Design and evaluation of universal 16S rRNA gene primers for high-throughput sequencing to simultaneously detect DAMO microbes and anammox bacteria

Remediation of arsenic- and nitrate-contaminated groundwater through iron-dependent autotrophic denitrifying culture

Groundwater contamination with arsenic and nitrate poses a pressing concern for the safety of local communities. Bioremediation, utilizing Fe(II)-oxidizing nitrate reducing bacteria, shows promise as a solution to this problem. However, the relatively weak environmental adaptability of a single bacterium hampers practical application. Therefore, this study explored the feasibility and characteristics of a mixed iron-dependent autotrophic denitrifying (IDAD) culture for effectively removing arsenic and nitrate from synthetic groundwater. The IDAD biosystem exhibited stable performace and arsenic resistance, even at a high As(III) concentration of 800 μg/L. Although the nitrogen removal efficiency of the IDAD biosystem decreased from 71.4% to 64.7% in this case, the arsenic concentration in the effluent remained below the standard (10 μg/L) set by WHO. The crystallinity of the lepidocrocite produced by the IDAD culture decreased with increasing arsenic concentration, but the relative abundance of the key iron-oxidizing bacteria norank_f_Gallionellaceae in the culture showed an opposite trend. Metagenomic analysis revealed that the IDAD culture possess arsenic detoxification pathways, including redox, methylation, and efflux of arsenic, which enable it to mitigate the adverse impact of arsenic stress. This study provides theoretical understanding and technical support for the remediation of arsenic and nitrate-contaminated groundwater using the IDAD culture.

Competitive bio-augmentation overcoming unusual direct inhibitor inefficacy in mainstream nitrite-oxidizing bacteria suppression: Unveiling the underpinnings in microbial and nitrogen metabolism aspects

The long-stabilized mainstream partial nitritation/Anammox (PN/A) process continues to encounter significant challenges from nitrite-oxidizing bacteria (NOB). Therefore, this study aimed to determine an efficient, rapid, and easily implementable strategy for inhibiting NOB. A laboratory-scale reactor was operated continuously for 325 days, experiencing NOB outbreak in mainstream and recovery with simulated sidestream support. The results show that direct inhibitory strategies including intermittent aeration and approximately 35 mg/L free ammonia had unusual weak inhibitory effects on NOB activity. Subsequently, the exogenous Anammox from sidestream employed as a competitive bio-augmentation approach rapidly inhibited NOB dynamics. Evidence suggests that the damaged hydroxyapatite granules under low pH conditions might have contributed to NOB dominance by diminishing Anammox bacteria activity, thereby creating a substrate-rich environment favoring NOB survival. In contrast, the introduction of exogenous Candidatus Kuenenia facilitated the nitrogen removal efficiency from 32.5 % to over 80 %. This coincided with a decrease in the relative abundance of Nitrospira from 16.5 % to 2.7 % and NOB activity from 0.34 to 0.07 g N/(g mixed liquor volatile suspended solid)/d. Metagenomic analysis reveals a decrease in the functional potential of most nitrite transport proteins, coupled with a significant increase in eukaryotic-like serine/threonine-protein kinase involved in cellular regulation, during the Anammox activity recovery. This study's findings reveal the feasibility of the bio-augmentation based on substrate competition, wherein sidestream processes support the mainstream PN/A integration, offering significant potential for practical applications.

The ecology of the sewer systems: Microbial composition, function, assembly, and network in different spatial locations

Microbial induced concrete corrosion (MICC) is the primary deterioration affecting global sewers. Disentangling ecological mechanisms in the sewer system is meaningful for implementing policies to protect sewer pipes using trenchless technology. It is necessary to understand microbial compositions, interaction networks, functions, alongside assembly processes in sewer microbial communities. In this study, sewer wastewater samples and microbial samples from the upper part (UP), middle part (MP) and bottom part (BP) of different pipes were collected for 16S rRNA gene amplicon analysis. It was found that BP harbored distinct microbial communities and the largest proportion of unique species (1141) compared to UP and MP. The community in BP tended to be more clustered. Furthermore, significant differences in microbial functions existed in different spatial locations, including the carbon cycle, nitrogen cycle and sulfur cycle. Active microbial sulfur cycling indicated the corrosion risk of MICC. Among the environmental factors, the oxidation‒reduction potential drove changes in BP, while sulfate managed changes in UP and BP. Stochasticity dominated community assembly in the sewer system. Additionally, the sewer microbial community exhibited numerous positive links. BP possessed a more complex, modular network with higher modularity. These deep insights into microbial ecology in the sewer system may guide engineering safety and disaster prevention in sewer infrastructure.

Nitrite-dependent anaerobic methane oxidation (N-DAMO) in global aquatic environments: A review

The vast majority of processes in the carbon and nitrogen cycles are driven by microorganisms. The nitrite-dependent anaerobic oxidation of methane (N-DAMO) process links carbon and nitrogen cycles, offering a novel approach for the simultaneous reduction of methane emissions and nitrite pollution. However, there is currently no comprehensive summary of the current status of the N-DAMO process in natural aquatic environments. Therefore, our study aims to fill this knowledge gap by conducting a comprehensive review of the global research trends in N-DAMO processes in various aquatic environments (excluding artificial bioreactors). Our review mainly focused on molecular identification, global study sites, and their interactions with other elemental cycling processes. Furthermore, we performed a data integration analysis to unveil the effects of key environmental factors on the abundance of N-DAMO bacteria and the rate of N-DAMO process. By combining the findings from the literature review and data integration analysis, we proposed future research perspectives on N-DAMO processes in global aquatic environments. Our overarching goal is to advance the understanding of the N-DAMO process and its role in synergistically reducing carbon emissions and removing nitrogen. By doing so, we aim to make a significant contribution to the timely achievement of China's carbon peak and carbon neutrality targets.

Correlation study on microbial communities and volatile flavor compounds in cigar tobacco leaves of diverse origins

To elucidate the significant influence of microorganisms on geographically dependent flavor formation by analyzing microbial communities and volatile flavor compounds (VFCs) in cigar tobacco leaves (CTLs) obtained from China, Dominica, and Indonesia. Microbiome analysis revealed that the predominant bacteria in CTLs were Staphylococcus, Aerococcus, Pseudomonas, and Lactobacillus, while the predominant fungi were Aspergillus, Wallemia, and Sampaiozyma. The microbial communities of CTLs from different origins differed to some extent, and the diversity and abundance of bacteria were greater than fungi. Metabolomic analysis revealed that 64 VFCs were identified, mainly ketones, of which 23 VFCs could be utilized to identify the geographical origins of CTLs. Sixteen VFCs with OAV greater than 1, including cedrol, phenylacetaldehyde, damascone, beta-damascone, and beta-ionone, play important roles in shaping the flavor profile of CTLs from different origins. Combined with the correlation analysis, bacterial microorganisms were more closely related to key VFCs and favored a positive correlation. Bacillus, Vibrio, and Sphingomonas were the main flavor-related bacteria. The study demonstrated that the predominant microorganisms were essential for the formation of key flavor qualities in CTLs, which provided a theoretical reference for flavor control of CTLs by microbial technology. KEY POINTS: • It is the high OAV VFCs that determine the flavor profile of CTLs. • The methylerythritol phosphate (MEP) pathway and the carotenoid synthesis pathway are key metabolic pathways for the formation of VFCs in CTLs. • Microbial interactions influence tobacco flavor, with bacterial microorganisms contributing more to the flavor formation of CTLs.

