Comparative Genome-Centric Analysis of Freshwater and Marine ANAMMOX Cultures Suggests Functional Redundancy in Nitrogen Removal Processes

Metagenomic unveils the promotion of mainstream PD-anammox process at lower nZVI concentration and inhibition at higher dosage

The partial-denitrification-anammox (PdNA) process exhibits great potential in enabling the simultaneous removal of NO3--N and NH4+-N. This study delved into the impact of exogenous nano zero-valent iron (nZVI) on the PdNA process. Adding 10 mg L-1 of nZVI increased nitrogen removal efficiency up to 83.12 % and maintained higher relative abundances of certain beneficial bacteria. The maximum relative abundance of Candidatus Brocadia (1.6 %), Candidatus Kuenenia (1.5 %), Ignavibacterium (1.3 %), and Azospira (1.2 %) was observed at 10 mg L-1 of nZVI. However, the greatest relative abundance of Thauera (1.3 %) was recorded under 50 mg L-1. Moreover, applying nZVI selectively enhanced the abundance of NO3--N reductase genes. So, keeping the nZVI concentration at 10 mg L-1 or below is advisable to ensure a stable PdNA process in mainstream conditions. Considering nitrogen removal efficiency, using nZVI in the PD-anammox process could be more cost-effective in enhancing its adoption in industrial and mainstream settings.

Emerging biotechnological applications of anaerobic ammonium oxidation

Anaerobic ammonium oxidation (anammox) is an energy-efficient method for nitrogen removal that opens the possibility for energy-neutral wastewater treatment. Research on anammox over the past decade has primarily focused on its implementation in domestic wastewater treatment. However, emerging studies are now expanding its use to novel biotechnological applications and wastewater treatment processes. This review highlights recent advances in the anammox field that aim to overcome conventional bottlenecks, and explores novel and niche-specific applications of the anammox process. Despite the promising results and potential of these advances, challenges persist for their real-world implementation. This underscores the need for a transition from laboratory achievements to practical, scalable solutions for wastewater treatment which mark the next crucial phase in the evolution of anammox research.

Long-distance electron transport in multicellular freshwater cable bacteria

Filamentous multicellular cable bacteria perform centimeter-scale electron transport in a process that couples oxidation of an electron donor (sulfide) in deeper sediment to the reduction of an electron acceptor (oxygen or nitrate) near the surface. While this electric metabolism is prevalent in both marine and freshwater sediments, detailed electronic measurements of the conductivity previously focused on the marine cable bacteria (Candidatus Electrothrix), rather than freshwater cable bacteria, which form a separate genus (Candidatus Electronema) and contribute essential geochemical roles in freshwater sediments. Here, we characterize the electron transport characteristics of Ca. Electronema cable bacteria from Southern California freshwater sediments. Current-voltage measurements of intact cable filaments bridging interdigitated electrodes confirmed their persistent conductivity under a controlled atmosphere and the variable sensitivity of this conduction to air exposure. Electrostatic and conductive atomic force microscopies mapped out the characteristics of the cell envelope's nanofiber network, implicating it as the conductive pathway in a manner consistent with previous findings in marine cable bacteria. Four-probe measurements of microelectrodes addressing intact cables demonstrated nanoampere currents up to 200 μm lengths at modest driving voltages, allowing us to quantify the nanofiber conductivity at 0.1 S/cm for freshwater cable bacteria filaments under our measurement conditions. Such a high conductivity can support the remarkable sulfide-to-oxygen electrical currents mediated by cable bacteria in sediments. These measurements expand the knowledgebase of long-distance electron transport to the freshwater niche while shedding light on the underlying conductive network of cable bacteria.

BASALT refines binning from metagenomic data and increases resolution of genome-resolved metagenomic analysis

Metagenomic binning is an essential technique for genome-resolved characterization of uncultured microorganisms in various ecosystems but hampered by the low efficiency of binning tools in adequately recovering metagenome-assembled genomes (MAGs). Here, we introduce BASALT (Binning Across a Series of Assemblies Toolkit) for binning and refinement of short- and long-read sequencing data. BASALT employs multiple binners with multiple thresholds to produce initial bins, then utilizes neural networks to identify core sequences to remove redundant bins and refine non-redundant bins. Using the same assemblies generated from Critical Assessment of Metagenome Interpretation (CAMI) datasets, BASALT produces up to twice as many MAGs as VAMB, DASTool, or metaWRAP. Processing assemblies from a lake sediment dataset, BASALT produces ~30% more MAGs than metaWRAP, including 21 unique class-level prokaryotic lineages. Functional annotations reveal that BASALT can retrieve 47.6% more non-redundant opening-reading frames than metaWRAP. These results highlight the robust handling of metagenomic sequencing data of BASALT.

