Elevated nitrate enriches microbial functional genes for potential bioremediation of complexly contaminated sediments

Biodegradation potential of polycyclic aromatic hydrocarbons in Taihu Lake sediments

ABSTRACTTo assess the biodegradation potential of polycyclic aromatic hydrocarbons (PAHs) in sediments, sediment microcosms were constructed with sediments collected from six lake zones with different trophic statuses in Taihu Lake. The presence and concentration of PAH-degrading bacteria (PDB) were estimated by the most probable number (MPN) method. After 85 d of aerobic and anaerobic incubation, spiked PAHs (phenanthrene, pyrene, and benzo[a]pyrene) were partially degraded by indigenous sediment microorganisms. Large differences in PAH degradation were observed depending on the molecular size of the PAHs. The PAH removal efficiency in sediments under aerobic conditions was higher than that under anaerobic conditions. MPN analyses showed a higher abundance of degrading microflora in the high PAH-contaminated sites than in the low PAH-contaminated sites. Moreover, the anaerobic PDB populations in the sediments from the six different sites were much higher than those of aerobic PDB. The PAH biodegradation capability in sediments was associated with the geochemical conditions and bacterial populations. PDB showed a broad spatial distribution, thereby implying that they played an important role in the natural attenuation and cycling of PAHs in Taihu Lake. This work indicates that PAHs remain a concern in Taihu Lake sediments and can provide useful information for further bioremediation of PAH-contaminated sediments.

Microbial and abiotic factors of flooded soil that affect redox biodegradation of lindane

Pollution induces pressure to soil microorganism; and conversely, the degradation of pollutants is reported largely regulated by the soil microbiome assembly in situ. However, the specific-dependent core taxa of degraders were barely confirmed, which is not conducive to improving the soil remediation strategy. Taking pollution of a typical organochlorine pesticide (OCP), lindane, as an example, we explored the microbial community assembly in flooded soils and simultaneously quantified the corresponding dynamics of typical soil redox processes. Contrasting initial status of microbial diversity was set up by gamma irradiation or not, with additives (acetate, NaNO_3, acetate + NaNO₃) capable of modifying microbial growth employed simultaneously. Microorganism under lindane stress was reflected by microbial adaptability within complex co-occurrence networks, wherein some environment-dependent core taxa (e.g., Clostridia, Bacteroidia, Bacilli) were highly resilient to pollution and sterilization disturbances. Lindane had higher degradation rate in irradiated soil (0.96 mg kg^-1 d^-1) than non-irradiated soil (0.83 mg kg^-1 d^-1). In non-irradiated soil, addition of acetate promoted lindane degradation and methanogenesis, whereas nitrate inhibited lindane degradation but promoted denitrification. No significant differences in lindane degradation were observed in irradiated soils, which exhibited low-diversity microbiomes in parallel to stronger Fe reduction and methanogenesis. The varied corresponding trigger effects on soil redox processes are likely due to differences of soil microbiome, specifically, deterministic or stochastic assembly, in response to pollution stress under high or low initial microbial diversity conditions. Our results improve the knowledge of the adaptability of disturbed microbiomes and their feedback on microbial functional development in OCP-polluted soils, achieving for a more reliable understanding with respect to the ecological risk of soils resided with OCPs under the fact of global microbial diversity loss.

Persistent contamination of polycyclic aromatic hydrocarbons (PAHs) and phthalates linked to the shift of microbial function in urban river sediments

Urban rivers were heavily polluted, which resulted in blackening and odorization (i.e., black-odor rivers). Nevertheless, very limited information is available on sediment contamination levels of black-odor rivers and their linkage to the patterns of microbial functional genes. This study investigated distribution of polycyclic aromatic hydrocarbons (PAHs) and phthalates (PAEs) and their linkages to bacterial community and related functional genes in river sediments. The results demonstrate that higher average levels of ∑16PAHs (1405 μg/kg, dry weight) and ∑6PAEs (7120 μg/kg) were observed in sediments from heavy black-odor rivers than the moderate ones (∑16PAHs: 462 μg/kg; ∑6PAEs: 2470 μg/kg). The taxon composition and diversities of bacterial community in sediments varied with significantly lower diversity indices in heavy black-odor rivers than moderate ones. Sediments from heavy black-odor rivers enriched certain PAH and PAE degrading bacteria and genes. Unfortunately, PAH and PAE contamination demonstrated negative influences on nitrogen and phosphorus metabolism related bacteria and function genes but significant positive influences on certain sulfur metabolism related bacterial taxa and sulfur reduction gene, which might cause nitrogen and phosphorus accumulation and black-odor phenomenon in heavy black-odor rivers. This study highlights PAH and PAE contamination in urban rivers may shift bacterial community and detrimentally affect their ecological functions.

Nitrogen species control the interaction between NO3--N reduction and aniline degradation and microbial community structure in the oxic-anoxic transition zone

Contrary to the fact that NO₃^--N can serve as electron acceptor to promote organics degradation, it was also found NO₃^--N reduction does not necessarily promote organics degradation. We speculate nitrogen (N) species may control the interaction between NO₃^--N reduction and organics degradation via shifting related microbial community structure. To prove the hypothesis, oxic-anoxic transition zone (OATZ) microcosms simulated by lake water and sediment were conducted with the addition of N species (NO₃^--N, NO₂^--N, and NH₄⁺-N) and aniline as typical organics. High-throughput sequencing was used to analyze the microbial community structure and functional enzyme in the microcosms. Results show that, NO₂^--N inhibited NO₃^--N reduction while enhanced aniline degradation. For NH₄⁺-N, it promoted NO₃^--N reduction when NH₄⁺-N/NO₃^--N concentration ratio ≤ 2 and inhibited aniline degradation when NH₄⁺-N/aniline concentration ratio ≥ 0.5. The presence of NO₂^--N or NH₄⁺-N weakened the interaction between NO₃^--N reduction and aniline degradation, which might be caused by significant changes in the diversity and abundance of microbial communities controlled by N species. The microbial mechanism indicates that NO₂^--N weakened the interaction by affecting both denitrification enzyme activity and electron transfer capability, while NH₄⁺-N weakened the interaction mainly by affecting electron transfer capability. These results imply that N species, as well as other electron acceptors and donors, in the contaminated OATZ should be fully considered, when performing in situ remediation technology of NO₃^--N reduction.

Bacterial community responses to the redox profile changes of mariculture sediment

Suspended mariculture has significantly influences on the benthic sediment. However, our understanding on how bacterial communities respond to mariculture induced changes in redox profiles is limited. In present study, sediments from two maricultures and reference areas were collected and incubated for 28 day. The results indicated that the dominant pathway of organic matter mineralization in the sediment varied from groups, in the reference, it was the iron reduction, but in the two mariculture groups it was the SO₄^2- reduction. Remarkable changes of bacteria community were recorded in the aerobic zone, where the abundances of 14 OTUs belonging to Gammaproteobacteria and Alphaproteobacteria were significantly higher than that in oxidation and anaerobic zones. However, 4 keystone OTUs were strictly anaerobic and belonging to Desulfobacteraceae (n = 3) and Marinilabiaceae (n = 1). The main environmental drivers determining sediment bacterial distribution were the particle organic carbon, dissolve oxygen, NO₃^-, and moisture content.

Laboratory investigation on calcium nitrate induced coupling reactions between nitrogen, phosphorus, sulfur, and metals in contaminated sediments

In recent years, calcium nitrate addition has become a promising and usually used method for in situ sediment remediation. In this study, excess calcium nitrate was applied to column sediments to explore the coupling reactions of elements such as N, Fe, S, and P. Diffusive gradients in thin film (DGT) devices were used to collect labile substances at the sediment-water interface. Rhizon samplers were used to collect soluble substances in interstitial water. Results showed that nitrate addition turned the surface sediment into a more oxidized state, and mobile Fe, S, P, and As were removed in surface ~ 10-cm sediment. Due to different nitrate distributions in corresponding sediment depths, the consumption rates of NH3-N and soluble reactive P were faster in the surface sediment than that in deeper layers. Different from previous researches, the transient increase of soluble Fe was observed in this study, which was probably attributed to the solvation of FeS in the autotrophic denitrification process. According to our results, we suggest that a dosage of far less than 141 g N/m2 and slightly more than 45.3 g N/m2 can be used for the remediation of black and odorous sediment and control of internal P by calcium nitrate.

Synergistic interactions of Desulfovibrio and Petrimonas for sulfate-reduction coupling polycyclic aromatic hydrocarbon degradation

Microbial sulfate-reduction coupling polycyclic aromatic hydrocarbon (PAH) degradation is an important process for the remediation of contaminated sediments. However, little is known about core players and their mechanisms in this process due to the complexity of PAH degradation and the large number of microorganisms involved. Here we analyzed potential core players in a black-odorous sediment using gradient-dilution culturing, isolation and genomic/metagenomic approaches. Along the dilution gradient, microbial PAH degradation and sulfate consumption were not decreased, and even a significant (p = 0.003) increase was observed in the degradation of phenanthrene although the microbial diversity declined. Two species, affiliated with Desulfovibrio and Petrimonas, were commonly present in all of the gradients as keystone taxa and showed as the dominant microorganisms in the single colony (SB8) isolated from the highest dilution culture with 93.49% and 4.73% of the microbial community, respectively. Desulfovibrio sp. SB8 and Petrimonas sp. SB8 could serve together as core players for sulfate-reduction coupling PAH degradation, in which Desulfovibrio sp. SB8 could degrade PAHs to hexahydro-2-naphthoyl through the carboxylation pathway while Petrimonas sp. SB8 might degrade intermediate metabolites of PAHs. This study provides new insights into the microbial sulfate-reduction coupling PAH degradation in black-odorous sediments.

