The impact of genome analyses on our understanding of ammonia-oxidizing bacteria

Microbial responses to changes in flow status in temporary headwater streams: a cross-system comparison

Microbial communities are responsible for the bulk of biogeochemical processing in temporary headwater streams, yet there is still relatively little known about how community structure and function respond to periodic drying. Moreover, the ability to sample temporary habitats can be a logistical challenge due to the limited capability to measure and predict the timing, intensity and frequency of wet-dry events. Unsurprisingly, published datasets on microbial community structure and function are limited in scope and temporal resolution and vary widely in the molecular methods applied. We compared environmental and microbial community datasets for permanent and temporary tributaries of two different North American headwater stream systems: Speed River (Ontario, Canada) and Parkers Creek (Maryland, USA). We explored whether taxonomic diversity and community composition were altered as a result of flow permanence and compared community composition amongst streams using different 16S microbial community methods (i.e., T-RFLP and Illumina MiSeq). Contrary to our hypotheses, and irrespective of method, community composition did not respond strongly to drying. In both systems, community composition was related to site rather than drying condition. Additional network analysis on the Parkers Creek dataset indicated a shift in the central microbial relationships between temporary and permanent streams. In the permanent stream at Parkers Creek, associations of methanotrophic taxa were most dominant, whereas associations with taxa from the order Nitrospirales were more dominant in the temporary stream, particularly during dry conditions. We compared these results with existing published studies from around the world and found a wide range in community responses to drying. We conclude by proposing three hypotheses that may address contradictory results and, when tested across systems, may expand understanding of the responses of microbial communities in temporary streams to natural and human-induced fluctuations in flow-status and permanence.

Metabolic engineering in methanotrophic bacteria

Methane, as natural gas or biogas, is the least expensive source of carbon for (bio)chemical synthesis. Scalable biological upgrading of this simple alkane to chemicals and fuels can bring new sustainable solutions to a number of industries with large environmental footprints, such as natural gas/petroleum production, landfills, wastewater treatment, and livestock. Microbial biocatalysis with methane as a feedstock has been pursued off and on for almost a half century, with little enduring success. Today, biological engineering and systems biology provide new opportunities for metabolic system modulation and give new optimism to the concept of a methane-based bio-industry. Here we present an overview of the most recent advances pertaining to metabolic engineering of microbial methane utilization. Some ideas concerning metabolic improvements for production of acetyl-CoA and pyruvate, two main precursors for bioconversion, are presented. We also discuss main gaps in the current knowledge of aerobic methane utilization, which must be solved in order to release the full potential of methane-based biosystems.

Genomic and proteomic characterization of "Candidatus Nitrosopelagicus brevis": an ammonia-oxidizing archaeon from the open ocean

Thaumarchaeota are among the most abundant microbial cells in the ocean, but difficulty in cultivating marine Thaumarchaeota has hindered investigation into the physiological and evolutionary basis of their success. We report here a closed genome assembled from a highly enriched culture of the ammonia-oxidizing pelagic thaumarchaeon CN25, originating from the open ocean. The CN25 genome exhibits strong evidence of genome streamlining, including a 1.23-Mbp genome, a high coding density, and a low number of paralogous genes. Proteomic analysis recovered nearly 70% of the predicted proteins encoded by the genome, demonstrating that a high fraction of the genome is translated. In contrast to other minimal marine microbes that acquire, rather than synthesize, cofactors, CN25 encodes and expresses near-complete biosynthetic pathways for multiple vitamins. Metagenomic fragment recruitment indicated the presence of DNA sequences >90% identical to the CN25 genome throughout the oligotrophic ocean. We propose the provisional name "Candidatus Nitrosopelagicus brevis" str. CN25 for this minimalist marine thaumarchaeon and suggest it as a potential model system for understanding archaeal adaptation to the open ocean.

Synthesis and characterization of ammonia-responsive polymer microgels

We report a polymer microgel that can undergo rapid, reversible, and highly-sensitive volume phase transitions upon varying ammonia concentrations in milieu.

Seasonality and depth distribution of the abundance and activity of ammonia oxidizing microorganisms in marine coastal sediments (North Sea)

Microbial processes such as nitrification and anaerobic ammonium oxidation (anammox) are important for nitrogen cycling in marine sediments. Seasonal variations of archaeal and bacterial ammonia oxidizers (AOA and AOB) and anammox bacteria, as well as the environmental factors affecting these groups, are not well studied. We have examined the seasonal and depth distribution of the abundance and potential activity of these microbial groups in coastal marine sediments of the southern North Sea. This was achieved by quantifying specific intact polar lipids as well as the abundance and gene expression of their 16S rRNA gene, the ammonia monooxygenase subunit A (amoA) gene of AOA and AOB, and the hydrazine synthase (hzsA) gene of anammox bacteria. AOA, AOB, and anammox bacteria were detected and transcriptionally active down to 12 cm sediment depth. In all seasons, the abundance of AOA was higher compared to the AOB abundance suggesting that AOA play a more dominant role in aerobic ammonia oxidation in these sediments. Anammox bacteria were abundant and active even in oxygenated and bioturbated parts of the sediment. The abundance of AOA and AOB was relatively stable with depth and over the seasonal cycle, while anammox bacteria abundance and transcriptional activity were highest in August. North Sea sediments thus seem to provide a common, stable, ecological niche for AOA, AOB, and anammox bacteria.

Characterisation of terrestrial acidophilic archaeal ammonia oxidisers and their inhibition and stimulation by organic compounds

Autotrophic ammonia oxidation is performed by two distinct groups of microorganisms: ammonia-oxidising archaea (AOA) and ammonia-oxidising bacteria (AOB). AOA outnumber their bacterial counterparts in many soils, at times by several orders of magnitude, but relatively little is known of their physiology due to the lack of cultivated isolates. Although a number of AOA have been cultivated from soil, Nitrososphaera viennensis was the sole terrestrial AOA in pure culture and requires pyruvate for growth in the laboratory. Here, we describe isolation in pure culture and characterisation of two acidophilic terrestrial AOA representing the Candidatus genus Nitrosotalea and their responses to organic acids. Interestingly, despite their close phylogenetic relatedness, the two Nitrosotalea strains exhibited differences in physiological features, including specific growth rate, temperature preference and to an extent, response to organic compounds. In contrast to N. viennensis, both Nitrosotalea isolates were inhibited by pyruvate but their growth yield increased in the presence of oxaloacetate. This study demonstrates physiological diversity within AOA species and between different AOA genera. Different preferences for organic compounds potentially influence the favoured localisation of ammonia oxidisers within the soil and the structure of ammonia-oxidising communities in terrestrial ecosystems.

The history of aerobic ammonia oxidizers: from the first discoveries to today

Nitrification, the oxidation of ammonia to nitrite and nitrate, has long been considered a central biological process in the global nitrogen cycle, with its first description dated 133 years ago. Until 2005, bacteria were considered the only organisms capable of nitrification. However, the recent discovery of a chemoautotrophic ammonia-oxidizing archaeon, Nitrosopumilus maritimus, changed our concept of the range of organisms involved in nitrification, highlighting the importance of ammonia-oxidizing archaea (AOA) as potential players in global biogeochemical nitrogen transformations. The uniqueness of these archaea justified the creation of a novel archaeal phylum, Thaumarchaeota. These recent discoveries increased the global scientific interest within the microbial ecology society and have triggered an analysis of the importance of bacterial vs archaeal ammonia oxidation in a wide range of natural ecosystems. In this mini review we provide a chronological perspective of the current knowledge on the ammonia oxidation pathway of nitrification, based on the main physiological, ecological and genomic discoveries.

