Complete Genome of Ignavibacterium album, a Metabolically Versatile, Flagellated, Facultative Anaerobe from the Phylum Chlorobi

A novel coupling process to replace the traditional multi-stage anammox process-sulfur autotrophic denitrification coupled anammox system

A novel coupling process to replace the traditional multi-stage anammox process-sulfur autotrophic denitrification (SAD) coupled anaerobic ammonium oxidation (anammox) system was designed, which solved problems of nitrate produced in anammox process and low nitrate conversion rate caused by nitrite accumulation in SAD process. Different filter structures (SAD filter and anammox granular sludge) were investigated to further explore the excellent performance of the novel integrated reactor. The results of sequential batch experiments indicated that nitrite accumulation occurred during SAD, which inhibited the conversion of nitrate to dinitrogen gas. When SAD filter and anammox granular sludge were added to packed bed reactor simultaneously, the nitrate removal rate increased by 37.21% and effluent nitrite concentration decreased by 100% compared to that achieved using SAD. The stratified filter structure solved groove flow. Different proportion influence of SAD filter and anammox granular sludge on the stratified filter structure was evaluated. More suitable ratio of SAD filter to anammox granular sludge was 2:1. Proteobacteria (57.26%), Bacteroidetes (20.12%) and Chloroflexi (9.95%) were the main phyla. The dominant genera of denitrification functional bacteria were Thiobacillus (39.80%), Chlorobaculum (3.99%), norank_f_PHOs-HE36 (2.90%) and Ignavibacterium (2.64%). The dominant genus of anammox bacterium was Candidatus_Kuenenia (3.05%).

Vertical spatial denitrification performance and microbial community composition in denitrification biofilters coupled with water electrolysis

In this study, a denitrification biofilter coupled with water electrolysis (DNBF-WE) was developed as a novel heterotrophic-hydrogen autotrophic denitrification system, which could enhance denitrification with limited organic carbon in the secondary effluent. The volumetric denitrification rate of DNBF-WE reached 152.16 g N m-3 d-1 (C/N = 2, I = 60 mA, and HRT = 5 h). Besides, the vertical spatial denitrification of DNBF-WE was explored, with the nitrate removal rate being 49.5%, 16.3%, and 29.3% in the top, middle, and bottom, respectively. The concentration of extracellular polymeric substances (EPSs) was consistent with the denitrification performance vertically. The high-throughput sequencing analysis results revealed that autotrophic denitrification bacteria (e.g. Thauera) gradually enriched along DNBF-WE from top to bottom. The functional gene prediction results illustrated the vertical stratification mechanisms of the denitrification. Both dissimilatory nitrate reduction and denitrification contributed to nitrate removal, and denitrification became more advantageous with an increase in the filter depth. The research on both the performance of DNBF-WE and the characteristics of microbial communities in the vertical zones of the biofilter may lay a foundation for the biofilter denitrification process in practice.

Accounting for the microbial assembly of each process in wastewater treatment plants (WWTPs): study of four WWTPs receiving similar influent streams

We evaluated a unique model in which four full-scale wastewater treatment plants (WWTPs) with the same treatment schematic and fed with similar influent wastewater were tracked over an 8-month period to determine whether the community assembly would differ in the activated sludge (AS) and sand filtration (SF) stages. For each WWTP, AS and SF achieved an average of 1-log10 (90%) and <0.02-log10 (5%) reduction of total cells, respectively. Despite the removal of cells, both AS and SF had a higher alpha and beta diversity compared to the influent microbial community. Using the Sloan neutral model, it was observed that AS and SF were individually dominated by different assembly processes. Specifically, microorganisms from influent to AS were predominantly determined by the selective niche process for all WWTPs, while the microbial community in the SF was relatively favored by a stochastic, random migration process, except two WWTPs. AS also contributed more to the final effluent microbial community compared with the SF. Given that each WWTP operates the AS independently and that there is a niche selection process driven mainly by the chemical oxygen demand concentration, operational taxonomic units unique to each of the WWTPs were also identified. The findings from this study indicate that each WWTP has its distinct microbial signature and could be used for source-tracking purposes.IMPORTANCEThis study provided a novel concept that microorganisms follow a niche assembly in the activated sludge (AS) tank and that the AS contributed more than the sand filtration process toward the final microbial signature that is unique to each treatment plant. This observation highlights the importance of understanding the microbial community selected by the AS stage, which could contribute toward source-tracking the effluent from different wastewater treatment plants.

Role of sulfide on DNRA distribution and the microbial community structure in a sulfide-driven nitrate reduction process

Microbial nitrate reduction processes involve two competing pathways: denitrification (DEN) and dissimilatory nitrate reduction to ammonium (DNRA). This study investigated the distribution of DNRA in a sole sulfur-driven nitrogen conversion process using a laboratory-scale sequencing biofilm batch reactor (SBBR) through a series of batch tests with varying sulfide/nitrate (S/N) ratios. The results showed that DNRA became more dominant in the sulfide-oxidizing autotrophic denitrification (SOAD) process as the S/N ratio increased to 1.5:1, 1.7:1, and 2:1, reaching a peak of 35.3% at the S/N ratio of 1.5:1. Oxidation-reduction potential (ORP) patterns demonstrated distinct inflection points for nitrate and nitrite consumption under the SOAD-only conditions, whereas these points overlapped when DNRA coexisted with SOAD. Analysis of 16S ribosomal RNA identified Ignavibacterium, Hydrogenophaga, and Geobacter as the dominant genera responsible for DNRA during autotrophic nitrate reduction. The findings of the DNRA divergence investigation provided valuable insights into enhancing biological nitrogen removal processes, particularly when coupled with the anammox.

Enhancement strategies of aerobic denitrification for efficient nitrogen removal from low carbon-to-nitrogen ratio shale oil wastewater

The strategy of high reflux ratio and long solids retention time was adopted to realize efficient nitrogen removal from real shale oil wastewater. This was undertaken with a low chemical oxygen demand to total nitrogen (COD/TN) ratio by strengthening aerobic denitrification in an anoxic/aerobic membrane bioreactor (A/O-MBR). The TN removal load climbed from 22 to 25 g N/(kg MLSS·d) as the COD/TN ratio declined from 8 to 3. The abundance of heterotrophic nitrifying and aerobic denitrifying (HNAD) bacteria increased by 13.8 times to 42.5%, displacing anoxic denitrifying bacteria as the predominant bacteria. The abundance of genes involved in denitrification (napAB, narGHI, norBC, nosZ) increased, however the genes related to assimilatory nitrate reduction (nirA, narB, nasC) decreased. The capacity of the dominant HNAD bacteria in an A/O-MBR to efficiently utilize a carbon source is the key to efficient nitrogen removal from shale oil wastewater with a low COD/TN ratio.

Direct interspecies electron transfer enables anaerobic oxidation of sulfide to elemental sulfur coupled with CO2-reducing methanogenesis

Electric syntrophy between fatty acid oxidizers and methanogens through direct interspecies electron transfer (DIET) is essential for balancing acidogenesis and methanogenesis in anaerobic digestion. Promoting DIET using electrically conductive additives proved effective in enhancing methanogenesis; however, its possibility to affect other microbial redox reactions in methanogenic systems has been little studied. This study provides the first confirmation of the electro-syntrophic coupling of sulfide oxidation to S0 with CO2-reducing methanogenesis in sulfur-rich methanogenic cultures supplemented with conductive magnetite (100-700-nm particle size). The H2S content in biogas, initially exceeding 5000 ppmv, decreased to below 1 ppmv along with an accumulation of extracellular S0 (60-70 mg/L; initially <1 mg/L) at a magnetite dose of 20 mM Fe, while there were no significant changes in methane yield. A comprehensive polyphasic approach demonstrated that the S0 formation occurs through electro-syntrophic oxidation of sulfide coupled with CO2-reducing methanogenesis, involving Methanothrix as the dominant methanogen.

Culture-independent assessment of the indigenous microbial diversity of Raniganj coal bed methane block, Durgapur

It is widely acknowledged that conventional mining and extraction techniques have left many parts of the world with depleting coal reserves. A sustainable method for improving the recovery of natural gas from coalbeds involves enhancing the production of biogenic methane in coal mines. By taking a culture-independent approach, the diversity of the microbial community present in the formation water of an Indian reservoir was examined using 16S rRNA gene amplification in order to study the potential of microbial-enhanced coal bed methane (CBM) production from the deep thermogenic wells at a depth of 800-1200 m. Physicochemical characterization of formation water and coal samples was performed with the aim of understanding the in situ reservoir conditions that are most favorable for microbial CBM production. Microbial community analysis of formation water showed that bacteria were more abundant than archaea. Proteobacteria, Firmicutes, and Bacteroidetes were found as the most prevalent phyla in all the samples. These phyla play a crucial role in providing substrate for the process of methanogenesis by performing fermentative, hydrolytic, and syntrophic functions. Considerable variation in the abundance of microbial genera was observed amongst the selected CBM wells, potentially due to variable local geochemical conditions within the reservoir. The results of our study provide insights into the impact of geochemical factors on microbial distribution within the reservoir. Further, the study demonstrates lab-scale enhancement in methane production through nutrient amendment. It also focuses on understanding the microbial diversity of the Raniganj coalbed methane block using amplicon sequencing and further recognizing the potential of biogenic methane enhancement through microbial stimulation. The findings of the study will help as a reference for better strategization and implementation of on-site microbial stimulation for enhanced biogenic methane production in the future.

