Microbial assemblages in water hyacinth silages with different initial moistures.

Making silage is a green process to use the fast-growing water hyacinth (Eichhornia crassipes) biomass. However, the high moisture (∼95%) of the water hyacinth is the biggest challenge to making silage while its effects on fermentation processes are less studied. In this study, water hyacinths silage with different initial moistures were conducted to investigate the fermentation microbial communities and their roles on the silage qualities. Results show that both silages with 70% (S70) and 90% (S90) of initial moistures achieved the target of silage fermentation, however, their microbial processes were significantly different. Their succession directions of microbial communities were different: Plant cells in S70 were destroyed by the air-dry treatment, thus there were more soluble carbohydrates, which helped the inoculated fermentative bacteria become dominant (Lactobacillus spp. > 69%) and produce abundant lactic acid; In contrast, stochastic succession became dominant over time in S90 (NST = 0.79), in which Lactobacillus spp. and Clostridium spp. produced butyric that also obviously decreased the pH and promoted the fermentation process. Different microbial succession led to different metabolic patterns: S70 had stronger starch and sucrose metabolisms while S90 had stronger amino acid and nitrogen metabolisms. Consequently, S70 had higher lactic acid, crude protein and lower ammonia nitrogen and S90 had higher in vitro digestibility of dry matter and higher relative feeding value. Moreover, the variance partitioning analysis indicated that moisture could only explain less information (5.9%) of the microbial assemblage than pH value (41.4%). Therefore, the colonization of acid-producing bacteria and establishment of acidic environment were suggested as the key on the silage fermentation no matter how much is the initial moisture. This work can provide a basis for the future preparation of high-moisture raw biomasses for silage.

Novosphingobium percolationis sp. nov. and Novosphingobium huizhouense sp. nov., isolated from landfill leachate of a domestic waste treatment plant.

Two strains designated as c1T and c7T, were isolated from the landfill leachate of a domestic waste treatment plant in Huizhou City, Guangdong Province, PR China. The cells of both strains were aerobic, rod-shaped, non-motile and formed yellow colonies on Reasoner's 2A agar plates. Strain c1T grew at 10-42 °C (optimum, 30 °C), pH 4.5-10.5 (optimum, pH 7.0) and 0-2.0 % (w/v) NaCl (optimum, 0-0.5 %). Strain c7T grew at 10-42 °C (optimum, 30 °C), pH 4.5-10.5 (optimum, pH 6.0) and 0-2.0 % (w/v) NaCl (optimum, 0-0.5 %). Phylogenetic analyses revealed that strains c1T and c7T belong to the genus Novosphingobium. The 16S rRNA gene sequence similarities of strains c1T and c7T to the type strains of Novosphingobium species were 94.5-98.2 % and 94.3-99.1 %, respectively. The calculated pairwise average nucleotide identity values among strains c1T, c7T and the reference strains were in the range of 75.2-85.9 % and the calculated pairwise average amino acid identity values among strains c1T, c7T and reference strains were in the range of 72.0-88.3 %. Their major respiratory quinone was Q-10, and the major cellular fatty acids were C18 : 1 ω7c, C18 : 0, C16 : 1 ω7c, C16 : 0 and C14 : 0 2OH. The major polar lipids of strains c1T and c7T were phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, sphingoglycolipid, unidentified lipids and unidentified phospholipid. Based on phenotypic, chemotaxonomic, phylogenetic and genomic results from this study, strains c1T and c7T should represent two independent novel species of Novosphingobium, for which the names Novosphingobium percolationis sp. nov. (type strain c1T=GDMCC 1.2555T=KCTC 82826T) and Novosphingobium huizhouense sp. nov. (type strain c7T=GDMCC 1.2556T=KCTC 82827T) are proposed. The gene function annotation results of strains c1T and c7T suggest that they could play an important role in the degradation of organic pollutants.

Duganella lactea sp. nov., Duganella guangzhouensis sp. nov., Duganella flavida sp. nov. and Massilia rivuli sp. nov., isolated from a subtropical stream in PR China and proposal to reclassify Duganella ginsengisoli as Massilia ginsengisoli comb. nov.

