A Chloroflexi bacterium dechlorinates polychlorinated biphenyls in marine sediments under in situ-like biogeochemical conditions

The biotechnological potential of the Chloroflexota phylum

In the next decades, the increasing material and energetic demand to support population growth and higher standards of living will amplify the current pressures on ecosystems and will call for greater investments in infrastructures and modern technologies. A valid approach to overcome such future challenges is the employment of sustainable bio-based technologies that explore the metabolic richness of microorganisms. Collectively, the metabolic capabilities of Chloroflexota, spanning aerobic and anaerobic conditions, thermophilic adaptability, anoxygenic photosynthesis, and utilization of toxic compounds as electron acceptors, underscore the phylum's resilience and ecological significance. These diverse metabolic strategies, driven by the interplay between temperature, oxygen availability, and energy metabolism, exemplify the complex adaptations that enabled Chloroflexota to colonize a wide range of ecological niches. In demonstrating the metabolic richness of the Chloroflexota phylum, specific members exemplify the diverse capabilities of these microorganisms: Chloroflexus aurantiacus showcases adaptability through its thermophilic and phototrophic growth, whereas members of the Anaerolineae class are known for their role in the degradation of complex organic compounds, contributing significantly to the carbon cycle in anaerobic environments, highlighting the phylum's potential for biotechnological exploitation in varying environmental conditions. In this context, the metabolic diversity of Chloroflexota must be considered a promising asset for a large range of applications. Currently, this bacterial phylum is organized into eight classes possessing different metabolic strategies to survive and thrive in a wide variety of extreme environments. This review correlates the ecological role of Chloroflexota in such environments with the potential application of their metabolisms in biotechnological approaches.

Chemical-physical parameters and microbial community changes induced by electrodes polarization inhibit PCB dechlorination in a marine sediment

Microbial reductive dechlorination of organohalogenated pollutants is often limited by the scarcity of electron donors, that can be overcome with microbial electrochemical technologies (METs). In this study, polarized electrodes buried in marine sediment microcosms were investigated to stimulate PCB reductive dechlorination under potentiostatic (-0.7 V vs Ag/AgCl) and galvanostatic conditions (0.025 mA·cm-2-0.05 mA·cm-2), using graphite rod as cathode and iron plate as sacrificial anode. A single circuit and a novel two antiparallel circuits configuration (2AP) were investigated. Single circuit polarization impacted the sediment pH and redox potential (ORP) proportionally to the intensity of the electrical input and inhibited PCB reductive dechlorination. The effects on the sediment's pH and ORP, along with the inhibition of PCB reductive dechlorination, were mitigated in the 2AP system. Electrodes polarization stimulated sulfate-reduction and promoted the enrichment of bacterial clades potentially involved in sulfate-reduction as well as in sulfur oxidation. This suggested the electrons provided were consumed by competitors of organohalide respiring bacteria and specifically sequestered by sulfur cycling, which may represent the main factor limiting the applicability of METs for stimulating PCB reductive dechlorination in marine sediments.

Efficient biostimulation of microbial dechlorination of polychlorinated biphenyls by acetate and lactate under nitrate reducing conditions: Insights into dechlorination pathways and functional genes

Microbial-catalyzed reductive dechlorination of polychlorinated biphenyls (PCBs) is largely affected by the indigenous sediment geochemical properties. In this study, the effects of nitrate on PCB dechlorination and microbial community structures were first investigated in Taihu Lake sediment microcosms. And biostimulation study was attempted supplementing acetate/lactate. PCB dechlorination was apparently inhibited under nitrate-reducing conditions. Lower PCB dechlorination rate and less PCB dechlorination extent were observed in nitrate amended sediment microcosms (T-N) than those in non-nitrate amended microcosms (T-1) during 66 weeks of incubation. The total PCB mass reduction in T-N was 17.6% lower than that in T-1. The flanked-para dechlorination was completely inhibited, while the ortho-flanked meta dechlorination was only partially inhibited in T-N. The 7.5 mM of acetate/lactate supplementation recovered PCB dechlorination by resuming ortho-flanked meta dechlorination. Repeated additions of lactate showed more effective biostimulation than acetate. Phylum Chloroflexi, containing most known PCB dechlorinators, was found to play a vital role on stability of the network structures. In T-N, putative dechlorinating Chloroflexi, Dehalococcoides and RDase genes rdh12, pcbA4, pcbA5 all declined. With acetate/lactate supplementation, Dehalococcoides grew by 1-2 orders of magnitude and rdh12, pcbA4, pcbA5 increased by 1-3 orders of magnitude. At Week 66, parent PCBs declined by 86.4% and 80.9% respectively in T-N-LA and T-N-AC compared to 69.9% in T-N. These findings provide insights into acetate/lactate biostimulation as a cost-effective approach for treating PCB contaminated sediments undergoing nitrate inhibition.

Sources of polychlorinated biphenyls (PCBs) in sediments of the East China marginal seas: Role of unintentionally-produced PCBs

The production and use of intentionally-produced polychlorinated biphenyls (PCBs) in China have a short history compared with countries of North America and Europe, where technical PCB mixtures were manufactured in large amounts for decades before being banned. Unintentionally-produced PCB emissions increased dramatically in China, leading to unique profiles of PCB burdens. This study first time evaluated 208 individual PCB congeners at 94 sites from surface sediments of the East China Marginal Seas (ECMSs) and explored their sources. Non-technical PCBs transported from atmospheric transport and river discharge played a dominant role in most areas of the ECMSs, while historical residuals of technical PCBs occupied the fine-grained sediments in muddy areas of the central Yellow Sea (YS), regarding to the low sedimentation rate in the central YS. Furthermore, emissions from Taizhou located on the coast of the East China Sea (ECS), which is an important electronic waste dismantling site in East China, contributed additional technical PCBs to the inner shelf of the ECS. Our results indicate that non-technical PCBs have become the dominant PCB species in the ECMSs, and emphasize the synergistic effects of large riverine input, long-range atmospheric transport, and muddy shelf deposition on PCB source and sink of in marginal seas.

Enrichment of Aerobic and Anaerobic Hydrocarbon-Degrading Bacteria from Multicontaminated Marine Sediment in Mar Piccolo Site (Taranto, Italy)

Marine sediments act as a sink for the accumulation of various organic contaminants such as polychlorobiphenyls (PCBs). These contaminants affect the composition and activity of microbial communities, particularly favoring those capable of thriving from their biodegradation and biotransformation under favorable conditions. Hence, contaminated environments represent a valuable biological resource for the exploration and cultivation of microorganisms with bioremediation potential. In this study, we successfully cultivated microbial consortia with the capacity for PCB removal under both aerobic and anaerobic conditions. The source of these consortia was a multicontaminated marine sediment collected from the Mar Piccolo (Taranto, Italy), one of Europe's most heavily polluted sites. High-throughput sequencing was employed to investigate the dynamics of the bacterial community of the marine sediment sample, revealing distinct and divergent selection patterns depending on the imposed reductive or oxidative conditions. The aerobic incubation resulted in the rapid selection of bacteria specialized in oxidative pathways for hydrocarbon transformation, leading to the isolation of Marinobacter salinus and Rhodococcus cerastii species, also known for their involvement in aerobic polycyclic aromatic hydrocarbons (PAHs) transformation. On the other hand, anaerobic incubation facilitated the selection of dechlorinating species, including Dehalococcoides mccartyi, involved in PCB reduction. This study significantly contributes to our understanding of the diversity, dynamics, and adaptation of the bacterial community in the hydrocarbon-contaminated marine sediment from one sampling point of the Mar Piccolo basin, particularly in response to stressful conditions. Furthermore, the establishment of consortia with biodegradation and biotransformation capabilities represents a substantial advancement in addressing the challenge of restoring polluted sites, including marine sediments, thus contributing to expanding the toolkit for effective bioremediation strategies.

