Intracellular localization of membrane-bound ATPases in the compartmentalized anammox bacterium 'Candidatus Kuenenia stuttgartiensis'

Oxygen-induced evolution of anammox granular sludge explains its unique responses during preservation

Anammox granular sludge (AnGS) preservation is indispensable for the application of anammox technology. Oxygen is a common and crucial factor for anammox, yet its long-term effects on AnGS during preservation remain incomplete clarification. This study investigated the effect of oxygen on AnGS in two simulated preservation systems with open and sealed conditions, and the mechanism was discussed. The results showed that the open system was in an oxidized state with an average dissolved oxygen (DO) concentration and oxidation-reduction potential (ORP) of (3.10 ± 1.36) mg·L-1 and (112.58 ± 46.78) mV, while a reduced state for the sealed system with no detected DO and a lower average ORP of (-153.96 ± 64.32) mV. Both systems showed declines in AnGS activity, while with different responses of AnGS demonstrated by the evolution in terms of granular morphology and structure, bacterial communities, bacteria survival, and bacteria antioxidation. In the open system, reactive oxygen species were generated and destroyed the unsaturated fatty acids in the cell membrane, further leading to the destructed cell structure and declined activity. However, in the sealed system, AnAOB tended to enter a dormant state after long-term preservation, contributing to better conditions in granular morphology and structure, higher AnAOB abundance, and higher live cell ratio. The findings of this study are expected to offer vital information and guidelines for the preservation technologies of AnGS.

Analysis of the regulation mechanism for salt-tolerant anammox process: process performance and metabolic insights

In this study, the start-up and microbial domestication of a salt-tolerant functional anammox system was investigated by gradually increasing the salinity level in a stabilized anammox system in the laboratory. After 44 days of stable operation, the salt-tolerant system was successfully activated, at which time the salinity of the influent water was 3 g/L, and the maximum removal efficiency of ammonia nitrogen and nitrite nitrogen in the system reached 94.18% and 96.66%, respectively, and then the ammonia nitrogen and nitrite nitrogen removal efficiency were stabilized at 88.17% and 96.48% after the enrichment domestication for 89 days. The system was operated in the salinity of 10 g/L, with the concentration of each nitrogen compound measured at the same time. The ammonia nitrogen removal efficiency decreased to 59.93% at a salinity of 10 g/L, which had a significant impact on the system. High-throughput sequencing revealed that the system was enriched with a large number of Chloroflexi, the relative abundance of which increased from 19.46% to 52.33%, and the genus of AnAOB was transformed from Candidatus Brocadia to Candidatus Kuenenia, Candidatus Kuenenia, with a percentage of 4.78%. The system successfully achieved the simultaneous removal of ammonia nitrogen and nitrite nitrogen under salinity stress, which to a certain extent indicated that AnAOB could achieve the initiation and enrichment domestication under salinity conditions, and could provide a basis for the efficient and low-consumption treatment of high salinity nitrogen-containing wastewater.

Potential Role of the Anammoxosome in the Adaptation of Anammox Bacteria to Salinity Stress

The underlying adaptative mechanisms of anammox bacteria to salt stress are still unclear. The potential role of the anammoxosome in modulating material and energy metabolism in response to salinity stress was investigated in this study. The results showed that anammox bacteria increased membrane fluidity and decreased mechanical properties by shortening the ladderane fatty acid chain length of anammoxosome in response to salinity shock, which led to the breakdown of the proton motive force driving ATP synthesis and retarded energy metabolism activity. Afterward, the fatty acid chain length and membrane properties were recovered to enhance the energy metabolic activity. The relative transmission electron microscopy (TEM) area proportion of anammoxosome decreased from 55.9 to 38.9% under salinity stress. The 3D imaging of the anammox bacteria based on Synchrotron soft X-ray tomography showed that the reduction in the relative volume proportion of the anammoxosome and the concave surfaces was induced by salinity stress, which led to the lower energy expenditure of the material transportation and provided more binding sites for enzymes. Therefore, anammox bacteria can modulate nitrogen and energy metabolism by changing the membrane properties and morphology of the anammoxosome in response to salinity stress. This study broadens the response mechanism of anammox bacteria to salinity stress.

Rapid start-up of an innovative pilot-scale staged PN/A continuous process for enhanced nitrogen removal from mature landfill leachate via robust NOB elimination and efficient biomass retention

The start-up and stable operation of partial nitritation-anammox (PN/A) treatment of mature landfill leachate (MLL) still face challenges. This study developed an innovative staged pilot-scale PN/A system to enhance nitrogen removal from MLL. The staged process included a PN unit, an anammox upflow enhanced internal circulation biofilm (UEICB) reactor, and a post-biofilm unit. Rapid start-up of the continuous flow PN process (full-concentration MLL) was achieved within 35 days by controlling dissolved oxygen and leveraging free ammonia and free nitrous acid to selectively suppress nitrite-oxidizing bacteria (NOB). The UEICB was equipped with an annular flow agitator combined with the enhanced internal circulation device of the guide tube, which achieved an efficient enrichment of Candidatus Kuenenia in the biofilm (relative abundance of 33.4 %). The nitrogen removal alliance formed by the salt-tolerant anammox bacterium (Candidatus Kuenenia) and denitrifying bacteria (unclassified SBR1031 and Denitratisoma) achieved efficient nitrogen removal of UEICB (total nitrogen removal percentage: 90.8 %) and at the same time effective treatment of the refractory organic matter (ROM). The dual membrane process of UEICB fixed biofilm combined with post-biofilm is effective in sludge retention, and can stably control the effluent suspended solids (SS) at a level of less than 5 mg/L. The post-biofilm unit ensured that effluent total nitrogen (TN) remained below the 40 mg/L discharge standard (98.5 % removal efficiency). Compared with conventional nitrification-denitrification systems, the staged PN/A process substantially reduced oxygen consumption, sludge production, CO2 emissions and carbon consumption by 22.8 %, 67.1 %, 87.1 % and 87.1 %, respectively. The 195-day stable operation marks the effective implementation of the innovative pilot-scale PN/A process in treating actual MLL. This study provides insights into strategies for rapid start-up, robust NOB suppression, and anammox biomass retention to advance the application of PN/A in high-ammonia low-carbon wastewater.