Aerobic and Anaerobic Biodegradability of Organophosphates in Activated Sludge Derived From Kitchen Garbage Biomass and Agricultural Residues

Organophosphates (also known as organophosphate esters, OPEs) have in recent years been found to be significant pollutants in both aerobic and anaerobic activated sludge. Food waste, such as kitchen garbage and agricultural residues, can be used as co-substrates to treat the active sludge in sewage treatment plants (STPs). We investigated the biodegradability of nine OPEs derived from kitchen garbage biomass and agricultural residues under different conditions. Under anaerobic conditions, the rate of removal of triphenyl ester OPEs was significantly higher than that of chloride and alkyl OPEs. The addition of FeCl₃ and Fe powder increased the rate of degradation of triphenyl ester OPEs, with a DT₅₀ for triphenyl ester OPEs of 1.7–3.8 d for FeCl₃ and 1.3–4.7 d for Fe powder, compared to a DT₅₀ of 4.3–6.9 d for the blank control. Addition of an electron donor and a rhamnolipid increased the rate of removal of chlorinated OPEs, with DT₅₀ values for tris(2-carboxyethyl)phosphine) (TCEP) and tris(1,3-dichloroisopropyl)phosphate (TDCPP) of 18.4 and 10.0 d, respectively, following addition of the electron donor, and 13.7 and 3.0 d, respectively, following addition of the rhamnolipid. However, addition of an electron donor, electron acceptor, surfactant, and Fe powder did not always increase the degradation of different kinds of OPEs, which was closely related to the structure of the OPEs. No treatment increased the removal of alkyl OPEs due to their low anaerobic degradability. Tween 80, a non-ionic surfactant, inhibited anaerobic degradation to some degree for all OPEs. Under aerobic conditions, alkyl OPEs were more easily degraded, chlorinated OPEs needed a long adaptation period to degrade and finally attain a 90% removal rate, while the rates of degradation of triphenyl ester OPEs were significantly affected by the concentration of sludge. Higher sludge concentrations help microorganisms to adapt and remove OPEs. This study provides new insights into methods for eliminating emerging pollutants using activated sludge cultured with kitchen garbage biomass and agricultural residues.

Mechanistic insights into organic carbon-driven water blackening and odorization of urban rivers

With rapid global urbanization, massive anthropogenic inputs of organic matter and inorganic nutrients are resulting in severe pollution of urban rivers and consequently altering the structure and function of their aquatic microbial communities. In contrast to nutrient-induced eutrophication of freshwaters, water blackening and odorization of urban rivers, as well as their microbial communities, are poorly understood at a mechanistic level. Here, in a one-year field study on the taxonomic composition, predicted function and spatiotemporal dynamics of water and sediment microbial communities in seven black-odorous urban rivers in a megacity in southern China, combined with laboratory water-sediment column experiments, we pinpointed organic carbon as a key parameter driving the overgrowth of aquatic heterogeneous microorganisms. These microorganisms are major constituents of suspended black flocs that mediate methanogenic digestion of organic carbon and consequent water blackening and odorization. Source tracking analysis revealed a strikingly high contribution of sewage communities to black-odorous water microbial communities, in which emerging pathogens are enriched. Our results provide mechanistic insight into organic carbon-driven water blackening and odorization of urban rivers, which brings up current remediation strategies in questioning and sheds light on the future sustainable management of urban aquatic ecosystems.

Anaerobic degradation of xenobiotic organic contaminants (XOCs): The role of electron flow and potential enhancing strategies

In groundwater, deep soil layer, sediment, the widespread of xenobiotic organic contaminants (XOCs) have been leading to the concern of human health and eco-environment safety, which calls for a better understanding on the fate and remediation of XOCs in anoxic matrices. In the absence of oxygen, bacteria utilize various oxidized substances, e.g. nitrate, sulphate, metallic (hydr)oxides, humic substance, as terminal electron acceptors (TEAs) to fuel anaerobic XOCs degradation. Although there have been increasing anaerobic biodegradation studies focusing on species identification, degrading pathways, community dynamics, systematic reviews on the underlying mechanism of anaerobic contaminants removal from the perspective of electron flow are limited. In this review, we provide the insight on anaerobic biodegradation from electrons aspect - electron production, transport, and consumption. The mechanism of the coupling between TEAs reduction and pollutants degradation is deconstructed in the level of community, pure culture, and cellular biochemistry. Hereby, relevant strategies to promote anaerobic biodegradation are proposed for guiding to an efficient XOCs bioremediation.

Combined impact of organic matter, phosphorus, nitrate, and ammonia nitrogen on the process of blackwater

Blackwater events are frequently reported over the world and become a serious environmental problem. However, the mechanisms of blackwater occurrence are not fully understood yet. This study simulated the process of blackwater with the combined pollution in an orthogonal experiment, which had 4 factors (TOC, TP, NH4+-N, and NO3--N) and 4 levels (None, Low, Middle, and High). Results showed that the process of water condition changes was divided into two parts, which were "exogenous" and "algae-derived" blackwater, and the influence of four different pollutants on the occurrence of the blackwater was ranked as follows: TOC > TP > NO3--N > NH4+-N. With the increase of organic matter addition, the anaerobic condition in water was prolonged and the concentration of Fe2+ had a significant increase. In addition, under the None phosphorus condition, the descent rates of DO and COD in the water were reduced, and the algae bloom was obviously deferred. Moreover, the addition of organic matter or phosphorus changed the microbial community structure and led to different water processes. Particularly, only on the condition of the high content of TOC and phosphorus, the diversity of sulfate-reducing bacteria (e.g., Pseudomonas, Paludibacter, and Bacteroides) increased significantly, which accounted for 51.4%, causing the significant production of S2- in the water. Water's lack of phosphorus showed a low rate of decomposition of organic matter, which might be the result of a considerable increase in the abundance of aerobic Trichococcus and Malikia. This study shows that organic matter and phosphorus have synergistic effect on blackwater occurrence. In the treatment of blackwater, the exogenous pollutant control should reduce the discharge of organic pollutants, and endogenous control should focus on phosphorus abatement and reduce nitrogen control.

Microscale heterogeneity of the soil nitrogen cycling microbial functional structure and potential metabolism

Soil aggregates, with complex spatial and nutritional heterogeneity, are clearly important for regulating microbial community ecology and biogeochemistry in soils. However, how the taxonomic composition and functional attributes of N-cycling-microbes within different soil particle-size fractions under a long-term fertilization treatment remains largely unknown. Here, we examined the composition and metabolic potential for urease activity, nitrification, N₂ O production and reduction of the microbial communities attached to different sized soil particles (2000-250, 250-53 and <53 μm) using a functional gene microarray (GeoChip) and functional assays. We found that urease activity and nitrification were higher in <53 μm fractions, whereas N₂ O production and reduction rates were greater in 2000-250 and 250-53 μm across different fertilizer regimes. The abundance of key N-cycling genes involved in anammox, ammonification, assimilatory and dissimilatory N reduction, denitrification, nitrification and N₂ -fixation detected by GeoChip increased as soil aggregate size decreased; and the particular key genes abundance (e.g., ureC, amoA, narG, nirS/K) and their corresponding activity were uncoupled. Aggregate fraction exerted significant impacts on N-cycling microbial taxonomic composition, which was significantly shaped by soil nutrition. Taken together, these findings indicate the important roles of soil aggregates in differentiating N-cycling metabolic potential and taxonomic composition, and provide empirical evidence that nitrogen metabolism potential and community are uncoupled due to aggregate heterogeneity.

Novel magnetic loofah sponge biochar enhancing microbial responses for the remediation of polycyclic aromatic hydrocarbons-contaminated sediment

Magnetic activated carbon and magnetic biochar have been widely used for contaminants removal due to the advantages of sequestration and recovery. However, the remediation function and microbial response of conductive magnetic carbonaceous materials for treating organic contaminated sediment are poorly understood. In this study we applied novel three-dimensional mesh magnetic loofah sponge biochar (MagLsBC), made from natural agricultural product, to remediate polycyclic aromatic hydrocarbons (PAHs)-contaminated sediment. Compared to other carbon-based materials, MagLsBC achieved the high reduction of PAHs content and bioavailability in sediment by respectively 31.9 % and 38.1 % after 350 days. Microbial analysis showed that MagLsBC amended sediment had different community diversity, structure and enriched dominant species associated with the aromatic hydrocarbon metabolism. And MagLsBC amendment significantly increased the aromatic compounds degradation function, which was not observed in other treatments, and methanogenesis function. Further analysis revealed that the enhanced microbial responses in MagLsBC amended sediment were related with the high conductivity of MagLsBC. These results give the new insights into the effect of magnetic carbon materials on microbial community and organic pollutants degradation function during the long period amendment, demonstrating MagLsBC as an effective material with the biostimulation potential for the risk control of PAHs contamination.

