Anaerobic naphthalene degradation by sulfate-reducing Desulfobacteraceae from various anoxic aquifers

Evaluating Natural Source Zone Depletion and Enhanced Source Zone Depletion in laboratory columns via soil redox continuous sensing and microbiome characterization

To optimally employ Natural Source Zone Depletion (NSZD) and Enhanced Source Zone Depletion (ESZD) at sites impacted by light non-aqueous phase liquids (LNAPL), monitoring strategies are required. Emerging use of subsurface oxidation-reduction potential (ORP) sensors shows promise for tracking redox evolution, which reflects ongoing biogeochemical processes. However, further understanding of how soil redox dynamics relate to subsurface microbial activity and LNAPL degradation pathways is needed. In this work, soil ORP sensors and DNA and RNA sequencing-based microbiome analysis were combined to elucidate NSZD and ESZD (biostimulation via periodic sulfate addition and biosparging) processes in columns containing LNAPL-impacted soils from a former petroleum refinery. Results show expected relationships between continuous soil redox and active microbial communities. Continuous data revealed spatial and temporal detail that informed interpretation of the hydrocarbon biodegradation data. Redox increases were transient for sulfate addition, and sequencing revealed how hydrocarbon concentration and composition impacted microbiome structure and naphthalene degradation. Periodic biosparging did not result in fully aerobic conditions suggesting observed biodegradation improvements could be explained by alternative anaerobic metabolisms (e.g., iron reduction due to air oxidizing reduced iron). Collectively, data suggest combining continuous redox sensing with microbiome analysis provides insights beyond those possible with either monitoring tool alone.

Transformation of sedimentary dissolved organic matter in electrokinetic remediation catalogued by FT-ICR mass spectrometry

In electrokinetic remediation (EKR), the sedimentary dissolved organic matter (DOM) could impede remediation by scavenging reactive species and generating unintended byproducts. Yet its transformation and mechanisms remained largely unknown. This study conducted molecular-level characterization of the water-extractable DOM (WEOM) in EKR using negative-ion electrospray ionization coupled to 21 tesla Fourier transform ion cyclotron resonance mass spectrometry (21 T FT-ICR MS). The results suggested that ∼55 % of the ∼7,000 WEOM compounds identified were reactive, and EKR lowered their diversity, molecular weight distribution, and double-bond equivalent (DBE) through a combination of electrochemical and microbial redox reactions. Heteroatom-containing WEOM (CHON and CHOS) were abundant (∼ 35% of the total WEOM), with CHOS generally being more reactive than CHON. Low electric potential (1 V/cm) promoted the growth of dealkylation and desulfurization bacteria, and led to anodic CO2 mineralization, anodic cleavage of -SO and -SO3, and cathodic cleavage of -SH2; high electric potential (2 V/cm) only enriched desulfurization bacteria, and differently, led to anodic oxygenation and cathodic hydrogenation of unsaturated and phenolic compounds, in addition to cathodic cleavage of -SH2. The long-term impact of these changes on soil quality and nitrogen-sulfur-carbon flux may be need to studied to identify unknown risks and new applications of EKR.

Effects of humic electron mediators on reductive dechlorination of polychlorinated biphenyl by consortia enriched from terrestrial and marine environments

Humic electron mediators can facilitate the reductive dehalogenation of organohalogenated compounds by accelerating electron transfer. To investigate the effect of humic electron mediators on the microbial anaerobic reductive dechlorination of Polychlorinated biphenyls (PCBs), three types of humic electron mediators, humin (HM), humic acid (HA), and anthraquinone-2,6-disulfonic acid (AQDS, HA analogs), were added to PCB dechlorination cultures enriched from different sources in terrestrial and marine environments (T and M cultures). The results showed that meta- and para-site dechlorination occurred in the M culture, while only meta-site dechlorination occurred in the T culture. The dechlorination process N and the dechlorination process H or H' are presented in both cultures. HM enhanced PCB dechlorination metabolic activity in both cultures mainly by promoting meta-site dechlorination. HA showed a weak promoting effect on the M culture by promoting para-chlorine removal but inhibited the dechlorination metabolism of the terrestrial-origin culture, inhibiting meta-chlorine removal. AQDS showed inhibitory effects on both cultures by inhibiting the microbial removal of meta-chlorine. High-throughput sequencing and qPCR results suggest that HM is not a carbon source for the potential dechlorinating metabolism of Dehalococcoides but may promote reductive dechlorination by changing the community structure, and AQDS may inhibit anaerobic reductive dechlorination of PCBs by inhibiting the growth of Dehalococcoides. This study provides insights into the mechanism of enhancing PCB microbial dechlorination mediated by humic substances and plays a significant role in extending the application prospects of PCBs bioremediation technology.

Progress of Crude Oil Gasification Technology Assisted by Microorganisms in Reservoirs

Crude oil gasification bacteria, including fermenting bacteria, hydrocarbon-oxidizing bacteria, reducing bacteria, and methanogenic bacteria, participate in multi-step reactions involving initial activation, intermediate metabolism, and the methanogenesis of crude oil hydrocarbons. These bacteria degrade crude oil into smaller molecules such as hydrogen, carbon dioxide, acetic acid, and formic acid. Ultimately, they convert it into methane, which can be utilized or stored as a strategic resource. However, the current challenges in crude oil gasification include long production cycles and low efficiency. This paper provides a summary of the microbial flora involved in crude oil gasification, the gasification metabolism pathways within reservoirs, and other relevant information. It specifically focuses on analyzing the factors that affect the efficiency of crude oil gasification metabolism and proposes suggestions for improving this efficiency. These studies deepen our understanding of the potential of reservoir ecosystems and provide valuable insights for future reservoir development and management.

Potential for the anaerobic oxidation of benzene and naphthalene in thermophilic microorganisms from the Guaymas Basin

Unsubstituted aromatic hydrocarbons (UAHs) are recalcitrant molecules abundant in crude oil, which is accumulated in subsurface reservoirs and occasionally enters the marine environment through natural seepage or human-caused spillage. The challenging anaerobic degradation of UAHs by microorganisms, in particular under thermophilic conditions, is poorly understood. Here, we established benzene- and naphthalene-degrading cultures under sulfate-reducing conditions at 50°C and 70°C from Guaymas Basin sediments. We investigated the microorganisms in the enrichment cultures and their potential for UAH oxidation through short-read metagenome sequencing and analysis. Dependent on the combination of UAH and temperature, different microorganisms became enriched. A Thermoplasmatota archaeon was abundant in the benzene-degrading culture at 50°C, but catabolic pathways remained elusive, because the archaeon lacked most known genes for benzene degradation. Two novel species of Desulfatiglandales bacteria were strongly enriched in the benzene-degrading culture at 70°C and in the naphthalene-degrading culture at 50°C. Both bacteria encode almost complete pathways for UAH degradation and for downstream degradation. They likely activate benzene via methylation, and naphthalene via direct carboxylation, respectively. The two species constitute the first thermophilic UAH degraders of the Desulfatiglandales. In the naphthalene-degrading culture incubated at 70°C, a Dehalococcoidia bacterium became enriched, which encoded a partial pathway for UAH degradation. Comparison of enriched bacteria with related genomes from environmental samples indicated that pathways for benzene degradation are widely distributed, while thermophily and capacity for naphthalene activation are rare. Our study highlights the capacities of uncultured thermophilic microbes for UAH degradation in petroleum reservoirs and in contaminated environments.