Diversity, composition, metabolic characteristics, and assembly process of the microbial community in sewer system at the early stage

Sewer systems play vital roles in wastewater treatment facilities, and the microbial communities contribute significantly to the transformation of domestic wastewater. Therefore, this study conducted a 180-day experiment on a sewer system and utilized the high-throughput sequencing technology to characterize the microbial communities. Additionally, community assembly analysis was performed to understand the early-stage dynamics within the sewer system. The results demonstrated that the overall diversity of microbial communities exhibited fluctuations as the system progressed. The dominant phyla observed were Chloroflexi, Bacteroidetes, Firmicutes, and Proteobacteria, accounting for over 85.4% of the total relative abundances. At the genus level, bacteria associated with fermentation displayed a high relative abundance, particularly during days 75 to 180. A random-forest machine-learning model identified a group of microbes that confirmed the substantial contribution of fermentation. During the process of fermentation, microorganisms predominantly utilized propionate formation as the main pathway for acidogenesis, followed by acetate and butyrate formation. In terms of nitrogen and sulfur cycles, dissimilatory nitrate reduction and assimilatory sulfate reduction played significant roles. Furthermore, stochastic ecological processes had a dominant effect during the experiment. Dispersal limitation primarily governed the assembly process almost the entire experimental period, indicating the strong adaptability and metabolic plasticity of microorganisms in response to environmental variations. This experiment provides valuable insights into the metabolic mechanisms and microbial assembly associated with sewer systems.

Long-term effect of acetate and biochar addition on enrichment and activity of denitrifying anaerobic methane oxidation microbes

The denitrifying anaerobic methane oxidation (DAMO) process plays a crucial role in the global carbon/nitrogen cycles and methane emission control, and also has application potential in biological wastewater treatment. However, given that DAMO microbes are susceptible to external conditions such as additional carbon source in the system, it is essential to evaluate the effect of alternative carbon substance on the enrichment efficiency and metabolic activity of DAMO microbes. To this end, this study investigated the effect of acetate (0.1 mmol/L-R2, 0.5 mmol/L-R3) and biochar addition (R4) on the enrichment and activity of DAMO microbes. The long-term operation showed that the NO2--N and CH4 consumption rates in the reactors almost presented the sequence of R4>R2>R3>R1. However, the short-term activity test with isotope labelling showed the sequence of R2>R4>R1>R3. Furthermore, the addition of acetate and biochar improved the electrochemical activity and extracellular polymeric substance (EPS) secretion in the systems. In R4 reactor, the proportion of DAMO bacteria was the highest (7.20%), indicating that the addition of biochar could promote the enrichment of DAMO bacteria, and Thauera was co-enriched with the proportion increasing from 0.26% to 6.73%. While in R1, R2 and R3 reactors, DAMO bacteria were enriched with relatively low abundances (0.10%, 0.23%, 0.15%, respectively), together with methanogens and denitrifiers. This study showed that biochar and acetate with appropriate concentration could enhance the enrichment and activity of DAMO bacteria, the results can provide reference for the enrichment of DAMO microbes and its application in the biological nitrogen removal of wastewater.

Aquaculture bacterial pathogen database: Pathogen monitoring and screening in coastal waters using environmental DNA

Increasingly diverse pathogen occurrence in coastal and mariculture areas demands improved monitoring platforms to prevent economic and public health implications. Accessible databases with up-to-date knowledge and taxonomy are critical for detecting and screening environmental pathogens. Condensed from over 3000 relevant reports in peer reviewed articles, we constructed an aquaculture bacterial pathogen database that provides specialized curation of over 210 bacterial pathogenic species impacting aquaculture. Application of the aquaculture bacterial pathogen database to environmental DNA metabarcoding monitoring data in Hong Kong coastal and mariculture waters effectively characterized regional pathogen profiles over a one-year period and improved identification of new potential pathogen targets. The results highlighted the increase in potential pathogen abundance related to aquaculture activity and the associated inorganic nitrogen load, which was chiefly due to the enrichment of Vibrio during the atypical dry winter season. The value of the aquaculture bacterial pathogen database for empowering environmental DNA-based approaches in coastal marine pathogen surveillance benefits water resource management and aquaculture development on a global scale.

Enhancement of denitrifying anaerobic methane oxidation via applied electric potential

In this study, single-chamber three-electrode electrochemical sequencing batch reactor (ESBR) was set up to investigate the impact of applying potential on denitrifying anaerobic methane oxidation (DAMO) process. When the applied potential was +0.8 V, the conversion rate of nitrite to nitrogen was superior to those of other potentials. With the optimal potential of +0.8 V for 60 days, the nitrite removal rate of ESBR could reach 3.34 ± 0.28 mg N/L/d, which was 4.5 times more than that of the non-current control (0.74 ± 0.16 mg N/L/d). The DAMO functional bacteria Candidatus Methylomirabilis exhibited noticeable enrichment under applying potential, and its functional gene of pmoA was significantly expressed. Through untargeted LC-MS metabolomics analysis, applied potential was shown to affect the regulation of prior metabolites including spermidine, spermine and glycerophosphocholine that were related to the metabolic pathways of glycerophospholipid metabolism and arginine and proline metabolism, which had positive effects on DAMO process. These results show that applying electric potential could be a useful strategy in DAMO process used for methane and nitrogen removal.

A novel sulfide-driven denitrification methane oxidation (SDMO) system: Operational performance and metabolic mechanisms

Microbial denitrification is a crucial biological process for the treatment of nitrogen-polluted water. Traditional denitrification process consumes external organic carbon leading to an increase in treatment costs. We developed a novel sulfide-driven denitrification methane oxidation (SDMO) system that integrates autotrophic denitrification (AD) and denitrification anaerobic methane oxidation (DAMO) for cost-effective denitrification and biogas utilization in situ. Two SDMO systems were operated for 735 days, with nitrate and nitrite serving as electron acceptors, to explore the performance of sewage denitrification and characterize metabolic mechanisms. Results showed SDMO system could reach as high as 100% efficiency of nitrogen removal and biogas desulfurization without an external carbon source when HRT was 10 days and inflow nitrogen concentrations were 50-100 mgN·L^-1. Besides, nitrate was a preferable electron acceptor for SDMO system. Biogas not only enhanced nitrogen removal but also intensified the DAMO, nitrogen removed through DAMO contribution doubled as original period from 2.9 mgN·(L·d)^-1 to 6.2 mgN·(L·d)^-1, and the ratio of nitrate removal through AD to DAMO was 1.2:1 with nitrate as electron acceptor. While nitrogen removed almost all through AD contribution and DAMO was weaken as before, the ratio of nitrate removal through AD to DAMO was 21.2:1 with nitrite as electron acceptor. Biogas introduced into SDMO system with nitrate inspired the growth of DAMO bacteria Candidatus Methylomirabilis from 0.3% to 19.6% and motivated its potentiality to remove nitrate without ANME archaea participation accompanying with gene mfnE upregulating ∼100 times. According to the reconstructed genome from binning analysis, the dramatically upregulated gene mfnE was derived from Candidatus Methylomirabilis, which may represent a novel metabolism pathway for DAMO bacteria to replace the role of archaea for nitrate reduction.