Functional guilds and drivers of diversity in seaweed-associated bacteria

Comparisons of functional and taxonomic profiles from bacterial communities in different habitats have suggested the existence of functional guilds composed of taxonomically or phylogenetically distinct members. Such guild membership is, however, rarely defined and the factors that drive functional diversity in bacteria remain poorly understood. We used seaweed-associated bacteria as a model to shed light on these important aspects of community ecology. Using a large dataset of over 1300 metagenome-assembled genomes from 13 seaweed species we found substantial overlap in the functionality of bacteria coming from distinct taxa, thus supporting the existence of functional guilds. This functional equivalence between different taxa was particularly pronounced when only functions involved in carbohydrate degradation were considered. We further found that bacterial taxonomy is the dominant driver of functional differences between bacteria and that seaweed species or seaweed type (i.e. brown, red and green) had relatively stronger impacts on genome functionality for carbohydrate-degradation functions when compared to all other cellular functions. This study provides new insight into the factors underpinning the functional diversity of bacteria and contributes to our understanding how community function is generated from individual members.

Validation of 16S rRNA gene sequencing and metagenomics for evaluating microbial immigration in a methanogenic bioreactor

To quantitatively evaluate the impact of microbial immigration from an upstream community on the microbial assembly of a downstream community, an ecological genomics (ecogenomics)-based mass balance (EGMB) model coupled with 16S rRNA gene sequencing was previously developed. In this study, a mock community was used to further validate the EGMB models and demonstrate the feasibility of using metagenome-based EGMB model to reveal both microbial activity and function. The mock community consisting of Aeromonas, Escherichia, and Pseudomonas was fed into a lab-scale methanogenic bioreactor together with dissolved organic substrate. Using qPCR, 16S rRNA gene, 16S rRNA gene copy number normalization (GCN), and metagenome, results showed highly comparable community profiles in the feed. In the bioreactor, Aeromonas and Pseudomonas exhibited negative growth rates throughout the experiment by all approaches. Escherichia's growth rate was negative by most biomarkers but was slightly positive by 16S rRNA gene. Still, all approaches showed a decreasing trend toward negative in the growth rate of Escherichia as reactor operation time increased. Uncultivated populations of phyla Desulfobacterota, Chloroflexi, Actinobacteriota, and Spirochaetota were observed to increase in abundance, suggesting their contribution in degrading the feed biomass. Based on metabolic reconstruction of metagenomes, these populations possessed functions of hydrolysis, fermentation, fatty acid degradation, or acetate oxidation. Overall results supported the application of both 16S rRNA gene- and metagenome-based EGMB models to measure the growth rate of microbes in the bioreactor, and the latter had advantage in providing insights into the microbial functions of uncultivated populations.

Surface-layer protein is a public-good matrix exopolymer for microbial community organisation in environmental anammox biofilms

Extracellular polymeric substances (EPS) are core biofilm components, yet how they mediate interactions within and contribute to the structuring of biofilms is largely unknown, particularly for non-culturable microbial communities that predominate in environmental habitats. To address this knowledge gap, we explored the role of EPS in an anaerobic ammonium oxidation (anammox) biofilm. An extracellular glycoprotein, BROSI_A1236, from an anammox bacterium, formed envelopes around the anammox cells, supporting its identification as a surface (S-) layer protein. However, the S-layer protein also appeared at the edge of the biofilm, in close proximity to the polysaccharide-coated filamentous Chloroflexi bacteria but distal to the anammox bacterial cells. The Chloroflexi bacteria assembled into a cross-linked network at the edge of the granules and surrounding anammox cell clusters, with the S-layer protein occupying the space around the Chloroflexi. The anammox S-layer protein was also abundant at junctions between Chloroflexi cells. Thus, the S-layer protein is likely transported through the matrix as an EPS and also acts as an adhesive to facilitate the assembly of filamentous Chloroflexi into a three-dimensional biofilm lattice. The spatial distribution of the S-layer protein within the mixed species biofilm suggests that it is a "public-good" EPS, which facilitates the assembly of other bacteria into a framework for the benefit of the biofilm community, and enables key syntrophic relationships, including anammox.

