Methylophilaceae link methanol oxidation to denitrification in freshwater lake sediment as suggested by stable isotope probing and pure culture analysis

Selenate bioreduction in a large in situ field trial

Removing selenium (Se) from mine effluent is a common challenge. A long-term, in situ experiment was conducted to bioremediate large volumes (up to 7500 mc d-1) of Se(VI)-contaminated water (mean 87 μg L-1) by injecting the water into a saturated waste rock fill (SRF) at a coal mining operation in Elk Valley, British Columbia, Canada. To stimulate/maintain biofilm growth in the SRF, labile organic carbon (methanol) and nutrients were added to the water prior to its injection. A conservative tracer (Br-) was also added to track the migration of injected water across the SRF, identify wells with minimal dilution and used to quantify the extent of bioreduction. The evolution of the Se species through the SRF was monitored in time and space for 201 d. Selenium concentrations of <3.8 μg L-1 were attained in monitoring wells located 38 m from the injection wells after 114 to 141 d of operation. Concentrations of Se species in water samples from complementary long-term (351-498 d) column experiments using influent Se(VI) concentrations of 1.0 mg L-1 were consistent with the results of the in situ experiment. Solid samples collected at the completion of the column experiments confirmed the presence of indigenous Se-reducing bacteria and that the sequestered Se was present as insoluble Se(0), likely in Se-S ring compounds. Based on the success of this ongoing bioremediation experiment, this technology is being applied at other mine sites.

Seasonal variation in metabolic profiles and microbial communities in a subarctic ore processing plant

The mining industry strives to reduce its water footprint by recycling water in ore processing. This leads to build-up of ions, flotation chemicals and microbial biomass, which may affect the process. The Boliden Kevitsa mine in Northern Finland is exposed to seasonal change and recycles up to 90% of the process water. We studied the variation in size, composition and putative functions of microbial communities in summer and winter in the ore processing plant. The raw water, Cu and Ni thickener overflow waters had statistically significantly higher bacterial numbers in winter compared to summer, and specific summer and winter communities were identified. Metagenomic analysis indicated that Cu and Hg resistance genes, sulphate/thiosulphate, molybdate, iron(III) and zinc ABC transporters, nitrate reduction, denitrification, thiosulphate oxidation and methylotrophy were more common in winter than in summer. Raw water drawn from the nearby river did not affect the microbial communities in the process samples, indicating that the microbial communities and metabolic capacities develop within the process over time in response to the conditions in the processing plant, water chemistry, used chemicals, ore properties and seasonal variation. We propose that the microbial community structures are unique to the Boliden Kevitsa mine and processing plant.

Using RNA-Stable isotope probing to investigate methane oxidation metabolites and active microbial communities in methane oxidation coupled to denitrification

The active denitrifying communities performing methane oxidation coupled to denitrification (MOD) were investigated using samples from an aerobic reactor (∼20% O2 and 2% CH4) and a microaerobic reactor (2% O2, 2% CH4) undertaking denitrification. The methane oxidation metabolites excreted in the reactors were acetate, methanol, formate and acetaldehyde. Using anaerobic batch experiments supplemented with exogenously supplied 13C-labelled metabolites, the active denitrifying bacteria were identified using 16S rRNA amplicon sequencing and RNA-stable isotope probing (RNA-SIP). With the aerobic reactor (AR) samples, the maximum NO3- removal rates were 0.43 mmol g-1 d-1, 0.40 mmol g-1 d-1, 0.33 mmol g-1 d-1 and 0.10 mmol g-1 d-1 for exogenously supplied acetate, formate, acetaldehyde and methanol batch treatments respectively, while with the microaerobic reactor (MR) samples, the maximum NO3- removal rates were 0.41 mmol g-1 d-1, 0.33 mmol g-1 d-1, 0.38 mmol g-1 d-1 and 0.14 mmol g-1 d-1 for exogenously supplied acetate, formate, acetaldehyde and methanol batch treatments respectively. The RNA-SIP experiments with 13C-labelled acetate, formate, and methanol identified Methyloversatilis, and Hyphomicrobium as the active methane-driven denitrifying bacteria in the AR samples, while Pseudoxanthomonas, Hydrogenophaga and Hyphomicrobium were the active MOD bacteria in the MR samples. Collectively, all the data indicate that formate is a key cross-feeding metabolite excreted by methanotrophs and consumed by denitrifiers performing MOD.

Biofilms on plastic litter in an urban river: Community composition and activity vary by substrate type

In aquatic ecosystems, plastic litter is a substrate for biofilms. Biofilms on plastic and natural surfaces share similar composition and activity, with some differences due to factors such as porosity. In freshwaters, most studies have examined biofilms on benthic substrates, while little research has compared the activity and composition of biofilms on buoyant plastic and natural surfaces. Additionally, the influence of substrate size and successional stage on biofilm composition has not been commonly assessed. We incubated three plastics of distinct textures that are buoyant in rivers, low-density polyethylene (rigid; 1.7 mm thick), low-density polyethylene film (flexible; 0.0254 mm thick), and foamed polystyrene (brittle; 6.5 mm thick), as well as wood substrates (untreated oak veneer; 0.6 mm thick) in the Chicago River. Each material was incubated at three sizes (1, 7.5, and 15 cm2 ). Substrates were incubated at 2-10 cm depths and removed weekly for 6 weeks. On each substrate we measured chlorophyll concentration, biofilm biomass, respiration, and flux of nitrogen gas. We sequenced 16S and 23S rRNA genes at Weeks 1, 3, and 6 to capture biofilm community composition across successional stages. Chlorophyll, biomass, and N2 flux were similar across substrates, but respiration was greater on wood than plastics. Bacterial and algal richness and diversity were highest on foam and wood compared to polyethylene substrates. Bacterial biofilm community composition was distinct between wood and plastic substrates, while the algal community was distinct on wood and foam, which were different from each other and polyethylene substrates. These results indicate that polymer properties influence biofilm alpha and beta diversity, which may affect transport and distribution of plastic pollution and associated microbes, as well as biogeochemical processes in urban rivers. This study provides valuable insights into the effects of substrate on biofilm characteristics, and the ecological impacts of plastic pollution on urban rivers. PRACTITIONER POINTS: Plastic physical and chemical properties act as forces of selection for biofilm. Biofilm activity was similar among three different types of plastic. Community composition between plastic and wood was different.

Elucidating microbial mechanisms of microcystin-LR degradation in Lake Erie beach sand through metabolomics and metatranscriptomics

As one of five Laurentian Great Lakes, Lake Erie ranks among the top freshwater drinking sources and ecosystems globally. Historical and current agriculture mismanagement and climate change sustains the environmental landscape for late summer cyanobacterial harmful algal blooms, and consequently, cyanotoxins such as microcystin (MC). Microcystin microbial degradation is a promising mitigation strategy, however the mechanisms controlling the breakdown of MCs in Lake Erie are not well understood. Pelee Island, Ontario, Canada is located in the western basin of Lake Erie and the bacterial community in the sand has demonstrated the capacity of metabolizing the toxin. Through a multi-omic approach, the metabolic, functional and taxonomical signatures of the Pelee Island microbial community during MC-LR degradation was investigated over a 48-hour period to comprehensively study the degradation mechanism. Cleavage of bonds surrounding nitrogen atoms and the upregulation of nitrogen deamination (dadA, alanine dehydrogenase, leucine dehydrogenase) and assimilation genes (glnA, gltB) suggests a targeted isolation of nitrogen by the microbial community for energy production. Methylotrophic pathways RuMP and H4MPT control assimilation and dissimilation of carbon, respectively and differential abundance of Methylophilales indicates an interconnected role through electron exchange of denitrification and methylotrophic pathways. The detected metabolites did not resolve a clear breakdown pathway, but rather the diversity of products in combination with taxonomic and functional results supports that a variety of strategies are applied, such as epoxidation, hydroxylation, and aromatic degradation. Annual repeated exposure to the toxin may have allowed the community to adaptatively establish a novel pathway through functional plasticity and horizontal gene transfer. The culmination of these results reveals the complexity of the Pelee Island sand community and supports a dynamic and cooperative metabolism between microbial species to achieve MC degradation.

Net-spinning caddisflies create denitrifier-enriched niches in the stream microbiome

Larval net-spinning caddisflies (Hydropsychidae) function as ecosystem engineers in streams where they construct protective retreats composed of organic and inorganic material affixed with silk filtration nets that alter streambed hydrology. We hypothesized that hydropsychid bio-structures (retreats, nets) are microhabitats for microbes with oxygen-sensitive metabolisms, and therefore increase the metabolic heterogeneity of streambed microbial assemblages. Metagenomic and 16 S rRNA gene amplicon analysis of samples from a montane stream (Cherry Creek, Montana, USA) revealed that microbiomes of caddisfly bio-structures are taxonomically and functionally distinct from those of the immediately adjacent rock biofilm (~2 cm distant) and enriched in microbial taxa with established roles in denitrification, nitrification, and methane production. Genes for denitrification, high oxygen affinity terminal oxidases, hydrogenases, oxidative dissimilatory sulfite reductases, and complete ammonia oxidation are significantly enriched in caddisfly bio-structures. The results suggest a novel ecosystem engineering effect of caddisflies through the creation of low-oxygen, denitrifier-enriched niches in the stream microbiome. Facilitation of metabolic diversity in streambeds may be a largely unrecognized mechanism by which caddisflies alter whole-stream biogeochemistry.

