Diversity, abundance, and consistency of microbial oxygenase expression and biodegradation in a shallow contaminated aquifer

Nitro-PAHs: Occurrences, ecological consequences, and remediation strategies for environmental restoration

Nitrated polycyclic aromatic hydrocarbons (nitro-PAHs) are persistent pollutants that have been introduced into the environment as a result of human activities. They are produced when PAHs undergo oxidation and are highly resistant to degradation, resulting in prolonged exposure and significant health risks for wildlife and humans. Nitro-PAHs' potential to induce cancer and mutations has raised concerns about their harmful effects. Furthermore, their ability to accumulate in the food chain seriously threatens the ecosystem and human health. Moreover, nitro-PAHs can disrupt the normal functioning of the endocrine system, leading to reproductive and developmental problems in humans and other organisms. Reducing nitro-PAHs in the environment through source management, physical removal, and chemical treatment is essential to mitigate the associated environmental and human health risks. Recent studies have focused on improving nitro-PAHs' phytoremediation by incorporating microorganisms and biostimulants. Microbes can break down nitro-PAHs into less harmful substances, while biostimulants can enhance plant growth and metabolic activity. By combining these elements, the effectiveness of phytoremediation for nitro-PAHs can be increased. This study aimed to investigate the impact of introducing microbial and biostimulant agents on the phytoremediation process for nitro-PAHs and identify potential solutions for addressing the environmental risks associated with these pollutants.

DARHD: A sequence database for aromatic ring-hydroxylating dioxygenase analysis and primer evaluation

Biodegradation of aromatic compounds is ubiquitous in the environment and important for controlling organic pollutants. Aromatic ring-hydroxylating dioxygenases (ARHDs) are responsible for the first and rate-limiting step of aerobic biodegradation of aromatic compounds. The ARHD α subunit is a good biomarker for studying functional microorganisms in the environment, however their diversity and corresponding primer coverage are unclear, both of which require a comprehensive sequence database for the ARHD α subunit. Here amino acid sequences of the ARHD α subunit were collected, and a total of 103 sequences were selected as seed sequences that were distributed in 72 bacterial genera with 34 gene names. Based on both homolog search and keyword confirmation against the GenBank, a sequence database of ARHD (DARHD) has been established and 6367 highly credible sequences were retrieved. DARHD contained 407 bacterial genera capable of degrading 38 aromatic substrates, and intricate relationships among the gene name, aromatic substrate and microbial taxa were observed. Thereafter, a total of 136 pairs of primers were collected and assessed. Results showed coverages of most published primers were low. Our research provides new insights for understanding the diversity of ARHD α subunit, and gives guidance on the design and application of primers in the future.

Estructura y función de las oxigenasas tipo Rieske/mononuclear

Las oxigenasas Rieske/mononuclear son un grupo de metaloenzimas que catalizan la oxidación de una variedad de compuestos, destaca su participación en la degradación de compuestos xenobióticos contaminantes; estas enzimas también participan en la biosíntesis de algunos compuestos de interés comercial. Poseen una amplia especificidad por el sustrato, convirtiéndolas en un grupo de enzimas con un alto potencial de aplicación en procesos biotecnológicos que hasta el momento no ha sido explotado. La presente revisión aborda aspectos generales acerca de la función y estructura de este importante grupo de enzimas. 

Groundwater Autochthonous Microbial Communities as Tracers of Anthropogenic Pressure Impacts: Example from a Municipal Waste Treatment Plant (Latium, Italy)