Elevated nitrate simplifies microbial community compositions and interactions in sulfide-rich river sediments

Excessive nitrate in water systems is prevailing and a global risk of human health. Polluted river sediments are dominated by anaerobes and often the hotspot of denitrification. So far, little is known about the ecological effects of nitrate pollution on microbial dynamics, especially those in sulfide-rich sediments. Here we simulated a nitrate surge and monitored the microbial responses, as well as the changes of important environmental parameters in a sulfide-rich river sediment for a month. Our analysis of sediment microbial communities showed that elevated nitrate led to (i) a functional convergence at denitrification and sulfide oxidation, (ii) a taxonomic convergence at Proteobacteria, and (iii) a significant loss of biodiversity, community stability and other functions. Two chemolithotrophic denitrifiers Thiobacillus and Luteimonas were enriched after nitrate amendment, although the original communities were dominated by methanogens and syntrophic bacteria. Also, serial dilutions of sediment microbial communities found that Thiobacillus thiophilus dominated 18/30 communities because of its capability of simultaneous nitrate reduction and sulfide oxidation. Additionally, our network analysis indicated that keystone taxa seemed more likely to be native auxotrophs (e.g., syntrophic bacteria, methanogens) rather than dominant denitrifiers, possibly because of the extensive interspecific cross-feeding they estabilished, while environment perturbations probably disrupted that cross-feeding and simplified microbial interactions. This study advances our understanding of microbial community responses to nitrate pollution and possible mechanism in the sulfide-rich river sediment.

Nitrate-assisted biodegradation of polycyclic aromatic hydrocarbons (PAHs) in the water-level-fluctuation zone of the three Gorges Reservoir, China: Insights from in situ microbial interaction analyses and a microcosmic experiment

An increase in polycyclic aromatic hydrocarbon (PAH) pollution poses significant challenges to human and ecosystem health in the Three Gorges Reservoir (TGR) of the Yangtze River. Based on the combination of PAH analysis with qPCR and high-throughput sequencing of bacteria, 32 topsoil samples collected from 16 sites along the TGR were used to investigate the distribution and biodegradation pathways of PAHs in the water-level-fluctuation zone (WLFZ). The results indicated that the concentrations of PAHs were 43.8-228.2 and 30.8-206.3 ng/g soil (dry weight) under the high- and low-water-level (HWL and LWL) conditions, respectively. The PAH concentration in urban areas was higher than that in rural areas. Under both the HWL and LWL conditions, the abundance of the bamA gene, a biomarker of anaerobic PAH biodegradation, was significantly higher than that of the ring-hydroxylating-dioxygenase (RHD) gene, a biomarker of aerobic PAH biodegradation. The abundance of the bamA gene was significantly positively correlated with PAHs (R² = 0.8), and the biodegradation percentage of PAHs incubated anaerobically was greater than that in the aerobically incubated microcosm experiments. These data implicated a key role of the anaerobic pathway in PAH biodegradation. Co-occurrence network analysis suggested that anaerobic Anaerolineaceae, Dechloromonas, Bacteroidetes_vadin HA17 and Geobacter were key participants in the biodegradation of PAHs. The diversity analysis of functional bacteria based on the bamA gene and microcosm experiments further demonstrated that nitrate was the primary electron acceptor for PAH biodegradation. These findings provide a new perspective on the mechanism of PAH biodegradation in the TGR and knowledge that can be used to develop strategies for environmental management.

Mechanism of ammonium sharp increase during sediments odor control by calcium nitrate addition and an alternative control approach by subsurface injection

Nitrate-driven sulfide/ferrous oxidation has been proved a cost-effective approach for river sediments in-situ odor control. However, calcium nitrate addition would sharply increase ammonium concentration in interstitial water and the mechanism was not yet clear. In this work, though sulfide and ferrous iron were efficiently oxidized, about 102% of NH₄⁺ concentration increased in interstitial water on the first day of calcium nitrate injection (30 mg kg dwt^-1), and about 31% more NH₄⁺ increase at the 21st days was observed. To discover the mechanism of ammonium sharp release, desorption kinetics experiment was conducted and the results suggested that the short-time sharp releases of ammonium when calcium nitrate was added could be attributed to the chemical extraction of exchangeable ammonium by calcium ion. Furthermore, at the end of treatment, many genus such as Thiobacillus, Sulfurimonas, Thermomonas, and Clostridium, which were closely related to sulfide and ferrous-driven denitrification and dissimilatory nitrate reduction to ammonium (DNRA), were identified by 16S rRNA Illumina sequencing method. These findings indicated the long-time increase of ammonium might be determined by the biochemical processes (e.g. DNRA) driven by nitrate reduction. Therefore, to avoid the impact of ammonium release, an alternative subsurface injection method was introduced in this work, and the results showed that ammonium releases could be well controlled when the injection position was beneath 10 cm of the sediment surface.

Availability of Nitrite and Nitrate as Electron Acceptors Modulates Anaerobic Toluene-Degrading Communities in Aquifer Sediments

Microorganisms are essential in the degradation of environmental pollutants. Aromatic hydrocarbons, e.g., benzene, toluene, ethylbenzene, and xylene (BTEX), are common aquifer contaminants, whose degradation in situ is often limited by the availability of electron acceptors. It is clear that different electron acceptors such as nitrate, iron, or sulfate support the activity of distinct degraders. However, this has not been demonstrated for the availability of nitrate vs. nitrite, both of which can be respired in reductive nitrogen cycling. Here via DNA-stable isotope probing, we report that nitrate and nitrite provided as electron acceptors in different concentrations and ratios not only modulated the microbial communities responsible for toluene degradation but also influenced how nitrate reduction proceeded. Zoogloeaceae members, mainly Azoarcus spp., were the key toluene degraders with nitrate-only, or both nitrate and nitrite as electron acceptors. In addition, a shift within Azoarcus degrader populations was observed on the amplicon sequence variant (ASV) level depending on electron acceptor ratios. In contrast, members of the Sphingomonadales were likely the most active toluene degraders when only nitrite was provided. Nitrate reduction did not proceed beyond nitrite in the nitrate-only treatment, while it continued when nitrite was initially also present in the microcosms. Likely, this was attributed to the fact that different microbial communities were stimulated and active in different microcosms. Together, these findings demonstrate that the availability of nitrate and nitrite can define degrader community selection and N-reduction outcomes. It also implies that nitrate usage efficiency in bioremediation could possibly be enhanced by an initial co-supply of nitrite, via modulating the active degrader communities.

Functional potential and assembly of microbes from sediments in a lake bay and adjoining river ecosystem for polycyclic aromatic hydrocarbon biodegradation

Lake and adjoining river ecosystems are ecologically and economically valuable and are heavily threatened by anthropogenic activities. Determining the inherent capacity of ecosystems for polycyclic aromatic hydrocarbon (PAH) biodegradation can help quantify environmental impacts on the functioning of ecosystems, especially on that of the microbial community. Here, PAH biodegradation potential was compared between sediments collected from a lake bay (LS) and an adjoining river (RS) ecosystem. Microbial community composition, function, and their co-occurrence patterns were also explored. In the RS, the biodegradation rates (K_D ) of pyrene or PAH were almost two orders of magnitude higher than those in the LS. Sediment functional community structure and network interactions were dramatically different between the LS and RS. Although PAH degradation genes (p450aro, quinoline, and qorl) were detected in the LS, the community activity of these genes needed to be biostimulated for accelerated bioremediation. In contrast, functional communities in the RS were capable of spontaneous natural attenuation of PAH. The degradation of PAH in the RS also required coordinated response of the complex functional community. Taken together, elucidating functions and network interactions in sediment microbial communities and their responses to environmental changes are very important for the bioremediation of anthropogenic toxic contaminants.

Bacterial community responses to tourism development in the Xixi National Wetland Park, China

A large number of urban wetland parks have been established, but knowledge about the effects of tourism development on the microbial diversity and ecosystem functioning remains limited. This study aimed to clarify the responses of bacterial communities to tourism development targeted the Xixi National Wetland Park, China. By analyzing the diversity, composition, assembly pattern, and environmental drivers of bacterial communities, we found that tourism development considerably affected the water quality, which further decreased the α-diversity but increased the β-diversity in open areas for landscaping and recreation. Specifically, there was higher Simpson dissimilarity across functional wetland areas, indicating that species replacement mainly explained β-diversity patterns of bacterial communities. RDA analysis and ecological processes quantification further suggested that TOC and TC were the major factors in the open areas driving bacterial communities in water and sediment, respectively. Also, typical anti-disturbance taxa (Gammaproteobacteria) and potential pathogens (Bacillus) were enriched in the wetlands under more anthropogenic disturbances. Findings of the present study highlighted the effects of tourism development on bacterial communities resulted in obvious spatial variation in the Xixi National Wetland Park. This study gives us useful information for ecological assessments of urban wetlands, and further can provide references in making appropriate strategies to manage wetland ecosystems.

Ciceribacter ferrooxidans sp. nov., a nitrate-reducing Fe(II)-oxidizing bacterium isolated from ferrous ion-rich sediment

A nitrate-reducing Fe(II)-oxidizing bacterial strain, F8825^T, was isolated from the Fe(II)-rich sediment of an urban creek in Pearl River Delta, China. The strain was Gram-negative, facultative chemolithotrophic, facultative anaerobic, non-spore-forming, and rod-shaped with a single flagellum. Phy-logenetic analysis based on 16S rRNA gene sequencing indicated that it belongs to the genus Ciceribacter and is most closely related to C. lividus MSSRFBL1^T (99.4%), followed by C. thiooxidans F43b^T (98.8%) and C. azotifigens A.slu09^T (98.0%). Fatty acid, polar lipid, respiratory quinone, and DNA G + C content analyses supported its classification in the genus Ciceribacter. Multilocus sequence analysis of concatenated 16S rRNA, atpD, glnII, gyrB, recA, and thrC suggested that the isolate was a novel species. DNA-DNA hybridization and genome sequence comparisons (90.88 and 89.86%, for values of ANIm and ANIb between strains F8825^T with MSSRFBL1^T, respectively) confirmed that strain F8825^T was a novel species, different from C. lividus MSSRFBL1^T, C. thiooxidans F43b^T, and C. azotifigens A.slu09^T. The physiological and biochemical properties of the strain, such as carbon source utilization, nitrate reduction, and ferrous ion oxidation, further supported that this is a novel species. Based on the polyphasic taxonomic results, strain F8825^T was identified as a novel species in the genus Ciceribacter, for which the name Ciceribacter ferrooxidans sp. nov. is proposed. The type strain is F8825^T (= CCTCC AB 2018196^T = KCTC 62948^T).