Site-specific response of sediment microbial community to supplementation of polyhydroxyalkanoates as biostimulants for PCB reductive dechlorination

The use of biodegradable plastics is constantly raising, increasing the likeliness for these polymers to end up in the environment. Environmental applications foreseeing the intentional release of biodegradable plastics have been also recently proposed, e.g., for polyhydroxyalkanoates (PHAs) acting as slow hydrogen releasing compounds to stimulate microbial reductive dehalogenation processes. However, the effects of their release into the environment on the ecosystems still need to be thoroughly explored. In this work, the use of PHAs to enhance the microbial reductive dechlorination of polychlorobiphenyls (PCBs) and their impact on the metabolic and compositional features of the resident microbial community have been investigated in laboratory microcosms of a polluted marine sediment from Mar Piccolo (Taranto, Italy), and compared with recent findings on a different contaminated marine sediment from Pialassa della Baiona (Ravenna, Italy). A decreased biostimulation efficiency of PHAs on PCBs reductive dechlorination was observed in the sediment from Mar Piccolo, with respect to the sediment from Pialassa della Baiona, suggesting that the sediments' physical-chemical characteristics and/or the biodiversity and composition of its microbial community might play a key role in determining the outcome of this biostimulation strategy. Regardless of the sediment origin, PHAs were found to have a specific and pervasive effect on the sediment microbial community, reducing its biodiversity, defining a newly arranged microbial core of primary degraders and consequently affecting, in a site-specific way, the abundance of subdominant bacteria, possibly cross-feeders. Such potential to dramatically change the structure of autochthonous microbial communities should be carefully considered, since it might have secondary effects, e.g., on the natural biogeochemical cycles.

Short-chain fatty acids facilitated long-term dechlorination of PCBs in Taihu Lake sediment microcosms: Evidence from PCB congener and microbial community analyses

Microbial reductive dechlorination hosts great promise as an in situ bioremediation strategy for polychlorinated biphenyls (PCBs) contamination. However, the slow dechlorination in sediments limits natural attenuation. Short-chain fatty acids, as preferred carbon sources and electron donors for dechlorinating microorganisms, might stimulate PCB dechlorination. Herein, two sets of short-chain fatty acids, sole acetate and a fatty acid mixture (acetate, propionate, and butyrate), were amended periodically into Taihu Lake (China) sediment microcosms containing nine PCB congeners (PCB5, 12, 64, 71, 105, 114, 149, 153, and 170) after 24 weeks of incubation. Short-chain fatty acids facilitated the long-term PCB dechlorination and the promoting effect of the fatty acid mixture compared favorably with that of sole acetate. By the end of 108 weeks, the total PCB mass concentrations in acetate amended and fatty acid mixture amended microcosms significantly declined by 7.6% and 10.3% compared with non-amended microcosms (P < 0.05), respectively. Short-chain fatty acids selectively favored the removal of flanked meta and single-flanked para chlorines. Notably, a rare ortho dechlorination pathway, PCB25 (24-3-CB) to PCB13 (3-4-CB), was enhanced. Supplementary fatty acids significantly increased reductive dehalogenases (RDase) gene pcbA5 instead of improving the growth of Dehalococcoides. These findings highlight the merits of low cost short-chain fatty acids on in situ biostimulation in treating PCBs contamination.

Occurrence and Distribution of Tetrabromobisphenol A and Diversity of Microbial Community Structure in the Sediments of Mangrove

The occurrence and distribution characteristics of tetrabromobisphenol A (TBBPA) and its relationship with microbial community diversity in different mangrove sediments need further investigation. The results of this study indicated levels of TBBPA in mangrove sediments from the Zhangjiang Estuary (ZJ), Jiulongjiang Estuary (JLJ), and Quanzhou Bay (QZ) in Southeast China ranging from 1.80 to 20.46, 3.47 to 40.77, and 2.37 to 19.83 ng/g dry weight (dw), respectively. Mangrove sediments from JLJ contained higher levels of TBBPA, possibly due to agricultural pollution. A correlation analysis revealed a significant correlation between total organic carbon (TOC), total nitrogen (TN), and TBBPA distribution in ZJ and JLJ mangrove sediments, but not in QZ mangrove sediments. TOC significantly affected the distribution of TBBPA in mangrove sediments, but pH had no effect. High-throughput 16S rRNA gene sequencing showed that Pseudomonadota dominated the sediment bacteria followed by Chloroflexota, Actinobacteota, Bacillota, Acidobacteriota, Bacteroidota, and Aminicenantes in mangrove sediments. Although the microbial community structure of the ZJ, JLJ, and QZ mangrove sediments was similar, the taxonomic profile of their sensitive responders differed markedly. The genus Anaerolinea was dominant in the mangrove sediments and was responsible for the in situ dissipation of TBBPA. Based on redundancy analysis, there was a correlation between TBBPA, TOC, TN, C/N, pH, and microbial community structure at the genus level. Combining TBBPA, TN, and TOC may induce variations in the microbial community of mangrove sediments.

Anoxic/oxic treatment without biomass recycle

The Anoxic/Oxic (A/O) process involves recirculating mixed liquor between its A and O tanks so that nitrate produced in the O tank can be used to for denitrification with influent COD in the A tank. Because biomass is recirculated along with nitrate, A/O operation leads to similar microbial communities in the A and O tanks, which may decrease the rates of denitrification and nitrification in each tank. Here, bench-scale experiments simulated this aspect of the A/O process by exchanging biomass between an anoxic flask and an oxic cylinder at exchange ratios of 0%, 20%, 30%, and 50%. Nitrification and denitrification rates were only 40% and 19% for 50% biomass exchange of that for no biomass exchange. Phylogenetic analysis documented that the microbial communities became much more similar with biomass exchange, and the finding was consistent with community composition in a full-scale A/O process in a municipal wastewater treatment plant. A two-stage vertical baffled bioreactor (VBBR) realized efficient total‑nitrogen removal in recirculation without biomass exchange. Average removals of COD and TN were respectively 6% and 22% higher for the two-stage VBBR than the conventional A/O process, but its hydraulic retention time (HRT) was 55% to 70% of the volume of a conventional A/O process treating the same influent wastewater. The VBBR was more efficient because its anoxic biofilm was enriched in denitrifying bacteria, while its oxic biofilm was enriched in nitrifying bacteria. For example, the phylum Chloroflexi was greater in the An-VBBR, while the phylum Proteobacteria was greater in the Ox-VBBR.

Anaerobic digestion of wood vinegar wastewater using domesticated sludge: Focusing on the relationship between organic degradation and microbial communities (archaea, bacteria, and fungi)

Thermochemical process of biomass is one of the promising renewable energy technologies; however, the by-product (wood vinegar wastewater) is rich in refractory organics, which is harmful to the environment and inhibits the conversion efficiency of microorganisms. Consequently, the dominant functional microbial communities corresponding to the various substrate were obtained through the continuous domestication, and the relationship between the dominant functional communities and the degradation of organic compounds was comprehensively analyzed. The bacterial community was absolutely dominant (approximately 85%), while archaea and fungi had similar relative abundance. The diversity showed that glucose was not conducive to the development of microbial diversity, while the substrate containing wood vinegar wastewater showed the opposite trend. The functional analysis revealed that the enrichment of bacteria associated with the hydrolysis and acidification of organics increased in the domestication process. Glucose facilitated hydrogen-trophic methanogenesis as the main methanogenic pathway in the methanogenic stage.

