Bioaugmentation potential of free and formulated 2,6-dichlorobenzamide (BAM) degrading Aminobacter sp. MSH1 in soil, sand and water

Bioaugmentation has temporary effect on anaerobic pesticide biodegradation in simulated groundwater systems

Groundwater is the most important source for drinking water in The Netherlands. Groundwater quality is threatened by the presence of pesticides, and biodegradation is a natural process that can contribute to pesticide removal. Groundwater conditions are oligotrophic and thus biodegradation can be limited by the presence and development of microbial communities capable of biodegrading pesticides. For that reason, bioremediation technologies such as bioaugmentation (BA) can help to enhance pesticide biodegradation. We studied the effect of BA using enriched mixed inocula in two column bioreactors that simulate groundwater systems at naturally occurring redox conditions (iron and sulfate-reducing conditions). Columns were operated for around 800 days, and two BA inoculations (BA1 and BA2) were conducted in each column. Inocula were enriched from different wastewater treatment plants (WWTPs) under different redox-conditions. We observed a temporary effect of BA1, reaching 100% removal efficiency of the pesticide 2,4-D after 100 days in both columns. In the iron-reducing column, 2,4-D removal was in general higher than under sulfate-reducing conditions demonstrating the influence of redox conditions on overall biodegradation. We observed a temporary shift in microbial communities after BA1 that is relatable to the increase in 2,4-D removal efficiency. After BA2 under sulfate-reducing conditions, 2,4-D removal efficiency decreased, but no change in the column microbial communities was observed. The present study demonstrates that BA with a mixed inoculum can be a valuable technique for improving biodegradation in anoxic groundwater systems at different redox-conditions.

Microbial community profiling in bio-stimulated municipal solid waste for effective removal of organic pollutants containing endocrine disrupting chemicals

The study was aimed to improve the degradation of organic pollutants in municipal solid waste (MSW) through the bio-stimulation process. The results showed that the physico-chemical properties of MSW (control) had a high value of pH (9.2 ± 0.02); total suspended solids (TSS: 1547 ± 23 mg/kg^-1), and total dissolved solids (TDS:76 ± 0.67 mg/kg^-1). After the biostimulation process (biostimulated MSW), the physico-chemical parameters of MSW were reduced as pH (7.1 ± 0.01); TSS (41 ± 0.01 mg/kg^-1), and TDS (789 ± 03 mg/kg^-1). Furthermore, the major organic pollutants detected from MSW by gas chromatography-mass spectroscopy (GC-MS) analysis at different retention time (RT) were hexadecane (RT-8.79); pentadecane (RT-9.36); and hexasiloxane (RT-9.43) while these organic pollutants were degraded after the biostimulation process. The whole-genome metagenome sequencing size (%) analyses showed major groups of bacteria (40.82%) followed by fungi (0.05%), virus (0.0032%), and archaea (0.0442%) in MSW. The species richness and evenness of the microbial community were decreased substantially due to the biostimulation treatment. The total number of genes in the biostimulated MSW (PS-3_11267) sample were 465302 whereas the number of genes in the control MSW (PS-4_11268) sample were 256807. Furthermore, the biostimulated MSW (PS-3_11267) aligned the reads to bacteria (19502525), fungi (40030), virus (3339), and archaea (12759) genomes whereas the control sample (PS-4_11268) aligned the reads to bacteria (17057259), fungi (19148), virus (1335), and archaea (18447) genomes. Moreover, the relative abundance at genus level in biostimulated MSW (PS-3_11267) (Ochrobactrum and Phenylobacterium), phylum; (Proteobacteria and Actinobacteria), and species (Chthoniobacter flavus and Vulgatibacter incomptus) level was the most abundant. The results provided valuable information regarding the degradation of organic pollutants in MSW by microbial communities through biostimulation for the prevention of soil pollution and health protection.

Phylogenomic Reconstruction and Metabolic Potential of the Genus Aminobacter

Bacteria belonging to the genus Aminobacter are metabolically versatile organisms thriving in both natural and anthropized terrestrial environments. To date, the taxonomy of this genus is poorly defined due to the unavailability of the genomic sequence of A. anthyllidis LMG 26462^T and the presence of unclassified Aminobacter strains. Here, we determined the genome sequence of A. anthyllidis LMG 26462^T and performed phylogenomic, average nucleotide identity and digital DNA-DNA hybridization analyses of 17 members of genus Aminobacter. Our results indicate that 16S rRNA-based phylogeny does not provide sufficient species-level discrimination, since most of the unclassified Aminobacter strains belong to valid Aminobacter species or are putative new species. Since some members of the genus Aminobacter can utilize certain C1 compounds, such as methylamines and methyl halides, a comparative genomic analysis was performed to characterize the genetic basis of some degradative/assimilative pathways in the whole genus. Our findings suggest that all Aminobacter species are heterotrophic methylotrophs able to generate the methylene tetrahydrofolate intermediate through multiple oxidative pathways of C1 compounds and convey it in the serine cycle. Moreover, all Aminobacter species carry genes implicated in the degradation of phosphonates via the C-P lyase pathway, whereas only A. anthyllidis LMG 26462^T contains a symbiosis island implicated in nodulation and nitrogen fixation.

