Haloalkaliphilic denitrifiers-dependent sulfate-reducing bacteria thrive in nitrate-enriched environments

Roles of nitrite in facilitating nitrogen and sulfur conversion in the hybrid bioreactor of Sulfate-reduced ammonium oxidation and anaerobic ammonium oxidation

The hybrid bioreactor combining sulfate-reducing ammonium oxidation (Sulfammox) and Anammox offered potential for simultaneous nitrogen and sulfur removal, but the removal efficiency and microbial mechanism remain unclear. This study demonstrated that in the hybrid bioreactor, the ammonium utilization rate (AUR) of Sulfammox increased by 5.42 times. The promotion of NO2- on nitrogen and sulfur conversion in Sulfammox could be attributed to: 1) Increasing extracellular polymers substance (EPS) accelerated the stratification of granule sludge; 2) Increasing the relative abundance of Candidatus Brocadia by 29.55 times and Candidatus Anammoxoglobus by 3.17 times; 3) Upregulating the expression of nitrification (amo, hao and nxr) and sulfur metabolism (sat, aprAB dsr and sox) genes, associated with the pathways NH4+→NH2OH → NO2-→NO3- and SO42-→S2-→SO42-. Moreover, Candida Brocadia sapporoensis emerged as a potential specie of Sulfammox, mediating nitrification by hao and nxr, and sulfate reduction by sat and aprAB, thereby enabling electron transfer between nitrogen and sulfur.

Hypersaline organic wastewater treatment: Biotechnological advances and engineering challenges

The sustainable treatment of hypersaline organic wastewater (HSOW) remains a significant challenge in industrial wastewater management, as conventional approaches often fail to meet stringent discharge standards and low-carbon sustainability targets. Halotolerant and halophilic microbial strains offer promising solutions, yet their application is hindered by limited stress resistance, thus hindering effective treatment and achieving near-zero liquid discharge. In this review, we systematically examine endogenous strategies, such as microbial mutualism and genetic engineering, alongside exogenous approaches, including functional materials, electrical and magnetic stimulation, and 3D bioprinting, to improve microbial resilience in hypersaline environments. Furthermore, we propose an integrated treatment framework that combines physicochemical and biochemical processes, leveraging biological detoxification and biological desalination to enhance the treatment of HSOW while minimizing environmental impact and carbon emissions. By advancing the understanding of microbial stress adaptation and optimization strategies, this review provides critical insights into the development of sustainable, low-carbon wastewater treatment solutions.

Investigating the genomic and metabolic abilities of PGPR Pseudomonas fluorescens in promoting plant growth and fire blight management

Pseudomonas fluorescens is commonly found in diverse environments and is well known for its metabolic and antagonistic properties. Despite its remarkable attributes, its potential role in promoting plant growth remains unexplored. This study examines these traits across 14 strains residing in diverse rhizosphere environments through pangenome and comparative genome analysis, alongside molecular docking studies against Erwinia amylovora to combat fire blight. Whole genome analysis revealed circular chromosome (6.01-7.07 Mb) with GC content averaging 59.95-63.39%. Predicted genes included 16S rRNA and protein-coding genes ranging from 4435 to 6393 bp and 1527 to 1541 bp, respectively. Pangenome analysis unveiled an open pangenome, shedding light on genetic factors influencing plant growth promotion and biocontrol, including nitrogen fixation, phosphorus solubilization, siderophore production, stress tolerance, flagella biosynthesis, and induced systemic resistance. Furthermore, pyrrolnitrin, phenazine-1-carboxylic acid, pyoluteorin, lokisin, 2,4-diacetylpholoroglucinol and pseudomonic acid were identified. Molecular docking against key proteins of E. amylovora highlighted the high binding affinities of 2,4-diacetylphloroglucinol, pseudomonic acid, and lokisin. These findings underscore the multifaceted role of P. fluorescens in plant growth promotion and biocontrol, with key biomolecules showing promising applications in plant growth and defense against pathogens.