Distribution of bound-PAH residues and their correlations with the bacterial community at different depths of soil from an abandoned chemical plant site

The situ pollutant residue and microbial characteristics in contaminated environments are crucial for ecological restoration and soil utilization. This work reported the variation of polycyclic aromatic hydrocarbon (PAH) residues and the bacterial community at different depths in an aged-abandoned site. These results unveiled that over 90% of low molecular weight (LMW) and medium molecular weight (MMW), 52.84-76.88% of high molecular weight (HMW) bound-PAH (BP) residues were sequestrated in humin (HM). The stresses of PAH and soil depth enhanced the frequency of bacteria associations, especially positive associations. We enriched and cultured PAH degradation bacteria (PDB) from the sampling site mainly consisting of Pseudomonas and Acinetobacter, which were originally 0.39-0.52% abundant in the sampling site. The abundances of PDB and PAH-degradation genes (PDGs) were higher at shallower depths and increased with high PAH concentration. Simultaneously, Pearson correlation analysis and experimental verification found that the process of PAH binding with SOM limited the further increase of PDB and PDGs in PAH-contaminated sites. These findings may illustrate possible ecological risks of contaminated soils and provide guidance for the isolation and application of PDB.

Polycyclic aromatic hydrocarbon (PAH) biodegradation capacity revealed by a genome-function relationship approach

BACKGROUND

Polycyclic aromatic hydrocarbon (PAH) contamination has been a worldwide environmental issue because of its impact on ecosystems and human health. Biodegradation plays an important role in PAH removal in natural environments. To date, many PAH-degrading strains and degradation genes have been reported. However, a comprehensive PAH-degrading gene database is still lacking, hindering a deep understanding of PAH degraders in the era of big data. Furthermore, the relationships between the PAH-catabolic genotype and phenotype remain unclear.

RESULTS

Here, we established a bacterial PAH-degrading gene database and explored PAH biodegradation capability via a genome-function relationship approach. The investigation of functional genes in the experimentally verified PAH degraders indicated that genes encoding hydratase-aldolase could serve as a biomarker for preliminarily identifying potential degraders. Additionally, a genome-centric interpretation of PAH-degrading genes was performed in the public genome database, demonstrating that they were ubiquitous in Proteobacteria and Actinobacteria. Meanwhile, the global phylogenetic distribution was generally consistent with the culture-based evidence. Notably, a few strains affiliated with the genera without any previously known PAH degraders (Hyphomonas, Hoeflea, Henriciella, Saccharomonospora, Sciscionella, Tepidiphilus, and Xenophilus) also bore a complete PAH-catabolic gene cluster, implying their potential of PAH biodegradation. Moreover, a random forest analysis was applied to predict the PAH-degrading trait in the complete genome database, revealing 28 newly predicted PAH degraders, of which nine strains encoded a complete PAH-catabolic pathway.

CONCLUSIONS

Our results established a comprehensive PAH-degrading gene database and a genome-function relationship approach, which revealed several potential novel PAH-degrader lineages. Importantly, this genome-centric and function-oriented approach can overcome the bottleneck of conventional cultivation-based biodegradation research and substantially expand our current knowledge on the potential degraders of environmental pollutants.

Anaerobic biodegradation of polycyclic aromatic hydrocarbons

Although many anaerobic microorganisms that can degrade PAHs have been harnessed, there is still a large gap between laboratory achievements and practical applications. Here, we review the recent advances in the biodegradation of PAHs under anoxic conditions and highlight the mechanistic insights into the metabolic pathways and functional genes. Achievements of practical application and enhancing strategies of anaerobic PAHs bioremediation in soil were summarized. Based on the concerned issues during research, perspectives of further development were proposed including time-consuming enrichment, byproducts with unknown toxicity, and activity inhibition with low temperatures. In addition, meta-omics, synthetic biology and engineering microbiome of developing microbial inoculum for anaerobic bioremediation applications are discussed. We anticipate that integrating the theoretical research on PAHs anaerobic biodegradation and its successful application will advance the development of anaerobic bioremediation.

Microbial communities in petroleum-contaminated sites: Structure and metabolisms

Over recent decades, hydrocarbon concentrations have been augmented in soil and water, mainly derived from accidents or operations that input crude oil and petroleum into the environment. Different techniques for remediation have been proposed and used to mitigate oil contamination. Among the available environmental recovery approaches, bioremediation stands out since these hydrocarbon compounds can be used as growth substrates for microorganisms. In turn, microorganisms can play an important role with significant contributions to the stabilization of impacted areas. In this review, we present the current knowledge about responses from natural microbial communities (using DNA barcoding, multiomics, and functional gene markers) and bioremediation experiments (microcosm and mesocosm) conducted in the presence of petroleum and chemical dispersants in different samples, including soil, sediment, and water. Additionally, we present metabolic mechanisms for aerobic/anaerobic hydrocarbon degradation and alternative pathways, as well as a summary of studies showing functional genes and other mechanisms involved in petroleum biodegradation processes.

Iron and sulfate reduction structure microbial communities in (sub-)Antarctic sediments

Permanently cold marine sediments are heavily influenced by increased input of iron as a result of accelerated glacial melt, weathering, and erosion. The impact of such environmental changes on microbial communities in coastal sediments is poorly understood. We investigated geochemical parameters that shape microbial community compositions in anoxic surface sediments of four geochemically differing sites (Annenkov Trough, Church Trough, Cumberland Bay, Drygalski Trough) around South Georgia, Southern Ocean. Sulfate reduction prevails in Church Trough and iron reduction at the other sites, correlating with differing local microbial communities. Within the order Desulfuromonadales, the family Sva1033, not previously recognized for being capable of dissimilatory iron reduction, was detected at rather high relative abundances (up to 5%) while other members of Desulfuromonadales were less abundant (<0.6%). We propose that Sva1033 is capable of performing dissimilatory iron reduction in sediment incubations based on RNA stable isotope probing. Sulfate reducers, who maintain a high relative abundance of up to 30% of bacterial 16S rRNA genes at the iron reduction sites, were also active during iron reduction in the incubations. Thus, concurrent sulfate reduction is possibly masked by cryptic sulfur cycling, i.e., reoxidation or precipitation of produced sulfide at a small or undetectable pool size. Our results show the importance of iron and sulfate reduction, indicated by ferrous iron and sulfide, as processes that shape microbial communities and provide evidence for one of Sva1033's metabolic capabilities in permanently cold marine sediments.