Applications of Sponge Iron and Effects of Organic Carbon Source on Sulfate-Reducing Ammonium Oxidation Process

The typical characteristics of wastewater produced from seafood, chemical, textile, and paper industries are that it contains ammonia, sulfate, and a certain amount of chemical oxygen demand (COD). The sulfate-reducing ammonium oxidation process is a biochemical reaction that allows both ammonia and sulfate removal, but its low growth rate and harsh reaction conditions limit its practical application. Due to the adsorption properties of the iron sponge and its robust structure, it provides a suitable living environment for microorganisms. To reduce the negative impact on the environment, we employed 4.8 kg of sponge iron in a 2.0 dm3 anaerobic sequencing batch reactor (ASBR). We investigated the effects of the type and concentration of carbon sources on the performance of the sulfate-reducing ammonium oxidation (SRAO) process. The results demonstrated that during a start-up period of 90 days, the average ammonium removal efficiency and the sulfate conversion efficiency of the reactor containing the sponge iron were 4.42% and 8.37% higher than those of the reactor without the sponge iron. The addition of the sponge iron shortens the start-up time of this greenhouse gas-free denitrification process and reduces future costs in practical applications. The removal of total nitrogen (TN) significantly increased after adding organic carbon sources and then declined sharply, while the most considerable reduction of ammonium removal efficiency from 98.4% to 30.5% was observed with adding phenol. The performance of the group employing glucose as the carbon source was recovered on the 28th day, with the average ammonium removal efficiency increasing from 49.03% to 83.5%. The results of this simulation study will help the rapid start-up of SRAO in the water treatment industry and can precisely guide the application of the SRAO process for wastewater containing different organic carbon sources.

Long-Term Dechlorination of Polychlorinated Biphenyls (PCBs) in Taihu Lake Sediment Microcosms: Identification of New Pathways, PCB-Driven Shifts of Microbial Communities, and Insights into Dechlorination Potential

Microbial reductive dechlorination of polychlorinated biphenyls (PCBs) is regarded as an alternative approach for in situ remediation and detoxification in the environment. To better understand the process of PCB dechlorination in freshwater lake sediment, a long-term (108 weeks) dechlorination study was performed in Taihu Lake sediment microcosms with nine parent PCB congeners (PCB5, 12, 64, 71, 105, 114, 149, 153, and 170). Within 108 weeks, the total PCBs declined by 32.8%, while parent PCBs declined by 84.8%. PCB dechlorinators preferred to attack meta- and para-chlorines, principally para-flanked meta and single-flanked para chlorines. A total of 58 dechlorination pathways were observed, and 20 of them were not in 8 processes, suggesting the broad spectrum of PCB dechlorination in the environment. Rare ortho dechlorination was confirmed to target the unflanked ortho chlorine, indicating a potential for complete dechlorination. PCBs drove the shifts of the microbial community structures, and putative dechlorinating bacteria were growth-linked to PCB dechlorination. The distinct jump of RDase genes ardA, rdh12, pcbA4, and pcbA5 was found to be consistent with the commencement of dechlorination. The maintained high level of putative dechlorinating phylum Chloroflexi (including Dehalococcoides and o-17/DF-1), genus Dehalococcoides, and four RDase genes at the end of incubation revealed the long-term dechlorination potential. This work provided insights into dechlorination potential for long-term remediation strategies at PCB-contaminated sites.

Distribution characteristics and environmental fate of PCBs in marine sediments at different latitudinal regions: Insights from congener profiles

Sediments were sampled from Hangzhou Bay (HB), the South China Sea (SCS), and Antarctica (AZ) to better understand the distribution characteristics and environmental fate of polychlorinated biphenyls (PCBs) at different latitudes. Numerous PCB congeners (68) were detected among the sampling sites, supporting the ubiquity of PCB congeners. High and low chlorinated congeners dominated the PCB profiles of AZ and SCS, respectively, whereas the PCB homologues were evenly distributed in the HB. As a fraction of low chlorinated PCBs originates from an exogenous input, the low mean ratios of ∑Tetra-CBs to ∑PCBs and ∑Tetra-CBs to the sum of ∑Tri- and ∑Di-CBs suggest that microbial transformation of PCBs is weak in marine surface sediments, if any occurs at all. Furthermore, PCB contamination levels in marine sediments may be primarily influenced by latitude rather than pollution sources. Thus, the findings of this study suggest that Antarctica is becoming a prospective hotspot for PCBs.

Combined heterotrophic and autotrophic system for advanced denitrification of municipal secondary effluent in full-scale plant and bacterial community analysis

Total nitrogen (TN) removal is the major technical challenge for wastewater treatment plants to meet the more stringent discharge standard. In this study, lab- (0.05 m³/d), pilot- (1000 m³/d) and full-scale (10,000 m³/d) combined heterotrophic and autotrophic denitrification reactors (HARs) were designed and operated to treat municipal secondary effluent. During the 110-day stable operation, the effluent TN was reduced below 2.5 mg/L without secondary pollution causing by the excessive addition of organics, close to Class IV of Environmental Quality Standards for Surface Water. The bacterial richness and diversity increased with the expansion of reactor scale. Denitrifying bacteria (DB) dominated in all reactors, however, Thiomonas (12.42%), Methylotenera (6.35%), Thiobacillus (20.62%), Methyloverstatilis (5.44%) and Thauera (8.21%) were the main genera in lab-, pilot- and full-scale reactors respectively. The denitrification efficiency temporarily deteriorated at the later stage, and redundancy analysis (RDA) indicated the obviously increased sulfate reducing bacteria (SRB) and sulfide were main contributors. Sludge supplement rapidly recovered the reactors performance in five days. This study suggests that HARs could be a promising technique for advanced denitrification of the municipal secondary effluent.

Inhibition and removal of trichloroacetaldehyde by biological acidification with glucose co-metabolism

Biological acidification plays a crucial role in biological removal of organic compounds during petrochemical wastewater treatment. Trichloroacetaldehyde is a typical organic pollutant in petrochemical wastewater, however, no studies have been conducted on its effect on biological acidification. In this study, batch bioassays of volatile fatty acids were conducted to explore the inhibitory effect of trichloroacetaldehyde on biological acidification, the variations of key enzymes and extracellular polymeric substances under trichloroacetaldehyde shock, and the mechanism of trichloroacetaldehyde removal. The results of these bioassays indicated that trichloroacetaldehyde inhibited the acid yield at higher concentrations (EC₅₀ 112.20 mg/L), and butyric fermentation was predominant. Moreover, the contents of extracellular polymeric substances and several key acidifying enzymes greatly decreased when the trichloroacetaldehyde concentration exceeded 100 mg/L, which was due to the toxicity that trichloroacetaldehyde poses to the microbes involved in biological acidification. The trichloroacetaldehyde mechanism was as follows: first, trichloroacetaldehyde was adsorbed by extracellular polymeric substances and anaerobic granular sludge, and then transformed into trichloroethanol, trichloroethane, dichloroacetaldehyde, and dichloroethanol under the combined action of the aldehyde reductase and reductive dehalogenases secreted from the microbial consortium. The ability of biological acidification to remove trichloroacetaldehyde was limited; therefore, trichloroacetaldehyde should be pretreated before it enters biological treatment systems.

Temporal and spatial variations in the bacterial community composition in Lake Bosten, a large, brackish lake in China

The bacteria inhabiting brackish lake environments in arid or semi-arid regions have not been thoroughly identified. In this study, the 454 pyrosequencing method was used to study the sedimentary bacterial community composition (BCC) and diversity in Lake Bosten, which is located in the arid regions of northwestern China. A total of 210,233 high-quality sequence reads and 8,427 operational taxonomic units (OTUs) were successfully obtained from 20 selected sediment samples. The samples were quantitatively dominated by members of Proteobacteria (34.1% ± 11.0%), Firmicutes (21.8% ± 21.9%) and Chloroflexi (13.8% ± 5.2%), which accounted for more than 69% of the bacterial sequences. The results showed that (i) Lake Bosten had significant spatial heterogeneity, and TOC(total organic carbon), TN(total nitrogen) and TP(total phosphorus) were the most important contributors to bacterial diversity; (ii) there was lower taxonomic richness in Lake Bosten, which is located in an arid region, than in reference lakes in eutrophic floodplains and marine systems; and (iii) there was a low percentage of dominant species in the BCC and a high percentage of unidentified bacteria. Our data help to better describe the diversity and distribution of bacterial communities in contaminated brackish lakes in arid regions and how microbes respond to environmental changes in these stable inland waters in arid or semi-arid regions.

