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

Engineering natural microbiomes toward enhanced bioremediation by microbiome modeling

Engineering natural microbiomes for biotechnological applications remains challenging, as metabolic interactions within microbiomes are largely unknown, and practical principles and tools for microbiome engineering are still lacking. Here, we present a combinatory top-down and bottom-up framework to engineer natural microbiomes for the construction of function-enhanced synthetic microbiomes. We show that application of herbicide and herbicide-degrader inoculation drives a convergent succession of different natural microbiomes toward functional microbiomes (e.g., enhanced bioremediation of herbicide-contaminated soils). We develop a metabolic modeling pipeline, SuperCC, that can be used to document metabolic interactions within microbiomes and to simulate the performances of different microbiomes. Using SuperCC, we construct bioremediation-enhanced synthetic microbiomes based on 18 keystone species identified from natural microbiomes. Our results highlight the importance of metabolic interactions in shaping microbiome functions and provide practical guidance for engineering natural microbiomes.

Piped-slow-release calcium nitrate dosing: A new approach to in-situ sediment odor control in rural areas

Calcium nitrate addition is economically viable and highly efficient for the in-situ treatment of contaminated sediment and enhancement of surface water quality, particularly in rural areas. However, conventional nitrate addition technologies have disadvantages such as excessive nitrate release, sharp ammonium increase, and weakened sulfide oxidation efficiency owing to rapid nitrate injection into the sediment. To resolve these defects, we propose a piped-slow-release (PSR) calcium nitrate dosing method and investigate its treatment efficiency and underlying mechanisms. The results illustrated that PSR dosing had a longer half-life (t1/2 = 5.08 days) and a lower maximum apparent nitrate escape rate of 1.28 % than conventional nitrate injection and other dosing methods. In addition, the PSR managed the inorganic nitrogen release into the overlying water, and after the treatment, the nitrate, ammonium, and nitrite concentrations of 0 mg/L, 8.60 mg/L, and 0 mg/L on day 28 were close to those of the control group (0 mg/L, 8.76 mg/L, and 0 mg/L, respectively). Moreover, the PSR method maintained a moderate nitrate concentration of approximately 3000 mg/L in sediment interstitial water by its controlled-release design, thus greatly enhancing the sulfide oxidation efficiency by relieving the inhibitory effects of high nitrate concentrations, with 83.0 % sulfide being eradicated within 5 days. Sulfide-ferrous nitrate reduction (denitrification and dissimilatory nitrate reduction to ammonium) genera (e.g., Sulfurimonas, Thiobacillus, and Thioalkalispira) were successively enhanced and dominated the microbial community, and the related functional genes displayed high relative abundances. These results imply that the PSR dosing method for calcium nitrate, characterized by flexible operation, high efficiency, low cost, and controllable processes, is appropriate for remediating black-odorous sediment in rural areas.

Dissolved organic matter influences the indigenous bacterial community and polycyclic aromatic hydrocarbons biodegradation in soils

In polycyclic aromatic hydrocarbon (PAH) contaminated soils, bioremediation is superior to other strategies owing to its low cost and environmental friendliness. However, dissolved organic matter (DOM) and indigenous bacterial communities can affect the efficiency of PAH-degrading bacteria (PDB). This study found that exogenous PDB (C1) including the genera Acinetobacter, Stenotrophomonas, and Comamonas, decreased the bacterial diversity of Alfisol, Ultisol, Inceptisol, and Mollisol, and DOM enhanced the diffusion of PDB and the bioavailability of PAH. In addition, bacteria preferred to ingest low molecular weight DOM fractions, and the abundances of lipid-like and protein-like substances decreased by 0.12-3.03 % and 1.73-4.60 %. The DOM fractions had a more marked influence on the indigenous bacteria than the exogenous PDB, and PDB dominated the PAH biodegradation process in the soils. More COO functional groups promoted the utilization of higher molecular weight-related homologue fractions by bacteria, and lower molecular weight fractions carrying more CH2 functional groups declined during biodegradation. This study investigated the variations in bacterial communities during biodegradation and revealed the effects of DOM fractions on biodegradation in PAH-contaminated soils at the molecular level. These results will promote the development of bioremediation strategies for organics-contaminated soil and provide guidance for prediction models of soil biodegradation kinetics.

Response of microbial communities to exogenous nitrate nitrogen input in black and odorous sediment

Since nitrate nitrogen (NO3--N) input has proved an effective approach for the treatment of black and odorous river waterbody, it was controversial whether the total nitrogen concentration standard should be raised when the effluent from the sewage treatment plant is discharged into the polluted river. To reveal the effect of exogenous nitrate (NO3--N) on black odorous waterbody, sediments with different features from contaminated rivers were collected, and the changes of physical and chemical characteristics and microbial community structure in sediments before and after the addition of exogenous NO3--N were investigated. The results showed that after the input of NO3--N, reducing substances such as acid volatile sulfide (AVS) in the sediment decreased by 80 % on average, ferrous (Fe2+) decreased by 50 %, yet the changing trend of ammonia nitrogen (NH4+-N) in some sediment samples increased while others decreased. High-throughput sequencing results showed that the abundance of Thiobacillus at most sites increased significantly, becoming the dominant genus in the sediment, and the abundance of functional genes in the metabolome increased, such as soxA, soxX, soxY, soxZ. Network analysis showed that sediment microorganisms evolved from a single sulfur oxidation ecological function to diverse ecological functions, such as nitrogen cycle nirB, nirD, nirK, nosZ, and aerobic decomposition. In summary, inputting an appropriate amount of exogenous NO3--N is beneficial for restoring and maintaining the oxidation states of river sediment ecosystems.

How redox gradient potentially influences nitrate reduction coupled with sulfur cycling: A new insight into nitrogen cycling in the hyporheic zone of effluent-dominated rivers

The coupled N and S cycling in variable redox gradients in the hyporheic zone (HZ) of the rivers receiving effluents from wastewater treatment plants is unclear. Using two representative effluent-dominated rivers as model systems, a metagenome approach was employed to explore the spatiotemporal redox zonation of the HZ and the N/S cycling processes within the system. The results manifested that nitrate reduction represented the fundamental nitrogen pathway in the HZ. Interestingly, DNRA coupled with sulfur reduction, and denitrification coupled with sulfur oxidation were respectively abundant in the oxic and anoxic zone. Lower nitrate concentration (0-2.72 mg-N/L) and more abundant genes involved in denitrification (napB, NarGHI) and sulfur oxidation (sseA, glpE) were detected in the anoxic zone. Contrarily, the nitrate concentration (0.07-4.87 mg-N/L) and the abundance of genes involved in sulfur reduction (ttrB, sudA) and DNRA (nirBD) were observed more abundant in the oxic zone. Therefore, the results verified the oxygen-limited condition did not suppress but rather facilitated the denitrification process in the presence of active S cycling. The high relative abundances of nosZ gene encoding sequence (3-5 % relative to all nitrogen-cycling processes) in both the effluent-discharging area and downstream area highly confirmed that HZ was capable of alleviating the N2O emission in the region. The functional keystone taxa were revealed through co-occurrence network analysis. The structural equation model shows that the genes of N/S cycling were positively impacted by functional keystone taxa, especially the N cycling genes. Functional keystone taxa were proven driven by the redox gradient, demonstrating their positive roles in mediating N/S cycling processes. The promoting effect on nitrate reduction coupled with sulfur cycling was clarified when redox conditions oscillated, providing a new perspective on mitigating nitrogen pollution and greenhouse gas emissions in effluent-receiving rivers.

