Identification of nitrite-oxidizing bacteria with monoclonal antibodies recognizing the nitrite oxidoreductase

Niche differentiation and influencing factors of nitrite oxidation bacteria Nitrospira in sediments of the Luan River estuary in China

In the estuarine sediment, the nitrite oxidation process mediated by bacteria significantly influences nitrification. Nitrospira is the most widely distributed nitrite-oxidizing bacteria (NOB) and can adapt to various environments. In this study, the Nitrospira-specific primer nxrB 169F-638R was used to analyze the microbial communities in the sediments of low-, middle-, and high-level zones in the Luan River estuary. The structure of the microbial community and its response to environmental factors were also assessed. The abundance and diversity of Nitrospira were the highest in the low-level zone and lowest in the high-level zone. Lineage II and lineage IV were the dominant Nitrospira at 43.58% and 32.09%, respectively. The distribution pattern of Nitrospira was also affected by complex environmental factors, such as the concentration of NH4+, Fe, and Cu cations. This study provides novel insights into the niche differentiation and adaptation strategies of Nitrospira in an estuarine sediment environment and will help to facilitate single-step nitrification.

Study of effect of various temperatures on the abundance of ammonia oxidizing archaea and bacteria

Temperature plays significant role in the oxidation of ammonia in filtration units of recirculating aquaculture system. The impact of temperature on the abundance of ammonia oxidizing archaea and bacteria, and the expression of ammonia oxidizing gene (amoA) at specific temperature was evaluated. The broken earthen pot pieces used as filter bed materials of recirculating system, showing the presence of microorganisms were introduced in glass containers (5 pieces/5l) filled with synthetic wastewater and exposed to four different temperatures of 10, 20, 30 and 40°C for 40 days. The ammonia oxidation rate was minimum at 10°C. In 20, 30 and 40°C treatments, 99% ammonia was reduced on day-18, 8 and 18, respectively compared to the initial day. Fresh ammonium chloride (2 mM) was added twice to maintain the ammonia concentration in all treatments, except 10°C one. Nitrite-N level was < 1 mg/l at 10°C. The level was highest on day-22 at 20° and 40°C and on day-12 at 30°C. The nitrification was 10 days delayed at 20°C and 40°C compared to 30°C treatment. Concentration of nitrate-N was lowest at 10°C. Highest concentration of nitrate-N was observed on day-40 at 20°C and 40°C and day-26 at 30°C. Highest copy number of bacterial amoA was recorded at 30°C (2.59×107) followed by 20°C (4.08×106), 40°C (1.45×106) and 10°C (5.664×103). Archaeal amoA was highest at 30°C (7.47×103) followed by 40°C (2.98×102) and 20°C (46.8) treatments. Hence it may be concluded that 30°C temperature was optimum for the efficient and faster oxidation of ammonia in the present recirculating system.

Some like it cold: The cellular organization and physiological limits of cold-tolerant nitrite-oxidizing Nitrotoga

Chemolithoautotrophic production of nitrate is accomplished by the polyphyletic functional group of nitrite-oxidizing bacteria (NOB). A widely distributed and important NOB clade in nitrogen removal processes at low temperatures is Nitrotoga, which however remains understudied due to the scarcity of cultivated representatives. Here, we present physiological, ultrastructural and genomic features of Nitrotoga strains from various habitats, including the first marine species enriched from an aquaculture system. Immunocytochemical analyses localized the nitrite-oxidizing enzyme machinery in the wide irregularly shaped periplasm, apparently without contact to the cytoplasmic membrane, confirming previous genomic data suggesting a soluble nature. Interestingly, in two strains we also observed multicellular complexes with a shared periplasmic space, which seem to form through incomplete cell division and might enhance fitness or survival. Physiological tests revealed differing tolerance limits towards dissolved inorganic nitrogen concentrations and confirmed the generally psychrotolerant nature of the genus was. Moreover, comparative analysis of 15 Nitrotoga genomes showed, e.g., a unique gene repertoire of the marine strain that could be advantageous in its natural habitat and confirmed the lack of genes for assimilatory nitrite reduction in a strain found to require ammonium for growth. Overall, these novel insights largely broaden our knowledge of Nitrotoga and elucidate the metabolic variability, physiological limits and thus potential ecological roles of this group of nitrite oxidizers. This article is protected by copyright. All rights reserved.