Probing the dynamics of three freshwater Anammox genera at different salinity levels in a partial nitritation and Anammox sequencing batch reactor treating landfill leachate

Partial nitritation/Anammox was applied to treat NaCl-amended landfill leachate. The reactor established robust nitrogen removal of 85.7 ± 2.4% with incremental salinity from 0.61% to 3.10% and achieved 0.91-1.05 kg N/m³/d at salinity of 2.96%-3.10%. Microbial community analysis revealed Nitrosomonas, Nitrospira, and denitrifiers occupied 4.1%, <0.2% and 10.9%, respectively. Salinity variations impelled the dynamics of Anammox bacteria. Jettenia shifted to Brocadia and Kuenenia at salinity of 0.61%-0.81%. Kuenenia outcompeted Brocadia and occupied 51.5% and 50.9% at salinity of 1.48%-1.54% and 2.96%-3.10%, respectively. High nitrite affinity and fast growth rate were proposed as key factors fostering Brocadia overgrew Jettenia. Functionalities of sodium-motive-force facilitated energy generation and intracellular osmotic pressure equilibrium regulation crucially determined Kuenenia's dominance at elevated salinity. Co-occurrence network further manifested beneficial symbiotic relationships boosted Kuenenia's preponderance. Knowledge gleaned deepen understanding on survival niches of freshwater Anammox genera at saline environments and lead to immediate benefits to its applications treating relevant wastewaters.

Specific and effective detection of anammox bacteria using PCR primers targeting the 16S rRNA gene and functional genes

Anaerobic ammonium-oxidizing (anammox) bacteria play an important role in the nitrogen cycle by coupling ammonium and nitrite to produce dinitrogen gas (N₂). Polymerase chain reaction (PCR) is a fast, simple, and sensitive method that is widely used to assess the diversity, abundance, and activity of the slow-growing bacteria. In this review, we summarize and evaluate the wide variety of PCR primers targeting the 16S rRNA gene and functional genes (hzo, nir, and hzs) of anammox bacteria for their effectiveness and efficiencies in detecting this group of bacteria in different sample types. Furthermore, the efficiencies of different universal high-throughput sequencing 16S rRNA gene primers in anammox bacteria investigations were also evaluated to provide a reference for primer selection. Based on our in silico evaluation results, none of the 16S rRNA gene primers could recover all of the known anammox bacteria, but multiple hzo and hzs gene primers could accomplish this task. However, uncertain copies (1-3 copies) of hzo genes were identified in the genomes, and the hydrazine oxidation reaction catalyzed by hydrazine oxidoreductases (HZOs) can also be catalyzed by other hydroxylamine oxidoreductases (HAOs) in anammox bacteria, which can potentially result in large deviations in hzo-based qPCR and RT-qPCR analyses and results. Therefore, the use of optimal primers targeting unique hzs genes are recommended, although the efficiencies of these newly designed primers need further verification in practical applications. This article provides comprehensive information for the effective and specific detection of anammox bacteria using specific primers targeting the 16S rRNA gene and functional genes and serves as a basis for future high-quality primer design.

Investigation of anaerobic phenanthrene biodegradation by a highly enriched co-culture, PheN9, with nitrate as an electron acceptor

In this study, we developed a highly enriched phenanthrene-degrading co-culture, PheN9, which uses nitrate as an electron acceptor under anaerobic conditions, and the processes mediating biodegradation were proposed. The dominant bacteria populations included Pseudomonas stutzeri (91.7% relative abundance), which shared 98% 16S rRNA-sequence similarity with the naphthalene-degrading, nitrate-reducing strain NAP-3-1, and Candidatus_Kuenenia (2.3% relative abundance), which is a type of anammox bacteria. Enrichment transformed 54% of the added phenanthrene, reduced nitrate, and generated significant amounts of nitrite. Enrichment also result in partial consumption of the produced nitrite by the anammox bacteria. The key initial steps of anaerobic phenanthrene biodegradation by PheN9 were methylation and carboxylation, which were identified for detection of metabolic products, as well as carboxylase and methyltransferase activities. The methylation product was then oxidized to 2-naphthoic acid and then underwent sequential biodegradation steps. Then, ring-system reducing occurred, and the metabolic products were identified as dihydro-, tetrahydro-, hexahydro-, and octahydro-2-phenanthroic acid. Downstream degradation proceeded via a substituted benzene series and cyclohexane derivatives. This study employed anaerobic phenanthrene-biodegradation processes with nitrate as an electron acceptor. These findings can improve our understanding of anaerobic polycyclic aromatic hydrocarbon (PAH) biodegradation processes and guide PAH bioremediation by adding nitrate to anaerobic environments.

Nitrogen loss by anaerobic ammonium oxidation in a mangrove wetland of the Zhangjiang Estuary, China

Anaerobic ammonium oxidation (anammox), a microbial process in which NH₄⁺ is oxidized to N₂ gas, is considered a significant nitrogen cycle process, but its significance in mangrove wetland sediments, particularly its depth- and genus-specific distribution and activity have remained uncertain. Here we report the vertical distribution, abundance, activity and role of anammox bacteria in mangrove sediments of Zhangjiang Estuary, China. We used stable isotope-tracer techniques, 16S rRNA and anammox bacterial functional gene (Hydrazine synthase B: hzsB) clone libraries and quantitative polymerase chain reaction (qPCR) assays, along with an assessment of nutrient profiles of sediment core samples. We observed a widespread occurrence of anammox bacteria at different depths of mangrove sediments. The abundance of anammox bacterial 16S rRNA and hzsB genes ranged from 0.41×10⁷ to 9.74×10⁷ and from 0.42×10⁶ to 6.44×10⁶ copies per gram of dry soil and peaked in the upper layer of mangrove sediments. We also verified the co-occurrence of different genera of anammox microorganisms in mangrove sediments, with Candidatus Scalindua and Candidatus Kuenenia being the dominant genera. Potential anammox rates ranged from 4.83 to 277.36 nmolN₂·g^-1·d^-1 at different depths of sediment cores, and the highest rates were found in the deeper layer (70-100cm) of mangrove sediments. Scaling our findings up to the entire mangrove system, we estimated that anammox hotspots accounted for a loss of 751 gN·m^-2·y^-1, and contributed to over 12% of the nitrogen lost from the deeper layer of mangrove sediments in this region.