Effect of Diet Supplemented With Rapeseed Meal or Hydrolysable Tannins on the Growth, Nutrition, and Intestinal Microbiota in Grass Carp (Ctenopharyngodon idellus)

Grass carp (Ctenopharyngodon idellus; n = 320) were received four different diets for 56 days. The experimental diets were: fishmeal (FM) containing 10% fishmeal (without rapeseed meal), and rapeseed meal (RM) containing 50% rapeseed meal (without fishmeal), and two semi-purified diets either without (T0) or with 1.25% (T1) supplemental hydrolysable tannin. The approximate content of tannin in the RM diet was 1.31%, which was close to that of T1, while the tannin content of FM was close to that of T0. The weight gain rate of grass carp of the RM group was significantly lower than that of the FM group, while the feeding conversion ratio and the feeding rate were significantly higher in the T1 group than in T0. The muscle lipid content was significantly lower in RM than in FM, while T1 was lower than T0. Intestinal activities of trypsin and α-amylase were significantly higher in T1 and RM groups compared with the other treatments. The hepatic activities of aspartate aminotransferase and alanine aminotransferase were lower in T1 and RM groups compared with the other treatments, while hepatic glycogen, and malonaldehyde were significantly higher in T1 and RM groups. In serum, the total protein and globulin contents were significantly higher in T1 and RM groups, while albumin was significantly lower in the RM group compared to the FM group. High-throughput sequencing showed that Proteobacteria, Firmicutes, and Actinobacteria were the dominant bacterial phyla among groups. The intestinal microbial diversity was higher in T1 and RM. Redundancy analysis showed that tannin, rapeseed meal, and intestinal trypsin activity were positively or negatively correlated with the relative abundance of several different intestinal microbiota at phylum and/or genus levels. The results indicated that 1.25% tannin could not be the main reason for the poor growth of grass carp of the RM group; however, the protein metabolism was disturbed, the absorption of carbohydrate was improved, and the accumulation of lipid had decreased. Furthermore, tannin and rapeseed meal supplementations modulated the intestinal microbiota, and may sequentially regulate the intestinal function by fermenting dietary nutrition, producing digestive enzymes, and modulating probiotics.

Reduction in sulfate inhibition of microbial dechlorination of polychlorinated biphenyls in Hudson and Grasse River sediments through fatty acid supplementation

Microbial dechlorination of polychlorinated biphenyls (PCBs) in aquatic sediments may reduce the need for dredging for remediation. To better understand this biotransformation route under different geochemical conditions, the influence of sulfate on dechlorination in sediments from the Hudson River and the Grasse River spiked with two PCB mixtures (PCB 5/12, 64/71, 105/114 and 149/153/170 in Mixture 1 and PCB 5/12, 64/71, 82/97/99, 144/170 in Mixture 2) was investigated. The results showed that PCB dechlorination was partially inhibited in the sulfate-amended sediment microcosms. The rate, extent and preference of dechlorination were mainly controlled by the indigenous differences (sulfate, carbon content etc.) in sediment, but also affected by the PCB mixture composition. An increase of Dehalococcoides 16S rRNA genes coincided with the resumption of dechlorination. Dechlorination preferences were identified using a modified dechlorination pathway analysis approach. The low carbon content and high background sulfate Hudson sediment exhibited more para dechlorination targeting flanked para chlorines. The high carbon content and low background sulfate Grasse sediment preferentially removed more para-flanked meta chlorines than flanked para chlorines. The supplementation of fatty acids (acetate or a mixture of acetate, propionate and butyrate) dramatically increased PCB dechlorination in the Grasse sediment by resuming ortho-flanked meta dechlorination. Rare ortho removals were found in the Grasse sediment after adding fatty acids. This study suggests that supplementary fatty acids might be used to stimulate PCB dechlorination under sulfate reducing conditions, but the effectiveness largely depends on sediment geochemistry.

Redox characteristics of humins and their coupling with potential PCB dechlorinators in southern Yellow Sea sediments

Natural attenuation of polychlorinated biphenyls (PCBs) by indigenous bacteria is an effective remediation strategy for polluted marine sediments. This study investigated the relationships between PCB concentrations in sediment pore water, humin electron transfer capacity, and potential PCB dechlorinators at eight sediment sampling sites in the southern Yellow Sea, China, with differential PCB contamination. Station A2 showed the highest PCB concentration (453.16 ng L^-1 for seven indicator PCBs), especially of less chlorinated PCB congeners (≤5 Cl atoms), humin redox activity, and Dehalococcoides abundance (p < 0.05). Statistical analyses revealed a highly positive correlation between Dehalococcoides abundance and PCB concentration (r = 0.836, p < 0.05) and the electron shuttling ability of humins (r = 0.952, p < 0.01), whereas this was not observed for total bacteria and other potential PCB dechlorinators, e.g., Dehalobacter and Dehalogenimonas. Based on these results, Dehalococcoides might play an important role in the in situ reductive dechlorination of PCBs involving humins in marine sediments, and the natural microbial PCB attenuation capacity at station A2 was high. Chemical characterizations, electrochemical properties, and Fourier transform infrared analysis suggested that humins at station A2 had the highest electron transfer capacity. Furthermore, quinones are likely to be the functional groups that shuttle electrons during PCB dechlorination. Overall, this study provides a useful foundation for evaluating the natural microbial attenuation potential and fates of PCBs in marine sediments and for determining the role of humins as redox mediators in in situ PCB dechlorination by putative indigenous dechlorinators.

Intracellular toxicity exerted by PCBs and role of VBNC bacterial strains in biodegradation

Polychlorinated biphenyls (PCBs) are xenobiotic compounds that persists in the environment for long-term, though its productivity is banned. Abatement of the pollutants have become laborious due to it's recalcitrant nature in the environment leading to toxic effects in humans and other living beings. Biphenyl degrading bacteria co-metabolically degrade low chlorinated PCBs using the active metabolic pathway. bph operon possess different genetic arrangements in gram positive and gram negative bacteria. The binding ability of the genes and the active sites were determined by PCB docking studies. The active site of bphA gene with conserved amino acid residues determines the substrate specificity and biodegradability. Accumulation of toxic intermediates alters cellular behaviour, biomass production and downturn the metabolic activity. Several bacteria in the environment attain unculturable state which is viable and metabolically active but not cultivable (VBNC). Resuscitation-promoting factor (Rpf) and Rpf homologous protein retrieve the culturability of the so far uncultured bacteria. Recovery of this adaptive mechanism against various physical and chemical stressors make a headway in understanding the functionality of both environmental and medically important unculturable bacteria. Thus, this paper review about the general aspects of PCBs, cellular toxicity exerted by PCBs, role of unculturable bacterial strains in biodegradation, genes involved and degradation pathways. It is suggested to extrapolate the research findings on extracellular organic matters produced in culture supernatant of VBNC thus transforming VBNC to culturable state.

