Anaerobic ammonium-oxidizing bacteria: unique microorganisms with exceptional properties

Occurrence, activity and contribution of anammox in some freshwater extreme environments

Anaerobic ammonium oxidation (anammox) widely occurs in marine ecosystems, and it plays an important role in the global nitrogen cycle. But in freshwater ecosystems its occurrence, distribution and contribution, especially in extreme environments, are still not well known. In this study, anammox process was investigated in some extreme environments of freshwater ecosystems, such as those with high (above 75°C) and low (below -35°C) temperature, high (pH > 8) and low (pH < 4) pH and eutrophy (the concentration of NH4 (+) -N > 300 mg kg(-1) ). The polymerase chain reaction (PCR) screening results showed that anammox bacteria were widespread in the examined sediments from freshwater extreme environments. Quantitative PCR showed that the abundance of anammox bacteria ranged from 6.94 × 10(4) to 8.05 × 10(6) hydrazine synthase (hzsB) gene copies g(-1) dry soil. (15) N-labelled incubation experiments indicated the occurrence of anammox in all examined sediments and the potential anammox rates ranged from 0.02 to 6.24 nmol N g(-1)  h(-1) , with a contribution of 3.45-58.74% of the total N2 production. In summary, these results demonstrate the occurrence of anammox in these extreme environments, inferring that anammox may harbour a wide ecological niche in the freshwater ecosystems.

Impact of Water Chemistry, Pipe Material and Stagnation on the Building Plumbing Microbiome

A unique microbiome establishes in the portion of the potable water distribution system within homes and other buildings (i.e., building plumbing). To examine its composition and the factors that shape it, standardized cold water plumbing rigs were deployed at the treatment plant and in the distribution system of five water utilities across the U.S. Three pipe materials (copper with lead solder, CPVC with brass fittings or copper/lead combined pipe) were compared, with 8 hour flush cycles of 10 minutes to simulate typical daily use patterns. High throughput Illumina sequencing of 16S rRNA gene amplicons was employed to profile and compare the resident bulk water bacteria and archaea. The utility, location of the pipe rig, pipe material and stagnation all had a significant influence on the plumbing microbiome composition, but the utility source water and treatment practices were dominant factors. Examination of 21 water chemistry parameters suggested that the total chlorine concentration, pH, P, SO₄^2- and Mg were associated with the most of the variation in bulk water microbiome composition. Disinfectant type exerted a notably low-magnitude impact on microbiome composition. At two utilities using the same source water, slight differences in treatment approaches were associated with differences in rare taxa in samples. For genera containing opportunistic pathogens, Utility C samples (highest pH of 9–10) had the highest frequency of detection for Legionella spp. and lowest relative abundance of Mycobacterium spp. Data were examined across utilities to identify a true universal core, special core, and peripheral organisms to deepen insight into the physical and chemical factors that shape the building plumbing microbiome.

Bacterial microcompartments: widespread prokaryotic organelles for isolation and optimization of metabolic pathways

Prokaryotes use subcellular compartments for a variety of purposes. An intriguing example is a family of complex subcellular organelles known as bacterial microcompartments (MCPs). MCPs are widely distributed among bacteria and impact processes ranging from global carbon fixation to enteric pathogenesis. Overall, MCPs consist of metabolic enzymes encased within a protein shell, and their function is to optimize biochemical pathways by confining toxic or volatile metabolic intermediates. MCPs are fundamentally different from other organelles in having a complex protein shell rather than a lipid-based membrane as an outer barrier. This unusual feature raises basic questions about organelle assembly, protein targeting and metabolite transport. In this review, we discuss the three best-studied MCPs highlighting atomic-level models for shell assembly, targeting sequences that direct enzyme encapsulation, multivalent proteins that organize the lumen enzymes, the principles of metabolite movement across the shell, internal cofactor recycling, a potential system of allosteric regulation of metabolite transport and the mechanism and rationale behind the functional diversification of the proteins that form the shell. We also touch on some potential biotechnology applications of an unusual compartment designed by nature to optimize metabolic processes within a cellular context.