A novel strategy for rapid development of a self-sustaining symbiotic algal-bacterial granular sludge: Applying algal-mycelial pellets as nuclei

Algal-bacterial granular sludge (ABGS) is a promising technology for wastewater treatment, benefiting from the synergetic interactions between algae and bacteria. However, the rapid start-up of the ABGS system is not trivial. Herein, a novel strategy was proposed by applying the algal-mycelial pellets (AMPs) as the primary nuclei for accelerating the development of a self-sustaining symbiotic ABGS system. The results indicated that by using this strategy complete granulation was shortened to 12 days, much shorter than the control system without AMPs dosage (28 days). The ABGS had a large particle diameter (3.3 mm), compact granular structure (1.0253 g/mL), and excellent settleability (SVI30 of 53.2 mL/g). Moreover, 98.6% of COD, 80.8% of TN and 80.0% of PO43--P were removed by the ABGS. The nuclei of targeted algae (Chlorella) and filamentous fungi (Aspergillus niger), the enhanced production of extracellular polymeric substances (especially proteins) and the enrichment of functional bacteria (such as Neomegalonema and Flavobacterium) facilitated the granules development. The low surface free energy (-69.56 mJ/m2) and energy barrier (89.93 KT) were the inherent mechanisms for the strong surface hydrophobicity, the easy bacterial adhesion, and the short granulation period. This study provides an economically feasible approach to accelerate ABGS granulation and sustain system stability.

Skin Microbiota Variation Among Bat Species in China and Their Potential Defense Against Pathogens

Host-associated skin bacteria are essential for resisting pathogen infections and maintaining health. However, we have little understanding of how chiropteran skin microbiota are distributed among bat species and their habitats, or of their putative roles in defending against Pseudogymnoascus destructans in China. In this study, we characterized the skin microbiomes of four bat species at five localities using 16S rRNA gene amplicon sequencing to understand their skin microbial composition, structure, and putative relationship with disease. The alpha- and beta-diversities of skin microbiota differed significantly among the bat species, and the differences were affected by environmental temperature, sampling sites, and host body condition. The chiropteran skin microbial communities were enriched in bacterial taxa that had low relative abundances in the environment. Most of the potential functions of skin microbiota in bat species were associated with metabolism. Focusing on their functions of defense against pathogens, we found that skin microbiota could metabolize a variety of active substances that could be potentially used to fight P. destructans. The skin microbial communities of bats in China are related to the environment and the bat host, and may be involved in the host's defense against pathogens.

Novel primers for 16S rRNA gene-based archaeal and bacterial community analysis in oceanic trench sediments

High-throughput sequencing of the 16S ribosomal RNA (16S rRNA) gene has been successfully applied to explore the microbial structure and dynamics in various environments. The distinctive microbial communities in oceanic trench sediments are expected because of the extremely high pressure and V-shape topology that caused the isolation from the other marine sediments. However, they have only been primarily targeted using 'universal' primers that provide variable performances for different environments. It is necessary to design specific primers to improve the detection resolution of unique microbial groups in oceanic trenches. Here, we designed one pair of bacterial and two pairs of archaeal specific primers based on 16S rRNA gene full-length sequences that truly come from trench sediment and tested their performances in 30 oceanic trench sediment samples. An in silico analysis showed that the V3-V4 hypervariable region was the most informative and representative for oceanic trench microbial groups. Compared with the 'universal' primers, 46 bacterial families were only detected by newly designed primer B344F/B749R, and eight archaeal families were only detected by the newly designed primer A306F/A713R which covered the one or two orders of magnitude more ASVs (amplicon sequence variants) (1,470,216) in the tested total 30 samples. Moreover, A306F/A713R had the largest number of observed ASVs suggesting its better performance in discovering more archaeal species which were easily ignored in universal primer-based experiments for oceanic trench sediments. The novel primers designed in this research could be a better option to access the unique microbial communities in extreme oceanic trench sediments.Key points• Defining V3-V4 as the most adequate hypervariable region for archaea and bacteria from oceanic trench sediments.• Three sets of bacterial and archaeal primers appear validity and advantage in revealing the real trench microbial communities.• The novel primers provide a better option to specifically detect the unique microbial communities in extreme oceanic trench sediments.

Acetate and electricity generation from methane in conductive fiber membrane- microbial fuel cells

Microbial conversion of methane to electricity, fuels, and liquid chemicals has attracted much attention. However, due to the low solubility of methane, it is not considered a suitable substrate for microbial fuel cells (MFCs). In this study, a conductive fiber membrane (CFM) module was constructed as the bioanode of methane-driven MFCs, directly delivering methane. After biofilm formation on the CFM surface, a steady voltage output of 0.6 to 0.7 V was recorded, and the CFM-MFCs obtained a maximum power density of 64 ± 2 mW/m². Moreover, methane oxidation produced a high concentration of intermediate acetate (up to 7.1 mM). High-throughput 16S rRNA gene sequencing suggests that the microbial community was significantly changed after electricity generation. Methane-related archaea formed a symbiotic consortium with characterized electroactive bacteria and fermentative bacteria, suggesting a combination of three types of microorganisms for methane conversion into acetate and electricity.

Application of electric potential improves ethanol production from xylose by active sludge

BACKGROUND

Low-cost raw materials such as lignocellulosic materials have been utilized in second-generation ethanol production process. However, the sequential and slow conversion of xylose into target products remains one of the main challenges for realizing efficient industrial lignocellulosic biorefinery.

RESULTS

By applying different constant potentials to different microbial electrolysis cells with xylose as the sole carbon source, we analyzed the output of metabolites, microbial community structures, electron flow, and carbon flow in the process of xylose electro-fermentation by domesticated activated sludge. The bioreactors produced currents when applying positive potentials. The peak currents of the + 0.242 V, + 0.542 V and + 0.842 V reactors were 0.96 × 10-6 A, 3.36 × 10-6 A and 6.43 × 10-6 A, respectively. The application of potentials promoted the xylose consumption, and the maximum consumption rate in the + 0.542 V reactor was 95.5%, which was 34.8 times that of the reactor without applied potential. The potential application also promoted the production of ethanol and acetate. The maximum ethanol yield (0.652 mol mol-1 xylose) was obtained in the + 0.842 V reactor. The maximum acetate concentration (1,874 µmol L-1) was observed in the + 0.842 V reactor. The optimal potential for ethanol production was + 0.842 V with the maximum ethanol yield and energy saving. The application of positive potential caused the microorganisms to carry out ethanol fermentation, and the application of negative potential forced the microorganisms to carry out acetic fermentation. The potential application changed the diversity and community structure of microorganisms in the reactors, and the two most significantly changed families were Paenibacillaceae and Bacillaceae.

CONCLUSION

The constructed microbial electrolysis cells with different potentials obtained better production yield and selectivity compared with the reactor without applied potential. Our work provides strategies for the subsequent fermentation processes with different needs.