Effects of Ferric Oxyhydroxide on Anaerobic Microbial Dechlorination of Polychlorinated Biphenyls in Hudson and Grasse River Sediment Microcosms: Dechlorination Extent, Preferences, Ortho Removal, and Its Enhancement

Microbial reductive dechlorination of polychlorinated biphenyls (PCBs) has been observed in many PCB-impacted sediments. However, this biodegradation is relatively site-specific and can be affected by PCB compositions and sediment geochemical conditions. To better understand the influence of a common competing electron acceptor, ferric oxyhydroxide (FeOOH), on dechlorination, two sediments (Hudson River and Grasse River sediments), and two PCB mixtures (PCB 5/12, 64/71, 105/114, and 149/153/170 in Mixture 1 and PCB 5/12, 64/71, 82/97/99, 144/170 in Mixture 2) were used for this microcosm study. The addition of 40 mmole/kg FeOOH completely inhibited PCB dechlorination in the Hudson sediment, but only moderately inhibited PCB dechlorination in the Grasse sediment with a 3-week longer lag time. The inhibitory effect in the Grasse sediment was mainly due to the loss of unflanked para dechlorination activity. Fe(II) analysis showed that dechlorination started prior to the consumption of Fe(III), which indicates PCB reduction and Fe(III) reduction were able to take place concurrently. Dehalococcoides 16S rRNA genes increased with the commencement of dechlorination in the Grasse sediment, but not in the completely inhibited Hudson sediment. Rare ortho dechlorination pathways were identified in FeOOH-amended Grasse sediment microcosms, dominated by transformations of PCB 25(24-3-CB) to PCB 13(3-4-CB) and PCB 28(24-4-CB) to PCB 15(4-4-CB). The addition of carbon sources (acetate or a fatty acid mixture with acetate, propionate, and butyrate) after 27 weeks of incubation reinitiated dechlorination in FeOOH-amended Hudson sediment microcosms. Also, the addition of carbon sources greatly enhanced ortho dechlorination in FeOOH-amended Grasse microcosms, indicating the utilization of acetate and/or the fatty acid mixture for ortho dechlorination-related microorganisms. A dechlorination pathway analysis approach revealed that para-flanked meta dechlorination was primarily preferred followed by ortho-/double-flanked meta dechlorination and single-/double-flanked para dechlorination in the Grasse sediment.

Diversity and Dynamics of Microbial Community Structure in Different Mangrove, Marine and Freshwater Sediments During Anaerobic Debromination of PBDEs

Little is known about the diversity and succession of indigenous microbial community during debromination of polybrominated diphenyl ethers (PBDEs). This study examined the diversity and dynamics of microbial community structure in eight saline (mangrove and marine) and freshwater sediment microcosms exhibiting different debrominating capabilities for hexa-BDE 153, a common congener in sediments, using terminal restriction fragment length polymorphism (T-RFLP) and clone library analyses. The results showed that microbial community structure greatly differed between the saline and freshwater microcosms, likely leading to distinct variations in their debrominating capabilities and pathways. Higher relative abundances of Chloroflexi and Deltaproteobacteria succeed by Alphaproteobacteria and Betaproteobacteria were detected in the two mangrove microcosms with the fastest debrominating capabilities mainly via para pathway, respectively; the dominance of Alphaproteobacteria resulted in less accumulation of tetra-BDEs and more complete debromination of lower brominated congeners (from di- to tetra-BDEs). Meanwhile, the shifts in both microbial community structure and PBDE profiles were relatively small in the less efficient freshwater microcosms, with relatively more ortho and meta brominated products of BDE-153 resulted. Coincidently, one of the freshwater microcosms showed sudden increases of Chloroflexi and Deltaproteobacteria by the end of incubation, which synchronized with the increase in the removal rate of BDE-153. The significant relationship between microbial community structure and PBDEs was confirmed by redundancy analysis (18.7% of total variance explained, P = 0.002). However, the relative abundance of the well-known dechlorinator Dehalococcoides showed no clear correlation with the debrominating capability across different microcosms. These findings shed light in the significance of microbial community network in different saline environments on enhancement of PBDE intrinsic debromination.

Natural Attenuation Potential of Polychlorinated Biphenyl-Polluted Marine Sediments

The marine environment in Kuwait is polluted with various hazardous chemicals of industrial origin. These include petroleum hydrocarbons, halogenated compounds and heavy metals. Bioremediation with dedicated microorganisms can be effectively applied for reclamation of the polluted marine sediments. However, information on the autochthonous microbes and their ecophysiology is largely lacking. We analyzed sediments from Shuwaikh harbor to detect polychlorinated biphenyls (PCBs) and total petroleum hydrocarbons (TPHs). Then we adopted both culture-dependent and culture-independent (PCR-DGGE) approaches to identify bacterial inhabitants of the polluted marine sediments from Shuwaikh harbor. The chemical analysis revealed spatial variation among the sampling stations in terms of total amount of PCBs, TPHs and the PCB congener fingerprints. Moreover, in all analyzed sediments, the medium-chlorine PCB congeners were more abundant than the low-chlorine and high-chlorine counterparts. PCR-DGGE showed the presence of members of the Proteobacteria, Spirochaetes, Firmicutes and Bacteroidetes in the analyzed sediments. However, Chloroflexi-related bacteria dominated the detected bacterial community. We also enriched a biphenyl-utilizing mixed culture using the W2 station sediment as an inoculum in chemically defined medium using biphenyl as a sole carbon and energy source. The enriched mixed culture consisted mainly of the Firmicute Paenibacillus spp. Sequences of genes encoding putative aromatic ring-hydroxylating dioxygenases were detected in sediments from most sampling stations and the enriched mixed culture. The results suggest the potential of bioremediation as a means for natural attenuation of Shuwaikh harbor sediments polluted with PCBs and TPHs.

Identification of two organohalide-respiring Dehalococcoidia associated to different dechlorination activities in PCB-impacted marine sediments

Background

Microbial reductive dechlorination of polychlorinated biphenyls (PCBs) plays a major role in detoxifying anoxic contaminated freshwater and marine sediments from PCBs. Known members of the phylum Chloroflexi are typically responsible for this activity in freshwater sediments, whereas less is known about the microorganisms responsible for this activity in marine sediments. PCB-respiring activities were detected in PCB-impacted marine sediments of the Venice Lagoon. The aim of this work was to identify the indigenous organohalide-respiring microorganisms in such environments and assess their dechlorination specificity against spiked Aroclor™ 1254 PCBs under laboratory conditions resembling the in situ biogeochemistry.

Results

High PCB dechlorination activities (from 150 ± 7 to 380 ± 44 μmol of chlorine removed kg⁻¹ week⁻¹) were detected in three out of six sediments sampled from different locations of the lagoon. An uncultured non-Dehalococcoides phylotype of the class Dehalococcoidia closely related to Dehalobium chlorocoercia DF-1, namely phylotype VLD-1, was detected and enriched up to 10⁹ 16S rRNA gene copies per gram of sediment where dechlorination activities were higher and 25-4/24-4 and 25-2/24-2/4-4 chlorobiphenyls (CB) accumulated as the main tri-/dichlorinated products. Conversely, a different phylotype closely related to the SF1/m-1 clade, namely VLD-2, also enriched highly where lower dechlorination activity and the accumulation of 25-3 CB as main tri-chlorinated product occurred, albeit in the simultaneous presence of VLD-1. Both phylotypes showed growth yields higher or comparable to known organohalide respirers and neither phylotypes enriched in sediment cultures not exhibiting dechlorination.

Conclusions

These findings confirm the presence of different PCB-respiring microorganisms in the indigenous microbial communities of Venice Lagoon sediments and relate two non-Dehalococcoides phylotypes of the class Dehalococcoidia to different PCB dechlorination rates and specificities.

Electronic supplementary material

The online version of this article (doi:10.1186/s12934-017-0743-4) contains supplementary material, which is available to authorized users.