The dynamics of the bacterial diversity in the redox transition and anoxic zones of the Cariaco Basin assessed by parallel tag sequencing

Massively parallel tag sequencing was applied to describe the bacterial diversity in the redox transition and anoxic zones of the Cariaco Basin. In total, 14 samples from the Cariaco Basin were collected over a period of eight years from two stations. A total of 244 357 unique bacterial V6 amplicons were sequenced. The total number of operational taxonomic units (OTUs) found in this study was 4692, with a range of 511-1491 OTUs per sample. Approximately 95% of the OTUs found in the redox transition zone and anoxic layers of Cariaco are represented by less than 50 amplicons suggesting that only about 5% of the bacterial OTUs are responsible for the bulk of the microbial processes in the basin redox transition and anoxic zones. The same dominant OTUs were observed across all eight years of sampling although periodic fluctuations in their proportion were apparent. No distinctive differences were observed between the bacterial communities from the redox transition and anoxic layers of the Cariaco Basin water column. The largest proportion of amplicons belongs to Gammaproteobacteria represented mostly by sulfide oxidizers, followed by Marine Group A (originally described as SAR406; Gordon and Giovannoni 1996), a group of uncultured bacteria hypothesized to be involved in metal reduction, and sulfate-reducing Deltaproteobacteria. Gammaproteobacteria, Deltaproteobacteria and Marine Group A make up 67-90% of all V6 amplicons sequenced in this study. This strongly suggests that the basin's microbial communities are actively involved in the sulfur-related metabolism and coupling of the sulfur and carbon cycles. According to detrended canonical correspondence analysis, ecological factors such as chemoautotrophy, nitrate and oxidized and reduced sulfur compounds influence the structuring and distribution of the Cariaco microbial communities.

Comparative evaluation of multiple methods to quantify and characterise granular anammox biomass

Six methodologically different approaches were evaluated and compared regarding their suitability to quantify and characterise granular anammox biomass. The investigated techniques were gravimetric analysis (GA), activity measurements (AM), Coulter counter analysis (CC), quantitative PCR (qPCR), heme protein quantification (HQ) and the novel image analysis technique Particle Tracking (PT). The focus was set on the development of fast, economic and user-friendly approaches for potential implementation in regular wastewater treatment plant (WWTP) monitoring. To test the effectiveness of each technique, two sample matrices were chosen at the WWTP Strass (Austria): i) sludge liquor of the DEMON tank, treating ammonium-rich reject water of anaerobic digestion via the deammonification process and rich in anammox biomass (SL), and ii) the mainstream biological stage, that has been enriched with anammox biomass for more than two years (B). In both of these plants hydro-cyclones are installed for density-fractioning of the sludge into a low- and a high-density fraction, thus leading to a characteristic anammox distribution in the investigated sample set. All investigated methods could statistically discriminate the SL samples. Heme quantification and qPCR were also able to correctly classify the B-samples and both methods showed a Pearson's correlation coefficient of 0.81. An asset of the PT and CC method is the additional qualitative characterization of granule size distribution that can help to better understand and optimise general process operation (cyclone operation duration and construction characteristics). In combination these two methods were able to elucidate the relationship of gross granule volume and actual biomass, excluding the dead volume of inner cavities and exopolymers. We found a linear sphere-equivalent-radius correction factor (3.96 ± 0.15) for investigated anammox granules, that can be used for the fast and reliable PT technique to avoid biomass overestimation. We also recommend routine HQ and PT analysis as ideal monitoring strategy for anammox abundance in wastewater facilities with the HQ technique entailing the further advantage of being also suited for non-granular anammox biomass.

