How to make a living from anaerobic ammonium oxidation

Ladderane phospholipids form a densely packed membrane with normal hydrazine and anomalously low proton/hydroxide permeability

Ladderane lipids are unique to anaerobic ammonium-oxidizing (anammox) bacteria and are enriched in the membrane of the anammoxosome, an organelle thought to compartmentalize the anammox process, which involves the toxic intermediate hydrazine (N2H4). Due to the slow growth rate of anammox bacteria and difficulty of isolating pure ladderane lipids, experimental evidence of the biological function of ladderanes is lacking. We have synthesized two natural and one unnatural ladderane phosphatidylcholine lipids and compared their thermotropic properties in self-assembled bilayers to distinguish between [3]- and [5]-ladderane function. We developed a hydrazine transmembrane diffusion assay using a water-soluble derivative of a hydrazine sensor and determined that ladderane membranes are as permeable to hydrazine as straight-chain lipid bilayers. However, pH equilibration across ladderane membranes occurs 5-10 times more slowly than across straight-chain lipid membranes. Langmuir monolayer analysis and the rates of fluorescence recovery after photobleaching suggest that dense ladderane packing may preclude formation of proton/hydroxide-conducting water wires. These data support the hypothesis that ladderanes prevent the breakdown of the proton motive force rather than blocking hydrazine transmembrane diffusion in anammox bacteria.

Organelle Formation in Bacteria and Archaea

Uncovering the mechanisms that underlie the biogenesis and maintenance of eukaryotic organelles is a vibrant and essential area of biological research. In comparison, little attention has been paid to the process of compartmentalization in bacteria and archaea. This lack of attention is in part due to the common misconception that organelles are a unique evolutionary invention of the "complex" eukaryotic cell and are absent from the "primitive" bacterial and archaeal cells. Comparisons across the tree of life are further complicated by the nebulous criteria used to designate subcellular structures as organelles. Here, with the aid of a unified definition of a membrane-bounded organelle, we present some of the recent findings in the study of lipid-bounded organelles in bacteria and archaea.

The cycle of nitrogen in river systems: sources, transformation, and flux

Nitrogen is a requisite and highly demanded element for living organisms on Earth. However, increasing human activities have greatly altered the global nitrogen cycle, especially in rivers and streams, resulting in eutrophication, formation of hypoxic zones, and increased production of N2O, a powerful greenhouse gas. This review focuses on three aspects of the nitrogen cycle in streams and rivers. We firstly introduce the distributions and concentrations of nitrogen compounds in streams and rivers as well as the techniques for tracing the sources of nitrogen pollution. Secondly, the overall picture of nitrogen transformations in rivers and streams conducted by organisms is described, especially focusing on the roles of suspended particle-water surfaces in overlying water, sediment-water interfaces, and riparian zones in the nitrogen cycle of streams and rivers. The coupling of nitrogen and other element (C, S, and Fe) cycles in streams and rivers is also briefly covered. Finally, we analyze the nitrogen budget of river systems as well as nitrogen loss as N2O and N2 through the fluvial network and give a summary of the effects and consequences of human activities and climate change on the riverine nitrogen cycle. In addition, future directions for the research on the nitrogen cycle in river systems are outlined.

Keeping a Completely Autotrophic Nitrogen Removal over Nitrite System Effective in Treating Low Ammonium Wastewater by Adopting an Alternative Low and High Ammonium Influent Regime

An alternative low and high ammonium influent regime was proposed and adopted to keep a completely autotrophic nitrogen removal over nitrite (CANON) effective when treating low ammonium wastewater. Results show that, by cyclic operating at an alternative low and high ammonium concentration for 10 days and 28 days, the CANON system could effectively treat low ammonium wastewater. Excessive proliferation of nitrite oxidizing bacteria (NOB) under low ammonium environment was still the challenge for the stable CANON operation; but with 28 days of a high ammonium treatment combined with a sludge retention time control, the NOB overproliferated in the low ammonium operational period could be under control. Specifically, when the nitrite oxidation rate reached 8 g N/m³/h, the CANON system should enter the high ammonium influent operating mode. 16S rDNA high-throughput sequencing results show that the appropriate sludge discharging provided an environment favoring Candidatus Jettenia.

Draft Genome Sequence of a "Candidatus Brocadia" Bacterium Enriched from Activated Sludge Collected in a Tropical Climate

Here, we present the draft genome sequence of an anaerobic ammonium-oxidizing bacterium (AnAOB), “Candidatus Brocadia,” which was enriched in an anammox reactor. A 3.2-Mb genome sequence comprising 168 contigs was assembled, in which 2,765 protein-coding genes, 47 tRNAs, and one each of 5S, 16S, and 23S rRNAs were annotated. No evidence for the presence of a nitric oxide-forming nitrite reductase was found.