Coupling methanotrophic denitrification to anammox in a moving bed biofilm reactor for nitrogen removal under hypoxic conditions

Simultaneous removal of ammonium and nitrate was achieved in a methane-fed moving bed biofilm reactor (MBBR). In the reactor, methanotrophic microorganisms oxidized methane under hypoxic conditions likely to methanol, hence providing an electron donor to denitrifiers to reduce nitrate to nitrite that then allowed anaerobic ammonium oxidizing bacteria (Anammox) to remove excess ammonium as N₂. The ammonium and nitrate removal rates reached 72.09 ± 5.81 mgNH₄⁺-N/L/d and 62.61 ± 4.17 mgNO₃^--N/L/d when the MBBR was operated in continuous mode. Nitrate removal by the methane-fed mixed consortia was confirmed in a batch test revealing a CH₄/NO₃^- molar removal ratio of 1.15. The functional populations were unveiled by FISH analysis and 16S rRNA gene sequencing, which showed that the biofilm was dominated by Anammox bacteria (Candidatus Kuenenia) and diverse taxa associated with the capacity for denitrification: aerobic methanotrophs (Methylobacter, Methylomonas, and unclassified Methylococcaceae), methylotrophic denitrifiers (Opitutaceae and Methylophilaceae), and other heterotrophic denitrifiers (Ignavibacteriaceae, Anaerolineaceae, Comamonadaceae, Rhodocyclaceae and Thauera). Neither DAMO archaea nor DAMO bacteria were found in the sequencing analysis, indicating that more unknown community members possess the metabolic capacity of methanotrophic denitrification.

Glutamate Enhances Osmoadaptation of Anammox Bacteria under High Salinity: Genomic Analysis and Experimental Evidence

An osmoprotectant that alleviates the bacterial osmotic stress can improve the bioreactor treatment of saline wastewater. However, proposed candidates are expensive, and osmoprotectants of anammox bacteria and their ecophysiological roles are not fully understood. In this study, a comparative analysis of 34 high-quality public metagenome-assembled genomes from anammox bacteria revealed two distinct groups of osmoadaptation. Candidatus Scalindua and Kuenenia share a close phylogenomic relation and osmoadaptation gene profile and have pathways for glutamate transport and metabolisms for enhanced osmoadaptation. The batch assay results demonstrated that the reduced Ca. Kuenenia activity in saline conditions was substantially alleviated with the addition and subsequent synergistic effects of potassium and glutamate. The operational test of two reactors demonstrated that the reduced anammox performance under brine conditions rapidly recovered by 35.7-43.1% as a result of glutamate treatment. The Ca. Kuenenia 16S rRNA and hydrazine gene expressions were upregulated significantly (p < 0.05), and the abundance increased by approximately 19.9%, with a decrease in dominant heterotrophs. These data demonstrated the effectiveness of glutamate in alleviating the osmotic stress of Ca. Kuenenia. This study provides genomic insight into group-specific osmoadaptation of anammox bacteria and can facilitate the precision management of anammox reactors under high salinity.

Microbial response on the first full-scale DEMON® biomass transfer for mainstream deammonification

Sidestream partial nitritation and deammonification (pN/A) of high-strength ammonia wastewater is a well-established technology. Its expansion to the mainstream is, however mainly impeded by poor retention of anaerobic ammonia oxidizing bacteria (AnAOB), insufficient repression of nitrite oxidizing bacteria (NOB) and difficult control of soluble chemical oxygen demand and nitrite levels. At the municipal wastewater treatment plant in Strass (Austria) the microbial consortium was exhaustively monitored at full-scale over one and a half year with regular transfer of sidestream DEMON® biomass and further retention and enrichment of granular anammox biomass via hydrocyclone operation. Routine process parameters were surveyed and the response and evolution of the microbiota was followed by molecular tools, ex-situ activity tests and further, AnAOB quantification through particle tracking and heme measurement. After eight months of operation, the first anaerobic, simultaneous depletion of ammonia and nitrite was observed ex-situ, together with a direction to higher nitrite generation (68% of total NO_x-N) as compared to nitrate under aerobic conditions. Our dissolved oxygen (DO) scheme allowed for transient anoxic conditions and had a strong influence on nitrite levels and the NOB community, where Nitrobacter eventually dominated Nitrospira. The establishment of a minor but stable AnAOB biomass was accompanied by the rise of Chloroflexi and distinct emergence of Chlorobi, a trend not seen in the sidestream system. Interestingly, the most pronounced switch in the microbial community and noticeable NOB repression occurred during unfavorable conditions, i.e. the cold winter season and high organic load. Further abatement of NOB was achieved through bioaugmentation of aerobic ammonia oxidizing bacteria (AerAOB) from the sidestream-DEMON® tank. Performance of the sidestream pN/A was not impaired by this operational scheme and the average volumetric nitrogen removal rate of the mainstream even doubled in the second half of the monitoring campaign. We conclude that a combination of both, regular sidestream-DEMON® biomass transfer and granular SRT increase via hydrocyclone operation was crucial for AnAOB establishment within the mainstream.