Simultaneous denitrification and electricity generation in a methane-powered bioelectrochemical system

Bioelectrochemical system is a novel method for controlling down nitrate pollution, yet the feasibility of using methane as the electron donors for denitrification in this system remains unknown. In this study, using the effluent from mother BESs as inocula, a denitrifying anaerobic methane oxidation bioelectrochemical system was successfully started up in 92 days. When operated with 50 mmol/L phosphate buffer solution at pH 7 and 30°C, the maximum methane consumption, nitrate, and total nitrogen removal load reached 0.23 ± 0.01 mmol/d, 551.0 ± 22.1 mg N/m3 /d, and 64.0 ± 18.8 mg N/m3 /d, respectively. Meanwhile, the peak voltage of 93 ± 4 mV, the anodic coulombic efficiency of 6.99 ± 0.20%, and the maximum power density of 219.86 mW/m3 were obtained. The metagenomics profiles revealed that the dominant denitrifying bacteria in the cathodic chamber reduced most nitrate to nitrite through denitrification and assimilatory reduction. In the anodic chamber, various archaea including methanotrophs and methanogens converted methane via reverse methanogenesis to form formate (or H2 ), acetate, and methyl compounds, which were than utilized by electroactive bacteria to generate electricity. PRACTITIONER POINTS: A denitrifying anaerobic methane oxidation BES was successfully started up in 92 d. Simultaneous removal of methane and nitrate was achieved in the DAMO-BES. Functional genes related to AMO and denitrification were detected in the DAMO-BES. Methylocystis can mediate AMO in the anode and denitrification in the cathode.

Combining biological denitrification and electricity generation in methane-powered microbial fuel cells

Methane has been demonstrated to be a feasible substrate for electricity generation in microbial fuel cells (MFCs) and denitrifying anaerobic methane oxidation (DAMO). However, these two processes were evaluated separately in previous studies and it has remained unknown whether methane is able to simultaneously drive these processes. Here we investigated the co-occurrence and performance of these two processes in the anodic chamber of MFCs. The results showed that methane successfully fueled both electrogenesis and denitrification. Importantly, the maximum nitrate removal rate was significantly enhanced from (1.4 ± 0.8) to (18.4 ± 1.2) mg N/(L·day) by an electrogenic process. In the presence of DAMO, the MFCs achieved a maximum voltage of 610 mV and a maximum power density of 143 ± 12 mW/m². Electrochemical analyses demonstrated that some redox substances (e.g. riboflavin) were likely involved in electrogenesis and also in the denitrification process. High-throughput sequencing indicated that the methanogen Methanobacterium, a close relative of Methanobacterium espanolae, catalyzed methane oxidation and cooperated with both exoelectrogens and denitrifiers (e.g., Azoarcus). This work provides an effective strategy for improving DAMO in methane-powered MFCs, and suggests that methanogens and denitrifiers may jointly be able to provide an alternative to archaeal DAMO for methane-dependent denitrification.

Metalloenzymes play major roles to achieve high-rate nitrogen removal in N-damo communities: Lessons from metaproteomics

Nitrite-driven anaerobic methane oxidation (N-damo) is a promising biological process to achieve carbon-neutral wastewater treatment solutions, aligned with the sustainable development goals. Here, the enzymatic activities in a membrane bioreactor highly enriched in N-damo bacteria operated at high nitrogen removal rates were investigated. Metaproteomic analyses, with a special focus on metalloenzymes, revealed the complete enzymatic route of N-damo including their unique nitric oxide dismutases. The relative protein abundance evidenced that "Ca. Methylomirabilis lanthanidiphila" was the predominant N-damo species, attributed to the induction of its lanthanide-binding methanol dehydrogenase in the presence of cerium. Metaproteomics also disclosed the activity of the accompanying taxa in denitrification, methylotrophy and methanotrophy. The most abundant functional metalloenzymes from this community require copper, iron, and cerium as cofactors which was correlated with the metal consumptions in the bioreactor. This study highlights the usefulness of metaproteomics for evaluating the enzymatic activities in engineering systems to optimize microbial management.

Autotrophic denitrification supported by sphalerite and oyster shells: Chemical and microbiome analysis

This research evaluated the metal-sulfide mineral, sphalerite, as an electron donor for autotrophic denitrification, with and without oyster shells (OS). Batch reactors containing sphalerite simultaneously removed NO₃^- and PO₄^3- from groundwater. OS addition minimized NO₂^- accumulation and removed 100% PO₄^3- in approximately half the time compared with sphalerite alone. Further investigation using domestic wastewater revealed that sphalerite and OS removed NO₃^- at a rate of 0.76 ± 0.36 mg NO₃^--N/(L · d), while maintaining consistent PO₄^3- removal (∼97%) over 140 days. Increasing the sphalerite and OS dose did not improve the denitrification rate. 16S rRNA amplicon sequencing indicated that sulfur-oxidizing species of Chromatiales, Burkholderiales, and Thiobacillus played a role in N removal during sphalerite autotrophic denitrification. This study provides a comprehensive understanding of N removal during sphalerite autotrophic denitrification, which was previously unknown. Knowledge from this work could be used to develop novel technologies for addressing nutrient pollution.

Gel-immobilized partial nitritation/anammox achieves reliable nitrogen removal at different concentrations of nitrogen and reactivation processes

A two-stage partial nitritation/anammox process based on microbial encapsulation (PN/A-E) was established. The nitrogen removal characteristics of PN/A-E under high and low ammonia nitrogen and after reactivation following a long-term shutdown were comprehensively investigated and compared with anammox granular sludge (AnGS). The stable PN process did not depend on high ammonia nitrogen, and the nitrite accumulation rate reached 95.2 ± 0.7 %. The overall nitrogen removal rate of encapsulated anammox bacteria was twice that of the AnGS, and it was more tolerant to external interference. Moreover, PN/A-E showed good reactivation performance, and the total nitrogen in the effluent was 10.0 ± 1.4 mg·L^-1 when the final hydraulic retention time was 2.18 h. The immobilized fillers support an increase in ammonia-oxidizing bacteria under restricted conditions and were more conducive to the dominance of functional bacteria and the stability of microbial community under low ammonia nitrogen. This study provides a positive method to achieve a reliable PN/A.

Discovering dominant ammonia assimilation: Implication for high-strength nitrogen removal in full scale biological treatment of landfill leachate

Landfill leachate containing high-strength nitrogen is generated in domestic waste landfilling. The integration of anoxic and aerobic process (AO) based on nitrification and denitrification, has been a mainstream process of biological nitrogen removal (BNR). But the high-strength organics as well as aerobic effluent reflux might change the biochemical environment designed and operated as AO. In view of the nitrogen balance in a full scale landfill leachate treatment plant with two-stage AO, we found that approximately 90% removal of total nitrogen (TN) and ammonia (NH₄⁺-N) focused on primary anoxic and aerobic stage. Meanwhile, the less nitrate and nitrite in the aerobic effluent were incapable of sustaining denitrification or anaerobic ammonia oxidation (anammox). The high reflux flow from aerobic to anoxic process enabled the similar microbial community and functional genes in anoxic and aerobic process units. However, the functional genes involving ammonia assimilation in all process units showcased the highest abundance compared to those correlated with other BNR pathways, including nitrification and denitrification, assimilatory and dissimilatory nitrate reduction, nitrogen fixation and anammox. The ammonia assimilation dominated the removals of TN and NH₄⁺-N, rather than other BNR mechanism. The insight of dominant ammonia assimilation is favorable for illustrating the authentic BNR mechanism of landfill leachate in AO, thereby guiding the optimization of engineering design and operation.

Dynamics of bacterial and archaeal communities during horse bedding and green waste composting

Organic waste decomposition can make up substantial amounts of municipal greenhouse emissions during decomposition. Composting has the potential to reduce these emissions as well as generate sustainable fertilizer. However, our understanding of how complex microbial communities change to drive the chemical and biological processes of composting is still limited. To investigate the microbiota associated with organic waste decomposition, initial composting feedstock (Litter), three composting windrows of 1.5 months (Young phase), 3 months (Middle phase) and 12 months (Aged phase) old, and 24-month-old mature Compost were sampled to assess physicochemical properties, plant cell wall composition and the microbial community using 16S rRNA gene amplification. A total of 2,612 Exact Sequence Variants (ESVs) included 517 annotated as putative species and 694 as genera which together captured 57.7% of the 3,133,873 sequences, with the most abundant species being Thermobifida fusca, Thermomonospora chromogena and Thermobifida bifida. Compost properties changed rapidly over time alongside the diversity of the compost community, which increased as composting progressed, and multivariate analysis indicated significant variation in community composition between each time-point. The abundance of bacteria in the feedstock is strongly correlated with the presence of organic matter and the abundance of plant cell wall components. Temperature and pH are the most strongly correlated parameters with bacterial abundance in the thermophilic and cooling phases/mature compost respectively. Differential abundance analysis revealed 810 ESVs annotated as species significantly varied in relative abundance between Litter and Young phase, 653 between the Young and Middle phases, 1182 between Middle and Aged phases and 663 between Aged phase and mature Compost. These changes indicated that structural carbohydrates and lignin degrading species were abundant at the beginning of the thermophilic phase, especially members of the Firmicute and Actinobacteria phyla. A high diversity of species capable of putative ammonification and denitrification were consistently found throughout the composting phases, whereas a limited number of nitrifying bacteria were identified and were significantly enriched within the later mesophilic composting phases. High microbial community resolution also revealed unexpected species which could be beneficial for agricultural soils enriched with mature compost or for the deployment of environmental and plant biotechnologies. Understanding the dynamics of these microbial communities could lead to improved waste management strategies and the development of input-specific composting protocols to optimize carbon and nitrogen transformation and promote a diverse and functional microflora in mature compost.