Mutualistic relationship between Nitrospira and concomitant heterotrophs

Nitrifying chemoautotrophs support the growth of diverse concomitant heterotrophs in natural or engineered environments by supplying organic compounds. In this study, we aimed to investigate this microbial association, especially (i) to distinguish whether the relationship between nitrifying chemoautotrophs and heterotrophs is commensal or mutualistic, and (ii) to clarify how heterotrophs promote the growth of autotrophic nitrite-oxidizing bacteria (Nitrospira). Pure cultured Nitrospira (Nitrospira sp. ND1) was employed in this study. Heterotrophs growing with metabolic by-products of Nitrospira as a sole carbon source were isolated from several environmental samples and used to test the growth-promoting activity of Nitrospira. Furthermore, liquid chromatography-mass spectrometry analysis was conducted to evaluate how heterotrophs consumed chemical compounds produced by Nitrospira and newly produced during co-cultivation. Notably, Nitrospira growth was stimulated by co-cultivation with some heterotrophs and the addition of spent media of some strains, suggesting that not only heterotrophs but also Nitrospira received benefits from their mutual co-existence. Furthermore, the data suggested that some of the growth-promoting heterotrophs provided as-yet-unidentified growth-promoting factors to Nitrospira. Overall, Nitrospira and heterotrophs thus appear to exhibit a mutualistic relationship. Such mutualistic relationships between autotrophs and heterotrophs would contribute to the stability and diversity of microbial ecosystems.

Relevance of Candidatus Nitrotoga for nitrite oxidation in technical nitrogen removal systems

Abstract

Many biotechnological applications deal with nitrification, one of the main steps of the global nitrogen cycle. The biological oxidation of ammonia to nitrite and further to nitrate is critical to avoid environmental damage and its functioning has to be retained even under adverse conditions. Bacteria performing the second reaction, oxidation of nitrite to nitrate, are fastidious microorganisms that are highly sensitive against disturbances. One important finding with relevance for nitrogen removal systems was the discovery of the mainly cold-adapted Cand. Nitrotoga, whose activity seems to be essential for the recovery of nitrite oxidation in wastewater treatment plants at low temperatures, e.g., during cold seasons. Several new strains of this genus have been recently described and ecophysiologically characterized including genome analyses. With increasing diversity, also mesophilic Cand. Nitrotoga representatives have been detected in activated sludge. This review summarizes the natural distribution and driving forces defining niche separation in artificial nitrification systems. Further critical aspects for the competition with Nitrospira and Nitrobacter are discussed. Knowledge about the physiological capacities and limits of Cand. Nitrotoga can help to define physico-chemical parameters for example in reactor systems that need to be run at low temperatures.

Key points

• Characterization of the psychrotolerant nitrite oxidizer Cand. Nitrotoga

• Comparison of the physiological features of Cand. Nitrotoga with those of other NOB

• Identification of beneficial environmental/operational parameters for proliferation

Supplementary Information

The online version contains supplementary material available at 10.1007/s00253-021-11487-5.

Desalinization via freshwater restoration highly improved microbial diversity, co-occurrence patterns and functions in coastal wetland soils

Saltwater intrusion has greatly impacted the functions of coastal wetland soils worldwide by increasing the salt stress; desalinization via freshwater restoration has been suggested to recover saline wetland soils and biodiversity, but its effectiveness is debated. To evaluate the desalinization effectiveness, we characterized the microbial communities and activities using high throughput 16S rRNA gene sequencing and ¹⁵N isotopic techniques in freshwater restored (≥10 years) and unrestored wetlands, and then compared the data with reported values of original freshwater wetlands in one of the most dynamic coastal areas, Yellow river estuary (YRE). Our data revealed that freshwater input significantly increased the soil organic carbon (SOC; P < 0.05) after 10 years of restoration, yet it was still 10 times lower than the reported values of original freshwater wetlands. In general, microbial community showed higher diversities and more co-occurrence interactions in the restored than unrestored wetlands. The recovered phylogenetic diversity and the relative abundance of Chloroflexi (9.8-16.3%), Actinobacteria (5.5-10%), Latescibacteria (0.5-1.5%), Nitrospirae (0.9-1.4%) were up to the similar levels of original freshwater wetlands in YRE. Specifically, Gemmatimonadetes_denitrifier clones, as the representatives of denitrifiers, were recovered up to 0.3% with 20 times higher concomitant denitrification rate than anammox rate, significantly contributing to the nitrate removal in restored wetlands; however the rate will be reduced by 80% with a short-term saltwater intrusion. Our study highlighted that freshwater input effectively improved the microbial diversity and their functions and provided a good insight into the desalinization effectiveness via freshwater restoration in coastal wetlands worldwide. ORIGINALITY-SIGNIFICANCE STATEMENT: Salinization is globally spreading with approximately one billion hectares area covered with saline and/or sodic soils on the earth, and the negative effects of salinity on soil microbial communities and their activities have been frequently reported in previous studies all around the world; however, it remains largely unknown about whether the microbial communities and their activities can be recovered or not in soil suffered salinization. Desalinization via freshwater restoration is supposed to offer a good solution to soil salinization in coastal area, but the effectiveness is debated. Here, we are presenting the long-term of field study related to the desalinization effects on microbial diversity, co-occurrence and functions, and find desalinization via freshwater restoration can recover most of microbial communities up to the similar levels of that in original freshwater wetlands, and highly improved microbial diversity and their functions, which sheds a positive light on soil desalinization via freshwater restoration at microenvironments.