Anaerobic phenanthrene biodegradation by a newly isolated sulfate-reducer, strain PheS1, and exploration of the biotransformation pathway

Phenanthrene is a widespread and harmful polycyclic aromatic hydrocarbon that is difficult to anaerobically biodegrade. Current challenges in anaerobic phenanthrene bioremediation are a lack of degrading cultures and limited knowledge of biotransformation pathways. Under sulfate-reducing conditions, pure-cultures and biotransformation processes for anaerobic phenanthrene biodegradation are poorly understood. In this study, strain PheS1, which is phylogenetically closely related to Desulfotomaculum, was found to be a sulfate-reducing phenanthrene-degrading bacterium. Anaerobic phenanthrene biodegradation using PheS1 was proposed based on metabolite and genome analyses, and the initial step was identified as carboxylation based on the detection of 2-phenanthroic acid, [¹³C]-2-phenanthroic acid, and [D9]-2- phenanthroic acid when phenanthrene+HCO₃^-, phenanthrene+H¹³CO₃^-, and [D10]-phenanthrene+HCO₃^- were used as the substrate, respectively. PheS1 genome ubiD gene encoding of carboxylase putatively involved in the biodegradation was performed. Next, benzene ring reduction and cleavage that produced benzene compounds and cyclohexane derivative were reported to occur in the downstream biotransformation processes. Additionally, benzene, naphthalene, benz[a]anthracene, and anthracene can be utilised by PheS1, whereas pyrene and benz[a]pyrene cannot. We discovered a new phenanthrene-degrading sulfate-reducer and provided the anaerobic phenanthrene biotransformation pathway under sulfate-reducing conditions, which can act as a reference for practical applications in bioremediation and for studying the molecular mechanisms of phenanthrene in anaerobic zones.

Aromatic compound-degrading taxa in an anoxic coal seam microbiome from the Surat Basin, Australia

Methane is an important energy resource internationally, and a large proportion of this methane is produced by microbial communities living in coal seams. Despite the value of this resource for human energy security, our understanding of the metabolic roles played by specific taxa during the biodegradation of coal to methane in situ is quite limited. In order to develop a greater understanding of microbial catabolism on coal, a community from a coal seam in the Surat Basin, Australia, was incubated on 10 different aromatic organic compounds: coronene, benzo[a]pyrene, pyrene, phenanthrene, naphthalene, ethylbenzene, phenol, benzoate, vanillate and syringate. Each of these aromatic compounds either occurs in coal or is a possible product of the coal biodegradation process. 16S rRNA sequencing revealed substantial changes to each community in response to each aromatic carbon substrate provided. Abundant taxa from these substrate-specific communities were identified and their probable catabolic roles proposed based on literature searches of related taxa. This study is the first to link specific coal seam taxa to aromatic substrates available in coal seam environments. Two conceptual models of the putative degradation pathways and key taxa responsible are proposed.

Nitric oxide-dependent biodegradation of phenanthrene and fluoranthene: The co-occurrence of anaerobic and intra-aerobic pathways

Polycyclic aromatic hydrocarbons (PAHs) pollution as well as the emissions of nitric oxide (NO) and greenhouse gas nitrous oxide (N₂O) in denitrification processes are currently two environmental issues of great concern. Although bioremediation of PAHs under denitrification is considered a promising approach, denitrification was an important contributor to N₂O and NO emissions. This long-term study confirmed for the first time that microorganisms could utilize NO to efficiently degrade phenanthrene and fluoranthene. When the two systems of NO-dependent phenanthrene and fluoranthene degradation were stable, the first-order rate constants of phenanthrene and fluoranthene in the two systems (0.1940 and 0.0825 day^-1, respectively) were close to those values (0.2290 and 0.1085 day^-1, respectively) observed at nitrate-reducing conditions. Further analysis of functional genes revealed that phenanthrene and fluoranthene might be degraded under the combined action of the anaerobic pathway mediated by NO reduction and intra-aerobic pathway mediated by NO dismutation. The genomic analysis showed that Nod genes had high diversity and most of them were similar to aquifer cluster group in the two systems. Microbial community structure analysis indicated that Pseudomonas and Ochrobactrum might be key participants in NO-dependent phenanthrene degradation system, and Azoarcus, Alicycliphilus and Moheibacter might play vital roles in NO-dependent fluoranthene degradation system. This study provides new perspective for anaerobic remediation of PAH pollution and simultaneously reducing NO and N₂O emissions during bioprocesses, which has important ecological significance for amending sediment and soil PAHs contamination and potential application for the removal of PAHs in flue gas.

Effect of Temperature on Acetate Mineralization Kinetics and Microbial Community Composition in a Hydrocarbon-Affected Microbial Community During a Shift From Oxic to Sulfidogenic Conditions

Aquifer thermal energy storage (ATES) allows for the seasonal storage and extraction of heat in the subsurface thus reducing reliance on fossil fuels and supporting decarbonization of the heating and cooling sector. However, the impacts of higher temperatures toward biodiversity and ecosystem services in the subsurface environment remain unclear. Here, we conducted a laboratory microcosm study comprising a hydrocarbon-degrading microbial community from a sulfidic hydrocarbon-contaminated aquifer spiked with ¹³C-labeled acetate and incubated at temperatures between 12 and 80°C to evaluate (i) the extent and rates of acetate mineralization and (ii) the resultant temperature-induced shifts in the microbial community structure. We observed biphasic mineralization curves at 12, 25, 38, and 45°C, arising from immediate and fast aerobic mineralization due to an initial oxygen exposure, followed by slower mineralization at sulfidogenic conditions. At 60°C and several replicates at 45°C, acetate was only aerobically mineralized. At 80°C, no mineralization was observed within 178 days. Rates of acetate mineralization coupled to sulfate reduction at 25 and 38°C were six times faster than at 12°C. Distinct microbial communities developed in oxic and strictly anoxic phases of mineralization as well as at different temperatures. Members of the Alphaproteobacteria were dominant in the oxic mineralization phase at 12–38°C, succeeded by a more diverse community in the anoxic phase composed of Deltaproteobacteria, Clostridia, Spirochaetia, Gammaproteobacteria and Anaerolinea, with varying abundances dependent on the temperature. In the oxic phases at 45 and 60°C, phylotypes affiliated to spore-forming Bacilli developed. In conclusion, temperatures up to 38°C allowed aerobic and anaerobic acetate mineralization albeit at varying rates, while mineralization occurred mainly aerobically between 45 and 60°C; thermophilic sulfate reducers being active at temperatures > 45°C were not detected. Hence, temperature may affect dissolved organic carbon mineralization rates in ATES while the variability in the microbial community composition during the transition from micro-oxic to sulfidogenic conditions highlights the crucial role of electron acceptor availability when combining ATES with bioremediation.

Powdered activated carbon (PAC) amendment enhances naphthalene biodegradation under strictly sulfate-reducing conditions

Capping represents an efficient and well-established practice to contain polycyclic aromatic hydrocarbons (PAHs) in sediments, reduce mobility, and minimize risks. Exposure to PAHs can encourage biodegradation, which can improve the performance of capping. This study investigates biodegradation of naphthalene (a model PAH) in highly reducing, sediment-like environments with amendment of different capping materials (PAC and sand). Microcosms were prepared with sediment enrichments, sulfate as an electron acceptor, and naphthalene. Results show that PAC stimulates naphthalene biodegradation and mineralization, as indicated by production of ¹⁴CO₂ from radiolabeled naphthalene. Mineralization in PAC systems correlates with the enrichment of genera (Geobacter and Desulfovirga) previously identified to biodegrade naphthalene (Spearman's, p < 0.05). Naphthalene decay in sand and media-free systems was not linked to biodegradation activity (ANOVA, p > 0.05), and microbial communities were correlated to biomass yields rather than metabolites. Naphthalene decay in PAC systems consists of three stages with respect to time: latent (0-88 days), exponential decay (88-210 days), and inactive (210-480 days). This study shows that PAC amendment enhances naphthalene biodegradation under strictly sulfate-reducing conditions and provides a kinetic and metagenomic characterization of systems demonstrating naphthalene decay.