Application of acclimated sewage sludge as a bio-augmentation/bio-stimulation strategy for remediating chlorpyrifos contamination in soil with/without cadmium

This experiment was performed to investigate the effects of acclimated sewage sludge (ASS) and sterilized ASS on the fates of chlorpyrifos (CP) in soil with or without cadmium (Cd), as well as the improvement of soil biochemical properties. Results showed that both ASS and sterilized ASS could significantly promote CP dissipation, and the groups with ASS had the highest efficiency on CP removal, whose degradation rates reached 71.3%-85.9% at the 30th day (40.4%-50.2% higher than non-sludge groups). Besides, the degradation rate of CP was not severely influenced by the existence of Cd, and the population of soil microorganism dramatically increased after adding sludge. The soil enzyme activities (dehydrogenase, acid phosphatase and FDA hydrolase activities) ranked from high to low were as follows: groups with sterilized ASS>groups with ASS>groups without sludge. Simultaneously, 16S rRNA gene sequencing revealed that ASS changed bacterial community structure and diversity in soil. In addition, alkali-hydrolyzable nitrogen and Olsen- phosphorus increased after application of sludge, indicating that the addition of ASS (or sterilized ASS) could effectively improve soil fertility.

Potential risk reduction of Aroclor 1254 by microbial dechlorination in anaerobic Grasse River sediment microcosms

Aroclor 1254 was the second most produced commercial PCB mixture and is found in soils, sediments and sewage throughout the globe. This commercial PCB mixture is considered particularly toxic because of the relatively high concentrations of congeners with dioxin-like properties. The potential for risk reduction by microbial reductive dechlorination of Aroclor 1254 (A1254) was investigated in sediment microcosms from Grasse River (GR), Massena, NY. The specificity of A1254 dechlorination was doubly- and singly-flanked chlorines in meta positions and to a less extent doubly-flanked para chlorines of 2345-substituted chlorobiphenyl rings. The average dechlorination rate of A1254 was 0.0153 Cl^-/biphenyl/day, and dechlorination rates of single congeners ranged between 0.001 and 0.0074 Cl^-/biphenyl/day. Potential risk associated with A1254 based on the toxic equivalency factors of the dioxin-like congeners was reduced by 83%. Additional potential risk associated with bioaccumulation in fish was reduced by 35% based on biota-sediment accumulation factor estimates for all detected congeners. Finally, the dechlorination end-products were tri- and tetra-chlorobiphenyls with unflanked chlorines, all of which are susceptible to further degradation by aerobic microorganisms. The combined results indicate that microbial reductive dechlorination has the potential for reducing risk associated with toxicity and bioaccumulation in fish in sites contaminated with A1254.

Phyto-rhizoremediation of polychlorinated biphenyl contaminated soils: An outlook on plant-microbe beneficial interactions

Polychlorinated biphenyls (PCBs) are toxic chemicals, recalcitrant to degradation, bioaccumulative and persistent in the environment, causing adverse effects on ecosystems and human health. For this reason, the remediation of PCB-contaminated soils is a primary issue to be addressed. Phytoremediation represents a promising tool for in situ soil remediation, since the available physico-chemical technologies have strong environmental and economic impacts. Plants can extract and metabolize several xenobiotics present in the soil, but their ability to uptake and mineralize PCBs is limited due to the recalcitrance and low bioavailability of these molecules that in turn impedes an efficient remediation of PCB-contaminated soils. Besides plant degradation ability, rhizoremediation takes into account the capability of soil microbes to uptake, attack and degrade pollutants, so it can be seen as the most suitable strategy to clean-up PCB-contaminated soils. Microbes are in fact the key players of PCB degradation, performed under both aerobic and anaerobic conditions. In the rhizosphere, microbes and plants positively interact. Microorganisms can promote plant growth under stressed conditions typical of polluted soils. Moreover, in this specific niche, root exudates play a pivotal role by promoting the biphenyl catabolic pathway, responsible for microbial oxidative PCB metabolism, and by improving the overall PCB degradation performance. Besides rhizospheric microbial community, also the endophytic bacteria are involved in pollutant degradation and represent a reservoir of microbial resources to be exploited for bioremediation purposes. Here, focusing on plant-microbe beneficial interactions, we propose a review of the available results on PCB removal from soil obtained combining different plant and microbial species, mainly under simplified conditions like greenhouse experiments. Furthermore, we discuss the potentiality of "omics" approaches to identify PCB-degrading microbes, an aspect of paramount importance to design rhizoremediation strategies working efficiently under different environmental conditions, pointing out the urgency to expand research investigations to field scale.

Impact of bio-palladium nanoparticles (bio-Pd NPs) on the activity and structure of a marine microbial community

Biogenic palladium nanoparticles (bio-Pd NPs) represent a promising catalyst for organohalide remediation in water and sediments. However, the available information regarding their possible impact in case of release into the environment, particularly on the environmental microbiota, is limited. In this study the toxicity of bio-Pd NPs on the model marine bacterium V. fischeri was assessed. The impacts of different concentrations of bio-Pd NPs on the respiratory metabolisms (i.e. organohalide respiration, sulfate reduction and methanogenesis) and the structure of a PCB-dechlorinating microbial community enriched form a marine sediment were also investigated in microcosms mimicking the actual sampling site conditions. Bio-Pd NPs had no toxic effect on V. fischeri. In addition, they had no significant effects on PCB-dehalogenating activity, while showing a partial, dose-dependent inhibitory effect on sulfate reduction as well as on methanogenesis. No toxic effects by bio-Pd NPs could be also observed on the total bacterial community structure, as its biodiversity was increased compared to the not exposed community. In addition, resilience of the microbial community to bio-Pd NPs exposure was observed, being the final community organization (Gini coefficient) of samples exposed to bio-Pd NPs similar to that of the not exposed one. Considering all the factors evaluated, bio-Pd NPs could be deemed as non-toxic to the marine microbiota in the conditions tested. This is the first study in which the impact of bio-Pd NPs is extensively evaluated over a microbial community in relevant environmental conditions, providing important information for the assessment of their environmental safety.

First evidence on the occurrence and dynamics of Dehalococcoides mccartyi PCB-dechlorinase genes in marine sediment during Aroclor1254 reductive dechlorination

The present study evaluates the PCB-dehalorespiring capabilities and dynamics of indigenous Dehalococcoides mccartyi population in a PCB contaminated marine sediment. Specialized PCB-dechlorinase genes pcbA1, pcbA4 and pcbA5 previously characterized in pure cultures of D. mccartyi, were here found for the first time in environmental samples. Reductive dechlorination was stimulated by spiking Aroclor1254 to the sediment and by imposing strictly anaerobic conditions both with and without bioaugmentation with a Dehalococcoides mccartyi enrichment culture. In line with the contaminant dechlorination kinetics, Dehalococcoides population increased during the entire incubation period showing growth yields of 4.94E+07 Dehalococcoides per μmolCl^-1 and 7.30E+05 Dehalococcoides per μmolCl^-1 in the marine sediment with and without bioaugmentation respectively. The pcbA4 and pcbA5 dechlorinase genes, and to a lesser extent pcbA1 gene, were enriched during the anaerobic incubation suggesting their role in Aroclor1254 dechlorination under salinity conditions.

Plant-assisted bioremediation of a historically PCB and heavy metal-contaminated area in Southern Italy

A plant-assisted bioremediation strategy was applied in an area located in Southern Italy, close to the city of Taranto, historically contaminated by polychlorinated biphenyls (PCBs) and heavy metals. A specific poplar clone (Monviso) was selected for its ability to promote organic pollutant degradation in the rhizosphere, as demonstrated elsewhere. Chemical and microbiological analyses were performed at the time of poplar planting in selected plots at different distances from the trunk (0.25-1m) and at different soil depths (0-20 and 20-40cm), at day 420. A significant decrease in PCB congeners and a reduction in all heavy metals was observed where the poplar trees were present. No evidence of PCB and heavy metal reduction was observed in the non poplar-vegetated soil. Microbial analyses (dehydrogenase activity, cell viability, microbial abundance) of the autochthonous microbial community showed an improvement in soil quality. In particular, microbial activity generally increased in the poplar-rhizosphere and a positive effect was observed in some cases at up to 1m distance from the trunk and up to 40cm depth. The Monviso clone was effective in promoting both a general decrease in contaminant occurrence and an increase in microbial activity in the chronically polluted area a little more than one year after planting.