Metal enzymes in "impossible" microorganisms catalyzing the anaerobic oxidation of ammonium and methane

Ammonium and methane are inert molecules and dedicated enzymes are required to break up the N-H and C-H bonds. Until recently, only aerobic microorganisms were known to grow by the oxidation of ammonium or methane. Apart from respiration, oxygen was specifically utilized to activate the inert substrates. The presumed obligatory need for oxygen may have resisted the search for microorganisms that are capable of the anaerobic oxidation of ammonium and of methane. However extremely slowly growing, these "impossible" organisms exist and they found other means to tackle ammonium and methane. Anaerobic ammonium-oxidizing (anammox) bacteria use the oxidative power of nitric oxide (NO) by forging this molecule to ammonium, thereby making hydrazine (N2H4). Nitrite-dependent anaerobic methane oxidizers (N-DAMO) again take advantage of NO, but now apparently disproportionating the compound into dinitrogen and dioxygen gas. This intracellularly produced dioxygen enables N-DAMO bacteria to adopt an aerobic mechanism for methane oxidation.Although our understanding is only emerging how hydrazine synthase and the NO dismutase act, it seems clear that reactions fully rely on metal-based catalyses known from other enzymes. Metal-dependent conversions not only hold for these key enzymes, but for most other reactions in the central catabolic pathways, again supported by well-studied enzymes from model organisms, but adapted to own specific needs. Remarkably, those accessory catabolic enzymes are not unique for anammox bacteria and N-DAMO. Close homologs are found in protein databases where those homologs derive from (partly) known, but in most cases unknown species that together comprise an only poorly comprehended microbial world.

Physiological characterization of anaerobic ammonium oxidizing bacterium 'Candidatus Jettenia caeni'

To date, six candidate genera of anaerobic ammonium-oxidizing (anammox) bacteria have been identified, and numerous studies have been conducted to understand their ecophysiology. In this study, we examined the physiological characteristics of an anammox bacterium in the genus 'Candidatus Jettenia'. Planctomycete KSU-1 was found to be a mesophilic (20-42.5°C) and neutrophilic (pH 6.5-8.5) bacterium with a maximum growth rate of 0.0020 h(-1) . Planctomycete KSU-1 cells showed typical physiological and structural features of anammox bacteria; i.e. (29) N2 gas production by coupling of (15) NH4 (+) and (14) NO2 (-) , accumulation of hydrazine with the consumption of hydroxylamine and the presence of anammoxosome. In addition, the cells were capable of respiratory ammonification with oxidation of acetate. Notably, the cells contained menaquinone-7 as a dominant respiratory quinone. Proteomic analysis was performed to examine underlying core metabolisms, and high expressions of hydrazine synthase, hydrazine dehydrogenase, hydroxylamine dehydrogenase, nitrite/nitrate oxidoreductase and carbon monoxide dehydrogenase/acetyl-CoA synthase were detected. These proteins require iron or copper as a metal cofactor, and both were dominant in planctomycete KSU-1 cells. On the basis of these experimental results, we proposed the name 'Ca. Jettenia caeni' sp. nov. for the bacterial clade of the planctomycete KSU-1.

A taxonomy of bacterial microcompartment loci constructed by a novel scoring method

Bacterial microcompartments (BMCs) are proteinaceous organelles involved in both autotrophic and heterotrophic metabolism. All BMCs share homologous shell proteins but differ in their complement of enzymes; these are typically encoded adjacent to shell protein genes in genetic loci, or operons. To enable the identification and prediction of functional (sub)types of BMCs, we developed LoClass, an algorithm that finds putative BMC loci and inventories, weights, and compares their constituent pfam domains to construct a locus similarity network and predict locus (sub)types. In addition to using LoClass to analyze sequences in the Non-redundant Protein Database, we compared predicted BMC loci found in seven candidate bacterial phyla (six from single-cell genomic studies) to the LoClass taxonomy. Together, these analyses resulted in the identification of 23 different types of BMCs encoded in 30 distinct locus (sub)types found in 23 bacterial phyla. These include the two carboxysome types and a divergent set of metabolosomes, BMCs that share a common catalytic core and process distinct substrates via specific signature enzymes. Furthermore, many Candidate BMCs were found that lack one or more core metabolosome components, including one that is predicted to represent an entirely new paradigm for BMC-associated metabolism, joining the carboxysome and metabolosome. By placing these results in a phylogenetic context, we provide a framework for understanding the horizontal transfer of these loci, a starting point for studies aimed at understanding the evolution of BMCs. This comprehensive taxonomy of BMC loci, based on their constituent protein domains, foregrounds the functional diversity of BMCs and provides a reference for interpreting the role of BMC gene clusters encoded in isolate, single cell, and metagenomic data. Many loci encode ancillary functions such as transporters or genes for cofactor assembly; this expanded vocabulary of BMC-related functions should be useful for design of genetic modules for introducing BMCs in bioengineering applications.