Fate of Trace Organic Compounds in Hyporheic Zone Sediments of Contrasting Organic Carbon Content and Impact on the Microbiome

The organic carbon in streambed sediments drives multiple biogeochemical reactions, including the attenuation of organic micropollutants. An attenuation assay using sediment microcosms differing in the initial total organic carbon (TOC) revealed higher microbiome and sorption associated removal efficiencies of trace organic compounds (TrOCs) in the high-TOC compared to the low-TOC sediments. Overall, the combined microbial and sorption associated removal efficiencies of the micropollutants were generally higher than by sorption alone for all compounds tested except propranolol whose removal efficiency was similar via both mechanisms. Quantitative real-time PCR and time-resolved 16S rRNA gene amplicon sequencing revealed that higher bacterial abundance and diversity in the high-TOC sediments correlated with higher microbial removal efficiencies of most TrOCs. The bacterial community in the high-TOC sediment samples remained relatively stable against the stressor effects of TrOC amendment compared to the low-TOC sediment community that was characterized by a decline in the relative abundance of most phyla except Proteobacteria. Bacterial genera that were significantly more abundant in amended relative to unamended sediment samples and thus associated with biodegradation of the TrOCs included Xanthobacter, Hyphomicrobium, Novosphingobium, Reyranella and Terrimonas. The collective results indicated that the TOC content influences the microbial community dynamics and associated biotransformation of TrOCs as well as the sorption potential of the hyporheic zone sediments.

Metagenomic Insights Into the Mechanisms for Biodegradation of Polycyclic Aromatic Hydrocarbons in the Oil Supply Chain

Petroleum is a very complex and diverse organic mixture. Its composition depends on reservoir location and in situ conditions and changes once crude oil is spilled into the environment, making the characteristics associated with every spill unique. Polycyclic aromatic hydrocarbons (PAHs) are common components of the crude oil and constitute a group of persistent organic pollutants. Due to their highly hydrophobic, and their low solubility tend to accumulate in soil and sediment. The process by which oil is sourced and made available for use is referred to as the oil supply chain and involves three parts: (1) upstream, (2) midstream and (3) downstream activities. As consequence from oil supply chain activities, crude oils are subjected to biodeterioration, acidification and souring, and oil spills are frequently reported affecting not only the environment, but also the economy and human resources. Different bioremediation techniques based on microbial metabolism, such as natural attenuation, bioaugmentation, biostimulation are promising approaches to minimize the environmental impact of oil spills. The rate and efficiency of this process depend on multiple factors, like pH, oxygen content, temperature, availability and concentration of the pollutants and diversity and structure of the microbial community present in the affected (contaminated) area. Emerging approaches, such as (meta-)taxonomics and (meta-)genomics bring new insights into the molecular mechanisms of PAH microbial degradation at both single species and community levels in oil reservoirs and groundwater/seawater spills. We have scrutinized the microbiological aspects of biodegradation of PAHs naturally occurring in oil upstream activities (exploration and production), and crude oil and/or by-products spills in midstream (transport and storage) and downstream (refining and distribution) activities. This work addresses PAH biodegradation in different stages of oil supply chain affecting diverse environments (groundwater, seawater, oil reservoir) focusing on genes and pathways as well as key players involved in this process. In depth understanding of the biodegradation process will provide/improve knowledge for optimizing and monitoring bioremediation in oil spills cases and/or to impair the degradation in reservoirs avoiding deterioration of crude oil quality.

Microaerated UASB reactor treating textile wastewater: The core microbiome and removal of azo dye Direct Black 22

Sequential anaerobic and aerobic processes have been recommended to treat textile wastewater reliably. In this work, the focus was on finding an energetically more competitive system to remove tetra-azo dye Direct Black 22 (DB22). We operated two upflow anaerobic sludge blanket (UASB) reactors (R1 and R2) in three phases (PI, PII, and PIII). R1 was operated as a conventional UASB, while R2 was microaerated in the upper part (0.18 ± 0.05 mg O₂. L^-1), aiming to remove DB22 simultaneously with the aromatic amine byproducts. PI consisted of feeding reactors with synthetic textile wastewater (STW), PII had higher salinity in the STW, and PIII was the same as PII, plus sulfate. The results showed that color and COD removal efficiencies were similar for both reactors (67-72% for R1 and 59-78% for R2) without a substantial influence of oxygen in R2. However, microaeration played a crucial role in R2 by removing the anaerobically formed aromatic amines; during PIII, the effluent was 16 times less toxic than that of R1. The microbial community that developed in the sludge bed of both reactors was quite similar, with the core microbiome represented by Trichococcus, Syntrophus and Methanosaeta genera. The increase in salinity in PII and PIII promoted a shift in the microbial community, excluding salty-sensitive genera from the core microbiome. The putative genera Brevundimonas and Ornatilinea were associated to aromatic amine microaerobic removal. Therefore, there is a potential application of a compact microaerated anaerobic system for textile wastewater treatment.

Investigation of anaerobic phenanthrene biodegradation by a highly enriched co-culture, PheN9, with nitrate as an electron acceptor

In this study, we developed a highly enriched phenanthrene-degrading co-culture, PheN9, which uses nitrate as an electron acceptor under anaerobic conditions, and the processes mediating biodegradation were proposed. The dominant bacteria populations included Pseudomonas stutzeri (91.7% relative abundance), which shared 98% 16S rRNA-sequence similarity with the naphthalene-degrading, nitrate-reducing strain NAP-3-1, and Candidatus_Kuenenia (2.3% relative abundance), which is a type of anammox bacteria. Enrichment transformed 54% of the added phenanthrene, reduced nitrate, and generated significant amounts of nitrite. Enrichment also result in partial consumption of the produced nitrite by the anammox bacteria. The key initial steps of anaerobic phenanthrene biodegradation by PheN9 were methylation and carboxylation, which were identified for detection of metabolic products, as well as carboxylase and methyltransferase activities. The methylation product was then oxidized to 2-naphthoic acid and then underwent sequential biodegradation steps. Then, ring-system reducing occurred, and the metabolic products were identified as dihydro-, tetrahydro-, hexahydro-, and octahydro-2-phenanthroic acid. Downstream degradation proceeded via a substituted benzene series and cyclohexane derivatives. This study employed anaerobic phenanthrene-biodegradation processes with nitrate as an electron acceptor. These findings can improve our understanding of anaerobic polycyclic aromatic hydrocarbon (PAH) biodegradation processes and guide PAH bioremediation by adding nitrate to anaerobic environments.

Anaerobic Microbial Degradation of Polycyclic Aromatic Hydrocarbons: A Comprehensive Review

Polycyclic aromatic hydrocarbons (PAHs) are a class of hazardous organic contaminants that are widely distributed in nature, and many of them are potentially toxic to humans and other living organisms. Biodegradation is the major route of detoxification and removal of PAHs from the environment. Aerobic biodegradation of PAHs has been the subject of extensive research; however, reports on anaerobic biodegradation of PAHs are so far limited. Microbial degradation of PAHs under anaerobic conditions is difficult because of the slow growth rate of anaerobes and low energy yield in the metabolic processes. Despite the limitations, some anaerobic bacteria degrade PAHs under nitrate-reducing, sulfate-reducing, iron-reducing, and methanogenic conditions. Anaerobic biodegradation, though relatively slow, is a significant process of natural attenuation of PAHs from the impacted anoxic environments such as sediments, subsurface soils, and aquifers. This review is intended to provide comprehensive details on microbial degradation of PAHs under various reducing conditions, to describe the degradation mechanisms, and to identify the areas that should receive due attention in further investigations.