Nitrospira as versatile nitrifiers: Taxonomy, ecophysiology, genome characteristics, growth, and metabolic diversity

The global nitrogen cycle is of paramount significance as it affects important processes like primary productivity and decomposition. Nitrification, the oxidation of ammonia to nitrate via nitrite, is a key process in the nitrogen cycle. The knowledge about nitrification has been challenged during the last few decades with inventions like anaerobic ammonia oxidation, ammonia-oxidizing archaea, and recently the complete ammonia oxidation (comammox). The discovery of comammox Nitrospira has made a paradigm shift in nitrification, before which it was considered as a two-step process, mediated by chemolithoautotrophic ammonia oxidizers and nitrite oxidizers. The genome of comammox Nitrospira equipped with molecular machineries for both ammonia and nitrite oxidation. The genus Nitrospira is ubiquitous, comes under phylum Nitrospirae, which comprises six sublineages consisting of canonical nitrite oxidizers and comammox. The single-step nitrification is energetically more feasible; furthermore, the existence of diverse metabolic pathways in Nitrospira is critical for its establishment in various habitats. The present review discusses the taxonomy, ecophysiology, isolation, identification, growth, and metabolic diversity of the genus Nitrospira; compares the genomes of canonical nitrite-oxidizing Nitrospira and comammox Nitrospira, and analyses the differences of Nitrospira with other nitrifying bacteria.

Low Temperature and Neutral pH Define "Candidatus Nitrotoga sp." as a Competitive Nitrite Oxidizer in Coculture with Nitrospira defluvii

Nitrification is an essential process for N removal in activated sludge to avoid toxicity of ammonium and nitrite. Besides Nitrospira, "Candidatus Nitrotoga" has been identified as a key nitrite-oxidizing bacterium (NOB) performing the second step of nitrification, nitrite oxidation to nitrate, in wastewater treatment plants (WWTPs). However, the driving forces for the dominance of Nitrotoga in certain plants have often remained unclear and could not be explained solely by temperature effects. In this study, we characterized the physiology of the ammonium-dependent Nitrotoga sp. BS with regard to temperature and pH variations and evaluated its competitiveness against Nitrospira defluvii Both NOB originated from the same WWTP and shared a comparable pH optimum of 7.3. Based on these results, coculturing experiments with these NOB were performed in batch reactors operated at either 17°C or 22°C to compare their abundances under optimal (pH 7.4) or suboptimal (pH 6.4) conditions using 1 mM nitrite. As revealed by quantitative PCR (qPCR), fluorescence in situ hybridization (FISH), and 16S amplicon sequencing, Nitrotoga sp. BS was clearly favored by its optimal growth parameters and dominated over Ns. defluvii at pH 7.4 and 17°C, whereas a pH of 6.4 was more selective for Ns. defluvii Our synthetic communities revealed that niche differentiation of NOB is influenced by a complex interaction of environmental parameters and has to be evaluated for single species.IMPORTANCE "Ca. Nitrotoga" is a NOB of high environmental relevance, but physiological data exist for only a few representatives. Initially, it was detected in specialized niches of low temperature and low nitrite concentrations, but later on, its ubiquitous distribution revealed its critical role for N removal in engineered systems like WWTPs. In this study, we analyzed the competition between Nitrotoga and Nitrospira in bioreactors and identified conditions where the K strategist Ns. defluvii was almost replaced by Nitrotoga sp. BS. We show that the pH value is an important factor that regulates the composition of the nitrite-oxidizing enrichment with a dominance of Nitrotoga sp. BS versus Ns. defluvii at a neutral pH of 7.4 in combination with a temperature of 17°C. The physiological diversity of novel Nitrotoga cultures improves our knowledge about niche differentiation of NOB with regard to functional nitrification under suboptimal conditions.

Genomic profiling of four cultivated Candidatus Nitrotoga spp. predicts broad metabolic potential and environmental distribution

Nitrite-oxidizing bacteria (NOB) play a critical role in the mitigation of nitrogen pollution by metabolizing nitrite to nitrate, which is removed via assimilation, denitrification, or anammox. Recent studies showed that NOB are phylogenetically and metabolically diverse, yet most of our knowledge of NOB comes from only a few cultured representatives. Using cultivation and genomic sequencing, we identified four putative Candidatus Nitrotoga NOB species from freshwater sediments and water column samples in Colorado, USA. Genome analyses indicated highly conserved 16S rRNA gene sequences, but broad metabolic potential including genes for nitrogen, sulfur, hydrogen, and organic carbon metabolism. Genomic predictions suggested that Ca. Nitrotoga can metabolize in low oxygen or anoxic conditions, which may support an expanded environmental niche for Ca. Nitrotoga similar to other NOB. An array of antibiotic and metal resistance genes likely allows Ca. Nitrotoga to withstand environmental pressures in impacted systems. Phylogenetic analyses highlighted a deeply divergent nitrite oxidoreductase alpha subunit (NxrA), suggesting a novel evolutionary trajectory for Ca. Nitrotoga separate from any other NOB and further revealing the complex evolutionary history of nitrite oxidation in the bacterial domain. Ca. Nitrotoga-like 16S rRNA gene sequences were prevalent in globally distributed environments over a range of reported temperatures. This work considerably expands our knowledge of the Ca. Nitrotoga genus and suggests that their contribution to nitrogen cycling should be considered alongside other NOB in wide variety of habitats.