Five Gram-stain-negative, catalase- and oxidase-positive, rod-shaped and motile strains (FT50WT, FT80WT, FT92WT, FT94W and FT135WT) were isolated from a subtropical stream in PR China. Comparisons based on 16S rRNA gene sequences showed that strains FT50WT, FT94W and FT135WT take strain Duganella sacchari Sac-22T, and strains FT80WT and FT92WT take strain Duganella ginsengisoli DCY83T as their closest neighbour in the phylogenetic trees, respectively. The G+C contents of strains FT50WT, FT80WT, FT92WT, FT94W and FT135WT were 63.3, 62.4, 62.8, 63.8 and 60.8 %, respectively. The reconstructed phylogenomic tree based on concatenated 92 core genes showed that strains FT50WT, FT80WT, FT94W and FT135WT clustered together with species of the genus Duganella, but strains FT92WT and D. ginsengisoli KCTC 42409T were located in the clades of the genus Massilia. The calculated pairwise average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values among strains FT50WT, FT80WT, FT92WT, FT94W, FT135WT and related strains were in the ranges of 75.6-87.8% and 20.3-33.8% except that the values between strains FT50WT and FT94W were 98.7 and 89.2%, respectively. The respiratory quinone of these five strains was Q-8. The major fatty acids were C16 : 1 ω7c, C16 : 0, C18 : 1 ω7c and C12 : 0. The polar lipids included phosphatidylethanolamine, phosphatidylglycerol and one unidentified phospholipid. Considering the distinct phylogenetic relationships of D. ginsengisoli with species of the genus Massilia in the phylogenomic tree, it was reasonable to transfer D. ginsengisoli to the genus Massilia as Massilia ginsengisoli comb. nov. Combining the results of phylogenomic analysis, ANI and dDDH data, and a range of physiological and biochemical characteristics together, strains FT50WT and FT94W should belong to the same species and be assigned to genus Duganella with strains FT80WT and FT135WT together, and strain FT92WT should be assigned to the genus Massilia, for which the names Duganella lactea sp. nov. (type strain FT50WT=GDMCC 1.1674T=KACC 21466T), Duganella guangzhouensis sp. nov. (FT80WT=GDMCC 1.1678T=KACC 21470T), Duganella flavida sp. nov. (FT135WT=GDMCC 1.1745T=KACC 21659T) and Massilia rivuli sp. nov. (FT92WT=GDMCC 1.1682T=KACC 21474T) are proposed.

Duganella alba sp. nov., Duganella aquatilis sp. nov., Duganella margarita sp. nov. and Duganella levis sp. nov., isolated from subtropical streams in China.

Six Gram-stain-negative, catalase- and oxidase-positive, rod-shaped and motile strains (FT9WT, FT25W, FT26WT, FT109WT, FT134W and CY42WT) were isolated from subtropical streams in China. Comparisons based on 16S rRNA gene sequences showed that the six strains shared similarities of less than 98.1 % with other species within the family Oxalobacteraceae and formed two separately distinct clades in phylogenetic trees. The 16S rRNA gene sequence similarities between strains FT9WT and FT25W, and between strains FT109WT and FT134W were both 99.7 %. The genome sizes of strains FT9WT, FT25W, FT26WT, FT109WT, FT134W and CY42WT were 6.45, 6.45, 6.54, 6.43, 6.52 and 6.74 Mbp with G+C contents of 64.0, 64.0, 63.8, 63.2, 63.2 and 62.5 %, respectively. The calculated pairwise average nucleotide (ANI) values among the six strains and other related species were less than 93.9 %, except that the values were 99.9 % between strains FT9WT and FT25W, 98.2 % between strains FT109WT and FT134W, and 95.0 and 95.1 % between strain FT26WT and strains FT9WT and FT25W, respectively. However, strain FT26WT shared 16S rRNA gene sequence similarities of only 98.3 and 98.2 % with FT9WT and FT25W, respectively. The respiratory quinone of the six strains was determined to be Q-8. The major fatty acids were C16 : 1ω7c, C16 : 0 and C12 : 0. The predominant polar lipids included phosphatidylethanolamine and phosphatidylglycerol. Considering the phenotypic, biochemical, genotypic and ANI data, strains FT9WT and FT25W, and FT109WT and FT134W may belong to the same species, respectively. Although the pairwise ANI values between strain FT26WT and each of strains FT9WT and FT25W were located in the transition region of species demarcation, the dissimilarities among them indicated that strain FT26WT could represent an independent novel species. The reconstructed phylogenomic tree based on a concatenation of 92 core genes showed that the six strains clustered closely with Duganella sacchari Sac-22T and Duganella radicis KCTC 22382T, and supported that these six strains belong to the genus Duganella. The names Duganella albus sp. nov. (type strain FT9WT=GDMCC 1.1637T=KACC 21313T), Duganella aquatilis sp. nov. (type strain FT26WT=GDMCC 1.1641T=KACC 21315T), Duganella pernnla sp. nov. (type strain FT109WT=GDMCC 1.1688T=KACC 21480T) and Duganella levis sp. nov. (type strain CY42WT=GDMCC 1.1673T=KACC 21465T) are proposed.