Geological gas-storage shapes deep life

Around the world, several dozen deep sedimentary aquifers are being used for storage of natural gas. Ad hoc studies of the microbial ecology of some of them have suggested that sulfate reducing and methanogenic microorganisms play a key role in how these aquifers' communities function. Here, we investigate the influence of gas storage on these two metabolic groups by using high-throughput sequencing and show the importance of sulfate-reducing Desulfotomaculum and a new monophyletic methanogenic group. Aquifer microbial diversity was significantly related to the geological level. The distance to the stored natural gas affects the ratio of sulfate-reducing Firmicutes to deltaproteobacteria. In only one aquifer, the methanogenic archaea dominate the sulfate-reducers. This aquifer was used to store town gas (containing at least 50% H₂ ) around 50 years ago. The observed decrease of sulfates in this aquifer could be related to stimulation of subsurface sulfate-reducers. These results suggest that the composition of the microbial communities is impacted by decades old transient gas storage activity. The tremendous stability of these gas-impacted deep subsurface microbial ecosystems suggests that in situ biotic methanation projects in geological reservoirs may be sustainable over time.

Oil degradation potential of microbial communities in water and sediment of Baltic Sea coastal area

Two long-term potentially oil exposed Baltic Sea coastal sites near old oil refineries and harbours were compared to nearby less exposed sites in terms of bacterial, archaeal and fungal microbiomes and oil degradation potential. The bacterial, archaeal and fungal diversities were similar in oil exposed and less exposed sampling sites based on bacterial and archaeal 16S rRNA gene and fungal 5.8S rRNA gene amplicon sequencing from both DNA and RNA fractions. The number of genes participating in alkane degradation (alkB) or PAH-ring hydroxylation (PAH–RHDα) were detected by qPCR in all water and sediment samples. These numbers correlated with the number of bacterial 16S rRNA gene copies in sediment samples but not with the concentration of petroleum hydrocarbons or PAHs. This indicates that both the clean and the more polluted sites at the Baltic Sea coastal areas have a potential for petroleum hydrocarbon degradation. The active community (based on RNA) of the coastal Baltic Sea water differed largely from the total community (based on DNA). The most noticeable difference was seen in the bacterial community in the water samples were the active community was dominated by Cyanobacteria and Proteobacteria whereas in total bacterial community Actinobacteria was the most abundant phylum. The abundance, richness and diversity of Fungi present in water and sediment samples was in general lower than that of Bacteria and Archaea. Furthermore, the sampling location influenced the fungal community composition, whereas the bacterial and archaeal communities were not influenced. This may indicate that the fungal species that are adapted to the Baltic Sea environments are few and that Fungi are potentially more vulnerable to or affected by the Baltic Sea conditions than Bacteria and Archaea.

The microbiomic and environmental analysis of sediments in the Indo-Pacific humpback dolphin (Sousa chinensis) habitat in the Northern Beibu Gulf, China

The northern Beibu Gulf is one of the major habitats for the Indo-Pacific humpback dolphin (Sousa chinensis) in China. In this habitat, the core distribution zone of humpback dolphins was confined to the Sanniang Bay (SNB) and Dafengjiang River Estuary (DRE) areas. In our present research, the sediments of 14 sampling sites across the SNB and DRE waters were collected and further conducted for microbiomic and environmental analysis to explore the ecosystem characteristics of major humpback dolphin habitats in Northern Beibu Gulf. The environmental condition includes ammonia nitrogen (NH₄⁺-N), nitrate nitrogen (NO₃^--N), dissolved reactive phosphorus (DRP), sulfur content in the form of sulfuric acid (SO₄^2--S), Fe, and heavy metals (including Cu, Zn, Cd, Pb, and As). The composition of the bacterial community was characterized by 16S ribosomal DNA analysis of the V3-V4 regions using the Illumina-based sequencing platform. The environmental characteristic of the nutrient elements and heavy metals indicated that SNB suffered more anthropogenic impact than DRE. The comparably higher concentration of NH₄⁺-N, NO₃^--N, DRP, Pb, and Cd in the SNB region was detected. The comparably higher nutrients in the SNB may have resulted in higher biomass and lower dissolved oxygen (DO) profile, which was further proved by Landsat thermal image data. The microbiome analysis showed that the DRE region was oligotrophic and SNB reflected an anaerobic environment in the sediments. Environmental factors rather than the spatial distance determined the similarity of bacterial community among different sites. Ecological associations between environmental, oceanographic, and bacterial characteristics were illustrated, which exhibited strong mutual associations. Our findings presented a feasibility that integrates empirical and remote sensing data to distinguish ecological features and evaluate ecosystem healthiness for the humpback dolphin habitats.

Anaerobic degradation of hexadecane and phenanthrene coupled to sulfate reduction by enriched consortia from northern Gulf of Mexico seafloor sediment

To advance understanding of the fate of hydrocarbons released from the Deepwater Horizon oil spill and deposited in marine sediments, this study characterized the microbial populations capable of anaerobic hydrocarbon degradation coupled with sulfate reduction in non-seep sediments of the northern Gulf of Mexico. Anaerobic, sediment-free enrichment cultures were obtained with either hexadecane or phenanthrene as sole carbon source and sulfate as a terminal electron acceptor. Phylogenetic analysis revealed that enriched microbial populations differed by hydrocarbon substrate, with abundant SSU rRNA gene amplicon sequences from hexadecane cultures showing high sequence identity (up to 98%) to Desulfatibacillum alkenivorans (family Desulfobacteraceae), while phenanthrene-enriched populations were most closely related to Desulfatiglans spp. (up to 95% sequence identity; family Desulfarculaceae). Assuming complete oxidation to CO2, observed stoichiometric ratios closely resembled the theoretical ratios of 12.25:1 for hexadecane and 8.25:1 for phenanthrene degradation coupled to sulfate reduction. Phenanthrene carboxylic acid was detected in the phenanthrene-degrading enrichment cultures, providing evidence to indicate carboxylation as an activation mechanism for phenanthrene degradation. Metagenome-assembled genomes (MAGs) revealed that phenanthrene degradation is likely mediated by novel genera or families of sulfate-reducing bacteria along with their fermentative syntrophic partners, and candidate genes linked to the degradation of aromatic hydrocarbons were detected for future study.

Enhancement of synchronous bio-reductions of vanadium (V) and chromium (VI) by mixed anaerobic culture

The co-occurrence of toxic vanadium (V) and chromium (VI) in groundwater receives incremental attention while knowledge on their interactions in biogeochemical processes is limited, with lack of efficient removal means. This study is the first to realize synchronous bio-reductions of V(V) and Cr(VI) with high efficiency by mixed anaerobic culture. After 72-h operation, 97.0 ± 1.0% of V(V) and 99.1 ± 0.7% of Cr(VI) were removed, respectively, with initial concentration of 1 mM for both V(V) and Cr(VI). Cr(VI) bio-reduction took priority while V(V) detoxification was inhibited. V(IV) and Cr(III) were the identified reduction products, both of which could precipitate naturally. Initial Cr(VI) and acetate concentrations as well as pH affected this process significantly. High-throughput 16S rRNA gene sequencing analysis indicated the accumulation of Anaerolineaceae, Spirochaeta and Spirochaetaceae, which could contribute to V(V) and Cr(VI) bio-reductions. The new knowledge obtained in this study will facilitate understanding the biogeochemical fate of co-existing V(V) and Cr(VI) in groundwater and development of bioremediation strategy for their induced combined pollution.