Carbon source shaped microbial ecology, metabolism and performance in denitrification systems

The limited information on microbial interactions and metabolic patterns in denitrification systems, especially those fed with different carbon sources, has hindered the establishment of ecological linkages between microscale connections and macroscopic reactor performance. In this work, denitrification performance, metabolic patterns, and ecological structure were investigated in parallel well-controlled bioreactors with four representative carbon sources, i.e., methanol, glycerol, acetate, and glucose. After long-term acclimation, significant differences were observed among the four bioreactors in terms of denitrification rates, organic utilization, and heterotrophic bacterial yields. Different carbon sources induced the succession of denitrifying microbiota toward different ecological structures and exhibited distinct metabolic patterns. Methanol-fed reactors showed distinctive microbial carbon utilization pathways and a more intricate microbial interaction network, leading to significant variations in organic utilization and metabolite production compared to other carbon sources. Three keystone taxa belonging to the Verrucomicrobiota phylum, SJA-15 order and the Kineosphaera genus appeared as network hubs in the methanol, glycerol, and acetate-fed systems, playing essential roles in their ecological functions. Several highly connected species were also identified within the glucose-fed system. The close relationship between microbial metabolites, ecological structures, and system performances suggests that this complex network relationship may greatly contribute to the efficient operation of bioreactors.

Methane-Oxidizing Activity Enhances Sulfamethoxazole Biotransformation in a Benthic Constructed Wetland Biomat

Ammonia monooxygenase and analogous oxygenase enzymes contribute to pharmaceutical biotransformation in activated sludge. In this study, we hypothesized that methane monooxygenase can enhance pharmaceutical biotransformation within the benthic, diffuse periphytic sediments (i.e., "biomat") of a shallow, open-water constructed wetland. To test this hypothesis, we combined field-scale metatranscriptomics, porewater geochemistry, and methane gas fluxes to inform microcosms targeting methane monooxygenase activity and its potential role in pharmaceutical biotransformation. In the field, sulfamethoxazole concentrations decreased within surficial biomat layers where genes encoding for the particulate methane monooxygenase (pMMO) were transcribed by a novel methanotroph classified as Methylotetracoccus. Inhibition microcosms provided independent confirmation that methane oxidation was mediated by the pMMO. In these same incubations, sulfamethoxazole biotransformation was stimulated proportional to aerobic methane-oxidizing activity and exhibited negligible removal in the absence of methane, in the presence of methane and pMMO inhibitors, and under anoxia. Nitrate reduction was similarly enhanced under aerobic methane-oxidizing conditions with rates several times faster than for canonical denitrification. Collectively, our results provide convergent in situ and laboratory evidence that methane-oxidizing activity can enhance sulfamethoxazole biotransformation, with possible implications for the combined removal of nitrogen and trace organic contaminants in wetland sediments.

Similar assembly mechanisms but distinct co-occurrence patterns of free-living vs. particle-attached bacterial communities across different habitats and seasons in shallow, eutrophic Lake Taihu

Eutrophication due to nitrogen and phosphorus input is an increasing problem in lake ecosystems. Free-living (FL) and particle-attached (PA) bacterial communities play a primary role in mediating biogeochemical processes in these lakes and in responding to eutrophication. However, knowledge of factors governing function, assembly mechanisms, and co-occurrence patterns of these communities remain poorly understood and are key challenges in microbial ecology. To address this knowledge gap, we collected 96 samples from Lake Taihu across four seasons and investigated the bacterial community using 16S rRNA gene sequencing. Our results demonstrate that the α-diversity, β-diversity, community composition, and functional composition of FL and PA bacterial communities exhibited differing spatiotemporal dynamics. FL and PA bacterial communities displayed similar distance-decay relationships across seasons. Deterministic processes (i.e., environmental filtering and species interaction) were the primary factors shaping community assembly in both FL and PA bacteria. Similar environmental factors shaped bacterial community structure while different environmental factors drove bacterial functional composition. Habitat filtering influenced enrichment of bacteria within specific functional groups. Among them, the FL bacterial community appeared to play a critical role in methane-utilization, whereas the PA bacteria contributed more to biogeochemical cycling of carbon. FL and PA bacterial communities exhibited distinct co-occurrence pattern across different seasons. In the FL network, Methylotenera and Methylophilaceae were identified as keystone taxa, while Burkholderiaceae and the hgcI clade were keystone taxa in the PA network. The PA bacterial community appeared to possess greater stability in the face of environmental change than did FL counterparts. These results broaden our knowledge of the driving factors, co-occurrence patterns, and assembly processes in FL and PA bacterial communities in eutrophic ecosystems and provide improved insight into the underlying mechanisms responsible for these results.

Denitrification performance and characteristics of untreated corncob for enhanced nitrogen removal of municipal sewage with low C/N ratio

Unpretreated corncob was applied in denitrification bio-filter (DNBF) and anoxic tank of AAO system, respectively, to treat sewage with low C/N ratio, and both two approaches achieved good denitrification performance. Although shorter HRT could effectively decrease effluent chroma and COD of corncob-DNBF, nitrogen removal efficiency declined unexpectedly. Higher internal reflux ratio was beneficial for corncob-AAO without damage to anoxic environment for denitrification, while there was no risk of effluent chroma and excessive COD. Different supplement modes could realize same denitrification effect with distinct advantages, which were higher specific denitrification rate and biomass amount, respectively. The latter mode, applying corncob at secondary treatment, was preferable for its operational stability and convenience. Stoichiometry analysis indicated the unit COD demand of AAO decreased from 5.70 to 5.04 g COD/g N after adding corncob, and the oxygen demand (or energy consumption of aeration) decreased as well. The dominant substrates decomposer in corncob-AAO altered to Kouleothrix (affiliated to phylum Chloroflexi), and the main denitrifying bacteria were unclassified_f__Methylophilaceae and Azospira. Accordingly, functional enzymes for degrading glucan, xylan and lignin and processing denitrification showed satisfying abundance in the integrated system, especially in the newly formed biofilm.

Nitrite reduction using a membrane biofilm reactor (MBfR) in a hypoxic environment with dilute methane under low pressures

Methane-based membrane biofilm reactors (MBfRs) can be an effective solution for nitrogen control in wastewater, but there is limited information on nitrite reduction for dilute wastewater (e.g., municipal wastewater) in hypoxic MBfRs. This study assessed the impacts of dilute (20 %), low-pressure methane (0.35-2.41 kPa) applied to MBfRs at hydraulic retention times (HRTs) of 2-12 h on nitrite removals, dissolved methane concentrations, and the resulting changes in the microbial community. High nitrite flux along with rapid and virtually complete (>99 %) nitrite removals were observed at methane pressures of 1.03-2.41 kPa at HRTs above 4 h, despite the use of diluted methane gas for the MBfR. The lowest methane pressure (0.35 kPa) was also able to achieve up to 98 % nitrite removals but required HRTs of up to 12 h. All scenarios had low dissolved methane concentrations (<10 mg/L), indicating that dilute methane at low supply pressures can effectively remove nitrite while meeting dissolved methane guidelines in treated effluent. Methylococcus genus was the key bacterium in MBfR biofilm grown at different HRTs and methane pressures, along with Methylocystis and other heterotrophic denitrifiers (Terrimonas and Hyphomicrobium). This study indicates that methane-based denitrification MBfRs can be a valuable tool to meet nitrogen limits for dilute wastewater coupled to partial nitrification, while limiting the release of methane to the environment.

Biofilm assemblage and activity on plastic in urban streams at a continental scale: Site characteristics are more important than substrate type

The fate of plastics in rivers is a key component of the global plastic cycle. Plastics entering freshwater ecosystems are colonized by microbial biofilms, and microbe-plastic interactions can influence ecosystem processes and plastic fate. While literature examining the role of geographic region on plastic biofilms is quickly expanding, research which covers large (i.e., continental) spatial scales and includes freshwater ecosystems is warranted. In addition, most research focuses on bacterial communities, while biofilm eukaryotes are less commonly studied. We assessed biofilm metabolism and community structure on plastic (foamed polystyrene and polyvinyl chloride; PVC) and natural substrates (unglazed ceramic tile) in urban streams spanning a nested geographic gradient in the continental United States. We measured biofilm biomass, community respiration, and chlorophyll a, in addition to assessing marker gene-based community diversity of bacterial, fungal, and algal assemblages. Results demonstrated some substrate-specific trends in biofilm characteristics, including higher biofilm biomass on polystyrene across sites, and lower diversity of bacterial assemblages on both types of plastic litter versus tile. However, there were no differences among substrates for chlorophyll, respiration, and the abundance and diversity of algal and fungal assemblages. Thus, we concluded that the primary driver of biofilm metabolism and community composition were site characteristics, rather than substrate type. Additional studies are needed to quantify which site-specific characteristics drive biofilm dynamics on plastic litter in streams (e.g., water chemistry, light, seasonality, hydrology). These results add to the growing literature on the biofilm 'plastisphere' in aquatic ecosystems, demonstrating that the factors which control the assembly and activity of biofilm communities on plastic substrates (including bacteria, algal, and fungal assemblages together) in urban streams are similar to those driving biofilm dynamics on natural substrates.