Anaerobic ammonium oxidation coupled with sulfate reduction links nitrogen with sulfur cycle

Sulfate-dependent ammonium oxidation (Sulfammox) is a critical process linking nitrogen and sulfur cycles. However, the metabolic pathway of microbes driven Sulfammox is still in suspense. The study demonstrated that ammonium was not consumed with sulfate as the sole electron acceptor during long-term enrichment, probably due to inhibition from sulfide accumulation, while ammonium was removed at ∼ 10 mg N/L/d with sulfate and nitrate as electron acceptors. Ammonium and sulfate were converted into nitrogen gas, sulfide, and elemental sulfur. Sulfammox was mainly performed by Candidatus Brocadia sapporoensis and Candidatus Brocadia fulgida, both of which encoded ammonium oxidation pathway and dissimilatory sulfate reduction pathway. Not sulfide-driven autotrophic denitrifiers but Candidatus Kuenenia stuttgartiensis converted nitrate to nitrite with sulfide. The results of this study reveal the specialized metabolism of Sulfammox bacteria (Candidatus Brocadia sapporoensis and Candidatus Brocadia fulgida) and provide insight into microbial relationships during the nitrogen and sulfur cycles.

Impact of Nitrate on the Removal of Pollutants from Water in Reducing Gas-Based Membrane Biofilm Reactors: A Review

The membrane biofilm reactor (MBfR) is a novel wastewater treatment technology, garnering attention due to its high gas utilization rate and effective pollutant removal capability. This paper outlines the working mechanism, advantages, and disadvantages of MBfR, and the denitrification pathways, assessing the efficacy of MBfR in removing oxidized pollutants (sulfate (SO4-), perchlorate (ClO4-)), heavy metal ions (chromates (Cr(VI)), selenates (Se(VI))), and organic pollutants (tetracycline (TC), p-chloronitrobenzene (p-CNB)), and delves into the role of related microorganisms. Specifically, through the addition of nitrates (NO3-), this paper analyzes its impact on the removal efficiency of other pollutants and explores the changes in microbial communities. The results of the study show that NO3- inhibits the removal of other pollutants (oxidizing pollutants, heavy metal ions and organic pollutants), etc., in the simultaneous removal of multiple pollutants by MBfR.

Contrasting response strategies of sulfate-reducing bacteria in a microbial consortium to As3+ stress under anaerobic and aerobic environments

The sulfate-reducing efficiency of sulfate-reducing bacteria (SRB) is strongly influenced by the presence of oxygen, but little is known about the oxygen tolerance mechanism of SRB and the effect of oxygen on the metalliferous immobilization by SRB. The performance evaluation, identification of bioprecipitates, and microbial and metabolic process analyses were used here to investigate the As3+ immobilization mechanisms and survival strategies of the SRB1 consortium under different oxygen-containing environments. Results indicated that the sulfate reduction efficiency was significantly decreased under aerobic (47.37%) compared with anaerobic conditions (66.72%). SEM analysis showed that under anaerobic and aerobic conditions, the morphologies of mineral particles were different, whereas XRD and XPS analyses showed that the most of As3+ bioprecipitates under both conditions were arsenic minerals such as AsS and As4S4. The abundances of Clostridium_sensu_stricto_1, Desulfovibrio, and Thiomonas anaerobic bacteria were significantly higher under anaerobic than aerobic conditions, whereas the aerobic Pseudomonas showed an opposite trend. Network analysis revealed that Desulfovibrio was positively correlated with Pseudomonas. Metabolic process analysis confirmed that under aerobic conditions the SRB1 consortium generated additional extracellular polymeric substances (rich in functionalities such as Fe-O, SO, CO, and -OH) and the anti-oxidative enzyme superoxide dismutase to resist As3+ stress and oxygen toxicity. New insights are provided here into the oxygen tolerance and detoxification mechanism of SRB and provide a basis for the future remediation of heavy metal(loid)-contaminated environments.