Revision of N2O-producing pathways in the ammonia-oxidizing bacterium Nitrosomonas europaea ATCC 19718

Nitrite reductase (NirK) and nitric oxide reductase (NorB) have long been thought to play an essential role in nitrous oxide (N2O) production by ammonia-oxidizing bacteria. However, essential gaps remain in our understanding of how and when NirK and NorB are active and functional, putting into question their precise roles in N2O production by ammonia oxidizers. The growth phenotypes of the Nitrosomonas europaea ATCC 19718 wild-type and mutant strains deficient in expression of NirK, NorB, and both gene products were compared under atmospheric and reduced O2 tensions. Anoxic resting-cell assays and instantaneous nitrite (NO2 (-)) reduction experiments were done to assess the ability of the wild-type and mutant N. europaea strains to produce N2O through the nitrifier denitrification pathway. Results confirmed the role of NirK for efficient substrate oxidation of N. europaea and showed that NorB is involved in N2O production during growth at both atmospheric and reduced O2 tensions. Anoxic resting-cell assays and measurements of instantaneous NO2 (-) reduction using hydrazine as an electron donor revealed that an alternate nitrite reductase to NirK is present and active. These experiments also clearly demonstrated that NorB was the sole nitric oxide reductase for nitrifier denitrification. The results of this study expand the enzymology for nitrogen metabolism and N2O production by N. europaea and will be useful to interpret pathways in other ammonia oxidizers that lack NirK and/or NorB genes.

Impacts of bioturbation on temporal variation in bacterial and archaeal nitrogen-cycling gene abundance in coastal sediments

In marine environments, macrofauna living in or on the sediment surface may alter the structure, diversity and function of benthic microbial communities. In particular, microbial nitrogen (N)-cycling processes may be enhanced by the activity of large bioturbating organisms. Here, we study the effect of the burrowing mud shrimp Upogebia deltaura upon temporal variation in the abundance of genes representing key N-cycling functional guilds. The abundance of bacterial genes representing different N-cycling guilds displayed different temporal patterns in burrow sediments in comparison with surface sediments, suggesting that the burrow provides a unique environment where bacterial gene abundances are influenced directly by macrofaunal activity. In contrast, the abundances of archaeal ammonia oxidizers varied temporally but were not affected by bioturbation, indicating differential responses between bacterial and archaeal ammonia oxidizers to environmental physicochemical controls. This study highlights the importance of bioturbation as a control over the temporal variation in nitrogen-cycling microbial community dynamics within coastal sediments.

Evaluation of autotrophic growth of ammonia-oxidizers associated with granular activated carbon used for drinking water purification by DNA-stable isotope probing

Nitrification is an important biological function of granular activated carbon (GAC) used in advanced drinking water purification processes. Newly discovered ammonia-oxidizing archaea (AOA) have challenged the traditional understanding of ammonia oxidation, which considered ammonia-oxidizing bacteria (AOB) as the sole ammonia-oxidizers. Previous studies demonstrated the predominance of AOA on GAC, but the contributions of AOA and AOB to ammonia oxidation remain unclear. In the present study, DNA-stable isotope probing (DNA-SIP) was used to investigate the autotrophic growth of AOA and AOB associated with GAC at two different ammonium concentrations (0.14 mg N/L and 1.4 mg N/L). GAC samples collected from three full-scale drinking water purification plants in Tokyo, Japan, had different abundance of AOA and AOB. These samples were fed continuously with ammonium and (13)C-bicarbonate for 14 days. The DNA-SIP analysis demonstrated that only AOA assimilated (13)C-bicarbonate at low ammonium concentration, whereas AOA and AOB exhibited autotrophic growth at high ammonium concentration. This indicates that a lower ammonium concentration is preferable for AOA growth. Since AOA could not grow without ammonium, their autotrophic growth was coupled with ammonia oxidation. Overall, our results point towards an important role of AOA in nitrification in GAC filters treating low concentration of ammonium.

Biodegradation and cometabolic modeling of selected beta blockers during ammonia oxidation

Accurate prediction of pharmaceutical concentrations in wastewater effluents requires that the specific biochemical processes responsible for pharmaceutical biodegradation be elucidated and integrated within any modeling framework. The fate of three selected beta blockers-atenolol, metoprolol, and sotalol-was examined during nitrification using batch experiments to develop and evaluate a new cometabolic process-based (CPB) model. CPB model parameters describe biotransformation during and after ammonia oxidation for specific biomass populations and are designed to be integrated within the Activated Sludge Models framework. Metoprolol and sotalol were not biodegraded by the nitrification enrichment culture employed herein. Biodegradation of atenolol was observed and linked to the activity of ammonia-oxidizing bacteria (AOB) and heterotrophs but not nitrite-oxidizing bacteria. Results suggest that the role of AOB in atenolol degradation may be disproportionately more significant than is otherwise suggested by their lower relative abundance in typical biological treatment processes. Atenolol was observed to competitively inhibit AOB growth in our experiments, though model simulations suggest inhibition is most relevant at atenolol concentrations greater than approximately 200 ng·L(-1). CPB model parameters were found to be relatively insensitive to biokinetic parameter selection suggesting the model approach may hold utility for describing pharmaceutical biodegradation during biological wastewater treatment.

Feasibility of bioengineered two-stages sequential batch reactor and filtration-adsorption process for complex agrochemical effluent

In the present study, the feasibility of a bioengineered two-stages sequential batch reactor (BTSSBR) followed by filtration-adsorption process was investigated to treat the agrochemical effluent by overcoming factor affecting process stability such as microbial imbalance and substrate sensitivity. An air stripper stripped 90% of toxic ammonia, and combined with other streams for bio-oxidation and filtration-adsorption. The BTSSBR system achieved bio-oxidation at 6 days hydraulic retention time by fending off microbial imbalance and substrate sensitivity. The maximum reduction in COD and BOD by heterotrophic bacteria in the first reactor was 87% and 90%, respectively. Removal of toxic ammoniacal-nitrogen by autotrophic bacteria in a post-second stage bio-oxidation was 97%. The optimum filtration and adsorption of pollutants were achieved at a filtration rate of 10 and 9 m(3)m(-2)h(-1), respectively. The treatment scheme comprising air stripper, BTSSBR and filtration-adsorption process showed a great promise for treating the agrochemical effluent.

Energy-mediated vs. ammonium-regulated gene expression in the obligate ammonia-oxidizing bacterium, Nitrosococcus oceani

Ammonia serves as the source of energy and reductant and as a signaling molecule that regulates gene expression in obligate ammonia-oxidizing chemolithotrophic microorganisms. The gammaproteobacterium, Nitrosococcus oceani, was the first obligate ammonia-oxidizer isolated from seawater and is one of the model systems for ammonia chemolithotrophy. We compared global transcriptional responses to ammonium and the catabolic intermediate, hydroxylamine, in ammonium-starved and non-starved cultures of N. oceani to discriminate transcriptional effects of ammonium from a change in overall energy and redox status upon catabolite availability. The most highly expressed genes from ammonium- or hydroxylamine-treated relative to starved cells are implicated in catabolic electron flow, carbon fixation, nitrogen assimilation, ribosome structure and stress tolerance. Catabolic inventory-encoding genes, including electron flow-terminating Complexes IV, FoF1 ATPase, transporters, and transcriptional regulators were among the most highly expressed genes in cells exposed only to ammonium relative to starved cells, although the differences compared to steady-state transcript levels were less pronounced. Reduction in steady-state mRNA levels from hydroxylamine-treated relative to starved-cells were less than five-fold. In contrast, several transcripts from ammonium-treated relative to starved cells were significantly less abundant including those for forward Complex I and a gene cluster of cytochrome c encoding proteins. Identified uneven steady-state transcript levels of co-expressed clustered genes support previously reported differential regulation at the levels of transcription and transcript stability. Our results differentiated between rapid regulation of core genes upon a change in cellular redox status vs. those responsive to ammonium as a signaling molecule in N. oceani, both confirming and extending our knowledge of metabolic modules involved in ammonia chemolithotrophy.