Nitrate input inhibited the biodegradation of erythromycin through affecting bacterial network modules and keystone species in lake sediments

Antibiotic contamination and excessive nitrate loads are generally concurrent in aquatic ecosystems. However, little is known about the effects of nitrate input on the biodegradation of antibiotics. In this study, the effects of nitrate input on microbial degradation of erythromycin, a typical macrolide antibiotic widely detected in lake sediments, were investigated. The results showed that the nitrate input significantly inhibited the erythromycin removal and such an inhibitory effect was strengthened with the increased input dosages. Nitrate input significantly increased sediment nitrite concentration, indicating enhanced denitrification under high nitrate pressure. Bacterial network module and keystone species analysis showed that nitrate input enriched the keystone species involved in denitrification (e.g., Simplicispira and Denitratisoma). In contrast, some potential erythromycin-degrading bacteria (e.g., Desulfatiglandales, Pseudomonadales, Nitrospira) were inhibited by nitrate input. The variations in dominant bacterial groups implied competition between denitrification and erythromycin degradation in response to nitrate input. Based on the partial least squares path modeling analysis, keystone species (total effect: 0.419) and bacterial module (total effect: 0.403) showed strong association with erythromycin removal percentage. This indicated that the inhibitory effect of nitrate input on erythromycin degradation was mainly explained by bacterial network modules and keystone species. These findings will help us to assess the bioremediation potential of antibiotic-contaminated sediments suffering from excessive nitrogen discharge concurrently.

Endophytic Fungal Diversity of Mangrove Ferns Acrostichum speciosum and A. aureum in China

Microbial communities are an important component of mangrove ecosystems. In order to reveal the diversity of endophytic fungi in the mangrove ferns Acrostichum speciosum and A. aureum in China, the internal transcribed spacer (ITS) regions of endophytic fungi in four plant tissues (leaves, petioles, roots, and rhizomes) from three locations (Zhanjiang, Haikou, and Wenchang) were sequenced. The richness, species composition, and community similarity were analyzed. The main results are as follows: the dominant fungi in A. speciosum and A. aureum belonged to the phyla Ascomycota and Basidiomycota, accounting for more than 75% of the total identified fungi; in terms of species composition at the operational taxonomic unit (OTU) level, the endophytic fungi in A. aureum were more diverse than those in A. speciosum, and the endophytic fungi in rhizomes were more diverse than in other tissues. In Zhanjiang, both A. speciosum and A. aureum showed the richest diversity of endophytic fungi, both at the OTU classification level and in terms of species composition. Conversely, the richness of endophytic fungi in the samples of A. speciosum from Wenchang and Haikou is extremely low. The regional differences in dominant fungi increase with the degrading of taxonomic levels, and there were also significant differences in the number of unique fungi among different origins, with Zhanjiang samples having a larger number of unique fungi than the other locations. There were significant differences in the dominant fungi among different tissues, with Xylariales being the dominant fungi in rhizomes of A. speciosum and Hypocreales being the dominant fungi in the petioles, roots, and rhizomes of A. aureum. Overall, the community similarity of endophytic fungi among locations is moderately dissimilar (26-50%), while the similarity between tissues is moderately similar (51-75%). The low diversity of endophytic fungi could be one of the main reasons for the endangerment of A. speciosum. The protection of the diversity of endophytic fungi in the underground parts of A. speciosum is essential for the conservation of this critically endangered mangrove fern.

Community assembly of organisms regulates soil microbial functional potential through dual mechanisms

Unraveling the influence of community assembly processes on soil ecosystem functioning presents a major challenge in the field of theoretical ecology, as it has received limited attention. Here, we used a series of long-term experiments spanning over 25 years to explore the assembly processes of bacterial, fungal, protist, and nematode communities using high-throughput sequencing. We characterized the soil microbial functional potential by the abundance of microbial genes associated with carbon, nitrogen, phosphorus, and sulfur cycling using GeoChip-based functional gene profiling, and determined how the assembly processes of organism groups regulate soil microbial functional potential through community diversity and network stability. Our results indicated that balanced fertilization (NPK) treatment improved the stochastic assembly of bacterial, fungal, and protist communities compared to phosphorus-deficient fertilization (NK) treatment. However, there was a nonsignificant increase in the normalized stochasticity ratio of the nematode community in response to fertilization across sites. Our findings emphasized that soil environmental factors influenced the assembly processes of the biotic community, which regulated soil microbial functional potential through dual mechanisms. One mechanism indicated that the high phosphorus levels and low soil nutrient stoichiometry may increase the stochasticity of bacterial, fungal, and protist communities and the determinism of the nematode community under NPK treatment, ultimately enhancing soil microbial functional potential by reinforcing the network stability of the biotic community. The other mechanism indicated that the low phosphorus levels and high soil nutrient stoichiometry may increase the stochastic process of the bacterial community and the determinism of the fungal, protist, and nematode communities under NK treatment, thereby enhancing soil microbial functional potential by improving the β-diversity of the biotic community. Taken together, these results provide valuable insights into the mechanisms underlying the assembly processes of the biotic community that regulate ecosystem functioning.

Microcystis blooms caused the decreasing richness of and interactions between free-living microbial functional genes in Lake Taihu, China

Microcystis blooms have a marked effect on microbial taxonomical diversity in eutrophic lakes, but their influence on the composition of microbial functional genes is still unclear. In this study, the free-living microbial functional genes (FMFG) composition was investigated in the period before Microcystis blooms (March) and during Microcystis blooms (July) using a comprehensive functional gene array (GeoChip 5.0). The composition and richness of FMFG in the water column was significantly different between these two periods. The FMFG in March was enriched in the functional categories of nitrogen, sulfur, and phosphorus cycling, whereas the FMFG in July was enriched in carbon cycling, organic remediation, and metal homeostasis. Molecular ecological network analysis further demonstrated fewer functional gene interactions and reduced complexity in July than in March. Module hubs of the March network were mediated by functional genes associated with carbon, nitrogen, sulfur, and phosphorus, whereas those in July by a metal homeostasis functional gene. We also observed stronger deterministic processes in the FMFG assembly in July than in March. Collectively, this study demonstrated that Microcystis blooms induced significant changes in FMFG composition and metabolic potential, and abundance-information, which can support the understanding and management of biogeochemical cycling in eutrophic lake ecosystems.

A multi-omics approach to unravelling the coupling mechanism of nitrogen metabolism and phenanthrene biodegradation in soil amended with biochar

The presence of polycyclic aromatic hydrocarbons (PAHs) in soil negatively affects the environment and the degradation of these contaminants is influenced by nitrogen metabolism. However, the mechanisms underlying the interrelationships between the functional genes involved in nitrogen metabolism and phenanthrene (PHE) biodegradation, as well as the effects of biochar on these mechanisms, require further study. Therefore, this study utilised metabolomic and metagenomic analysis to investigate primary nitrogen processes, associated functional soil enzymes and functional genes, and differential soil metabolites in PHE-contaminated soil with and without biochar amendment over a 45-day incubation period. Results showed that dissimilatory nitrate reduction to ammonium (DNRA) and denitrification were the dominant nitrogen metabolism processes in PHE-contaminated soil. The addition of biochar enhanced nitrogen modules, exhibiting discernible temporal fluctuations in denitrification and DNRA proportions. Co-occurrence networks and correlation heatmap analysis revealed potential interactions among functional genes and enzymes responsible for PHE biodegradation and nitrogen metabolism. Notably, enzymes associated with denitrification and DNRA displayed significant positive correlation with enzymes involved in downstream phenanthrene degradation. Of particular interest was stronger correlation observed with the addition of biochar. However, biochar amendment inhibited the 9-phenanthrol degradation pathway, resulting in elevated levels of glutathione (GSH) in response to environmental stress. These findings provide new insights into the interactions between nitrogen metabolism and PHE biodegradation in soil and highlight the dual effects of biochar on these processes.