Elucidating the negative effect of denitrification on aromatic humic substance formation during sludge aerobic fermentation

Humic substance (HS), as an aromatic compound, is the core product of aerobic fermentation. Denitrification-dependent degradation of aromatic compounds have been repeatedly observed in environment. However, few studies have elucidated the relationship between denitrification and aromatic HS during sludge aerobic fermentation. This study was conducted to investigate the effect of enhanced denitrification on aromatic HS formation. On the 24th day of sludge aerobic fermentation, five tests (CK, Run1, Run2, Run3 and Run4) were executed, and nitrate concentrations were adjusted to 480 ± 20, 500 ± 20, 1000 ± 20, 1500 ± 20 and 2000 ± 20 mg/kg with potassium nitrate, respectively. Analytical results demonstrated that nitrate addition increased denitrifying genes abundance and enhanced denitrification, which further reduced aromatic HS formation (p < 0.05). Especially in Run3, the concentrations of HS and humic acid on the 52nd day dramatically decreased by 12.9 % and 34.2 % in comparison with those on the 31st day. High-throughput sequencing revealed that enhanced denitrification effectively stimulated the metabolism of denitrifying microorganisms with aromatic-degrading capability. Co-occurring network analysis indicated that some keystone taxa of denitrification aromatic-degrading microorganisms involved in the conversion of nitrate to nitrite were the most crucial for enhancing denitrification and reducing aromatic HS formation.

Interactions of PAH-degradation and nitrate-/sulfate-reducing assemblages in anaerobic sediment microbial community

Nitrate and sulfate are electron acceptors (EAs) for biodegradation of polycyclic aromatic hydrocarbons (PAHs) in anaerobic sediments. The efficiency of PAHs biodegradation depends on the strength of the interactions between PAH-degradation and EA-reduction assemblages. However, these interactions are less studied. In this study, microbial response and PAH degradation efficiencies in river sediment were investigated using nitrate and sulfate stimulation. Results showed that the functional assemblages (PAH-degraders, nitrate- and sulfate- reducers) were low connectivity in the microbial network without EA adding. Nitrate input rapidly (<1 day) raised the nitrate reduction intensity. And the PAH-degraders and nitrate reducers established significant and direct correlations under nitrate stimulation, seen from the 13 connectors (nodes) in the microbial network. In contrast, sulfate reducers slowly increased in abundance (>20 days) and were connected to PAH-degraders through indirect connection under sulfate stimulation. The null model suggested that nitrate led to a higher level of directional selection, which implied that nitrate was a more favorable EA to trigger the deterministic succession. As a result, PAHs degradation was faster with nitrate stimulation (t_1/2 = 68.3 d) than with sulfate stimulation (t_1/2 = 164.6 d). These mechanistic understandings can serve as the guidelines for EA selection in bioremediation.

Revealing the Inner Dynamics of Fulvic Acid from Different Compost-Amended Soils through Microbial and Chemical Analyses

The formation of fulvic acid (FA), an aromatic compound, is affected by the compost amendment. This study aimed to assess the extent of the humification of FA in soil amended with seven different composts. Results showed that composts improved the FA concentration in soil. Parallel factor (PARAFAC) analysis, combined with hetero-two-dimensional correlation spectroscopy (hetero-2DCOS), indicated that the inner changes in FA components determined the evolution of mineralization. The diversity in the composts used and the dominant microbes present might be responsible for the evolution of different mechanisms of FA transformation. Structural equation models (SEMs) demonstrated that the FA components were transformed directly by microbes, or indirectly via changes in the total organic carbon (TOC) and total nitrogen (TN) contents, C:N ratio, humic substance (HS) levels, and humic acid (HA): FA ratio, which regulate the microbial community structure. Our results will be useful for improving the bioavailability of compost products and realizing sustainable utilization of the soil.

Metagenomics as a Public Health Risk Assessment Tool in a Study of Natural Creek Sediments Influenced by Agricultural and Livestock Runoff: Potential and Limitations

Little is known about the public health risks associated with natural creek sediments that are affected by runoff and fecal pollution from agricultural and livestock practices. For instance, the persistence of foodborne pathogens such as Shiga toxin-producing Escherichia coli (STEC) originating from these practices remains poorly quantified. Towards closing these knowledge gaps, the water-sediment interface of two creeks in the Salinas River Valley of California was sampled over a 9-month period using metagenomics and traditional culture-based tests for STEC. Our results revealed that these sediment communities are extremely diverse and have functional and taxonomic diversity comparable to that observed in soils. With our sequencing effort (∼4 Gbp per library), we were unable to detect any pathogenic E. coli in the metagenomes of 11 samples that had tested positive using culture-based methods, apparently due to relatively low abundance. Furthermore, there were no significant differences in the abundance of human- or cow-specific gut microbiome sequences in the downstream impacted sites compared to that in upstream more pristine (control) sites, indicating natural dilution of anthropogenic inputs. Notably, the high number of metagenomic reads carrying antibiotic resistance genes (ARGs) found in all samples was significantly higher than ARG reads in other available freshwater and soil metagenomes, suggesting that these communities may be natural reservoirs of ARGs. The work presented here should serve as a guide for sampling volumes, amount of sequencing to apply, and what bioinformatics analyses to perform when using metagenomics for public health risk studies of environmental samples such as sediments.IMPORTANCE Current agricultural and livestock practices contribute to fecal contamination in the environment and the spread of food- and waterborne disease and antibiotic resistance genes (ARGs). Traditionally, the level of pollution and risk to public health are assessed by culture-based tests for the intestinal bacterium Escherichia coli However, the accuracy of these traditional methods (e.g., low accuracy in quantification, and false-positive signal when PCR based) and their suitability for sediments remain unclear. We collected sediments for a time series metagenomics study from one of the most highly productive agricultural regions in the United States in order to assess how agricultural runoff affects the native microbial communities and if the presence of Shiga toxin-producing Escherichia coli (STEC) in sediment samples can be detected directly by sequencing. Our study provided important information on the potential for using metagenomics as a tool for assessment of public health risk in natural environments.

Aerobic and anoxic degradation and detoxification of profenofos insecticide by Pseudomonas plecoglossicida strain PF1

Profenofos insecticide is one of the most broadly used organophosphorus pesticides causing the contamination of soil and groundwater. Since dissolved oxygen concentration in groundwater is limited, this study aimed to investigate profenofos biodegradation and detoxification under aerobic and anoxic conditions using the profenofos-degrading Pseudomonas plecoglossicida strain PF1 (PF1). Anoxic biodegradation under the presence of nitrate was the focus. The results showed that profenofos at 10-150 mg/L was degraded under aerobic and anoxic conditions with removal efficiencies of 38-55% and 27-45%, respectively. Kinetic analysis following the Michaelis-Menten model revealed that the maximum substrate degradation rates and the Michaelis constants were 13.07 and 8.92 mg/L/d and 92.07 and 84.76 mg/L under aerobic and anoxic conditions, respectively. The culture preferred an aerobic environment resulting in better biodegradation performance. During the degradation experiment, 4-bromo-2-chlorophenol and 1,1-dimethylethylphenol were detected as profenofos biodegradation intermediate products. Microbial toxicity, phytotoxicity, and cytogenotoxicity assays showed that the toxicity of the contaminated water significantly decreased after both aerobic and anoxic biodegradation by PF1. The results from this study indicated that PF1 has the potential for bioremediation in a profenofos-contaminated environment under the presence or absence of oxygen.

How did the bacterial community respond to the level of urbanization along the Yangtze River?

Bacterial communities in the sediment of the Yangtze River influenced by rapid urbanization have thus far been under-investigated despite the importance of microorganisms as mass transporters. Here, the response patterns of the bacterial community along the Yangtze River to different levels of urbanization were generated using 16S rRNA Miseq sequencing. The results reveal that economic aspects have made the largest contribution (41.8%) to the urbanization along the Yangtze River. A clear declining tendency in the abundance of Chloroflexi and Acidobacteria and a significant increase in the abundance of Bacteroidetes were observed with an elevated urbanization level gradient. Bacterial diversity showed a negative relevance (P < 0.01) to the demographic, economic and social urbanization index. Per capita gross domestic product (GDP) (PCGDP) and the GDP of tertiary industry (GDP3) exhibited significantly (P < 0.05) negative correlations with the bacterial diversity, while a positive relationship between the pH and α-diversity (P < 0.05) was observed. Redundancy analysis revealed that PCGDP was significantly correlated (13.9%, P < 0.01) with the overall bacterial compositions, followed by temperature (10.8%, P < 0.01) and GDP3 (8.4%, P < 0.05). Meanwhile, the GDP3 (35.9%), the ratio of total nitrogen and total phosphorus (N/P) (12.9%) and the PCGDP (8.8%) were revealed to be most significantly related to the metabolic bacteria (P < 0.05). The metabolic functions of the bacteria related to the N-cycle and S-cycle were significant in the sediment of the Yangtze River. The variations of the bacterial community and metabolic function responding to the rapid urbanization were related to the economic development via the influence of the 'mass effect'. In brief, the tertiary industry was significantly correlated with the variations in the composition of the metabolic community and the variations in the overall bacteria were both related to the tertiary and secondary industry.