Brevibacterium rongguiense sp. nov., isolated from freshwater sediment.

A Gram stain-positive, non-spore-forming, non-motile and rod-shaped actinomycete, strain 5221T, was isolated from the sediment of a river collected at Ronggui in the Pearl River Delta, PR China. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the strain formed a distinct lineage within the genus Brevibacterium and had the highest sequence similarity to Brevibacterium pityocampae Tp12T (96.7 %), followed by Brevibacterium daeguense 2C6-41T (96.5 %), Brevibacterium samyangense SST-8T (96.0 %) and Brevibacterium ravenspurgense 20T (95.9 %). The results of chemotaxonomic analyses, including detecting anteiso-C15 : 0, anteiso-C17 : 0, and C16 : 0 as the major cellular fatty acids, diphosphatidylglycerol, phosphatidylglycerol and three phosphoglycolipids as the polar lipids, MK-8(H2) as the major menaquinone, and a DNA G+C content of 72.4 mol%, supported that strain 5221T is a member of the genus Brevibacterium. Furthermore, low sequence similarities of 16S rRNA gene sequences, differences in fatty acid compositions and differential physiological characteristics such as enzyme activity and carbon sources utilization ability distinguished the isolate from its close relatives. Therefore, strain 5221T represents a novel species of the genus Brevibacterium, for which the name Brevibacterium rongguiense sp. nov. is proposed, with the type strain 5221T (=GDMCC 1.1766T=KACC 21700T).

Janthinobacterium violaceinigrum sp. nov., Janthinobacterium aquaticum sp. nov. and Janthinobacterium rivuli sp. nov., isolated from a subtropical stream in China.

Four strains assigned the names FT13WT, FT14W, FT58WT and FT68WT were isolated from a subtropical stream in PR China. All the strains were Gram-stain-negative, catalase- and oxidase-positive, rod-shaped and motile with flagella. Comparisons based on 16S rRNA gene sequences showed that strains FT13WT, FT14W, FT58WT and FT68WT belonged to genus Janthinobacterium and shared 16S rRNA gene similarities in the range of 98.8-99.7 % with Janthinobacterium lividum DSM 1522T, Janthinobacterium agaricidamnosum DSM 9628T and 'Janthinobacterium svalbardensis JA-1', respectively. The calculated pairwise average nucleotide identity (ANI) values among the genomes of above seven strains were in the range of 79.0-92.2 %, except that the ANI value was 96.8 % between strain FT13WT and FT14W. The respiratory quinone of strains FT13WT, FT14W, FT58WT and FT68WT was determined to be Q-8. The major fatty acids were C16 : 1 ω7c, C16 : 0, C18 : 1 ω7c and C12 : 0. The polar lipids included phosphatidylethanolamine, phosphatidylglycerol and one unidentified phospholipid. The genome sizes of strains FT13WT, FT14W, FT58WT and FT68WT were 6.45, 6.38, 5.73 and 6.37 Mbp with G+C contents of 63.4, 63.7, 61.6 and 63.1 mol%, respectively. Combining phenotypic, biochemical, genotypic and ANI data, strain FT13WT and FT14W should belong to the same species. The four strains were considered to represent three novel species within genus Janthinobacterium, for which the names Janthinobacterium violaceinigrum sp. nov. (type strain FT13WT=GDMCC 1.1638T=KACC 21319T), Janthinobacterium aquaticum sp. nov. (FT58WT=GDMCC 1.1676T=KACC 21468T) and Janthinobacterium rivuli sp. nov. (FT68WT=GDMCC 1.1677T=KACC 21469T) are proposed.

Functional response of sediment bacterial community to iron-reducing bioaugmentation with Shewanella decolorationis S12.