Moderate anthropogenic disturbance stimulates versatile microbial taxa contributing to denitrification and aromatic compound degradation

Wastewater treatment plants (WWTPs) effluent often contains a significant amount of residual organic pollutants and nutrients, causing disturbance to the coastal effluent receiving areas (ERA). Microbial communities in coastal ERA sediments may benefit from the coexistence of organic pollutants and nutrients, promoting the emergence of versatile taxa that are capable of eliminating these substances simultaneously. However, the identification and exploration of versatile taxa in natural environments under anthropogenic disturbances remain largely uncharted territory. In this study, we specifically focused on the versatile taxa coupled by the degradation of aromatic compounds (ACs) and denitrification, using Hangzhou Bay in China as our study area. We explored how WWTPs effluent disturbance would affect the versatile taxa, and particularly examined the role of disturbance intensity in shaping their composition. Intriguingly, we found that versatile taxa were mainly derived from denitrifiers like Pseudomonas, suggesting the fulfilled potential of denitrifiers regarding ACs degradation. We also discovered that moderate disturbance stimulated the diversity of versatile taxa, resulting in strengthened functional redundancy. Through correlation network analysis, we further demonstrated that moderate disturbance enhanced the community-level cooperation. Thus, moderate disturbance serves as a catalyst for versatile taxa to maintain community function, making them more resilient to effluent disturbances. Additionally, we identified COD and NO3--N concentrations as significant environmental factors influencing the versatile taxa. Overall, our findings reveal the role of effluent disturbances in the promotion of versatile taxa, and highlight moderate disturbance can foster more robust versatile taxa that are better equipped to handle effluent disturbances.

Distribution, sources, ecological risk and microbial response of polycyclic aromatic hydrocarbons in Qingdao bays, China

Bay ecosystem has garnered significant attention due to the severe threat posed by organic pollutants, particularly polycyclic aromatic hydrocarbons (PAHs). However, there is a dearth of information regarding the extent of PAHs pollutant risk and its impact on microbial communities and metabolism within this environment. In this study, the distribution, sources, ecological risk, and microbial community and metabolic response of PAHs in Jiaozhou Bay, Aoshan Bay, and Lingshan Bay in Qingdao, China were investigated. The results showed that the average concentration of ∑PAHs ranged from 120 to 614 ng/L across three bays, with Jiaozhou and Aoshan Bay exhibiting a higher risk than Lingshan Bay due to an increased concentration of high-molecular-weight PAHs. Further analysis revealed a negative correlation between dissolved organic carbon concentration and ∑PAHs concentration in water. Metagenomic analysis demonstrated that higher levels of PAHs can lead to decreased microbial diversity, while the abundance of PAHs-degrading bacteria is enhanced. Additionally, the Erythrobacter, Jannaschia and Ruegeria genera were found to have a significant correlation with low-molecular-weight PAH concentrations. In terms of microbial metabolism, higher PAH concentrations were beneficial for carbohydrate metabolic pathway but unfavorable for amino acid metabolic pathways and membrane transport pathways in natural bay environments. These findings provide a foundation for controlling PAHs pollution and offer insights into the impact of PAHs on bacterial communities and metabolism in natural bay environments.

Microbial community structure and its driving mechanisms in the Hangbu estuary of Chaohu Lake under different sedimentary areas

Estuaries are known for their high ecological diversity and biological productivity. Sediment microorganisms, as crucial components of estuarine ecosystems, play a pivotal role in reflecting the intricate and dynamic ecological niches. However, our research on microbial community characteristics in estuarine ecosystems under different sedimentary types remains limited. In this study, we collected a total of 27 samples from three sampling sites at Hangbu estuary in Chaohu Lake, and three sedimentary areas were classified based on the overlying water flow conditions and sediment particle properties to elucidate their microbial community structure, environmental drivers, assembly processes, and co-occurrence network characteristics. Our results showed significant differences in microbial community composition and diversity among three sedimentary areas. Redundancy analysis indicated that the differences in microbial community composition at the OTU level among the three sedimentary areas were mainly determined by nitrate-nitrogen, temperature, and water content. Phylogenetic bin-based null model analysis revealed that temperature was a key factor influencing deterministic processes among the three sedimentary areas, while stochastic processes predominantly governed the assembly of microbial communities. In addition, co-occurrence network analysis demonstrated that the network in the hydraulically driven sedimentary area of the lake, consisting mainly of medium and fine silt, had the highest complexity, stability, and cohesion, but was missing potential keystone taxa. The remaining two sedimentary areas had 5 and 8 potential keystone taxa, respectively. Overall, our study proposes the delineation of sedimentary types and comprehensively elucidates the microbial community characteristics under different sedimentary areas, providing a new perspective for studying sediment microbial community structure and helping future scholars systematically study ecological dynamics in estuaries.

Black odorous water concentrating by forward osmosis: rejection performance of characteristic pollutants based on cation exchange

This study aimed to investigate pollutant concentration and nitrogen interception characteristics of a forward osmosis (FO) process for concentrating black odorous water. The membrane cell was operated in active layer facing feed solution (AL-FS) mode with aquaporin (AQP) as the membrane material and NaCl solution as the draw solution (DS). The organic pollutants (COD), TP, NH+4-N, NO-3-N, TN, Fe and Mn in black odorous water were concentrated non-intermittently for 24 h, and their interception characteristics were investigated. The results showed that the average interception rates of COD, TP, NO- 3-N, TN, Fe and Mn were 97.2%, 98.0%, 58.7%, 54.3%, 61.8% and 60.0%, respectively, while the average interception rate of NH+4-N was only 1.27%-3.47%. To explore the characteristics of nitrogen interception, a comparison was conducted between AQP membrane and thin film composite (TFC) membrane. Because the surface electronegativity of AQP membrane was stronger than that of TFC, the effect of cation exchange on ammonia nitrogen interception was more serious with AQP membrane. With NaCl solution as DS, the reverse osmosis flux of Na+ was (0.53 ± 0.02 mol·m-2·h-1), which was significantly higher than that of Cl- (0.29 ± 0.03 mol·m-2·h-1) (P < 0.05). The interception effect of AQP membrane on TN was related to the proportion of NH+4-N in TN. The pretreatment of black odorous water by aeration could transform part of NH+4-N into NO-3-N, and reduce the negative effect of cation exchange effect on nitrogen interception. The TN interception rate increased from 54.3% to 66.1%.