The groundwater behavior at a municipal solid waste disposal dump, located in Central Italy, was studied using a multi-parameter monitoring over 1 year consisting of 4 seasonal samples. The hydrological and hydrogeological dynamics of water circulation, microbiological parameters (microbial abundance and cell viability of the autochthonous microbial community), dissolved organic carbon, and several contaminants were evaluated and related to the geological structures in both two and three dimensions and used for geostatistical analysis in order to obtain 3D maps. Close relationships between geological heterogeneity, water circulation, pollutant diffusion, dissolved organic carbon, and cell viability were revealed. The highest cell viability values were found with dissolved organic carbon (DOC) values ≤0.5 mg/L; above this value, DOC negatively affected the microbial community. The highest DOC values were detected in groundwater at some sampling points within the site indicating its probable origin from the waste disposal dump. Although legislation limits for the parameters measured were not exceeded (except for a contaminant in one piezometer), the 1-year multi-parameter monitoring approach made it possible to depict both the dynamics and the complexity of the groundwater flux and, with “non-legislative parameters” such as microbial cell viability and DOC, identify the points with the highest vulnerability and their origin. This approach is useful for identifying the most vulnerable sites in a groundwater body.

Community dynamics and functional characteristics of naphthalene-degrading populations in contaminated surface sediments and hypoxic/anoxic groundwater

Earlier research on the biogeochemical factors affecting natural attenuation in coal-tar contaminated groundwater, at South Glens Falls, NY, revealed the importance of anaerobic metabolism and trophic interactions between degrader and bacterivore populations. Field-based characterizations of both phenomena have proven challenging, but advances in stable isotope probing (SIP), single-cell imaging and shotgun metagenomics now provide cultivation-independent tools for their study. We tracked carbon from ¹³ C-labelled naphthalene through microbial populations in contaminated surface sediments over 6 days using respiration assays, secondary ion mass spectrometry imaging and shotgun metagenomics to disentangle the contaminant-based trophic web. Contaminant-exposed communities in hypoxic/anoxic groundwater were contrasted with those from oxic surface sediments to identify putative features of anaerobic catabolism of naphthalene. In total, six bacteria were responsible for naphthalene degradation. Cupriavidus, Ralstonia and Sphingomonas predominated at the earliest stages of SIP incubations and were succeeded in later stages by Stenotrophomonas and Rhodococcus. Metagenome-assembled genomes provided evidence for the ecological and functional characteristics underlying these temporal shifts. Identical species of Stenotrophomonas and Rhodococcus were abundant in the most contaminated, anoxic groundwater. Apparent increases in bacterivorous protozoa were observed following exposure to naphthalene, though insignificant amounts of carbon were transferred between bacterial degraders and populations of secondary feeders.

Benzene Degradation by a Variovorax Species within a Coal Tar-Contaminated Groundwater Microbial Community

Investigations of environmental microbial communities are crucial for the discovery of populations capable of degrading hazardous compounds and may lead to improved bioremediation strategies. The goal of this study was to identify microorganisms responsible for aerobic benzene degradation in coal tar-contaminated groundwater. Benzene degradation was monitored in laboratory incubations of well waters using gas chromatography mass spectrometry (GC-MS). Stable isotope probing (SIP) experiments using [¹³C]benzene enabled us to obtain ¹³C-labled community DNA. From this, 16S rRNA clone libraries identified Gammaproteobacteria and Betaproteobacteria as the active benzene-metabolizing microbial populations. Subsequent cultivation experiments yielded nine bacterial isolates that grew in the presence of benzene; five were confirmed in laboratory cultures to grow on benzene. The isolated benzene-degrading organisms were genotypically similar (>97% 16S rRNA gene nucleotide identities) to the organisms identified in SIP experiments. One isolate, Variovorax MAK3, was further investigated for the expression of a putative aromatic ring-hydroxylating dioxygenase (RHD) hypothesized to be involved in benzene degradation. Microcosm experiments using Variovorax MAK3 revealed a 10-fold increase in RHD (Vapar_5383) expression, establishing a link between this gene and benzene degradation. Furthermore, the addition of Variovorax MAK3 to microcosms prepared from site waters accelerated community benzene degradation and correspondingly increased RHD gene expression. In microcosms using uninoculated groundwater, quantitative (q)PCR assays (with 16S rRNA and RDH genes) showed that Variovorax was present and responsive to added benzene. These data demonstrate how the convergence of cultivation-dependent and -independent techniques can boost understandings of active populations and functional genes in complex benzene-degrading microbial communities.

