed in 2 bioreactors, M and P, operated for 16 months under anaerobic conditions to favor dehalogenation and for an additional 16 months under aerobic conditions to achieve complete mineralization. Samples were taken every 4 months for toxicity and microbial analyses. The results showed a 64% removal of total CPs (ΣCPs) in reactor P after just 18 months of remediation, whereas similar depletion in reactor M occurred after ∼25 months, indicating that the grinding decelerated the remediation. By the end of the experiment, both reactors achieved 93.5-95% removal. The toxicity tests showed a decrease in toxicity as the remediation progressed. The succession of bacterial communities over time was significantly associated with pH, anaerobic/aerobic phase and the concentration of the majority of CP congeners. Our data indicate that the supplementation of contaminated soil with sludge and further incubation in pilot-scale bioreactors under consecutive anaerobic-aerobic conditions proved to be effective at the remediation of CP-contaminated soil.

Bacterial Biotransformation of Pentachlorophenol and Micropollutants Formed during Its Production Process.

Pentachlorophenol (PCP) is a toxic and persistent wood and cellulose preservative extensively used in the past decades. The production process of PCP generates polychlorinated dibenzo-p-dioxins and polychlorinated dibenzofurans (PCDD/Fs) as micropollutants. PCDD/Fs are also known to be very persistent and dangerous for human health and ecosystem functioning. Several physico-chemical and biological technologies have been used to remove PCP and PCDD/Fs from the environment. Bacterial degradation appears to be a cost-effective way of removing these contaminants from soil while causing little impact on the environment. Several bacteria that cometabolize or use these pollutants as their sole source of carbon have been isolated and characterized. This review summarizes current knowledge on the metabolic pathways of bacterial degradation of PCP and PCDD/Fs. PCP can be successfully degraded aerobically or anaerobically by bacteria. Highly chlorinated PCDD/Fs are more likely to be reductively dechlorinated, while less chlorinated PCDD/Fs are more prone to aerobic degradation. The biochemical and genetic basis of these pollutants' degradation is also described. There are several documented studies of effective applications of bioremediation techniques for the removal of PCP and PCDD/Fs from soil and sediments. These findings suggest that biodegradation can occur and be applied to treat these contaminants.