Nitrification rates in Arctic soils are associated with functionally distinct populations of ammonia-oxidizing archaea

The functioning of Arctic soil ecosystems is crucially important for global climate, and basic knowledge regarding their biogeochemical processes is lacking. Nitrogen (N) is the major limiting nutrient in these environments, and its availability is strongly dependent on nitrification. However, microbial communities driving this process remain largely uncharacterized in Arctic soils, namely those catalyzing the rate-limiting step of ammonia (NH3) oxidation. Eleven Arctic soils were analyzed through a polyphasic approach, integrating determination of gross nitrification rates, qualitative and quantitative marker gene analyses of ammonia-oxidizing archaea (AOA) and bacteria (AOB) and enrichment of AOA in laboratory cultures. AOA were the only NH3 oxidizers detected in five out of 11 soils and outnumbered AOB in four of the remaining six soils. The AOA identified showed great phylogenetic diversity and a multifactorial association with the soil properties, reflecting an overall distribution associated with tundra type and with several physico-chemical parameters combined. Remarkably, the different gross nitrification rates between soils were associated with five distinct AOA clades, representing the great majority of known AOA diversity in soils, which suggests differences in their nitrifying potential. This was supported by selective enrichment of two of these clades in cultures with different NH3 oxidation rates. In addition, the enrichments provided the first direct evidence for NH3 oxidation by an AOA from an uncharacterized Thaumarchaeota-AOA lineage. Our results indicate that AOA are functionally heterogeneous and that the selection of distinct AOA populations by the environment can be a determinant for nitrification activity and N availability in soils.

L-Malate dehydrogenase activity in the reductive arm of the incomplete citric acid cycle of Nitrosomonas europaea

The autotrophic nitrifying bacterium Nitrosomonas europaea does not synthesize 2-oxoglutarate (α-ketoglutarate) dehydrogenase under aerobic conditions and so has an incomplete citric acid cycle. L-malate (S-malate) dehydrogenase (MDH) from N. europaea was predicted to show similarity to the NADP(+)-dependent enzymes from chloroplasts and was separated from the NAD(+)-dependent proteins from most other bacteria or mitochondria. MDH activity in a soluble fraction from N. europaea ATCC 19718 was measured spectrophotometrically and exhibited simple Michaelis-Menten kinetics. In the reductive direction, activity with NADH increased from pH 6.0 to 8.5 but activity with NADPH was consistently lower and decreased with pH. At pH 7.0, the K m for oxaloacetate was 20 μM; the K m for NADH was 22 μM but that for NADPH was at least 10 times higher. In the oxidative direction, activity with NAD(+) increased with pH but there was very little activity with NADP(+). At pH 7.0, the K m for L-malate was 5 mM and the K m for NAD(+) was 24 μM. The reductive activity was quite insensitive to inhibition by L-malate but the oxidative activity was very sensitive to oxaloacetate. MDH activity was not strongly activated or inhibited by glycolytic or citric acid cycle metabolites, adenine nucleotides, NaCl concentrations, or most metal ions, but increased with temperature up to about 55 °C. The reductive activity was consistently 10-20 times higher than the oxidative activity. These results indicate that the L-malate dehydrogenase in N. europaea is similar to other NAD(+)-dependent MDHs (EC 1.1.1.37) but physiologically adapted for its role in a reductive biosynthetic sequence.

Novel hydrocarbon monooxygenase genes in the metatranscriptome of a natural deep-sea hydrocarbon plume

Particulate membrane-associated hydrocarbon monooxygenases (pHMOs) are critical components of the aerobic degradation pathway for low molecular weight hydrocarbons, including the potent greenhouse gas methane. Here, we analysed pHMO gene diversity in metagenomes and metatranscriptomes of hydrocarbon-rich hydrothermal plumes in the Guaymas Basin (GB) and nearby background waters in the deep Gulf of California. Seven distinct phylogenetic groups of pHMO were present and transcriptionally active in both plume and background waters, including several that are undetectable with currently available polymerase chain reaction (PCR) primers. The seven groups of pHMOs included those related to a putative ethane oxidizing Methylococcaceae-like group, a group of the SAR324 Deltaproteobacteria, three deep-sea clades (Deep sea-1/symbiont-like, Deep sea-2/PS-80 and Deep sea-3/OPU3) within gammaproteobacterial methanotrophs, one clade related to Group Z and one unknown group. Differential abundance of pHMO gene transcripts in plume and background suggests niche differentiation between groups. Corresponding 16S rRNA genes reflected similar phylogenetic and transcriptomic abundance trends. The novelty of transcriptionally active pHMOs we recovered from a hydrocarbon-rich hydrothermal plume suggests there are significant gaps in our knowledge of the diversity and function of these enzymes in the environment.

Impacts of silver nanoparticles on cellular and transcriptional activity of nitrogen-cycling bacteria

The widespread use of silver nanoparticles (AgNPs) raises the potential for environmental releases that could impact microbial ecosystem services. In the present study, the authors address how the AgNPs and Ag(+) that they release may impact nitrogen-cycling bacteria. The authors studied the cellular and transcriptional response of the denitrifier Pseudomonas stutzeri, the nitrogen fixer Azotobacter vinelandii, and the nitrifier Nitrosomonas europaea exposed to 35 nm (carbon-coated) AgNPs or to Ag(+) (added as AgNO3 ). Based on minimum inhibitory concentrations (MICs), Ag(+) was 20 times to 48 times more toxic to the tested strains than AgNPs (including Ag(+) released during exposure). Exposure to sublethal concentrations of AgNPs or Ag(+) (representing 10% of the respective MIC for AgNO3 ) resulted in no significant effect on the expression of the denitrifying genes narG, napB, nirH, and norB in P. stutzeri or the nitrogen-fixing genes nifD, nifH, vnfD, and anfD in A. vinelandii, whereas nitrifying genes (amoA1 and amoC2) in N. europaea were upregulated (2.1- to 3.3-fold). This stimulatory effect disappeared at higher silver concentrations (60% of the Ag(+) MIC), and toxicity was exerted at concentrations higher than 60% of the Ag(+) MIC. The MIC for N. europaea was 8 times to 24 times lower than for the other strains, indicating higher susceptibility to AgNPs. This was corroborated by the lower half-lethal concentration for N. europaea (87 µg/L) compared with P. stutzeri (124 µg/L) and A. vinelandii (>250 µg/L) when cells were exposed with Ag(+) for 24 h in 1 mM bicarbonate buffer. This suggests that ammonia oxidation would be the most vulnerable nitrogen-cycling process in wastewater treatment plants receiving AgNPs and in agricultural soils amended with biosolids that concentrate them.