Exploratory analysis of the microbial community profile of the municipal solid waste leachate treatment system: A case study

Studies on the degradation dynamics of landfill leachate indicate that the microbial community profile is a valuable and sensitive tool for landfill monitoring programs. Although knowledge about the microbial community can improve the efficiency of leachate treatment systems, little is known about the microbial profile changes that occur throughout the leachate attenuation process. In the present work, an exploratory analysis of the microbial community profile of the MSW leachate treatment system in the municipality of Osório (Brazil) was conducted. In this way, a comprehensive analysis of chemical parameters, isotopic signature and microbial profile data were applied to monitor the changes in the structure of the microbial community throughout the leachate attenuation process and to describe the relationship between the microbial community structure and the attenuation of chemical and isotopic parameters. From data analysis, it was possible to assess the microbial community structure and relate it to the attenuation of chemical and isotopic parameters. Based on massive parallel 16S rRNA gene sequencing, it was possible to observe that each leachate treatment unit has a specific microbial consortium, reflecting the adaptation of different microorganisms to changes in leachate characteristics throughout treatment. From our results, we concluded that the structure of the microbial community is sensitive to the leachate composition and can be applied to study the municipal solid waste management system.

Microbial Diversity of Adult Aedes aegypti and Water Collected from Different Mosquito Aquatic Habitats in Puerto Rico

Mosquitoes, the major vectors of viruses like dengue, are naturally host to diverse microorganisms, which play an important role in their development, fecundity, immunity, and vector competence. The composition of their microbiota is strongly influenced by the environment, particularly their aquatic larval habitat. In this study, we used 2×300 bp 16s Illumina sequencing to compare the microbial profiles of emerging adult Aedes aegypti mosquitoes and the water collected from common types of aquatic habitat containers in Puerto Rico, which has endemic dengue transmission. We sequenced 141 mosquito and 46 water samples collected from plastic containers, septic tanks, discarded tires, underground trash cans, tree holes, or water meters. We identified 9 bacterial genera that were highly prevalent in the mosquito microbiome, and 77 for the microbiome of the aquatic habitat. The most abundant mosquito-associated bacterial OTUs were from the families Burkholderiaceae, Pseudomonadaceae, Comamonadaceae, and Xanthomonadaceae. Microbial profiles varied greatly between mosquitoes, and there were few major differences explained by container type; however, the microbiome of mosquitoes from plastic containers was more diverse and contained more unique taxa than the other groups. Container water was significantly more diverse than mosquitoes, and our data suggest that mosquitoes filter out many bacteria, with Alphaproteobacteria in particular being far more abundant in water. These findings provide novel insight into the microbiome of mosquitoes in the region and provide a platform to improve our understanding of the fundamental mosquito-microbe interactions.

Temporal changes of microbial community structure and nitrogen cycling processes during the aerobic degradation of phenanthrene

Phenanthrene (PHE) is frequently detected in worldwide soils. But it is still not clear that how the microbial community succession happens and the nitrogen-cycling processes alter during PHE degradation. In this study, the temporal changes of soil microbial community composition and nitrogen-cycling processes during the biodegradation of PHE (12 μg g^-1) were explored. The results showed that the biodegradation of PHE followed the second-order kinetics with a half-life of 7 days. QPCR results demonstrated that the bacteria numbers increased by 67.1%-194.7% with PHE degradation, whereas, no significant change was observed in fungi numbers. Thus, high-throughput sequencing based on 16 S rRNA was conducted and showed that the abundances of Methylotenera, Comamonadaceae, and Nocardioides involved in PHE degradation and denitrification were significantly increased, while those of nitrogen-metabolism-related genera such as Nitrososphaeraceae, Nitrospira, Gemmatimonadacea were decreased in PHE-treated soil. Co-occurrence network analysis suggested that more complex interrelations were constructed, and Proteobacteria instead of Acidobacteriota formed intimate associations with other microbes in responding to PHE exposure. Additionally, the abundances of nifH and narG were significantly up-regulated in PHE-treated soil, while that of amoA especially AOAamoA was down-regulated. Finally, correlation analysis found several potential microbes (Methylotenera, Comamonadaceae, and Agromyces) that could couple PHE degradation and nitrogen transformation. This study confirmed that PHE could alter microbial community structure, change the native bacterial network, and disturb nitrogen-cycling processes.

Spatial Variation of Cladophora Epiphytes in the Nan River, Thailand

Cladophora is an algal genus known to be ecologically important. It provides habitats for microorganisms known to provide ecological services such as biosynthesis of cobalamin (vitamin B12) and nutrient cycling. Most knowledge of microbiomes was obtained from studies of lacustrine Cladophora species. However, whether lotic freshwater Cladophora microbiomes are as complex as the lentic ones or provide similar ecological services is not known. To illuminate these issues, we used amplicons of 16S rDNA, 18S rDNA, and ITS to investigate the taxonomy and diversity of the microorganisms associated with replicate Cladophora samples from three sites along the Nan River, Thailand. Results showed that the diversity of prokaryotic and eukaryotic members of Cladophora microbiomes collected from different sampling sites was statistically different. Fifty percent of the identifiable taxa were shared across sampling sites: these included organisms belonging to different trophic levels, decomposers, and heterotrophic bacteria. These heterogeneous assemblages of bacteria, by functional inference, have the potential to perform various ecological functions, i.e., cellulose degradation, cobalamin biosynthesis, fermentative hydrogen production, ammonium oxidation, amino acid fermentation, dissimilatory reduction of nitrate to ammonium, nitrite reduction, nitrate reduction, sulfur reduction, polyphosphate accumulation, denitrifying phosphorus-accumulation, and degradation of aromatic compounds. Results suggested that river populations of Cladophora provide ecologically important habitat for microorganisms that are key to nutrient cycling in lotic ecosystems.

RNA stable isotope probing and high-throughput sequencing to identify active microbial community members in a methane-driven denitrifying biofilm

AIMS

Aerobic methane oxidation coupled to denitrification (AME-D) is a promising process for removing nitrate from groundwater and yet its microbial mechanism and ecological implications are not fully understood. This study used RNA stable isotope probing (RNA-SIP) and high-throughput sequencing to identify the micro-organisms that are actively involved in aerobic methane oxidation within a denitrifying biofilm.

METHODS AND RESULTS

Two RNA-SIP experiments were conducted to investigate labelling of RNA and methane monooxygenase (pmoA) transcripts when exposed to ¹³ C-labelled methane over a 96-hour time period and to determine active bacteria involved in methane oxidation in a denitrifying biofilm. A third experiment was performed to ascertain the extent of ¹³ C labelling of RNA using isotope ratio mass spectrometry (IRMS). All experiments used biofilm from an established packed bed reactor. IRMS confirmed ¹³ C enrichment of the RNA. The RNA-SIP experiments confirmed selective enrichment by the shift of pmoA transcripts into heavier fractions over time. Finally, high-throughput sequencing identified the active micro-organisms enriched with ¹³ C.

CONCLUSIONS

Methanotrophs (Methylovulum spp. and Methylocystis spp.), methylotrophs (Methylotenera spp.) and denitrifiers (Hyphomicrobium spp.) were actively involved in AME-D.

SIGNIFICANCE AND IMPACT OF THE STUDY

This is the first study to use RNA-SIP and high-throughput sequencing to determine the bacteria active within an AME-D community.

Research on microbial structures, functions and metabolic pathways in an advanced denitrification system coupled with aerobic methane oxidation based on metagenomics

Methanotrophs can oxidize methane as the sole carbon and energy, and the resulting intermediate products can be simultaneously utilized by coexistent denitrifying bacteria to remove the nitrogen, which named Aerobic Methane Oxidation Coupled to Denitrification (AME-D). In this paper, an AME-D system was built in an improved denitrification bio-filter, to analyze the nitrogen removal efficiency and mechanism. The maximum TN removal rate reached 95.05%. As shown in Raman spectroscopy, in the effluent wave crests generated by the symmetric expansion and contraction of NO₃^- disappeared, and the distortion of olefin CH₂ and C-OH stretching of alcohols appeared. Metagenomics revealed Methylotenera and Methylobacter were the dominated methanotrophs. There was a completed methane and nitrogen metabolism pathway with the synergism of nxrAB, narGHI, nasAB, pmo-amoABC and mmo genes. Dissimilatory reduction pathway was the primary nitrate removal pathway. Moreover, Bradyrhizobium could participate in methane and nitrogen metabolism simultaneously.