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.

The responses of bacterial community and N2O emission to nitrogen input in lake sediment: Estrogen as a co-pollutant

Excessive nitrogen (N) input is one of the most important causative factors of lake eutrophication, which has aroused increasing public attention in past decades. Estrogen contamination is also an increasing environmental problem in aquatic systems around the world. Although both substances usually co-exist in aquatic ecosystems, many researches have only investigated the influences of either N or estrogen individually on sediment bacterial community and nitrous oxide (N₂O) emission. Knowledge regarding the combined effects of N and estrogen is still very limited. In this study, a 30-day laboratory incubation experiment was performed to examine the impacts of different N sources (ammonium and nitrate) combined with 17β-estradiol (E2) on sediment bacterial community. High-throughput 16S rRNA gene sequencing technique was used and N₂O emission was measured. The results revealed that the relative abundances of Proteobacteria and Bacteroidetes were higher in nitrate treatment than ammonium treatment. Compared to N treatments, N and E2 combined treatments showed higher relative abundances of Proteobacteria, Bacteroidetes, and Firmicutes, but lower relative abundances of Chloroflexi, Acidobacteria, and Actinobacteria over entire incubation period. At the genus level, the relative abundances of genera Flavobacterium, Pseudomonas, Arenimonas, Novosphingobium, Massilia, Aquabacterium, and Bacillus were enhanced by N treatments and especially N and E2 combined treatments, compared to sediment without addition of N and E2. However, the relative abundances of Sporacetigenium, Gaiella, Desulfatiglans, Nitrospira, and Haliangium were decreased in N treatments. Apart from the changes in bacterial community structure, N₂O emission was also influenced by different treatments. Nitrate exerted a more significant positive effect on N₂O emission than ammonium, and the cumulative emission of N₂O was highest in nitrate and E2 combined treatment. Very low abundances of ammonia monooxygenase (amoA) gene and hydroxylamine oxidase (hao) gene were observed in sediments compared to other genes involved in N cycles (such as nitrate reductase (narG and napA) genes, nitrite reductase (nirB, nirK, and nrfA) genes, and nitric oxide reductase (norB) gene), implying that denitrification rather than nitrification played an important role in sediments. The abundances of napA, nirK, and norB were higher in N and E2 combined treatments, indicating that E2 might provide a carbon source for denitrifiers. Moreover, decrease in the abundance of nitrous oxide reductase (nosZ) gene during the denitrifying process in N and E2 combined treatment might be an important reason for increases of N₂O emission. These results indicated that alterations of the bacterial community structure due to the co-existence of N and E2 could also change the abundances of genes involved in N cycle.

A new method to overall immobilization of phosphorus in sediments through combined application of capping and oxidizing agents

A new method has been developed for improving the overall immobilization efficiency of phosphorus (P) in sediment. A capping agent (lanthanum modified bentonite, LMB) was sprinkled on the sediment surface to prevent the release of P in the top sediment layer. Meanwhile, an oxidizing agent (calcium nitrate, CN) was injected into the sediment layer (~5 cm) to immobilize labile P in deep sediment layers. High-resolution sampling techniques, including diffusive gradients in thin films (DGT) and high-resolution dialysis (HR-Peeper) were employed to investigate the fine-scale changes of labile and/or soluble nitrogen, P, sulfide and iron in sediments, respectively. The results showed that the combined application of LMB and CN had significant advantages over the individual treatments. The average concentrations of soluble reactive phosphorus (SRP) (0.01 mg/L) in the overlying water after a 68-day incubation were only 10%, 21% and 4% for the CK, LMB and CN treatments, respectively. Furthermore, the immobilization effect caused by the combined treatment reached from the sediment-water interface to a depth of 60 mm in the sediment, and the effective depth was much >20 mm caused by LMB treatment. The concentrations of SRP in the sediment profile were also lower than those of the other treatments. The results of this work indicate that the combined application of capping and oxidizing agents is a promising method to control water eutrophication by preventing the release of P from both the top and deep sediment layers.

Long-term harvesting of reeds affects greenhouse gas emissions and microbial functional genes in alkaline wetlands

Reed (Phragmites australis) is dominant vegetation in alkaline wetlands that is harvested annually due to its economic value. To reveal the effects of harvesting reeds on the emission of greenhouse gases (GHG), the annual soil physicochemical characteristics and flux of GHGs in a reed wetland without harvesting (NHRW) and with harvesting (HRW) were measured. The results showed that after the harvesting of reeds, the total organic carbon (TOC) and total nitrogen (TN) significantly decreased, and soil temperature significantly increased. The annual cumulative N₂O emissions decreased from 0.73 ± 0.20 kg ha^-1 to -0.57 ± 0.49 kg ha^-1 with the harvesting of reeds. The annual cumulative CH₄ emissions also decreased from 561.88 ± 18.61 kg ha^-1 to 183.13 ± 18.77 kg ha^-1 with the harvesting of reeds. However, harvesting of reeds had only a limited influence on the annual cumulative CO₂ emissions. A Pearson correlation analysis revealed that the CO₂ and N₂O emissions were more sensitive to temperature than the CH₄ emissions. Both structural equation modeling (SEM) analysis and slurry incubation confirmed that higher temperatures offset the reduction of CO₂ emissions after reed harvesting. Metagenomics showed that the abundance of functional genes involved in both GHG sink and source decreased with reed harvesting. This study presents a comprehensive view of reed harvesting on GHG emissions in alkaline wetlands, yielding new insight into the microbial response and offering a novel perspective on the potential impacts of wetland management.

The dissipation and risk alleviation mechanism of PAHs and nitrogen in constructed wetlands: The role of submerged macrophytes and their biofilms-leaves

The role of submerged macrophytes (Vallisneria natans, Hydrilla verticillata and artificial plant) and their biofilms-leaves for the dissipation and risk alleviation mechanism of PAHs (phenanthrene and pyrene) and nitrogen in constructed wetland systems with PAH-polluted sediments were investigated. Biofilms-leaves/surface might contribute to PAHs degradation, which was positively correlated with PAHs degrading bacteria. Nitrogen-fixing bacteria in biofilms on surface might cause total nitrogen in sediment (TNs) increasing by 4% from 14th d to 28th d indirectly when suffering PAHs pollution. The relative abundance of nitrogen-fixing bacteria significantly increased with the increase of PAHs concentrations in early period (p < 0.01), which might lead to risk of nitrogen accumulation further. Heat maps showed that the relative abundance of functional bacteria were influenced in order of attached surface > incubation time > spiking concentration of PAHs. Interestingly, differences of deduced bacterial functions were affected in order of incubation time > attached surface > spiking concentration. Thus, submerged macrophytes and their biofilms on leaves not only played an important role in PAHs degradation, but also regulated the nitrogen cycling in constructed wetland systems, which could reduce these pollutants risk for natural environment, organisms and human health.

Nitrate addition promotes the nitrogen cycling processes under the co-contaminated tetrabromobisphenol A and copper condition in river sediment

Tetrabromobisphenol A (TBBPA) and copper (Cu) are the main pollutants at e-waste recycling sites and the effects of their biotoxicity on microorganisms have drawn extensive attention. Nitrate-based bioremediation has been applied to organic pollutant-contaminated sediments since nitrate is a favorable electron acceptor for microbes. However, the effects of TBBPA and Cu on nitrogen (N)-cycling microorganisms and bioremediation in co-contaminated sediments remain unclear. Thus, our study examined the effects of TBBPA and Cu with/without nitrate addition on the TBBPA biodegradation efficiencies, microbial activities, and N functional genes. It was found the biodegradation efficiencies of TBBPA were improved by the nitrate addition from 34.7% to 59.3% and from 22.6% to 42.8% in the TBBPA and TBBPA-Cu contaminated groups, respectively. The inhibitions of the catalase activity increased with the nitrate addition because of the anaerobic respiration of the microorganisms. In addition, the potential denitrification rate exhibited an increasing trend from 6.46 to 8.23 mg-N kg^-1 dry sediment day^-1 during the period of 15-90 days after adding nitrate to the co-contaminated group, whereas the potential nitrification rate exhibited an opposite trend and decreased from 4.47 to 3.19 mg-N kg^-1 dry sediment day^-1. The denitrification gene abundances of the N-cycling genes were 10⁷-10⁸ orders of magnitude higher and significantly increased in the nitrate addition groups. The amoA gene abundances were lower than the denitrification gene abundances and were 10⁵-10⁶ orders of magnitude in the same groups. Moreover, the interaction types of the pollutants on the gene abundances were changed from synergistic to antagonistic as nitrate addition. Our study emphasized the gap of knowledge on nitrate addition affecting N-cycling microbes in the combined pollutants exposure sediments, and will be helpful for further bioremediation in different contaminated scenarios.