Risk assessment and microbial community structure in agricultural soils contaminated by vanadium from stone coal mining

High health risks of vanadium (V) released by the mining of vanadium titanomagnetite (VTM) have been widely recognized, but little is known about the risks and microbial community responses of V pollution as a consequence of the stone coal mining (SCM), another important resource for V mining. In this study, the topsoils and the profile soils were collected from the agricultural soils around a typical SCM in Hunan Province, China, with the investigation of ecological, health risks and microbial community structures. The results showed that ∼97.6% of sampling sites had levels of total V exceeding the Chinese National standard (i.e., 130 mg/kg), and up to 41.1% of V speciation in the topsoils was pentavalent vanadium (V(V)). Meanwhile, the proportions of HQ > 1 and 0.6-1 in the topsoils were ∼8.3% and ∼31.0% respectively, indicating that V might pose a non-carcinogenic risk to children. In addition, the microbial community varied between the topsoils and the profile soils. Both sulfur-oxidizing bacteria (e.g. Thiobacillus, MND1, Ignavibacterium) and sulfate-reducing bacteria (e.g. Desulfatiglans, GOUTB8, GOUTA6) might have been involved in V(V) reductive detoxification. This study helps better understand the pollution and associated risks of V in the soils of SCM and provides a potential strategy for bioremediation of the V-contaminated environment.

Effects of carbon load on nitrate reduction during riverbank filtration: Field monitoring and batch experiment

Riverbank filtration (RBF) is a well-established technique worldwide, and is critical for the maintenance of groundwater quality and production of clean drinking water. Evaluation of the decay of exogenous nitrate (NO₃^-) in river water and the enrichment of ammonium (NH₄⁺) in groundwater during RBF is important; these two processes are mainly influenced by denitrification (DNF) and dissimilatory nitrate reduction to ammonium (DNRA) controlled by the groundwater carbon load. In this study, the effects of carbon load (organic carbon [OC]: NO₃^-) on the competing nitrate reduction (DNRA and DNF) were assessed during RBF using field monitoring and a laboratory batch experiment. Results show the groundwater OC: NO₃^- ratio did not directly affect the reaction rate of DNRA and DNF, however, it could control the competitive partitioning between the two. In the near-shore zone, the groundwater OC: NO₃^- ratio shows significant seasonal variations along the filtration path owing to the changing conditions of redox, OC-rich, and NO₃^--limited. A greater proportion of NO₃^- would be available for DNRA in the wet season with higher OC: NO₃^- ratio (> 10), resulting in a significantly NH₄⁺-N enrichment rate (from 1.43 × 10^-3 to 9.54 × 10^-4 mmol L^-1 d^-1) in the near-shore zone where the zone of Mn (IV) oxide reduction. However, the activity of DNRA was suppressed with lower OC: NO₃^- ratio (< 10) in the dry season, resulting in a stable NH₄⁺-N enrichment rate (from 3.12 × 10^-4 to 1.30 × 10^-4 mmol L^-1 d^-1). Benefiting from seasonal variation of OC-rich and NO₃^--limited conditions, DNRA bacteria outcompeted denitrifiers, which eventually led to seasonal differences in NO₃^- reduction in the near-shore zone. Overall, under the effect of DNRA induced by continuous high carbon load in RBF systems, nitrogen input is not permanently removed but rather retained in groundwater during RBF.

Nitrogen removal performance of anammox immobilized fillers in response to seasonal temperature variations and different operating modes: Substrate utilization and microbial community analysis

Four anaerobic ammonium oxidation (anammox) immobilized filler reactors (R1: 33 °C-normal, R2: seasonal temperature-normal, R3: seasonal temperature-feast, R4: seasonal temperature-starvation) were established to study the response of anammox immobilized fillers to seasonal temperature changes and different operating modes. The results showed that the anammox immobilized filler could better adapt to the seasonal temperature drop and maintain the activity potential by adjusting the hydraulic retention time (HRT). During the temperature rise phase, R2 activity increased rapidly with the highest nitrogen removal rate reaching 1.26 kgN·(m³·d)^-1, which was equivalent to control sample R1 (1.33 kgN·(m³·d)^-1). However, feasting and famine conditions severely impaired anammox performance and changed stoichiometric ratios; feasting, in particular, significantly lowered the nitrogen removal potential of R3. The specific anammox activity of R2, R3 and R4 was 92.2%, 52.6% and 67.9%, respectively, that of R1, respectively, where the accumulation of functional bacteria was the reason for the higher activity of R2. Degradation kinetics and NO₂^--N inhibition curves showed that R3 was less sensitive to high concentrations of NH₄⁺-N, while R4 responded earlier to low concentrations of NH₄⁺-N, and the reduction of IC50 at low temperature was the reason for the inhibition of R3 activity. Furthermore, seasonal temperature fluctuations had little effect on the microbial community structure but had a considerable impact on bacteria abundance. The anammox functional bacteria Candidatus Kuenenia was found to be the dominant genus in R1-R4; however, the relative abundance of most bacteria, including anammox bacteria, decreased in R3, while the proportion of fermentation bacteria and denitrifying bacteria increased in R4. These findings highlight the necessity of rational regulation of HRT for the adaptation of anammox immobilized fillers to seasonal temperature changes, which could enhance our understanding of the synergistic effect of seasonal temperature changes and different operating modes on nitrogen removal.

Efficient nitrogen removal from leachate by coupling Anammox and sulfur-siderite-driven denitrification

High concentrations of nitrate can be generated during anaerobic ammonium oxidation (Anammox) wastewater treatment processes. Addition of sulfur to Anammox reactors stimulates the growth of sulfur-driven denitrifying (SADN) bacteria that can reduce nitrate to nitrogen gas. However, protons released during the SADN process lower the pH of the system and inhibit Anammox activity. The system will keep stable when pH is in the range of 7.5-8.5. This study showed that addition of siderite stabilized the reactor system and significantly improved the nitrogen removal process. In fact, even when concentrations of total nitrogen were 477.15 ± 16.84 mg/L, the sulfur/siderite reactor maintained nitrogen removal efficiencies >90%, while efficiencies in the sulfur reactor were < 80%. Anammox accounted for 31% of the bacterial sequences in the sulfur/siderite reactor compared to only 14% in the sulfur reactor with the majority of sequences clustering with Ca. Brocadia. An abundance of c-type cytochromes in anammox aggregates in the sulfur-siderite reactor also indicated that anammox activity was higher in this system.

Phylogenomic Analyses and Molecular Signatures Elucidating the Evolutionary Relationships amongst the Chlorobia and Ignavibacteria Species: Robust Demarcation of Two Family-Level Clades within the Order Chlorobiales and Proposal for the Family Chloroherpetonaceae fam. nov

Evolutionary relationships amongst Chlorobia and Ignavibacteria species/strains were examined using phylogenomic and comparative analyses of genome sequences. In a phylogenomic tree based on 282 conserved proteins, the named Chlorobia species formed a monophyletic clade containing two distinct subclades. One clade, encompassing the genera Chlorobaculum, Chlorobium, Pelodictyon, and Prosthecochloris, corresponds to the family Chlorobiaceae, whereas another clade, harboring Chloroherpeton thalassium, Candidatus Thermochlorobacter aerophilum, Candidatus Thermochlorobacteriaceae bacterium GBChlB, and Chlorobium sp. 445, is now proposed as a new family (Chloroherpetonaceae fam. nov). In parallel, our comparative genomic analyses have identified 47 conserved signature indels (CSIs) in diverse proteins that are exclusively present in members of the class Chlorobia or its two families, providing reliable means for identification. Two known Ignavibacteria species in our phylogenomic tree are found to group within a larger clade containing several Candidatus species and uncultured Chlorobi strains. A CSI in the SecY protein is uniquely shared by the species/strains from this “larger Ignavibacteria clade”. Two additional CSIs, which are commonly shared by Chlorobia species and the “larger Ignavibacteria clade”, support a specific relationship between these two groups. The newly identified molecular markers provide novel tools for genetic and biochemical studies and identification of these organisms.