Regulation of potential denitrification rates in sediments by microbial-driven elemental coupled metabolisms

Microbial driven coupled processes between denitrification and methane/sulfur metabolism play a very substantial role in accelerating nitrogen removal in river sediments. Until now, little is known about how element coupling processes alter nitrogen metabolism by the microbial functional communities. The primary objective of this research was to clarify the contributory role of microbial-mediated coupled processes in controlling denitrification. Specifically, the study sought to identify the key bioindicators (or metabolic pathway) for preferably regulating and predicting potential denitrification rate (PDR). Here, a total of 40 sediment samples were collected from the inflow rivers of Chaohu Lake under nitrogen stress. The results revealed the ecological importance of methanogens and sulfate reducing bacteria in the microbial interaction network. Correlations between quantitative or predicted genes showed that the methanogenic gene (mcrA) was synergistic with denitrifying genes, further unraveling that the key role of methanogenesis in denitrification process for facilitating nitrogen removal. The PDR of sediments ranged from 0.03 to 133.21 μg N·g-1·h-1. The study uncovered specific environmental factors (NH4+ and OM) and microbial indicators (nosZ, mcrA, Paracoccus, Thauera, Methanobrevibacter and Desulfomicrobium) as potential contributors to the variations in PDR. Structural Equation Model (SEM) analysis revealed a significant direct effect of NH4+ on PDR, evidenced by a standardized coefficient (λ) of 0.77 (P < 0.001). Additionally, the findings also emphasized the salient role of methanogens (Methanobrevibacter) and methanogenic gene (mcrA) in indicating PDR. The research's aforementioned findings shed light on the substantial consequences of methanogenesis on nitrogen metabolism in coupled processes, enabling improved control of nitrogen pollution in river sediments. This study provided fresh perspectives on the effects of multiple functional taxa on denitrification, and reinforces the significance of coupling processes for nitrogen removal.

Effective removal of nitrate in water by continuous-flow electro-dialysis ion exchange membrane bioreactor (CF-EDIMB): Performance optimization and microbial analysis

The use of nitrogen fertilizer has been causing nitrate pollution in groundwater, and there is an urgent need for efficient approach to remove nitrate from groundwater. In our job, a novel continuous-flow electrodialysis ion exchange membrane bioreactor system (CF-EDIMB) was set up to remove nitrate (NO3-) from water for the first time. Nitrate removal was positively dependent on water chamber HRT and voltage; voltage had significant effect on the water chamber effluent pH; acetate utilization efficiency was closely correlated with acetate dosage. The optimal conditions forecasted through response surface method (RSM) were given as follows: water chamber HRT was 20 h, biological chamber HRT was 24 h, voltage was 6.65 V and acetate dosage was 454.99 mg/L, dedicating to nitrate removal of 81.90% (83.70% in prediction), water chamber effluent pH of 7.10 (7.00 in prediction) and acetate utilization efficiency of 92.87% (96.51% in prediction). Meanwhile, microorganisms are crucial for nitrate removal, and the microbial community was not sensitive to the variation of acetate dosage. The microbial analysis results indicated that when CF-EDIMB system was operated for 20 d, the sulfate-reducing bacteria Sediminibacterium appeared in the biological chamber, and the effluent sulfate concentration of biological chamber was decreased. During the whole operation, Thauera was the dominant genus. Denitrifying functional genes nirS presented a better expression than the gene narG, and there was no accumulation of nitrite.

Effects of microplastics on denitrification and associated N2O emission in estuarine and coastal sediments: insights from interactions between sulfate reducers and denitrifiers

Global estuarine and coastal zones are facing severe microplastics (MPs) pollution. Sulfate reducers (SRB) and denitrifiers (DNB) are two key functional microorganisms in these zones, exhibiting intricate interactions. However, whether and how MPs modulate the interactions between SRB and DNB, with implications for denitrification and associated N2O emissions, remains poorly understood. Here, we simultaneously investigated the spatial response patterns of SRB-DNB interactions and denitrification and associated N2O emissions to different MPs exposure along an estuarine gradient in the Yangtze Estuary. Spatial responses of denitrification to polyvinyl chloride (PVC) and polyadipate/butylene terephthalate (PBAT) MPs exposure were heterogeneous, while those of N2O emissions were not. Gradient-boosted regression tree and multiple regression model analyses showed that sulfide, followed by nitrate (NO3-), controlled the response patterns of denitrification to MPs exposure. Further mechanistic investigation revealed that exposure to MPs resulted in a competitive and toxic (sulfide accumulation) inhibition of SRB on DNB, ultimately inhibiting denitrification at upstream zones with high sulfide but low NO3- levels. Conversely, MPs exposure induced a competitive inhibition of DNB on SRB, generally promoting denitrification at downstream zones with low sulfide but high NO3- levels. These findings advance the current understanding of the impacts of MPs on nitrogen cycle in estuarine and coastal zones, and provide a novel insight for future studies exploring the response of biogeochemical cycles to MPs in various ecosystems.