Methanotrophic denitrification in wastewater treatment: microbial aspects and engineering strategies

Anaerobic technologies are consolidated for sewage treatment and are the core processes for mining marketable products from waste streams. However, anaerobic effluents are supersaturated with methane, which represents a liability regarding greenhouse gas emissions. Meanwhile, anaerobic technologies are not capable of nitrogen removal, which is required to ensure environmental protection. Methane oxidation and denitrification processes can be combined to address both issues concurrently. Aerobic methane oxidizers can release intermediate organic compounds that can be used by conventional denitrifiers as electron donors. Alternatively, anoxic methanotrophic species combine methane oxidation with either nitrate or nitrite reduction in the same metabolism. Engineered systems need to overcome the long doubling times and low NO_x consumption rates of anoxic methanotrophic microorganisms. Another commonly reported bottleneck of methanotrophic denitrification relates to gas-liquid mass transfer limitations. Although anaerobic effluents are supersaturated with methane, experimental setups usually rely on methane supply in a gaseous mode. Hence, possibilities for the application of methane-oxidation coupled to denitrification in full scale might be overlooked. Moreover, syntrophic relationships among methane oxidizers, denitrifiers, nitrifiers, and other microorganisms (such as anammox) are not well understood. Integrating mixed populations with various metabolic abilities could allow for more robust methane-driven wastewater denitrification systems. This review presents an overview of the metabolic capabilities of methane oxidation and denitrification and discusses technological aspects that allow for the application of methanotrophic denitrification at larger scales.

Implications of Climate Change: How Does Increased Water Temperature Influence Biofilm and Water Quality of Chlorinated Drinking Water Distribution Systems?

Temperature variation can promote physico-chemical and microbial changes in the water transported through distribution systems and influence the dynamics of biofilms attached to pipes, thus contributing to the release of pathogens into the bulk drinking water. An experimental real-scale chlorinated DWDS was used to study the effect of increasing temperature from 16 to 24°C on specific pathogens, bacterial-fungal communities (biofilm and water samples) and determine the risk of material accumulation and mobilisation from the pipes into the bulk water. Biofilm was developed for 30 days at both temperatures in the pipe walls, and after this growth phase, a flushing was performed applying 4 gradual steps by increasing the shear stress. The fungal-bacterial community characterised by Illumina MiSeq sequencing, and specific pathogens were studied using qPCR: Mycobacterium spp., Mycobacterium avium complex, Acanthamoeba spp., Pseudomonas aeruginosa, Legionella pneumophilia, and Stenotrophomonas maltophilia. Sequencing data showed that temperature variation significantly modified the structure of biofilm microbial communities from the early stages of biofilm development. Regarding bacteria, Pseudomonas increased its relative abundance in biofilms developed at 24°C, while fungal communities showed loss of diversity and richness, and the increase in dominance of Fusarium genus. After the mobilisation phase, Pseudomonas continued being the most abundant genus at 24°C, followed by Sphingobium and Sphingomonas. For biofilm fungal communities after the mobilisation phase, Helotiales incertae sedis and Fusarium were the most abundant taxa. Results from qPCR showed a higher relative abundance of Mycobacterium spp. on day 30 and M. avium complex throughout the growth phase within the biofilms at higher temperatures. The temperature impacts were not only microbial, with physical mobilisation showing higher discolouration response and metals release due to the increased temperature. While material accumulation was accelerated by temperature, it was not preferentially to either stronger or weaker biofilm layers, as turbidity results during the flushing steps showed. This research yields new understanding on microbial challenges that chlorinated DWDS will undergo as global temperature rises, this information is needed in order to protect drinking water quality and safety while travelling through distribution systems.

Analysis of Different Size Fractions Provides a More Complete Perspective of Viral Diversity in a Freshwater Embayment

Inspired by recent discoveries of the prevalence of large viruses in the environment, we reassessed the longstanding approach of filtering water through small-pore-size filters to separate viruses from cells before metagenomic analysis. We collected samples from three sites in Hamilton Harbour, an embayment of Lake Ontario, and studied 6 data sets derived from <0.45-μm- and >0.45-μm-size fractions to compare the diversity of viruses in these fractions. At the level of virus order/family, we observed highly diverse and distinct virus communities in the >0.45-μm-size fractions, whereas the <0.45-μm-size fractions were composed primarily of Caudovirales The relative abundances of Caudovirales for which hosts could be inferred varied widely between size fractions, with higher relative abundances of cyanophages in the >0.45-μm-size fractions, potentially indicating replication within cells during ongoing infections. Many viruses of eukaryotes, such as Mimiviridae, Phycodnaviridae, Iridoviridae, and Poxviridae, were detected exclusively in the often-disregarded >0.45-μm-size fractions. In addition to observing unique virus communities associated with each size fraction from every site we examined, we detected viruses common to both fractions, suggesting that these are candidates for further exploration because they could be the product of ongoing or recent lytic events. Most importantly, our observations indicate that analysis of either fraction alone provides only a partial perspective of double-stranded DNA (dsDNA) viruses in the environment, highlighting the need for more comprehensive approaches for analyzing virus communities inferred from metagenomic sequencing.IMPORTANCE Most studies of aquatic virus communities analyze DNA sequences derived from the smaller-size "free-virus" fraction. Our study demonstrates that analysis of virus communities using only the smaller-size fraction can lead to erroneously low diversity estimates for many of the larger viruses such as Mimiviridae, Phycodnaviridae, Iridoviridae, and Poxviridae, whereas analyzing only the larger->0.45-μm-size fraction can lead to underestimates of Caudovirales diversity and relative abundance. Similarly, our data show that examining only the smaller-size fraction can lead to underestimations of virophage and cyanophage relative abundances that could, in turn, cause researchers to assume their limited ecological importance. Given the considerable differences we observed in this study, we recommend cautious interpretations of environmental virus community assemblages and dynamics when based on metagenomic data derived from different size fractions.

Simultaneous enhancement of nitrate removal flux and methane utilization efficiency in MBfR for aerobic methane oxidation coupled to denitrification by using an innovative scalable double-layer membrane

Endevours on the enhancement of nitrate removal efficiency during methane oxidation coupled with denitrification (AME-D) has always overlooked the role of membrane employed. It would be highly beneficial to enrich the biomass content and to manage biofilm on the membrane, in the utilization of methane and denitrification. In this study, an innovative and scalable double-layer membrane (DLM) was designed and prepared for a membrane biofilm reactor (MBfR), to simultaneously enhance nitrate removal flux and methane utilization efficiency during aerobic methane oxidation coupled with the denitrification (AME-D) process. The DLM allowed quick bacterial attachment and biomass accumulation for biofilm growth, which would be then self-regulated for well distribution of functional microbes on/within the DLM. Upon a high biofilm density of over 70 g-VSS m^-2 achieved on the DLM, the methane utilization efficiency of the MBfR was enhanced significantly to over 1.3 times than the control MBfR with conventional polypropylene membrane. The MBfR employed DLM also demonstrated the maximum nitrate removal flux of 740 mg-NO₃^--N m^-2 d^-1 that was approximately 1.64 times of that in control MBfR at continuous-mode operation. This DLM indeed favored the enrichment of Type II aerobic methanotrophs of Methylocystaceae, and methanol-utilization denitrifiers of Rhodocyclaceae that preferentially utilize methanol as the cross-feeding intermediates to promote the methane utilization efficiency, and thus to enhance the nitrate removal flux. These results raised from new designed DLM confirmed the importance of membrane surface properties on the effectiveness of MBfR, and offered great potential to address challenging problems of MBfRs during engineering application.

Stable-isotopic and metagenomic analyses reveal metabolic and microbial link of aerobic methane oxidation coupled to denitrification at different O2 levels

Aerobic methane (CH₄) oxidation coupled to denitrification (AME-D) can not only mitigate CH₄ emission into the atmosphere, but also potentially alleviate nitrogen pollution in surface waters and engineered ecosystems, and it has attracted substantial research interest. O₂ concentration plays a key role in AME-D, yet little is understood about how it impacts microbial interactions. Here, we applied isotopically labeled K¹⁵NO₃ and ¹³CH₄ and metagenomic analyses to investigate the metabolic and microbial link of AME-D at different O₂ levels. Among the four experimental O₂ levels of 21%,10%, 5% and 2.5% and a CH₄ concentration of 8% (i.e., the O₂/CH₄ ratios of 2.62, 1.26, 0.63 and 0.31), the highest NO₃^--N removal occurred in the AME-D system incubated at the O₂ concentration of 10%. Methanol and acetate may serve as the trophic linkage between aerobic methanotrophs and denitrifers in the AME-D systems. Methylotrophs including Methylophilus, Methylovorus, Methyloversatilis and Methylotenera were abundant under the O₂-sufficient condition with the O₂ concentration of 21%, while denitrifiers such as Azoarcus, Thauera and Thiobacillus dominated in the O₂-limited environment with the O₂ concentration of 10%. The competition of denitrifiers and methylotrophs in the AME-D system for CH₄-derived carbon, such as methanol and acetate, might be influenced by chemotactic responses. More methane-derived carbon flowed into methylotrophs under the O₂-sufficient condition, while more methane-derived carbon was used for denitrification in the O₂-limited environment. These findings can aid in evaluating the distribution and contribution of AME-D and in developing strategies for mitigating CH₄ emission and nitrogen pollution in natural and engineered ecosystems.