Some enzymatic transformations have undesirable side reactions, produce toxic or volatile intermediates, or are inefficient; these shortcomings can be alleviated through their sequestration with their substrates in a confined space, as in the membrane-bound organelles of eukaryotes. Recently, it was discovered that bacteria also form organelles–bacterial microcompartments (BMCs)–composed of a protein shell that surrounds functionally related enzymes. BMCs long evaded detection because they typically form only in the presence of the substrate they metabolize, and they can only be visualized by electron microscopy. A few BMCs have been experimentally characterized; they have diverse functions in CO₂ fixation, pathogenesis, and niche colonization. While the encapsulated enzymes differ among functionally distinct BMCs, the shell architecture is conserved. This enables their detection computationally, as genes for shell proteins are typically nearby genes for the encapsulated enzymes. We developed a novel algorithm to comprehensively identify and categorize BMCs in sequenced bacterial genomes. We show that BMCs are often encoded adjacent to genes that play supporting roles to the organelle's function. Our results provide the first glimpse of the extent of BMC metabolic diversity and will inform design of genetic modules encoding BMCs for introduction of new metabolic functions in a plug-and-play approach.

Nitrososphaera viennensis gen. nov., sp. nov., an aerobic and mesophilic, ammonia-oxidizing archaeon from soil and a member of the archaeal phylum Thaumarchaeota

A mesophilic, neutrophilic and aerobic, ammonia-oxidizing archaeon, strain EN76(T), was isolated from garden soil in Vienna (Austria). Cells were irregular cocci with a diameter of 0.6-0.9 µm and possessed archaella and archaeal pili as cell appendages. Electron microscopy also indicated clearly discernible areas of high and low electron density, as well as tubule-like structures. Strain EN76(T) had an S-layer with p3 symmetry, so far only reported for members of the Sulfolobales. Crenarchaeol was the major core lipid. The organism gained energy by oxidizing ammonia to nitrite aerobically, thereby fixing CO2, but growth depended on the addition of small amounts of organic acids. The optimal growth temperature was 42 °C and the optimal pH was 7.5, with ammonium and pyruvate concentrations of 2.6 and 1 mM, respectively. The genome of strain EN76(T) had a DNA G+C content of 52.7 mol%. Phylogenetic analyses of 16S rRNA genes showed that strain EN76(T) is affiliated with the recently proposed phylum Thaumarchaeota, sharing 85% 16S rRNA gene sequence identity with the closest cultivated relative 'Candidatus Nitrosopumilus maritimus' SCM1, a marine ammonia-oxidizing archaeon, and a maximum of 81% 16S rRNA gene sequence identity with members of the phyla Crenarchaeota and Euryarchaeota and any of the other recently proposed phyla (e.g. 'Korarchaeota' and 'Aigarchaeota'). We propose the name Nitrososphaera viennensis gen. nov., sp. nov. to accommodate strain EN76(T). The type strain of Nitrososphaera viennensis is strain EN76(T) ( = DSM 26422(T) = JMC 19564(T)). Additionally, we propose the family Nitrososphaeraceae fam. nov., the order Nitrososphaerales ord. nov. and the class Nitrososphaeria classis nov.

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.