The Discovery of Twenty-Eight New Encapsulin Sequences, Including Three in Anammox Bacteria

Many prokaryotes encode protein-based encapsulin nanocompartments, including anaerobic ammonium oxidizing (anammox) bacteria. This study expands the list of known anammox encapsulin systems from freshwater species to include the marine genus Scalindua. Two novel systems, identified in "Candidatus Scalindua rubra" and "Candidatus Scalindua sp. SCAELEC01 167" possess different architectures than previously studied freshwater anammox encapsulins. Characterization of the S. rubra encapsulin confirms that it can self-assemble to form compartments when heterologously expressed in Escherichia coli. BLASTp and HMMER searches of additional genomes and metagenomes spanning a range of environments returned 26 additional novel encapsulins, including a freshwater anammox encapsulin identified in "Candidatus Brocadia caroliniensis". Phylogenetic analysis comparing these 28 new encapsulin sequences and cargo to that of their closest known relatives shows that encapsulins cluster by cargo protein type and therefore likely evolved together. Lastly, prokaryotic encapsulins may be more common and diverse than previously thought. Through searching a small sample size of all public metagenomes and genomes, many new encapsulin systems were unearthed by this study. This suggests that many additional encapsulins likely remain to be discovered.

Trending topics and open questions in anaerobic ammonium oxidation

Anaerobic ammonium-oxidizing (anammox) bacteria are major players in the biological nitrogen cycle and can be applied in wastewater treatment for the removal of nitrogen compounds. Anammox bacteria anaerobically convert the substrates ammonium and nitrite into dinitrogen gas in a specialized intracellular compartment called the anammoxosome. The anammox cell biology, physiology and biochemistry is of exceptional interest but also difficult to study because of the lack of a pure culture, standard cultivation techniques and genetic tools. Here we review the most important recent developments regarding the cell structure - anammoxosome and cell envelope - and anammox energy metabolism - nitrite reductase, hydrazine synthase and energy conversion - including the trending topics electro-anammox, extracellular polymeric substances and ladderane lipids.

Increased salinity triggers significant changes in the functional proteins of ANAMMOX bacteria within a biofilm community

Anaerobic ammonium oxidation (ANAMMOX) processes can potentially be influenced by salinity related to variable salinity in water environment. Here, we used 16S rRNA sequencing analysis combining with iTRAQ-based quantitative proteomic approach to reveal the response of microbial community and functional proteins to salinity, which was increased from 0 to 20 g L^-1 with a step of 5 g L^-1 (designed as S5, S10, S15 and S20) compared to control reactor (without salinity stress desined as S0). The 16S rRNA sequencing analysis showed that a high salinity (20 g L^-1, S20) decreased the abundance of genus Candidatus Jettenia but increased that of Candidatus Kuenenia. A total of 1609 differentially expressed proteins were acquired in the three comparison groups (S5:S0, S20:S0 and S20:S5). Of these, 39 proteins co-occurred in the three salt-exposed samples. Hydrazine dehydrogenase (HDH; Q1PW30) and nitrate reductase (Q1PZD8) were up-regulated more than 3-folds in the exposure of 20 g-NaCl/L. The functional enrichment analysis further showed that some proteins responsible for ion binding, catalysis and oxidation-reduction reaction were up-regulated, which explained the physiological resilience of ANAMMOX bacteria under salinity stress. Additionally, ANAMMOX bacteria responded to salinity by modulating the electron transport systems, indicating that the cells retained a high potential for proton pumping, as well as the ATP production. Furthermore, the over-expression of HDH which associated with ANAMMOX metabolism, was potentially related to the increased abundance of halophilic Candidatus Kuenenia. These findings provide a comprehensive baseline for understanding the roles of salinity stresses in shaping the functional proteins of 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.

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.

Determining the bacterial cell biology of Planctomycetes

Bacteria of the phylum Planctomycetes have been previously reported to possess several features that are typical of eukaryotes, such as cytosolic compartmentalization and endocytosis-like macromolecule uptake. However, recent evidence points towards a Gram-negative cell plan for Planctomycetes, although in-depth experimental analysis has been hampered by insufficient genetic tools. Here we develop methods for expression of fluorescent proteins and for gene deletion in a model planctomycete, Planctopirus limnophila, to analyse its cell organization in detail. Super-resolution light microscopy of mutants, cryo-electron tomography, bioinformatic predictions and proteomic analyses support an altered Gram-negative cell plan for Planctomycetes, including a defined outer membrane, a periplasmic space that can be greatly enlarged and convoluted, and an energized cytoplasmic membrane. These conclusions are further supported by experiments performed with two other Planctomycetes, Gemmata obscuriglobus and Rhodopirellula baltica. We also provide experimental evidence that is inconsistent with endocytosis-like macromolecule uptake; instead, extracellular macromolecules can be taken up and accumulate in the periplasmic space through unclear mechanisms.

Horizontal gene transfer drives the evolution of Rh50 permeases in prokaryotes

Background

Rh50 proteins belong to the family of ammonia permeases together with their Amt/MEP homologs. Ammonia permeases increase the permeability of NH₃/NH₄⁺ across cell membranes and are believed to be involved in excretion of toxic ammonia and in the maintenance of pH homeostasis. RH50 genes are widespread in eukaryotes but absent in land plants and fungi, and remarkably rare in prokaryotes. The evolutionary history of RH50 genes in prokaryotes is just beginning to be unveiled.

Results

Here, a molecular phylogenetic approach suggests horizontal gene transfer (HGT) as a primary force driving the evolution and spread of RH50 among prokaryotes. In addition, the taxonomic distribution of the RH50 gene among prokaryotes turned out to be very narrow; a single-copy RH50 is present in the genome of only a small proportion of Bacteria, and, first evidence to date, in only three methanogens among Euryarchaea. The coexistence of RH50 and AMT in prokaryotes seems also a rare event. Finally, phylogenetic analyses were used to reconstruct the HGT network along which prokaryotic RH50 evolution has taken place.