MEGAN-LR: new algorithms allow accurate binning and easy interactive exploration of metagenomic long reads and contigs

Background

There are numerous computational tools for taxonomic or functional analysis of microbiome samples, optimized to run on hundreds of millions of short, high quality sequencing reads. Programs such as MEGAN allow the user to interactively navigate these large datasets. Long read sequencing technologies continue to improve and produce increasing numbers of longer reads (of varying lengths in the range of 10k-1M bps, say), but of low quality. There is an increasing interest in using long reads in microbiome sequencing, and there is a need to adapt short read tools to long read datasets.

Methods

We describe a new LCA-based algorithm for taxonomic binning, and an interval-tree based algorithm for functional binning, that are explicitly designed for long reads and assembled contigs. We provide a new interactive tool for investigating the alignment of long reads against reference sequences. For taxonomic and functional binning, we propose to use LAST to compare long reads against the NCBI-nr protein reference database so as to obtain frame-shift aware alignments, and then to process the results using our new methods.

Results

All presented methods are implemented in the open source edition of MEGAN, and we refer to this new extension as MEGAN-LR (MEGAN long read). We evaluate the LAST+MEGAN-LR approach in a simulation study, and on a number of mock community datasets consisting of Nanopore reads, PacBio reads and assembled PacBio reads. We also illustrate the practical application on a Nanopore dataset that we sequenced from an anammox bio-rector community.

Reviewers

This article was reviewed by Nicola Segata together with Moreno Zolfo, Pete James Lockhart and Serghei Mangul.

Conclusion

This work extends the applicability of the widely-used metagenomic analysis software MEGAN to long reads. Our study suggests that the presented LAST+MEGAN-LR pipeline is sufficiently fast and accurate.

Effect of dissolved oxygen on nitrogen removal and the microbial community of the completely autotrophic nitrogen removal over nitrite process in a submerged aerated biological filter

Dissolved oxygen (DO) is a crucial parameter of the completely autotrophic nitrogen removal over nitrite (CANON) process. This study determined the nitrogen removal performance and microbial community of the CANON process in a laboratory-scale submerged aerated biological filter (SABF) over a DO concentration range from 0 to 1.2 mg·L^-1. The results showed that the optimum DO (0.2-0.3 mg·L^-1) corresponded to an average ammonium nitrogen removal efficiency of 93.4% and a total nitrogen removal efficiency of 81.0%. A 16S rRNA gene high-throughput sequencing technology confirmed that the phyla Proteobacteria and Nitrospirae enriched, whereas the phylum Planctomycetes was inhibited with increasing DO concentration. At the genus level, the increase of DO concentration resulted in the enrichment of genera Dok59 and Nitrospira, but restrained the genus Candidatus Brocadia. This research can be used to improve the nitrogen removal ability of the CANON process in an SABF in the future.

Using low frequency and intensity ultrasound to enhance start-up and operation performance of Anammox process inoculated with the conventional sludge

A lab-scale ultrasound enhancing Anammox reactor (R1) was established and irradiated once a week by ultrasound with the optimal parameter (frequency of 25 kHz, intensity of 0.2 W cm^-2 and exposure time of 3 min) obtained by batch experiments. R1 and the controlled Anammox reactor (R2) without exposure to the ultrasound were operated in parallel. The start-up period of Anammox process (53 days) in R1 was shorter than that (61 days) in R2. The nitrogen loading-enhancing period (day 53-day 135) in R1 was also shorter than that (day 61-day 151) in R2. At the end of the nitrogen loading-enhancing period, NLR (0.76 kg N m^-3 d^-1) and NRR (0.68 kg N m^-3 d^-1) of R1 were both higher than NLR (0.66 kg N m^-3 d^-1) and NRR (0.56 kg N m^-3 d^-1) of R2. Moreover, The stability of Anammox process in R1 was better than that in R2. The results demonstrated that the periodical irradiation of ultrasound enhanced the start-up and operational performance of Anammox reactor. Microbial community analysis indicated that the ultrasound accelerated the microbial succession from some other bacteria to Anammox bacteria so that shorten the start-up period of Anammox process from the conventional activated sludge. It also indicated that the ultrasound strengthened the competitive advantage of Candidatus Kuenenia stuttgartiensis in Anammox bacteria of the mature sludge so as to enhance the nitrogen removal performance of the Anammox reactor under the operation condition of high nitrogen loading.