Host-specific assemblages typify gut microbial communities of related insect species

Mutualisms between microbes and insects are ubiquitous and facilitate exploitation of various trophic niches by host insects. Dictyopterans (mantids, cockroaches and termites) exhibit trophisms that range from omnivory to strict wood-feeding and maintain beneficial symbioses with the obligate endosymbiont, Blattabacterium, and/or diverse gut microbiomes that include cellulolytic and diazotrophic microbes. While Blattabacterium in omnivorous Periplaneta is fully capable of provisioning essential amino acids, in wood-feeding dictyopterans it has lost many genes for their biosynthesis (Mastotermes and Cryptocercus) or is completely absent (Heterotermes). The conspicuous functional degradation and absence of Blattabacterium in most strict wood-feeding dictyopteran insects suggest that alternative means of acquiring nutrients limited in their diet are being employed. A 16S rRNA gene amplicon resequencing approach was used to deeply sample the composition and diversity of gut communities in related dictyopteran insects to explore the possibility of shifts in symbiont allegiances during termite and cockroach evolution. The gut microbiome of Periplaneta, which has a fully functional Blattabacterium, exhibited the greatest within-sample operational taxonomic unit (OTU) diversity and abundance variability than those of Mastotermes and Cryptocercus, whose Blattabacterium have shrunken genomes and reduced nutrient provisioning capabilities. Heterotermes lacks Blattabacterium and a single OTU that was 95% identical to a Bacteroidia-assigned diazotrophic endosymbiont of an anaerobic cellulolytic protist termite gut inhabitant samples consistently dominates its gut microbiome. Many host-specific OTUs were identified in all host genera, some of which had not been previously detected, indicating that deep sampling by pyrotag sequencing has revealed new taxa that remain to be functionally characterized. Further analysis is required to uncover how consistently detected taxa in the cockroach and termite gut microbiomes, as well as the total community, contribute to host diet choice and impact the fate of Blattabacterium in dictyopterans.

Shotgun metagenomic data reveals significant abundance but low diversity of "Candidatus Scalindua" marine anammox bacteria in the Arabian Sea oxygen minimum zone

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 both water columns and sediments worldwide belong almost exclusively to “Candidatus Scalindua” species. Recently the genome assembly of a marine anammox enrichment culture dominated by “Candidatus Scalindua profunda” became available and can now be used as a template to study metagenome data obtained from various oxygen minimum zones (OMZs). Here, we sequenced genomic DNA from suspended particulate matter recovered at the upper (170 m deep) and center (600 m) area of the OMZ in the Arabian Sea by SOLiD and Ion Torrent technology. The genome of “Candidatus Scalindua profunda” served as a template to collect reads. Based on the mapped reads marine anammox Abundance was estimated to be at least 0.4% in the upper and 1.7% in the center area. Single nucleotide variation (SNV) analysis was performed to assess diversity of the “Candidatus Scalindua” populations. Most highly covered were the two diagnostic anammox genes hydrazine synthase (scal_01318c, hzsA) and hydrazine dehydrogenase (scal_03295, hdh), while other genes involved in anammox metabolism (narGH, nirS, amtB, focA, and ACS) had a lower coverage but could still be assembled and analyzed. The results show that “Candidatus Scalindua” is abundantly present in the Arabian Sea OMZ, but that the diversity within the ecosystem is relatively low.

Characterization of a planctomycetal organelle: a novel bacterial microcompartment for the aerobic degradation of plant saccharides

Bacterial microcompartments (BMCs) are organelles that encapsulate functionally linked enzymes within a proteinaceous shell. The prototypical example is the carboxysome, which functions in carbon fixation in cyanobacteria and some chemoautotrophs. It is increasingly apparent that diverse heterotrophic bacteria contain BMCs that are involved in catabolic reactions, and many of the BMCs are predicted to have novel functions. However, most of these putative organelles have not been experimentally characterized. In this study, we sought to discover the function of a conserved BMC gene cluster encoded in the majority of the sequenced planctomycete genomes. This BMC is especially notable for its relatively simple genetic composition, its remote phylogenetic position relative to characterized BMCs, and its apparent exclusivity to the enigmatic Verrucomicrobia and Planctomycetes. Members of the phylum Planctomycetes are known for their morphological dissimilarity to the rest of the bacterial domain: internal membranes, reproduction by budding, and lack of peptidoglycan. As a result, they are ripe for many discoveries, but currently the tools for genetic studies are very limited. We expanded the genetic toolbox for the planctomycetes and generated directed gene knockouts of BMC-related genes in Planctomyces limnophilus. A metabolic activity screen revealed that BMC gene products are involved in the degradation of a number of plant and algal cell wall sugars. Among these sugars, we confirmed that BMCs are formed and required for growth on l-fucose and l-rhamnose. Our results shed light on the functional diversity of BMCs as well as their ecological role in the planctomycetes, which are commonly associated with algae.