Conclusions

The eukaryotic or bacterial “origin” of the RH50 gene remains unsolved. The RH50 prokaryotic HGT network suggests a preferential directionality of transfer from aerobic to anaerobic organisms. The observed HGT events between archaeal methanogens, anaerobic and aerobic ammonia-oxidizing bacteria suggest that syntrophic relationships play a major role in the structuring of the network, and point to oxygen minimum zones as an ecological niche that might be of crucial importance for HGT-driven evolution.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-016-0850-6) contains supplementary material, which is available to authorized users.

Cytochromes c in Archaea: distribution, maturation, cell architecture, and the special case of Ignicoccus hospitalis

Cytochromes c (Cytc) are widespread electron transfer proteins and important enzymes in the global nitrogen and sulfur cycles. The distribution of Cytc in more than 300 archaeal proteomes deduced from sequence was analyzed with computational methods including pattern and similarity searches, secondary and tertiary structure prediction. Two hundred and fifty-eight predicted Cytc (with single, double, or multiple heme c attachment sites) were found in some but not all species of the Desulfurococcales, Thermoproteales, Archaeoglobales, Methanosarcinales, Halobacteriales, and in two single-cell genome sequences of the Thermoplasmatales, all of them Cren- or Euryarchaeota. Other archaeal phyla including the Thaumarchaeota are so far free of these proteins. The archaeal Cytc sequences were bundled into 54 clusters of mutual similarity, some of which were specific for Archaea while others had homologs in the Bacteria. The cytochrome c maturation system I (CCM) was the only one found. The highest number and variability of Cytc were present in those species with known or predicted metal oxidation and/or reduction capabilities. Paradoxical findings were made in the haloarchaea: several Cytc had been purified biochemically but corresponding proteins were not found in the proteomes. The results are discussed with emphasis on cell morphologies and envelopes and especially for double-membraned Archaea-like Ignicoccus hospitalis. A comparison is made with compartmentalized bacteria such as the Planctomycetes of the Anammox group with a focus on the putative localization and roles of the Cytc and other electron transport proteins.

Immunogold Localization of Key Metabolic Enzymes in the Anammoxosome and on the Tubule-Like Structures of Kuenenia stuttgartiensis

Anaerobic ammonium-oxidizing (anammox) bacteria oxidize ammonium with nitrite as the terminal electron acceptor to form dinitrogen gas in the absence of oxygen. Anammox bacteria have a compartmentalized cell plan with a central membrane-bound "prokaryotic organelle" called the anammoxosome. The anammoxosome occupies most of the cell volume, has a curved membrane, and contains conspicuous tubule-like structures of unknown identity and function. It was suggested previously that the catalytic reactions of the anammox pathway occur in the anammoxosome, and that proton motive force was established across its membrane. Here, we used antibodies raised against five key enzymes of the anammox catabolism to determine their cellular location. The antibodies were raised against purified native hydroxylamine oxidoreductase-like protein kustc0458 with its redox partner kustc0457, hydrazine dehydrogenase (HDH; kustc0694), hydroxylamine oxidase (HOX; kustc1061), nitrite oxidoreductase (NXR; kustd1700/03/04), and hydrazine synthase (HZS; kuste2859-61) of the anammox bacterium Kuenenia stuttgartiensis. We determined that all five protein complexes were exclusively located inside the anammoxosome matrix. Four of the protein complexes did not appear to form higher-order protein organizations. However, the present data indicated for the first time that NXR is part of the tubule-like structures, which may stretch the whole length of the anammoxosome. These findings support the anammoxosome as the locus of catabolic reactions of the anammox pathway.

IMPORTANCE

Anammox bacteria are environmentally relevant microorganisms that contribute significantly to the release of fixed nitrogen in nature. Furthermore, the anammox process is applied for nitrogen removal from wastewater as an environment-friendly and cost-effective technology. These microorganisms feature a unique cellular organelle, the anammoxosome, which was proposed to contain the energy metabolism of the cell and tubule-like structures with hitherto unknown function. Here, we purified five native enzymes catalyzing key reactions in the anammox metabolism and raised antibodies against these in order to localize them within the cell. We showed that all enzymes were located within the anammoxosome, and nitrite oxidoreductase was located exclusively at the tubule-like structures, providing the first insights into the function of these subcellular structures.

Subcellular localization of an ATPase in anammox bacteria using proteomics and immunogold electron microscopy

Anaerobic ammonium oxidation (anammox) has received significant attention during optimization of waste-water treatment and constitutes an important pathway for the removal of bioavailable nitrogen from natural environments. Studies of key catabolic enzymes indicate that the anammox reaction takes place inside the anammoxosome, an organelle-like membranous compartment of anammox bacteria. The anammoxosome has also been suggested as a site for ATP synthesis. A lipid-based protein immobilization technique, previously used to identify proteins essential for the anammox reaction, was in this study used to select linear epitopes for antibodies specifically targeted against an identified ATPase. The approach of using proteomics and bioinformatics as tools for selecting antibody targets for immunolocalization provides an important alternative to traditional methods for selection of specific antibodies. Immunogold electron microscopy and statistical evaluations indicated that the antibodies against the ATPase were exclusively found associated with the anammoxosome membrane. This provides strong evidence for ATP synthesis by an intracellular proton motive force in anammox bacteria. Within prokaryotes, an ATP synthase associated with an intracellular compartment is a feature unique for anammox bacteria.

A new addition to the cell plan of anammox bacteria: "Candidatus Kuenenia stuttgartiensis" has a protein surface layer as the outermost layer of the cell

Anammox bacteria perform anaerobic ammonium oxidation (anammox) and have a unique compartmentalized cell consisting of three membrane-bound compartments (from inside outwards): the anammoxosome, riboplasm, and paryphoplasm. The cell envelope of anammox bacteria has been proposed to deviate from typical bacterial cell envelopes by lacking both peptidoglycan and a typical outer membrane. However, the composition of the anammox cell envelope is presently unknown. Here, we investigated the outermost layer of the anammox cell and identified a proteinaceous surface layer (S-layer) (a crystalline array of protein subunits) as the outermost component of the cell envelope of the anammox bacterium "Candidatus Kuenenia stuttgartiensis." This is the first description of an S-layer in the phylum of the Planctomycetes and a new addition to the cell plan of anammox bacteria. This S-layer showed hexagonal symmetry with a unit cell consisting of six protein subunits. The enrichment of the S-layer from the cell led to a 160-kDa candidate protein, Kustd1514, which has no homology to any known protein. This protein is present in a glycosylated form. Antibodies were generated against the glycoprotein and used for immunogold localization. The antiserum localized Kustd1514 to the S-layer and thus verified that this protein forms the "Ca. Kuenenia stuttgartiensis" S-layer.