Bioaugmentation with exogenously functional microbes is a widely used technology in bioengineering and environmental remediation. Generally, the colonization of inoculated bacteria is considered to be the determining factor in technical success. However, increasing reports have shown that bioaugmentation was still effective when the colonization of inoculated bacteria was unsuccessful. Here, an augmentation study with iron-reducing bacteria (IRB, Shewanella decolorationis S12) was conducted in Fe(II)-poor sediments to elucidate the role of exogenously inoculated bacteria for bioaugmentation performance. The results showed that a sufficient amount of IRB inputs enhanced the iron reduction in bioaugmented sediments, even though the exogenous IRB did not colonize after the beginning of the experiment (less than 1% at day 3). The iron reduction function responded to stimulation of the indigenous IRB community such as Clostridium, Cupriavidus, Fervidicella, and Acinetobacter, which comprised less than 1% in the initial sediments. Moreover, compared with microbial community in control sediment, more positive correlations between OTUs were observed for that in S12-added sediments upon network analysis. The pH and oxidation-reduction potential of sediment were found to be the predominant factors shaping the iron-reducing microbial communities. It meant that exogenous IRB successfully trigged functional community via altering microenvironment by the inoculated bacteria. Overall, this study provides a new insight into the understanding of the role of single strain addition in iron-reducing bioaugmentation.

Correlating microbial community with physicochemical indices and structures of a full-scale integrated constructed wetland system.

Microorganisms play a key role in removal of pollutants in constructed wetlands (CWs). The aim of this study was to investigate the composition and diversity of microbes in a full-scale integrated constructed wetland system and examine how microbial assemblages were shaped by the structures and physicochemical properties of the sediments. The microbial assemblages were determined using 16S rRNA high-throughput sequencing. Results showed that the microbial phenotypes were more diverse in the system than in single CWs. The genera of Zoogloea, Comamonas, Thiobacillus, Nitrosospira, Denitratisoma, Azonexus, and Azospira showed relatively high abundances, which contributed to the removal of organic matter and nitrogen. The interactions among the three CWs in series acted a key role in the increase of phylogenetic diversity and high percentage of shared operational taxonomic units. In the system, some core microbes always existed even with the changing environment. Redox potential and NH4-N were the important factors affecting the overall microbial community patterns. Total organic carbon had a relatively high impact on some denitrifiers. The results from this study should be useful to better understand the microbial mechanism of wastewater treatment in integrated constructed wetland systems.

Impacts of MnO2 on tomato (Lycopersicon esculentum Mill.) growth: A study with MnO2-amended organic fertilizer.

Manganese dioxide (MnO2), as a catalyst in composting processes, can accumulate in soil over multiple fertilizations. However, its impact on crop growth remains to be explored. In this study, a pot experiment was conducted to investigate the impacts of MnO2 on the tomato plant performance across various growth stages. Results showed that MnO2 reduced the plant height, leaf number and length by 35.53 %, 27.61 %, and 37.00 %, respectively, and decreased the fruit weight (23.16 %) and sugar-acid ratio (29.7 %) of fruits compared to the MnO2-free control. The adverse impacts of MnO2 on plant growth might be attributed to the inhibition of microbial activity in soil reflected by the reduction of soil urease (9.30 %) and acid phosphatase (12.52 %) activities, which decreased the efficiency of nutrients conversion and uptake. The decrease of nutrient elements in roots resulted in oxidative stress in the plant, inhibiting the plasma membrane H+-ATPase activity thereby reducing the translocation of nutrients (e.g., calcium, magnesium, and phosphorus) translocation from roots to leaves. Furthermore, the phytohormones indolebutyric acid, gibberellin, and jasmonic acid of leaves were disturbed. This study reveals the risks associated with the application of MnO2-containing organic fertilizers.

Cable bacteria accelerate the anaerobic removal of pyrene in black odorous river sediments.

Cable bacteria play an essential role in biogeochemical processes in sediments by long-distance electron transport (LDET). A potential relationship has been found between cable bacteria and organic contaminant removal; however, the mechanisms remain unclear. In this study, the response of cable bacteria to pyrene was investigated in sediments with and without pyrene, and the effect of cable bacteria on pyrene removal was explored by connecting and blocking the paths of cable bacteria to the suboxic zones. The results showed that pyrene significantly influenced the microbial community structure and the composition of cable bacteria. The pyrene removal efficiencies significantly increased with the enrichment of cable bacteria, while sulfur-reducing microorganisms and aromatic compound degraders were also significantly enriched and correlated with cable bacteria abundance. Metagenomic analysis showed that cable bacteria have a potential LDET-bound acetate/formate respiratory pathway to gain energy. The presence of pyrene probably selects and enriches cable bacteria with a high tolerance to organic contaminants and changes the related functional microbial community, leading to the acceleration of pyrene removal. This study provides new insights into the interaction mechanisms between contaminants and cable bacteria, shedding light on the applications of cable bacteria in the bioremediation of contaminants in sediments.