Structure and function of microbial community associated with phenol co-substrate in degradation of benzo[a]pyrene in coking wastewater

Coking wastewater (CWW) contains high contents of phenols and other toxic and refractory compounds including polycyclic aromatic hydrocarbons (PAHs) with the most carcinogenic benzo[a]pyrene (BaP) among them. The mechanism of PAHs/BaP degradation in activated sludge of CWW treatment with phenol as co-substrate was studied. For characterizing the structure and functions of microbial community associated with BaP degradation with phenol as co-substrate, high-throughput MiSeq sequencing was used to examine the 16S rRNA genes of microbiology, revealing noticeable shifts in CWW activated sludge bacterial populations. Major genera involved in anaerobic degradation were Tissierella_Soehngenia, Diaphorobacter and Geobacter, whereas in aerobic degradation Rhodanobacter, Dyella and Thauera prevailed. BaP degradation with phenol as co-substrate induced bacterial diversification in CWW activated sludge in opposite trends when anaerobic and aerobic conditions were applied. In order to predict the microbial community functional profiling, a bioinformatics software package of phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) was run to find that some dominant genera enriched in the BaP pathway may own the ability to degrade PAHs/BaP. Further experiments should focus on testing the dominant genera in BaP degradation at different oxygen levels.

A pollution gradient contributes to the taxonomic, functional, and resistome diversity of microbial communities in marine sediments

BACKGROUND

Coastal marine environments are one of the most productive ecosystems on Earth. However, anthropogenic impacts exert significant pressure on coastal marine biodiversity, contributing to functional shifts in microbial communities and human health risk factors. However, relatively little is known about the impact of eutrophication-human-derived nutrient pollution-on the marine microbial biosphere.

RESULTS

Here, we tested the hypothesis that benthic microbial diversity and function varies along a pollution gradient, with a focus on human pathogens and antibiotic resistance genes. Comprehensive metagenomic analysis including taxonomic investigation, functional detection, and ARG annotation revealed that zinc, lead, total volatile solids, and ammonia nitrogen were correlated with microbial diversity and function. We propose several microbes, including Planctomycetes and sulfate-reducing microbes as candidates to reflect pollution concentration. Annotation of antibiotic resistance genes showed that the highest abundance of efflux pumps was found at the most polluted site, corroborating the relationship between pollution and human health risk factors. This result suggests that sediments at polluted sites harbor microbes with a higher capacity to reduce intracellular levels of antibiotics, heavy metals, or other environmental contaminants.

CONCLUSIONS

Our findings suggest a correlation between pollution and the marine sediment microbiome and provide insight into the role of high-turnover microbial communities as well as potential pathogenic organisms as real-time indicators of water quality, with implications for human health and demonstrate the inner functional shifts contributed by the microcommunities.

Occurrence and distribution of antibiotic resistance genes in the sediments of the East China Sea bays

The coastal area of the East China Sea has experienced rapid urbanization and industrialization in China since 1980s, resulting in severe pollution of its environments. Antibiotic resistance genes (ARGs) are regarded as a kind of emerging pollutant with potential high risk. The sediment samples were collected from Hangzhou Bay (HB), Xiangshan Bay (XB), and Taizhou Bay (TB) to investigate the spatial occurrence and distribution of 27 ARGs and class I integron-integrase gene (intI1) in the coastal area of the East China Sea. The PCR results showed the frequent presence of 11 ARGs and intI1 in the sediments of the three bays. The qPCR results further showed that sulfonamide resistance was the most prevalent ARG type and antibiotic target replacement and protection were the most important resistance mechanisms in the sediments. Regarding the subtype of ARGs, sulI, tetW, and dfrA13 were the most abundant ARGs, in which sulI was higher in TB (based on both the absolute and relative abundances) and dfrA13 was higher in HB (based on the relative abundances). The network analysis revealed that intI1 had significant correlations with tetC, sulI, sulII, and bla_PSE-1. Oil was the key connected factor, which had positive connections with sulI, sulII, and bla_PSE-1. In addition, the joint effect of heavy metals and nutrients & organic pollutants might be crucial for the fate of ARGs in the coastal sediments.

Mediation of functional gene and bacterial community profiles in the sediments of eutrophic Chaohu Lake by total nitrogen and season

Microbes in sediments contribute to nutrient release and play an important role in lake eutrophication. However, information about the profiles of functional genes and bacterial communities and the most important environmental factor affecting them in the sediments of eutrophic lake remains unrevealed. In this work, the real-time fluorescent quantitative polymerase chain reaction (qPCR) assay and 16S ribosomal RNA gene next generation sequencing analysis were used to explore the profiles of functional genes and bacterial communities in the sediments of Chaohu Lake. The selected 18 functional genes involved in C, N and P cycles were detected in most of samples. Seasonal variation and sediment variables were found to affect the profiles of functional genes and bacterial communities, and total nitrogen was the dominant environmental factor to drive the formation of bacterial community structure. Proteobacteria and Firmicutes were observed to be the two dominant phyla in the sediments with relative abundance ranging from 10.8% to 36.0% and 7.7%-46.7%, respectively. Three bacterial phyla, i.e., Actinobacteria, Proteobacteria, and Spirochaetes, were found to be significantly positively correlated with the C, N and P-cycle related functional genes. Bacterial community structure was the most important driver to shape the profiles of functional genes. Seasonal variation also influenced the co-occurrence patterns between functional genes and bacterial taxa as revealed by network analysis. The findings from this work facilitate a better understanding about the C, N, and P cycles in the sediments of eutrophic lakes.

Exploring co-occurrence patterns between organic micropollutants and bacterial community structure in a mixed-use watershed

Complex mixtures of low concentrations of organic micropollutants are commonly found in rivers and streams, but their relationship to the structure of native bacterial communities that underlie critical ecological goods and services in these systems is poorly understood. To address this knowledge gap, we used correlation-based network analysis to explore co-occurrence patterns between measured micropollutant concentrations and the associated surface water and sediment bacterial communities in a restored riparian zone of the Des Plaines River (DPR) in Illinois that is impacted by both wastewater treatment plant (WWTP) effluent and agricultural runoff. Over a two year period, we collected 55 grab samples at 11 sites along the DPR and one of its tributaries (48 surface water samples) and from WWTP effluent (7 samples), and screened for 126 organic micropollutants. In parallel, we used high-throughput 16S rRNA gene amplicon sequencing to characterize the bacterial community in sediment and surface water. Our results revealed quantifiable levels of 102 micropollutants in at least one surface water or WWTP effluent sample, 85 of which were detected in at least one surface water sample. While micropollutants were temporally and spatially variable in terms of both presence and concentration, 21 micropollutants were measured in over 75% of the 48 surface water samples. 16S rRNA gene sequencing documented diverse bacterial communities along the DPR transect, with highly distinct community structures observed in sediment and water. Bacterial community structure in surface water, but not in sediment, was significantly associated with concentrations of micropollutants, based on a Mantel test. Correlation-based network analyses revealed diverse strong and significant co-occurrence and co-exclusion patterns between specific bacterial OTUs and both micropollutant groups (defined based on k-means clustering on chemical substructure) and individual micropollutants. Significantly more associations were documented between micropollutants and bacterial taxa in the water compared to the sediment microbiomes. Taken together, our results document a significant link between complex mixtures of micropollutants commonly found in aquatic systems and associated bacterial community structure. Furthermore, our results suggest that micropollutants may exert a more significant impact on water-associated than on sediment-associated bacterial taxa.

Contrasting impact of elevated atmospheric CO2 on nitrogen cycle in eutrophic water with or without Eichhornia crassipes (Mart.) Solms

The elevation of atmospheric CO₂ is an inevitable trend that would lead to significant impact on the interrelated carbon and nitrogen cycles through microbial activities in the aquatic ecosystem. Eutrophication has become a common trophic state of inland waters throughout the world, but how the elevated CO₂ affects N cycles in such eutrophic water with algal bloom, and how vegetative restoration helps to mitigate N₂O emission remains unknown. We conducted the experiments to investigate the effects of ambient and elevated atmospheric CO₂ (a[CO₂], e[CO₂]; 400, 800 μmol﹒mol^-1) with and without the floating aquatic plant, Eichhornia crassipes (Mart.) Solms, on N-transformation in eutrophic water using the ¹⁵N tracer method. The nitrification could be slightly inhibited by e[CO₂], due mainly to the competition for dissolved inorganic carbon between algae and nitrifiers. The e[CO₂] promoted denitrification and N₂O emissions from eutrophic water without growth of plants, leading to aggravation of greenhouse effect and forming a vicious cycle. However, growth of the aquatic plant, Eichhornia crassipes, slightly promoted nitrification, but reduced N₂O emissions from eutrophic water under e[CO₂] conditions, thereby attenuating the negative effect of e[CO₂] on N₂O emissions. In the experiment, the N transformation was influenced by many factors such as pH, DO and algae density, except e[CO₂] and plant presence. The pH could be regulated through diurnal photosynthesis and respiration of algae and mitigated the acidification of water caused by e[CO₂], leading to an appropriate pH range for both nitrifying and denitrifying microbes. Algal respiration at night could consume DO and enhance abundance of denitrifying functional genes (nirK, nosZ) in water, which was also supposed to be a critical factor affecting denitrification and N₂O emissions. This study clarifies how the greenhouse effect caused by e[CO₂] mediates N biogeochemical cycle in the aquatic ecosystem, and how vegetative restoration mitigates greenhouse gas emission.