454 pyrosequencing-based characterization of the bacterial consortia in a well established nitrifying reactor

This present study aimed to characterize the bacterial community in a well-established nitrifying reactor by high-throughput sequencing of 16S rRNA amplicons. The laboratory-scale continuous stirred tank reactor has been supplied with ammonium (NH(4)(+)) as sole energy source for over 5 years, while no organic carbon has been added, assembling thus a unique planktonic community with a mean NH(4)(+) removal rate of 86 ± 1.4 mg NH(4)(+)-N/(L d). Results showed a nitrifying community composed of bacteria belonging to Nitrosomonas (relative abundance 11.0%) as the sole ammonia oxidizers (AOB) and Nitrobacter (9.3%) as the sole nitrite oxidizers (NOB). The Alphaproteobacteria (42.3% including Nitrobacter) were the most abundant class within the Proteobacteria (62.8%) followed by the Gammaproteobacteria (9.4%). However, the Betaproteobacteria (excluding AOB) contributed only 0.08%, confirming that Alpha- and Gammaproteobacteria thrived in low-organic-load environments while heterotrophic Betaproteobacteria are not well adapted to these conditions. Bacteroidetes, known to metabolize extracellular polymeric substances produced by nitrifying bacteria and secondary metabolites of the decayed biomass, was the second most abundant phylum (30.8%). It was found that Nitrosomonas and Nitrobacter sustained a broad population of heterotrophs in the reactor dominated by Alpha- and Gammaproteobacteria and Bacteroidetes, in a 1:4 ratio of total nitrifiers to all heterotrophs.

Comparison of oxidation kinetics of nitrite-oxidizing bacteria: nitrite availability as a key factor in niche differentiation

Nitrification has an immense impact on nitrogen cycling in natural ecosystems and in wastewater treatment plants. Mathematical models function as tools to capture the complexity of these biological systems, but kinetic parameters especially of nitrite-oxidizing bacteria (NOB) are lacking because of a limited number of pure cultures until recently. In this study, we compared the nitrite oxidation kinetics of six pure cultures and one enrichment culture representing three genera of NOB (Nitrobacter, Nitrospira, Nitrotoga). With half-saturation constants (Km) between 9 and 27 μM nitrite, Nitrospira bacteria are adapted to live under significant substrate limitation. Nitrobacter showed a wide range of lower substrate affinities, with Km values between 49 and 544 μM nitrite. However, the advantage of Nitrobacter emerged under excess nitrite supply, sustaining high maximum specific activities (Vmax) of 64 to 164 μmol nitrite/mg protein/h, contrary to the lower activities of Nitrospira of 18 to 48 μmol nitrite/mg protein/h. The Vmax (26 μmol nitrite/mg protein/h) and Km (58 μM nitrite) of "Candidatus Nitrotoga arctica" measured at a low temperature of 17°C suggest that Nitrotoga can advantageously compete with other NOB, especially in cold habitats. The kinetic parameters determined represent improved basis values for nitrifying models and will support predictions of community structure and nitrification rates in natural and engineered ecosystems.

Characterization of a new marine nitrite oxidizing bacterium, Nitrospina watsonii sp. nov., a member of the newly proposed phylum "Nitrospinae"

Nitrite oxidizing bacteria are an integral part of the nitrogen cycle in marine waters, but the knowledge about their diversity is limited. Recently, a high abundance of Nitrospina-like 16S rRNA gene sequences has been detected in oceanic habitats with low oxygen content by molecular methods. Here, we describe a new strain of Nitrospina, which was sampled in 100m depth from the Black Sea. It coexisted with a not-yet cultivated chemoorganotrophic gammaproteobacterium and could be purified by classical isolation methods including Percoll density gradient centrifugation. The new Nitrospina-like bacterium grew lithoautotrophically at 28°C in diluted seawater supplemented with inorganic salts and nitrite. Gram-negative rods were characterized morphologically, physiologically and partly biochemically. The 16S rRNA gene of the new strain of Nitrospina is 97.9% similar to the described species N. gracilis and DNA/DNA hybridization experiments revealed a relatedness of 30.0%. The data from both Nitrospina species and environmental clones were used for an extensive 16S rRNA based phylogenetic study applying high quality filtering. Treeing analyses confirm the newly defined phylum status for "Nitrospinae" [18]. The results of phylogenetic and genotypic analyses support the proposal of a novel species Nitrospina watsonii sp. nov. (type strain 347(T), LMG 27401(T), NCIMB 14887(T)).