Response of the nitrogen processing bacterial community to water level fluctuation and nitrate availability in an intact marsh soil column

Wetlands are known to experience fluctuations in water levels and receive exogenous nitrogen inputs that affect various organisms, including soil microorganisms. To study the impact of these factors on microbial diversity, we collected intact soil columns from a Phragmites australis-dominated site in the Qixing River National Nature Reserve in Northeast China. In a laboratory experiment, we simulated water level fluctuations and exogenous nitrogen inputs to the soil columns and examined the associated changes in the relative abundance of 51 bacterial genera involved in nitrogen cycling processes. Our findings revealed that different bacterial genera exhibited varying relative abundances across treatments. Specifically, Massilia showed the highest total relative abundance at the genus level, while Planctomyces had the second highest, and Campylobacter had the lowest abundance. The DESeq2 model, based on negative binomial distribution, revealed that the tags of bacterial genera were significantly correlated with soil depth, but not with water levels or nitrogen concentrations. However, the addition of a 30 mg/L nitrate solution caused a decrease in the relative abundances of bacterial genera with decreasing water levels, while a 60 mg/L concentration of nitrogen resulted in a decrease and then an increase in the relative abundances of bacterial genera with decreasing water levels. Our study provides valuable insights into the response of nitrogen-cycling bacteria to changes in different environmental conditions.

Species' functional traits and interactions drive nitrate-mediated sulfur-oxidizing community structure and functioning

IMPORTANCE

Understanding the processes and mechanisms governing microbial community assembly and their linkages to ecosystem functioning has long been a core issue in microbial ecology. An in-depth insight still requires combining with analyses of species' functional traits and microbial interactions. Our study showed how species' functional traits and interactions determined microbial community structure and functions by a well-controlled laboratory experiment with nitrate-mediated sulfur oxidation systems using high-throughput sequencing and culture-dependent technologies. The results provided solid evidences that species' functional traits and interactions were the intrinsic factors determining community structure and function. More importantly, our study established quantitative links between community structure and function based on species' functional traits and interactions, which would have important implications for the design and synthesis of microbiomes with expected functions.

Anaerobic biodegradation of pyrene and benzo[a]pyrene by a new sulfate-reducing Desulforamulus aquiferis strain DSA

The study of anaerobic high molecular weight polycyclic aromatic hydrocarbons (HMW-PAHs) biodegradation under sulfate-reducing conditions by microorganisms, including microbial species responsible for biodegradation and relative metabolic processes, remains in its infancy. Here, we found that a new sulfate-reducer, designated as Desulforamulus aquiferis strain DSA, could biodegrade pyrene and benzo[a]pyrene (two kinds of HMW-PAHs) coupled with the reduction of sulfate to sulfide. Interestingly, strain DSA could simultaneously biodegrade pyrene and benzo[a]pyrene when they co-existed in culture. Additionally, the metabolic processes for anaerobic pyrene and benzo[a]pyrene biodegradation by strain DSA were newly proposed in this study based on the detection of intermediates, quantum chemical calculations and analyses of the genome and RTqPCR. The initial activation step for anaerobic pyrene and benzo[a]pyrene biodegradation by strain DSA was identified as the formation of pyrene-2-carboxylic acid and benzo[a]pyrene-11-carboxylic acid by carboxylation Thereafter, CoA ligase, ring reduction through hydrogenation, and ring cracking occurred, and short-chain fatty acids and carbon dioxide were identified as the final products. Additionally, DSA could also utilize benzene, naphthalene, anthracene, phenanthrene, and benz[a]anthracene as carbon sources. Our study can provide new guidance for the anaerobic HMW-PAHs biodegradation under sulfate-reducing conditions.

Synthetic Denitrifying Communities Reveal a Positive and Dynamic Biodiversity-Ecosystem Functioning Relationship during Experimental Evolution

Biodiversity is vital for ecosystem functions and services, and many studies have reported positive, negative, or neutral biodiversity-ecosystem functioning (BEF) relationships in plant and animal systems. However, if the BEF relationship exists and how it evolves remains elusive in microbial systems. Here, we selected 12 Shewanella denitrifiers to construct synthetic denitrifying communities (SDCs) with a richness gradient spanning 1 to 12 species, which were subjected to approximately 180 days (with 60 transfers) of experimental evolution with generational changes in community functions continuously tracked. A significant positive correlation was observed between community richness and functions, represented by productivity (biomass) and denitrification rate, however, such a positive correlation was transient, only significant in earlier days (0 to 60) during the evolution experiment (180 days). Also, we found that community functions generally increased throughout the evolution experiment. Furthermore, microbial community functions with lower richness exhibited greater increases than those with higher richness. Biodiversity effect analysis revealed positive BEF relationships largely attributable to complementary effects, which were more pronounced in communities with lower richness than those with higher richness. This study is one of the first studies that advances our understanding of BEF relationships and their evolutionary mechanisms in microbial systems, highlighting the crucial role of evolution in predicting the BEF relationship in microbial systems. IMPORTANCE Despite the consensus that biodiversity supports ecosystem functioning, not all experimental models of macro-organisms support this notion with positive, negative, or neutral biodiversity-ecosystem functioning (BEF) relationships reported. The fast-growing, metabolically versatile, and easy manipulation nature of microbial communities allows us to explore well the BEF relationship and further interrogate if the BEF relationship remains constant during long-term community evolution. Here, we constructed multiple synthetic denitrifying communities (SDCs) by randomly selecting species from a candidate pool of 12 Shewanella denitrifiers. These SDCs differ in species richness, spanning 1 to 12 species, and were monitored continuously for community functional shifts during approximately 180-day parallel cultivation. We demonstrated that the BEF relationship was dynamic with initially (day 0 to 60) greater productivity and denitrification among SDCs of higher richness. However, such pattern was reversed thereafter with greater productivity and denitrification increments in lower-richness SDCs, likely due to a greater accumulation of beneficial mutations during the experimental evolution.

Response of microbial taxonomic and nitrogen functional attributes to elevated nitrate in suburban groundwater

Anthropogenic nitrogen (N) input has led to elevated levels of nitrate nitrogen (NO₃^--N) in the groundwater. However, insights into the responses of the microbial community and its N metabolic functionality to elevated NO₃^--N in suburban groundwater are still limited. Here, we explored the microbial taxonomy, N metabolic attributes, and their responses to NO₃^--N pollution in groundwaters from Chaobai River catchment (CR) and Huai River catchment (HR) in Beijing, China. Results showed that average NO₃^--N and NH₄⁺-N concentrations in CR groundwater were 1.7 and 3.0 folds of those in HR. NO₃^--N was the dominant nitrogen specie both in HR and CR groundwater (over 80 %). Significantly different structures and compositions of the microbial communities and N cycling gene profiles were found between CR groundwater and HR groundwater (p < 0.05), with CR groundwater harboring significantly lower microbial richness and abundance of N metabolic genes. However, denitrification was the dominant microbial N cycling process in both CR and HR groundwater. Strong associations among NO₃^--N, NH₄⁺-N, microbial taxonomic, and N functional attributes were found (p < 0.05), suggesting denitrifiers and Candidatus_Brocadia might serve as potential featured biomarkers for the elevated NO₃^--N and NH₄⁺-N concentration in groundwater. Path analysis further revealed the significant effect of NO₃^--N on the overall microbial N functionality and microbial denitrification (p < 0.05). Collectively, our results provide field evidence that elevated levels of NO₃^--N and NH₄⁺-N under different hydrogeologic conditions had a significant effect on the microbial taxonomic and N functional attributes in groundwater, with potential implications for improving sustainable N management and risk assessment of groundwater.