Autochthonous Bioaugmentation-Modified Bacterial Diversity of Phenanthrene Degraders in PAH-Contaminated Wastewater as Revealed by DNA-Stable Isotope Probing

To reveal the mechanisms of autochthonous bioaugmentation (ABA) in wastewater contaminated with polycyclic aromatic hydrocarbons (PAHs), DNA-stable-isotope-probing (SIP) was used in the present study with the addition of an autochthonous microorganism Acinetobacter tandoii LJ-5. We found LJ-5 inoculum produced a significant increase in phenanthrene (PHE) mineralization, but LJ-5 surprisingly did not participate in indigenous PHE degradation from the SIP results. The improvement of PHE biodegradation was not explained by the engagement of LJ-5 but attributed to the remarkably altered diversity of PHE degraders. Of the major PHE degraders present in ambient wastewater ( Rhodoplanes sp., Mycobacterium sp., Xanthomonadaceae sp. and Enterobacteriaceae sp.), only Mycobacterium sp. and Enterobacteriaceae sp. remained functional in the presence of strain LJ-5, but five new taxa Bacillus, Paenibacillus, Ammoniphilus, Sporosarcina, and Hyphomicrobium were favored. Rhodoplanes, Ammoniphilus, Sporosarcina, and Hyphomicrobium were directly linked to, for the first time, indigenous PHE biodegradation. Sequences of functional PAH-RHD_α genes from heavy fractions further proved the change in PHE degraders by identifying distinct PAH-ring hydroxylating dioxygenases between ambient degradation and ABA. Our findings indicate a new mechanism of ABA, provide new insights into the diversity of PHE-degrading communities, and suggest ABA as a promising in situ bioremediation strategy for PAH-contaminated wastewater.

Bioaugmentation of thiabendazole-contaminated soils from a wastewater disposal site: Factors driving the efficacy of this strategy and the diversity of the indigenous soil bacterial community

The application of the fungicide thiabendazole (TBZ) in fruit packaging plants (FPP) results in the production of effluents which are often disposed in adjacent field sites. These require remediation to prevent further environmental dispersal of TBZ. We assessed the bioaugmentation potential of a newly isolated TBZ-degrading bacterial consortium in a naturally contaminated soil (NCS) exhibiting a natural gradient of TBZ levels (12000, 400, 250 and 12 mg kg^-1). The effect of aging on bioaugmentation efficacy was comparatively tested in a soil with similar physicochemical properties and soil microbiota, which was artificially, contaminated with the same TBZ levels (ACS). The impact of bioaugmentation and TBZ on the bacterial diversity in the NCS was explored via amplicon sequencing. Bioaugmentation effectively removed TBZ from both soils at levels up to 400 mg kg^-1 but failed at the highest contamination level (12000 mg kg^-1). Dissipation of TBZ in bioaugmented samples showed a concentration-dependent pattern, while aging of TBZ had a slight effect on bioaugmentation efficiency. Bioaugmentation had no impact on the soil bacterial diversity, in contrast to TBZ contamination. Soils from the hotspots of TBZ contamination (12000 mg kg^-1) showed a drastically lower α-diversity driven by the dominance of β- and γ-proteobacteria at the expense of all other bacterial phyla, especially Actinobacteria. Overall, bioaugmentation with specialized microbial inocula could be an effective solution for the recovery of disposal sites contaminated with persistent chemicals like TBZ.

Groundwater contamination with 2,6-dichlorobenzamide (BAM) and perspectives for its microbial removal

The pesticide metabolite 2,6-dichlorobenzamide (BAM) is very persistent in both soil and groundwater and has become one of the most frequently detected groundwater micropollutants. BAM is not removed by the physico-chemical treatment techniques currently used in drinking water treatment plants (DWTP); therefore, if concentrations exceed the legal threshold limit, it represents a sizeable problem for the stability and quality of drinking water production, especially in places that depend on groundwater for drinking water. Bioremediation is suggested as a valuable strategy for removing BAM from groundwater by deploying dedicated BAM-degrading bacteria in DWTP sand filters. Only a few bacterial strains with the capability to degrade BAM have been isolated, and of these, only three isolates belonging to the Aminobacter genus are able to mineralise BAM. Considerable effort has been made to elucidate degradation pathways, kinetics and degrader genes, and research has recently been presented on the application of strain Aminobacter sp. MSH1 for the purification of BAM-contaminated water. The aim of the present review was to provide insight into the issue of BAM contamination and to report on the current status and knowledge with regard to the application of microorganisms for purification of BAM-contaminated water resources. This paper discusses the prospects and challenges for bioaugmentation of DWTP sand filters with specific BAM-degrading bacteria and identifies relevant perspectives for future research.