Isolation of sublineage I Nitrospira by a novel cultivation strategy

Nitrification is an important process in the biogeochemical nitrogen cycle and is widely exploited in biological wastewater treatment. Recently, Nitrospira has been recognized as the numerically dominant nitrite-oxidizing bacterial genus and is primarily responsible for the second step of aerobic nitrification. Nevertheless, the physiological properties of Nitrospira remain poorly understood because the organisms are difficult to isolate and culture. Here, we report a novel cultivation strategy for obtaining members of the Nitrospira sublineage I in pure culture. The method combines: (i) selective enrichment of Nitrospira using a continuous feeding reactor and (ii) purification followed by sub-cultivation via a cell sorting system by focusing on the unique characteristics of Nitrospira forming spherical micro-colonies. This strategy is potentially applicable to other uncultured or unisolated Nitrospira and could accelerate the physiological and biochemical understandings of this important group of organisms.

Isolation of Nitrospira belonging to sublineage II from a wastewater treatment plant

Nitrite oxidation is a key step in nitrogen removal in biological wastewater treatment plants. Recently, two phylogenetically different Nitrospira (sublineages I and II) have been recognized as the numerically dominant nitrite-oxidizing bacteria in wastewater treatment plants. However, Nitrospira sublineage II inhabiting activated sludge was not isolated and its detailed properties were unclear. In this study, we developed a new method for the isolation of Nitrospira forming micro-colonies using a cell sorter. We obtained a novel pure strain "Nitrospira japonica" from the activated sludge. Subsequently, phylogenetic and physiological analyses revealed that Nitrospira japonica belongs to sublineage II and grew in medium containing formate. This method has the potential to isolate other uncultured microorganisms forming micro-colonies.

The nitrite-oxidizing community in activated sludge from a municipal wastewater treatment plant determined by fatty acid methyl ester-stable isotope probing

Metabolically-active autotrophic nitrite oxidizers from activated sludge were labeled with (13)C-bicarbonate under exposure to different temperatures and nitrite concentrations. The labeled samples were characterized by FAME-SIP (fatty acid methyl ester-stable isotope probing). The compound cis-11-palmitoleic acid, which is the major lipid of the most abundant nitrite oxidizer in activated sludge, Candidatus Nitrospira defluvii, showed (13)C-incorporation in all samples exposed to 3 mM nitrite. Subsequently, the lipid cis-7-palmitoleic acid was labeled, and it indicated the activity of a nitrite oxidizer that was different from the known Nitrospira taxa in activated sludge. The highest incorporation of cis-7-palmitoleic acid label was found after incubation with a nitrite concentration of 0.3 mM at 17 and 22°C. While activity of Nitrobacter populations could not be detected by the FAME-SIP approach, an unknown nitrite oxidizer with the major lipid cis-9 isomer of palmitoleic acid exhibited (13)C-incorporation at 28°C with 30 mM nitrite. These results indicated flexibility of nitrite-oxidizing guilds in a complex community responding to different conditions. Labeled lipids so far not described for activated sludge-associated nitrifiers indicated the presence of unknown nitrite oxidizers in this habitat. The FAME-SIP-based information can be used to define appropriate conditions for the enrichment of nitrite-oxidizing guilds from complex samples.

Selective enrichment of two different types of Nitrospira-like nitrite-oxidizing bacteria from a wastewater treatment plant

Nitrification is an important step in nitrogen removal in biological wastewater treatment processes. Recently, Nitrospira have been recognized as the numerically dominant nitrite-oxidizing bacterial genus primarily responsible for the second step of aerobic nitrification; however, Nitrospira usually resist cultivation under laboratory conditions and only one species enriched from activated sludge has been described. In this study, a novel enrichment method for Nitrospira was successfully developed using continuous feeding bioreactors. By controlling nitrite concentrations strictly in the bioreactor at low levels below 10 mg-N L⁻¹, coexisting members of sublineages I and II of the genus Nitrospira were enriched selectively. The maximum ratios of sublineages I and II to total microbial cells achieved 88.3% and 53.8%, respectively. This enrichment method is potentially applicable to other uncultured Nitrospira.