Microbiome Dynamics of a Polychlorobiphenyl (PCB) Historically Contaminated Marine Sediment under Conditions Promoting Reductive Dechlorination

The toxicity of polychlorinated biphenyls (PCB) can be efficiently reduced in contaminated marine sediments through the reductive dechlorination (RD) process lead by anaerobic organohalide bacteria. Although the process has been extensively investigated on PCB-spiked sediments, the knowledge on the identity and metabolic potential of PCB-dechlorinating microorganisms in real contaminated matrix is still limited. Aim of this study was to explore the composition and the dynamics of the microbial communities of the marine sediment collected from one of the largest Sites of National Interest (SIN) in Italy (Mar Piccolo, Taranto) under conditions promoting the PCBs RD. A long-term microcosm study revealed that autochthonous bacteria were able to sustain the PCB dechlorination at a high extent and the successive addition of an external fermentable organic substrate (lactate) caused the further depletion of the high-chlorinated PCBs (up to 70%). Next Generation Sequencing was used to describe the core microbiome of the marine sediment and to follow the changes caused by the treatments. OTUs affiliated to sulfur-oxidizing ε-proteobacteria, Sulfurovum, and Sulfurimonas, were predominant in the original sediment and increased up to 60% of total OTUs after lactate addition. Other OTUs detected in the sediment were affiliated to sulfate reducing (δ-proteobacteria) and to organohalide respiring bacteria within Chloroflexi phylum mainly belonging to Dehalococcoidia class. Among others, Dehalococcoides mccartyi was enriched during the treatments even though the screening of the specific reductive dehalogenase genes revealed the occurrence of undescribed strains, which deserve further investigations. Overall, this study highlighted the potential of members of Dehalococcoidia class in reducing the contamination level of the marine sediment from Mar Piccolo with relevant implications on the selection of sustainable bioremediation strategies to clean-up the site.

Distribution of bacterial communities across plateau freshwater lake and upslope soils

Microorganisms are involved in a variety of biogeochemical processes in natural environments. The differences between bacterial communities in freshwaters and upslope soils remain unclear. The present study investigated the bacterial distribution in a plateau freshwater lake, Erhai Lake (southwestern China), and its upslope soils. Illumina MiSeq sequencing illustrated high bacterial diversity in lake sediments and soils. Sediment and soil bacterial communities were mainly composed of Proteobacteria, Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi and Planctomycetes. However, a distinctive difference in bacterial community structure was found between soil and sediment ecosystems. Water content, nitrogen and pH affected the distribution of the bacterial community across Erhai Lake and its upslope soils. Moreover, the soil bacterial community might also be shaped by plant types. This work could provide some new insights into plateau aquatic and terrestrial microbial ecology.

Reductive dechlorination of tetrachloroethene in marine sediments: Biodiversity and dehalorespiring capabilities of the indigenous microbes

Chlorinated compounds pose environmental concerns due to their toxicity and wide distribution in several matrices. Microorganisms specialized in leading anaerobic reductive dechlorination (RD) processes, including Dehalococcoides mccartyi (Dhc), are able to reduce chlorinated compounds to harmless products or to less toxic forms. Here we report the first detailed study dealing with the RD potential of heavy polluted marine sediment by evaluating the biodegradation kinetics together with the composition, dynamics and activity of indigenous microbial population. A microcosm study was conducted under strictly anaerobic conditions on marine sediment collected near the marine coast of Sarno river mouth, one of the most polluted river in Europe. Tetrachloroethene (PCE), used as model pollutant, was completely converted to ethene within 150 days at reductive dechlorination rate equal to 0.016 meq L(-1) d(-1). Consecutive spikes of PCE allowed increasing the degradation kinetics up to 0.1 meq L(-1)d(-1) within 20 days. Strictly anaerobiosis and repeated spikes of PCE stimulated the growth of indigenous Dhc cells (growth yield of ~7.0 E + 07 Dhc cells per μM Cl(-1) released). Dhc strains carrying the reductive dehalogenase genes tceA and vcrA were detected in the original marine sediment and their number increased during the treatment as demonstrated by the high level of tceA expression at the end of the microcosm study (2.41 E + 05 tceA gene transcripts g(-1)). Notably, the structure of the microbial communities was fully described by Catalysed Reporter Deposition Fluorescence In Situ Hybridization (CARD-FISH) as wells as the dynamics of the dechlorinating bacteria during the microcosms operation. Interestingly, a direct role of Dhc cells was ascertained suggesting the existence of strains adapted at salinity conditions. Additionally, non-Dhc Chloroflexi were retrieved in the original sediment and were kept stable over time suggesting their likely flanking role of the RD process.

Ecogenomics reveals metals and land-use pressures on microbial communities in the waterways of a megacity

Networks of engineered waterways are critical in meeting the growing water demands in megacities. To capture and treat rainwater in an energy-efficient manner, approaches can be developed for such networks that use ecological services from microbial communities. Traditionally, engineered waterways were regarded as homogeneous systems with little responsiveness of ecological communities and ensuing processes. This study provides ecogenomics-derived key information to explain the complexity of urban aquatic ecosystems in well-managed watersheds with densely interspersed land-use patterns. Overall, sedimentary microbial communities had higher richness and evenness compared to the suspended communities in water phase. On the basis of PERMANOVA analysis, variation in structure and functions of microbial communities over space within same land-use type was not significant. In contrast, this difference was significant between different land-use types, which had similar chemical profiles. Of the 36 environmental parameters from spatial analysis, only three metals, namely potassium, copper and aluminum significantly explained between 7% and 11% of the variation in taxa and functions, based on distance-based linear models (DistLM). The ecogenomics approach adopted here allows the identification of key drivers of microbial communities and their functions at watershed-scale. These findings can be used to enhance microbial services, which are critical to develop ecologically friendly waterways in rapidly urbanizing environments.

Spatial patterns of metals, PCDDs/Fs, PCBs, PBDEs and chemical status of sediments from a coastal lagoon (Pialassa Baiona, NW Adriatic, Italy)

The European Water Framework Directive (WFD) establishes a framework for the protection and improvement of all water bodies including transitional waters; its final objective is to achieve at least 'good status' by 2015. In the present work, a hierarchical sampling design was applied to analyze the influence of anthropogenic inputs on the spatial distribution of metals, polychlorinated dibenzo-p-dioxins (PCDDs) dibenzofurans (PCDFs), polychlorinated biphenyls (PCBs) and polybrominated diphenyl ethers (PBDEs) in sediment at four areas in Pialassa Baiona coastal lagoon. In order to assess the chemical status, levels of priority substances and other pollutants were compared with the recently developed national Environmental Quality Standards (EQS) and site specific background levels for metals. Levels of mercury and PCBs were particularly high and exceeded their national EQS values at all sampled areas, thus not contributing to the achievement of a good chemical status of this transitional water body according to the WFD classification.

Phytoremediation and bioremediation of polychlorinated biphenyls (PCBs): state of knowledge and research perspectives

This review summarizes the bioremediation and phytoremediation technologies proposed so far to detoxify PCB-contaminated sites. A critical analysis about the potential and limits of the PCB pollution treatment strategies by means of plants, fungi and bacteria are elucidated, including the new insights emerged from recent studies on the rhizosphere potential and on the implementation of simultaneous aerobic and anaerobic biodegradation processes. The review describes the biodegradation and phytoremediation processes and elaborates on the environmental variables affecting contaminant degradation rates, summarizing the amendments recommended to enhance PCB degradation. Additionally, issues connected with PCB toxicology, actual field remediation strategies and economical evaluation are discussed.