Anaerobic biodegradation of polycyclic aromatic hydrocarbons

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

Elevated antimony concentration stimulates rare taxa of potential autotrophic bacteria in the Xikuangshan groundwater

Microbial communities composed of few abundant and many rare species are widely involved in the biogeochemical cycles of elements. Yet little is known about the ecological roles of rare taxa in antimony (Sb) contaminated groundwater. Groundwater samples were collected along an Sb concentration gradient in the Xikuangshan antimony mine area and subjected to high through-put sequencing of 16S rRNA genes to investigate the bacterial communities. Results suggested that both abundant and rare sub-communities were dominated by Betaproteobacteria, Gammaproteobacteria, and Alphaproteobacteria, whereas rare sub-communities showed higher alpha-diversities. Multivariate analysis showed that both the abundant and rare taxa were under the stress of Sb, but the impact on rare taxa was greater. Nitrate explained a large part for the variation of the abundant sub-communities, indicating the critical role of nitrate for their activities under anoxic conditions. In contrast, bicarbonate significantly impacted rare sub-communities, suggesting their potential autotrophic characteristics. To further explore the role of rare taxa in the communities and the mechanism of affecting the community composition, a network was constructed to display the co-occurrence pattern of bacterial communities. The rare taxa contributed most of the network nodes and served as keystone species to maintain the stability of community. Abiotic factors (mainly Sb and pH) and bacterial interspecific interactions (interactions between keystone species and other bacterial groups) jointly affect the community dynamics. Functional prediction was performed to further reveal the ecological function of rare taxa in the Sb-disturbed groundwater environment. The results indicated that the rare taxa harbored much more diverse functions than their abundant counterparts. Notably, elevated Sb concentration promoted some potential autotrophic functions in rare taxa such as the oxidation of S-, N-, and Fe(II)-compounds. These results offer new insights into the roles of rare species in elemental cycles in the Sb-impacted groundwater.

Nitrogen transformation promotes the anaerobic degradation of PAHs in water level fluctuation zone of the Three Gorges Reservoir in Yangtze River, China: Evidences derived from in-situ experiment

Polycyclic aromatic hydrocarbons (PAHs) pose a great threat to human health and ecological system safety. The interception of nitrogen is common found in the riparian zone. However, there is no evidence on how nitrogen addition affects the anaerobic degradation of PAHs in soil of the water-level-fluctuation zone (WLFZ) of the Three Gorges Reservoir (TGR) in Yangtze River, China. Here, we investigated the PAHs degradation rate, the variation of key functional genes and microbial communities after nitrogen addition in soil that experienced a flooding period of water-level-fluctuation. The results revealed that the ∑16PAHs were decreased 16.19 %-36.65 % and more 3-5-rings PAHs were biodegraded with nitrogen addition in WLFZ. The most genes involved in PAHs-anaerobic degradation and denitrification were up-regulated by nitrate addition, and phyla Firmicutes, Actinobacteria and Proteobacteria were more advantages in nitrogen addition groups. The Tax4Fun based genome function analysis revealed that the microbial activity of PAHs-degradation increased with nitrate addition. The co-occurrence network analysis indicated that nitrogen addition accelerated the metabolism of nitrogen and PAHs. It is the first time to provide the direct experimental evidences that nitrogen transformation in the WLFZ soil promotes anaerobic PAHs degradation. This work is of importance to understand the effect of nitrogen intercepted in the WLFZ soil of TGR in Yangtze River, China.

Cyclohexanecarboxylic acid degradation with simultaneous nitrate removal by Marinobacter sp. SJ18

Naphthenic acid (NA) is a toxic pollutant with potential threat to human health. However, NA transformations in marine environments are still unclear. In this study, the characteristics and pathways of cyclohexanecarboxylic acid (CHCA) biodegradation were explored in the presence of nitrate. The results showed that CHCA was completely degraded with pseudo-first-order kinetic reaction under aerobic and anaerobic conditions, accompanied by nitrate removal rates exceeding 70%, which was positively correlated with CHCA degradation (P < 0.05). In the proposed CHCA degradation pathways, cyclohexane is dehydrogenated to form cyclohexene, followed by ring-opening by dioxygenase to generate fatty acid under aerobic conditions or cleavage of cyclohexene through β-oxidation under anaerobic conditions. Whole genome analysis indicated that nitrate was removed via assimilation and dissimilation pathways under aerobic conditions and via denitrification pathway under anaerobic conditions. These results provide a basis for alleviating combined pollution of NA and nitrate in marine environments with frequent anthropogenic activities.

Metagenomes from Coastal Sediments of Kuwait: Insights into the Microbiome, Metabolic Functions and Resistome

Coastal sediments in the proximity of wastewater and emergency outfalls are often sinks of pharmaceutical compounds and other organic and inorganic contaminants that are likely to affect the microbial community. The metabolites of these contaminants affect microbial diversity and their metabolic processes, resulting in undesirable effects on ecosystem functioning, thus necessitating the need to understand their composition and functions. In the present investigation, we studied the metagenomes of 12 coastal surface sediments through whole genome shot-gun sequencing. Taxonomic binning of the genes predicted about 86% as bacteria, 1% as archaea, >0.001% as viruses and Eukaryota, and 12% as other communities. The dominant bacterial, archaeal, and fungal genera were Woeseia, Nitrosopumilus, and Rhizophagus, respectively. The most prevalent viral families were Myoviridae and Siphoviridae, and the T4 virus was the most dominant bacteriophage. The unigenes further aligned to 26 clusters of orthologous genes (COGs) and five carbohydrate-active enzymes (CAZy) classes. Glycoside hydrolases (GH) and glycoside transferase (GT) were the highest-recorded CAzymes. The Kyoto Encyclopedia of Genes and Genomes (KEGG) level 3 functions were subjugated by purine metabolism > ABC transporters > oxidative phosphorylation > two-component system > pyrimidine metabolism > pyruvate metabolism > quorum sensing > carbon fixation pathways > ribosomes > and glyoxalate and dicarboxylate metabolism. Sequences allying with plasmids, integrons, insertion sequences and antibiotic-resistance genes were also observed. Both the taxonomies and functional abundances exhibited variation in relative abundances, with limited spatial variability (ANOVA p > 0.05; ANOSIM-0.05, p > 0.05). This study underlines the dominant microbial communities and functional genes in the marine sediments of Kuwait as a baseline for future biomonitoring programs.

Novel synergistic metabolic processes for phenanthrene biodegradation by a nitrate-reducing phenanthrene-degrading culture and an anammox culture