Bioinformatic analyses of integral membrane transport proteins encoded within the genome of the planctomycetes species, Rhodopirellula baltica

Rhodopirellula baltica (R. baltica) is a Planctomycete, known to have intracellular membranes. Because of its unusual cell structure and ecological significance, we have conducted comprehensive analyses of its transmembrane transport proteins. The complete proteome of R. baltica was screened against the Transporter Classification Database (TCDB) to identify recognizable integral membrane transport proteins. 342 proteins were identified with a high degree of confidence, and these fell into several different classes. R. baltica encodes in its genome channels (12%), secondary carriers (33%), and primary active transport proteins (41%) in addition to classes represented in smaller numbers. Relative to most non-marine bacteria, R. baltica possesses a larger number of sodium-dependent symporters but fewer proton-dependent symporters, and it has dimethylsulfoxide (DMSO) and trimethyl-amine-oxide (TMAO) reductases, consistent with its Na(+)-rich marine environment. R. baltica also possesses a Na(+)-translocating NADH:quinone dehydrogenase (Na(+)-NDH), a Na(+) efflux decarboxylase, two Na(+)-exporting ABC pumps, two Na(+)-translocating F-type ATPases, two Na(+):H(+) antiporters and two K(+):H(+) antiporters. Flagellar motility probably depends on the sodium electrochemical gradient. Surprisingly, R. baltica also has a complete set of H(+)-translocating electron transport complexes similar to those present in α-proteobacteria and eukaryotic mitochondria. The transport proteins identified proved to be typical of the bacterial domain with little or no indication of the presence of eukaryotic-type transporters. However, novel functionally uncharacterized multispanning membrane proteins were identified, some of which are found only in Rhodopirellula species, but others of which are widely distributed in bacteria. The analyses lead to predictions regarding the physiology, ecology and evolution of R. baltica.

Identification of the type II cytochrome c maturation pathway in anammox bacteria by comparative genomics

Background

Anaerobic ammonium oxidizing (anammox) bacteria may contribute up to 50% to the global nitrogen production, and are, thus, key players of the global nitrogen cycle. The molecular mechanism of anammox was recently elucidated and is suggested to proceed through a branched respiratory chain. This chain involves an exceptionally high number of c-type cytochrome proteins which are localized within the anammoxosome, a unique subcellular organelle. During transport into the organelle the c-type cytochrome apoproteins need to be post-translationally processed so that heme groups become covalently attached to them, resulting in mature c-type cytochrome proteins.

Results

In this study, a comparative genome analysis was performed to identify the cytochrome c maturation system employed by anammox bacteria. Our results show that all available anammox genome assemblies contain a complete type II cytochrome c maturation system.

Conclusions

Our working model suggests that this machinery is localized at the anammoxosome membrane which is assumed to be the locus of anammox catabolism. These findings will stimulate further studies in dissecting the molecular and cellular basis of cytochrome c biogenesis in anammox bacteria.

From genome mining to phenotypic microarrays: Planctomycetes as source for novel bioactive molecules

Most members of the phylum Planctomycetes share many unusual traits that are unique for bacteria, since they divide independent of FtsZ through asymmetric budding, possess a complex life cycle and comprise a compartmentalized cell plan. Besides their complex cell biological features Planctomycetes are environmentally important and play major roles in global matter fluxes. Such features have been successfully employed in biotechnological applications such as the anaerobic oxidation of ammonium in wastewater treatment plants or the utilization of enzymes for biotechnological processes. However, little is known about planctomycetal secondary metabolites. This is surprising as Planctomycetes have several key features in common with known producers of small bioactive molecules such as Streptomycetes or Myxobacteria: a complex life style and large genome sizes. Planctomycetal genomes with an average size of 6.9 MB appear as tempting targets for drug discovery approaches. To enable the hunt for bioactive molecules from Planctomycetes, we performed a comprehensive genome mining approach employing the antiSMASH secondary metabolite identification pipeline and found 102 candidate genes or clusters within the analyzed 13 genomes. However, as most genes and operons related to secondary metabolite production are exclusively expressed under certain environmental conditions, we optimized Phenotype MicroArray protocols for Rhodopirellula baltica and Planctomyces limnophilus to allow high throughput screening of putative stimulating carbon sources. Our results point towards a previously postulated relationship of Planctomycetes with algae or plants, which secrete compounds that might serve as trigger to stimulate the secondary metabolite production in Planctomycetes. Thus, this study provides the necessary starting point to explore planctomycetal small molecules for drug development.

Cell biology of unique anammox bacteria that contain an energy conserving prokaryotic organelle

Anammox bacteria obtain their energy for growth from the anaerobic oxidation of ammonium with nitrite to dinitrogen gas. This property has made anammox bacteria very valuable for industry where they are applied for the removal of nitrogen compounds from industrial and domestic wastewaters. Anammox bacteria are also important in nature where they contribute significantly to oceanic nitrogen loss. Further, anammox bacteria have similarities to both Archaea and Eukarya, making them extremely interesting from a cell biological perspective. The anammox cell does not conform to the typical prokaryotic cell plan: single bilayer membranes divide the anammox cell into three distinct cellular compartments that possibly also have distinct cellular functions. The innermost and largest compartment, the anammoxosome, is the location of the energy metabolism. The middle compartment, the riboplasm, contains the nucleoid and ribosomes and thus has a genetic, information processing function. Finally, the outermost compartment, the paryphoplasm, has an as yet unknown function. In addition, anammox bacteria are proposed to have an atypical cell wall devoid of both peptidoglycan and a typical outer membrane. Here, I review the current knowledge on the cell biology of this enigmatic group of bacteria.

The PVC superphylum: exceptions to the bacterial definition?