Host-Specificity and Core Taxa of Seagrass Leaf Microbiome Identified Across Tissue Age and Geographical Regions

The seagrass Zostera marina is a widespread foundational species in temperate coastal ecosystems that supports diverse communities of epiphytes and grazers. Bacteria link the production of seagrass to higher trophic levels and are thought to influence seagrass biology and health. Yet, we lack a clear understanding of the factors that structure the seagrass microbiome, or whether there is a consistent microbial community associated with seagrass that underpins functional roles. We sampled surface microbiome (epibiota) from new and old growth seagrass leaves and the surrounding seawater in eight meadows among four regions along the Central Coast of British Columbia, Canada to assess microbiome variability across space and as leaves age. We found that the seagrass leaf microbiome differs strongly from seawater. Microbial communities in new and old growth leaves are different from each other and from artificial seagrass leaves we deployed in one meadow. The microbiome on new leaves is less diverse and there is a small suite of core OTUs (operational taxonomic units) consistently present across regions. The overall microbial community for new leaves is more dispersed but with little regional differentiation, while the epiphytes on old leaves are regionally distinct. Many core OTUs on old leaves are commonly associated with marine biofilms. Together these observations suggest a stronger role for host filtering in new compared to old leaves, and a stronger influence of the environment and environmental colonization in old leaves. We found 11 core microbial taxa consistently present on old and new leaves and at very low relative abundance on artificial leaves and in the water column. These 11 taxa appear to be strongly associated with Z. marina. These core taxa may perform key functions important for the host such as detoxifying seagrass waste products, enhancing plant growth, and controlling epiphyte cover.

Bacterial community composition and function succession under aerobic and anaerobic conditions impacts the biodegradation of 17β-estradiol and its environmental risk

The widespread detection of 17β-estradiol (E2) in the environment has become an emerging concern worldwide due to its endocrine disrupting effects. This work focuses on the aerobic and anaerobic biodegradations of E2 in various sedimentary environments with different availabilities of electron acceptors, including O₂, NO₃^-, Fe³⁺, SO₄^2-, or HCO₃^-. The highest removal efficiency (98.9%) and shortest degradation half-life of E2 (t_1/2 = 5.0 d) were achieved under aerobic condition, followed by nitrate-reducing, ferric-reducing, sulfate-reducing and methanogenic conditions. We propose four different degradation pathways of E2 based on the metabolites identified under various redox conditions. Although most of E2 was effectively removed under aerobic condition, the potential environmental risk still needs to be considered due to the residual estrogenic activity induced by estrone (E1) formation. The endocrine-disrupting activities, as indicated by estradiol equivalent (EEQ) values, were related to E2 degradation rate and metabolite formation. We further analyzed the succession of bacterial community compositions and functions using Illumina HiSeq sequencing and Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt). The findings herein evidenced that bacterial community compositions and metabolic functions associated with different redox conditions impact the biodegradation of E2 and its endocrine-disrupting activity. This knowledge will be useful in predicting the environmental fates of estrogenic hormones in various sedimentary environments and aid in establishing appropriate strategies for eliminating potential environmental risks.

Bacterial community in a freshwater pond responding to the presence of perfluorooctanoic acid (PFOA)

Microbial community is an essential component of freshwater, providing valuable self-purification ecosystem service. Poly-and perfluoroalkyl substances (PFAS) have attracted increasing concerns in light of their potential ecotoxicological effects and ubiquitous occurrence in the aquatic environment. Knowledge about their influences on the microbial community, however, remains largely unknown. In the present study, Illumina high-throughput sequencing of 16S ribosomal DNA was applied to explore the changes in the dynamic and composition of the bacterial community upon exposure to perfluorooctanoic acid (PFOA) at different concentrations, i.e. 0.45 µg L^-1, 130 µg L^-1 and 5.0 mg L^-1. Principal component analysis (PCA) revealed variations of 57.2% for Principal Component 1 and 16.0% for Principal Component 2 of the total community. This clearly demonstrated changes in the bacterial community structure between the controls and PFOA-amended water samples. At the phylum level, the predominant bacteria in the original pond water included Proteobacteria (64.47%), Armatimonadetes (11.87%), Actinobacteria (10.81%), Bacteroidetes (6.36%), Chloroflexi (1.44%), Verrucomicrobia (0.61%) and Firmicutes (0.14%). The relative abundance of Actinobacteria, Bacteroidetes, and Verrucomicrobia decreased 26.5-38.8%, 40.5-70.7%, and 47.4-87.5%, respectively, upon PFOA exposure. By contrast, PFOA led to an obvious increase of Proteobacteria, by 12.5-18.6% and Chloroflexi by 19.1-74.4%. Results from this study provided the needed evidence that PFAS at high concentrations could affect the microbial community in a freshwater ecosystem. Principle Component Analysis (PCA) results suggest clear distinctions of bacterial community structure between the original pond water and the water samples spiked with PFOA based on pyrosequencing of 16S rRNA gene.

Environmental and Microbial Interactions Shape Methane-Oxidizing Bacterial Communities in a Stratified Lake

In stratified lakes, methane-oxidizing bacteria (MOB) are strongly mitigating methane fluxes to the atmosphere by consuming methane entering the water column from the sediments. MOB communities in lakes are diverse and vertically structured, but their spatio-temporal dynamics along the water column as well as physico-chemical parameters and interactions with other bacterial species that drive the community assembly have so far not been explored in depth. Here, we present a detailed investigation of the MOB and bacterial community composition and a large set of physico-chemical parameters in a shallow, seasonally stratified, and sub-alpine lake. Four highly resolved vertical profiles were sampled in three different years and during various stages of development of the stratified water column. Non-randomly assembled MOB communities were detected in all compartments. We could identify methane and oxygen gradients and physico-chemical parameters like pH, light, available copper and iron, and total dissolved nitrogen as important drivers of the MOB community structure. In addition, MOB were well-integrated into a bacterial-environmental network. Partial redundancy analysis of the relevance network of physico-chemical variables and bacteria explained up to 84% of the MOB abundances. Spatio-temporal MOB community changes were 51% congruent with shifts in the total bacterial community and 22% of variance in MOB abundances could be explained exclusively by the bacterial community composition. Our results show that microbial interactions may play an important role in structuring the MOB community along the depth gradient of stratified lakes.

Methanol-linked synergy between aerobic methanotrophs and denitrifiers enhanced nitrate removal efficiency in a membrane biofilm reactor under a low O2:CH4 ratio

Nitrate removal efficiency of aerobic methane oxidation coupled with denitrification (AME-D) process was elevated by enhancing the methanol-linked synergy in a membrane biofilm reactor (MBfR) under a low O₂:CH₄ ratio. After 140 days' enrichment, the nitrate removal rate increased significantly from 3 to 4 mg-N L^-1 d^-1 to 22.09 ± 1.21 mg-N L^-1 d^-1 and the indicator, mol CH₄ consumed/mol reduced NO₃^--N (C/N ratio), decreased to 1.79 which was very close to the theoretical minimum value (1.27-1.39). The increased nitrate removal efficiency was largely related to the enhanced relationship between aerobic methanotrophs and methanol-utilizing denitrifiers. Type I methanotrophs and some denitrifiers, especially those potential methanol-utilizing denitrifiers from Methylobacillus, Methylotenera, Methylophilus and Methyloversatilis, were abundant in the MBfR sludge. Aerobic methanotrophs and potential methanol-utilizing denitrifiers were closely associated in many globular aggregates (5-10 μm diameter) in the MBfR sludge, which may have promoted the denitrifiers to capture methanol released by methanotrophs efficiently. If we assume methanol is the only cross-feeding intermediate in the MBfR, about 38-60% of the CH₄ supplied would be converted to methanol and secreted rather than continuing to be oxidized. At least 63% of this secreted methanol should be utilized for denitrification instead of being oxidized by oxygen in the MBfR. These findings suggest that the nitrate removal efficiency of the AME-D process could be significantly improved.

Sludge alkaline fermentation enhanced anaerobic- multistage anaerobic/oxic (A-MAO) process to treat low C/N municipal wastewater: Nutrients removal and microbial metabolic characteristics

This study aimed to present a strategy that utilizing semi-continuous flow primary sludge fermentation liquor as carbon source for anaerobic- multistage anaerobic/oxic (A-MAO) process to treat low chemical oxygen demand (COD) and total nitrogen (TN) (C/N) ratio municipal wastewater. The results showed that adding fermentation liquor resulted in average TN and total phosphorus (TP) concentration in effluent decreased from 33 and 2.80 mg L^-1 to 9.2 and 0.23 mg L^-1, respectively, which met wastewater discharge standard. High-throughput sequencing results indicated that bacterial richness increased and diversity decreased with fermentation liquor adding, and the dominant genera varied from Methylophilaceae and Methylotenera to unclassified_f_Rhodocyclaceae, noran k_f__env.OPS_17, and Azospira. Meanwhile, the abundance of metabolism and organismal systems in A-MAO process rose from 48.42% and 0.74% to 49.52% and 0.78%. The improvement of nitrogen and phosphorus removal with fermentation adding was based on the increment of enzyme coding genes in nitrogen and phosphorus pathway.