The synergistic metabolism by anammox cultures and nitrate-reducers for anaerobic PAH biodegradation is largely unknown, including whether anammox culture and which kind of anammox bacterium can perform nitrogen metabolism in the anaerobic PAH biodegradation processes, the inhibitory effect of PAH on anammox activity and nitrite on PAH-degrading nitrate-reducers activity, and the synergistic metabolic processes. Herein, an anammox culture that can eliminate nitrite accumulation and decrease inorganic carbon emission during anaerobic phenanthrene (a model of PAH in this study) biodegradation, the synergistic mechanism for phenanthrene biodegradation by a nitrate-reducer and such anammox culture, and the inhibition effect of phenanthrene on such anammox culture and nitrite on a phenanthrene-degrading nitrate-reducer were newly discussed. The results showed that nitrite largely accumulated during anaerobic phenanthrene biodegradation (nitrate accumulation is a common phenomenon for the biodegradation of refractory matter, including PAHs, by nitrate-reducers) by a nitrate-reducer, PheN2, which mineralizes phenanthrene to inorganic carbon, and nitrite was verified as an inhibiting factor for further biodegradation. Anaerobic phenanthrene biodegradation rates and nitrite concentrations (0-7 mM) appeared to have a negative linear correlation. The anammox culture that mainly contained Candidatus Kuenenia was newly found to efficiently reduce nitrite accumulation and inorganic carbon emissions and significantly promote biodegradation efficiency by ∼1.94-fold. Our results showed that phenanthrene absorbed in and on anammox cells had a more direct relationship with the inhibitory effect on anammox activity than phenanthrene in the environment, and 15.2 mg/gVSS phenanthrene absorbed in and on the cells (4 mM concentration in the culture) showed nearly complete inhibition of anammox culture in this study. In addition, few (less than 2% abundance) anammox bacteria were found to be enough for the removal of nitrite produced from anaerobic phenanthrene biodegradation. In an ideal world, co-pollutants of ammonia, nitrate, phenanthrene, and nitrite could be converted to nitrogen gas and biomass by the synergistic metabolism of anammox cultures and nitrate reducers. Our study reveals a new synergistic process that may exist in our environments for PAH elimination by an anammox culture and a nitrate-reducer, which provides a new strategy for the bioremediation of PAH-polluted anoxic zones.

Nitrate determines the bacterial habitat specialization and impacts microbial functions in a subsurface karst cave

Karst caves are usually considered as natural laboratories to study pristine microbiomes in subsurface biosphere. However, effects of the increasingly detected nitrate in underground karst ecosystem due to the acid rain impact on microbiota and their functions in subsurface karst caves have remained largely unknown. In this study, samples of weathered rocks and sediments were collected from the Chang Cave, Hubei province and subjected to high-throughput sequencing of 16S rRNA genes. The results showed that nitrate significantly impacted bacterial compositions, interactions, and functions in different habitats. Bacterial communities clustered according to their habitats with distinguished indicator groups identified for each individual habitat. Nitrate shaped the overall bacterial communities across two habitats with a contribution of 27.2%, whereas the pH and TOC, respectively, structured bacterial communities in weathered rocks and sediments. Alpha and beta diversities of bacterial communities increased with nitrate concentration in both habitats, with nitrate directly affecting alpha diversity in sediments, but indirectly on weathered rocks by lowering pH. Nitrate impacted more on bacterial communities in weathered rocks at the genus level than in sediments because more genera significantly correlated with nitrate concentration in weathered rocks. Diverse keystone taxa involved in nitrogen cycling were identified in the co-occurrence networks such as nitrate reducers, ammonium-oxidizers, and N₂-fixers. Tax4Fun2 analysis further confirmed the dominance of genes involved in nitrogen cycling. Genes of methane metabolism and carbon fixation were also dominant. The dominance of dissimilatory and assimilatory nitrate reduction in nitrogen cycling substantiated nitrate impact on bacterial functions. Our results for the first time revealed the impact of nitrate on subsurface karst ecosystem in terms of bacterial compositions, interactions, and functions, providing an important reference for further deciphering the disturbance of human activities on the subsurface biosphere.

Ecological influence by colonization of fluoride-resistant Streptococcus mutans in oral biofilm

Background

Dental caries is one of the oldest and most common infections in humans. Improved oral hygiene practices and the presence of fluoride in dentifrices and mouth rinses have greatly reduced the prevalence of dental caries. However, increased fluoride resistance in microbial communities is concerning. Here, we studied the effect of fluoride-resistant Streptococcus mutans (S. mutans) on oral microbial ecology and compare it with wild-type S. mutans in vitro.

Methods

Biofilm was evaluated for its polysaccharide content, scanning electron microscopy (SEM) imaging, acid-producing ability, and related lactic dehydrogenase (LDH), arginine deiminase (ADS), and urease enzymatic activity determination. Fluorescence in situ hybridization (FISH) and quantitative real-time polymerase chain reaction (qRT-PCR) were used to evaluate the S. mutans ratio within the biofilm. It was followed by 16S rRNA sequencing to define the oral microbial community.

Results

Fluoride-resistant S. mutans produced increased polysaccharides in presence of NaF (P < 0.05). The enzymatic activities related to both acid and base generation were less affected by the fluoride. In presence of 275 ppm NaF, the pH in the fluoride-resistant strain sample was lower than the wild type. We observed that with the biofilm development and accumulative fluoride concentration, the fluoride-resistant strain had positive relationships with other bacteria within the oral microbial community, which enhanced its colonization and survival. Compared to the wild type, fluoride-resistant strain significantly increased the diversity and difference of oral microbial community at the initial stage of biofilm formation (4 and 24 h) and at a low fluoride environment (0 and 275 ppm NaF) (P < 0.05). Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that fluoride-resistant strain enhanced the metabolic pathways and glucose transfer.

Conclusions

Fluoride-resistant S. mutans affected the microecological balance of oral biofilm and its cariogenic properties in vitro, indicating its negative impact on fluoride's caries prevention effect.

Polycyclic aromatic hydrocarbon removal from subsurface soil mediated by bacteria and archaea under methanogenic conditions: Performance and mechanisms

In situ anoxic bioremediation is an easy-to-use technology to remediate polycyclic aromatic hydrocarbon (PAH)-contaminated soil. Degradation of PAHs mediated by soil bacteria and archaea using CO₂ as the electron acceptor is an important process for eliminating PAHs under methanogenic conditions; however, knowledge of the performance and mechanisms involved is poorly unveiled. In this study, the effectiveness and efficiency of NaHCO₃ (CO₂) as an electron acceptor to stimulate the degradation of PAHs by bacteria and archaea in highly contaminated soil were investigated. The results showed that CO₂ addition (EC2000) promoted PAH degradation compared to soil without added CO₂ (EC0), with 4.18%, 9.01%-8.05%, and 6.19%-12.45% increases for 2-, 3- and 4-ring PAHs after 250 days of incubation, respectively. Soil bacterial abundances increased with increasing incubation time, especially for EC2000 (2.90 × 10⁸ g^-1 soil higher than EC0, p < 0.05). Different succession patterns of the soil bacterial and archaeal communities during PAH degradation were observed. According to the PCoA and ANOSIM results, the soil bacterial communities were greatly (ANOSIM: R = 0.7232, P = 0.001) impacted by electron acceptors, whereas significant differences in the archaeal communities were not observed (ANOSIM: R = 0.553, P = 0.001). Soil bacterial and archaeal co-occurrence network analyses showed that positive correlations outnumbered the negative correlations throughout the incubation period for both treatments (e.g., EC0 and EC2000), suggesting the prevalence of coexistence/cooperation within and between these two domains rather than competition. The higher complexity, connectance, edge, and node numbers in EC2000 revealed stronger linkage and a more stable co-occurrence network compared to EC0. The results of this study could improve the knowledge on the removal of PAHs and the responses of soil bacteria and archaea to CO₂ application, as well as a scientific basis for the in situ anoxic bioremediation of PAH-contaminated industrial sites.

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.