Spatial and temporal dynamics of bacterioplankton community composition in a subtropical dammed karst river of southwestern China

River damming influences the hydro‐physicochemical variations in karst water; however, such disruption in bacterioplankton communities has seldom been studied. Here, three sampling sites (city‐river section, reservoir area, and outflow area) of the Ca²⁺–Mg²⁺–HCO₃⁻–SO₄²⁻ water type in the dammed Liu River were selected to investigate the bacterioplankton community composition as identified by high‐throughput 16S rRNA gene sequencing. In the dammed Liu River, thermal regimes have been altered, which has resulted in considerable spatial‐temporal differences in total dissolved solids (TDSs), oxidation‐reduction potential (Eh), dissolved oxygen (DO), and pH and in a different microenvironment for bacterioplankton. Among the dominant bacterioplankton phyla, Proteobacteria, Actinobacteria, Bacteroidetes, and Cyanobacteria account for 38.99%–87.24%, 3.75%–36.55%, 4.77%–38.90%, and 0%–14.44% of the total reads (mean relative frequency), respectively. Bacterioplankton communities are dominated by Brevundimonas, Novosphingobium, Zymomonas, the Actinobacteria hgcIclade, the CL500‐29 marine group, Sediminibacterium, Flavobacterium, Pseudarcicella, Cloacibacterium, and Prochlorococcus. Their abundances covary with spatial‐temporal variations in hydro‐physicochemical factors, as also demonstrated by beta diversity analyses. In addition, temperature plays a pivotal role in maintaining bacterioplankton biodiversity and hydro‐physicochemical variations. This result also highlights the concept that ecological niches for aquatic bacteria in dammed karst rivers do not accidentally occur but are the result of a suite of environmental forces. In addition, bacterioplankton can alter the aquatic carbon/nitrogen cycle and contribute to karst river metabolism.

Performance of physical and chemical methods in the co-reduction of internal phosphorus and nitrogen loading from the sediment of a black odorous river

The continuous release of nutrients from sediment is a major barrier to the remediation of black odorous rivers. This study used a long-term laboratory incubation experiment to investigate the effectiveness of sediment dredging, intermittent aeration, and in situ inactivation with modified clays to reduce the internal loading of sediment from a seriously polluted river. The results indicated that intermittent aeration and in situ inactivation were effective in reducing the TN and NH₄⁺ concentrations in the water column. However, sediment dredging did not consistently reduce the TN and NH₄⁺ concentrations in the water column. In contrast, the three methods were all effective in controlling the TP and PO₄^3- concentrations in the water column. Except for dredging, >30% of NH₄⁺ and 40% of PO₄^3- fluxes from sediment were reduced when compared with a control sample after 120 days of remediation. Dredging induced a significant release of NH₄⁺ from sediment. Dredging and aeration made nearly no change to the amount of extractable nitrogen in the sediment. However, inactivation may increase sediment-extractable ammonium in deep sediment layers with time due to vertical transportation of clay by intensive bioturbation. Dredging is the most effective way to reduce surface mobile phosphorus over time while the transported clays can reduce a large percentage of the mobile phosphorus in deeper sediment. The relative abundance of Nitrospira in the surface sediment increased significantly with each remediation measure, creating favorable conditions for the reduction of the ammonium released from sediment. Altogether, the results of this study indicated that clay inactivation is the best method for controlling the internal loading of both phosphorus and nitrogen in seriously polluted river sediment.

Co-occurrence patterns of the microbial community in polycyclic aromatic hydrocarbon-contaminated riverine sediments

Understanding environmental and spatial gradient influences on sediment microbial communities, especially the communities of highly contaminated subsurface sediments, has received great attention with respect to natural attenuation and bioremediation. Here, we investigated the spatial variation and the co-occurrence patterns of microbial communities in polycyclic aromatic hydrocarbon (PAH)-contaminated riverine sediments by using spatial-series 16S rRNA gene data. The results showed that species from the surface and subsurface sediment samples tended to show greater co-occurrence patterns and facilitative interactions in the sediment microbial community as environmental severity increased. Microorganisms in the heavier PAH-contaminated sediment have stronger relationships and are more centrally clustered within the network compared to microorganisms in the lower PAH-contaminated sediment. The core communities harbored the keystone species (Dechloromonas, Crenothrix, Desulfuromonadales, Xanthomonadales, Anaerolineaceae and Dehalococcoidales), which responded to changes in the environmental and spatial gradients. The sediment PAH concentrations, ferrous iron and vertical distance were identified as the main drivers in determining the bacterial community assembly. The keystone species were linked to PAHs biodegradation coupled with iron cycling in sediments and could orchestrate core communities to perform ecosystem processes. Overall, these findings provide new insight into microbial community assembly and contribute to harnessing their functions in ecosystems for bioremediation.

Bioremediation of contaminated urban river sediment with methanol stimulation: Metabolic processes accompanied with microbial community changes

The intense pollution of urban river sediments with rapid urbanization has attracted considerable attention. Complex contaminated sediments urgently need to be remediated to conserve the ecological functions of impacted rivers. This study investigated the effect of using methanol as a co-substrate on the stimulation of the indigenous microbial consortium to enhance the bioremediation of petroleum hydrocarbons (PHs) and polycyclic aromatic hydrocarbons (PAHs) in an urban river sediment. After 65 days of treatment, the PAHs degradation efficiencies in the sediment adding methanol were 4.87%-40.3% higher than the control. The removal rate constant of C31 was 0.0749 d^-1 with 100 mM of supplied methanol, while the corresponding rate was 0.0399 d^-1 in the control. Four-ring PAHs were effectively removed at a degradation efficiency of 65%-69.8%, increased by 43.3% compared with the control. Sulfate reduction and methanogenesis activity were detected, and methane-producing archaea (such as Methanomethylovorans, with a relative abundance of 25.87%-58.53%) and the sulfate-reducing bacteria (SRB, such as Desulfobulbus and Desulfobacca) were enriched. In addition, the chemolithoautotrophic sulfur-oxidizing bacteria (SOB, such as Sulfuricurvum, with a relative abundance of 34%-39.2%) were predominant after the depletion of total organic carbon (TOC), and markedly positively correlated with the PHs and PAHs degradation efficiencies (P < 0.01). The SRB and SOB populations participated in the sulfur cycle, which was associated with PHs and PAHs degradation. Other potential functional bacteria (such as Dechloromonas) were also obviously enriched and significantly positively correlated with the TOC concentration after methanol injection (P < 0.001). This study provides a new insight into the succession of the indigenous microbial community with methanol as a co-substrate for the enhanced bioremediation of complexly contaminated urban river sediments.

Index for nitrate dosage calculation on sediment odor control using nitrate-dependent ferrous and sulfide oxidation interactions

Nitrate-driven sulfide and ferrous oxidation have received great concern in researches on sediments odor control with calcium nitrate addition. However, interrelations among sulfide oxidation, ferrous oxidation and their associated microbes during the nitrate reduction process are rarely reported. In this work, a n_NO3/n_(S+Fe) ratio (mole ratio of NO₃^- concentration to S^2- and Fe²⁺ concentration) was first introduced as an index for calcium nitrate dosage calculation. Then certain amount of calcium nitrate was added to four sediment systems with various sulfide and ferrous initial concentration to create four gradients of n_NO3/n_(S+Fe) ratio (0.6, 0.9, 1.5 and 2.0) for treatment. Furthermore, the significant variations of sulfide and ferrous oxidation, microbial diversity and community structure were observed. The results revealed that at low n_NO3/n_(S+Fe) ratio (0.6 and 0.9) systems, sulfide seemed prior to ferrous to be oxidized and no obvious ferrous oxidation occurred. Meanwhile, sulfide oxidizing associated genus Sulfurimonas sp. became dominant in these systems. In contrast, sulfide and ferrous oxidation rate increased when n_NO3/n_(S+Fe) ratio reached 1.5 and 2.0 (two and three times of theoretically required amount for sulfide and ferrous oxidation), which made Thiobacillus sp. more dominant than Sulfurimonas sp. Hence, when n_NO3/n_(S+Fe) ratio of 1.5 and 2.0 were used, sulfide and ferrous could be simultaneously oxidized and no sulfide regeneration appeared in two months. These results demonstrated that for sulfide- and ferrous-rich sediment treatment, the nitrate consumed by ferrous oxidation should be taken into account when calculating the nitrate injecting dosage. Moreover, n_NO3/n_(S+Fe) ratio was feasible as a key parameter to control the oxidation process and as an index for calcium nitrate dosage calculation.

Response of environmental variables and microbial community to sodium percarbonate addition to contaminated sediment

Sodium percarbonate (SPC) is a common reagent used for in situ remediation of contaminated soil. Current studies focus on the effects of SPC on pollutant removal; however, a knowledge gap exists for the biochemical process following SPC addition. In this study, a microcosm batch experiment was conducted to investigate the residual effect caused by different doses of SPC addition on native microbial communities, as well as on the environmental variables of contaminated sediments. The obtained results showed that the more SPC was added, the more dissolved matters were generated and the oxidation-reduction potential was lowered. Furthermore, the metabolic activities of the microbial community were enhanced and the microbial community structure responded differently to different SPC doses: the microbes that increased at high SPC dose mainly belonged to the phylum Firmicutes, the class Clostridia, and the genera Petrimonas and Proteiniclasticum. The microbes that increased at medium SPC dose mainly belonged to the class Alphaproteobacteria and the genus Brevundimonas. In contrast, vulnerable microbes mainly belonged to the phylum Acidobacteria, the class Caldisericia, Holophagae, and the genus Sulfuricurvum. Microbes capable of fermentation, ureolysis, and chemohetrotrophy increased. These results indicate that SPC addition could indirectly provide both electron acceptors and donors, thus improving the metabolic activities of the microorganisms in the contaminated sediment. Furthermore, the utilized SPC dose should be considered to achieve the optimal benefit for in situ remediation. This study forms a valuable reference for the application of SPC in ecological engineering.