The Genome of Nitrospina gracilis Illuminates the Metabolism and Evolution of the Major Marine Nitrite Oxidizer

In marine systems, nitrate is the major reservoir of inorganic fixed nitrogen. The only known biological nitrate-forming reaction is nitrite oxidation, but despite its importance, our knowledge of the organisms catalyzing this key process in the marine N-cycle is very limited. The most frequently encountered marine NOB are related to Nitrospina gracilis, an aerobic chemolithoautotrophic bacterium isolated from ocean surface waters. To date, limited physiological and genomic data for this organism were available and its phylogenetic affiliation was uncertain. In this study, the draft genome sequence of N. gracilis strain 3/211 was obtained. Unexpectedly for an aerobic organism, N. gracilis lacks classical reactive oxygen defense mechanisms and uses the reductive tricarboxylic acid cycle for carbon fixation. These features indicate microaerophilic ancestry and are consistent with the presence of Nitrospina in marine oxygen minimum zones. Fixed carbon is stored intracellularly as glycogen, but genes for utilizing external organic carbon sources were not identified. N. gracilis also contains a full gene set for oxidative phosphorylation with oxygen as terminal electron acceptor and for reverse electron transport from nitrite to NADH. A novel variation of complex I may catalyze the required reverse electron flow to low-potential ferredoxin. Interestingly, comparative genomics indicated a strong evolutionary link between Nitrospina, the nitrite-oxidizing genus Nitrospira, and anaerobic ammonium oxidizers, apparently including the horizontal transfer of a periplasmically oriented nitrite oxidoreductase and other key genes for nitrite oxidation at an early evolutionary stage. Further, detailed phylogenetic analyses using concatenated marker genes provided evidence that Nitrospina forms a novel bacterial phylum, for which we propose the name Nitrospinae.

Nitrification performance and microbial ecology of nitrifying bacteria in a full-scale membrane bioreactor treating TFT-LCD wastewater

This study investigated nitrification performance and nitrifying community in one full-scale membrane bioreactor (MBR) treating TFT-LCD wastewater. For the A/O MBR system treating monoethanolamine (MEA) and dimethyl sulfoxide (DMSO), no nitrification was observed, due presumably to high organic loading, high colloidal COD, low DO, and low hydraulic retention time (HRT) conditions. By including additional A/O or O/A tanks, the A/O/A/O MBR and the O/A/O MBR were able to perform successful nitrification. The real-time PCR results for quantification of nitrifying populations showed a high correlation to nitrification performance, and can be a good indicator of stable nitrification. Terminal restriction fragment length polymorphism (T-RFLP) results of functional gene, amoA, suggest that Nitrosomonas oligotropha-like AOB seemed to be important to a good nitrification in the MBR system. In the MBR system, Nitrobacter- and Nitrospira-like NOB were both abundant, but the low nitrite environment is likely to promote the growth of Nitrospira-like NOB.

Nitrification expanded: discovery, physiology and genomics of a nitrite-oxidizing bacterium from the phylum Chloroflexi

Nitrite-oxidizing bacteria (NOB) catalyze the second step of nitrification, a major process of the biogeochemical nitrogen cycle, but the recognized diversity of this guild is surprisingly low and only two bacterial phyla contain known NOB. Here, we report on the discovery of a chemolithoautotrophic nitrite oxidizer that belongs to the widespread phylum Chloroflexi not previously known to contain any nitrifying organism. This organism, named Nitrolancetus hollandicus, was isolated from a nitrifying reactor. Its tolerance to a broad temperature range (25–63 °C) and low affinity for nitrite (K_s=1 mℳ), a complex layered cell envelope that stains Gram positive, and uncommon membrane lipids composed of 1,2-diols distinguish N. hollandicus from all other known nitrite oxidizers. N. hollandicus grows on nitrite and CO₂, and is able to use formate as a source of energy and carbon. Genome sequencing and analysis of N. hollandicus revealed the presence of all genes required for CO₂ fixation by the Calvin cycle and a nitrite oxidoreductase (NXR) similar to the NXR forms of the proteobacterial nitrite oxidizers, Nitrobacter and Nitrococcus. Comparative genomic analysis of the nxr loci unexpectedly indicated functionally important lateral gene transfer events between Nitrolancetus and other NOB carrying a cytoplasmic NXR, suggesting that horizontal transfer of the NXR module was a major driver for the spread of the capability to gain energy from nitrite oxidation during bacterial evolution. The surprising discovery of N. hollandicus significantly extends the known diversity of nitrifying organisms and likely will have implications for future research on nitrification in natural and engineered ecosystems.

Graph-based deconvolution analysis of multiplex sandwich microarray immunoassays: applications for environmental monitoring

The sandwich microarray immunoassay (SMI) is a powerful technique for the analysis and characterization of environmental samples, from the identification of microorganisms to specific bioanalytes. As the number of antibodies increases, however, unspecific binding and cross-reactivity can become a problem. To cope with such difficulties, we present here the concept of antibody graph associated to a sandwich antibody microarray. Antibody graphs give valuable information about the antibody cross-reactivity network and all the players involved in the sandwich format: capturing and tracer antibodies, the antigenic sample and the degree of cross-reactivity between antibodies. Making use of the information contained in the antibody graph, we have developed a deconvolution method that disentangles the antibody cross-reactivity events and gives qualitative information about the composition of the experimental sample under study. We have validated the method by using a 66 antibody-containing microarray to describe known antigenic mixtures as well as natural environmental samples characterized by 16S-RNA gene phylogenetic analysis. The application of our antibody graph and deconvolution method allowed us to discriminate between true specific antigen-antibody reactions and spurious signals on a microarray designed for environmental monitoring.