Resolving the complete genome of Kuenenia stuttgartiensis from a membrane bioreactor enrichment using Single-Molecule Real-Time sequencing

Anaerobic ammonium-oxidizing (anammox) bacteria are a group of strictly anaerobic chemolithoautotrophic microorganisms. They are capable of oxidizing ammonium to nitrogen gas using nitrite as a terminal electron acceptor, thereby facilitating the release of fixed nitrogen into the atmosphere. The anammox process is thought to exert a profound impact on the global nitrogen cycle and has been harnessed as an environment-friendly method for nitrogen removal from wastewater. In this study, we present the first closed genome sequence of an anammox bacterium, Kuenenia stuttgartiensis MBR1. It was obtained through Single-Molecule Real-Time (SMRT) sequencing of an enrichment culture constituting a mixture of at least two highly similar Kuenenia strains. The genome of the novel MBR1 strain is different from the previously reported Kuenenia KUST reference genome as it contains numerous structural variations and unique genomic regions. We find new proteins, such as a type 3b (sulf)hydrogenase and an additional copy of the hydrazine synthase gene cluster. Moreover, multiple copies of ammonium transporters and proteins regulating nitrogen uptake were identified, suggesting functional differences in metabolism. This assembly, including the genome-wide methylation profile, provides a new foundation for comparative and functional studies aiming to elucidate the biochemical and metabolic processes of these organisms.

Understanding the sorption and biotransformation of organic micropollutants in innovative biological wastewater treatment technologies

New technologies for wastewater treatment have been developed in the last years based on the combination of biological reactors operating under different redox conditions. Their efficiency in the removal of organic micropollutants (OMPs) has not been clearly assessed yet. This review paper is focussed on understanding the sorption and biotransformation of a selected group of 17 OMPs, including pharmaceuticals, hormones and personal care products, during biological wastewater treatment processes. Apart from considering the role of "classical" operational parameters, new factors such as biomass conformation and particle size, upward velocity applied or the addition of adsorbents have been considered. It has been found that the OMP removal by sorption not only depends on their physico-chemical characteristics and other parameters, such as the biomass conformation and particle size, or some operational conditions also relevant. Membrane biological reactors (MBR), have shown to enhance sorption and biotransformation of some OMPs. The same applies to technologies bases on direct addition of activated carbon in bioreactors. The OMP biotransformation degree and pathway is mainly driven by the redox potential and the primary substrate activity. The combination of different redox potentials in hybrid reactor systems can significantly enhance the overall OMP removal efficiency. Sorption and biotransformation can be synergistically promoted in biological reactors by the addition of activated carbon. The deeper knowledge of the main parameters influencing OMP removal provided by this review will allow optimizing the biological processes in the future.

Characterization of the first planctomycetal outer membrane protein identifies a channel in the outer membrane of the anammox bacterium Kuenenia stuttgartiensis

Planctomycetes are a bacterial phylum known for their complex intracellular compartmentalization. While most Planctomycetes have two compartments, the anaerobic ammonium oxidizing (anammox) bacteria contain three membrane-enclosed compartments. In contrast to a long-standing consensus, recent insights suggested the outermost Planctomycete membrane to be similar to a Gram-negative outer membrane (OM). One characteristic component that differentiates OMs from cytoplasmic membranes (CMs) is the presence of outer membrane proteins (OMPs) featuring a β-barrel structure that facilitates passage of molecules through the OM. Although proteomic and genomic evidence suggested the presence of OMPs in several Planctomycetes, no experimental verification existed of the pore-forming function and localization of these proteins in the outermost membrane of these exceptional microorganisms. Here, we show via lipid bilayer assays that at least two typical OMP-like channel-forming proteins are present in membrane preparations of the anammox bacterium Kuenenia stuttgartiensis. One of these channel-forming proteins, the highly abundant putative OMP Kustd1878, was purified to homogeneity. Analysis of the channel characteristics via lipid bilayer assays showed that Kustd1878 forms a moderately cation-selective channel with a high current noise and an average single-channel conductance of about 170-190pS in 1M KCl. Antibodies were raised against the purified protein and immunogold localization indicated Kustd1878 to be present in the outermost membrane. Therefore, this work clearly demonstrates the presence of OMPs in anammox Planctomycetes and thus firmly adds to the emerging view that Planctomycetes have a Gram-negative cell envelope.

Inhibitory effects of veterinary antibiotics on anammox activity: short- and long-term tests

The suitability of the anammox process for the treatment of swine digester liquor was assessed through the evaluation of the short- and long-term inhibitory effect of three veterinary antibiotics commonly administered to Italian swine livestock. The toxicity of doxycycline, tiamulin and enrofloxacin was evaluated through batch tests designed to estimate specific anammox activity. Moreover, the short-term toxicity of combined concentrations of doxycycline and enrofloxacin was evaluated so as to verify whether a synergistic effect could be established. According to the inhibition recorded in the presence of the maximum antibiotics concentrations predicted for digester liquor, target compounds do not seem to represent a real hazard for anammox bacteria because at those concentration levels, the activity was just slightly reduced. Moreover, in granular systems, inhibition could be easily counterbalanced by increasing the biomass concentration in the reactor, thus assuring the design treatment capacity for antibiotic-rich wastewaters.