IMPORTANCE

Benzene is a human carcinogen whose presence in contaminated groundwater drives environmental cleanup efforts. Although the aerobic biodegradation of benzene has long been established, knowledge of the identity of the microorganisms in complex naturally occurring microbial communities responsible for benzene biodegradation has evaded scientific inquiry for many decades. Here, we applied a molecular biology technique known as stable isotope probing (SIP) to the microbial communities residing in contaminated groundwater samples to identify the community members active in benzene biodegradation. We complemented this approach by isolating and growing in the laboratory a bacterium representative of the bacteria found using SIP. Further characterization of the isolated bacterium enabled us to track the expression of a key gene that attacks benzene both in pure cultures of the bacterium and in the naturally occurring groundwater microbial community. This work advances information regarding the documentation of microbial processes, especially the populations and genes that contribute to bioremediation.

Spatial Patterns of bphA Gene Diversity Reveal Local Adaptation of Microbial Communities to PCB and PAH Contaminants

Biphenyl dioxygenases, encoded by the bphA gene, initiate the oxidation of polychlorinated biphenyls (PCBs) and specify the substrate range of PCB congeners metabolized by bacteria. Increased bphA gene diversity within microbial communities may allow a broader range of PCB congeners to be catabolized, thus resulting in greater PCB degradation. To assess the role of PCBs in modulating bphA gene diversity, 16S ribosomal RNA (rRNA) gene and bphA environmental DNA libraries were generated from bacterial communities in sediments with a steep gradient of PCB contamination. Multiple measures of sequence diversity revealed greater heterogeneity of bphA sequences in polluted compared to unpolluted locations. Codon-based signatures of selection in bphA sequences provided evidence of purifying selection. Unifrac analysis of 16S rRNA sequences revealed independent taxonomic lineages from polluted and unpolluted locations, consistent with the presence of locally adapted bacterial communities. Phylogenetic analysis of bphA sequences indicated that dioxygenases from sediments were closely related to previously characterized dioxygenases that metabolize PCBs and polynuclear aromatic hydrocarbons (PAHs), consistent with high levels of these contaminants within the studied sediments. Structural analyses indicated that the BphA protein of Rhodococcus jostii, capable of metabolizing both PCBs and PAHs, provided a more optimal modeling template for bphA sequences reported in this study than a BphA homologue with more restricted substrate specificity. Results from this study suggest that PCBs and PAHs may drive local adaptation of microbial communities by acting as strong selective agents for biphenyl dioxygenases capable of metabolizing a wide range of congeners.

Re-evaluation of dioxygenase gene phylogeny for the development and validation of a quantitative assay for environmental aromatic hydrocarbon degraders

Rieske non-heme iron oxygenases enzymes have been widely studied, as they catalyse essential reactions initiating the bacterial degradation of organic compounds, for instance aromatic hydrocarbons. The genes encoding these enzymes offer a potential target for studying aromatic hydrocarbon-degrading organisms in the environment. However, previously reported primer sets that target dioxygenase gene sequences or the common conserved Rieske centre of aromatics dioxygenases have limited specificity and/or target non-dioxygenase genes. In this work, an extensive database of dioxygenase α-subunit gene sequences was constructed, and primer sets targeting the conserved Rieske centre were developed. The high specificity of the primers was confirmed by polymerase chain reaction analysis, agarose gel electrophoresis and sequencing. Quantitative polymerase chain reaction (qPCR) assays were also developed and optimized, following MIQE guidelines (Minimum Information for Publication of Quantitative Real-Time PCR Experiments). Comparison of the qPCR quantification of dioxygenases in spiked sediment samples and in pure cultures demonstrated an underestimation of the Ct value, and the requirement for a correction factor at gene abundances below 10⁸ gene copies per g of sediment. Externally validated qPCR provides a valuable tool to monitor aromatic hydrocarbon degrader population abundances at contaminated sites.