The PVC superphylum is a grouping of distinct phyla of the domain bacteria proposed initially on the basis of 16S rRNA gene sequence analysis. It consists of a core of phyla Planctomycetes, Verrucomicrobia and Chlamydiae, but several other phyla have been considered to be members, including phylum Lentisphaerae and several other phyla consisting only of yet-to-be cultured members. The genomics-based links between Planctomycetes, Verrucomicrobia and Chlamydiae have been recently strengthened, but there appear to be other features which may confirm the relationship at least of Planctomycetes, Verrucomicrobia and Lentisphaerae. Remarkably these include the unique planctomycetal compartmentalized cell plan differing from the cell organization typical for bacteria. Such a shared cell plan suggests that the common ancestor of the PVC superphylum members may also have been compartmentalized, suggesting this is an evolutionarily homologous feature at least within the superphylum. Both the PVC endomembranes and the eukaryote-homologous membrane-coating MC proteins linked to endocytosis ability in Gemmata obscuriglobus and shared by PVC members suggest such homology may extend beyond the bacteria to the Eukarya. If so, either our definition of bacteria may have to change or PVC members admitted to be exceptions. The cases for and against considering the PVC superphylum members as exceptions to the bacteria are discussed, and arguments for them as exceptions presented. Recent critical analysis has favoured convergence and analogy for explaining eukaryote-like features in planctomycetes and other PVC organisms. The case is made for constructing hypotheses leaving the possibility of homology and evolutionary links to eukaryote features open. As the case of discovery of endocytosis-like protein uptake in planctomycetes has suggested, this may prove a strong basis for the immediate future of experimental research programs in the PVC scientific community.

Three-dimensional reconstruction of bacteria with a complex endomembrane system

The apparently complex membrane organization of Gemmata obscuriglobus, and probably all PVC superphylum members, comprises interconnected invaginations and is topologically identical to the “classical” Gram-negative bacterial membrane system.

The division of cellular space into functionally distinct membrane-defined compartments has been one of the major transitions in the history of life. Such compartmentalization has been claimed to occur in members of the Planctomycetes, Verrucomicrobiae, and Chlamydiae bacterial superphylum. Here we have investigated the three-dimensional organization of the complex endomembrane system in the planctomycete bacteria Gemmata obscuriglobus. We reveal that the G. obscuriglobus cells are neither compartmentalized nor nucleated as none of the spaces created by the membrane invaginations are closed; instead, they are all interconnected. Thus, the membrane organization of G. obscuriglobus, and most likely all PVC members, is not different from, but an extension of, the “classical” Gram-negative bacterial membrane system. Our results have implications for our definition and understanding of bacterial cell organization, the genesis of complex structure, and the origin of the eukaryotic endomembrane system.

The compartmentalization of cellular space has been an important evolutionary innovation, allowing for the functional specialization of cellular space. This compartmentalization is extensively developed in eukaryotes and although not as complex and developed, compartments with specialized function are known to occur in bacteria and can be surprisingly sophisticated. Nevertheless, members of the Planctomycetes, Verrucomicrobiae, and Chlamydiae (PVC) bacterial superphylum are exceptional in displaying diverse and extensive intracellular membranous organization. We investigated the three-dimensional organization of the complex endomembrane system in the planctomycete bacterium Gemmata obscuriglobus. We reveal that the G. obscuriglobus cells are neither compartmentalized nor nucleated, contrary to previous claims, as none of the spaces created by the membrane invaginations is topologically closed; instead, they are all interconnected. The organization of cellular space is similar to that of a classical Gram-negative bacterium modified by the presence of large invaginations of the inner membrane inside the cytoplasm. Thus, the membrane organization of G. obscuriglobus, and most likely all PVC members, is not fundamentally different from, but is rather an extension of, the “classical” Gram-negative bacterial membrane system.

The metagenome of the marine anammox bacterium 'Candidatus Scalindua profunda' illustrates the versatility of this globally important nitrogen cycle bacterium

Anaerobic ammonium-oxidizing (anammox) bacteria are responsible for a significant portion of the loss of fixed nitrogen from the oceans, making them important players in the global nitrogen cycle. To date, marine anammox bacteria found in marine water columns and sediments worldwide belong almost exclusively to the 'Candidatus Scalindua' species, but the molecular basis of their metabolism and competitive fitness is presently unknown. We applied community sequencing of a marine anammox enrichment culture dominated by 'Candidatus Scalindua profunda' to construct a genome assembly, which was subsequently used to analyse the most abundant gene transcripts and proteins. In the S. profunda assembly, 4756 genes were annotated, and only about half of them showed the highest identity to the only other anammox bacterium of which a metagenome assembly had been constructed so far, the freshwater 'Candidatus Kuenenia stuttgartiensis'. In total, 2016 genes of S. profunda could not be matched to the K. stuttgartiensis metagenome assembly at all, and a similar number of genes in K.stuttgartiensis could not be found in S. profunda. Most of these genes did not have a known function but 98 expressed genes could be attributed to oligopeptide transport, amino acid metabolism, use of organic acids and electron transport. On the basis of the S. profunda metagenome, and environmental metagenome data, we observed pronounced differences in the gene organization and expression of important anammox enzymes, such as hydrazine synthase (HzsAB), nitrite reductase (NirS) and inorganic nitrogen transport proteins. Adaptations of Scalindua to the substrate limitation of the ocean may include highly expressed ammonium, nitrite and oligopeptide transport systems and pathways for the transport, oxidation, and assimilation of small organic compounds that may allow a more versatile lifestyle contributing to the competitive fitness of Scalindua in the marine realm.

Multiple Rieske/cytb complexes in a single organism

Most organisms contain a single Rieske/cytb complex. This enzyme can be integrated in any respiratory or photosynthetic electron transfer chain that is quinone-based and sufficiently energy rich to allow for the turnover of three enzymes - a quinol reductase, a Rieske/cytb complex and a terminal oxidase. Despite this universal usability of the enzyme a variety of phylogenetically distant organisms have multiple copies thereof and no reason for this redundancy is obvious. In this review we present an overview of the distribution of multiple copies among species and describe their properties from the scarce experimental results, analysis of their amino acid sequences and genomic context. We discuss the predicted redox properties of the Rieske cluster in relation to the nature of the pool quinone. It appears that acidophilic iron-oxidizing bacteria specialized one of their two copies for reverse electron transfer, archaeal Thermoprotei adapted their three copies to the interaction with different oxidases and several, phylogenetically unrelated species imported a second complex with a putative heme ci that may confer some yet to be determined properties to the complex. These hypothesis and all the more the so far completely unexplained cases call for further studies and we put forward a number of suggestions for future research that we hope to be stimulating for the field. This article is part of a Special Issue entitled: Respiratory complex III and related bc complexes.