The Paradigms They Are a-Changin': past, present and future of PVC bacteria research

These are exciting times for PVC researchers! The PVC superphylum is composed of the bacterial phyla Planctomycetes, Verrucomicrobia, Chlamydiae (those three founders giving it its name), Lentisphaerae and Kirimatiellaeota as well as some uncultured candidate phyla, such as the Candidatus Omnitrophica (previously known as OP3). Despite early debates, most of the disagreements that surround this group of bacteria have been recently resolved. In this article, we review the history of the study of PVC bacteria, with a particular focus on the misinterpretations that emerged early in the field and their resolution. We begin with a historical perspective that describes the relevant facts of PVC research from the early times when they were not yet termed PVC. Those were controversial times and we refer to them as the “discovery age” of the field. We continue by describing new discoveries due to novel techniques and data that combined with the reinterpretations of old ones have contributed to solve most of the discordances and we refer to these times as the “illumination age” of PVC research. We follow by arguing that we are just entering the “golden age” of PVC research and that the future of this growing community is looking bright. We finish by suggesting a few of the directions that PVC researches might take in the future.

Synthesis of ent-[3]-Ladderanol: Development and Application of Intramolecular Chirality Transfer [2+2] Cycloadditions of Allenic Ketones and Alkenes

An enantioselective synthesis of ent-[3]-ladderanol is presented. The ladderanes are an interesting class of molecules for their unique structure of fused cyclobutane rings as well as their perceived biological function of organism protection. The route hinges on the development and application of a chirality transfer [2+2] cycloaddition of an allenic ketone and alkene. Further stereocontrolled transformations allowed for completion of the synthesis. The scope of the chirality transfer [2+2] cycloaddition is also presented.

Genetic diversity of marine anaerobic ammonium-oxidizing bacteria as revealed by genomic and proteomic analyses of 'Candidatus Scalindua japonica'

Anaerobic ammonium-oxidizing (anammox) bacteria affiliated with the genus 'Candidatus Scalindua' are responsible for significant nitrogen loss in oceans, and thus their ecophysiology is of great interest. Here, we enriched a marine anammox bacterium, 'Ca. S. japonica' from a Hiroshima bay sediment in Japan, and comparative genomic and proteomic analyses of 'Ca. S. japonica' were conducted. Sequence of the 4.81-Mb genome containing 4019 coding regions of genes (CDSs) composed of 47 contigs was determined. In the proteome, 1762 out of 4019 CDSs in the 'Ca. S. japonica' genome were detected. Based on the genomic and proteomic data, the core anammox process and carbon fixation of 'Ca. S. japonica' were further investigated. Additionally, the present study provides the first detailed insights into the genetic background responsible for iron acquisition and menaquinone biosynthesis in anammox bacterial cells. Comparative analysis of the 'Ca. Scalindua' genomes revealed that the 1502 genes found in the 'Ca. S. japonica' genome were not present in the 'Ca. S. profunda' and 'Ca. S. rubra' genomes, showing a high genomic diversity. This result may reflect a high phylogenetic diversity of the genus 'Ca. Scalindua'.

Emergence of cytochrome bc complexes in the context of photosynthesis

The cytochrome bc (cyt bc) complexes are involved in Q-cycling; they oxidize membrane quinols by high-potential electron acceptors, such as cytochromes or plastocyanin, and generate transmembrane proton gradient. In several prokaryotic lineages, and also in plant chloroplasts, the catalytic core of the cyt bc complexes is built of a four-helical cytochrome b (cyt b) that contains three hemes, a three-helical subunit IV, and an iron-sulfur Rieske protein (cytochrome b₆ f-type complexes). In other prokaryotic lineages, and also in mitochondria, the cyt b subunit is fused with subunit IV, yielding a seven- or eight-helical cyt b with only two hemes (cyt bc₁ -type complexes). Here we present an updated phylogenomic analysis of the cyt b subunits of cyt bc complexes. This analysis provides further support to our earlier suggestion that (1) the ancestral version of cyt bc complex contained a small four-helical cyt b with three hemes similar to the plant cytochrome b₆ and (2) independent fusion events led to the formation of large cyts b in several lineages. In the search for a primordial function for the ancestral cyt bc complex, we address the intimate connection between the cyt bc complexes and photosynthesis. Indeed, the Q-cycle turnover in the cyt bc complexes demands high-potential electron acceptors. Before the Great Oxygenation Event, the biosphere had been highly reduced, so high-potential electron acceptors could only be generated upon light-driven charge separation. It appears that an ancestral cyt bc complex capable of Q-cycling has emerged in conjunction with the (bacterio)chlorophyll-based photosynthetic systems that continuously generated electron vacancies at the oxidized (bacterio)chlorophyll molecules.