An overview of the direct and indirect effects of acid rain on plants: Relationships among acid rain, soil, microorganisms, and plants.

Acid rain (AR) causes numerous environmental problems and complex negative effects on plants globally. Many studies have previously reported on direct effects of AR or its depositional substances on plant injury and performance. However, few studies have addressed the indirect effects of AR on plants as mediated by soil microorganisms and the abiotic environment of the soil rhizosphere. The indirect effects (e.g., AR â†’ soil microorganisms→plants) need greater attention, because acidic deposition not only affects the distribution, composition, abundance, function, and activity of plant-associated microorganisms, but also influences the dynamics of some substances in the soil in a way that may be harmful to plants. Therefore, this review not only focused on the direct effects of AR on plant performance, growth, and biomass allocations from a whole-plant perspective, but also addressed the pathway of AR-soil chemical characteristics-plants, which explains how soil solute leaching and acidification by AR will reduce the availability of essential nutrients and increase the availability of heavy metals for plants, affecting carbon and nitrogen cycles. Mainly, we evaluated the AR-soil microorganisms-plants pathway by: 1) synthesizing the potential roles of soil microbes in alleviating soil acidic stress on plants and the adverse effects of AR on plant-associated soil microorganisms; 2) exploring how plant mycorrhizal types affect the detection of AR effect on plants. The meta-analysis showed that the effects of AR-induced pH on leaf chlorophyll content, plant height, and plant root biomass were dependent on plant mycorrhizal types. Some possible reasons for different synergy between mycorrhizal symbiotic types and plants were discussed. Future research relating to the effects of AR on plants should focus on the combined direct and indirect effects to evaluate how AR affects plant performance comprehensively.

Pyrethroid bioaccumulation in wild fish linked to geographic distribution and feeding habit.

The accumulation of pyrethroid insecticides in aquatic food webs has attracted increased research attention. Fish are key species in aquatic food webs, directly connecting invertebrates and human consumption. However, little is known about the bioaccumulation of pyrethroids in wild fish species. In this study, 19 species of wild fish were collected from 11 sites in the Pearl River, China, and the levels of seven pyrethroids in the fish were determined. Linear mixed-effects models were applied to estimate the means of pyrethroid concentrations, in which sample site and fish species were set as random effects. The concentrations of Σ7 pyrethroids in fish ranged from 4.99 to 50.82 ng/g. Permethrin and bifenthrin were present at the highest concentration (8.89 ± 1.47 ng/g) and frequency (100%) in fish muscle, respectively. The composition patterns of pyrethroids varied in fish organs. Fish species contributed a higher proportion of the variance than geographic distribution (28.6% vs. 26.4%). The pyrethroids in carnivorous fish (23.5 ± 2.9 ng/g) were significantly higher than in omnivorous (14.6 ± 1.9 ng/g) and phytophagous fish (16.0 ± 4.7 ng/g). To our knowledge, this is the first report examining the effect of feeding habits on pyrethroid bioaccumulation in wild fish. The results can provide evidence for the risk of pyrethroid pollution in aquatic ecosystems.

Risk control and assessment of sulfide-rich sediment remediation by controlled-release calcium nitrate.

Nitrate stimulation is widely used in sediment remediation to eliminate sulfides, degrade organic pollutants and immobilize phosphorus. However, the environmental risks of nitrate escape and the subsequent release of pollutants (e.g. nitrite, ammonium and trace metals) to water bodies during its application has received less attention. In this study, controlled-release nitrate pellets (SedCaN pellets) were manufactured and applied at different sediment depths to examine their effectiveness in controlling the risk of nitrate escape and subsequent pollutant release. The germination of submerged plant was also analyzed to assess the ecological risks associated with the remediated sediment. The results showed that the SedCaN pellets slowly released calcium nitrate, which led to denitrifying sulfide oxidation, organic matter degradation and the immobilization of phosphorus as a calcium-bound species. Gas production by denitrification increased the sediment porosity (0.3-2.2%) and led to the concomitant release of nitrite, ammonium, and heavy metals, creating secondary risks. Application of the SedCaN pellets at depth decreased the nitrate escape and the secondary risks, presumably by means of a capping effect of the upper sediment. The release of nitrate, ammonium, Ni and Cu were partially limited by 91.6%, 19.0%, 61.6% and 57.4% when SedCaN pellets were incorporated into deeper sediments (7-9 cm). Moreover, the range of sulfide oxidation extended to the upper and lower sediments in the profile (column), while the sulfide oxidation efficiency reached 85.9-95.0%. Finally, increased germination of Bacopa monnieri (20.0-26%) demonstrated that in comparison to reference materials the ecological risks of the treated sediments was reduced and the habitat function of sediment was restored after nitrate-stimulating remediation. The results of this study provide valuable guidelines for nitrate-stimulating remediation of sulfide-rich (black-odor) sediments.