Geosphere-biosphere interactions in bio-activity volcanic lakes: evidences from Hule and Rìo Cuarto (Costa Rica)

Hule and Río Cuarto are maar lakes located 11 and 18 km N of Poás volcano along a 27 km long fracture zone, in the Central Volcanic Range of Costa Rica. Both lakes are characterized by a stable thermic and chemical stratification and recently they were affected by fish killing events likely related to the uprising of deep anoxic waters to the surface caused by rollover phenomena. The vertical profiles of temperature, pH, redox potential, chemical and isotopic compositions of water and dissolved gases, as well as prokaryotic diversity estimated by DNA fingerprinting and massive 16S rRNA pyrosequencing along the water column of the two lakes, have highlighted that different bio-geochemical processes occur in these meromictic lakes. Although the two lakes host different bacterial and archaeal phylogenetic groups, water and gas chemistry in both lakes is controlled by the same prokaryotic functions, especially regarding the CO2-CH4 cycle. Addition of hydrothermal CO2 through the bottom of the lakes plays a fundamental priming role in developing a stable water stratification and fuelling anoxic bacterial and archaeal populations. Methanogens and methane oxidizers as well as autotrophic and heterotrophic aerobic bacteria responsible of organic carbon recycling resulted to be stratified with depth and strictly related to the chemical-physical conditions and availability of free oxygen, affecting both the CO2 and CH4 chemical concentrations and their isotopic compositions along the water column. Hule and Río Cuarto lakes were demonstrated to contain a CO2 (CH4, N2)-rich gas reservoir mainly controlled by the interactions occurring between geosphere and biosphere. Thus, we introduced the term of bio-activity volcanic lakes to distinguish these lakes, which have analogues worldwide (e.g. Kivu: D.R.C.-Rwanda; Albano, Monticchio and Averno: Italy; Pavin: France) from volcanic lakes only characterized by geogenic CO2 reservoir such as Nyos and Monoun (Cameroon).

The role of environmental biotechnology in exploring, exploiting, monitoring, preserving, protecting and decontaminating the marine environment

In light of the Marine Strategy Framework Directive (MSFD) and the EU Thematic Strategy on the Sustainable Use of Natural Resources, environmental biotechnology could make significant contributions in the exploitation of marine resources and addressing key marine environmental problems. In this paper 14 propositions are presented focusing on (i) the contamination of the marine environment, and more particularly how to optimize the use of biotechnology-related tools and strategies for predicting and monitoring contamination and developing mitigation measures; (ii) the exploitation of the marine biological and genetic resources to progress with the sustainable, eco-compatible use of the maritime space (issues are very diversified and include, for example, waste treatment and recycling, anti-biofouling agents; bio-plastics); (iii) environmental/marine biotechnology as a driver for a sustainable economic growth.

Trichloroethylene aerobic cometabolism by suspended and immobilized butane-growing microbial consortia: a kinetic study

A kinetic study of butane uptake and trichloroethylene (TCE) aerobic cometabolism was conducted by two suspended-cell (15 and 30°C) and two attached-cell (15 and 30°C) consortia obtained from the indigenous biomass of a TCE-contaminated aquifer. The shift from suspended to attached cells resulted in an increase of butane (15 and 30°C) and TCE (15°C) biodegradation rates, and a significant decrease of butane inhibition on TCE biodegradation. The TCE 15°C maximum specific biodegradation rate was equal to 0.011 mg(TCE ) mg(protein)(-1) d(-1) with suspended cells and 0.021 mg(TCE) mg(protein)(-1) d(-1) with attached cells. The type of mutual butane/TCE inhibition depended on temperature and biomass conditions. On the basis of a continuous-flow simulation, a packed-bed PFR inoculated with the 15 or 30°C attached-cell consortium could attain a 99.96% conversion of the studied site's average TCE concentration with a 0.4-0.5-day hydraulic residence time, with a low effect of temperature on the TCE degradation performances.

In situ treatment of PCBs by anaerobic microbial dechlorination in aquatic sediment: are we there yet?

The remediation of polychlorinated biphenyls (PCBs) in soils and sediments remains a particularly difficult problem to solve. The possibility of in situ degradation by microorganisms has been pursued for many years since this approach has the potential to provide a cost-effective and environmentally sustainable alternative to dredging for treatment of PCB impacted sites. Being hydrophobic, PCBs partition into organic material and accumulate in anoxic environments well poised to support anaerobic dechlorination of highly chlorinated congeners; products of which are susceptible to complete aerobic degradation. Laboratory research over the past 25 years is now leading to new microbial technologies that could soon be tested for treatment of PCB impacted sediments in the field.

Phylogenetically distinct bacteria involve extensive dechlorination of aroclor 1260 in sediment-free cultures

Microbial reductive dechlorination of the persistent polychlorinated biphenyls (PCBs) is attracting much attention in cleanup of the contaminated environment. Nevertheless, most PCB dechlorinating cultures require presence of sediment or sediment substitutes to maintain their dechlorination activities which hinders subsequent bacterial enrichment and isolation processes. The information on enriching sediment-free PCB dechlorinating cultures is still limited. In this study, 18 microcosms established with soils and sediments were screened for their dechlorination activities on a PCB mixture – Aroclor 1260. After one year of incubation, 10 out of 18 microcosms showed significant PCB dechlorination with distinct dechlorination patterns (e.g., Process H, N and T classified based on profiles of PCB congeners loss and new congeners formation). Through serial transfers in defined medium, six sediment-free PCB dechlorinating cultures (i.e., CW-4, CG-1, CG-3, CG-4, CG-5 and SG-1) were obtained without amending any sediment or sediment-substitutes. PCB dechlorination Process H was the most frequently observed dechlorination pattern, which was found in four sediment-free cultures (CW-4, CG-3, CG-4 and SG-1). Sediment-free culture CG-5 showed the most extensive PCB dechlorination among the six cultures, which was mediated by Process N, resulting in the accumulation of penta- (e.g., 236-24-CB) and tetra-chlorobiphenyls (tetra-CBs) (e.g., 24-24-CB, 24-25-CB, 24-26-CB and 25-26-CB) via dechlorinating 30.44% hepta-CBs and 59.12% hexa-CBs after three months of incubation. For culture CG-1, dechlorinators mainly attacked double flanked meta-chlorines and partially ortho-chlorines, which might represent a novel dechlorination pattern. Phylogenetic analysis showed distinct affiliation of PCB dechlorinators in the microcosms, including Dehalogenimonas and Dehalococcoides species. This study broadens our knowledge in microbial reductive dechlorination of PCBs, and provides essential information for culturing and stimulating PCB dechlorinators for in situ bioremediation applications.

Distribution of dehalogenation activity in subseafloor sediments of the Nankai Trough subduction zone

Halogenated organic matter buried in marine subsurface sediment may serve as a source of electron acceptors for anaerobic respiration of subseafloor microbes. Detection of a diverse array of reductive dehalogenase-homologous (rdhA) genes suggests that subseafloor organohalide-respiring microbial communities may play significant ecological roles in the biogeochemical carbon and halogen cycle in the subseafloor biosphere. We report here the spatial distribution of dehalogenation activity in the Nankai Trough plate-subduction zone of the northwest Pacific off the Kii Peninsula of Japan. Incubation experiments with slurries of sediment collected at various depths and locations showed that degradation of several organohalides tested only occurred in the shallow sedimentary basin, down to 4.7 metres below the seafloor, despite detection of rdhA in the deeper sediments. We studied the phylogenetic diversity of the metabolically active microbes in positive enrichment cultures by extracting RNA, and found that Desulfuromonadales bacteria predominate. In addition, for the isolation of genes involved in the dehalogenation reaction, we performed a substrate-induced gene expression screening on DNA extracted from the enrichment cultures. Diverse DNA fragments were obtained and some of them showed best BLAST hit to known organohalide respirers such as Dehalococcoides, whereas no functionally known dehalogenation-related genes such as rdhA were found, indicating the need to improve the molecular approach to assess functional genes for organohalide respiration.