Shifts between ammonia-oxidizing bacteria and archaea in relation to nitrification potential across trophic gradients in two large Chinese lakes (Lake Taihu and Lake Chaohu)

Ammonia oxidation plays a pivotal role in the cycling and removal of nitrogen in aquatic ecosystems. Recent findings have expanded the known ammonia-oxidizing prokaryotes from Bacteria to Archaea. However, the relative importance of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) in nitrification is still debated. Here we showed that, in two large eutrophic lakes in China (Lake Taihu and Lake Chaohu), the abundance of AOA and AOB varied in opposite patterns according to the trophic state, although both AOA and AOB were abundant. In detail, from mesotrophic to eutrophic sites, the AOA abundance decreased, while the AOB increased in abundance and outnumbered the AOA at hypertrophic sites. In parallel, the nitrification rate increased along these trophic gradients and was significantly correlated with both the AOB abundance and the numerical ratio of AOB to AOA. Phylogenetic analysis of bacterial amoA sequences showed that Nitrosomonas oligotropha- and Nitrosospira-affiliated AOB dominated in both lakes, while Nitrosomonas communis-related AOB were only detected at the eutrophic sites. The diversity of AOB increased from mesotrophic to eutrophic sites and was positively correlated with the nitrification rate. Overall, this study enhances our understanding of the ecology of ammonia-oxidizing prokaryotes by elucidating conditions that AOB may numerically predominated over AOA, and indicated that AOA may play a less important role than AOB in the nitrification process of eutrophic lakes.

Complete genome sequence of Nitrosomonas sp. Is79, an ammonia oxidizing bacterium adapted to low ammonium concentrations

Nitrosomonas sp. Is79 is a chemolithoautotrophic ammonia-oxidizing bacterium that belongs to the family Nitrosomonadaceae within the phylum Proteobacteria. Ammonia oxidation is the first step of nitrification, an important process in the global nitrogen cycle ultimately resulting in the production of nitrate. Nitrosomonas sp. Is79 is an ammonia oxidizer of high interest because it is adapted to low ammonium and can be found in freshwater environments around the world. The 3,783,444-bp chromosome with a total of 3,553 protein coding genes and 44 RNA genes was sequenced by the DOE-Joint Genome Institute Program CSP 2006.

Hydroxylamine as an intermediate in ammonia oxidation by globally abundant marine archaea

The ammonia-oxidizing archaea have recently been recognized as a significant component of many microbial communities in the biosphere. Although the overall stoichiometry of archaeal chemoautotrophic growth via ammonia (NH(3)) oxidation to nitrite (NO(2)(-)) is superficially similar to the ammonia-oxidizing bacteria, genome sequence analyses point to a completely unique biochemistry. The only genomic signature linking the bacterial and archaeal biochemistries of NH(3) oxidation is a highly divergent homolog of the ammonia monooxygenase (AMO). Although the presumptive product of the putative AMO is hydroxylamine (NH(2)OH), the absence of genes encoding a recognizable ammonia-oxidizing bacteria-like hydroxylamine oxidoreductase complex necessitates either a novel enzyme for the oxidation of NH(2)OH or an initial oxidation product other than NH(2)OH. We now show through combined physiological and stable isotope tracer analyses that NH(2)OH is both produced and consumed during the oxidation of NH(3) to NO(2)(-) by Nitrosopumilus maritimus, that consumption is coupled to energy conversion, and that NH(2)OH is the most probable product of the archaeal AMO homolog. Thus, despite their deep phylogenetic divergence, initial oxidation of NH(3) by bacteria and archaea appears mechanistically similar. They however diverge biochemically at the point of oxidation of NH(2)OH, the archaea possibly catalyzing NH(2)OH oxidation using a novel enzyme complex.

Nitrous oxide emissions from wastewater treatment processes

Nitrous oxide (N(2)O) emissions from wastewater treatment plants vary substantially between plants, ranging from negligible to substantial (a few per cent of the total nitrogen load), probably because of different designs and operational conditions. In general, plants that achieve high levels of nitrogen removal emit less N(2)O, indicating that no compromise is required between high water quality and lower N(2)O emissions. N(2)O emissions primarily occur in aerated zones/compartments/periods owing to active stripping, and ammonia-oxidizing bacteria, rather than heterotrophic denitrifiers, are the main contributors. However, the detailed mechanisms remain to be fully elucidated, despite strong evidence suggesting that both nitrifier denitrification and the chemical breakdown of intermediates of hydroxylamine oxidation are probably involved. With increased understanding of the fundamental reactions responsible for N(2)O production in wastewater treatment systems and the conditions that stimulate their occurrence, reduction of N(2)O emissions from wastewater treatment systems through improved plant design and operation will be achieved in the near future.

The genome of the ammonia-oxidizing Candidatus Nitrososphaera gargensis: insights into metabolic versatility and environmental adaptations

The cohort of the ammonia-oxidizing archaea (AOA) of the phylum Thaumarchaeota is a diverse, widespread and functionally important group of microorganisms in many ecosystems. However, our understanding of their biology is still very rudimentary in part because all available genome sequences of this phylum are from members of the Nitrosopumilus cluster. Here we report on the complete genome sequence of Candidatus Nitrososphaera gargensis obtained from an enrichment culture, representing a different evolutionary lineage of AOA frequently found in high numbers in many terrestrial environments. With its 2.83 Mb the genome is much larger than that of other AOA. The presence of a high number of (active) IS elements/transposases, genomic islands, gene duplications and a complete CRISPR/Cas defence system testifies to its dynamic evolution consistent with low degree of synteny with other thaumarchaeal genomes. As expected, the repertoire of conserved enzymes proposed to be required for archaeal ammonia oxidation is encoded by N. gargensis, but it can also use urea and possibly cyanate as alternative ammonia sources. Furthermore, its carbon metabolism is more flexible at the central pyruvate switch point, encompasses the ability to take up small organic compounds and might even include an oxidative pentose phosphate pathway. Furthermore, we show that thaumarchaeota produce cofactor F420 as well as polyhydroxyalkanoates. Lateral gene transfer from bacteria and euryarchaeota has contributed to the metabolic versatility of N. gargensis. This organisms is well adapted to its niche in a heavy metal-containing thermal spring by encoding a multitude of heavy metal resistance genes, chaperones and mannosylglycerate as compatible solute and has the genetic ability to respond to environmental changes by signal transduction via a large number of two-component systems, by chemotaxis and flagella-mediated motility and possibly even by gas vacuole formation. These findings extend our understanding of thaumarchaeal evolution and physiology and offer many testable hypotheses for future experimental research on these nitrifiers.

Role for urea in nitrification by polar marine Archaea

Despite the high abundance of Archaea in the global ocean, their metabolism and biogeochemical roles remain largely unresolved. We investigated the population dynamics and metabolic activity of Thaumarchaeota in polar environments, where these microorganisms are particularly abundant and exhibit seasonal growth. Thaumarchaeota were more abundant in deep Arctic and Antarctic waters and grew throughout the winter at surface and deeper Arctic halocline waters. However, in situ single-cell activity measurements revealed a low activity of this group in the uptake of both leucine and bicarbonate (<5% Thaumarchaeota cells active), which is inconsistent with known heterotrophic and autotrophic thaumarchaeal lifestyles. These results suggested the existence of alternative sources of carbon and energy. Our analysis of an environmental metagenome from the Arctic winter revealed that Thaumarchaeota had pathways for ammonia oxidation and, unexpectedly, an abundance of genes involved in urea transport and degradation. Quantitative PCR analysis confirmed that most polar Thaumarchaeota had the potential to oxidize ammonia, and a large fraction of them had urease genes, enabling the use of urea to fuel nitrification. Thaumarchaeota from Arctic deep waters had a higher abundance of urease genes than those near the surface suggesting genetic differences between closely related archaeal populations. In situ measurements of urea uptake and concentration in Arctic waters showed that small-sized prokaryotes incorporated the carbon from urea, and the availability of urea was often higher than that of ammonium. Therefore, the degradation of urea may be a relevant pathway for Thaumarchaeota and other microorganisms exposed to the low-energy conditions of dark polar waters.