Our study aimed to re-evaluate the phylogeny of Rieske non-heme iron dioxygenases using only retrieved primary nucleic acid sequences for the development of quantitative real-time PCR primers.

Taxonomic profiling and metagenome analysis of a microbial community from a habitat contaminated with industrial discharges

Industrial units, manufacturing dyes, chemicals,solvents, and xenobiotic compounds, produce liquid and solid wastes, which upon conventional treatment are released in the nearby environment and thus are the major cause of pollution. Soil collected from contaminated Kharicut Canalbank (N 22°57.878′; E 072°38.478′), Ahmeda bad, Gujarat,India was used for metagenomic DNA preparation to study the capabilities of intrinsic microbial community in dealing with xenobiotics. Sequencing of metagenomic DNA on the Genome Sequencer FLX System using titanium chemistry resulted in 409,782 reads accounting for 133,529,997 bases of sequence information. Taxonomic analyses and gene annotations were carried out using the bioinformatics platform Sequence Analysis and Management System for Metagenomic Datasets. Taxonomic profiling was carried out by three different complementary approaches: (a) 16S rDNA, (b) environmental gene tags, and (c) lowest common ancestor. The most abundant phylum and genus were found to be “Proteobacteria”and “Pseudomonas,” respectively. Metagenome reads were mapped on sequenced microbial genomes and the highest numbers of reads were allocated to Pseudomonas stutzeri A1501. Assignment of obtained metagenome reads to Gene Ontology terms, Clusters of Orthologous Groups of protein categories, protein family numbers, and Kyoto Encyclopedia of Genes and Genomes hits revealed genomic potential of indigenous microbial community. In total, 157,024 reads corresponded to 37,028 different KEGG hits, and amongst them, 11,574 reads corresponded to 131 different enzymes potentially involved in xenobiotic biodegradation. These enzymes were mapped on biodegradation pathways of xenobiotics to elucidate their roles in possible catalytic reactions. Consequently, information obtained from the present study will act as a baseline which, subsequently along with other“-omic” studies, will help in designing future bioremediation strategies in effluent treatment plants and environmental cleanup projects.

Pyrosequencing analysis of the bacterial community in drinking water wells

Wells used for drinking water often have a large biomass and a high bacterial diversity. Current technologies are not always able to reduce the bacterial population, and the threat of pathogen proliferation in drinking water sources is omnipresent. The environmental conditions that shape the microbial communities in drinking water sources have to be elucidated, so that pathogen proliferation can be foreseen. In this work, the bacterial community in nine water wells of a groundwater aquifer in Northern Mexico were characterized and correlated to environmental characteristics that might control them. Although a large variation was observed between the water samples, temperature and iron concentration were the characteristics that affected the bacterial community structure and composition in groundwater wells. Small increases in the concentration of iron in water modified the bacterial communities and promoted the growth of the iron-oxidizing bacteria Acidovorax. The abundance of the genera Flavobacterium and Duganella was correlated positively with temperature and the Acidobacteria Gp4 and Gp1, and the genus Acidovorax with iron concentrations in the well water. Large percentages of Flavobacterium and Pseudomonas bacteria were found, and this is of special concern as bacteria belonging to both genera are often biofilm developers, where pathogens survival increases.

Taxonomic Profiling and Metagenome Analysis of a Microbial Community from a Habitat Contaminated with Industrial Discharges