Pre-exposure to nitrite in the absence of ammonium strongly inhibits anammox

Anaerobic ammonium oxidizing bacteria (Anammox) are known to be inhibited by their substrate, nitrite. However, the mechanism of inhibition and the physiological conditions under which nitrite impacts the performance of anammox bioreactors are still unknown. This study investigates the role of pre-exposing anammox bacteria to nitrite alone on their subsequent activity and metabolism after ammonium has been added. Batch experiments were carried out with anammox granular biofilm pre-exposed to nitrite over a range of concentrations and durations in the absence of ammonium. The effect of pre-exposure to nitrite alone compared to nitrite simultaneously fed with ammonium was evaluated by measuring the anammox activity and the accumulation of the intermediate, nitric oxide. The results show that the inhibitory effect was more dramatic when bacteria were pre-exposed to nitrite in absence of ammonium, as revealed by the lower activity and the higher accumulation of nitric oxide. The nitrite concentration causing 50% inhibition was 53 and 384 mg N L(-1) in the absence or the presence of ammonium, respectively. The nitrite inhibition was thus 7.2-fold more severe in the absence of ammonium. Biomass exposure to nitrite (25 mg N L(-1)), in absence of ammonium, led to accumulation of nitric oxide. On the other hand when the biomass was exposed to nitrite in presence of ammonium, accumulation of nitric oxide was only observed at much higher nitrite concentrations (500 mg N L(-1)). The inhibitory effect of nitrite in the absence of ammonium was very rapid. The rate of decay of the anammox activity was equivalent to the diffusion rate of nitrite up to 46% of activity loss. The results taken as a whole suggest that nitrite inhibition is more acute when anammox cells are not actively metabolizing. Accumulation of nitric oxide in the headspace most likely indicates disruption of the anammox biochemistry by nitrite inhibition, caused by an interruption of the hydrazine synthesis step.

Cultivation of planktonic anaerobic ammonium oxidation (anammox) bacteria using membrane bioreactor

Enrichment cultures of anaerobic ammonium oxidation (anammox) bacteria as planktonic cell suspensions are essential for studying their ecophysiology and biochemistry, while their cultivation is still laborious. The present study aimed to cultivate two phylogenetically distinct anammox bacteria, "Candidatus Brocadia sinica" and "Ca. Scalindua sp." in the form of planktonic cells using membrane bioreactors (MBRs). The MBRs were continuously operated for more than 250 d with nitrogen loading rates of 0.48-1.02 and 0.004-0.09 kgN m(-3) d(-1) for "Ca. Brocadia sinica" and "Ca. Scalindua sp.", respectively. Planktonic anammox bacterial cells were successfully enriched (>90%) in the MBRs, which was confirmed by fluorescence in-situ hybridization and 16S rRNA gene sequencing analysis. The decay rate and half-saturation constant for NO2(-) of "Ca. Brocadia sinica" were determined to be 0.0029-0.0081 d(-1) and 0.47 mgN L(-1), respectively, using enriched planktonic cells. The present study demonstrated that MBR enables the culture of planktonic anammox bacterial cells, which are suitable for studying their ecophysiology and biochemistry.