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.

Sulfate-Reducing Naphthalene Degraders Are Picky Eaters

Polycyclic aromatic hydrocarbons (PAHs) are common organic contaminants found in anoxic environments. The capacity for PAH biodegradation in unimpacted environments, however, has been understudied. Here we investigate the enrichment, selection, and sustainability of a microbial community from a pristine environment on naphthalene as the only amended carbon source. Pristine coastal sediments were obtained from the Jacques Cousteau National Estuarine Research Reserve in Tuckerton, New Jersey, an ecological reserve which has no direct input or source of hydrocarbons. After an initial exposure to naphthalene, primary anaerobic transfer cultures completely degraded 500 µM naphthalene within 139 days. Subsequent transfer cultures mineralized naphthalene within 21 days with stoichiometric sulfate loss. Enriched cultures efficiently utilized only naphthalene and 2-methylnaphthalene from the hydrocarbon mixtures in crude oil. To determine the microorganisms responsible for naphthalene degradation, stable isotope probing was utilized on cultures amended with fully labeled ¹³C-naphthalene as substrate. Three organisms were found to unambiguously synthesize ¹³C-DNA from ¹³C-naphthalene within 7 days. Phylogenetic analysis revealed that 16S rRNA genes from two of these organisms are closely related to the known naphthalene degrading isolates NaphS2 and NaphS3 from PAH-contaminated sites. A third 16S rRNA gene was only distantly related to its closest relative and may represent a novel naphthalene degrading microbe from this environment.

Fermentative Spirochaetes mediate necromass recycling in anoxic hydrocarbon-contaminated habitats

Spirochaetes are frequently detected in anoxic hydrocarbon- and organohalide-polluted groundwater, but their role in such ecosystems has remained unclear. To address this, we studied a sulfate-reducing, naphthalene-degrading enrichment culture, mainly comprising the sulfate reducer Desulfobacterium N47 and the rod-shaped Spirochete Rectinema cohabitans HM. Genome sequencing and proteome analysis suggested that the Spirochete is an obligate fermenter that catabolizes proteins and carbohydrates, resulting in acetate, ethanol, and molecular hydrogen (H₂) production. Physiological experiments inferred that hydrogen is an important link between the two bacteria in the enrichment culture, with H₂ derived from fermentation by R. cohabitans used as reductant for sulfate reduction by Desulfobacterium N47. Differential proteomics and physiological experiments showed that R. cohabitans utilizes biomass (proteins and carbohydrates) released from dead cells of Desulfobacterium N47. Further comparative and community genome analyses indicated that other Rectinema phylotypes are widespread in contaminated environments and may perform a hydrogenogenic fermentative lifestyle similar to R. cohabitans. Together, these findings indicate that environmental Spirochaetes scavenge detrital biomass and in turn drive necromass recycling at anoxic hydrocarbon-contaminated sites and potentially other habitats.

Typical Soil Redox Processes in Pentachlorophenol Polluted Soil Following Biochar Addition

Reductive dechlorination is the primary pathway for environmental removal of pentachlorophenol (PCP) in soil under anaerobic condition. This process has been verified to be coupled with other soil redox processes of typical biogenic elements such as carbon, iron and sulfur. Meanwhile, biochar has received increasing interest in its potential for remediation of contaminated soil, with the effect seldom investigated under anaerobic environment. In this study, a 120-day anaerobic incubation experiment was conducted to investigate the effects of biochar on soil redox processes and thereby the reductive dechlorination of PCP under anaerobic condition. Biochar addition (1%, w/w) enhanced the dissimilatory iron reduction and sulfate reduction while simultaneously decreased the PCP reduction significantly. Instead, the production of methane was not affected by biochar. Interestingly, however, PCP reduction was promoted by biochar when microbial sulfate reduction was suppressed by addition of typical inhibitor molybdate. Together with Illumina sequencing data regarding analysis of soil bacteria and archaea responses, our results suggest that under anaerobic condition, the main competition mechanisms of these typical soil redox processes on the reductive dechlorination of PCP may be different in the presence of biochar. In particularly, the effect of biochar on sulfate reduction process is mainly through promoting the growth of sulfate reducer (Desulfobulbaceae and Desulfobacteraceae) but not as an electron shuttle. With the supplementary addition of molybdate, biochar application is suggested as an improved strategy for a better remediation results by coordinating the interaction between dechlorination and its coupled soil redox processes, with minimum production of toxic sulfur reducing substances and relatively small emission of greenhouse gas (CH4) while maximum removal of PCP.

Anaerobic biodegradation of biofuels and their impact on the corrosion of a Cu-Ni alloy in marine environments

Fuel biodegradation linked to sulfate reduction can lead to corrosion of the metallic infrastructure in a variety of marine environments. However, the biological stability of emerging biofuels and their potential impact on copper-nickel alloys commonly used in marine systems has not been well documented. Two potential naval biofuels (Camelina-JP5 and Fisher-Tropsch-F76) and their petroleum-derived counterparts (JP5 and F76) were critically assessed in seawater/sediment incubations containing a metal coupon (70/30 Cu-Ni alloy). Relative to a fuel-unamended control (1.2 ± 0.4 μM/d), Camelina-JP5 (86.4 ± 1.6 μM/d) and JP5 (77.6 ± 8.3 μM/d) stimulated much higher rates of sulfate reduction than either FT-F76 (11.4 ± 2.7 μM/d) or F76 (38.4 ± 3.7 μM/d). The general corrosion rate (r² = 0.91) and pitting corrosion (r² = 0.92) correlated with sulfate loss in these incubations. Despite differences in microbial community structure on the metal or in the aqueous or sediment phases, sulfate reducing bacteria affiliated with Desulfarculaceae and Desulfobacteraceae became predominant upon fuel amendment. The identification of alkylsuccinates and alkylbenzylsuccinates attested to anaerobic metabolism of fuel hydrocarbons. Sequences related to Desulfobulbaceae were highly enriched (34.2-64.8%) on the Cu-Ni metal surface, regardless of whether the incubation received a fuel amendment. These results demonstrate that the anaerobic metabolism of biofuel linked to sulfate reduction can exacerbate the corrosion of Cu-Ni alloys. Given the relative lability of Camelina-JP5, particular precaution should be taken when incorporating this hydroprocessed biofuel into marine environments serviced by a Cu-Ni metallic infrastructure.

Microbial reduction of vanadium (V) in groundwater: Interactions with coexisting common electron acceptors and analysis of microbial community

Vanadium (V) pollution in groundwater has posed serious risks to the environment and public health. Anaerobic microbial reduction can achieve efficient and cost-effective remediation of V(V) pollution, but its interactions with coexisting common electron acceptors such as NO₃^-, Fe³⁺, SO₄^2- and CO₂ in groundwater remain unknown. In this study, the interactions between V(V) reduction and reduction of common electron acceptors were examined with revealing relevant microbial community and identifying dominant species. The results showed that the presence of NO₃^- slowed down the removal of V(V) in the early stage of the reaction but eventually led to a similar reduction efficiency (90.0% ± 0.4% in 72-h operation) to that in the reactor without NO₃^-. The addition of Fe³⁺, SO₄^2-, or CO₂ decreased the efficiency of V(V) reduction. Furthermore, the microbial reduction of these coexisting electron acceptors was also adversely affected by the presence of V(V). The addition of V(V) as well as the extra dose of Fe³⁺, SO₄^2- and CO₂ decreased microbial diversity and evenness, whereas the reactor supplied with NO₃^- showed the increased diversity. High-throughput 16S rRNA gene pyrosequencing analysis indicated the accumulation of Geobacter, Longilinea, Syntrophobacter, Spirochaeta and Anaerolinea, which might be responsible for the reduction of multiple electron acceptors. The findings of this study have demonstrated the feasibility of anaerobic bioremediation of V(V) and the possible influence of coexisting electron acceptors commonly found in groundwater.