How to make a living from anaerobic ammonium oxidation

Anaerobic ammonium-oxidizing (anammox) bacteria primarily grow by the oxidation of ammonium coupled to nitrite reduction, using CO2 as the sole carbon source. Although they were neglected for a long time, anammox bacteria are encountered in an enormous species (micro)diversity in virtually any anoxic environment that contains fixed nitrogen. It has even been estimated that about 50% of all nitrogen gas released into the atmosphere is made by these 'impossible' bacteria. Anammox catabolism most likely resides in a special cell organelle, the anammoxosome, which is surrounded by highly unusual ladder-like (ladderane) lipids. Ammonium oxidation and nitrite reduction proceed in a cyclic electron flow through two intermediates, hydrazine and nitric oxide, resulting in the generation of proton-motive force for ATP synthesis. Reduction reactions associated with CO2 fixation drain electrons from this cycle, and they are replenished by the oxidation of nitrite to nitrate. Besides ammonium or nitrite, anammox bacteria use a broad range of organic and inorganic compounds as electron donors. An analysis of the metabolic opportunities even suggests alternative chemolithotrophic lifestyles that are independent of these compounds. We note that current concepts are still largely hypothetical and put forward the most intriguing questions that need experimental answers.

Anammox--growth physiology, cell biology, and metabolism

Anaerobic ammonium-oxidizing (anammox) bacteria are the last major addition to the nitrogen-cycle (N-cycle). Because of the presumed inert nature of ammonium under anoxic conditions, the organisms were deemed to be nonexistent until about 15 years ago. They, however, appear to be present in virtually any anoxic place where fixed nitrogen (ammonium, nitrate, nitrite) is found. In various mar`ine ecosystems, anammox bacteria are a major or even the only sink for fixed nitrogen. According to current estimates, about 50% of all nitrogen gas released into the atmosphere is made by these bacteria. Besides this, the microorganisms may be very well suited to be applied as an efficient, cost-effective, and environmental-friendly alternative to conventional wastewater treatment for the removal of nitrogen. So far, nine different anammox species divided over five genera have been enriched, but none of these are in pure culture. This number is only a modest reflection of a continuum of species that is suggested by 16S rRNA analyses of environmental samples. In their environments, anammox bacteria thrive not just by competition, but rather by delicate metabolic interactions with other N-cycle organisms. Anammox bacteria owe their position in the N-cycle to their unique property to oxidize ammonium in the absence of oxygen. Recent research established that they do so by activating the compound into hydrazine (N(2)H(4)), using the oxidizing power of nitric oxide (NO). NO is produced by the reduction of nitrite, the terminal electron acceptor of the process. The forging of the N-N bond in hydrazine is catalyzed by hydrazine synthase, a fairly slow enzyme and its low activity possibly explaining the slow growth rates and long doubling times of the organisms. The oxidation of hydrazine results in the formation of the end product (N(2)), and electrons that are invested both in electron-transport phosphorylation and in the regeneration of the catabolic intermediates (N(2)H(4), NO). Next to this, the electrons provide the reducing power for CO(2) fixation. The electron-transport phosphorylation machinery represents another unique characteristic, as it is most likely localized on a special cell organelle, the anammoxosome, which is surrounded by a glycerolipid bilayer of ladder-like ("ladderane") cyclobutane and cyclohexane ring structures. The use of ammonium and nitrite as sole substrates might suggest a simple metabolic system, but the contrary seems to be the case. Genome analysis and ongoing biochemical research reveal an only partly understood redundancy in respiratory systems, featuring an unprecedented collection of cytochrome c proteins. The presence of the respiratory systems lends anammox bacteria a metabolic versatility that we are just beginning to appreciate. A specialized use of substrates may provide different anammox species their ecological niche.

Anaerobic ammonium-oxidizing bacteria: unique microorganisms with exceptional properties

Anaerobic ammonium-oxidizing (anammox) bacteria defy many microbiological concepts and share numerous properties with both eukaryotes and archaea. Among their most intriguing characteristics are their compartmentalized cell plan and archaeon-like cell wall. Here we review our current knowledge about anammox cell biology. The anammox cell is divided into three separate compartments by bilayer membranes. The anammox cell consists of (from outside to inside) the cell wall, paryphoplasm, riboplasm, and anammoxosome. Not much is known about the composition or function of both the anammox cell wall and the paryphoplasm compartment. The cell wall is proposed to be proteinaceous and to lack both peptidoglycan and an outer membrane typical of Gram-negative bacteria. The function of the paryphoplasm is unknown, but it contains the cell division ring. The riboplasm resembles the standard cytoplasmic compartment of other bacteria; it contains ribosomes and the nucleoid. The anammoxosome occupies most of the cell volume and is a so-called "prokaryotic organelle" analogous to the eukaryotic mitochondrion. This is the site where the anammox reaction takes place, coupled over the curved anammoxosome membrane, possibly giving rise to a proton motive force and subsequent ATP synthesis. With these unique properties, anammox bacteria are food for thought concerning the early evolution of the domains Bacteria, Archaea, and Eukarya.