Exerting applied voltage promotes microbial activity of marine anammox bacteria for nitrogen removal in saline wastewater treatment

To date, the application of marine anammox bacteria (MAB) is still a challenge in saline wastewater treatment due to the low growth rate and high sensitivity. Herein, bioelectrochemical system with applied voltage was exerted for the first time to promote the activity of MAB for removing nitrogen from saline wastewater. At the optimal voltage of 1.5 V, the mean total nitrogen removal rate (TNRR) reached the maximum of 0.65 kg/m³•d, which was 27.45% higher than that without applied voltage. Besides, applied voltage reduced the microbial diversity of MAB-based consortia, but the relative abundance of Candidatus Scalindua increased by 4.63% at 1.5 V compared with that without applied voltage. Also, proper applied voltage promoted the secretion of EPS and heme c, which resulted in the enhancement of MAB activity. Based on the remodified Logistic model analysis, the lag time of the nitrogen removal process was shortened by 0.72 h at the voltage of 1.5 V. Furthermore, it was found that higher voltage (> 2.0 V) had a negative effect on the MAB activity for low TNRR of 0.33 kg/m³•d (2.5 V). However, TNRR increased back to 0.61 kg/m³•d after removing the high applied voltage, which implied that the bioactivity was recoverable after being inhibited. These findings demonstrated that external electrical stimulation is an effective strategy to promote nitrogen removal and MAB activity for treating saline wastewater.

Phylogeny, distribution and potential metabolism of candidate bacterial phylum KSB1

Candidate phylum KSB1 is composed of uncultured bacteria and has been reported across various environments. However, the phylogeny and metabolic potential of KSB1 have not been studied comprehensively. In this study, phylogenomic analysis of KSB1 genomes from public databases and eleven metagenome-assembled genomes (MAGs) from marine and hydrothermal sediments revealed that those genomes were clustered into four clades. Isolation source and relative abundance of KSB1 genomes showed that clade I was particularly abundant in bioreactor sludge. Genes related to dissimilatory reduction of nitrate to ammonia (DNRA), the last step of denitrification converting nitrous oxide to nitrogen and assimilatory sulfur reduction were observed in the expanded genomes of clade I, which may due to horizontal gene transfer that frequently occurred in bioreactor. Annotation and metabolic reconstruction of clades II and IV showed flagellum assembly and chemotaxis genes in the genomes, which may indicate that exploration and sensing for nutrients and chemical gradients are critical for the two clades in deep-sea and hydrothermal sediment. Metabolic potentials of fatty acids and short-chain hydrocarbons utilization were predicted in clades I and IV of KSB1. Collectively, phylogenomic and metabolic analyses of KSB1 clades provide insight into their anaerobic heterotrophic lifestyle and differentiation in potential ecological roles.

Metabolic Diversity and Aero-Tolerance in Anammox Bacteria from Geochemically Distinct Aquifers