Pairing denitrifying phosphorus accumulating organisms with anaerobic ammonium oxidizing bacteria for simultaneous N and P removal

Coupling of denitrifying polyphosphate accumulating organisms (DPAO) with anaerobic ammonium oxidizing (Anammox) bacteria in a single treatment scheme has so far been unsuccessful but could offer substantial energy savings, minimize sludge production, while achieving simultaneous carbon, nitrogen and phosphate removal. However, both organisms compete for nitrite and have vastly different growth rates and therefore the goal of this study was to uncouple their solid retention time (SRT) by growing them in different sludge fractions and to determine their biomass specific kinetic properties. Anammox bacteria were grown in a biofilm for longer SRTs and DPAO in flocs to allow shorter SRTs. Exposure of DPAO to anaerobic conditions was accomplished by recycling the flocs to a separate reactor by which simultaneous P, N, and C removal was accomplished. The diffusion limited biofilm lowered the biomass specific nitrite affinity for Anammox (K_s^AMX = 0.091 mM), which gave DPAO a competitive edge to consume nitrite (K_s^DPAO = 0.022 mM) in the suspended floc fraction. However, DPAO are more sensitive to nitrite (K_i^DPAO = 0.377 mM) than Anammox bacteria and (K_i^AMX > 1.786 mM), and therefore the DPAO would be better suited to grow in the protective biofilm, showing that both biomass growth types (flocs and granules) have advantages (and disadvantages) depending on the setting. This work is an important steppingstone to understanding resource competition amongst Anammox and DPAO and SRT management strategies to allow their pairing in combined reactor configurations.

Evaluation of Three Prokaryote Primers for Identification of Prokaryote Community Structure and Their Abode Preference in Three Distinct Wetland Ecosystems

The ultimate role of prokaryote (bacteria and archaea), the decomposer of the wetland ecosystem, depends on its community structure and its interaction with the environment. The present study has used three universal prokaryote primers to compare prokaryote community structure and diversity of three distinctly different wetlands. The study results revealed that α-diversity indices and phylogenetic differential abundance patterns did not differ significantly among primers, but they did differ significantly across wetlands. Microbial community composition revealed a distinct pattern for each primer in each wetland. Overall comparison of prokaryote communities in sediments of three wetlands revealed the highest prokaryote richness and diversity in Bhomra (freshwater wetland) followed by Malencho (brackish-water wetland) and East Kolkata wetland (EKW) (sewage-fed wetland). Indicator genus analysis identified 21, 4, and 29 unique indicator genera, having preferential abode for Bhomra, EKW, and Malencho, respectively. Prediction of potential roles of these microbes revealed a preference for sulfate-reducing microbes in Malencho and methanogens in Bhomra. The distinct phylogenetic differential abundance pattern, microbial abode preference, and their potential functional role predict ecosystem variables shaping microbial diversity. The variation in community composition of prokaryotes in response to ecosystem variables can serve as the most sensitive bioindicator of wetland ecosystem assessment and management.

A novel identified Pseudomonas aeruginosa, which exhibited nitrate- and nitrite-dependent methane oxidation abilities, could alleviate the disadvantages caused by nitrate supplementation in rumen fluid fermentation

After the occurrence of nitrate-dependent anaerobic methane oxidation (AMO) in rumen fluid culture was proved, the organisms that perform the denitrifying anaerobic methane oxidizing (DAMO) process in the rumen of dairy goat were investigated by establishing two enrichment culture systems, which were supplied with methane as the sole carbon source and NaNO3 or NaNO2 as the electron acceptor. Several Operational Taxonomic Units (OTU) belonging to Proteobacteria became dominant in the two enrichment systems. The identified Pseudomonas aeruginosa, which was isolated from the NaNO2 enrichment system, could individually perform a whole denitrifying anaerobic methane oxidizing process. Further in vitro rumen fermentation showed that supplementation with the isolated P. aeruginosa could reduce methane emissions, alleviate the nitrite accumulation and prevent the decrease in propionic acid product caused by nitrate supplementation.

Enhancement of nitrite-dependent anaerobic methane oxidation via Geobacter sulfurreducens

Nitrite-dependent anaerobic methane-oxidation (n-damo) is a potential novel technology for nitrogen removal in anaerobic wastewater treatment. In this study, Geobacter sulfurreducens (G) was applied to stimulate n-damo activity. Conductive materials such as nano-magnetite (M) or aggregating agents such as hydroxylapatite (H) were co-added with G. sulfurreducens to further investigate the enhancement effect. Results showed that the nitrite reduction activity of the n-damo culture was promoted by G. sulfurreducens, with 1.71-2.38 times higher in treatment G, G + M, and G + H than that in the control, but was inhibited by the single addition of hydroxylapatite. N-damo bacterial abundances based on the qPCR of the n-damo-specific pmoA gene increased in treatments with G. sulfurreducens, compared with that of the control. High-throughput sequencing analysis revealed the enrichment of uncultured phylum WPS-2 in treatments with G. sulfurreducens. Fluorescence in situ hybridization verified the co-occurrence pattern of n-damo bacteria (NC10), G. sulfurreducens, and type-I aerobic methanotrophs (Methylomonas spp.). The above results corroborated the microbial interspecies electron transfer (MIET) potentiality of the n-damo enrichment. Our study provides a novel pathway for enhancing MIET to stimulate n-damo process.

Enhancement of nitrite reduction and enrichment of Methylomonas via conductive materials in a nitrite-dependent anaerobic methane oxidation system

Nitrite-dependent anaerobic methane-oxidizing (n-damo) process has a promising prospect in anaerobic wastewater treatment, utilizing methane as the sole electron source to remove nitrite. However, the metabolic activity of n-damo bacteria is too low for practical application. This study aimed to stimulate n-damo process by introducing conductive nano-magnetite and/or electron shuttle anthraquinone-2,6-disulfonate (AQDS), and also set a comparative treatment of adding insulated ferrihydrite. The results showed that the nitrite reduction rate was enhanced the most significantly in treatment with nano-magnetite, approximately 1.6 times higher than that of the control without any supplement. While ferrihydrite application showed an adverse effect on n-damo process. The well-known aerobic methane oxidizer Methylomonas spp. was found to be enriched under n-damo condition with the supplementation of nano-magnetite and/or AQDS, but abundance of n-damo bacteria did not exhibit significant increase. It was hypothesized that Methylomonas spp. could be survived under anaerobic n-damo condition using oxygen produced by n-damo bacteria for the self-growth, and the nitrite reduction could be promoted through the enhancement of microbial interspecies electron transfer triggered by the introduction of conductive materials. It opens a new direction for the stimulation of n-damo activity, which needs more evidences to verify the hypothetic mechanism.

Identification of Fungi in the Debitterizing Water of Apricot Kernels and Their Preliminary Evaluation on Degrading Amygdalin

Debitterizing water contains a great amount of amygdalin, a potential toxic compound, so it is mandatory the degradation of amygdalin to reduce the water’s toxicity and environmental pollution. In this paper, the suspended mycelia in debitterizing water were firstly investigated by digital microscope, cold field emission scanning electron microscope, and internal transcribed spacers (ITS) high-throughput sequencing. Thereafter, the degradation of commercial amygdalin by the identified species was assessed by determining the changes of amygdalin content and the β-glucosidase activity. The results indicate that the mycelia matched with genus of lower fungi, mainly including Irpex, Trichoderma and white rot fungus. Among them, Irpex lacteus had a definite promoting effect on the degradation of amygdalin, which was not caused by producing β-glucosidase, and the suitable degrading colony numbers ranged from 6.4 × 106 CFU/mL to 6.4 × 107 CFU/mL. In conclusion, this research might provide a potential novel approach to treat debitterizing water, so as to reduce the water pollution in the processing industry of apricot kernels.