Humic Lake Exhibits Higher Microbial Functional Gene Diversity and Weaker Gene Interaction Efficiency than a Common Alkaline Lake

Humic lakes (HLs) are special water bodies (high organic matter content, low pH, and low transparency) that are important sources of major greenhouse gases. The knowledge about microbial functional potentials and the interactions among different genes in HL water has been scarcely understood. In this study, we used 16S rRNA gene sequencing and the GeoChip 5.0 to investigate microbial community compositions and functional gene structures in an HL and a reference weakly alkaline lake (RAL). The HL microbial communities showed distinct compositions and functional gene structures than those in the RAL. The functional gene diversity was significantly higher in the HL than in the RAL. Specifically, higher gene relative intensities in carbon and nitrogen fixations, the degradation of various types of carbon, methane oxidation and methanogenesis, ammonification, denitrification, and assimilatory N reduction were observed in the HL samples. By contrast, the metabolic potentials of microorganisms involved in dissimilatory N reduction, phosphorus degradation, and sulfur oxidation were weaker in the HL than in the RAL. Despite higher functional gene diversity, the interaction efficiency among genes (reflected by network geodesic distance and clustering coefficient) might be reduced in the HL. Different functional microbes may develop less interdependent relationships in acquiring nutrients given the high resource availability in the HL. Overall, the enhanced microbial metabolic potentials and less efficient functional interactions might have great consequences on nutrient cycling and greenhouse gas emissions in the HL ecosystem.

Effects of lead pollution on bacterial communities in biofilm attached to submerged plants

Submerged plants and biofilms have significant advantages in hydro-ecology rehabilitation, but their tolerance and physiological responses to heavy metal stress have thus far been under-investigated. This study investigated the influence of lead on physiological and biochemical responses, as well as variation in bacterial communities and functional characteristics of submerged plant biofilms. The results showed that chlorophyll a content of two submerged plants decreased with increased lead concentration. The concentration of malondialdehyde of both submerged plants was higher under high lead concentrations than under low lead concentrations, and the concentrations of malondialdehyde and hydrogen peroxide in Vallisneria natans were more stable. The antioxidant enzyme systems of the two plants played protective roles against lead stress. High lead concentration can inhibit the bacterial community and lead to decreased diversity. The most abundant bacterial phyla were Proteobacteria (40.9%), Cyanobacteria (21.5%), and Bacteroidetes (14.3%). Proteobacteria abundance decreased with increased lead concentration, while Cyanobacteria abundance increased. The lead concentration in plants (19.7%, P < 0.01) and the lead concentration in aquatic environment (17.7%, P < 0.01) were significantly correlated with variation in bacterial communities. High lead concentration inhibits the activity of these bacteria related to the conversion of nitrogen and sulfur.

Nitrogen addition enhanced the polycyclic aromatic hydrocarbons dissipation through increasing the abundance of related degrading genes in the soils

High concentrations of Polycyclic Aromatic Hydrocarbons (PAHs) in the soils cause significant threats to human health. Since nitrogen plays a crucial role in controlling microbial composition and functions in terrestrial ecosystems, bio-stimulation based on nitrogen has been used in PAHs contaminated environments remediation. Recent studies show that microbial community composition and organic pollutants dissipation correlate with nitrogen addition. Here, we investigated the effect of nitrogen addition on the abundance of microbial community, degrading genes, and their relationship to PAHs dissipation. After a 32-day experiment, PAHs residues in nitrogen treatment soil were reduced by 23.23%-34.21%. The application of 80 mg·kg^-1 nitrate and ammonium nitrogen resulted in higher PAHs removal efficiency, and the dissipation rate of PAHs was 59.61% and 62.09%, respectively. Nitrogen application could improve the abundance and the diversity of soil microbial community. Degrading genes involved in PAH detoxification were enhanced after nitrogen addition, particularly those encoding ring-hydroxylating and catechol dioxygenases such as nahAc and nidA, thus, accelerating PAH dissipation in the soil. The results will facilitate the development of beneficial microbiome-based remediation strategies and improve agricultural production safety in PAHs-contaminated soils.

Per-, poly-fluoroalkyl substances (PFASs) and planktonic microbiomes: Identification of biotic and abiotic regulations in community coalescence and food webs

The importance of per-, poly-fluoroalkyl substances (PFASs) effects on riverine microbiomes is receiving increased recognition in the environmental sciences. However, few studies have explored how PFASs affect microbiomes across trophic levels, specifically through predator-prey interactions. This study examined the community profiles of planktonic archaea, bacteria, fungi, algae, protozoa, and metazoa in a semi-industrial and agricultural river alongside their interactions with 15 detected PFASs. As abiotic factors, PFASs affected community coalescence more than biogenic substances (p < 0.05). For biotic regulations, sub-communities in rare biospheres (including always rare taxa-ART and critically rare taxa-CRT) contributed to spatial community coalescence more than sub-communities in abundant biospheres (always abundant taxa-AAT and critically abundant taxa-CAT) (p < 0.05). Metazoa-bacteria (Modularity = 1.971) and protozoa-fungi (1.723) were determined to be the most stable predator-prey networks. Based on pathway models, short-chain PFBA (C4) was shown to weaken the trophic transfer efficiencies from heterotrophic bacteria (HB) to heterotrophic flagellates (HF) (p < 0.05). Long-chain PFTeDA (C14) promoted HB to amoeba (p < 0.05), which we postulate is the pathway for PFTeDA to enter the microbial food chain. Our preliminary results elucidated the influence of PFASs on planktonic microbial food webs and highlighted the need to consider protecting and remediating riverine ecosystems containing PFASs.

New insights into denitrification and phosphorus removal with degradation of polycyclic aromatic hydrocarbons in two-sludge system

Polycyclic aromatic hydrocarbons (PAHs) have led to failure of waste water treatment plant operations. In this study, a two-sludge system was used to solve this problem of simultaneously removing phosphorus, nitrogen, and PAHs. The results showed that increasing the maximum PAHs concentration to 15 mg/L did not have any negative effect on the removal rates of total nitrogen (79.68%) and chemical oxygen demand (75.94%); however, the phosphorus removal efficiency decreased to 61.16%. The system exhibited a stronger degradation ability for phenanthrene. Thauera, Hydrogenophaga, and Hyphomicrobium were enriched, which resulted in good denitrification, and contributed to PAHs removal. PAHs mixture promoted PAHs functional genes but restrained denitrification functional genes. However, single naphthalene enhanced denitrification functional genes, which confirmed the feasibility of denitrification coupled with PAHs degradation. In conclusion, for the removal of pollutants from sewage treatment, nitrogen and phosphorus removal coupled with PAHs could be maintained by selecting a two-sludge system.

Microbial community coalescence: does it matter in the Three Gorges Reservoir?

The microbial community coalescence describes the mixing of microbial communities and the merging of their surrounding environments. Despite its prevalence in natural ecosystems and its potential influence on ecological processes, little research focused on the extent of coalescence between aquatic microbial communities. In this research, we analyzed the microbial communities in the Three Gorges Reservoir, a typical deep-water reservoir on the Yangtze River. The biogeography and the coalescence of microbial communities in water and sediment were illustrated and analyzed based on 16S rRNA gene amplicon sequence variants (ASVs). Differences in composition and diversity were identified between microbial communities in water and sediment, and microbial communities in sediment were more diverse than those in water. Between adjacent communities, by calculating the proportion of overlapped taxa, adopting the SourceTracker algorithm, and quantifying the connectivity of microbial cohesion, we found that the extent of intra-medium coalescence was strong (19.8%) and inter-media coalescence was faint (0.2%). 50 keystone species were selected using the cohesion metric. They displayed a stronger coalescence extent than average, and formed an accumulating pattern from upstream to downstream in the Three Gorges Reservoir, exhibiting their importance in the ecological network. Potential influencing factors of microbial community coalescence in aquatic environments were discussed, including environmental conditions, types of habitats, suspended particles in water, and microscale microbial activities. To summarize, this research depicted the coalescence of microbial communities in a deep-water reservoir and emphasized its ecological importance. We anticipate more attention and further research on the processes of microbial coalescence in the aquatic environment, which might provide new insights into turnover of microbial keystone species and changes in aquatic ecological conditions.