Metagenomic Insights Into Competition Between Denitrification and Dissimilatory Nitrate Reduction to Ammonia Within One-Stage and Two-Stage Partial-Nitritation Anammox Bioreactor Configurations

Anaerobic ammonia oxidizing bacteria (Anammox) are implemented in high-efficiency wastewater treatment systems operated in two general configurations; one-stage systems combine aerobic ammonia oxidizing bacteria (AOB) and Anammox within a single aerated reactor, whereas two-stage configurations separate these processes into discrete tanks. Within both configurations heterotrophic populations that perform denitrification or dissimilatory nitrate reduction to ammonia (DNRA) compete for carbon and nitrate or nitrite and can impact reactor performance because DNRA retains nitrogen in the system. Therefore, it is important to understand how selective pressures imposed by one-stage and two-stage reactor configurations impact the microbial community structure and associated nitrogen transforming functions. We performed 16S rRNA gene and metagenomic sequencing on different biomass fractions (granules, flocs, and suspended biomass) sampled from two facilities treating sludge dewatering centrate: a one-stage treatment facility (Chambers Creek, Tacoma, WA) and a two-stage system (Rotterdam, Netherlands). Similar microbial populations were identified across the different samples, but relative abundances differed between reactor configurations and biomass sources. Analysis of metagenome assembled genomes (MAGs) indicated different lifestyles for abundant heterotrophic populations. Acidobacteria, Bacteroidetes, and Chloroflexi MAGs had varying capacity for DNRA and denitrification. Acidobacteria MAGs possessed high numbers of glycosyl hydrolases and glycosyl transferases indicating a role in biomass degradation. Ignavibacteria and Phycosphaerae MAGs contributed to the greater relative abundance of DNRA associated nrf genes in the two-stage granules and contained genomic features suggesting a preference for an anoxic or microoxic niche. In the one-stage granules a MAG assigned to Burkholderiales accounted for much of the abundant denitrification genes and had genomic features, including the potential for autotrophic denitrification using reduced sulfur, that indicate an ability to adapt its physiology to varying redox conditions. Overall, the competition for carbon substrates between denitrifying and DNRA performing heterotrophs may be impacted by configuration specific selective pressures. In one-stage systems oxygen availability in the bulk liquid and the oxygen gradient within granules would provide a greater niche space for heterotrophic populations capable of utilizing both oxygen and nitrate or nitrite as terminal electron acceptors, compared to two-stage systems where a homogeneous anoxic environment would favor heterotrophic populations primarily adapted to anaerobic metabolism.

Activity-based, genome-resolved metagenomics uncovers key populations and pathways involved in subsurface conversions of coal to methane

Microbial metabolisms and interactions that facilitate subsurface conversions of recalcitrant carbon to methane are poorly understood. We deployed an in situ enrichment device in a subsurface coal seam in the Powder River Basin (PRB), USA, and used BONCAT-FACS-Metagenomics to identify translationally active populations involved in methane generation from a variety of coal-derived aromatic hydrocarbons. From the active fraction, high-quality metagenome-assembled genomes (MAGs) were recovered for the acetoclastic methanogen, Methanothrix paradoxum, and a novel member of the Chlorobi with the potential to generate acetate via the Pta-Ack pathway. Members of the Bacteroides and Geobacter also encoded Pta-Ack and together, all four populations had the putative ability to degrade ethylbenzene, phenylphosphate, phenylethanol, toluene, xylene, and phenol. Metabolic reconstructions, gene analyses, and environmental parameters also indicated that redox fluctuations likely promote facultative energy metabolisms in the coal seam. The active "Chlorobi PRB" MAG encoded enzymes for fermentation, nitrate reduction, and multiple oxygenases with varying binding affinities for oxygen. "M. paradoxum PRB" encoded an extradiol dioxygenase for aerobic phenylacetate degradation, which was also present in previously published Methanothrix genomes. These observations outline underlying processes for bio-methane from subbituminous coal by translationally active populations and demonstrate activity-based metagenomics as a powerful strategy in next generation physiology to understand ecologically relevant microbial populations.

A comprehensive root cause analysis of anammox bioreactor performance decline

The cultivation of anaerobic ammonia oxidizing bacteria (anammox) has gained enormous awareness over the last few decades. Although numerous studies focus massively on successfully growing these anammox to different enrichment environments, in reality, the failure rates are somewhat comparable to the reported success rates. This study combines a variety of measurement techniques to observe and monitor the sequence of a bioreactor performance decline following elevated influent substrate concentration. After attaining stable substrate removal throughout a nitrogen loading rate (NLR) range of 0.691 to 1.669 kg-N·m^-3·d^-1, the performance of the lab-scale anammox-sequencing batch reactor (SBR) abruptly broke down as the NLR reached 2.01 kg-N·m^-3·d^-1. The gathered information showed that the increased NLR firstly caused a significant and unfavorable change in the free ammonia (FA) and free nitrous acid (FNA) concentration in the bioreactor. A subsequent drop in N₂ production and a decline from a peak high of 0.381 to a low of 0.012 kg-N·kg-VSS^-3·d^-1 of the specific nitrogen removal rate (SNRR) led to an 82% absurd decline in microbial cellular energy production. Prior to these anammox switching to survival mode and secreting larger quantities (32% higher) of extracellular polymeric substances (EPS), the activity of syntrophic decomposers increased substantially leading to the internal production of excess CO₂ in the bioreactor and thereby diverging the bioreactor pH to lower levels. The purposes of this study are to understand the reason an anammox process shows different signals during a decline phase and to enable immediate response to performance deterioration.

Weakened resilience of benthic microbial communities in the face of climate change

Increased ocean temperature associated with climate change is especially intensified in coastal areas and its influence on microbial communities and biogeochemical cycling is poorly understood. In this study, we sampled a Baltic Sea bay that has undergone 50 years of warmer temperatures similar to RCP5-8.5 predictions due to cooling water release from a nuclear power plant. The system demonstrated reduced oxygen concentrations, decreased anaerobic electron acceptors, and higher rates of sulfate reduction. Chemical analyses, 16S rRNA gene amplicons, and RNA transcripts all supported sediment anaerobic reactions occurring closer to the sediment-water interface. This resulted in higher microbial diversities and raised sulfate reduction and methanogenesis transcripts, also supporting increased production of toxic sulfide and the greenhouse gas methane closer to the sediment surface, with possible release to oxygen deficient waters. RNA transcripts supported prolonged periods of cyanobacterial bloom that may result in increased climate change related coastal anoxia. Finally, while metatranscriptomics suggested increased energy production in the heated bay, a large number of stress transcripts indicated the communities had not adapted to the increased temperature and had weakened resilience. The results point to a potential feedback loop, whereby increased temperatures may amplify negative effects at the base of coastal biochemical cycling.

Biological treatment of volatile organic compounds (VOCs)-containing wastewaters from wet scrubbers in semiconductor industry

This study investigated biological treatment for two kinds of volatile organic compounds (VOCs)-containing wastewaters collected from wet scrubbers in a semiconductor industry. Batch test results indicated that one wastewater containing highly volatile organic compounds was not suitable for aerated treatment conditions while the other containing much lower volatile organic compounds was suitable for aerobic treatment. Accordingly, two moving bed bioreactors, by adding commercial biocarrier BioNET, were operated under aerobic and anoxic conditions for treating low volatility wastewater (LVW) and high volatility wastewater (HVW), respectively. During 280 days of operation, the aerobic LVW bioreactor attained the highest chemical oxygen demand (COD) removal rate of 98.9 mg-COD/L/h with 81% of COD removal efficiency at hydraulic retention time (HRT) of 1 day. The anoxic HVW bioreactor performed above 80% of COD removal efficiency with the highest COD removal rate of 16.5 mg-COD/L/h at HRT of 2 days after 380 days of operation. The specific COD removal rates at different initial substrate-to-biomass (S₀/X₀) ratios, using either suspended sludge or microorganisms attached onto BioNET from both bioreactors, followed the Monod-type kinetics, while the half-saturation coefficients were generally higher for the microorganisms onto BioNET due presumably to relatively poor mass transfer efficiency. Based on the results of microbial community analysis using the next generation sequencing technique, the dominant communities of suspended sludge and BioNET, including nitrifiers, denitrifiers, and degraders for polycyclic aromatic hydrocarbons, were similar in the corresponded bioreactors, but microbial community shifts were observed with increased organic loadings.

Fe(II) enhances simultaneous phosphorus removal and denitrification in heterotrophic denitrification by chemical precipitation and stimulating denitrifiers activity

Using Fe(II) salt as the precipitant in heterotrophic denitrification achieves improved TP removal, and enhancement in denitrification was often observed. This study aimed to obtain a better understanding of Fe(II)-enhanced denitrification with sufficient carbon source supply. Laboratory-scale experiments were conducted in SBRs with or without Fe(II) addition. Remarkably improved TP removal was experienced. TP removal efficiency in Fe(II) adding reactor was 85.8 ± 3.4%; whereas, that in the reactor without Fe(II) addition was 31.1 ± 2.8%. Besides improved TP removal, better TN removal efficiency (94.1 ± 1.1%) were recorded when Fe(II) was added, and that in the reactor without Fe(II) addition was 89 ± 0.8%. The specific denitrification rate were observed increase by 12.6% when Fe(II) was added. Further microbial analyses revealed increases in the abundances of typical denitrifiers (i.e. Niastella, Opitutus, Dechloromonas, Ignavibacterium, Anaeromyxobacter, Pedosphaera, and Myxococcus). Their associated denitrifying genes, narG, nirS, norB, and nosZ, were observed had 14.2%, 19.4%, 21.6%, and 9.9% elevation, respectively. Such enhancement in denitrification shall not be due to nitrate-dependent ferrous oxidation, which prevails in organic-deficient environments. In an environment with a continuous supply of Fe(II) and plenty of carbon sources, a cycle of denitrifying enzyme activity enhancement in the presence of Fe(II) facilitating nitrogen substrate utilization, stimulating denitrifier metabolism and growth, elevating denitrifying genes abundance, and increasing denitrifying enzymes expression were thought to be responsible for the Fe(II)-enhanced heterotrophic denitrification. Fe(II) salt is often a less expensive precipitant and has recently become attractive for TP removal in wastewater. The findings of this study solidify previous observation of enhancement of both TP and TN removal by adding Fe(II) in denitrification, and would be helpful for developing cost-effective pollutant removal processes.