Seasonal variations of microbial community structure, assembly processes, and influencing factors in karst river

The physicochemical properties and microbial communities have significant annual and seasonal changes in karst aquifers. To explore the changes of microbial community and their relationships with environmental factors, water samples were collected from a typical karst river. Microbial communities in winter (Jan-2017 and Jan-2019) were stable with high similarity in spite of the 2 years sampling interval, but the microbial communities in Aug-2017 was different from that in Aug-2018. In four sampling times, there were 275 shared genera, whose average relative abundance ranging from 89.04 to 96.27%. The winter and summer specific genera were mainly from the recharge of tributary site K6 and discharge of waste water treatment plant (K2 and K3), respectively. The deterministic processes had a more significant effect on the microbial community assembly in winter than that in summer, which was affected by environmental pressure from pollution. Furthermore, antibiotics and inorganic nitrogen pollution affected element cycles of nitrogen and sulfur indirectly through microbial ecological modules in karst river, and the denitrification and desulfurization processes were potentially inhibited. These findings contributed to understand the changes and its assembly mechanism of microbial community, as well as the feedback to environment in polluted karst river.

Periphytic biofilms function as a double-edged sword influencing nitrogen cycling in paddy fields

It remains unclear whether periphytic biofilms are beneficial to N cycling in paddy fields. Here, based on a national-scale field investigation covering 220 rice fields in China, the N accumulation potential of periphytic biofilms was found to decrease from 8.8 ± 2.4 to 4.5 ± 0.7 g/kg and 3.1 ± 0.6 g/kg with increasing habitat latitude and longitude, respectively. The difference in abundant and rare subcommunities likely accounts for their geo-difference in N accumulation potential. The N cycling pathways involved in periphytic biofilms inferred that soil N and N₂ were two potential sources for N accumulation in periphytic biofilms. Meanwhile, some of the accumulated N may be lost via N₂ , N₂ O, NO, or NH₃ outputs. Superficially, periphytic biofilms are double-edged swords to N cycling by increasing soil N through biological N fixation but accelerating greenhouse gas emissions. Essentially, augmented periphytic biofilms increased change of TN (ΔTN) content in paddy soil from -231.9 to 31.9 mg/kg, indicating that periphytic biofilms overall benefit N content enhancement in paddy fields. This study highlights the contribution of periphytic biofilms to N cycling in rice fields, thus, drawing attention to their effect on rice production and environmental security.

RETRACTED: The adaptive mechanism of halophilic Brachybacterium muris in response to salt stress and its mitigation of copper toxicity in hydroponic plants

This article has been retracted: please see Elsevier Policy on Article Withdrawal (http://www.elsevier.com/locate/withdrawalpolicy). This article has been retracted at the request of the Authors who have indicated that there are significant errors with the scientific data upon which this study is based. Specifically, the authors have subsequently discovered that the 16S rDNA sequencing of Brachybacterium muris may not be reliable because of the limited identification methods from a few years ago. The authors are now repeating their experiments to reconfirm their data. The Authors take full responsibility for these errors and offer their sincere apologies.

The Metabolic Adaptation in Response to Nitrate Is Critical for Actinobacillus pleuropneumoniae Growth and Pathogenicity under the Regulation of NarQ/P

Nitrate metabolism is an adaptation mechanism used by many bacteria for survival in anaerobic environments. As a by-product of inflammation, nitrate is used by the intestinal bacterial pathogens to enable gut infection. However, the responses of bacterial respiratory pathogens to nitrate are less well understood. Actinobacillus pleuropneumoniae is an important bacterial respiratory pathogen of swine. Previous studies have suggested that adaptation of A. pleuropneumoniae to anaerobiosis is important for infection. In this work, A. pleuropneumoniae growth and pathogenesis in response to the nitrate were investigated. Nitrate significantly promoted A. pleuropneumoniae growth under anaerobic conditions in vitro and lethality in mice. By using narQ and narP deletion mutants and single-residue-mutated complementary strains of ΔnarQ, the two-component system NarQ/P was confirmed to be critical for nitrate-induced growth, with Arg50 in NarQ as an essential functional residue. Transcriptome analysis showed that nitrate upregulated multiple energy-generating pathways, including nitrate metabolism, mannose and pentose metabolism, and glycerolipid metabolism via the regulation of NarQ/P. Furthermore, narQ, narP, and its target gene encoding the nitrate reductase Nap contributed to the pathogenicity of A. pleuropneumoniae. The Nap inhibitor tungstate significantly reduced the survival of A. pleuropneumoniae in vivo, suggesting that Nap is a potential drug target. These results give new insights into how the respiratory pathogen A. pleuropneumoniae utilizes the alternative electron acceptor nitrate to overcome the hypoxia microenvironment, which can occur in the inflammatory or necrotic infected tissues.