Anaerobic degradation of 1-methylnaphthalene by a member of the Thermoanaerobacteraceae contained in an iron-reducing enrichment culture

An anaerobic culture (1MN) was enriched with 1-methylnaphthalene as sole source of carbon and electrons and Fe(OH)₃ as electron acceptor. 1-Naphthoic acid was produced as a metabolite during growth with 1-methylnaphthalene while 2-naphthoic acid was detected with naphthalene and 2-methylnaphthalene. This indicates that the degradation pathway of 1-methylnaphthalene might differ from naphthalene and 2-methylnaphthalene degradation in sulfate reducers. Terminal restriction fragment length polymorphism and pyrosequencing revealed that the culture is mainly composed of two bacteria related to uncultured Gram-positive Thermoanaerobacteraceae and uncultured gram-negative Desulfobulbaceae. Stable isotope probing showed that a ¹³C-carbon label from ¹³C₁₀-naphthalene as growth substrate was mostly incorporated by the Thermoanaerobacteraceae. The presence of putative genes involved in naphthalene degradation in the genome of this organism was confirmed via assembly-based metagenomics and supports that it is the naphthalene-degrading bacterium in the culture. Thermoanaerobacteraceae have previously been detected in oil sludge under thermophilic conditions, but have not been shown to degrade hydrocarbons so far. The second member of the community belongs to the Desulfobulbaceae and has high sequence similarity to uncultured bacteria from contaminated sites including recently proposed groundwater cable bacteria. We suggest that the gram-positive Thermoanaerobacteraceae degrade polycyclic aromatic hydrocarbons while the Desulfobacterales are mainly responsible for Fe(III) reduction.

Characterization of the chemicals used in hydraulic fracturing fluids for wells located in the Marcellus Shale Play

Hydraulic fracturing, coupled with the advances in horizontal drilling, has been used for recovering oil and natural gas from shale formations and has aided in increasing the production of these energy resources. The large volumes of hydraulic fracturing fluids used in this technology contain chemical additives, which may be toxic organics or produce toxic degradation byproducts. This paper investigated the chemicals introduced into the hydraulic fracturing fluids for completed wells located in Pennsylvania and West Virginia from data provided by the well operators. The results showed a total of 5071 wells, with average water volumes of 5,383,743 ± 2,789,077 gal (mean ± standard deviation). A total of 517 chemicals was introduced into the formulated hydraulic fracturing fluids. Of the 517 chemicals listed by the operators, 96 were inorganic compounds, 358 chemicals were organic species, and the remaining 63 cannot be identified. Many toxic organics were used in the hydraulic fracturing fluids. Some of them are carcinogenic, including formaldehyde, naphthalene, and acrylamide. The degradation of alkylphenol ethoxylates would produce more toxic, persistent, and estrogenic intermediates. Acrylamide monomer as a primary degradation intermediate of polyacrylamides is carcinogenic. Most of the chemicals appearing in the hydraulic fracturing fluids can be removed when adopting the appropriate treatments.

Benzene degradation in a denitrifying biofilm reactor: activity and microbial community composition

Benzene is an aromatic compound and harmful for the environment. Biodegradation of benzene can reduce the toxicological risk after accidental or controlled release of this chemical in the environment. In this study, we further characterized an anaerobic continuous biofilm culture grown for more than 14 years on benzene with nitrate as electron acceptor. We determined steady state degradation rates, microbial community composition dynamics in the biofilm, and the initial anaerobic benzene degradation reactions. Benzene was degraded at a rate of 0.15 μmol/mg protein/day and a first-order rate constant of 3.04/day which was fourfold higher than rates reported previously. Bacteria belonging to the Peptococcaceae were found to play an important role in this anaerobic benzene-degrading biofilm culture, but also members of the Anaerolineaceae were predicted to be involved in benzene degradation or benzene metabolite degradation based on Illumina MiSeq analysis of 16S ribosomal RNA genes. Biomass retention in the reactor using a filtration finger resulted in reduction of benzene degradation capacity. Detection of the benzene carboxylase encoding gene, abcA, and benzoic acid in the culture vessel indicated that benzene degradation proceeds through an initial carboxylation step.

Exploited application of sulfate-reducing bacteria for concomitant treatment of metallic and non-metallic wastes: a mini review

A variety of multidimensional anthropogenic activities, especially of industrial level, are contaminating our aquatic and terrestrial environments with a variety of metallic and non-metallic pollutants. The metallic and non-metallic pollutants addressed specifically in this review are heavy metals and various compound forms of sulfates, respectively. Direct and indirect deleterious effects of the both types of pollutants to all forms of life are well-known. The treatment of such pollutants is therefore much necessary before their final discharge into the environment. This review summarizes the productive utility of sulfate-reducing bacteria (SRB) for economical and concomitant treatment of the above mentioned wastes. Utilization of agro-industrial wastes and some environmental contaminants including hydrocarbons, as economical growth substrates for SRB, is also suggested and proved efficient in this review. Mechanistically, SRB will utilize sulfates as their terminal electron acceptors during respiration while utilizing agro-industrial and/or hydrocarbon wastes as electron donors/carbon sources and generate H₂S. The biogenic H₂S will then react vigorously with dissolved metals present in the wastewaters thus forming metal sulfide. The metal sulfide being water insoluble and heavier than water will settle down in the water as precipitates. In this way, three types of pollutants i.e., metals, sulfates and agro-industrial and/or hydrocarbon wastes will be treated simultaneously.

Polycyclic Aromatic Hydrocarbon-Induced Changes in Bacterial Community Structure under Anoxic Nitrate Reducing Conditions

Although bacterial anaerobic degradation of mono-aromatic compounds has been characterized in depth, the degradation of polycyclic aromatic hydrocarbons (PAHs) such as naphthalene has only started to be understood in sulfate reducing bacteria, and little is known about the anaerobic degradation of PAHs in nitrate reducing bacteria. Starting from a series of environments which had suffered different degrees of hydrocarbon pollution, we used most probable number (MPN) enumeration to detect and quantify the presence of bacterial communities able to degrade several PAHs using nitrate as electron acceptor. We detected the presence of a substantial nitrate reducing community able to degrade naphthalene, 2-methylnaphthalene (2MN), and anthracene in some of the sites. With the aim of isolating strains able to degrade PAHs under denitrifying conditions, we set up a series of enrichment cultures with nitrate as terminal electron acceptor and PAHs as the only carbon source and followed the changes in the bacterial communities throughout the process. Results evidenced changes attributable to the imposed nitrate respiration regime, which in several samples were exacerbated in the presence of the PAHs. The presence of naphthalene or 2MN enriched the community in groups of uncultured and poorly characterized organisms, and notably in the Acidobacteria uncultured group iii1-8, which in some cases was only a minor component of the initial samples. Other phylotypes selected by PAHs in these conditions included Bacilli, which were enriched in naphthalene enrichments. Several nitrate reducing strains showing the capacity to grow on PAHs could be isolated on solid media, although the phenotype could not be reproduced in liquid cultures. Analysis of known PAH anaerobic degradation genes in the original samples and enrichment cultures did not reveal the presence of PAH-related nmsA-like sequences but confirmed the presence of bssA-like genes related to anaerobic toluene degradation. Altogether, our results suggest that PAH degradation by nitrate reducing bacteria may require the contribution of different strains, under culture conditions that still need to be defined.