Nitrate removal by anammox biomass with intracellular carbon source as electron donors via DNRA pathway

In this work, a novel nitrate (NO₃^-) reduction pathway by anaerobic ammonium oxidation (anammox) biomass was firstly discovered with the intracellular carbon sources as the only electron donors. And the possible reaction mechanism was deduced to be intracellular dissimilatory nitrate reduction to ammonium (DNRA) pathway according to the experimental results. In batch experiments, without any external electron donors, NO₃^--N (about 50 mg/L) was reduced to N₂ within 48 h, and a small amount of NO₂^--N was detected (the maximum of 2 mg/L) with the anammox biomass concentration of 4400 mg/L. Acetylene (4.46 mmol/L) addition resulted in obvious NH₄⁺ accumulation during NO₃^- degradation by anammox biomass, since acetylene mainly interfered in hydrazine (N₂H₄) generation from NH₄⁺ and NO. Without HCO₃^- addition, the NO₃^--N degradation rate was slower than that with HCO₃^- addition. Simultaneously, glycogen contents inside anammox biomass decreased to 133.22 ± 1.21 mg/g VSS and 129.79 ± 1.21 mg/g VSS with and without HCO₃^-, respectively, from 142.20 ± 0.61 mg/g VSS. In the long-term experiment, anammox biomass stably degraded NO₃^--N without external electron donors addition, and the maximum removal efficiency of NO₃^--N reached 55.4%. The above results indicated the anammox bacteria utilized the DNRA pathway to reduce NO₃^- to NO₂^- and further NH₄⁺, then normal anammox metabolism would continue to convert the produced NO₂^- and NH₄⁺ to N₂. The intracellular stored carbon sources (e.g., glycogen) were supposed to be electron donors for NO₃^- degradation. This capability would enhance the viability and living space of anammox bacteria in different natural ecosystems, and make it plausible that complete nitrogen removal could be implemented only by the anammox process.

Enrichment of Autotrophic Denitrifiers From Anaerobic Sludge Using Sulfurous Electron Donors

This study compared the rates and microbial community development in batch bioassays on autotrophic denitrification using elemental sulfur (S0), pyrite (FeS2), thiosulfate (S2O3 2-), and sulfide (S2-) as electron donor. The performance of two inocula was compared: digested sludge (DS) from a wastewater treatment plant of a dairy industry and anaerobic granular sludge (GS) from a UASB reactor treating dairy wastewater. All electron donors supported the development of a microbial community with predominance of autotrophic denitrifiers during the enrichments, except for sulfide. For the first time, pyrite revealed to be a suitable substrate for the growth of autotrophic denitrifiers developing a microbial community with predominance of the genera Thiobacillus, Thioprofundum, and Ignavibacterium. Thiosulfate gave the highest denitrification rates removing 10.94 mM NO3 - day-1 and 8.98 mM NO3 - day-1 by DS and GS, respectively. This was 1.5 and 6 times faster than elemental sulfur and pyrite, respectively. Despite the highest denitrification rates observed in thiosulfate-fed enrichments, an evaluation of the most relevant parameters for a technological application revealed elemental sulfur as the best electron donor for autotrophic denitrification with a total cost of 0.38 € per m3 of wastewater treated.

Functional Interrelationships of Microorganisms in Iron-Based Anaerobic Wastewater Treatment

This study explicated the functional activities of microorganisms and their interrelationships under four previously reported iron reducing conditions to identify critical factors that governed the performance of these novel iron-dosed anaerobic biological wastewater treatment processes. Various iron-reducing bacteria (FeRB) and sulfate reducing bacteria (SRB) were identified as the predominant species that concurrently facilitated organics oxidation and the main contributors to removal of organics. The high organic contents of wastewater provided sufficient electron donors for active growth of both FeRB and SRB. In addition to the organic content, Fe (III) and sulfate concentrations (expressed by Fe/S ratio) were found to play a significant role in regulating the microbial abundance and functional activities. Various fermentative bacteria contributed to this FeRB-SRB synergy by fermenting larger organic compounds to smaller compounds, which were subsequently used by FeRB and SRB. Feammox (ferric reduction coupled to ammonium oxidation) bacterium was identified in the bioreactor fed with wastewater containing ammonium. Organic substrate level was a critical factor that regulated the competitive relationship between heterotrophic FeRB and Feammox bacteria. There were evidences that suggested a synergistic relationship between FeRB and nitrogen-fixing bacteria (NFB), where ferric iron and organics concentrations both promoted microbial activities of FeRB and NFB. A concept model was developed to illustrate the identified functional interrelationships and their governing factors for further development of the iron-based wastewater treatment systems.

Metagenomic insights into mixotrophic denitrification facilitated nitrogen removal in a full-scale A2/O wastewater treatment plant

Wastewater treatment plants (WWTPs) are important for pollutant removal from wastewater, elimination of point discharges of nutrients into the environment and water resource protection. The anaerobic/anoxic/oxic (A2/O) process is widely used in WWTPs for nitrogen removal, but the requirement for additional organics to ensure a suitable nitrogen removal efficiency makes this process costly and energy consuming. In this study, we report mixotrophic denitrification at a low COD (chemical oxygen demand)/TN (total nitrogen) ratio in a full-scale A2/O WWTP with relatively high sulfate in the inlet. Nitrogen and sulfur species analysis in different units of this A2/O WWTP showed that the internal sulfur cycle of sulfate reduction and reoxidation occurred and that the reduced sulfur species might contribute to denitrification. Microbial community analysis revealed that Thiobacillus, an autotrophic sulfur-oxidizing denitrifier, dominated the activated sludge bacterial community. Metagenomics data also supported the potential of sulfur-based denitrification when high levels of denitrification occurred, and sulfur oxidation and sulfate reduction genes coexisted in the activated sludge. Although most of the denitrification genes were affiliated with heterotrophic denitrifiers with high abundance, the narG and napA genes were mainly associated with autotrophic sulfur-oxidizing denitrifiers. The functional genes related to nitrogen removal were actively expressed even in the unit containing relatively highly reduced sulfur species, indicating that the mixotrophic denitrification process in A2/O could overcome not only a shortage of carbon sources but also the inhibition by reduced sulfur of nitrification and denitrification. Our results indicate that a mixotrophic denitrification process could be developed in full-scale WWTPs and reduce the requirement for additional carbon sources, which could endow WWTPs with more flexible and adaptable nitrogen removal.

Microbial Community Characteristics Largely Unaffected by X-Ray Computed Tomography of Sediment Cores

X-ray computed tomography (CT) scanning is used to study the physical characteristics of soil and sediment cores, allowing scientists to analyze stratigraphy without destroying core integrity. Microbiologists often work with geologists to understand the microbial properties in such cores; however, we do not know whether CT scanning alters microbial DNA such that DNA sequencing, a common method of community characterization, changes as a result of X-ray exposure. Our objective was to determine whether CT scanning affects the estimates of the composition of microbial communities that exist in cores. Sediment cores were extracted from a salt marsh and then submitted for CT scanning. We observed a minimal effect of CT scanning on microbial community composition in the sediment cores either when the cores were examined shortly after recovery from the field or after the cores had been stored for several weeks. In contrast, properties such as sediment layer and marsh location did affect microbial community structure. While we observed that CT scanning did not alter microbial community composition as a whole, we identified a few amplicon sequence variants (13 out of 7,037) that showed differential abundance patterns between scanned and unscanned samples among paired sample sets. Our overall conclusion is that the CT-scanning conditions typically used to obtain images for geological core characterization do not significantly alter microbial community structure. We stress that minimizing core exposure to X-rays is important if cores are to be studied for biological properties. Future investigations might consider variables, such as the length and energy of radiation exposure, the volume of the core, or the degree, to which microbial communities are stressed as important factors in assessing the impact of X-rays on microbes in geological cores.

Understanding complete ammonium removal mechanism in single-chamber microbial fuel cells based on microbial ecology

The removal of organics and ammonium from domestic wastewater was successfully achieved by a flat-panel air-cathode microbial fuel cell (FA-MFC). To elucidate the reason for complete ammonium removal in the single-chamber MFCs, microbial communities were analyzed in biofilms on the surface of each anode, separator, and cathode of separator-electrode assemblies (SEAs). The spatial distribution of bacterial families related to the nitrogen cycle varied based on local conditions. Since oxygen diffusing from the air-cathode created a locally aerobic condition, ammonia-oxidizing bacteria (AOB) Nitrosomonadacea and nitrite-oxidizing bacteria (NOB) Nitrospiraceae were present near the cathode. NOB (~12.1%) was more abundant than AOB (~4.4%), suggesting that the nitrate produced by NOB may be reduced back to nitrite by heterotrophic denitrifiers such as Rhodocyclaceae (~21.7%) and Comamonadaceae (~5%) in the anoxic zone close to the NOB layer. Near that zone, the "nitrite loop" also substantially enriched two nitrite-reducing bacterial families: Ignavibacteriaceae (~18.1%), facultative heterotrophs, and Brocadiaceae (~11.2%), anaerobic ammonium oxidizing autotrophs. A larger inner area of biofilm contained abundant heterotrophic denitrifiers and fermentation bacteria. These results indicate that the large-surface SEA of FA-MFC allows counter-diffusion between substrates and oxygen, resulting in interactions of bacteria involved in the nitrogen cycle for complete ammonium removal.