Cultivation, growth physiology, and chemotaxonomy of nitrite-oxidizing bacteria

Lithoautotrophic nitrite-oxidizing bacteria (NOB) are known as fastidious microorganisms, which are hard to maintain and not many groups are trained to keep them in culture. They convert nitrite stoichiometrically to nitrate and growth is slow due to the poor energy balance. NOB are comprised of five genera, which are scattered among the phylogenetic tree. Because NOB proliferate in a broad range of environmental conditions (terrestrial, marine, acidic) and have diverse lifestyles (lithoautotrophic, mixotrophic, and heterotrophic), variation in media composition is necessary to match their individual growth requirements in the laboratory. From Nitrobacter and Nitrococcus relatively high cell amounts can be achieved by consumption of high nitrite concentrations, whereas accumulation of cells belonging to Nitrospira, Nitrospina, or the new candidate genus Nitrotoga needs prolonged feeding procedures. Isolation is possible for planktonic cells by dilution series or plating techniques, but gets complicated for strains with a tendency to develop microcolonies like Nitrospira. Physiological experiments including determination of the temperature or pH-optimum can be conducted with active laboratory cultures of NOB, but the attainment of reference values like cell protein content or cell numbers might be hard to realize due to the formation of flocs and the low cell density. Monitoring of laboratory enrichments is necessary especially if several species or genera coexist within the same culture and due to population shifts over time. Chemotaxonomy is a valuable method to identify and quantify NOB in biofilms and pure cultures alike, since fatty acid profiles reflect their phylogenetic heterogeneity. This chapter focusses on methods to enrich, isolate, and characterize NOB by various cultivation-based techniques.

Enrichment and physiological characterization of a novel Nitrospira-like bacterium obtained from a marine sponge

Members of the nitrite-oxidizing genus Nitrospira are most likely responsible for the second step of nitrification, the conversion of nitrite (NO(2)(-)) to nitrate (NO(3)(-)), within various sponges. We succeeded in obtaining an enrichment culture of Nitrospira derived from the mesohyl of the marine sponge Aplysina aerophoba using a traditional cultivation approach. Electron microscopy gave first evidence of the shape and ultrastructure of this novel marine Nitrospira-like bacterium (culture Aa01). We characterized these bacteria physiologically with regard to optimal incubation conditions, especially the temperature and substrate range in comparison to other Nitrospira cultures. Best growth was obtained at temperatures between 28 degrees C and 30 degrees C in mineral medium with 70% North Sea water and a substrate concentration of 0.5 mM nitrite under microaerophilic conditions. The Nitrospira culture Aa01 is very sensitive against nitrite, because concentrations higher than 1.5 mM resulted in a complete inhibition of growth. Sequence analyses of the 16S rRNA gene revealed that the novel Nitrospira-like bacterium is separated from the sponge-specific subcluster and falls together with an environmental clone from Mediterranean sediments (98.6% similarity). The next taxonomically described species Nitrospira marina is only distantly related, with 94.6% sequence similarity, and therefore the culture Aa01 represents a novel species of nitrite-oxidizing bacteria.

Advanced imaging techniques for assessment of structure, composition and function in biofilm systems

Scientific imaging represents an important and accepted research tool for the analysis and understanding of complex natural systems. Apart from traditional microscopic techniques such as light and electron microscopy, new advanced techniques have been established including laser scanning microscopy (LSM), magnetic resonance imaging (MRI) and scanning transmission X-ray microscopy (STXM). These new techniques allow in situ analysis of the structure, composition, processes and dynamics of microbial communities. The three techniques open up quantitative analytical imaging possibilities that were, until a few years ago, impossible. The microscopic techniques represent powerful tools for examination of mixed environmental microbial communities usually encountered in the form of aggregates and films. As a consequence, LSM, MRI and STXM are being used in order to study complex microbial biofilm systems. This mini review provides a short outline of the more recent applications with the intention to stimulate new research and imaging approaches in microbiology.