Natural attenuation of spilled crude oil by cold-adapted soil bacterial communities at a decommissioned High Arctic oil well site

Romulus C-42 is a decommissioned oil well on Ellesmere Island in the Canadian High Arctic, and is the northernmost well to have produced oil and gas anywhere in the world. The remote site has been untouched since a crude oil spill in 1972, offering a rare opportunity to examine natural attenuation in Arctic soils >40 years after a pollution event. Bacterial community composition in crude oil contaminated soils was significantly different from adjacent background soils. Two members of the genus Rhodanobacter (Alphaproteobacteria) were found consistently in contaminated soils, whereas two members of the genus Sphingomonas (Gammaproteobacteria) appeared opposite to each other, one consistently within the oil contaminated soil and the other consistently in non-oil contaminated soils. GC of soil hydrocarbon extracts revealed moderate levels of biodegradation relative to the original oil produced in 1972. Despite conditions permissive for bacterial activity (>0 °C) being limited to only a few months each year, natural attenuation by cold adapted soil microbial communities has taken place since the oil spill over 40 years ago. Rhodanobacter and Sphingomonas lineages are associated with contaminated and baseline conditions in this extreme environment, revealing the utility of bacterial diversity measurements for assessing long-term responses of Arctic soils to pollution. ORIGINALITY-SIGNIFICANCE STATEMENT: Romulus C-42, the northernmost onshore drilling well in the world, was decommissioned following a small crude oil spill in 1972. Soil bacterial diversity profiles obtained >40 years later revealed significant differences in oil contaminated soils relative to adjacent non-oil contaminated background soils, consistent with evidence for moderate biodegradation of spilled crude oil having taken place since 1972. The results indicate that microbial diversity profiling is an effective tool for assessing natural attenuation in remote High Arctic soils with a history of oil pollution.

High-rate anaerobic decolorization of methyl orange from synthetic azo dye wastewater in a methane-based hollow fiber membrane bioreactor

Anaerobic biological techniques are widely used in the reductive decolorization of textile wastewater. However, the decolorization efficiency of textile wastewater by conventional anaerobic biological techniques is generally limited due to the low biomass retention capacity and short hydraulic retention time (HRT). In this study, a methane-based hollow fiber membrane bioreactor (HfMBR) was initially inoculated with an enriched anaerobic methane oxidation (AOM) culture to rapidly form an anaerobic biofilm. Then, synthetic azo dye wastewater containing methyl orange (MO) was fed into the HfMBR. MO decolorization efficiency of ∼ 100 % (HRT = 2 to 1.5 days) and maximum decolorization rate of 883 mg/L/day (HRT = 0.5 day) were obtained by the stepwise increase of the MO loading rate into the methane-based HfMBR. Scanning electron microscopy (SEM) and fluorescence in situ hybridization (FISH) analysis visually revealed that archaea clusters formed synergistic consortia with adjacent bacteria. Quantitative PCR (qPCR), phylogenetic and high-throughput sequencing analysis results further confirmed the biological consortia formation of methane-related archaea and partner bacteria, which played a synergistic role in MO decolorization. The high removal efficiency and stable microbial structure in HfMBR suggest it is a potentially effective technique for high-toxic azo dyes removal from textile wastewater.

Exclusive microbially driven autotrophic iron-dependent denitrification in a reactor inoculated with activated sludge

Autotrophic iron-dependent denitrification (AIDD) is arising as a promising process for nitrogen removal from wastewater with a low carbon to nitrogen ratio. However, there is still a debate about the existence of such a process in activated sludge systems. This work provides evidence and elucidated the feasibility of autotrophic Fe(II)-oxidizing nitrate-reducing culture for nitrogen removal by long-term reactor operation, batch experimental verification, unstructured kinetic modeling and microbial community analyses. A relatively stable nitrate removal rate was achieved coupled with the oxidation of ferrous ions in 3-month operation of reactor. The kinetic modeling suggests that the iron oxidation was a growth-associated process in AIDD. Utilization of extracellular polymeric substances (and/or soluble microbial products) as electron donor for denitrification by heterotrophic denitrifiers was not mainly responsible for nitrogen removal in the reactor. After long-term operation of the reactor with activated sludge as inoculum, the enrichment culture KS-like consortium, dominated by Fe(II) oxidizer, Gallionellaceae, was successfully acclimated for autotrophic Fe(II)-oxidizing nitrate reduction. This work extents our understanding about the existence of such an autotrophic Fe(II)-oxidizing nitrate-reducing culture in both natural and engineered systems, and opens a door for its potential application in wastewater treatment.

Effect of aquaculture salinity on nitrification and microbial community in moving bed bioreactors with immobilized microbial granules

The novel immobilized microbial granules (IMG) shows a significant effect of nitrification for freshwater aquaculture. However, there is lack of evaluation study on the performance of nitrification at high salinity due to the concentration of recycled water or seawater utilization. A laboratory scale moving bed bioreactor (MBBR) with IMG was tested on recycled synthetic aquaculture wastewater for the nitrification at 2.5 mg/L NH₃-N daily. The results indicated that IMG showed a high salinity tolerance and effectively converted ammonia to nitrate up to 92% at high salinity of 35.0 g/L NaCl. As salinity increased from near zero to 35.0 g/L, the microbial activity of nitrite oxidation bacteria (NOB) in the IMG decreased by 86.32%. The microbial community analysis indicated that salinity significantly influenced the community structure. It was found that Nitrosomonas sp. and Nitrospira sp. were the dominant genera for ammonia oxidation bacteria (AOB) and NOB respectively at different salinity levels.

TARGETING THE 16S RRNA GENE FOR BACTERIAL IDENTIFICATION IN COMPLEX MIXED SAMPLES: COMPARATIVE EVALUATION OF SECOND (ILLUMINA) AND THIRD (OXFORD NANOPORE TECHNOLOGIES) GENERATION SEQUENCING TECHNOLOGIES

Rapid, accurate bacterial identification in biological samples is an important task for microbiology laboratories, for which 16S~rRNA gene Sanger sequencing of cultured isolates is frequently used. In contrast, next-generation sequencing does not require intermediate culturing steps and can be directly applied on communities, but its performance has not been extensively evaluated. We present a comparative evaluation of second (Illumina) and third (Oxford Nanopore Technologies (ONT)) generation sequencing technologies for 16S targeted genomics using a well-characterized reference sample. Different 16S gene regions were amplified and sequenced using the Illumina MiSeq, and analyzed with Mothur. Correct classification was variable, depending on the region amplified. Using a majority vote over all regions, most false positives could be eliminated at the genus level but not the species level. Alternatively, the entire 16S gene was amplified and sequenced using the ONT MinION, and analyzed with Mothur, EPI2ME, and GraphMap. Although >99\% of reads were correctly classified at the genus level, up to $\approx$40\% were misclassified at the species level. Both~technologies, therefore, allow reliable identification of bacterial genera, but can potentially misguide identification of bacterial species, and constitute viable alternatives to Sanger sequencing for rapid analysis of mixed samples without requiring any culturing steps.

Enhanced butyrate production by transition metal particles during the food waste fermentation

Butyrate is an important precursor for fine chemicals and biofuels. The aim of this study is to investigate butyrate production as affected by transition metal addition of food waste fermentation including, nickel, Raney nickel and copper particles. Performance of fermentation showed nickel particles achieved the highest butyrate concentration, 7.3 g/L, which was 38.5% higher than that in the control trial. Raney nickel also showed similar effect on the enhancement of butyrate production. However, increased dosage of transition metal particle addition led to decreased butyrate production. The theoretical link between metal-assisted dark fermentation and butyrate production was tentatively explored. Redox potential affected by nickel addition was assumed to be an essential factor for butyrate production. Microbial community analysis found Clostridium sensu stricto 11 may be the dominant functional species for butyrate production. The study demonstrates that development on transition metal catalyst may contribute to waste biorefinery for added value products/energy production.