Industrial units, manufacturing dyes, chemicals, solvents, and xenobiotic compounds, produce liquid and solid wastes, which upon conventional treatment are released in the nearby environment and thus are the major cause of pollution. Soil collected from contaminated Kharicut Canal bank (N 22°57.878'; E 072°38.478'), Ahmedabad, Gujarat, India was used for metagenomic DNA preparation to study the capabilities of intrinsic microbial community in dealing with xenobiotics. Sequencing of metagenomic DNA on the Genome Sequencer FLX System using titanium chemistry resulted in 409,782 reads accounting for 133,529,997 bases of sequence information. Taxonomic analyses and gene annotations were carried out using the bioinformatics platform Sequence Analysis and Management System for Metagenomic Datasets. Taxonomic profiling was carried out by three different complementary approaches: (a) 16S rDNA, (b) environmental gene tags, and (c) lowest common ancestor. The most abundant phylum and genus were found to be "Proteobacteria" and "Pseudomonas," respectively. Metagenome reads were mapped on sequenced microbial genomes and the highest numbers of reads were allocated to Pseudomonas stutzeri A1501. Assignment of obtained metagenome reads to Gene Ontology terms, Clusters of Orthologous Groups of protein categories, protein family numbers, and Kyoto Encyclopedia of Genes and Genomes hits revealed genomic potential of indigenous microbial community. In total, 157,024 reads corresponded to 37,028 different KEGG hits, and amongst them, 11,574 reads corresponded to 131 different enzymes potentially involved in xenobiotic biodegradation. These enzymes were mapped on biodegradation pathways of xenobiotics to elucidate their roles in possible catalytic reactions. Consequently, information obtained from the present study will act as a baseline which, subsequently along with other "-omic" studies, will help in designing future bioremediation strategies in effluent treatment plants and environmental clean-up projects.

Spatio-temporal patterns of microbial communities in a hydrologically dynamic pristine aquifer

Seasonal patterns of groundwater and sediment microbial communities were explored in a hydrologically dynamic alpine oligotrophic porous aquifer, characterized by pronounced groundwater table fluctuations. Rising of the groundwater level in consequence of snow melting water recharge was accompanied by a dramatic drop of bacterial Shannon diversity in groundwater from H' = 3.22 ± 0.28 in autumn and winter to H' = 1.31 ± 0.35 in spring and summer, evaluated based on T-RFLP community fingerprinting. Elevated numbers of bacteria in groundwater in autumn followed nutrient inputs via recharge from summer rains and correlated well with highest concentrations of assimilable organic carbon. Sterile sediments incubated to groundwater in monitoring wells were readily colonized reaching maximum cell densities within 2 months, followed by a consecutive but delayed increase and leveling-off of bacterial diversity. After 1 year of incubation, the initially sterile sediments exhibited a similar number of bacteria and Shannon diversity when compared to vital sediment from a nearby river incubated in parallel. The river bed sediment microbial communities hardly changed in composition, diversity, and cell numbers during 1 year of exposure to groundwater. Summing up, the seasonal hydrological dynamics were found to induce considerable dynamics of microbial communities suspended in groundwater, while sediment communities seem unaffected and stable in terms of biomass and diversity.

Abundance, dynamics, and biogeographic distribution of seven polycyclic aromatic hydrocarbon dioxygenase gene variants in coastal sediments of Patagonia

Novel polycyclic aromatic hydrocarbon dioxygenase gene variants were present in abundances similar to or higher than those of phnA1 from Cycloclasticus spp. at a chronically polluted subantarctic coastal marine environment in Patagonia. These novel gene variants were detected over a 6-year time span and were also present in sediments from temperate Patagonian sites.

Simplified MPN method for enumeration of soil naphthalene degraders using gaseous substrate

We describe a simplified microplate most-probable-number (MPN) procedure to quantify the bacterial naphthalene degrader population in soil samples. In this method, the sole substrate naphthalene is dosed passively via gaseous phase to liquid medium and the detection of growth is based on the automated measurement of turbidity using an absorbance reader. The performance of the new method was evaluated by comparison with a recently introduced method in which the substrate is dissolved in inert silicone oil and added individually to each well, and the results are scored visually using a respiration indicator dye. Oil-contaminated industrial soil showed slightly but significantly higher MPN estimate with our method than with the reference method. This suggests that gaseous naphthalene was dissolved in an adequate concentration to support the growth of naphthalene degraders without being too toxic. The dosing of substrate via gaseous phase notably reduced the work load and risk of contamination. The result scoring by absorbance measurement was objective and more reliable than measurement with indicator dye, and it also enabled further analysis of cultures. Several bacterial genera were identified by cloning and sequencing of 16S rRNA genes from the MPN wells incubated in the presence of gaseous naphthalene. In addition, the applicability of the simplified MPN method was demonstrated by a significant positive correlation between the level of oil contamination and the number of naphthalene degraders detected in soil.