Research trends and hotspots related to ammonia oxidation based on bibliometric analysis

Ammonia oxidation is the rate-limiting and central step in global biogeochemistry cycle of nitrogen. A bibliometric analysis based on 4314 articles extracted from Science Citation Index Expanded database was carried out to provide insights into publication performances and research trends of ammonia oxidation in the period 1991-2014. These articles were originated from a wide range of 602 journals and 95 Web of Science Categories, among which Applied and Environmental Microbiology and Environmental Sciences took the leading position, respectively. Furthermore, co-citation analysis conducted with help of CiteSpace software clearly illustrated that ammonia-oxidizing bacteria (AOB), ammonia-oxidizing archaea (AOA), and anaerobic ammonia oxidation (anammox) were three dominant research themes. A total of 15 landmark works identified with the highest co-citation frequencies at every 8 years were extracted, which demonstrated that the establishments of culture-independent molecular biotechnologies as well as the discoveries of anammox and AOA played the most significant roles in promoting the evolution and development of ammonia oxidation research. Finally, word cluster analysis further suggested that microbial abundance and community of AOA and AOB was the most prominent hotspot, with soil and high-throughput sequencing as the most promising ecosystem and molecular biotechnology. In addition, application of anammox in nitrogen removal from wastewater has become another attractive research hotspot. This study provides a basis for better understanding the situations and prospective directions of the research field of ammonia oxidation.

Achieving Mainstream Nitrogen Removal through Coupling Anammox with Denitratation

Achieving maintream anammox is critical for energy-neutral sewage treatment. This study presents a new way to achieve mainstream anammox, which couples anammox with denitratation (nitrate reduction to nitrite) instead of nitritation (ammonium oxidation to nitrite). An anoxic/oxic (A/O) biofilm system treating systhetic domestic wastewater was used to demonstrate this concept for over 400 days. This A/O biofilm system achieved a total nitrogen (TN) removal efficiency of 80 ± 4% from the influent with a low C/N ratio of 2.6 and a TN concentration of 60.5 mg/L. Nitrogen removal via anammox was found to account for 70% of dinitrogen production in the anoxic reactor. Batch tests confirmed that the anoxic biofilm could oxidize ammonium using nitrite as electron acceptor, and that it had a higher nitrate reduction rate than the nitrite reduction rate, thus producing nitrite for the anammox reaction. Metagenomic analysis showed that Candidatus Jettenia caeni and Candidatus Kuenenia stuttgartiensis were the top two dominant species in anoxic biofilm. Genes involved in the metabolism of the anammox process were detected in anoxic biofilm. The abundance of nitrate reductase (73360 hits) was much higher than nitrite reductase (13114 hits) in anoxic biofilm. This system can be easily integrated with the high-rate activated sludge technology, which produces an effluent with a low C/N ratio. While this new design consumes 21% more oxygen in comparison to the currently studied nitritation/anammox process, the nitrite-producing process appears to be more stable.

Ecological Energetic Perspectives on Responses of Nitrogen-Transforming Chemolithoautotrophic Microbiota to Changes in the Marine Environment

Transformation and mobilization of bioessential elements in the biosphere, lithosphere, atmosphere, and hydrosphere constitute the Earth’s biogeochemical cycles, which are driven mainly by microorganisms through their energy and material metabolic processes. Without microbial energy harvesting from sources of light and inorganic chemical bonds for autotrophic fixation of inorganic carbon, there would not be sustainable ecosystems in the vast ocean. Although ecological energetics (eco-energetics) has been emphasized as a core aspect of ecosystem analyses and microorganisms largely control the flow of matter and energy in marine ecosystems, marine microbial communities are rarely studied from the eco-energetic perspective. The diverse bioenergetic pathways and eco-energetic strategies of the microorganisms are essentially the outcome of biosphere-geosphere interactions over evolutionary times. The biogeochemical cycles are intimately interconnected with energy fluxes across the biosphere and the capacity of the ocean to fix inorganic carbon is generally constrained by the availability of nutrients and energy. The understanding of how microbial eco-energetic processes influence the structure and function of marine ecosystems and how they interact with the changing environment is thus fundamental to a mechanistic and predictive understanding of the marine carbon and nitrogen cycles and the trends in global change. By using major groups of chemolithoautotrophic microorganisms that participate in the marine nitrogen cycle as examples, this article examines their eco-energetic strategies, contributions to carbon cycling, and putative responses to and impacts on the various global change processes associated with global warming, ocean acidification, eutrophication, deoxygenation, and pollution. We conclude that knowledge gaps remain despite decades of tremendous research efforts. The advent of new techniques may bring the dawn to scientific breakthroughs that necessitate the multidisciplinary combination of eco-energetic, biogeochemical and “omics” studies in this field.