High rate production of concentrated sulfides from metal bearing wastewater in an expanded bed hydrogenotrophic sulfate reducing bioreactor

Metallurgical wastewaters contain high concentrations of sulfate, up to 15 g L-1. Sulfate-reducing bioreactors are employed to treat these wastewaters, reducing sulfates to sulfides which subsequently co-precipitate metals. Sulfate loading and reduction rates are typically restricted by the total H2S concentration. Sulfide stripping, sulfide precipitation and dilution are the main strategies employed to minimize inhibition by H2S, but can be adversely compromised by suboptimal sulfate reduction, clogging and additional energy costs. Here, metallurgical wastewater was treated for over 250 days using two hydrogenotrophic granular activated carbon expanded bed bioreactors without additional removal of sulfides. H2S toxicity was minimized by operating at pH 8 ± 0.15, resulting in an average sulfate removal of 7.08 ± 0.08 g L-1, sulfide concentrations of 2.1 ± 0.2 g L-1 and peaks up to 2.3 ± 0.2 g L-1. A sulfate reduction rate of 20.6 ± 0.9 g L-1 d-1 was achieved, with maxima up to 27.2 g L-1 d-1, which is among the highest reported considering a literature review of 39 studies. The rates reported here are 6-8 times higher than those reported for other reactors without active sulfide removal and the only reported for expanded bed sulfate-reducing bioreactors using H2. By increasing the influent sulfate concentration and maintaining high sulfide concentrations, sulfate reducers were promoted while fermenters and methanogens were suppressed. Industrial wastewater containing 4.4 g L-1 sulfate, 0.036 g L-1 nitrate and various metals (As, Fe, Tl, Zn, Ni, Sb, Co and Cd) was successfully treated with all metal(loid)s, nitrates and sulfates removed below discharge limits.

Sedimentary Nitrogen and Sulfur Reduction Functional-Couplings Interplay With the Microbial Community of Anthropogenic Shrimp Culture Pond Ecosystem

Sediment nitrogen and sulfur cycles are essential biogeochemical processes that regulate the microbial communities of environmental ecosystems, which have closely linked to environment ecological health. However, their functional couplings in anthropogenic aquaculture sedimentary ecosystems remain poorly understood. Here, we explored the sediment functional genes in shrimp culture pond ecosystems (SCPEs) at different culture stages using the GeoChip gene array approach with 16S amplicon sequencing. Dissimilarity analysis showed that the compositions of both functional genes and bacterial communities differed at different phases of shrimp culture with the appearance of temporal distance decay (p < 0.05). During shrimp culture, the abundances of nitrite and sulfite reduction functional genes decreased (p < 0.05), while those of nitrate and sulfate reduction genes were enriched (p < 0.05) in sediments, implying the enrichment of nitrites and sulfites from microbial metabolism. Meanwhile, nitrogen and sulfur reduction genes were found to be linked with carbon degradation and phosphorous metabolism (p < 0.05). The influence pathways of nutrients were demonstrated by structural equation modeling through environmental factors and the bacterial community on the nitrogen and sulfur reduction functions, indicating that the bacterial community response to environmental factors was facilitated by nutrients, and led to the shifts of functional genes (p < 0.05). These results indicate that sediment nitrogen and sulfur reduction functions in SCPEs were coupled, which are interconnected with the SCPEs bacterial community. Our findings will be helpful for understanding biogeochemical cycles in anthropogenic aquaculture ecosystems and promoting sustainable management of sediment environments through the framework of an ecological perspective.