Insights into glycogen metabolism in chemolithoautotrophic bacteria from distinctive kinetic and regulatory properties of ADP-glucose pyrophosphorylase from Nitrosomonas europaea

Nitrosomonas europaea is a chemolithoautotroph that obtains energy by oxidizing ammonia in the presence of oxygen and fixes CO(2) via the Benson-Calvin cycle. Despite its environmental and evolutionary importance, very little is known about the regulation and metabolism of glycogen, a source of carbon and energy storage. Here, we cloned and heterologously expressed the genes coding for two major putative enzymes of the glycogen synthetic pathway in N. europaea, ADP-glucose pyrophosphorylase and glycogen synthase. In other bacteria, ADP-glucose pyrophosphorylase catalyzes the regulatory step of the synthetic pathway and glycogen synthase elongates the polymer. In starch synthesis in plants, homologous enzymes play similar roles. We purified to homogeneity the recombinant ADP-glucose pyrophosphorylase from N. europaea and characterized its kinetic, regulatory, and oligomeric properties. The enzyme was allosterically activated by pyruvate, oxaloacetate, and phosphoenolpyruvate and inhibited by AMP. It had a broad thermal and pH stability and used different divalent metal ions as cofactors. Depending on the cofactor, the enzyme was able to accept different nucleotides and sugar phosphates as alternative substrates. However, characterization of the recombinant glycogen synthase showed that only ADP-Glc elongates the polysaccharide, indicating that ATP and glucose-1-phosphate are the physiological substrates of the ADP-glucose pyrophosphorylase. The distinctive properties with respect to selectivity for substrates and activators of the ADP-glucose pyrophosphorylase were in good agreement with the metabolic routes operating in N. europaea, indicating an evolutionary adaptation. These unique properties place the enzyme in a category of its own within the family, highlighting the unique regulation in these organisms.

Diversity, physiology, and niche differentiation of ammonia-oxidizing archaea

Nitrification, the aerobic oxidation of ammonia to nitrate via nitrite, has been suggested to have been a central part of the global biogeochemical nitrogen cycle since the oxygenation of Earth. The cultivation of several ammonia-oxidizing archaea (AOA) as well as the discovery that archaeal ammonia monooxygenase (amo)-like gene sequences are nearly ubiquitously distributed in the environment and outnumber their bacterial counterparts in many habitats fundamentally revised our understanding of nitrification. Surprising insights into the physiological distinctiveness of AOA are mirrored by the recognition of the phylogenetic uniqueness of these microbes, which fall within a novel archaeal phylum now known as Thaumarchaeota. The relative importance of AOA in nitrification, compared to ammonia-oxidizing bacteria (AOB), is still under debate. This minireview provides a synopsis of our current knowledge of the diversity and physiology of AOA, the factors controlling their ecology, and their role in carbon cycling as well as their potential involvement in the production of the greenhouse gas nitrous oxide. It emphasizes the importance of activity-based analyses in AOA studies and formulates priorities for future research.

Diversity and evolution of bioenergetic systems involved in microbial nitrogen compound transformations

Nitrogen is an essential element of life that needs to be assimilated in its most reduced form, ammonium. On the other hand, nitrogen exists in a multitude of oxidation states and, consequently, nitrogen compounds (NCs) serve as electron donor and/or acceptors in many catabolic pathways including various forms of microbial respiration that contribute to the global biogeochemical nitrogen cycle. Some of these NCs are also known as reactive nitrogen species able to cause nitrosative stress because of their high redox reactivity. The best understood processes of the nitrogen cycle are denitrification and ammonification (both beginning with nitrate reduction to nitrite), nitrification (aerobic oxidation of ammonium and nitrite) and anaerobic ammonium oxidation (anammox). This review presents examples of the diverse architecture, either elucidated or anticipated, and the high degree of modularity of the corresponding respiratory electron transport processes found in Bacteria and Archaea, and relates these to their respective bioenergetic mechanisms of proton motive force generation. In contrast to the multiplicity of enzymes that catalyze NC transformations, the number of proteins or protein modules involved in connecting electron transport to and from these enzymes with the quinone/quinol pool is comparatively small. These quinone/quinol-reactive protein modules consist of cytochromes b and c and iron-sulfur proteins. Conclusions are drawn towards the evolutionary relationships of bioenergetic systems involved in NC transformation and deduced aspects of the evolution of the biogeochemical nitrogen cycle are presented. This article is part of a Special Issue entitled: The evolutionary aspects of bioenergetic systems.

Impact of short-term acidification on nitrification and nitrifying bacterial community dynamics in soilless cultivation media

Soilless medium-based horticulture systems are highly prevalent due to their capacity to optimize growth of high-cash crops. However, these systems are highly dynamic and more sensitive to physiochemical and pH perturbations than traditional soil-based systems, especially during nitrification associated with ammonia-based fertilization. The objective of this study was to assess the impact of nitrification-generated acidification on ammonia oxidation rates and nitrifying bacterial community dynamics in soilless growth media. To achieve this goal, perlite soilless growth medium from a commercial bell pepper greenhouse was incubated with ammonium in bench-scale microcosm experiments. Initial quantitative real-time PCR analysis indicated that betaproteobacterial ammonia oxidizers were significantly more abundant than ammonia-oxidizing archaea, and therefore, research focused on this group. Ammonia oxidation rates were highest between 0 and 9 days, when pH values dropped from 7.4 to 4.9. Pyrosequencing of betaproteobacterial ammonia-oxidizing amoA gene fragments indicated that r-strategist-like Nitrosomonas was the dominant ammonia-oxidizing bacterial genus during this period, seemingly due to the high ammonium concentration and optimal growth conditions in the soilless media. Reduction of pH to levels below 4.8 resulted in a significant decrease in both ammonia oxidation rates and the diversity of ammonia-oxidizing bacteria, with increased relative abundance of the r-strategist-like Nitrosospira. Nitrite oxidizers (Nitrospira and Nitrobacter) were on the whole more abundant and less sensitive to acidification than ammonia oxidizers. This study demonstrates that nitrification and nitrifying bacterial community dynamics in high-N-load intensive soilless growth media may be significantly different from those in in-terra agricultural systems.

Nitrous oxide (N2O) emission from aquaculture: a review

Nitrous oxide (N(2)O) is an important greenhouse gas (GHG) which has a global warming potential 310 times that of carbon dioxide (CO(2)) over a hundred year lifespan. N(2)O is generated during microbial nitrification and denitrification, which are common in aquaculture systems. To date, few studies have been conducted to quantify N(2)O emission from aquaculture. Additionally, very little is known with respect to the microbial pathways through which N(2)O is formed in aquaculture systems. This review suggests that aquaculture can be an important anthropogenic source of N(2)O emission. The global N(2)O-N emission from aquaculture in 2009 is estimated to be 9.30 × 10(10) g, and will increase to 3.83 × 10(11)g which could account for 5.72% of anthropogenic N(2)O-N emission by 2030 if the aquaculture industry continues to increase at the present annual growth rate (about 7.10%). The possible mechanisms and various factors affecting N(2)O production are summarized, and two possible methods to minimize N(2)O emission, namely aquaponic and biofloc technology aquaculture, are also discussed. The paper concludes with future research directions.