Evaluating the potential for dissimilatory nitrate reduction by anammox bacteria for municipal wastewater treatment

Anammox bacteria can perform dissimilatory nitrate reduction to ammonium (DNRA) with nitrite as intermediate coupled to the oxidation of volatile fatty acids (VFA). Batch tests with enriched anammox and a co-culture of anammox and heterotrophic bacteria showed the capacity of Candidatus 'Brocadia fulgida' to perform the DNRA coupled to the anammox reaction (DNRA-anammox) at a high rate although the culture was not previously adapted to VFA. From thermodynamic calculations it could be stated that low COD/N influent ratios favour the DNRA-anammox transformation over heterotrophic conversions since more free energy is gained. A process scheme is proposed for an innovative nitrogen removal system in which the nitrate produced by nitrite oxidizing bacteria and/or anammox bacteria is converted during DNRA-anammox pathway, resulting in a sustainable nitrogen removal from municipal wastewater while circumventing the troublesome out-selection of nitrite oxidizing bacteria encountered in mainstream applications.

Metabolic network analysis reveals microbial community interactions in anammox granules

Microbial communities mediating anaerobic ammonium oxidation (anammox) represent one of the most energy-efficient environmental biotechnologies for nitrogen removal from wastewater. However, little is known about the functional role heterotrophic bacteria play in anammox granules. Here, we use genome-centric metagenomics to recover 17 draft genomes of anammox and heterotrophic bacteria from a laboratory-scale anammox bioreactor. We combine metabolic network reconstruction with metatranscriptomics to examine the gene expression of anammox and heterotrophic bacteria and to identify their potential interactions. We find that Chlorobi-affiliated bacteria may be highly active protein degraders, catabolizing extracellular peptides while recycling nitrate to nitrite. Other heterotrophs may also contribute to scavenging of detritus and peptides produced by anammox bacteria, and potentially use alternative electron donors, such as H2, acetate and formate. Our findings improve the understanding of metabolic activities and interactions between anammox and heterotrophic bacteria and offer the first transcriptional insights on ecosystem function in anammox granules.

Simultaneous domestic wastewater and nitrate sewage treatment by DEnitrifying AMmonium OXidation (DEAMOX) in sequencing batch reactor

A novel DEAMOX system was developed for nitrogen removal from domestic wastewater and nitrate (NO₃^--N) sewage in sequencing batch reactor (SBR). High nitrite (NO₂^--N) was produced from NO₃^--N reduction in partial-denitrification process, which served as electron acceptor for anammox and was removed with ammonia (NH₄⁺-N) in domestic wastewater simultaneously. A 500-days operation demonstrated that the efficient and stable nitrogen removal performance could be achieved by DEAMOX. The total nitrogen (TN) removal efficiency was as high as 95.8% with influent NH₄⁺-N of 63.58 mg L^-1 and NO₃^--N of 69.24 mg L^-1. The maximum NH₄⁺-N removal efficiency reached up to 94.7%, corresponding to the NO₃^--N removal efficiency of 97.8%. The biomass of partial-denitrification and anammox bacteria was observed to be wall-growth. The deteriorated nitrogen removal performance occurred due to excess denitrifying microbial growth in the outer layer of sludge consortium, which prevented the substrate transfer for anammox inside. However, an excellent nitrogen removal could be guaranteed by scrapping the superficial denitrifying biomass at regular intervals. Furthermore, the high-throughput sequencing analysis revealed that the Thauera genera (26.33%) was possibly responsible for the high NO₂^--N accumulation in partial-denitrification and Candidatus Brocadia (1.7%) was the major anammox species.

Whole-Community Metagenomics in Two Different Anammox Configurations: Process Performance and Community Structure

Anaerobic ammonia oxidation (anammox) combined with partial nitritation (PN) is an innovative treatment process for energy-efficient nitrogen removal from wastewater. In this study, we used genome-based metagenomics to investigate the overall community structure and anammox species enriched in suspended growth (SGR) and attached growth packed-bed (AGR) anammox reactors after 220 days of operation. Both reactors removed more than 85% of the total inorganic nitrogen. Metagenomic binning and phylogenetic analysis revealed that two anammox population genomes, affiliated with the genus Candidatus Brocadia, were differentially abundant between the SGR and AGR. Both of the genomes shared an average nucleotide identify of 83%, suggesting the presence of two different species enriched in both of the reactors. Metabolic reconstruction of both population genomes revealed key aspects of their metabolism in comparison to known anammox species. The community composition of both the reactors was also investigated to identify the presence of flanking community members. Metagenomics and 16S rRNA gene amplicon sequencing revealed the dominant flanking community members in both reactors were affiliated with the phyla Anaerolinea, Ignavibacteria, and Proteobacteria. Findings from this research adds two new species, Ca. Brocadia sp. 1 and Ca. Brocadia sp. 2, to the genus Ca. Brocadia and sheds light on their metabolism in engineered ecosystems.