Anaerobic ammonium oxidation (anammox) is important for converting bioavailable nitrogen into dinitrogen gas, particularly in carbon-poor environments. However, the diversity and prevalence of anammox bacteria in the terrestrial subsurface-a typically oligotrophic environment-are little understood. To determine the distribution and activity of anammox bacteria across a range of aquifer lithologies and physicochemistries, we analyzed 16S rRNA genes and quantified hydrazine synthase genes and transcripts sampled from 59 groundwater wells and metagenomes and metatranscriptomes from an oxic-to-dysoxic subset. Data indicate that anammox and anammox-associated bacteria (class "Candidatus Brocadiae") are prevalent in the aquifers studied, and that anammox community composition is strongly differentiated by dissolved oxygen (DO), but not ammonia/nitrite. While "Candidatus Brocadiae" diversity decreased with increasing DO, "Candidatus Brocadiae" 16S rRNA genes and hydrazine synthase (hzsB) genes and transcripts were detected across a wide range of bulk groundwater DO concentrations (0 to 10 mg/L). Anammox genes and transcripts correlated significantly with those involved in aerobic ammonia oxidation (amoA), potentially representing a major source of nitrite for anammox. Eight "Candidatus Brocadiae" genomes (63 to 95% complete), representing 2 uncharacterized families and 6 novel species, were reconstructed. Six genomes have genes characteristic of anammox, all for chemolithoautotrophy. Anammox and aerotolerance genes of up to four "Candidatus Brocadiae" genomes were transcriptionally active under oxic and dysoxic conditions, although activity was highest in dysoxic groundwater. The coexpression of nrfAH nitrite reductase genes by "Candidatus Brocadiae" suggests active regeneration of ammonia for anammox. Our findings indicate that anammox bacteria contribute to loss of fixed N across diverse anoxic-to-oxic aquifer conditions, which is likely supported by nitrite from aerobic ammonia oxidation. IMPORTANCE Anammox is increasingly shown to play a major role in the aquatic nitrogen cycle and can outcompete heterotrophic denitrification in environments low in organic carbon. Given that aquifers are characteristically oligotrophic, anammox may represent a major route for the removal of fixed nitrogen in these environments, including agricultural nitrogen, a common groundwater contaminant. Our research confirms that anammox bacteria and the anammox process are prevalent in aquifers and occur across diverse lithologies (e.g., sandy gravel, sand-silt, and volcanic) and groundwater physicochemistries (e.g., various oxygen, carbon, nitrate, and ammonium concentrations). Results reveal niche differentiation among anammox bacteria largely driven by groundwater oxygen contents and provide evidence that anammox is supported by proximity to oxic niches and handoffs from aerobic ammonia oxidizers. We further show that this process, while anaerobic, is active in groundwater characterized as oxic, likely due to the availability of anoxic niches.

Metagenomic Analysis of Five Phylogenetically Distant Anammox Bacterial Enrichment Cultures

Anaerobic ammonium-oxidizing (anammox) bacteria are slow-growing and fastidious bacteria, and limited numbers of enrichment cultures have been established. A metagenomic ana-lysis of our 5 established anammox bacterial enrichment cultures was performed in the present study. Fourteen high-quality metagenome-assembled genomes (MAGs) were obtained, including those of 5 anammox Planctomycetota (Candidatus Brocadia, Ca. Kuenenia, Ca. Jettenia, and Ca. Scalindua), 4 Bacteroidota, and 3 Chloroflexota. Based on the gene sets of metabolic pathways involved in the degradation of polymeric substances found in Chloroflexota and Bacteroidota MAGs, they are expected to be scavengers of extracellular polymeric substances and cell debris.

Differences in the Effects of Calcium and Magnesium Ions on the Anammox Granular Properties to Alleviate Salinity Stress

Divalent cations were known to alleviate salinity stress on anammox bacteria. Understanding the mechanism of reducing the salinity stress on anammox granules is essential for the application of the anammox process for saline wastewater treatment. In this study, the effect of Ca2+ and Mg2+ augmentation on the recovery of the activity of freshwater anammox granules affected by salinity stress was evaluated. At the condition of a salinity stress of 5 g NaCl/L, the specific anammox activity (SAA) of the granule decreased to 50% of that of the SAA without NaCl treatment. Augmentation of Ca2+ at the optimum concentration of 200 mg/L increased the SAA up to 78% of the original activity, while the augmentation of Mg2+ at the optimum concentration of 70 mg/L increased the SAA up to 71%. EPS production in the granules was increased by the augmentation of divalent cations compared with the granules affected by salinity stress. In the soluble EPS, the ratio of protein to polysaccharides was higher in the granules augmented by Ca2+ than with Mg2+, and the functional groups of the EPS differed from each other. The amount of Na+ sequestered in the soluble EPS was increased by the augmentation of divalent cations, which seems to contribute to the alleviation of salinity stress. Ca. Kuenenia-like anammox bacteria, which were known to be salinity stress-tolerant, were predominant in the granules and there was no significant difference in the microbial community of the granules by the salinity stress treatment. Our results suggest that the alleviation effect of the divalent cations on the salinity stress on the anammox granules might be associated with the increased production of different EPS rather than in changes to the anammox bacteria.