Electron shuttles enhance anaerobic oxidation of methane coupled to iron(III) reduction

Anaerobic oxidation of methane (AOM) has recently been coupled with the reduction of insoluble electron acceptors such as iron minerals. However, effects of electron shuttles (ESs) on this process and the underlying coupling mechanisms remain not well understood. Here, we evaluated AOM-coupled ferrihydrite reduction by a mixed culture in the absence and presence of ESs. The results showed that ESs (AQS, flavin, HA and AQDS) significantly enhanced the rate (up to 7.4 times) of AOM-dependent ferrihydrite reduction compared with the control. The enhancements were linearly related with the electron transfer capacity of ESs. Illumina high-throughput sequencing and DNA-based stable isotope probing revealed that the AOM-coupled iron reduction depended on the syntrophic interaction of Methanobacterium and the partner bacteria. Methanobacterium as the dominant microorganism, did not assimilate methane into its biomasses. However, it played a crucial role in the partial oxidation of methane into an intermediate (i.e. propionate), which was then assimilated by the partner bacteria (e.g. Cellulomonas, Desulfovibrio, Actinotalea, etc.) for ferrihydrite reduction. This work suggests that ESs in natural environments can mitigate the methane emissions by facilitating the AOM process and biogeochemical cycles of iron.

Heterogeneity spacers in 16S rDNA primers improve analysis of mouse gut microbiomes via greater nucleotide diversity

Illumina-based amplicon sequencing suffers from the deleterious effects of highly homogenous nucleotide composition, limiting the number of high-quality reads generated per run. We attempted to alleviate this limitation by comparing the results obtained from 16S ribosomal DNA (16S rDNA) sequencing of mouse gut microbiomes using Illumina V3-V4 primers (Run 1) and custom primers that incorporate a heterogeneity spacer (0-7 nucleotides) upstream of the 16S priming region (Run 2). Overall, Run 2 had higher quality sequences, a more diverse microbial profile, and higher precision within, and variation between, experimental groups than Run 1. Our primer design offers a simple way to increase the quality of 16S rDNA sequencing and increases the number of useable reads generated per Illumina run.

Efficient acetogenesis of anaerobic co-digestion of food waste and maize straw in a HSAD reactor

In this study, food waste and maize straw were used as feedstock, and the two-phase high-solid anaerobic digestion (TP-HSAD) technology was used to optimize the process parameters of leachate reflux in acid-production stage. Results indicated that compared with other waste activated sludge, pig manure digestate (PM) as leachate can achieve better hydrolysis and acidification effect. The increase of leachate reflux ratio can shorten the fermentation time of the acid-producing stage and increase the fermentation efficiency. When the reflux ratio was 32:1, peak concentration of volatile fatty acids (VFAs) was 45.4 g/L and the volatile solids (VS) removal rate was 61.7%. Reflux frequency has minimal effect on the concentration of VFAs and the degree of degradation of VS, but a higher reflux frequency will prolong the reaction time of acid-production stage. When PM is used as reflux leachate, the HSAD reactor can improve the hydrolysis and acidification of the anaerobic fermentation.

Spatial variations of microbial communities in abyssal and hadal sediments across the Challenger Deep

Microbial communities in hadal sediments are least explored in hadal zone (>6,000 m), especially in the Challenger Deep with high pressure (∼110 M pa at the bottom). In this study, we investigated the microbial communities in the sediments of the slope and trench-axis bottom of the Challenger Deep in the Mariana Trench. Classification of the reads of the 16S rRNA gene amplicons showed vertical distribution of prokaryotic microbial inhabitants from the surface to up to 60 centimeter below surface floor (cmbsf). The most dominant phyla were Proteobacteria, Chloroflexi, Actinobacteria, Planctomycetes and candidate phyla Patescibacteria and Marinimicrobia. Distinct dominant groups in the microbial communities were observed in trench-axis sediment (water depth >8,600 m), compared to the slopes of the Challenger Deep. A sampling site at the northern slope was enriched with archaea from mesophilic Euryarchaeota Marine Group II (MGII) as a biomarker of specific geochemical setting. Among archaeal community, Thaumarchaeota represented by Nitrosopumilus were dominant in the upper layers and diminished drastically in the deeper layers. “Ca. Woesearchaeota”, however, became the dominant group in the deeper layers. Overall, our study provides a better understanding on the pattern of the microbial communities in the deepest hadal sediments on Earth, and highlights the extraordinary diversity still waiting to be discovered.

Heavy metal exposure causes changes in the metabolic health-associated gut microbiome and metabolites

BACKGROUND

Exposure to arsenic and cadmium is common. Epidemiological and animal studies have suggested that exposure to these two heavy metals can cause metabolic health problems, including type 2 diabetes (T2DM). It has been hypothesized that T2DM could be mediated through the gut microbiome and the metabolites it produces. Although many studies have investigated the association between the gut microbiome and T2DM, few have focused on the connection to arsenic and cadmium.

RESULTS

We applied 16S rRNA gene amplicon sequencing and untargeted LC-MS/MS metabolomics to examine the changes in the gut microbiome and metabolite profiles of exposed mice to relevant levels of cadmium and arsenic in the drinking water over two weeks. Cadmium chloride (Cd) exposure significantly changed the mice gut microbiome and resulted in a significantly lower microbial diversity whereas sodium arsenite (As) caused a non-significant decrease in microbial diversity. For Cd and As treatment respectively, we identified 5 and 2 phyla with significant changes and 42 and 24 genera. Bacterial genera that were observed to decline upon both treatments, included several butyrate-producers. Both As and Cd treatment perturbed the metabolome significantly, with 50 ppm Cd compound exposure having the greatest effect when compared to 50 ppm As compound exposure. Two unidentified features were differentially abundant in the As group, while 33 features changed in the Cd group. Differential abundance analysis of all bile acid associated molecular components showed differences under both treatments. Finally, integrative network analysis via bipartite correlation networks suggested that several genera, including the metabolically important Blautia, Eisenbergiella, Clostridium_XlVa, etc. declined in numbers of metabolite interactions.

CONCLUSIONS

These results demonstrated that As and Cd exposure caused significant changes to the gut microbiome and metabolome by affecting bile acids, amino acids and taxa associated with metabolic health.

Mass transfer affects reactor performance, microbial morphology, and community succession in the methane-dependent denitrification and anaerobic ammonium oxidation co-culture

Denitrifying anaerobic methane oxidation (DAMO) combining anaerobic ammonium oxidation (Anammox) process is a novel nitrogen removal technology. However, the roles of methane transfer (gas phase) and nitrogen transfer (liquid phase) in the heterogeneous process remain unclear. In this study, granular DAMO and Anammox co-cultures were inoculated from a hollow-fiber membrane bioreactor into a sequence batch reactor (SBR). Since the methane transfer became limited in SBR, the nitrate removal rate first decreased and then increased to 10 mg/(L∙day), while the ammonium removal rate did not recover and was around 2 mg/(L∙day). The activity of DAMO archaea and Anammox bacteria decreased noticeably. Furthermore, granular aggregates dispersed into small granules and ultimately became flocs with poor settleability in SBR. The content of extracellular polymeric substances decreased, especially that of proteins and humics. DAMO archaea decreased by 94.6% and Anammox bacteria decreased by 72%. In summary, the limitation of methane transfer affected DAMO and Anammox processes more notably than nitrogen transfer, resulting in lower nitrogen removal, granule disruption, and microbial community succession.