In-Situ Metatranscriptomic Analyses Reveal the Metabolic Flexibility of the Thermophilic Anoxygenic Photosynthetic Bacterium Chloroflexus aggregans in a Hot Spring Cyanobacteria-Dominated Microbial Mat

Chloroflexus aggregans is a metabolically versatile, thermophilic, anoxygenic phototrophic member of the phylum Chloroflexota (formerly Chloroflexi), which can grow photoheterotrophically, photoautotrophically, chemoheterotrophically, and chemoautotrophically. In hot spring-associated microbial mats, C. aggregans co-exists with oxygenic cyanobacteria under dynamic micro-environmental conditions. To elucidate the predominant growth modes of C. aggregans, relative transcription levels of energy metabolism- and CO₂ fixation-related genes were studied in Nakabusa Hot Springs microbial mats over a diel cycle and correlated with microscale in situ measurements of O₂ and light. Metatranscriptomic analyses indicated two periods with different modes of energy metabolism of C. aggregans: (1) phototrophy around midday and (2) chemotrophy in the early morning hours. During midday, C. aggregans mainly employed photoheterotrophy when the microbial mats were hyperoxic (400–800 µmol L⁻¹ O₂). In the early morning hours, relative transcription peaks of genes encoding uptake hydrogenase, key enzymes for carbon fixation, respiratory complexes as well as enzymes for TCA cycle and acetate uptake suggest an aerobic chemomixotrophic lifestyle. This is the first in situ study of the versatile energy metabolism of C. aggregans based on gene transcription patterns. The results provide novel insights into the metabolic flexibility of these filamentous anoxygenic phototrophs that thrive under dynamic environmental conditions.

Heavy metal reduction coupled to methane oxidation：Mechanisms, recent advances and future perspectives

Methane emission has contributed greatly to the global warming and climate change, and the pollution of heavy metals is an important concern due to their toxicity and environmental persistence. Recently, multiple heavy metals have been demonstrated to be electron acceptors for methane oxidation, which offers a potential for simultaneous methane emission mitigation and heavy metal detoxification. This review provides a comprehensive discussion of heavy metals reduction coupled to methane oxidation, and identifies knowledge gaps and opportunities for future research. The functional microorganisms and possible mechanisms are detailed in groups under aerobic, hypoxic and anaerobic conditions. The potential application and major environmental significances for global methane mitigation, the elements cycle and heavy metals detoxification are also discussed. The future research opportunities are also discussed to provide insights for further research and efficient practical application.

Nitrogen removal and microbial community diversity in single-chamber electroactive biofilm reactors with different ratios of the cathode surface area to reactor volume

Removal of nitrogen compounds is particularly important domestic wastewater treatment. Our recent study reported the successful removal of nitrogen in single-chamber electroactive biofilm reactors (EBRs) under aeration-free conditions. We hypothesized that the oxygen diffused from the air-cathode is a key factor in the removal of nitrogen in the EBR. If so, the effect of the penetrated oxygen would vary according to the ratio of the air-cathode surface area to the reactor volume (AV ratio) and the hydraulic retention time (HRT). In this study, single-chamber EBRs with three different AV ratios: 125 m²/m³ (EBR-125), 250 m²/m³ (EBR-250), and 500 m²/m³ (EBR-500) were evaluated for the removal of nitrogen under different HRTs of 0.5-6 h. The higher the AV ratio, the greater the increase in nitrification. The total nitrogen (TN) removal efficiency of EBR-125 and EBR-250 decreased as the HRT decreased, while that of EBR-500 increased. EBR-250 showed the highest TN removal (62.0%) with well-balanced nitrification (83.9%) and denitrification (75.1%) at an HRT of 6 h. However, EBR-500 appeared to be superior for practical application because it showed a comparable TN removal (59%) at a substantially short HRT of 1 h. The microbial communities that were involved in the nitrogen cycle varied according to whether the biofilms were located on the anodes, separators, and cathodes but were similar among EBRs with different AV ratios. Nitrifying bacteria were detected in the biofilms that were presented on the cathodes (approximately 7.8% of the total phylotypes), while denitrifying bacteria were mainly found in biofilm that were located on the anodes (approximately 23.3%). Anammox bacteria were also detected on the anode (approximately 3.7%) and in the separator biofilms (approximately 1.9%) of all the EBRs. These results suggest that both the A/V ratio and the HRT could affect the counter diffusion of substrates (NH₄⁺ and organic compounds) and oxygen in the biofilms and allow interactions between a diversity of microorganisms for the successful removal of nitrogen in EBRs. These findings are expected to aid in the development of new applications using EBR for energy-saving wastewater treatment.

Successional Dynamics of Molecular Ecological Network of Anammox Microbial Communities under Elevated Salinity

Response of microbial interactions to environmental perturbations has been a central issue in wastewater treatment system. However, the interactions among anammox microbial community under salt perturbation is still unclear. Here, we used random matrix theory (RMT)-based network analysis to investigate the dynamics of networks under elevated salinity in an anammox system. Results showed that high salinity (20 and 30 g/L NaCl) inhibited anammox performance. Salinity led to closer and more complex networks for the overall network and subnetwork of Planctomycetes and Proteobacteria, especially under low salinity (5 g/L NaCl), which could serve as a strategy to survive under salt perturbation. Planctomycetes, most dominant phylum and playing crucial roles in anammox, possessed higher proportion of competitive relationships (64.3%) under 30 g/L NaCl. OTU 109 (closely related to Ignavibacterium), the only network hub detected in the anammox system, also had larger amount of competitive relationships (27.3%) than the control (0%) under 30 g/L NaCl. Similar result was found for the most abundant keystone bacteria Candidatus Kuenenia. These increasing competitions at different taxa level could be responsible for the deterioration of nitrogen removal. Besides, all the network topological features tended to reach the values of the original network, which showed the network of microbial community could gradually adapt to the elevated salinity. Microbial network analysis adds a different dimension for our understanding of the response in microbial community to elevated salinity.

Microbial Life in the Deep Subsurface Aquifer Illuminated by Metagenomics

To get insights into microbial diversity and biogeochemical processes in the terrestrial deep subsurface aquifer, we sequenced the metagenome of artesian water collected at a 2.8 km deep oil exploration borehole 5P in Western Siberia, Russia. We obtained 71 metagenome-assembled genomes (MAGs), altogether comprising 93% of the metagenome. Methanogenic archaea accounted for about 20% of the community and mostly belonged to hydrogenotrophic Methanobacteriaceae; acetoclastic and methylotrophic lineages were less abundant. ANME archaea were not found. The most numerous bacteria were the Firmicutes, Ignavibacteriae, Deltaproteobacteria, Chloroflexi, and Armatimonadetes. Most of the community was composed of anaerobic heterotrophs. Only six MAGs belonged to sulfate reducers. These MAGs accounted for 5% of the metagenome and were assigned to the Firmicutes, Deltaproteobacteria, Candidatus Kapabacteria, and Nitrospirae. Organotrophic bacteria carrying cytochrome c oxidase genes and presumably capable of aerobic respiration mostly belonged to the Chloroflexi, Ignavibacteriae, and Armatimonadetes. They accounted for 13% of the community. The first complete closed genomes were obtained for members of the Ignavibacteriae SJA-28 lineage and the candidate phylum Kapabacteria. Metabolic reconstruction of the SJA-28 bacterium, designated Candidatus Tepidiaquacella proteinivora, predicted that it is an anaerobe growing on proteinaceous substrates by fermentation or anaerobic respiration. The Ca. Kapabacteria genome contained both the sulfate reduction pathway and cytochrome c oxidase. Presumably, the availability of buried organic matter of Mesozoic marine sediments, long-term recharge of the aquifer with meteoric waters and its spatial heterogeneity provided the conditions for the development of microbial communities, taxonomically and functionally more diverse than those found in oligotrophic underground ecosystems.

Characteristics and mechanism of anammox granular sludge with different granule size in high load and low rising velocity sewage treatment

An integrated investigation to structural, activity and microbial diversity of anammox granular sludge (AnGS) in a wastewater treatment system with high ammonia nitrogen load was performed and aimed to establish the relationship between granular size and performance. With the increase in granule size, the main component of extracellular polymeric substances (EPS) changed from slime EPS to tightly-bound EPS, while the organic component remained the same, and the specific anammox activity increased. However, the results of qPCR and high-throughput sequencing showed that for granules with sizes inferior than 4.75 mm, the abundance of ammonia-oxidizing bacteria (AnAOB) increased as the size increased, and the copies of AnAOB decreased when the granule size increased above 4.75 mm, and the community complexity increased. According to the correlation analysis results, AnAOB first accumulated and then optimized the flora structure to improve efficiency and 2.8 mm to 4.75 mm was the optimal size of AnGS.