Application of stable isotope tools for evaluating natural and stimulated biodegradation of organic pollutants in field studies

Stable isotope tools are increasingly applied for in-depth evaluation of biodegradation of organic pollutants at contaminated field sites. They can be divided into three methods i) determination of changes in natural abundance of stable isotopes using compound-specific stable isotope analysis (CSIA), ii) detection of incorporation of stable-isotope label from a stable-isotope labelled target compound into degradation and/or mineralisation products and iii) determination of stable-isotope label incorporation into biomarkers using stable isotope probing (SIP). Stable isotope tools have been applied as key monitoring tools for multiple-line-of-evidence-approaches (MLEA) for sensitive evaluation of pollutant biodegradation. This review highlights the application of CSIA, SIP and MLEA including stable isotope tools for assessing natural and stimulated biodegradation of organic pollutants in field studies dealing with soil and groundwater contaminations.

Hydrogen Isotope Fractionation As a Tool to Identify Aerobic and Anaerobic PAH Biodegradation

Aerobic and anaerobic polycyclic aromatic hydrocarbon (PAH) biodegradation was characterized by compound specific stable isotope analysis (CSIA) of the carbon and hydrogen isotope effects of the enzymatic reactions initiating specific degradation pathways, using naphthalene and 2-methylnaphtalene as model compounds. Aerobic activation of naphthalene and 2-methylnaphthalene by Pseudomonas putida NCIB 9816 and Pseudomonas fluorescens ATCC 17483 containing naphthalene dioxygenases was associated with moderate carbon isotope fractionation (εC = -0.8 ± 0.1‰ to -1.6 ± 0.2‰). In contrast, anaerobic activation of naphthalene by a carboxylation-like mechanism by strain NaphS6 was linked to negligible carbon isotope fractionation (εC = -0.2 ± 0.2‰ to -0.4 ± 0.3‰). Notably, anaerobic activation of naphthalene by strain NaphS6 exhibited a normal hydrogen isotope fractionation (εH = -11 ± 2‰ to -47 ± 4‰), whereas an inverse hydrogen isotope fractionation was observed for the aerobic strains (εH = +15 ± 2‰ to +71 ± 6‰). Additionally, isotope fractionation of NaphS6 was determined in an overlaying hydrophobic carrier phase, resulting in more reliable enrichment factors compared to immobilizing the PAHs on the bottle walls without carrier phase. The observed differences especially in hydrogen fractionation might be used to differentiate between aerobic and anaerobic naphthalene and 2-methylnaphthalene biodegradation pathways at PAH-contaminated field sites.

Anaerobic Degradation of Benzene and Polycyclic Aromatic Hydrocarbons

Aromatic hydrocarbons such as benzene and polycyclic aromatic hydrocarbons (PAHs) are very slowly degraded without molecular oxygen. Here, we review the recent advances in the elucidation of the first known degradation pathways of these environmental hazards. Anaerobic degradation of benzene and PAHs has been successfully documented in the environment by metabolite analysis, compound-specific isotope analysis and microcosm studies. Subsequently, also enrichments and pure cultures were obtained that anaerobically degrade benzene, naphthalene or methylnaphthalene, and even phenanthrene, the largest PAH currently known to be degradable under anoxic conditions. Although such cultures grow very slowly, with doubling times of around 2 weeks, and produce only very little biomass in batch cultures, successful proteogenomic, transcriptomic and biochemical studies revealed novel degradation pathways with exciting biochemical reactions such as for example the carboxylation of naphthalene or the ATP-independent reduction of naphthoyl-coenzyme A. The elucidation of the first anaerobic degradation pathways of naphthalene and methylnaphthalene at the genetic and biochemical level now opens the door to studying the anaerobic metabolism and ecology of anaerobic PAH degraders. This will contribute to assessing the fate of one of the most important contaminant classes in anoxic sediments and aquifers.

Stable Isotope Probing Approaches to Study Anaerobic Hydrocarbon Degradation and Degraders

Stable isotope probing (SIP) techniques have become state-of-the-art in microbial ecology over the last 10 years, allowing for the targeted detection and identification of organisms, metabolic pathways and elemental fluxes active in specific processes within complex microbial communities. For studying anaerobic hydrocarbon-degrading microbial communities, four stable isotope techniques have been used so far: DNA/RNA-SIP, PLFA (phospholipid-derived fatty acids)-SIP, protein-SIP, and single-cell-SIP by nanoSIMS (nanoscale secondary ion mass spectrometry) or confocal Raman microscopy. DNA/RNA-SIP techniques are most frequently applied due to their most meaningful phylogenetic resolution. Especially using ¹³C-labeled benzene and toluene as model substrates, many new hydrocarbon degraders have been identified by SIP under various electron acceptor conditions. This has extended the current perspective of the true diversity of anaerobic hydrocarbon degraders relevant in the environment. Syntrophic hydrocarbon degradation was found to be a common mechanism for various electron acceptors. Fundamental concepts and recent advances in SIP are reflected here. A discussion is presented concerning how these techniques generate direct insights into intrinsic hydrocarbon degrader populations in environmental systems and how useful they are for more integrated approaches in the monitoring of contaminated sites and for bioremediation.

Responses of Aromatic-Degrading Microbial Communities to Elevated Nitrate in Sediments

A high number of aromatic compounds that have been released into aquatic ecosystems have accumulated in sediment because of their low solubility and high hydrophobicity, causing significant hazards to the environment and human health. Since nitrate is an essential nitrogen component and a more thermodynamically favorable electron acceptor for anaerobic respiration, nitrate-based bioremediation has been applied to aromatic-contaminated sediments. However, few studies have focused on the response of aromatic-degrading microbial communities to nitrate addition in anaerobic sediments. Here we hypothesized that high nitrate inputs would stimulate aromatic-degrading microbial communities and their associated degrading processes, thus increasing the bioremediation efficiency in aromatic compound-contaminated sediments. We analyzed the changes of key aromatic-degrading genes in the sediment samples from a field-scale site for in situ bioremediation of an aromatic-contaminated creek in the Pearl River Delta before and after nitrate injection using a functional gene array. Our results showed that the genes involved in the degradation of several kinds of aromatic compounds were significantly enriched after nitrate injection, especially those encoding enzymes for central catabolic pathways of aromatic compound degradation, and most of the enriched genes were derived from nitrate-reducing microorganisms, possibly accelerating bioremediation of aromatic-contaminated sediments. The sediment nitrate concentration was found to be the predominant factor shaping the aromatic-degrading microbial communities. This study provides new insights into our understanding of the influences of nitrate addition on aromatic-degrading microbial communities in sediments.