Degradation of organic pollutants by anaerobic methane-oxidizing microorganisms using methyl orange as example

Anaerobic oxidation of methane (AOM) microorganisms widespread in nature and they are able to utilize methane as electron donor to reduce sulfate, nitrate, nitrite, and high valence metals. However, whether persistent organic contaminants can also be degraded remains unknown. In this study, the organic pollutant methyl orange (MO) was used to address this open question. The initial concentration of MO affected its degradation efficiency and higher concentration (>100 mg/L) caused considerable inhibition. A ¹³CH₄ isotope experiment indicated that methane oxidation was involved in MO degradation, which produced N, N-dimethyl-p-phenylenediamine, and 4-aminobenzenesulfonic acid corresponded stoichiometrically. During the long-term experiment, the maximum degradation rate was 47.91 mg/(L·d). The percentage of Candidatus Methanoperedens and Pseudoxanthomonas significantly increased after 30-d of MO degradation under CH₄ conditions; moreover, Candidatus Methanoperedens dominated (46.83%) the microbial community. Candidatus Methanoperedens, either alone or in combination with Pseudoxanthomonas, utilized methane as the sole carbon source to degrade MO via direct interspecies electron transfer or the syntrophy pathway. This study will add to our understanding of the functions and applications of AOM microorganisms.

Response of treatment performance and microbial community structure to the temporary suspension of an industrial anaerobic bioreactor

In this study, a novel type of mesophilic anaerobic bioreactor-an expanded granular sludge bed (EGSB)-was utilized to explore the effect of suspending reactor operation on the treatment performance and the microbial community structure. The parameters of performance and bacterial community before and after a four-week suspension were compared for the starch processing wastewater treatment bioreactor. The results indicate that the removal rate of the organic matter remained higher than 90%, although the biomass significantly decreased after restarting the reactor. However, the relatively stable microbial community structure before the suspension was altered significantly during the restart and post-running stages. This change was primarily due to variability in satellite species and the substitution effect of different dominant bacteria. For example, some non-major carbohydrate-degrading bacteria that were sensitive to nutrition deficiency, such as Desulfovibrio and Geobacter, were dramatically reduced after the suspension. In contrast, the stress of starvation stimulated the reproduction of hydrolytic bacteria, such as Macellibacteroides. However, the high bacterial diversity index (6.12-6.65) and the longstanding core species, including Chloroflexi, Cloacimonetes, Ignavibacteriae, Thermotogae and Euryarchaeota, maintained the functional stability of the reactor. Consequently, although the total bacteria decreased significantly after reactor operation was suspended, sufficient functional bacteria supported by the high diversity, as well as the longstanding core species, guaranteed the effective degradation after suspension.

Long-term nitrate removal through methane-dependent denitrification microorganisms in sequencing batch reactors fed with only nitrate and methane

Denitrifying anaerobic methane oxidation (damo) bioprocesses can remove nitrate using methane as the electron donor, which gains great concern due to the current stringent discharge standard of nitrogen in wastewater treatment plants. To obtain an engineering acceptable nitrogen removal rate (NRR) and demonstrate the long-term stable ability of damo system under conditions of nitrate and methane, two sequencing batch reactors (SBRs) fed with only nitrate and methane were operated for more than 600 days at 30 °C. The NRR of 21.91 ± 0.73 mg NO3--N L-1 day-1 was obtained which is, to the best of our knowledge, the highest rate observed in the literatures under such conditions. The temperature was found to significantly affect the system performance. Furthermore, the microbial community was analyzed by using real-time PCR technique. The results showed that the microbial consortium contained damo archaea and bacteria. These two microbes cooperated to maintain the long-term stability. And the number of damo archaea was higher than that of damo bacteria with the ratio of 1.77. By using methane as the electron donor, damo archaea reduced nitrate to nitrite coupled to methane oxidation and damo bacteria reduce the generated nitrite to nitrogen gas. The first step of nitrate to nitrite taken by damo archaea might be the limiting step of this cooperation system. SBR could be a suitable reactor configuration to enrich slow-growing microbes like damo culture. These results demonstrated the potential application of damo processes for nitrogen removal of wastewater containing low C/N ratios.

Different clusters of Candidatus 'Methanoperedens nitroreducens'-like archaea as revealed by high-throughput sequencing with new primers

The newly discovered Candidatus ‘Methanoperedens nitroreducens’ (M. nitroreducens), mediating nitrate-dependent anaerobic oxidation of methane, is an important microorganism in linking carbon and nitrogen cycles. In order to explore the diversity of M. nitroreducens-like archaea in various environmental niches with advanced high-throughput sequencing, new primers based on alpha subunit of methyl-coenzyme M reductase gene were designed. The PCR results demonstrated that the new primers could effectively detect M. nitroreducens-like archaea from an enrichment culture dominated by M. nitroreducens as well as samples collected from a natural freshwater lake and a full-scale wastewater treatment plant (WWTP). By high-throughput sequencing, more than 30,000 M. nitroreducens-like sequences were obtained. Phylogenetic analysis of these sequences along with published sequences showed that M. nitroreducens-like archaea could be divided into three sub-branches (named as Group A, Group B and Group C in this study). Clear geographical difference was observed, with Group A and Group B dominating samples in Queensland (Australia) and in European ecosystems, respectively. Further quantitative PCR revealed that the M. nitroreducens-like archaea were more abundant in WWTP than the freshwater lake. The study provided a large number of sequences for M. nitroreducens-like archaeal communities, thus expanded our understanding on the ecological diversity of M. nitroreducens-like archaea.

The content of trace element iron is a key factor for competition between anaerobic ammonium oxidation and methane-dependent denitrification processes

Coupling of anaerobic ammonium oxidation (Anammox) with denitrifying anaerobic methane oxidation (DAMO) is a sustainable pathway for nitrogen removal and reducing methane emissions from wastewater treatment processes. However, studies on the competitive relation between Anammox bacteria and DAMO bacteria are limited. Here, we investigated the effects of variations in the contents of trace element iron on Anammox and DAMO microorganisms. The short-term results indicated that optimal concentrations of iron, which obviously stimulated the activity of Amammox bacteria, DAMO bacteria and DAMO archaea, were 80, 20, and 80 μM, respectively. The activity of Amammox bacteria increased more significant than DAMO bacteria with increasing contents of trace element iron. After long-term incubation with high content of trace element iron of 160 μM in the medium, Candidatus Brocadia (Amammox bacteria) outcompeted Candidatus Methylomirabilis oxyfera (DAMO bacteria), and ANME-2d (DAMO archaea) remarkably increased in number and dominated the co-culture systems (64.5%). Meanwhile, with further addition of iron, the removal rate of ammonium and nitrate increased by 13.6 and 9.2 times, respectively, when compared with that noted in the control. As far as we know, this study is the first to explore the important role of trace element iron contents in the competition between Anammox bacteria and DAMO bacteria and further enrichment of DAMO archaea by regulating the contents of trace element iron.