Naphthenic acid anaerobic biodegrading consortia enriched from pristine sediments underlying oil sands tailings ponds

Seepage from oil sands tailings ponds (OSTP), which contain toxic naphthenic acids (NAs), can infiltrate into groundwater. Clay sediment layer beneath is a critical barrier for reducing the infiltration of NAs into the sand sediment layer, where groundwater channels reside. Biodegradation has great potential as a strategy for NAs removal, but little is known about NAs biodegradability and potential functional microbes in these pristine sediments. This study investigated the potential for anaerobic biodegradation of NAs by microbial consortia enriched from clay and sand sediments underlying OSTP, amended with either acid extracted organics or Merichem NAs, under nitrate- and sulfate-reducing conditions. Degradation of NAs only be detected after DOC concentration reached to steady state after 163 days. Microbial community analysis shows that different electron acceptors, sediment types, and NAs sources associated with specific microbial taxa and can explain 14.8, 13.9 % and 5% of variation of microbial community structures, respectively. The DOC and methane were the most important geochemical properties for microbial community variations. This study approved the potential capability of indigenous microbial communities from the pristine sediments in NA degradation, demonstrating the barrier function of pristine clay sediments underlying OSTP in prohibiting organic contaminants from entering into groundwater.

Auxiliary voltage enhanced microbial methane oxidation co-driven by nitrite and sulfate reduction

In this study, single-chamber bioelectrochemical reactors (EMNS) were used to investigate the methane oxidation driven by sulfate and nitrite reduction with the auxiliary voltage. Results showed that the methane oxidation was simultaneously driven by sulfate and nitrite reduction, with more methane being converted using the auxiliary voltage. When the voltage was 1.6 V, the maximum removal rate was achieved at 8.05 mg L^-1 d^-1. Carbon dioxide and methanol were the main products of methane oxidation. Simultaneously, nitrogen, nitrous oxide, sulfur ions, and hydrogen sulfide were detected as products of sulfate and nitrite reduction. Microbial populations were analyzed by qPCR and high-throughput sequencing. The detected methanotrophs included Methylocaldum sp., Methylocystis sp., Methylobacter sp. and M. oxyfera. The highest abundance of M. oxyfera was (3.97 ± 0.32) × 10⁶ copies L^-1 in the EMNS-1.6. The dominant nitrite-reducing bacteria were Ignavibacterium sp., Hyphomicrobium sp., Alicycliphilus sp., and Anammox bacteria. Desulfovibrio sp., Desulfosporosinus sp. and Thiobacillus sp. were related to the sulfur cycle. Ignavibacterium sp., Thiobacillus sp. and Desulfovibrio sp. may transfer electrons with electrodes using humic acids as the electronic shuttle. The possible pathways included (1) Methane was mainly oxidized to carbon dioxide and dissolved organic matters by methanotrophs utilizing the oxygen produced by the disproportionation in the cells of M. oxyfera. (2) Nitrite was reduced to nitrogen by heterotrophic denitrifying bacteria with dissolved organic compounds. (3) Desulfovibrio sp. and Desulfosporosinus sp. reduced sulfate to sulfur ions. Thiobacillus sp. oxidized sulfur ions to sulfur or sulfate using nitrite as the electron acceptor.

Microbial taxonomic, nitrogen cycling and phosphorus recycling community composition during long-term organic greenhouse farming

Understanding the interplay between the farming system and soil microbiomes could aid the design of a sustainable and efficient farming system. A comparative greenhouse experiment consisting of organic (ORG), integrated (INT) and conventional (CON) farming systems was established in northern China in 2002. The effects of 12 years of organic farming on soil microbiomes were explored by metagenomic and 16S rRNA gene amplicon sequencing analyses. Long-term ORG shifted the community composition of dominant phyla, especially Acidobacteria, increased the relative abundance of Ignavibacteria and Acidobacteria Gp6 and decreased the relative abundance of Nitrosomonas, Bacillus and Paenibacillus. Metagenomic analysis further revealed that relative abundance of ammonia oxidizing microorganisms (Bacteria and Archaea) and anaerobic ammonium oxidation bacteria decreased during ORG. Conversely, the relative abundance of bacteria-carrying periplasmic nitrate reductases (napA) was slightly higher for ORG. Long-term organic farming also caused significant alterations to the community composition of functional groups associated with ammonia oxidation, denitrification and phosphorus recycling. In summary, this study provides key insights into the composition of soil microbiomes and long-term organic farming under greenhouse conditions.

Roles of hydroxylamine and hydrazine in the in-situ recovery of one-stage partial nitritation-anammox process: Characteristics and mechanisms

Nitrate built-up is a serious operational difficulty in one-stage partial nitritation anammox (PN/A) process. To investigate an effective method for in-situ restoration, hydroxylamine (NH₂OH) and hydrazine (N₂H₄) of 2 mgN/L were dosed in PN/A process with nitrate built-up in a comparative study. NH₂OH treatment showed better performances on TN removal and nitrate reduction than N₂H₄ and blank control. Through 104 days' addition of NH₂OH, MRNN (mole ratio of NO₃^--N production to NH₄⁺-N removal) was decreased from 70% to 19.91%; TN removal was increased from 0.01 to 0.18 kgN/(m³ d). After stopping the chemical addition, nitrate rebounded for N₂H₄ treatment, but the restoration effect was stable and persistent for NH₂OH. NH₂OH addition resulted in a low reductive potential (-250 mV) and exerted strong inhibitions on nitrite oxidizing bacteria activities. Additionally, rapid enhancement of ammonia oxidizing bacteria activities, functional gene (hao) and Nitrosomonas gave rise to the restoration of PN/A with NH₂OH addition.

Aquatic Macrophytes and Local Factors Drive Bacterial Community Distribution and Interactions in a Riparian Zone of Lake Taihu

Aquatic macrophytes rhizosphere are biogeochemical cycling hotspots in freshwater ecosystems. However, little is known regarding the effect of aquatic macrophytes on bacterial community and interactions in the riparian zones. We investigated the bacterial community composition and network structures along a gradient of the riparian zone as follows: The supralittoral and eulittoral zones with Phragmites australis, the eulittoral and infralittoral zones without P. australi. The bacterial communities in the four zones differed significantly based on taxonomic dissimilarity, but the two zones with P. australis exhibited phylogenetic closeness of the bacterial communities. The characteristics of the bacterial networks, such as connectivity, modularity, and topological roles of OTUs, were totally different between the P. australis and non-P. australis zones. Some bacterial phyla enriched in the P. australis zones were found to be putative keystone taxa in the networks, which might be involved in the regulation of bacterial interactions and plant growth. Moreover, the hydrological regime and particle size were shown to be determinants of the bacterial community and network structures in the riparian zones. In summary, our results show that the role of P. australis and local factors are crucial for constructing bacterial community and interactions in the riparian zones of lakes.

A novel anammox granules-circulating expanded granular sludge bed reactor for the efficient circulation and retention of floating anammox granules

In application of anammox process, the operation of the conventional expanded granular sludge bed reactor (EGSB_conv.) is severely limited by the blocking and decay of floating anammox granules.To address this emerging issue, a novel three-phase separator configuration was designed and an anammox granules circulating EGSB (EGSB_GC) was proposed in this study. In the EGSB_GC, an influent scour on floating granules, whose effect was confirmed by simulation with a three-dimensional flow model, was obtained by integrating the external three-phase separator with the influent and the external cycle. After 166-d operation, the nitrogen removal efficiency of the EGSB_GC reached 75.6%, being 1.28-times that of the EGSB_conv. (58.9%). The sludge concentration in the main body of the EGSB_GC reached 3112 ± 65 mg/L, compared with 2613 ± 42 mg/L in the EGSB_conv. (p < 0.05). Moreover, the severe granules blockage and decay problem that is frequently encountered in the EGSB_conv. no longer occurred in the EGSB_GC. The relative abundance of anammox bacteria in granules from the three-phase separator of the EGSB_GC was 29.7%, significantly higher than that from the EGSB_conv. (16.1%, p < 0.05). The blockage and decay of granules in the three-phase separator of the EGSB_conv. led to an obvious proliferation of heterotrophic bacteria, with their relative abundance increased by 9.4% compared with the seed sludge (38.6% vs. 29.2%). This study proposed a practical three-phase separator configuration to sustain efficient and stable operation of anammox processes toward the promotion of granules circulation, retention and reaction.