Petroleum hydrocarbon rich oil refinery sludge of North-East India harbours anaerobic, fermentative, sulfate-reducing, syntrophic and methanogenic microbial populations

Background

Sustainable management of voluminous and hazardous oily sludge produced by petroleum refineries remains a challenging problem worldwide. Characterization of microbial communities of petroleum contaminated sites has been considered as the essential prerequisite for implementation of suitable bioremediation strategies. Three petroleum refinery sludge samples from North Eastern India were analyzed using next-generation sequencing technology to explore the diversity and functional potential of inhabitant microorganisms and scope for their on-site bioremediation.

Results

All sludge samples were hydrocarbon rich, anaerobic and reduced with sulfate as major anion and several heavy metals. High throughput sequencing of V3-16S rRNA genes from sludge metagenomes revealed dominance of strictly anaerobic, fermentative, thermophilic, sulfate-reducing bacteria affiliated to Coprothermobacter, Fervidobacterium, Treponema, Syntrophus, Thermodesulfovibrio, Anaerolinea, Syntrophobacter, Anaerostipes, Anaerobaculum, etc., which have been well known for hydrocarbon degradation. Relatively higher proportions of archaea were detected by qPCR. Archaeal 16S rRNA gene sequences showed presence of methanogenic Methanobacterium, Methanosaeta, Thermoplasmatales, etc. Detection of known hydrocarbon utilizing aerobic/facultative anaerobic (Mycobacterium, Pseudomonas, Longilinea, Geobacter, etc.), nitrate reducing (Gordonia, Novosphigobium, etc.) and nitrogen fixing (Azovibrio, Rhodobacter, etc.) bacteria suggested niche specific guilds with aerobic, facultative anaerobic and strict anaerobic populations. Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) predicted putative genetic repertoire of sludge microbiomes and their potential for hydrocarbon degradation; lipid-, nitrogen-, sulfur- and methane- metabolism. Methyl coenzyme M reductase A (mcrA) and dissimilatory sulfite reductase beta-subunit (dsrB) genes phylogeny confirmed methanogenic and sulfate-reducing activities within sludge environment endowed by hydrogenotrophic methanogens and sulfate-reducing Deltaproteobacteria and Firmicutes members.

Conclusion

Refinery sludge microbiomes were comprised of hydrocarbon degrading, fermentative, sulfate-reducing, syntrophic, nitrogen fixing and methanogenic microorganisms, which were in accordance with the prevailing physicochemical nature of the samples. Analysis of functional biomarker genes ascertained the activities of methanogenic and sulfate-reducing organisms within sludge environment. Overall data provided better insights on microbial diversity and activity in oil contaminated environment, which could be exploited suitably for in situ bioremediation of refinery sludge.

Electronic supplementary material

The online version of this article (10.1186/s12866-018-1275-8) contains supplementary material, which is available to authorized users.

Deciphering the Anode-Enhanced Azo Dye Degradation in Anaerobic Baffled Reactors Integrating With Microbial Fuel Cells

Microbial anode respiration in microbial fuel cells (MFCs) can enhance the degradations of many electron acceptor-type contaminants which are presumed to be competitive to anode respiration. The mechanisms underlying those counterintuitive processes are important for MFCs application but are unclear. This study integrated MFCs with anaerobic baffled reactor (ABR), termed MFC-ABR, to enhance the reduction of azo dye acid orange-7 (AO-7). Compare with ABR, MFC-ABR enhanced the degradation of AO-7, especially at high AO-7 concentration (800 mg/L). Acute toxicity test suggested a higher detoxication efficiency in MFC-ABR. Higher microbial viability, dehydrogenase activity and larger sludge granule size were also observed in MFC-ABR. MFC-ABR significantly enriched and reshaped the microbial communities relative to ABR. Bacteria with respiratory versatility, e.g., Pseudomonas, Geobacter, and Shewanella, were significantly enriched. Functional prediction showed that six metabolism functions (manganese-, iron-, fumarate- and nitrate-respiration, oil bioremediation and chemoheterotrophy) were significantly stimulated while methanogenesis, sulfate-respiration, hydrogen-oxidation were suppressed in MFC-ABR relative to ABR. The results provided important information for understanding the role of microbial anode respiration in contaminated environments.

Fertilizer N application rate impacts plant-soil feedback in a sanqi production system

Replant failure caused by negative plant-soil feedback (NPFS) in agricultural ecosystems is a critical factor restricting the development of sustainable agriculture. Soil nutrient availability has the capacity to affect plant-soil feedback. Here, we used sanqi (Panax notoginseng), which is severely threatened by NPSF, as a model plant to decipher the overall effects of nitrogen (N) rates on NPSF and the underlying mechanism. We found that a high rate of N at 450kgNha^-1 (450N) aggravated the NPSF through the accumulation of pathogens in the soil compared with the optimal 250N. The increased N rates resulted in a significant increase in the soil electrical conductivity and available nitrogen but a decrease in the soil pH and C/N ratio. GeoChip 5.0 data demonstrated that these changed soil properties caused the soil to undergo stress (acidification, salinization and carbon starvation), as indicated by the enriched soil microbial gene abundances related to stress response and nutrition cycling (N, C and S). Accordingly, increased N rates reduced the richness and diversity of soil fungi and bacteria and eventually caused a shift in soil microbes from a bacterial-dominant community to a fungal-dominant community. In particular, the high 450N treatment significantly suppressed the abundance of copiotrophic bacteria, including beneficial genera Bacillus and Pseudomonas, thus weakening the antagonistic activity of these bacteria against fungal pathogens. Moreover, 450N application significantly enriched the abundance of pathogen pathogenicity-related genes. Once sanqi plants were grown in this N-stressed soil, their host-specific fungal pathogen Fusarium oxysporum significantly accumulated, which aggravated the process of NPSF. This study suggested that over-application of nitrogen is not beneficial for disease management or the reduction of fungicide application in agricultural production.

Response of humic acid formation to elevated nitrate during chicken manure composting

Nitrate can stimulate microbes to degrade aromatic compounds, whereas humic acid (HA) as a high molecular weight aromatic compound, its formation may be affected by elevated nitrate during composting. Therefore, this study is conducted to determine the effect of elevated nitrate on HA formation. Five tests were executed by adding different nitrate concentrations to chicken manure composting. Results demonstrate that the concentration of HA in treatment group is significantly decreased compared with control group (p < 0.05), especially in the highest nitrate concentration group. RDA indicates that the microbes associated with HA and environmental parameters are influenced by elevated nitrate. Furthermore, structural equation model reveals that elevated nitrate reduces HA formation by mediating microbes directly, or by affecting ammonia and pH as the indirect drivers to regulate microbial community structure.

Sediment bacterial community structures and their predicted functions implied the impacts from natural processes and anthropogenic activities in coastal area

Coastal ecosystem structures and functions are changing under natural and anthropogenic influences. In this study, surface sediment samples were collected from disturbed zone (DZ), near estuary zone (NEZ), and far estuary zone (FEZ) of Hangzhou Bay, one of the most seriously polluted bays in China. The bacterial community structures and predicted functions varied significantly in different zones. Firmicutes were found most abundantly in DZ, highlighting the impacts of anthropogenic activities. Sediment total phosphorus was most influential on the bacterial community structures. Predicted by PICRUSt analysis, DZ significantly exceeded FEZ and NEZ in the subcategory of Xenobiotics Biodegradation and Metabolism; and DZ enriched all the nitrate reduction related genes, except nrfA gene. Seawater salinity and inorganic nitrogen, respectively as the representative natural and anthropogenic factor, performed exact-oppositely in nitrogen metabolism functions. The changes of bacterial community compositions and predicted functions provide a new insight into human-induced pollution impacts on coastal ecosystem.

Patterns of Change in Metabolic Capabilities of Sediment Microbial Communities in River and Lake Ecosystems

Information on the biodegradation potential of lake and river microbial communities is essential for watershed management. The water draining into the lake ecosystems often carries a significant amount of suspended sediments, which are transported by rivers and streams from the local drainage basin. The organic carbon processing in the sediments is executed by heterotrophic microbial communities, whose activities may vary spatially and temporally. Thus, to capture and apprehend some of these variabilities in the sediments, we sampled six sites: three from the Saint Clair River (SC1, SC2, and SC3) and three from Lake Saint Clair in the spring, summer, fall, and winter of 2016. Here, we investigated the shifts in metabolic profiles of sediment microbial communities, along Saint Clair River and Lake Saint Clair using Biolog EcoPlates, which test for the oxidation of 31 carbon sources. The number of utilized substrates was generally higher in the river sediments (upstream) than in the lake sediments (downstream), suggesting a shift in metabolic activities among microbial assemblages. Seasonal and site-specific differences were also found in the numbers of utilized substrates, which were similar in the summer and fall, and spring and winter. The sediment microbial communities in the summer and fall showed more versatile substrate utilization patterns than spring and winter communities. The functional fingerprint analyses clearly distinguish the sediment microbial communities from the lake sites (downstream more polluted sites), which showed a potential capacity to use more complex carbon substrates such as polymers. This study establishes a close linkage between physical and chemical properties (temperature and organic matter content) of lake and river sediments and associated microbial functional activities.