Effect of advanced oxidation on N-nitrosodimethylamine (NDMA) formation and microbial ecology during pilot-scale biological activated carbon filtration

Water treatment combining advanced oxidative processes with subsequent exposure to biological activated carbon (BAC) holds promise for the attenuation of recalcitrant pollutants. Here we contrast oxidation and subsequent biofiltration of treated wastewater effluent employing either ozone or UV/H₂O₂ followed by BAC during pilot-scale implementation. Both treatment trains largely met target water quality goals by facilitating the removal of a suite of trace organics and bulk water parameters. N-nitrosodimethylamine (NDMA) formation was observed in ozone fed BAC columns during biofiltration and to a lesser extent in UV/H₂O₂ fed columns and was most pronounced at 20 min of empty bed contact time (EBCT) when compared to shorter EBCTs evaluated. While microbial populations were highly similar in the upper reaches, deeper samples revealed a divergence within and between BAC filtration systems where EBCT was identified to be a significant environmental predictor for shifts in microbial populations. The abundance of Nitrospira in the top samples of both columns provides an explanation for the oxidation of nitrite and corresponding increases in nitrate concentrations during BAC transit and support interplay between nitrogen cycling with nitrosamine formation. The results of this study demonstrate that pretreatments using ozone versus UV/H₂O₂ impart modest differences to the overall BAC microbial population structural and functional attributes, and further highlight the need to evaluate NDMA formation prior to full-scale implementation of BAC in potable reuse applications.

Discovery and metagenomic analysis of an anammox bacterial enrichment related to Candidatus "Brocadia caroliniensis" in a full-scale glycerol-fed nitritation-denitritation separate centrate treatment process

A distinctive red biofilm was observed in a glycerol-fed digester liquid effluent treatment process coupling partial nitrification (nitritation) and partial denitrification (denitritation) processes. Based on initial phylogenetic screening using 16S rRNA clone libraries and quantitative polymerase chain reaction, the biofilm was enriched in novel anaerobic ammonium oxidizing bacteria (AMX/anammox) closely related to Candidatus "Brocadia caroliniensis". The metabolic functionality of the C. "Brocadia caroliniensis" enrichment was further explored using high-throughput sequencing and de novo metagenome assembly. The population anammox genome that was binned from the metagenome consisted of 209 contigs with a total of 3.73 Mbp consensus sequences having 43.3% GC content, and 27.4 average coverage depth. The assembled metagenome bin was comprised of 3582 open reading frames (ORFs). Based on 16S rRNA similarity the binned metagenome was closely related with Candidatus "Brocadia caroliniensis", Candidatus "Brocadia fulgida", planctomycete KSU-1, and Candidatus "Kuenenia stuttgartiensis" with 99%, 96%, 92% and 93% similarity, respectively. Essential genes in anammox metabolic functions including ammonium and nitrite transport, hydrazine synthesis, electron transfer for catabolism, and inorganic carbon fixation, among several other anabolic pathways, were also observed in the population genome of the C. "Brocadia caroliniensis" related enrichment. Our results demonstrate the wider profusion of anammox bacteria in engineered nitrogen removal systems than expected. The utility of metagenomics approaches to deciphering such novel functionality in these systems is also highlighted.

Rapid adaptation of activated sludge bacteria into a glycogen accumulating biofilm enabling anaerobic BOD uptake

Glycogen accumulating organisms (GAO) are known to allow anaerobic uptake of biological oxygen demand (BOD) in activated sludge wastewater treatment systems. In this study, we report a rapid transition of suspended activated sludge biomass to a GAO dominated biofilm by selective enrichment using sequences of anaerobic loading followed by aerobic exposure of the biofilm to air. The study showed that within eight weeks, a fully operational, GAO dominated biofilm had developed, enabling complete anaerobic BOD uptake at a rate of 256mg/L/h. The oxygen uptake by the biofilm directly from the atmosphere had been calculated to provide significant energy savings. This study suggests that wastewater treatment plant operators can convert activated sludge systems readily into a "passive aeration" biofilm that avoids costly oxygen transfer to bulk wastewater solution. The described energy efficient BOD removal system provides an opportunity to be coupled with novel nitrogen removal processes such as anammox.

Fuerstia marisgermanicae gen. nov., sp. nov., an Unusual Member of the Phylum Planctomycetes from the German Wadden Sea