Comparison of the specificities and efficacies of primers for aromatic dioxygenase gene analysis of environmental samples

Aromatic dioxygenase genes have long been of interest for bioremediation and aromatic carbon cycling studies. To date, 115 primers and probes have been designed and used to analyze dioxygenase gene diversities in environmental samples. Here we analyze those primers' specificities, coverages, and PCR product lengths compared to known aromatic dioxygenase genes based on in silico analysis as well as summarize their differing advantages or effectiveness from over 50 reported experimental studies. We also provide some guidance for primer use in future studies.

Soil type-dependent responses to phenanthrene as revealed by determining the diversity and abundance of polycyclic aromatic hydrocarbon ring-hydroxylating dioxygenase genes by using a novel PCR detection system

A novel PCR primer system that targets a wide range of polycyclic aromatic hydrocarbon ring-hydroxylating dioxygenase (PAH-RHD(alpha)) genes of both Gram-positive and Gram-negative bacteria was developed and used to study their abundance and diversity in two different soils in response to phenanthrene spiking. The specificities and target ranges of the primers predicted in silico were confirmed experimentally by cloning and sequencing of PAH-RHD(alpha) gene amplicons from soil DNA. Cloning and sequencing showed the dominance of phnAc genes in the contaminated Luvisol. In contrast, high diversity of PAH-RHD(alpha) genes of Gram-positive and Gram-negative bacteria was observed in the phenanthrene-spiked Cambisol. Quantitative real-time PCR based on the same primers revealed that 63 days after phenanthrene spiking, PAH-RHD(alpha) genes were 1 order of magnitude more abundant in the Luvisol than in the Cambisol, while they were not detected in both control soils. In conclusion, sequence analysis of the amplicons obtained confirmed the specificity of the novel primer system and revealed a soil type-dependent response of PAH-RHD(alpha) gene-carrying soil bacteria to phenanthrene spiking.

Subsurface cycling of nitrogen and anaerobic aromatic hydrocarbon biodegradation revealed by nucleic Acid and metabolic biomarkers

Microbial processes are crucial for ecosystem maintenance, yet documentation of these processes in complex open field sites is challenging. Here we used a multidisciplinary strategy (site geochemistry, laboratory biodegradation assays, and field extraction of molecular biomarkers) to deduce an ongoing linkage between aromatic hydrocarbon biodegradation and nitrogen cycling in a contaminated subsurface site. Three site wells were monitored over a 10-month period, which revealed fluctuating concentrations of nitrate, ammonia, sulfate, sulfide, methane, and other constituents. Biodegradation assays performed under multiple redox conditions indicated that naphthalene metabolism was favored under aerobic conditions. To explore in situ field processes, we measured metabolites of anaerobic naphthalene metabolism and expressed mRNA transcripts selected to document aerobic and anaerobic microbial transformations of ammonia, nitrate, and methylated aromatic contaminants. Gas chromatography-mass spectrometry detection of two carboxylated naphthalene metabolites and transcribed benzylsuccinate synthase, cytochrome c nitrite reductase, and ammonia monooxygenase genes indicated that anaerobic metabolism of aromatic compounds and both dissimilatory nitrate reduction to ammonia (DNRA) and nitrification occurred in situ. These data link formation (via DNRA) and destruction (via nitrification) of ammonia to in situ cycling of nitrogen in this subsurface habitat, where metabolism of aromatic pollutants has led to accumulation of reduced metabolic end products (e.g., ammonia and methane).