Classification of uncultivated anammox bacteria and Candidatus Uabimicrobium into new classes and provisional nomenclature as Candidatus Brocadiia classis nov. and Candidatus Uabimicrobiia classis nov. of the phylum Planctomycetes and novel family Candidatus Scalinduaceae fam. nov to accommodate the genus Candidatus Scalindua

The phylum Planctomycetes is metabolically unique group of bacteria divided in two classes Planctomycetia and Phycisphaerae. Anaerobic ammonia-oxidizing (anammox) bacteria are the uncultured representatives of the phylum Planctomycetes. Anammox bacterial genera are placed in the family Candidatus (Ca.) Brocadiaceae of the order Ca. Brocadiales, assigned to the class Planctomycetia. Phylogenetic analysis, showed that the anammox bacteria and Ca. Uabimicrobium form a divergent clade from the rest of the cultured representatives of the phylum Planctomycetes. The phylogenetic study, pairwise distance and Average Amino acid Identity (AAI) showed that anammox bacteria don't belong to the classes Planctomycetia and Phycisphaerae. Anammox bacteria and Ca. Uabimicrobium form a deep-branching third clade in the phylogenetic analysis indicating that it is the most ancient third class within the phylum Planctomycetes. Phenotypic characters also separate anammox bacteria from classes Planctomycetia and Phycisphaerae. Therefore, based on phenotypic, phylogenetic, pairwise distance, AAI and phylogenomic analysis we propose a novel class Ca. Brocadiia to accommodate the order Ca. Brocadiales of anammox bacteria except Ca. Anammoximicrobium. Genera Ca. Jettenia, Ca. Anammoxoglobus, Ca. Kuenenia and Ca. Brocadia show their phylogenetic affiliation to the family Ca. Brocadiaceae. However, Ca. Scalindua showed a distant relationship with the family Ca. Brocadiaceae. Therefore, we suggest the exclusion of the genus Ca. Scalindua from the family Ca. Brocadiaceae; and propose its inclusion under a novel family with a provisional name as Ca. Scalinduaceae fam. nov. Similarly, Ca. Uabimicrobium amporphum showed distinct phylogenetic affiliation, therefore we propose a novel class Ca. Uabimicrobiia classis nov. to accommodate the genus Ca. Uabimicrobium.

Nitrate- and Nitrite-Sensing Histidine Kinases: Function, Structure, and Natural Diversity

Under anaerobic conditions, bacteria may utilize nitrates and nitrites as electron acceptors. Sensitivity to nitrous compounds is achieved via several mechanisms, some of which rely on sensor histidine kinases (HKs). The best studied nitrate- and nitrite-sensing HKs (NSHKs) are NarQ and NarX from Escherichia coli. Here, we review the function of NSHKs, analyze their natural diversity, and describe the available structural information. In particular, we show that around 6000 different NSHK sequences forming several distinct clusters may now be found in genomic databases, comprising mostly the genes from Beta- and Gammaproteobacteria as well as from Bacteroidetes and Chloroflexi, including those from anaerobic ammonia oxidation (annamox) communities. We show that the architecture of NSHKs is mostly conserved, although proteins from Bacteroidetes lack the HAMP and GAF-like domains yet sometimes have PAS. We reconcile the variation of NSHK sequences with atomistic models and pinpoint the structural elements important for signal transduction from the sensor domain to the catalytic module over the transmembrane and cytoplasmic regions spanning more than 200 Å.

Gut Microbiomes of Freshwater Mussels (Unionidae) Are Taxonomically and Phylogenetically Variable across Years but Remain Functionally Stable

Freshwater mussels perform essential ecosystem functions, yet we have no information on how their microbiomes fluctuate over time. In this study, we examined temporal variation in the microbiome of six mussel species (Lampsilis ornata, Obovaria unicolor, Elliptio arca, Fusconaia cerina, Cyclonaias asperata, and Tritogonia verrucosa) sampled from the same river in 2016 and 2019. We examined the taxonomic, phylogenetic, and inferred functional (from 16S rRNA sequences) facets of their microbiome diversity. Significant differences between the two years were identified in five of the six species sampled. However, not all species that exhibited a temporally variable microbiome were functionally distinct across years, indicating functional redundancy within the mussel gut microbiome. Inferred biosynthesis pathways showed temporal variation in pathways involved in degradation, while pathways involved in cellular metabolism were stable. There was no evidence for phylosymbiosis across any facet of microbiome biodiversity. These results indicate that temporal variation is an important factor in the assembly of the gut microbiomes of freshwater mussels and provides further support that the mussel gut microbiome is involved in host development and activity.