Expression, and molecular and enzymatic characterization of Cu-containing nitrite reductase from a marine ammonia-oxidizing gammaproteobacterium, Nitrosococcus oceani

Ammonia-oxidizing bacteria (AOB) remove intracellular nitrite to prevent its toxicity by a nitrifier denitrification pathway involving two denitrifying enzymes, nitrite reductase and nitric oxide reductase. Here, a Cu-containing nitrite reductase from Nitrosococcus oceani strain NS58, a gammaproteobacterial marine AOB, was expressed in Escherichia coli and purified to homogeneity. Sequence homology analysis indicated that the nitrite reductase from N. oceani was phylogenetically closer to its counterparts from denitrifying bacteria than that of the betaproteobacterium Nitrosomonas europaea. The recombinant enzyme was a homotrimer of a 32 kDa subunit molecule. The enzyme was green in the oxidized state with absorption peaks at 455 nm and 575 nm. EPR spectroscopy indicated the presence of type 2 Cu. Molecular activities and the affinity constant for the nitrite were determined to be 1.6×10(3) s(-1) and 52 μM, respectively.

Relative susceptibility and transcriptional response of nitrogen cycling bacteria to quantum dots

Little is known about the potential impacts of accidental or incidental releases of manufactured nanomaterials to microbial ecosystem services (e.g., nutrient cycling). Here, quantum dots (QDs) coated with cationic polyethylenimine (PEI) were more toxic to pure cultures of nitrogen-cycling bacteria than QDs coated with anionic polymaleic anhydride-alt-1-octadecene (PMAO). Nitrifying bacteria (i.e., Nitrosomonas europaea) were much more susceptible than nitrogen fixing (i.e., Azotobacter vinelandii, Rhizobium etli, and Azospirillum lipoferum) and denitrifying bacteria (i.e., Pseudomonas stutzeri). Antibacterial activity was mainly exerted by the QDs rather than by their organic coating or their released QD components (e.g., Cd and Zn), which under the near-neutral pH tested (to minimize QD weathering) were released into the bacterial growth media at lower levels than their minimum inhibitory concentrations. Sublethal exposure to QDs stimulated the expression of genes associated with nitrogen cycling. QD-PEI (10 nM) induced three types of nitrogenase genes (nif, anf, and vnf) in A. vinelandii, and one ammonia monooxygenase gene (amoA) in N. europaea was up-regulated upon exposure to 1 nM QD-PEI. We previously reported up-regulation of denitrification genes in P. stutzeri exposed to low concentrations of QD-PEI. (1) Whether this surprising stimulation of nitrogen cycling activities reflects the need to generate more energy to overcome toxicity (in the case of nitrification or denitrification) or to synthesize organic nitrogen to repair or replace damaged proteins (in the case of nitrogen fixation) remains to be determined.

Inhibition of bacterial ammonia oxidation by organohydrazines in soil microcosms

Hydroxylamine oxidation by hydroxylamine oxidoreductase (HAO) is a key step for energy-yielding in support of the growth of ammonia-oxidizing bacteria (AOB). Organohydrazines have been shown to inactivate HAO from Nitrosomonas europaea, and may serve as selective inhibitors to differentiate bacterial from archaeal ammonia oxidation due to the absence of bacterial HAO gene homolog in known ammonia-oxidizing archaea (AOA). In this study, the effects of three organohydrazines on activity, abundance, and composition of AOB and AOA were evaluated in soil microcosms. The results indicate that phenylhydrazine and methylhydrazine at the concentration of 100 μmol g⁻¹ dry weight soil completely suppressed the activity of soil nitrification. Denaturing gradient gel electrophoresis fingerprinting and sequencing analysis of bacterial ammonia monooxygenase subunit A gene (amoA) clearly demonstrated that nitrification activity change is well paralleled with the growth of Nitrosomonas europaea-like AOB in soil microcosms. No significant correlation between AOA community structure and nitrification activity was observed among all treatments during the incubation period, although incomplete inhibition of nitrification activity occurred in 2-hydroxyethylhydrazine-amended soil microcosms. These findings show that the HAO-targeted organohydrazines can effectively inhibit bacterial nitrification in soil, and the mechanism of organohydrazine affecting AOA remains unclear.

Environmental factors determining ammonia-oxidizing organism distribution and diversity in marine environments

Ammonia-oxidizing bacteria (AOB) and archaea (AOA) play a vital role in bridging the input of fixed nitrogen, through N-fixation and remineralization, to its loss by denitrification and anammox. Yet the major environmental factors determining AOB and AOA population dynamics are little understood, despite both groups having a wide environmental distribution. This study examined the relative abundance of both groups of ammonia-oxidizing organisms (AOO) and the diversity of AOA across large-scale gradients in temperature, salinity and substrate concentration and dissolved oxygen. The relative abundance of AOB and AOA varied across environments, with AOB dominating in the freshwater region of the Chesapeake Bay and AOA more abundant in the water column of the coastal and open ocean. The highest abundance of the AOA amoA gene was recorded in the oxygen minimum zones (OMZs) of the Eastern Tropical South Pacific (ETSP) and the Arabian Sea (AS). The ratio of AOA : AOB varied from 0.7 in the Chesapeake Bay to 1600 in the Sargasso Sea. Relative abundance of both groups strongly correlated with ammonium concentrations. AOA diversity, as determined by phylogenetic analysis of clone library sequences and archetype analysis from a functional gene DNA microarray, detected broad phylogenetic differences across the study sites. However, phylogenetic diversity within physicochemically congruent stations was more similar than would be expected by chance. This suggests that the prevailing geochemistry, rather than localized dispersal, is the major driving factor determining OTU distribution.

Effect of salinity on hydroxylamine oxidation in a marine ammonia-oxidizing gammaproteobacterium, Nitrosococcus oceani strain NS58: molecular and catalytic properties of tetraheme cytochrome c-554

Tetraheme cytochrome c-554 is a physiological electron acceptor of hydroxylamine oxidoreductase (HAO), a core enzyme of ammonia oxidation in chemoautotrophic nitrifiers. Here we report the purification of cytochrome c-554 from Nitrosococcus oceani strain NS58, a marine gammaproteobacterial ammonia-oxidizing bacterium. The NS58 cytochrome is a 25 kDa-protein having four hemes c. The absorption spectrum of the cytochrome showed peaks at 420 nm, 523 nm, and 554 nm, with shoulders at around 430 nm and 580 nm in the reduced state. In contrast to the highly basic counterpart from the betaproteobacterium Nitrosomonas europaea, the NS58 cytochrome c-554 was an acidic protein whose isoelectric point was 4.6. HAO was also purified, and the reaction with the NS58 cytochrome was found to be salt-tolerant. Compared with the activity observed in a non-salt solution, 60% of the activity remained in a saline concentration comparable to that of seawater.