Genomic analysis indicates the presence of an asymmetric bilayer outer membrane in planctomycetes and verrucomicrobia

Bacteria of the phylum Planctomycetes are of special interest for the study of compartmental cellular organization. Members of this phylum share a very unusual prokaryotic cell plan, featuring several membrane-bound compartments. Recently, it was shown that this cellular organization might extend to certain members of the phylum Verrucomicrobia. The Planctomycete cell plan has been defined as featuring a proteinaceous cell wall, a cytoplasmic membrane surrounding the paryphoplasm, and an intracytoplasmic membrane defining the riboplasm. So far it was presumed that Planctomycetes did not have an asymmetric bilayer outer membrane as observed in Gram-negative bacteria. However, recent work on outer membrane biogenesis has provided several marker genes in the outer membrane protein (OMP) assembly and the lipopolysaccharide (LPS) insertion complexes. Additionally, advances in computational prediction of OMPs provided new tools to perform more accurate genomic screening for such proteins. Here we searched all 22 Planctomycetes and Verrucomicrobia genomes available in GenBank, plus the recently published genome of "Candidatus Scalindua profunda," for markers of outer membrane biogenesis and OMPs. We were able to identify the key components of LPS insertion, OMP assembly and at least eight OMPs in all genomes tested. Additionally, we have analyzed the transcriptome and proteome data of the Planctomycetes "Candidatus Kuenenia stuttgartiensis" and "Ca. S. profunda" and could confirm high expression of several predicted OMPs, including the biomarkers of outer membrane biogenesis. These analyses provide a strong indication that an asymmetrical outer membrane may be present in bacteria of both phyla. However, previous experiments have made obvious that the cell envelope of Planctomycetes is clearly divergent from both the Gram-negative and Gram-positive cell types. Thus, the functional implications of the presence of an outer membrane for the Planctomycete cell plan and compartmentalization are discussed and a revised model including an outer membrane is proposed. Although this model agrees with most experimental data, we do note that the presence, location, and role of an outer membrane within the Planctomycetes and Verrucomicrobia awaits further experimental validation.

Keys to eukaryality: planctomycetes and ancestral evolution of cellular complexity

Planctomycetes are known to display compartmentalization via internal membranes, thus resembling eukaryotes. Significantly, the planctomycete Gemmata obscuriglobus has not only a nuclear region surrounded by a double-membrane, but is also capable of protein uptake via endocytosis. In order to clearly analyze implications for homology of their characters with eukaryotes, a correct understanding of planctomycete structure is an essential starting point. Here we outline the major features of such structure necessary for assessing the case for or against homology with eukaryote cell complexity. We consider an evolutionary model for cell organization involving reductive evolution of Planctomycetes from a complex proto-eukaryote-like last universal common ancestor, and evaluate alternative models for origins of the unique planctomycete cell plan. Overall, the structural and molecular evidence is not consistent with convergent evolution of eukaryote-like features in a bacterium and favors a homologous relationship of Planctomycetes and eukaryotes.

The ultrastructure of the compartmentalized anaerobic ammonium-oxidizing bacteria is linked to their energy metabolism

The most striking example of a complex prokaryotic intracytoplasmic organization can be found in the members of the phylum Planctomycetes. Among them are the anammox (anaerobic ammonium-oxidizing) bacteria, which possess a unique cell compartment with an unprecedented function in bacteria: the anammoxosome is a prokaryotic cell organelle evolved for energy metabolism. It is an independent entity, which is enclosed by a contiguous membrane. Several lines of evidence indicate its importance in the anammox reaction and the unusual subcellular organization may well be essential for the lifestyle of anammox bacteria. The present review summarizes our knowledge about the ultrastructure of anammox cells and the connection between the anammoxosome and the energy metabolism of the cell. In the future, much more research will be necessary to validate the current models and to answer questions on the functional cell biology of anammox bacteria.

Planctomycetes and eukaryotes: a case of analogy not homology

Planctomycetes, Verrucomicrobia and Chlamydia are prokaryotic phyla, sometimes grouped together as the PVC superphylum of eubacteria. Some PVC species possess interesting attributes, in particular, internal membranes that superficially resemble eukaryotic endomembranes. Some biologists now claim that PVC bacteria are nucleus-bearing prokaryotes and are considered evolutionary intermediates in the transition from prokaryote to eukaryote. PVC prokaryotes do not possess a nucleus and are not intermediates in the prokaryote-to-eukaryote transition. Here we summarise the evidence that shows why all of the PVC traits that are currently cited as evidence for aspiring eukaryoticity are either analogous (the result of convergent evolution), not homologous, to eukaryotic traits; or else they are the result of horizontal gene transfers.

Beyond the bacterium: planctomycetes challenge our concepts of microbial structure and function

Planctomycetes form a distinct phylum of the domain Bacteria and possess unusual features such as intracellular compartmentalization and a lack of peptidoglycan in their cell walls. Remarkably, cells of the genus Gemmata even contain a membrane-bound nucleoid analogous to the eukaryotic nucleus. Moreover, the so-called 'anammox' planctomycetes have a unique anaerobic, autotrophic metabolism that includes the ability to oxidize ammonium; this process is dependent on a characteristic membrane-bound cell compartment called the anammoxosome, which might be a functional analogue of the eukaryotic mitochondrion. The compartmentalization of planctomycetes challenges our hypotheses regarding the origins of eukaryotic organelles. Furthermore, the recent discovery of both an endocytosis-like ability and proteins homologous to eukaryotic clathrin in a planctomycete marks this phylum as one to watch for future research on the origin and evolution of the eukaryotic cell.

Proteins and protein complexes involved in the biochemical reactions of anaerobic ammonium-oxidizing bacteria

It has been less than two decades since anammox (anaerobic ammonium oxidation) coupled to nitrite reduction has been discovered. Already, this process has been recognized as an important sink for fixed nitrogen in the natural environment and has been implemented as a cost-effective ammonium removal technology. Still, little is known about the molecular mechanism of this remarkable reaction. In this mini review, we present an insight into how ammonium and nitrite are combined to form dinitrogen gas.

New insights into the distribution of WXG100 protein secretion systems

Protein secretion is an important aspect of bacterial interaction with the environment. The WXG100 secretion system is a poorly understood pathway for the secretion of members of the WXG100 protein family in Firmicutes and Actinobacteria, notably Mycobacteria. This pathway has also been termed the Type VII secretion system but there are semantic problems with this nomenclature. This Perspective reviews the phylum level distribution of WXG100 secretion systems and presents comparative genomic evidence that these systems are present in several Chloroflexi and in some members of the phyla Cyanobacteria, Lentisphaerae, Proteobacteria (notably Helicobacter pylori) and Verrucomicrobiae. These findings have implications for the nomenclature of the WXG100 secretion pathway.