Effects of PVP-coated silver nanoparticles on enzyme activity, bacterial and archaeal community structure and function in a yellow-brown loam soil

The undesirable effects of silver nanoparticles (AgNPs) on soil environment have caused much concern. The previous studies, however, focused on sandy soil, with little known on others. In present study, the effects of polyvinylpyrrolidone-coated AgNPs (0, 1, 10, and 100 mg kg^- 1 soil) on enzyme activities (urease and dehydrogenase), ammonia-oxidizing bacteria (AOB) and archaea (AOA), bacterial and archaeal communities, and microbial function profile in a yellow-brown loam soil were investigated. The significant dose-response inhibitions of AgNPs on enzyme activities were observed, with dehydrogenase more susceptible to AgNPs. Both of bacterial and archaeal amoA genes were reduced by AgNPs above 10 mg kg^- 1, with AOB more susceptible to AgNPs than AOA. AgNPs at 100 mg kg^- 1 caused reductions on the dominant Nitrosospira and Nitrosomonas, and even disappearance on Nitrosovibrio, while increase on Nitrososphaera significantly. AgNPs also changed bacterial and archaeal community structure. Exposure to AgNPs at 100 mg kg^- 1 caused significant increases by 186.79% and 44.89% for Bacteroidetes and Proteobacteria, while decreases by 47.82%, 44.09%, 43.67%, and 80.44% for Actinobacteria, Chloroflexi, Planctomycetes, and Verrucomicrobia, respectively. Moreover, three dominant archaeal phyla (Thaumarchaeota, Euryarchaeota, and Parvarchaeota) were also reduced in the presence of AgNPs, especially Thaumarchaeota with the significant reduction of 13.71%. PICRUSt prediction revealed that AgNPs indeed had the potential to change soil microbial community's functional contributions. It must be cautious on the interference of AgNPs to soil ecological functions in the future.

Bacterioplankton community variation in Bohai Bay (China) is explained by joint effects of environmental and spatial factors

Parsing the relative importance of environmental (recent disturbances) and spatial factors (historical processes) in determining community structure is a core issue in ecology. The Bohai Bay is a typical semi‐enclosed bay located in the north of China, surrounding by the metropolitan area with anthropogenic disturbances made it a complex marine coastal system with pollution gradients, where the distributions and determinants of bacterioplankton communities remain unclear. In this study, we collected surface water samples from 19 sites across Bohai Bay at about 100 km scale to investigate the relative roles of local environments and regional spatial factors in shaping bacterioplankton community composition (BCC). The environmental parameters in the sampling region showed gradient change according to the geographic variation. Several abundant OTUs were significantly correlated with the pollution parameters in the studied area, and 16 OTUs of them showed distinct distribution pattern in different polluted regions with obvious geographic segmentation, which indicated the effects of pollution gradient and dispersal limitation on specific taxon. The BCCs did not show obviously clustering effect between different polluted regions, which indicated the complexity for explaining the BCC variation in the studied region. The partial Mantel test revealed stronger spatial effects on beta diversity than those of local environmental factors, which indicated that dispersal limitation accounted more for the beta diversity than environmental heterogeneity. Furthermore, variation partitioning analysis (VPA) conducted by combining the environmental variables, linear trends, and principal coordinates of the variables from neighbor matrices (PCNM) showed that it was the joint effects of environmental and spatial factors contributed to the explained variation of BCC in the studied area. Considering the special human geography characteristics of Bohai Bay, the unmeasured biotic/abiotic factors, stochastic factors, and anthropogenic disturbances may be responsible for the unexplained variation of the BCC.

Microbial vanadate and nitrate reductions coupled with anaerobic methane oxidation in groundwater

Vanadate contaminant in groundwater receives increasing attentions, but little is known on its biogeochemical transformation with gaseous electron donors. This study investigated bio-reduction of vanadate coupled with anaerobic methane oxidation and its relationship with nitrate reduction. Results showed 95.8 ± 3.1% of 1 mM vanadate was removed within 7 days using methane as the sole electron donor. Tetravalent vanadium compounds were the main reduction products, which precipitated naturally in groundwater environment. The introduction of nitrate inhibited vanadate reduction, though both were reduced in parallel. Accumulations of volatile fatty acids (VFAs) were observed from methane oxidation. Preliminary microbial community structure and metabolite analyses indicated that vanadate was likely reduced via Methylomonas coupled with methane oxidation or through synergistic relationships between methane oxidizing bacteria and heterotrophic vanadate reducers with VFAs served as the intermediates.

Microbial communities of the Laurentian Great Lakes reflect connectivity and local biogeochemistry

The Laurentian Great Lakes are a vast, interconnected freshwater system spanning strong physicochemical gradients, thus constituting a powerful natural laboratory for addressing fundamental questions about microbial ecology and evolution. We present a comparative analysis of pelagic microbial communities across all five Laurentian Great Lakes, focusing on Bacterial and Archaeal picoplankton characterized via 16S rRNA amplicon sequencing. We collected samples throughout the water column from the major basins of each lake in spring and summer over 2 years. Two oligotypes, classified as LD12 (Alphaproteobacteria) and acI‐B1 (Actinobacteria), were among the most abundant in every sample. At the same time, microbial communities showed distinct patterns with depth during summer stratification. Deep hypolimnion samples were frequently dominated by a Chloroflexi oligotype that reached up to 19% relative abundance. Stratified surface communities differed between the colder, less productive upper lakes (Superior, Michigan, Huron) and warmer, more productive lower lakes (Erie, Ontario), in part due to an Actinobacteria oligotype (acI‐C2) that averaged 7.7% of sequences in the lower lakes but <0.2% in the upper lakes. Together, our findings suggest that both hydrologic connectivity and local selective pressures shape microbial communities in the Great Lakes and establish a framework for future investigations.

A Plant Growth-Promoting Microbial Soil Amendment Dynamically Alters the Strawberry Root Bacterial Microbiome

Despite growing interest in utilizing microbial-based methods for improving crop growth, much work still remains in elucidating how beneficial plant-microbe associations are established, and what role soil amendments play in shaping these interactions. Here, we describe a set of experiments that test the effect of a commercially available soil amendment, VESTA, on the soil and strawberry (Fragaria x ananassa Monterey) root bacterial microbiome. The bacterial communities of the soil, rhizosphere, and root from amendment-treated and untreated fields were profiled at four time points across the strawberry growing season using 16S rRNA gene amplicon sequencing on the Illumina MiSeq platform. In all sample types, bacterial community composition and relative abundance were significantly altered with amendment application. Importantly, time point effects on composition are more pronounced in the root and rhizosphere, suggesting an interaction between plant development and treatment effect. Surprisingly, there was slight overlap between the taxa within the amendment and those enriched in plant and soil following treatment, suggesting that VESTA may act to rewire existing networks of organisms through an, as of yet, uncharacterized mechanism. These findings demonstrate that a commercial microbial soil amendment can impact the bacterial community structure of both roots and the surrounding environment.

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.

Bacterial Communities in Areas of Oil and Methane Seeps in Pelagic of Lake Baikal

We have assessed the diversity of bacteria near oil-methane (area I) and methane (area II) seeps in the pelagic zone of Lake Baikal using massive parallel sequencing of 16S rRNA, pmoA, and mxaF gene fragments amplified from total DNA. At depths from the surface to 100 m, sequences belonging to Cyanobacteria dominated. In the communities to a depth of 200 m of the studied areas, Proteobacteria dominated the deeper layers of the water column. Alphaproteobacteria sequences were predominant in the community near the oil-methane seep, while the community near the methane seep was characterized by the prevalence of Alpha- and Gammaproteobacteria. Among representatives of these classes, type I methanotrophs prevailed in the 16S rRNA gene libraries from the near-bottom area, and type II methanotrophs were detected in minor quantities at different depths. In the analysis of the libraries of the pmoA and mxaF functional genes, we observed the different taxonomic composition of methanotrophic bacteria in the surface and deep layers of the water column. All pmoA sequences from area I were type II methanotrophs and were detected at a depth of 300 m, while sequences of type I methanotrophs were the most abundant in deep layers of the water column of area II. All mxaF gene sequences belonged to Methylobacterium representatives. Based on comparative analyses of 16S rRNA, pmoA, and mxaF gene fragment libraries, we suggest that there must be a wider spectrum of functional genes facilitating methane oxidation that were not detected with the primers used.

Are dominant microbial sub-surface communities affected by water quality and soil characteristics?

Subsurface microorganisms must deal with quite extreme environmental conditions. The lack of light, oxygen, and potentially nutrients are the main environmental stresses faced by subsurface microbial communities. Likewise, environmental disruptions providing an unbalanced positive input of nutrients force microorganisms to adapt to varying conditions, visible in the changes in microbial community diversity. In order to test microbial community adaptation to environmental changes, we performed a study in a surface Managed Aquifer Recharge facility, consisting of a settlement basin (two-day residence time) and an infiltration pond. Data on groundwater hydrochemistry, soil texture, and microbial characterization was compiled from surface water, groundwater, and soil samples at two distinct recharge operation conditions. Multivariate statistics by means of Principal Component Analysis (PCA) was the technique used to map the relevant dimensionality reduced combinations of input variables that properly describe the system behavior. The methodology selected allows including variables of different nature and displaying very different range values. Strong differences in the microbial assemblage under recharge conditions were found, coupled to hydrochemistry and grain-size distribution variables. Also, some microbial groups displayed correlations with either carbon or nitrogen cycles, especially showing abundant populations of denitrifying bacteria in groundwater. A significant correlation was found between Methylotenera mobilis and the concentrations of NO₃ and SO₄, and also between Vogesella indigofera and the presence of DOC in the infiltrating water. Also, microbial communities present at the bottom of the pond correlated with representative descriptors of soil grain size distribution.