Lysozyme and penicillin inhibit the growth of anaerobic ammonium-oxidizing planctomycetes

Anaerobic ammonium-oxidizing (anammox) planctomycetes oxidize ammonium in the absence of molecular oxygen with nitrite as the electron acceptor. Although planctomycetes are generally assumed to lack peptidoglycan in their cell walls, recent genome data imply that the anammox bacteria have the genes necessary to synthesize peptidoglycan-like cell wall structures. In this study, we investigated the effects of two antibacterial agents that target the integrity and synthesis of peptidoglycan (lysozyme and penicillin G) on the anammox bacterium Kuenenia stuttgartiensis. The effects of these compounds were determined in both short-term batch incubations and long-term (continuous-cultivation) growth experiments in membrane bioreactors. Lysozyme at 1 g/liter (20 mM EDTA) lysed anammox cells in less than 60 min, whereas penicillin G did not have any observable short-term effects on anammox activity. Penicillin G (0.5, 1, and 5 g/liter) reversibly inhibited the growth of anammox bacteria in continuous-culture experiments. Furthermore, transcriptome analyses of the penicillin G-treated reactor and the control reactor revealed that penicillin G treatment resulted in a 10-fold decrease in the ribosome levels of the cells. One of the cell division proteins (Kustd1438) was downregulated 25-fold. Our results suggested that anammox bacteria contain peptidoglycan-like components in their cell wall that can be targeted by lysozyme and penicillin G-sensitive proteins were involved in their synthesis. Finally, we showed that a continuous membrane reactor system with free-living planktonic cells was a very powerful tool to study the physiology of slow-growing microorganisms under physiological conditions.

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.

Nitrate-dependent ferrous iron oxidation by anaerobic ammonium oxidation (anammox) bacteria

We examined nitrate-dependent Fe(2+) oxidation mediated by anaerobic ammonium oxidation (anammox) bacteria. Enrichment cultures of "Candidatus Brocadia sinica" anaerobically oxidized Fe(2+) and reduced NO3(-) to nitrogen gas at rates of 3.7 ± 0.2 and 1.3 ± 0.1 (mean ± standard deviation [SD]) nmol mg protein(-1) min(-1), respectively (37°C and pH 7.3). This nitrate reduction rate is an order of magnitude lower than the anammox activity of "Ca. Brocadia sinica" (10 to 75 nmol NH4(+) mg protein(-1) min(-1)). A (15)N tracer experiment demonstrated that coupling of nitrate-dependent Fe(2+) oxidation and the anammox reaction was responsible for producing nitrogen gas from NO3(-) by "Ca. Brocadia sinica." The activities of nitrate-dependent Fe(2+) oxidation were dependent on temperature and pH, and the highest activities were seen at temperatures of 30 to 45°C and pHs ranging from 5.9 to 9.8. The mean half-saturation constant for NO3(-) ± SD of "Ca. Brocadia sinica" was determined to be 51 ± 21 μM. Nitrate-dependent Fe(2+) oxidation was further demonstrated by another anammox bacterium, "Candidatus Scalindua sp.," whose rates of Fe(2+) oxidation and NO3(-) reduction were 4.7 ± 0.59 and 1.45 ± 0.05 nmol mg protein(-1) min(-1), respectively (20°C and pH 7.3). Co-occurrence of nitrate-dependent Fe(2+) oxidation and the anammox reaction decreased the molar ratios of consumed NO2(-) to consumed NH4(+) (ΔNO2(-)/ΔNH4(+)) and produced NO3(-) to consumed NH4(+) (ΔNO3(-)/ΔNH4(+)). These reactions are preferable to the application of anammox processes for wastewater treatment.

Molecular detection of Candidatus Scalindua pacifica and environmental responses of sediment anammox bacterial community in the Bohai Sea, China