Coupling oxidation of acid volatile sulfide, ferrous iron, and ammonia nitrogen from black-odorous sediment via autotrophic denitrification-anammox by nitrate addition

The coupling removal of acid volatile sulfide (AVS), ferrous iron, and ammonia nitrogen has been applied for black-odorous sediment remediation. In this study, calcium nitrate with different N/(S + Fe) ratios (0.45, 0.90, 1.20 and 1.80) was added into black-odorous sediment in four systems named R1, R2, R3, and R4. Results showed that the removal rate of AVS was 76.40% in the R1, which was lower compared with rates in R2-R4 around 96.70%. The ferrous oxidation rate was approximately 87.00% in R2-R4, which was considerably higher than that in the R1 (24.62%). And the ammonia was reduced by 81.02%, 88.00%, 100%, and 57.18% in R1, R2, R3 and R4, respectively. During the reaction, nitrite accumulation was observed, indicating partial denitrification. Moreover, microbes related to autotrophic denitrification (e.g., genus Thiobacillus, Dok59, GOUTA19, Gallionella, with the highest abundance of 15.40%, 13.21%, 8.79%, 9.44%, respectively) were detected in all systems. Furthermore, the anammox bacteria Candidatus_Brocadia with the highest abundance of 3.44% and 4.00% in R2 and R3, respectively was also found. These findings confirmed that AVS, ferrous iron, and ammonia nitrogen could be simultaneously removed via autotrophic denitrification coupled with anammox in black-odorous sediment by nitrate addition.

Dissolved oxygen disturbs nitrate transformation by modifying microbial community, co-occurrence networks, and functional genes during aerobic-anoxic transition

No consensus has been achieved among researchers on the effect of dissolved oxygen (DO) on nitrate (NO₃^--N) transformation and the microbial community, especially during aerobic-anoxic transition. To supplement this knowledge, NO₃^--N transformation, microbial communities, co-occurrence networks, and functional genes were investigated during aerobic-anoxic transition via microcosm simulation. NO₃^--N transformation rate in the early stage (DO ≥2 mg/L) was always significantly higher than that in the later stage (DO <2 mg/L) during aerobic-anoxic transition, and NO₂^--N accumulation was more significant during the anoxic stage, consistent with the result obtained under constant DO conditions. These NO₃^--N transformation characteristics were not affected by other environmental factors, indicating the important role of DO in NO₃^--N transformation during aerobic-anoxic transition. Changes in DO provoked significant alterations in microbial diversity and abundance of functional bacteria dominated by Massilia, Bacillus, and Pseudomonas, leading to the variation in NO₃^--N transformation. Co-occurrence network analysis revealed that NO₃^--N transformation was performed by the interactions between functional bacteria including symbiotic and competitive relationship. In the presence of oxygen, these interactions accelerated the NO₃^--N transformation rate, and bacterial metabolization proceeded via increasingly varied pathways including aerobic and anoxic respiration, which was demonstrated through predicted genes. The higher relative abundance of genes narG, narH, and napA suggested the occurrence of coupled aerobic-anoxic denitrification in the early stage. NO₃^--N transformation rate decreased accompanied by a significant NO₂^--N accumulation with the weakening of coupled aerobic-anoxic denitrification during aerobic-anoxic transition. Structural equation modeling further demonstrated the relationship between DO and NO₃^--N transformation. DO affects NO₃^--N transformation by modifying microbial community, bacterial co-occurrence, and functional genes during aerobic-anoxic transition.

Evaluation of humic acid conversion during composting under amoxicillin stress: Emphasizes the driving role of core microbial communities

This study aimed to investigate the effects of various amoxicillin (AMX) concentrations on humic acid (HA) formation and the bacterial community structure (BCS) during chicken manure aerobic composting. The findings showed that AMX caused a rise in pH and a shortening of the thermophilic cycle during the thermophilic period. Moreover, a high concentration of AMX (150 mg/kg) inhibited community succession and humification at maturity. In addition to influencing environmental factors, AMX increased the relative abundance (RA) of the dominant bacteria in the thermophilic phase (Firmicutes) and decreased the RA of the dominant bacteria in the mature phase (Proteobacteria). From carbon conversion, AMX promoted fulvic acid (FA) anabolism in the early period and inhibited HA accumulation in the later period. As a result, the primary impact of AMX on HA transformation was the alteration of the BCS, ultimately affecting the quality of compost.

Effects of black carbon-based thin-layer capping for nitrogen-overloaded sediment remediation on microbial community assembly

Black carbon is considered as a promising material for thin-layer capping for sediment remediation. However, the effects of black carbon-based thin-layer capping on microbial communities have not been thoroughly studied. Here, the preparation conditions of capping material were optimized, and the interaction and assembly mechanisms of the microbial community in sediment under black carbon capping were studied. The results showed that concentration of NH₄⁺-N in the overlying water was stably lower than 0.5 mg/L after capping. The abundance of key genes related to nitrogen transformation in the sediment was increased. Denitrification was the dominant nitrogen removal pathway under coarse granule capping, while aromatic compound degradation was dominant under fine granule capping and dissimilatory N reduction to ammonium was regarded as the dominant nitrogen removal pathway. Community assembly was mainly driven by deterministic processes (≥ 80%). Interactions between rare and common operational taxonomic units were most frequent. The functional zoning of nitrogen transformation in the vertical aerobic, hypoxic, and anaerobic zones of the sediment was strengthened because of black carbon capping. Overall, these results expand our current understanding of the ecological significance of black carbon capping for remediating contaminated sediment.

Investigation of the combined use of capping and oxidizing agents in the immobilization of arsenic in sediments

The combined use of capping (lanthanum modified bentonite; LMB) and oxidizing (calcium nitrate; CN) agents was investigated to immobilize arsenic (As) in sediments. The vertical changes in labile As and dissolved As were measured using diffusive gradients in thin films (DGT) and Rhizon devices. The results showed that the combined application of LMB and CN had the optimal effect on the immobilization of both DGT-labile As and dissolved As, compared to single treatments using LMB or CN. After 60 days of incubation, the maximum reduction efficiencies of DGT-labile As at sediment depths were 76.4%, 70.8%, and 44.9% of those treated with LMB + CN, CN, and LMB, respectively. After 32 days of incubation, the average concentrations of dissolved total As throughout the depths decreased from 7.71 μg/L after the control treatment without any amendments to 5.25, 4.03, and 3.15 μg/L after the addition of LMB, CN, and LMB + CN, respectively. The larger part of exchangeable As at sediment depths was converted into the reducible As mainly bound Fe/Mn oxide-hydroxides after combining LMB and CN. Due to the As(III) existing mainly in the form of electrically neutral H₃AsO₃ in sediments, it is hard to adsorb As(III) for the LMB and iron/manganese oxide-hydroxides formed by the oxidation effect of calcium nitrate. Thus, the single or combined LMB and CN use had much weaker effect on the immobilization of As(III) compared with As(V). The results of current study indicated that the combined use of LMB and CN could be a promising method to control the potential release of As from the sediment to the overlying water. However, this method needs further improvement to achieve a better immobilization effect on As(III) in 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.