Genome of a Novel Bacterium "Candidatus Jettenia ecosi" Reconstructed From the Metagenome of an Anammox Bioreactor

The microbial community of a laboratory-scale bioreactor based on the anammox process was investigated by using metagenomic approaches and fluorescent in situ hybridization (FISH). The bioreactor was initially inoculated with activated sludge from the denitrifying bioreactor of a municipal wastewater treatment station. By constantly increasing the ammonium and nitrite load, a microbial community containing the novel species of anammox bacteria "Candidatus Jettenia ecosi" developed in the bioreactor after 5 years when the maximal daily nitrogen removal rate reached 8.5 g/L. Sequencing of the metagenome of anammox granules and the binning of the contigs obtained, allowed a high quality draft genome of the dominant anammox bacterium, "Candidatus Jettenia ecosi" to be assembled. Annotation of the 3.9 Mbp long genome revealed 3970 putative protein-coding genes, 45 tRNA genes, and genes for 16S/23S rRNAs. Analysis of the genome of "Candidatus Jettenia ecosi" revealed genes involved in anammox metabolism, including nitrite and ammonium transporters, copper-containing nitrite reductase, a nitrate reductase complex, hydrazine synthase, and hydrazine dehydrogenase. Autotrophic carbon fixation could be accomplished through the Wood Ljungdahl pathway. The composition of the community was investigated through a search of 16S rRNA sequences in the metagenome and FISH analysis of the anammox granules. The presence of the members of Ignavibacteriae, Betaproteobacteria, Chloroflexi and other microbial lineages reflected the complexity of the microbial processes in the studied bioreactor performed by anammox Planctomycetes, fermentative bacteria, and denitrifiers.

Changes in microbial communities of a passive coal mine drainage bioremediation system

Drainage from abandoned mines is one factor greatly affecting the streams and vegetation in and around Pittsburgh and the Appalachian Mountains where coal mining occurred. This drainage may be more acidic, alkaline, or metal based. Different methods for remediation exist. Passive remediation is one method used to naturally allow the metals to precipitate out and aid in cleaning up the water. The goal of this study is to sample different holding ponds in a sequential passive remediation system and determine microbial communities present at each site of an abandoned coal mine drainage site. Sequencing of the 16S rRNA gene of the sediment indicated the most abundant phyla at each of the 5 ponds and wetland area included Proteobacteria (36%–43%), Bacteroidetes (12%–37%), Firmicutes (3%–11%), and Verrucomicrobia (6%–11%). Analysis of genera between the first, and most polluted, pond included Solitalea, Pedosphaera, and Rhodocyclus, whereas the microbial community from the wetland site at the end of the remediation system included Ignavibacterium, Pelotomaculum, and Petrimonas. The results of our microbial community composition study of sediment from a passive treatment system are in line with organisms commonly found in sediment regardless of iron oxide precipitation, while others are preferentially found in the less polluted wetland site.

Geomicrobiology of the carbon, nitrogen and sulphur cycles in Powell Lake: a permanently stratified water column containing ancient seawater

We present the first geomicrobiological characterization of the meromictic water column of Powell Lake (British Columbia, Canada), a former fjord, which has been stably stratified since the last glacial period. Its deepest layers (300-350 m) retain isolated, relict seawater from that period. Fine-scale vertical profiling of the water chemistry and microbial communities allowed subdivision of the water column into distinct geomicrobiological zones. These zones were further characterized by phylogenetic and functional marker genes from amplicon and shotgun metagenome sequencing. Binning of metagenomic reads allowed the linkage of function to specific taxonomic groups. Statistical analyses (analysis of similarities, Bray-Curtis similarity) confirmed that the microbial community structure followed closely the geochemical zonation. Yet, our characterization of the genetic potential relevant to carbon, nitrogen and sulphur cycling of each zone revealed unexpected features, including potential for facultative anaerobic methylotrophy, nitrogen fixation despite high ammonium concentrations and potential micro-aerobic nitrifiers within the chemocline. At the oxic-suboxic interface, facultative anaerobic potential was found in the widespread freshwater lineage acI (Actinobacteria), suggesting intriguing ecophysiological similarities to the marine SAR11. Evolutionary divergent lineages among diverse phyla were identified in the ancient seawater zone and may indicate novel adaptations to this unusual environment.

Change in the microbial community of saline geothermal fluids amended with a scaling inhibitor: effects of heat extraction and nitrate dosage

Geothermal plants are often affected by corrosion caused by microbial metabolites such as H₂S. In the Bad Blumau (Austria) geothermal system, an increase in microbially produced H₂S was observed in the hot (107 °C) and scaling inhibitor-amended saline fluids and in fluids that had cooled down (45 °C). Genetic fingerprinting and quantification revealed the dominance, increasing abundance and diversity of sulfate reducers such as Desulfotomaculum spp. that accompanied the cooling and processing of the geothermal fluids. In addition, a δ³⁴S isotopic signature showed the microbial origin of the H₂S that has been produced either chemolithotrophically or chemoorganotrophically. A nitrate addition test in a test pipe as a countermeasure against the microbial H₂S formation caused a shift from a biocenosis dominated by bacteria of the phylum Firmicutes to a community of Firmicutes and Proteobacteria. Nitrate supported the growth of nitrate-reducing sulfur-oxidizing Thiobacillus thioparus, which incompletely reduced nitrate to nitrite. The addition of nitrate led to a change in the composition of the sulfate-reducing community. As a result, representatives of nitrate- and nitrite-reducing SRB, such as Desulfovibrio and Desulfonatronum, emerged as additional community members. The interaction of sulfate-reducing bacteria and nitrate-reducing sulfur-oxidizing bacteria (NR-SOB) led to the removal of H₂S, but increased the corrosion rate in the test pipe.

Spatial and temporal heterogeneity in the structure and function of sediment bacterial communities of a tropical mangrove forest

Bacterial communities of mangrove sediments are well appreciated for their role in nutrient cycling. However, spatiotemporal variability in these communities over large geographical scale remains understudied. We investigated sediment bacterial communities and their metabolic potential in an intertidal mangrove forest of India, Bhitarkanika, using high-throughput sequencing of 16S rRNA genes and community-level physiological profiling. Bulk surface sediments from five different locations representing riverine and bay sites were collected over three seasons. Seasonality largely explained the variation in the structural and metabolic patterns of the sediment bacterial communities. Freshwater Actinobacteria were more abundant in monsoon, whereas γ-Proteobacteria demonstrated higher abundance in summer. Distinct differences in the bacterial community composition were noted between riverine and bay sites. For example, salt-loving marine bacteria affiliated to Oceanospirillales were more prominent in the bay sites than the riverine sites. L-asparagine, N-acetyl-D-glucosamine, and D-mannitol were the preferentially utilized carbon sources by bacterial communities. Bacterial community composition was largely governed by salinity and organic carbon content of the sediments. Modeling analysis revealed that the abundance of δ-Proteobacteria increased with salinity, whereas β-Proteobacteria displayed an opposite trend. Metabolic mapping of taxonomic data predicted biogeochemical functions such as xylan and chitin degradation, ammonia oxidation, nitrite reduction, and sulfate reduction in the bacterial communities suggesting their role in carbon, nitrogen, and sulfur cycling in mangrove sediments. This study has provided valuable clues about spatiotemporal heterogeneity in the structural and metabolic patterns of bacterial communities and their environmental determinants in a tropical mangrove forest.

"Candidatus Thermonerobacter thiotrophicus," A Non-phototrophic Member of the Bacteroidetes/Chlorobi With Dissimilatory Sulfur Metabolism in Hot Spring Mat Communities

In this study we present evidence for a novel, thermophilic bacterium with dissimilatory sulfur metabolism, tentatively named “Candidatus Thermonerobacter thiotrophicus,” which is affiliated with the Bacteroides/Ignavibacteria/Chlorobi and which we predict to be a sulfate reducer. Dissimilatory sulfate reduction (DSR) is an important and ancient metabolic process for energy conservation with global importance for geochemical sulfur and carbon cycling. Characterized sulfate-reducing microorganisms (SRM) are found in a limited number of bacterial and archaeal phyla. However, based on highly diverse environmental dsrAB sequences, a variety of uncultivated and unidentified SRM must exist. The recent development of high-throughput sequencing methods allows the phylogenetic identification of some of these uncultured SRM. In this study, we identified a novel putative SRM inhabiting hot spring microbial mats that is a member of the OPB56 clade (“Ca. Kapabacteria”) within the Bacteroidetes/Chlorobi superphylum. Partial genomes for this new organism were retrieved from metagenomes from three different hot springs in Yellowstone National Park, United States, and Japan. Supporting the prediction of a sulfate-reducing metabolism for this organism during period of anoxia, diel metatranscriptomic analyses indicate highest relative transcript levels in situ for all DSR-related genes at night. The presence of terminal oxidases, which are transcribed during the day, further suggests that these organisms might also perform aerobic respiration. The relative phylogenetic proximity to the sulfur-oxidizing, chlorophototrophic Chlorobi further raises new questions about the evolution of dissimilatory sulfur metabolism.

Bioelectricity generation using microalgal biomass as electron donor in a bio-anode microbial fuel cell

In this study, microalgal biomass waste (Chlorella regularis) was treated while simultaneously producing bioelectricity in a microbial fuel cell (MFC). Algal biomass was the sole electron donor and was enriched with easily biodegradable proteins (46%) and carbohydrates (22%). The generated power density was 0.86 W/m² and the columbic efficiency reached ∼61.5%.The power generation could be further increased to 1.07 W/m² by using a biomass waste concentration enhancement strategy with maximum chemical oxygen demand (COD) removal of ∼65.2%. Via direct comparison, the power generation and COD removal capability of the algal-fed MFC was close to that of the commercial acetate-fed MFC. The algae-fed MFC presented superior electrochemical characteristics that were attributed to the complicated composition of the biomass anolyte. It possessed a multiple anode respiring bacterial group and diverse microbial community. Hence, this study provides a new strategy for the utilization of microalgal biomass as a bioresource.