Cometabolism of the Superphylum Patescibacteria with Anammox Bacteria in a Long-Term Freshwater Anammox Column Reactor

Although the anaerobic ammonium oxidation (anammox) process has attracted attention regarding its application in ammonia wastewater treatment based on its efficiency, the physiological characteristics of anammox bacteria remain unclear because of the lack of pure-culture representatives. The coexistence of heterotrophic bacteria has often been observed in anammox reactors, even in those fed with synthetic inorganic nutrient medium. In this study, we recovered 37 draft genome bins from a long-term-operated anammox column reactor and predicted the metabolic pathway of coexisting bacteria, especially Patescibacteria (also known as Candidate phyla radiation). Genes related to the nitrogen cycle were not detected in Patescibacterial bins, whereas nitrite, nitrate, and nitrous oxide-related genes were identified in most of the other bacteria. The pathway predicted for Patescibacteria suggests the lack of nitrogen marker genes and its ability to utilize poly-N-acetylglucosamine produced by dominant anammox bacteria. Coexisting Patescibacteria may play an ecological role in providing lactate and formate to other coexisting bacteria, supporting growth in the anammox reactor. Patescibacteria-centric coexisting bacteria, which produce anammox substrates and scavenge organic compounds produced within the anammox reactor, might be essential for the anammox ecosystem.

Geochemical transition zone powering microbial growth in subsurface sediments

No other environment hosts as many microbial cells as the marine sedimentary biosphere. While the majority of these cells are expected to be alive, they are speculated to be persisting in a state of maintenance without net growth due to extreme starvation. Here, we report evidence for in situ growth of anaerobic ammonium-oxidizing (anammox) bacteria in ∼80,000-y-old subsurface sediments from the Arctic Mid-Ocean Ridge. The growth is confined to the nitrate-ammonium transition zone (NATZ), a widespread geochemical transition zone where most of the upward ammonium flux from deep anoxic sediments is being consumed. In this zone the anammox bacteria abundances, assessed by quantification of marker genes, consistently displayed a four order of magnitude increase relative to adjacent layers in four cores. This subsurface cell increase coincides with a markedly higher power supply driven mainly by intensified anammox reaction rates, thereby providing a quantitative link between microbial proliferation and energy availability. The reconstructed draft genome of the dominant anammox bacterium showed an index of replication (iRep) of 1.32, suggesting that 32% of this population was actively replicating. The genome belongs to a Scalindua species which we name Candidatus Scalindua sediminis, so far exclusively found in marine sediments. It has the capacity to utilize urea and cyanate and a mixotrophic lifestyle. Our results demonstrate that specific microbial groups are not only able to survive unfavorable conditions over geological timescales, but can proliferate in situ when encountering ideal conditions with significant consequences for biogeochemical nitrogen cycling.

Larger Anammox Granules not only Harbor Higher Species Diversity but also Support More Functional Diversity

Granule-based partial nitritation and anammox (PN/A) represents one of the most energy-efficient biotechniques for ammonium removal from wastewater. The PN/A granules appear in a continuum of sizes, yet little is known about the extent to which microbial communities and microbial metabolisms are partitioned between size-fractionated granules. Here, we divided granules harvested from a pilot-scale PN/A reactor into five discrete size fractions (<0.2, 0.2-0.5, 0.5-0.8, 0.8-1.0, and >1.0 mm). The composition and functional attribute of five pools of the size-fractionated granules were characterized by 16S ribosomal RNA (rRNA) gene amplicon and metagenomic and metatranscriptomic sequencing to provide a comprehensive insight into the key microbial group in a PN/A system. Larger granules were shown to not only harbor higher microbial diversity but also support more diverse functions than smaller granules. De novo coassembly and binning of metagenomic reads yielded 22 draft genomes of dominant microorganisms, which allowed us to infer an ecological model of the microbial ecosystem in anammox-based granules. This genome-based ecological model indicates that nitrifying organisms in smaller granules feed nitrite to anammox bacteria in larger granules. The results improve our understanding of the PN/A system, especially for the metabolic interactions between small and large granules.