Chromium isotope fractionation during Cr(VI) reduction in a methane-based hollow-fiber membrane biofilm reactor

Chromium (Cr) isotope fractionation analysis is a promising tool for monitoring Cr(VI) reduction in natural aqueous systems. In addition, large amounts of CH₄ in natural aqueous sediments are oxidized to CO₂ through methanotrophs, thereby mitigating emissions to the atmosphere. However, the investigations on the Cr(VI) reduction process with methanotrophs, and the associated Cr isotope fractionation patterns are scarce. In this study, we have shown that Cr(VI) reduction can occur in the presence of CH₄ as the sole electron donor in a hollow-fiber membrane reactor (HfMBR) after direct bacteria enrichment from sediment samples. Products of the methane oxidation by the methanotrophs are used by microbes to reduce Cr(VI) as shown by the progressive increase in δ⁵³Cr with time in the CH₄ feed reactor. The isotope fractionation factor (ε) of -2.62 ± 0.20‰ was obtained from the application of the Rayleigh distillation model. The results of Cr isotope fractionation analysis also explained the decrease of Cr(VI) concentration in the N₂ feed reactor, where the δ⁵³Cr values remained steady in the first two weeks but significantly increased in the last two weeks, indicating that physical adsorption and subsequent Cr(VI) reduction occurred. This study extended the application of Cr isotope fractionation, showing the suitability of this method for clarifying different Cr(VI) removal processes.

Screening and optimizing of inhibitors for ammonia-oxidizing bacteria in sediments of malodorous river

The proper use of selective ammonia-oxidizing archaea (AOA) and/or ammonia-oxidizing bacteria (AOB) inhibitors is critical to distinguish AOA and AOB contribution. In this research, three inhibitors including ampicillin, dicyandiamide (DCD), and allylthiourea (ATU) were examined mainly focusing on inhibiting dosage, adaptability, and effects. The results showed that the optimized inhibitory dosage of ampicillin, DCD, and ATU was separately 1.5 g L^-1, 1 mM, and 25 μM. Among the three inhibitors, ATU exhibited the strongest and persistent inhibition effects and resulted in up to 90% inhibition in the AOB-enriched culture. The seemingly weakening inhibiting effects of ATU in the simulated river systems can be attributed to the involved role of AOA, the uneven spatial distribution of ATU, and protection by sediment structure in complex malodorous rivers. The high-throughput pyrosequencing analysis showed the AOB-related genus Nitrosomonas and Nitrosococcus were mostly affected by ATU in the enrichments and the river systems, respectively. The inhibition of ATU was realized mainly by reducing the abundance and activity of AOB. The decrease of the ratio of AOB/AOA amoA gene copy numbers after addition of ATU further confirmed the inhibiting effectiveness of ATU in complex microbial community of malodorous rivers.

Hollow fiber membrane bioreactor affects microbial community and morphology of the DAMO and Anammox co-culture system

Denitrifying anaerobic methane oxidation (DAMO) and Anammox co-culture system was investigated in hollow fiber membrane bioreactor (HfMBR) for the change of microbial community morphology and proportion. NO₃^--N and NH₄⁺-N removal rates reached 85.33 and 37.95mg/L/d on 193d. The inoculum microorganisms were flocs and the proportion of DAMO archaea, DAMO bacteria and Anammox bacteria was 11.0, 24.2 and 0.4%, respectively, but it changed to 74.3, 11.8, 5.6% in HfMBR, respectively. Interestingly, microorganisms formed biofilms on fibers surface and the biofilms included two layers: inner layer was thin and dominated by DAMO bacteria and Anammox bacteria; while the outer layer was thick made up of granules with 100-200μm diameter and dominated by DAMO archaea. The spatial distribution of microorganisms in HfMBR was different from simulation results in the literature. Likely, HfMBR changed the interaction between DAMO and Anammox microorganisms, and the reactor configuration was beneficial for DAMO archaea growth.

High-calorific biogas production from anaerobic digestion of food waste using a two-phase pressurized biofilm (TPPB) system

To obtain high calorific biogas via anaerobic digestion without additional upgrading equipment, a two-phase pressurized biofilm system was built up, including a conventional continuously stirred tank reactor and a pressurized biofilm anaerobic reactor (PBAR). Four different pressure levels (0.3, 0.6, 1.0 and 1.7MPa) were applied to the PBAR in sequence, with the organic loading rate maintained at 3.1g-COD/L/d. Biogas production, gas composition, process stability parameters were measured. Results showed that with the pressure increasing from 0.3MPa to 1.7MPa, the pH value decreased from 7.22±0.19 to 6.98±0.05, the COD removal decreased from 93.0±0.9% to 79.7±1.2% and the methane content increased from 80.5±1.5% to 90.8±0.8%. Biogas with higher calorific value of 36.2MJ/m³ was obtained at a pressure of 1.7MPa. Pressure showed a significant effect on biogas production and gas quality in methanogenesis reactor.

Cr(VI) reduction coupled with anaerobic oxidation of methane in a laboratory reactor

The process of anaerobic oxidation of methane (AOM) is globally important because of its contribution to the carbon cycle in the environment. Besides, microorganisms play important roles in the environmental fate of chromium. However, there have been no studies to date on the interaction between methane and chromium in batch reactor systems. In this study, biological Cr(VI) reduction was investigated using methane as the sole electron donor. Isotopic (13)CH4 in the batch experiments and long-term performance in the reactor demonstrated that Cr(VI) reduction is coupled with methane oxidation. High-throughput sequencing of the 16S rRNA genes demonstrated that the microbial community had changed substantially after Cr(VI) reduction. The populations of ANME-2d archaea were enhanced, and they became the only predominant AOM-related microbe. Interestingly, other bacteria with significant increases in abundance were not reported as having the ability to reduce Cr(VI). According to these results, two mechanisms were proposed: 1) Cr(VI) is reduced by ANME-2d alone; 2) Cr(VI) is reduced by unknown Cr(VI)-reducing microbes coupled with ANME-2d. This study revealed the potential relationship between Cr(VI) reduction and CH4 oxidation, and extended our knowledge of the relationship between the AOM process and biogeochemical cycles.

Comparison of community structures of Candidatus Methylomirabilis oxyfera-like bacteria of NC10 phylum in different freshwater habitats

Methane oxidation coupled to nitrite reduction is mediated by 'Candidatus Methylomirabilis oxyfera' (M. oxyfera), which belongs to the NC10 phylum. In this study, the community composition and diversity of M. oxyfera-like bacteria of NC10 phylum were examined and compared in four different freshwater habitats, including reservoir sediments (RS), pond sediments (PS), wetland sediments (WS) and paddy soils (PAS), by using Illumina-based 16S rRNA gene sequencing. The recovered NC10-related sequences accounted for 0.4-2.5% of the 16S rRNA pool in the examined habitats, and the highest percentage was found in WS. The diversity of NC10 bacteria were the highest in RS, medium in WS, and lowest in PS and PAS. The observed number of OTUs (operational taxonomic unit; at 3% cut-off) were 97, 46, 61 and 40, respectively, in RS, PS, WS and PAS. A heterogeneous distribution of NC10 bacterial communities was observed in the examined habitats, though group B members were the dominant bacteria in each habitat. The copy numbers of NC10 bacterial 16S rRNA genes ranged between 5.8 × 10(6) and 3.2 × 10(7) copies g(-1) sediment/soil in the examined habitats. These results are helpful for a systematic understanding of NC10 bacterial communities in different types of freshwater habitats.