The membrane-associated monooxygenase in the butane-oxidizing Gram-positive bacterium Nocardioides sp. strain CF8 is a novel member of the AMO/PMO family

The Gram-positive bacterium Nocardioides sp. strain CF8 uses a membrane-associated monooxygenase (pBMO) to grow on butane. The nucleotide sequences of the genes encoding this novel monooxygenase were revealed through analysis of a de novo assembled draft genome sequence determined by high-throughput sequencing of the whole genome. The pBMO genes were in a similar arrangement to the genes for ammonia monooxygenase (AMO) from the ammonia-oxidizing bacteria and for particulate methane monooxygenase (pMMO) from the methane-oxidizing bacteria. The pBMO genes likely constitute an operon in the order bmoC, bmoA and bmoB. The nucleotide sequence was less than 50% similar to the genes for AMO and pMMO. The operon for pBMO was confirmed to be a single copy in the genome by Southern and computational analyses. In an incubation on butane the increase of transcriptional activity of the pBmoA gene was congruent with the increase of pBMO activity and suggested correspondence between gene expression and the utilization of butane. Phylogenetic comparison revealed distant but significant similarity of all three pBMO subunits to homologous members of the AMO/pMMO family and indicated that the pBMO represents a deeply branching third lineage of this group of particulate monooxygenases. No other bmoCAB-like genes were found to cluster with pBMO lineage in phylogenetic analysis by database searches including genomic and metagenomic sequence databases. pBMO is the first example of the AMO/pMMO-like monooxygenase from Gram-positive bacteria showing similarities to proteobacterial pMMO and AMO sequences.

Enrichment and characterization of ammonia-oxidizing archaea from the open ocean: phylogeny, physiology and stable isotope fractionation

Archaeal genes for ammonia oxidation are widespread in the marine environment, but direct physiological evidence for ammonia oxidation by marine archaea is limited. We report the enrichment and characterization of three strains of pelagic ammonia-oxidizing archaea (AOA) from the North Pacific Ocean that have been maintained in laboratory culture for over 3 years. Phylogenetic analyses indicate the three strains belong to a previously identified clade of water column-associated AOA and possess 16S ribosomal RNA genes and ammonia monooxygenase subunit a (amoA) genes highly similar (98-99% identity) to those recovered in DNA and complementary DNA clone libraries from the open ocean. The strains grow in natural seawater-based liquid medium while stoichiometrically converting ammonia (NH(3)) to nitrite (NO(2)(-)). Ammonia oxidation by the enrichments is only partially inhibited by allylthiourea at concentrations known to completely inhibit cultivated ammonia-oxidizing bacteria. The three strains were used to determine the nitrogen stable isotope effect ((15)ɛ(NH3)) during archaeal ammonia oxidation, an important parameter for interpreting stable isotope ratios in the environment. Archaeal (15)ɛ(NH3) ranged from 13‰ to 41‰, within the range of that previously reported for ammonia-oxidizing bacteria. Despite low amino acid identity between the archaeal and bacterial Amo proteins, their functional diversity as captured by (15)ɛ(NH3) is similar.

Continuous cultivation and thermodynamic aspects of niche definition in the nitrogen cycle

The study of model organisms in pure culture has provided detailed information about the physiology and biochemistry of nitrification and related processes. Metagenomic sequencing of environmental samples is providing information to what extent this understanding also applies to natural microbial communities. Here, we outline a conceptual and experimental strategy that links these two approaches. It consists of the mathematical modeling of nitrification and related processes. The model predictions are subsequently validated experimentally by the study of natural microbial communities in continuous cultures under precisely defined environmental conditions. Combined with calorimetry and metagenomic monitoring this form of "experimental metagenomics" enables the answering of current questions in the ecology of the nitrogen cycle.

A novel family of functional operons encoding methane/ammonia monooxygenase-related proteins in gammaproteobacterial methanotrophs

Genomes of alphaproteobacterial and verrucomicrobial methane-oxidizing bacteria (MOB) encode sequence-divergent copies of particulate methane monooxygenase [pMMO = (PmoABC); pmoCAB]. In contrast, sequenced gammaproteobacterial MOB (Gamma-MOB) genomes contain single or multiple near-identical copies of pmoCAB operons. In betaproteobacterial ammonia-oxidizing bacteria (Beta-AOB), near-identical amoCAB operons encode ammonia monooxygenase (AMO), a homologue of pMMO. Here, we report that Gamma-MOB in the genera Methylomonas, Methylobacter and Methylomicrobium also encode a sequence-divergent particulate monooxygenase (pXMO). Whereas all known genes encoding pMMO or AMO cluster in the order 'CAB', the genes encoding pXMO are uniquely organized in the non-canonical form 'pxmABC.' Steady state pxm mRNA was detected in cultures of Methylomonas sp. as well as in freshwater creek sediment samples, demonstrating that pxm genes are expressed in culture and in situ. Inclusion of PxmA and PxmB proteins in phylogenetic analyses of the Pmo/Amo protein superfamilies created trifurcated trees with three major clades: (i) Pmo of Alpha- and Gamma-MOB and Amo of Gamma-AOB; (ii) Amo of Beta-AOB, Pmo of putative ethane-oxidizing Gamma-MOB and Pxm of Gamma-MOB; and (iii) verrucomicrobial Pmo and Amo of ammonia-oxidizing Archaea. These data support but do not prove the hypothesis that oxygen-dependent methane and ammonia monooxygenases evolved from a substrate-promiscuous ancestor after horizontal transfer while being integrated into the catabolic contexts of their extant hosts.

Nitrosococcus watsonii sp. nov., a new species of marine obligate ammonia-oxidizing bacteria that is not omnipresent in the world's oceans: calls to validate the names 'Nitrosococcus halophilus' and 'Nitrosomonas mobilis'

Local associations between anammox bacteria and obligate aerobic bacteria in the genus Nitrosococcus appear to be significant for ammonia oxidation in oxygen minimum zones. The literature on the genus Nitrosococcus in the Chromatiaceae family of purple sulfur bacteria (Gammaproteobacteria, Chromatiales) contains reports on four described species, Nitrosococcus nitrosus, Nitrosococcus oceani, 'Nitrosococcus halophilus' and 'Nitrosomonas mobilis', of which only N. nitrosus and N. oceani are validly published names and only N. oceani is omnipresent in the world's oceans. The species 'N. halophilus' with Nc4(T) as the type strain was proposed in 1990, but the species is not validly published. Phylogenetic analyses of signature genes, growth-physiological studies and an average nucleotide identity analysis between N. oceani ATCC19707(T) (C-107, Nc9), 'N. halophilus' strain Nc4(T) and Nitrosococcus sp. strain C-113 revealed that a proposal for a new species is warranted. Therefore, the provisional taxonomic assignment Nitrosococcus watsonii is proposed for Nitrosococcus sp. strain C-113(T) . Sequence analysis of Nitrosococcus haoAB signature genes detected in cultures enriched from Jiaozhou Bay sediments (China) identified only N. oceani-type sequences, suggesting that different patterns of distribution in the environment correlate with speciation in the genus Nitrosococcus.

Responses of aerobic and anaerobic ammonia/ammonium-oxidizing microorganisms to anthropogenic pollution in coastal marine environments

Up to date, numerous studies have shown that the community structure of aerobic ammonia oxidizers including ammonia-oxidizing Betaproteobacteria (Beta-AOB) and ammonia-oxidizing archaea (AOA) and, more recently, the anaerobic ammonium-oxidizing (anammox) bacteria is responsive to environmental conditions including salinity, pH, selected metal ions, concentrations of inorganic nitrogen, total phosphorus, the ratio of organic carbon and nitrogen, and sedimentological factors such as the sediment median grain size. Identification of these responses to known anthropogenic pollution is of particular interest to better understand the growth dynamics and activities of nitrogen transforming microorganisms in marine environments. This chapter discusses currently available methods including molecular ecological analysis using clone library constructions with specific molecular genetic markers for delineating community changes of Beta-AOB, AOA, and anammox bacteria. Using data on ammonia-oxidizing microbial community structures from Jiaozhou Bay in North China and three marine environments with anthropogenic pollution gradients in South China from coastal Mai Po Nature Reserve of Hong Kong to the South China Sea as examples, statistical analyses packages (DOTUR, UniFrac, and Canoco) are presented as useful tools to illustrate the relationship between changes in nitrogen metabolizing microbial communities and established environmental variables.