The Bohai Sea is a large semi-enclosed shallow water basin, which receives extensive river discharges of various terrestrial and anthropogenic materials such as sediments, nutrients and contaminants. How these terrigenous inputs may influence the diversity, community structure, biogeographical distribution, abundance and ecophysiology of the sediment anaerobic ammonium oxidation (anammox) bacteria was unknown. To answer this question, an investigation employing both 16S rRNA and hzo gene biomarkers was carried out. Ca. Scalindua bacteria were predominant in the surface sediments of the Bohai Sea, while non-Scalindua anammox bacteria were also detected in the Yellow River estuary and inner part of Liaodong Bay that received strong riverine and anthropogenic impacts. A novel 16S rRNA gene sequence clade was identified, putatively representing an anammox bacterial new candidate species tentatively named "Ca. Scalindua pacifica". Several groups of environmental factors, usually with distinct physicochemical or biogeochemical natures, including general marine and estuarine physicochemical properties, availability of anammox substrates (inorganic N compounds), alternative reductants and oxidants, environmental variations caused by river discharges and associated contaminants such as heavy metals, were identified to likely play important roles in influencing the ecology and biogeochemical functioning of the sediment anammox bacteria. In addition to inorganic N compounds that might play a key role in shaping the anammox microbiota, organic carbon, organic nitrogen, sulfate, sulfide and metals all showed the potentials to participate in the anammox process, releasing the strict dependence of the anammox bacteria upon the direct availability of inorganic N nutrients that might be limiting in certain areas of the Bohai Sea. The importance of inorganic N nutrients and certain other environmental factors to the sediment anammox microbiota suggests that these bacteria were active for the in situ N transforming process and maintained a versatile life style well adapted to the varying environmental conditions of the studied coastal ocean.

The prokaryotic Mo/W-bisPGD enzymes family: a catalytic workhorse in bioenergetic

Over the past two decades, prominent importance of molybdenum-containing enzymes in prokaryotes has been put forward by studies originating from different fields. Proteomic or bioinformatic studies underpinned that the list of molybdenum-containing enzymes is far from being complete with to date, more than fifty different enzymes involved in the biogeochemical nitrogen, carbon and sulfur cycles. In particular, the vast majority of prokaryotic molybdenum-containing enzymes belong to the so-called dimethylsulfoxide reductase family. Despite its extraordinary diversity, this family is characterized by the presence of a Mo/W-bis(pyranopterin guanosine dinucleotide) cofactor at the active site. This review highlights what has been learned about the properties of the catalytic site, the modular variation of the structural organization of these enzymes, and their interplay with the isoprenoid quinones. In the last part, this review provides an integrated view of how these enzymes contribute to the bioenergetics of prokaryotes. This article is part of a Special Issue entitled: Metals in Bioenergetics and Biomimetics Systems.

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.

Metagenome Analysis of a Complex Community Reveals the Metabolic Blueprint of Anammox Bacterium "Candidatus Jettenia asiatica"

Anaerobic ammonium-oxidizing (anammox) bacteria are key players in the global nitrogen cycle and responsible for significant global nitrogen loss. Moreover, the anammox process is widely implemented for nitrogen removal from wastewaters as a cost-effective and environment-friendly alternative to conventional nitrification-denitrification systems. Currently, five genera of anammox bacteria have been identified, together forming a deep-branching order in the Planctomycetes-Verrucomicrobium-Chlamydiae superphylum. Members of all genera have been detected in wastewater treatment plants and have been enriched in lab-scale bioreactors, but genome information is not yet available for all genera. Here we report the metagenomic analysis of a granular sludge anammox reactor dominated (∼50%) by “Candidatus Jettenia asiatica.” The metagenome was sequenced using both Illumina and 454 pyrosequencing. After de novo assembly 37,432 contigs with an average length of 571 nt were obtained. The contigs were then analyzed by BLASTx searches against the protein sequences of “Candidatus Kuenenia stuttgartiensis” and a set of 25 genes essential in anammox metabolism were detected. Additionally all reads were mapped to the genome of an anammox strain KSU-1 and de novo assembly was performed again using the reads that could be mapped on KSU-1. Using this approach, a gene encoding copper-containing nitrite reductase NirK was identified in the genome, instead of cytochrome cd₁-type nitrite reductase (NirS, present in “Ca. Kuenenia stuttgartiensis” and “Ca. Scalindua profunda”). Finally, the community composition was investigated through MetaCluster analysis, 16S rRNA gene analysis and read mapping, which showed the presence of other important community members such as aerobic ammonia-oxidizing bacteria, methanogens, and the denitrifying methanotroph “Ca. Methylomirabilis oxyfera”, indicating a possible active methane and nitrogen cycle in the bioreactor under the prevailing operational conditions.