Members of the phylum Planctomycetes are ubiquitous bacteria that dwell in aquatic and terrestrial habitats. While planctomycetal species are important players in the global carbon and nitrogen cycle, this phylum is still undersampled and only few genome sequences are available. Here we describe strain NH11^T, a novel planctomycete obtained from a crustacean shell (Wadden Sea, Germany). The phylogenetically closest related cultivated species is Gimesia maris, sharing only 87% 16S rRNA sequence identity. Previous isolation attempts have mostly yielded members of the genus Rhodopirellula from water of the German North Sea. On the other hand, only one axenic culture of the genus Pirellula was obtained from a crustacean thus far. However, the 16S rRNA gene sequence of strain NH11^T shares only 80% sequence identity with the closest relative of both genera, Rhodopirellula and Pirellula. Thus, strain NH11^T is unique in terms of origin and phylogeny. While the pear to ovoid shaped cells of strain NH11^T are typical planctomycetal, light-, and electron microscopic observations point toward an unusual variation of cell division through budding: during the division process daughter- and mother cells are connected by an unseen thin tubular-like structure. Furthermore, the periplasmic space of strain NH11^T was unusually enlarged and differed from previously known planctomycetes. The complete genome of strain NH11^T, with almost 9 Mb in size, is among the largest planctomycetal genomes sequenced thus far, but harbors only 6645 protein-coding genes. The acquisition of genomic components by horizontal gene transfer is indicated by the presence of numerous putative genomic islands. Strikingly, 45 “giant genes” were found within the genome of NH11^T. Subsequent analysis of all available planctomycetal genomes revealed that Planctomycetes as such are especially rich in “giant genes”. Furthermore, Multilocus Sequence Analysis (MLSA) tree reconstruction support the phylogenetic distance of strain NH11^T from other cultivated Planctomycetes of the same phylogenetic cluster. Thus, based on our findings, we propose to classify strain NH11^T as Fuerstia marisgermanicae gen. nov., sp. nov., with the type strain NH11^T, within the phylum Planctomycetes.

Chemical Synthesis and Self-Assembly of a Ladderane Phospholipid

Ladderane lipids produced by anammox bacteria constitute some of the most structurally fascinating yet poorly studied molecules among biological membrane lipids. Slow growth of the producing organism and the inherent difficulty of purifying complex lipid mixtures have prohibited isolation of useful amounts of natural ladderane lipids. We have devised a highly selective total synthesis of ladderane lipid tails and a full phosphatidylcholine to enable biophysical studies on chemically homogeneous samples of these molecules. Additionally, we report the first proof of absolute configuration of a natural ladderane.

Nitrate Reverses Severe Nitrite Inhibition of Anaerobic Ammonium Oxidation (Anammox) Activity in Continuously-Fed Bioreactors

Nitrite (NO₂^-) substrate under certain conditions can cause failure of N-removal processes relying on anaerobic ammonium oxidizing (anammox) bacteria. Detoxification of NO₂^- can potentially be achieved by using exogenous nitrate (NO₃^-). In this work, continuous experiments in bioreactors with anammox bacteria closely related to "Candidatus Brocadia caroliniensis" were conducted to evaluate the effectiveness of short NO₃^- additions to reverse NO₂^- toxicity. The results show that a timely NO₃^- addition immediately after a NO₂^- stress event completely reversed the NO₂^- inhibition. This reversal occurs without NO₃^- being metabolized as evidence by lack of any ³⁰N₂ formation from ¹⁵N-NO₃^-. The maximum recovery rate was observed with 5 mM NO₃^- added for 3 days; however, slower but significant recovery was also observed with 5 mM NO₃^- for 1 day or 2 mM NO₃^- for 3 days. Without NO₃^- addition, long-term NO₂^- inhibition of anammox biomass resulted in irreversible damage of the cells. These results suggest that a short duration dose of NO₃^- to an anammox bioreactor can rapidly restore the activity of NO₂^--stressed anammox cells. On the basis of the results, a hypothesis about the detoxification mechanism related to narK genes in anammox bacteria is proposed and discussed.

Ammonium and nitrite oxidation at nanomolar oxygen concentrations in oxygen minimum zone waters

A major percentage of fixed nitrogen (N) loss in the oceans occurs within nitrite-rich oxygen minimum zones (OMZs) via denitrification and anammox. It remains unclear to what extent ammonium and nitrite oxidation co-occur, either supplying or competing for substrates involved in nitrogen loss in the OMZ core. Assessment of the oxygen (O2) sensitivity of these processes down to the O2 concentrations present in the OMZ core (<10 nmol⋅L(-1)) is therefore essential for understanding and modeling nitrogen loss in OMZs. We determined rates of ammonium and nitrite oxidation in the seasonal OMZ off Concepcion, Chile at manipulated O2 levels between 5 nmol⋅L(-1) and 20 μmol⋅L(-1) Rates of both processes were detectable in the low nanomolar range (5-33 nmol⋅L(-1) O2), but demonstrated a strong dependence on O2 concentrations with apparent half-saturation constants (Kms) of 333 ± 130 nmol⋅L(-1) O2 for ammonium oxidation and 778 ± 168 nmol⋅L(-1) O2 for nitrite oxidation assuming one-component Michaelis-Menten kinetics. Nitrite oxidation rates, however, were better described with a two-component Michaelis-Menten model, indicating a high-affinity component with a Km of just a few nanomolar. As the communities of ammonium and nitrite oxidizers were similar to other OMZs, these kinetics should apply across OMZ systems. The high O2 affinities imply that ammonium and nitrite oxidation can occur within the OMZ core whenever O2 is supplied, for example, by episodic intrusions. These processes therefore compete with anammox and denitrification for ammonium and nitrite, thereby exerting an important control over nitrogen loss.