Nitrogen metabolism and kinetics of ammonia-oxidizing archaea

The discovery of ammonia-oxidizing mesophilic and thermophilic Group I archaea changed the century-old paradigm that aerobic ammonia oxidation is solely mediated by two small clades of Beta- and Gammaproteobacteria. Group I archaea are extremely diverse and ubiquitous in marine and terrestrial environments, accounting for 20-30% of the microbial plankton in the global oceans. Recent studies indicated that many of these organisms carry putative ammonia monooxygenase genes and are more abundant than ammonia-oxidizing bacteria in most natural environments suggesting a potentially significant role in the nitrogen cycle. The isolation of Nitrosopumilus maritimus strain SCM1 provided the first direct evidence that Group I archaea indeed gain energy from ammonia oxidation. To characterize the physiology of this archaeal nitrifier, we developed a respirometry setup particularly suited for activity measurements in dilute microbial cultures with extremely low oxygen uptake rates. Here, we describe the setup and review the kinetic experiments conducted with N. maritimus and other nitrifying microorganisms. These experiments demonstrated that N. maritimus is adapted to grow on ammonia concentrations found in oligotrophic open ocean environments, far below the survival threshold of ammonia-oxidizing bacteria. The described setup and experimental procedures should facilitate physiological studies on other nitrifying archaea and oligotrophic microorganisms in general.

Evolution of the Kdo2-lipid A biosynthesis in bacteria

Background

Lipid A is the highly immunoreactive endotoxic center of lipopolysaccharide (LPS). It anchors the LPS into the outer membrane of most Gram-negative bacteria. Lipid A can be recognized by animal cells, triggers defense-related responses, and causes Gram-negative sepsis. The biosynthesis of Kdo₂-lipid A, the LPS substructure, involves with nine enzymatic steps.

Results

In order to elucidate the evolutionary pathway of Kdo₂-lipid A biosynthesis, we examined the distribution of genes encoding the nine enzymes across bacteria. We found that not all Gram-negative bacteria have all nine enzymes. Some Gram-negative bacteria have no genes encoding these enzymes and others have genes only for the first four enzymes (LpxA, LpxC, LpxD, and LpxB). Among the nine enzymes, five appeared to have arisen from three independent gene duplication events. Two of such events happened within the Proteobacteria lineage, followed by functional specialization of the duplicated genes and pathway optimization in these bacteria.

Conclusions

The nine-enzyme pathway, which was established based on the studies mainly in Escherichia coli K12, appears to be the most derived and optimized form. It is found only in E. coli and related Proteobacteria. Simpler and probably less efficient pathways are found in other bacterial groups, with Kdo₂-lipid A variants as the likely end products. The Kdo₂-lipid A biosynthetic pathway exemplifies extremely plastic evolution of bacterial genomes, especially those of Proteobacteria, and how these mainly pathogenic bacteria have adapted to their environment.

Diversity of nitrifying bacteria in a full-scale petroleum refinery wastewater treatment plant experiencing unstable nitrification

We have investigated bacterial populations relevant to nitrification in a full-scale activated sludge plant receiving wastewater from a petroleum refinery showing unstable nitrification. Inhibition of ammonia oxidation was related to phenol concentration according to a model of non-competitive inhibition. While the number of ammonia-oxidizing bacteria (AOB) did not correlate with nitrification performance, the total number of nitrite-oxidizing bacteria (NOB) dropped considerably during periods of nitrite accumulation or no nitrification. Diversity of nitrifiers in the sludge of the full-scale facility was examined at a time of full nitrification with the construction of clone libraries of ammonia monooxygenase (amoA) gene and of the 16S rRNA gene of NOB. Nucleotide sequences of amoA gene belonged to one dominant population, associated with Nitrosomonas europaea, and to a minor population related to the Nitrosomonas nitrosa lineage. The majority of sequences retrieved in the NOB-like clone library also clustered within a single operational taxonomic unit. The high dominance of Nitrobacter over Nitrospira and the low diversity of nitrifying bacteria observed in this wastewater treatment plant might account for the increased risk of failure in the presence of disturbances.

Diversity, abundance, and spatial distribution of sediment ammonia-oxidizing Betaproteobacteria in response to environmental gradients and coastal eutrophication in Jiaozhou Bay, China

Ongoing anthropogenic eutrophication of Jiaozhou Bay offers an opportunity to study the influence of human activity on bacterial communities that drive biogeochemical cycling. Nitrification in coastal waters appears to be a sensitive indicator of environmental change, suggesting that function and structure of the microbial nitrifying community may be associated closely with environmental conditions. In the current study, the amoA gene was used to unravel the relationship between sediment aerobic obligate ammonia-oxidizing Betaproteobacteria (Beta-AOB) and their environment in Jiaozhou Bay. Protein sequences deduced from amoA gene sequences grouped within four distinct clusters in the Nitrosomonas lineage, including a putative new cluster. In addition, AmoA sequences belonging to three newly defined clusters in the Nitrosospira lineage were also identified. Multivariate statistical analyses indicated that the studied Beta-AOB community structures correlated with environmental parameters, of which nitrite-N and sediment sand content had significant impact on the composition, structure, and distribution of the Beta-AOB community. Both amoA clone library and quantitative PCR (qPCR) analyses indicated that continental input from the nearby wastewater treatment plants and polluted rivers may have significant impact on the composition and abundance of the sediment Beta-AOB assemblages in Jiaozhou Bay. Our work is the first report of a direct link between a sedimentological parameter and the composition and distribution of the sediment Beta-AOB and indicates the potential for using the Beta-AOB community composition in general and individual isolates or environmental clones in the Nitrosomonas oligotropha lineage in particular as bioindicators and biotracers of pollution or freshwater or wastewater input in coastal environments.

Nitrosopumilus maritimus genome reveals unique mechanisms for nitrification and autotrophy in globally distributed marine crenarchaea

Ammonia-oxidizing archaea are ubiquitous in marine and terrestrial environments and now thought to be significant contributors to carbon and nitrogen cycling. The isolation of Candidatus "Nitrosopumilus maritimus" strain SCM1 provided the opportunity for linking its chemolithotrophic physiology with a genomic inventory of the globally distributed archaea. Here we report the 1,645,259-bp closed genome of strain SCM1, revealing highly copper-dependent systems for ammonia oxidation and electron transport that are distinctly different from known ammonia-oxidizing bacteria. Consistent with in situ isotopic studies of marine archaea, the genome sequence indicates N. maritimus grows autotrophically using a variant of the 3-hydroxypropionate/4-hydroxybutryrate pathway for carbon assimilation, while maintaining limited capacity for assimilation of organic carbon. This unique instance of archaeal biosynthesis of the osmoprotectant ectoine and an unprecedented enrichment of multicopper oxidases, thioredoxin-like proteins, and transcriptional regulators points to an organism responsive to environmental cues and adapted to handling reactive copper and nitrogen species that likely derive from its distinctive biochemistry. The conservation of N. maritimus gene content and organization within marine metagenomes indicates that the unique physiology of these specialized oligophiles may play a significant role in the biogeochemical cycles of carbon and nitrogen.