A review on the advanced leachate treatment technologies and their performance comparison: an opportunity to keep the environment safe

Landfill application is the most common approach for biowaste treatment via leachate treatment system. When municipal solid waste deposited in the landfills, microbial decomposition breaks down the wastes generating the end products, such as carbon dioxide, methane, volatile organic compounds, and liquid leachate. However, due to the landfill age, the fluctuation in the characteristics of landfill leachate is foreseen in the leachate treatment plant. The focuses of the researchers are keeping leachate from contaminating groundwater besides keeping potent methane emissions from reaching the atmosphere. To address the above issues, scientists are required to adopt green biological methods to keep the environment safe. This review focuses on the assorting of research papers on organic content and nitrogen removal from the leachate via recent effective biological technologies instead of conventional nitrification and denitrification process. The published researches on the characteristics of various Malaysian landfill sites were also discussed. The understanding of the mechanism behind the nitrification and denitrification process will help to select an optimized and effective biological treatment option in treating the leachate waste. Recently, widely studied technologies for the biological treatment process are aerobic methane oxidation coupled to denitrification (AME-D) and partial nitritation-anammox (PN/A) process, and both were discussed in this review article. This paper gives the idea of the modification of the conventional treatment technologies, such as combining the present processes to make the treatment process more effective. With the integration of biological process in the leachate treatment, the effluent discharge could be treated in shortcut and novel pathways, and it can lead to achieving "3Rs" of reduce, reuse, and recycle approach.

Comprehensive insights into the key components of bacterial assemblages in pharmaceutical wastewater treatment plants

Due to complexity and variety of pharmaceutical wastewater composition, little is known as for functionally important microflora of pharmaceutical wastewater treatment plants (pWWTPs). We compared bacterial composition and diversity of pWWTPs (27 sludge samples collected from 12 full-scale pWWTPs) with those of other industrial (iWWTPs) (27 samples) and municipal wastewater treatment plants (mWWTPs) (27 samples) through meta-analysis based on 16S rRNA gene amplicon sequencing, and identified putatively important organisms and their ecological correlations. Non-metric multidimensional scaling indicated that the pWWTPs, iWWTPs and mWWTPs showed distinctive differences in bacterial community composition (P < 1e-04), and the pWWTPs had significantly lower bacterial diversity than the mWWTPs (P < 1e-06). Thermotogae and Synergistetes phyla only strictly dominated in the pWWTPs, and 26, 30 and 6 specific genera were identified in the pWWTPs, mWWTPs and iWWTPs, respectively. Totally, 15 and 1300 OTUs were identified as core and occasional groups, representing 23.2% and 66.2% of the total read abundance of the pWWTPs, respectively. Permutational multivariate analysis of variance revealed that the bacterial components were clearly clustered corresponding to the types of pharmaceutical wastewater, and a total of 129 local specific OTUs were identified in the pWWTPs, among which anticancer antibiotics pWWTPs had the highest number of specific OTUs (40 ones). Co-occurrence network revealed that the species dominating in the same type of pWWTPs tended to co-occur much more frequently than theoretical random expectation. The results may extend our knowledge regarding the ecological status and correlation of the key microflora in pWWTPs.

Methane oxidation coupled to denitrification under microaerobic and hypoxic conditions in leach bed bioreactors

Managing nitrogen and carbon cycles in landfills is an environmental challenge. In this study, our purpose was to test two types of methane oxidation processes coupled to denitrification inside landfills: microaerobic and hypoxic methane oxidation coupled to denitrification (MAME-D and HYME-D). Leach bed bioreactors were designed and operated for >100 d with NO₃^--N concentration ranging from 100 to 400 mg N/L. During six runs of the leach bed bioreactor experiment, leach bed bioreactor 2 (MAME-D) reached 100% denitrification efficiency and the highest average specific denitrification rate of 20.36 mg N/(L·d) in run 5, while leach bed bioreactor 3 (HYME-D) achieved 75% denitrification efficiency and the highest average specific denitrification rate of 8.09 mg N/(L·d) in run 6. Subsequently, waste from leach bed bioreactors 1, 2, and 3 was inoculated into anaerobic bottles to run a batch experiment for 13 d. The total consumed methane, oxygen, and nitrate amounts in the microaerobic system with no methane and oxygen supplement were 2.33, 2.38, and 2.04 mmol, respectively, which almost matched the theoretical equation of aerobic methane oxidation coupled to denitrification. In the hypoxic system, the total consumed methane and nitrate amounts were 0.23 and 0.41 mmol, respectively, the ratio of which closely matched the HYME-D. In addition, via the diverse functional community analysis, methane oxidation in the microaerobic system was confirmed to be conducted by methanotrophs (i.e., Methylobacter and Methylomonas) using oxygen as an electron acceptor. Subsequently, the generated organic compounds could support denitrifiers (i.e., Methylophilaceae) to complete denitrification. In the hypoxic system, Methylomonas and Methylobacter utilized nitrate as a direct electron acceptor to oxidize methane. The two landfill processes characterized here will expand our understanding of the environmental role of methanotrophs and methylotrophs in both carbon and nitrogen cycles.

Biodegradation of methamphetamine and ketamine in aquatic ecosystem and associated shift in bacterial community

Methamphetamine (METH) and ketamine (KET) are widely detected in surface waters and thus may pose threat to aquatic organisms. However, their degradation in aquatic systems and the effects on bacterial community were unknown. The present study investigated the biodegradation process of METH and KET in river waters and sediments. Three microcosms were examined over 40-days' incubation under (i) aerobic and illumination conditions, (ii) anaerobic condition exposed to light, (iii) anaerobic-dark condition. Statistically significant biodegradation of METH and KET (1 mg L^-1) was observed in all treatments. The half-lives under the examined conditions indicate that the two drugs were refractory in aquatic environment. Moreover, there were no pronounced absorption and photolysis observed in this work. Illumina MiSeq sequencing analysis revealed that Methylophilaceae, Saprospiraceae, WCHB1-69, Desulfobulbaceae, Porphyromonadaceae, FamilyXI, Peptococcaceae, and Rhizobiaceae were the predominant candidatus families during KET and METH biodegradation, and the preponderance would impair other microorganisms' prosperity since them were scarcely detected in the wild. Meanwhile, canonical correlation analysis (CCA) indicates that METH as an environmental factor may affect bacterial community structure in field water samples.

Microbial communities in the rhizosphere and the root of lettuce as affected by Salmonella-contaminated irrigation water

Reclaimed wastewater is increasingly used as a source of irrigation water in croplands. The enteric pathogens in reclaimed wastewater may accumulate in soil and plants and cause food safety concerns. The objective of this study was to determine the effects of irrigation water containing Salmonella on the microbial communities in the rhizosphere and in the root of lettuce. The effects were also examined with three variables (soil texture, lettuce cultivar and harvest time) in a factorial design. Analyses of the 16S rRNA gene sequences show that the microbial communities in the root were significantly different from those in the rhizosphere, although ∼80% of the microbes in the root originated from the rhizosphere. Salmonella in irrigation water significantly altered the structure of the microbial community in the rhizosphere, but not in the root. Salmonella internalized in lettuce root was observed when contaminated water was used for irrigation. Compared to lettuce cultivar and harvest time, soil texture played a more significant role in shaping the bacterial communities in the rhizosphere and in the root. Results from this study could advance understanding about the long-term impact of reclaimed wastewater as a source of irrigation water on the microbiota associated with leafy green vegetables.

Emerging Biodegradation of the Previously Persistent Artificial Sweetener Acesulfame in Biological Wastewater Treatment

The persistence of acesulfame (ACE) in wastewater treatment (and subsequently the aquatic environment) has led to its use as a marker substance for wastewater input into surface water and groundwater. However, ACE degradation of >85% during summer and autumn was observed in nine German wastewater treatment plants (WWTPs). Annual removal performance was more stable in larger plants, enhanced by low biological oxygen demand and impeded by water temperatures below 10 °C. Literature data suggest that the potential to degrade ACE emerged in WWTPs around the year 2010. This development is ongoing, as illustrated by ACE content in the German rivers Elbe and Mulde: Between 2013 and 2016 the ACE mass load decreased by 70-80%. In enrichment cultures with ACE as sole carbon source the carbonaceous fraction of ACE was removed completely, indicating catabolic biotransformation and the inorganic compound sulfamic acid formed in quantitative amounts. Sequencing of bacterial 16S rRNA genes suggests that several species are involved in ACE degradation, with proteobacterial species affiliated to Phyllobacteriaceae, Methylophilaceae, Bradyrhizobiaceae, and Pseudomonas becoming specifically enriched. ACE appears to be the first micropollutant for which the evolution of a catabolic pathway in WWTPs has been witnessed. It can yet only be speculated whether the emergence of ACE removal in WWTPs in different regions of the world is due to independent evolution or to global spreading of genes or adapted microorganisms.