Water quality drives the distribution of freshwater cable bacteria.

Cable bacteria are a group of recently found filamentous sulfide-oxidizing Desulfobulbaceae that significantly impact biogeochemical cycling. However, the limited understanding of cable bacteria distribution patterns and the driving force hindered our abilities to evaluate and maximize their contribution to environmental health. We evaluated cable bacteria assemblages from ten river sediments in the Pearl River Delta, China. The results revealed a clear biogeographic distribution pattern of cable bacteria, and their communities were deterministically assembled through water quality-driven selection. Cable bacteria are diverse in the river sediments with a few generalists and many specialists, and the water quality IV and V environments are the "hot spot." We then provided evidence on their morphology, function, and genome to demonstrate how water quality might shape the cable bacteria assemblages. Reduced cell width, inhibited function, and water quality-related adaptive genomic traits were detected in sulfide-limited water quality III and contaminant-stressed water quality VI environments. Specifically, those genomic traits were contributed to carbon and sulfur metabolism in the water quality III environment and stress resistance in the water quality VI environment. Overall, these findings provided a helpful baseline in evaluating the contribution of cable bacteria in the freshwater ecosystem and suggested that their high diversity and flexibility in phylogeny, morphology, and genome allowed them to adapt and contribute to various environmental conditions.

Microorganisms in sediment microbial fuel cells: Ecological niche, microbial response, and environmental function.

A sediment microbial fuel cell (SMFC) is a device that harvests electrical energy from sediments rich in organic matter. SMFCs have been attracting increasing amounts of interest in environmental remediation, since they are capable of providing a clean and inexhaustible source of electron donors or acceptors and can be easily controlled by adjusting the electrochemical parameters. The microorganisms inhabiting sediments and the overlying water play a pivotal role in SMFCs. Since the SMFC is applied in an open environment rather than in an enclosed chamber, the effects of the environment on the microbes should be intense and the microbial community succession should be extremely complex. Thus, this review aims to provide an overview of the microorganisms in SMFCs, which few previous review papers have reported. In this study, the anodic and cathodic niches for the microorganisms in SMFCs are summarized, how the microbial population and community interact with the SMFC environment is discussed, a new microbial succession strategy called the electrode stimulation succession is proposed, and recent developments in the environmental functions of SMFCs are discussed from the perspective of microorganisms. Future studies are needed to investigate the electrode stimulation succession, the environmental function and the electron transfer mechanism in order to boost the application of SMFCs for power generation and environmental remediation.

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.

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 (t1/2 = 68.3 d) than with sulfate stimulation (t1/2 = 164.6 d). These mechanistic understandings can serve as the guidelines for EA selection in bioremediation.

Linking microbial community and biological functions to redox potential during black-odor river sediment remediation.

The black-odor phenomenon in polluted urban rivers is a serious environmental problem that has received increasing attention in the recent years. The low redox potential (less than - 100 mV) in the sediment is considered to be the key factor causing the occurrence of black-odor phenomenon. Here, we studied the structure and function of the microbial community during the remediation of urban rivers. Results showed a clear improvement in water quality after undergoing river remediation processes. The on-site treatments showed a succession in the microbial composition and their predicted functions. The primary iron- and sulfur-reducing bacteria (Thiobacillus, Sulfuricurvum, and Sulfursoma) and the related reactions rapidly decreased after the dredging treatment but reappeared after a year. The structure and abundance of nitrogen and methane participants were also affected by river remediation process. These results indicated that although the water quality temporarily improved shortly after a dredging process, a recurrence of the black-odor phenomenon may occur as a result of the rebound in the microbial communities.

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, F8825T, 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 MSSRFBL1T (99.4%), followed by C. thiooxidans F43bT (98.8%) and C. azotifigens A.slu09T (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 F8825T with MSSRFBL1T, respectively) confirmed that strain F8825T was a novel species, different from C. lividus MSSRFBL1T, C. thiooxidans F43bT, and C. azotifigens A.slu09T. 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 F8825T was identified as a novel species in the genus Ciceribacter, for which the name Ciceribacter ferrooxidans sp. nov. is proposed. The type strain is F8825T (= CCTCC AB 2018196T = KCTC 62948T).