Purification of eutrophic water containing chlorpyrifos by aquatic plants and its effects on planktonic bacteria

In this study, the removal of nutrients and chlorpyrifos as well as shifts of planktonic bacterial communities in constructed microcosms were investigated to evaluate the influence of Phragmites australis, Nymphaea alba, and Myriophyllum verticillatum, and their combination, on the restoration of eutrophic water containing chlorpyrifos. Plant-treated groups showed a higher pollutant removal rate than did no-remediation controls, indicating that treatment with plants is effective at remediation of eutrophic water containing chlorpyrifos. Different plants showed different performance on the remediation of eutrophic water, e.g., P. australis manifested stronger capacity for removal of sediment chlorpyrifos. This finding indicated that an appropriate plant combination is needed to deal with complex wastewater. During the treatments, the planktonic bacterial communities were influenced by the concentrations of nutrients and pollutants. The changes of composition of bacterial communities indicated a strong correlation between the bacterial communities and the concentrations of pollutants. The plants also influenced the planktonic bacterial communities, especially at the early phase of treatments. For example, P. australis increased the abundance of Limnohabitans and Nevskia significantly and decreased the abundance of Devosia, Luteolibacter, Methylibium, and Caulobacter significantly. The abundance of Hydrocarboniphaga significantly increased in N. alba-treated microcosms, whereas in M. verticillatum-treated microcosms, the abundance of Limnohabitans and Bdellovibrio significantly increased. Our results suggest that the planktonic bacterial communities may be altered during phytoremediation, and the functions of the affected bacteria should be concerned.

Aerobic proteobacterial methylotrophs in Movile Cave: genomic and metagenomic analyses

BACKGROUND

Movile Cave (Mangalia, Romania) is a unique ecosystem where the food web is sustained by microbial primary production, analogous to deep-sea hydrothermal vents. Specifically, chemoautotrophic microbes deriving energy from the oxidation of hydrogen sulphide and methane form the basis of the food web.

RESULTS

Here, we report the isolation of the first methane-oxidizing bacterium from the Movile Cave ecosystem, Candidatus Methylomonas sp. LWB, a new species and representative of Movile Cave microbial mat samples. While previous research has suggested a prevalence of anoxic conditions in deeper lake water and sediment, using small-scale shotgun metagenome sequencing, we show that metabolic genes encoding enzymes for aerobic methylotrophy are prevalent in sediment metagenomes possibly indicating the presence of microoxic conditions. Moreover, this study also indicates that members within the family Gallionellaceae (Sideroxydans and Gallionella) were the dominant taxa within the sediment microbial community, thus suggesting a major role for microaerophilic iron-oxidising bacteria in nutrient cycling within the Movile Cave sediments.

CONCLUSIONS

In this study, based on phylogenetic and metabolic gene surveys of metagenome sequences, the possibility of aerobic microbial processes (i.e., methylotrophy and iron oxidation) within the sediment is indicated. We also highlight significant gaps in our knowledge on biogeochemical cycles within the Movile Cave ecosystem, and the need to further investigate potential feedback mechanisms between microbial communities in both lake sediment and lake water.

Denitrifying metabolism of the methylotrophic marine bacterium Methylophaga nitratireducenticrescens strain JAM1

BACKGROUND

Methylophaga nitratireducenticrescens strain JAM1 is a methylotrophic, marine bacterium that was isolated from a denitrification reactor treating a closed-circuit seawater aquarium. It can sustain growth under anoxic conditions by reducing nitrate ([Formula: see text]) to nitrite ([Formula: see text]). These physiological traits are attributed to gene clusters that encode two dissimilatory nitrate reductases (Nar). Strain JAM1 also contains gene clusters encoding two nitric oxide (NO) reductases and one nitrous oxide (N2O) reductase, suggesting that NO and N2O can be reduced by strain JAM1. Here we characterized further the denitrifying activities of M. nitratireducenticrescens JAM1.

METHODS

Series of oxic and anoxic cultures of strain JAM1 were performed with N2O, [Formula: see text] or sodium nitroprusside, and growth and N2O, [Formula: see text], [Formula: see text] and N2 concentrations were measured. Ammonium ([Formula: see text])-free cultures were also tested to assess the dynamics of N2O, [Formula: see text] and [Formula: see text]. Isotopic labeling of N2O was performed in 15NH4+-amended cultures. Cultures with the JAM1ΔnarG1narG2 double mutant were performed to assess the involvement of the Nar systems on N2O production. Finally, RT-qPCR was used to measure the gene expression levels of the denitrification genes cytochrome bc-type nitric oxide reductase (cnorB1 and cnorB2) and nitrous oxide reductase (nosZ), and also nnrS and norR that encode NO-sensitive regulators.

RESULTS

Strain JAM1 can reduce NO to N2O and N2O to N2 and can sustain growth under anoxic conditions by reducing N2O as the sole electron acceptor. Although strain JAM1 lacks a gene encoding a dissimilatory [Formula: see text] reductase, [Formula: see text]-amended cultures produce N2O, representing up to 6% of the N-input. [Formula: see text] was shown to be the key intermediate of this production process. Upregulation in the expression of cnorB1, cnorB2, nnrS and norR during the growth and the N2O accumulation phases suggests NO production in strain JAM1 cultures.

DISCUSSION

By showing that all the three denitrification reductases are active, this demonstrates that M. nitratireducenticrescens JAM1 is one of many bacteria species that maintain genes associated primarily with denitrification, but not necessarily related to the maintenance of the entire pathway. The reason to maintain such an incomplete pathway could be related to the specific role of strain JAM1 in the denitrifying biofilm of the denitrification reactor from which it originates. The production of N2O in strain JAM1 did not involve Nar, contrary to what was demonstrated in Escherichia coli. M. nitratireducenticrescens JAM1 is the only reported Methylophaga species that has the capacity to grow under anoxic conditions by using [Formula: see text] and N2O as sole electron acceptors for its growth. It is also one of a few marine methylotrophs that is studied at the physiological and genetic levels in relation to its capacity to perform denitrifying activities.

Prokaryote species richness is positively correlated with eukaryote abundance in wastewater treatment biofilms

Biological treatment represents a key step in nutrient removal from wastewater. Until now these process has mainly been considered prokaryotic, with the interactions between prokaryotes and eukaryotes not being properly explored. We therefore investigated the co-occurrence of eukaryotes and prokaryotes in biological nitrogen removal biofilms. We found that biofilms in the nitrifying reactor contained the highest diversity and abundance of both prokaryotes and eukaryotes, with nearly three times higher prokaryote species richness than for the denitrifying reactor. The positive associations between eukaryote abundance and prokaryote diversity could potentially be explained by mutualism - and/or predator/prey interactions. Further mechanistic insight, however, is needed to determine the main diversifying mechanisms. In summary, eukaryote and prokaryote interactions seem to play a fundamental yet underexplored role in biological wastewater treatment.

SIGNIFICANCE AND IMPACT OF THE STUDY

Eukaryote and prokaryote interactions may play an important role in wastewater treatment. This study found that prokaryote species richness was nearly three times higher in the aerobe nitrification than in an anaerobe denitrification reactor, coinciding with the highest level of eukaryotes. This knowledge can be important in process control, and potentially in the development of novel approaches based on nitrate accumulating denitrifying eukaryotes.

Salinity and macrophyte drive the biogeography of the sedimentary bacterial communities in a brackish water tropical coastal lagoon

Brackish water coastal lagoons are least understood with respect to the seasonal and temporal variability in their sedimentary bacterial communities. These coastal lagoons are characterized by the steep environmental gradient and provide an excellent model system to decipher the biotic and abiotic factors that determine the bacterial community structure over time and space. Using Illumina sequencing of the 16S rRNA genes from a total of 100 bulk surface sediments, we investigated the sedimentary bacterial communities, their spatiotemporal distribution, and compared them with the rhizosphere sediment communities of a common reed; Phragmites karka and a native seagrass species; Halodule uninervis in Chilika Lagoon. Spatiotemporal patterns in bacterial communities were linked to specific biotic factors (e.g., presence and type of macrophyte) and abiotic factors (e.g., salinity) that drove the community composition. Comparative assessment of communities highlighted bacterial lineages that were responsible for segregating the sediment communities over distinct salinity regimes, seasons, locations, and presence and type of macrophytes. Several bacterial taxa were specific to one of these ecological factors suggesting that species-sorting processes drive specific biogeographical patterns in the bacterial populations. Modeling of proteobacterial lineages against salinity gradient revealed that α- and γ-Proteobacteria increased with salinity, whereas β-Proteobacteria displayed the opposite trend. The wide variety of biogeochemical functions performed by the rhizosphere microbiota of P. karka must be taken into consideration while formulating the management and conservation plan for this reed. Overall, this study provides a comprehensive understanding of the spatiotemporal dynamics and functionality of sedimentary bacterial communities and highlighted the role of biotic and abiotic factors in generating the biogeographical patterns in the bacterial communities of a tropical brackish water coastal lagoon.