Temperature influences the population structure of nitrite-oxidizing bacteria in activated sludge

Activated sludge from the municipal waste water treatment plant in Hamburg was seeded with mineral nitrite medium and incubated at 10°C, 17°C and 28°C. Dominant lithoautotrophic nitrite-oxidizing bacteria have been identified by electron microscopy, denaturing and temperature gradient gel electrophoresis and PCR with genus-specific primer pairs. The results have revealed the existence of three different genera of nitrite-oxidizing bacteria, namely Nitrospira, Nitrobacter and a novel cold-adapted nitrite oxidizer. As shown by electron microscopy members of the novel genus coexisted in activated sludge together with Nitrospira. A temperature-dependent shift in the population structure was demonstrated by cultivation-based approaches. The novel nitrite oxidizer was enriched at temperatures of 10°C and 17°C. Representatives of Nitrospira were able to grow in a broad temperature range between 10°C and 28°C and members of Nitrobacter were enriched during incubations at 17°C and 28°C. By subsequent 16S rDNA sequencing, the cold-adapted nitrite oxidizer was shown to be closely related to the betaproteobacterium 'Candidatus Nitrotoga arctica'. These findings demonstrated that the population structure of nitrite-oxidizing bacteria in activated sludge is more complex than previously thought and responds strongly to long-term temperature changes.

Nitrifying community structures and nitrification performance of full-scale municipal and swine wastewater treatment plants

This study evaluated nitrification performance and microbial ecology of nitrifying sludge in two full-scale wastewater treatment plants (WWTPs) including a municipal WWTP treating 20mgNL(-1) of ammonium and a swine WWTP treating 220mgNL(-1) of ammonium. These two plants differed in both wastewater characteristics and operating parameters, such as influent COD, TKN, ammonium, hydraulic retention time, and solids retention time, even though both plants achieve >85% nitrification efficiency. By employing molecular techniques, including terminal restriction fragment length polymorphism, cloning-sequencing and phylogenetic analyses targeting the 16S ribosomal RNA and group specific ammonia-monooxygenase functional gene (amoA), microbial community structures of nitrifying sludge and their significance to nitrification performance were evaluated. The results reveal that for the municipal WWTP Nitrosomonas marina-like AOB (ammonia-oxidizing bacteria) and Nitrospira-like NOB (nitrite-oxidizing bacteria) were the ubiquitously dominant nitrifiers, while Nitrosomonas europaea-, Nitrosomonas oligotropha-, and Nitrosospira-like AOB and Nitrobacter- and Nitrospira-like NOB were the major nitrifying populations found in the swine WWTP. The observed dissimilar nitrifying populations prevailing in these two plants may be related to niche differentiation concerning ammonium concentrations, system operation, and salinity. Moreover, our results suggest that the swine nitrifying sludge, involving relatively diverse AOB and NOB populations that perform the same task but with distinct growth and survival characters, may allow communities to maintain nitrifying capabilities when conditions change such as sudden increases in ammonium concentrations as examined with nitrification kinetic batch tests.

A 200-antibody microarray biochip for environmental monitoring: searching for universal microbial biomarkers through immunoprofiling

Environmental biomonitoring approaches require the measurement of either unequivocal biomarkers or specific biological profiles. Antibody microarrays constitute new tools for fast and reliable analysis of up to hundreds of biomarkers simultaneously. Herein we report 150 new polyclonal antibodies against microbial strains and environmental extracts, as well as the construction and validation of an antibody microarray (EMCHIP200, for "Environmental Monitoring Chip") containing 200 different antibodies. Each antibody was tested against its antigen for its specificity and cross-reactivity by a sandwich microarray immunoassay. The limit of detection was 0.2 ng mL (-1) for some proteins and 10 (4)-10 (5) cells mL (-1) for bacterial cells and spores. Partial biochemical characterization allowed identification of polymeric compounds (proteins and polysaccharides) as some of the targets recognized by the antibodies. We have successfully used the EMCHIP200 for the detection of biological polymers in samples from extreme environments around the world (e.g., a deep South African mine, Antarctica's dry valleys, Yellowstone National Park, Iceland, and Rio Tinto surface and subsurface). Clustering analysis permitted us to associate similar immunoprofiles or patterns to samples from apparently very different environments, indicating that they indeed share similar universal biomarkers. Our EMCHIP200 constitutes a new generation of immunosensors for biomarker detection and profiling, for either environmental, industrial, biotechnological, or astrobiological applications.

Nitrite-oxidizing bacteria guild ecology associated with nitrification failure in a continuous-flow reactor

Nitrification is an important process for nitrogen removal in many wastewater treatment plants, which requires the mutualistic oxidation of ammonia to nitrate by ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB). However, this process can be quite unpredictable because both guilds are conditionally sensitive to small changes in operating conditions. Here, dynamics are examined within the NOB guild in two parallel chemostats operated at low and high dilution rates (0.10 and 0.83 day(-1), respectively) during periods of varying nitrification performance. NOB and AOB guild abundances and nitrogen-oxidation efficiency were relatively constant over time in the 0.10 day(-1) reactor; however, the 0.83 day(-1) reactor had two major disturbance episodes that caused destabilization of the NOB guild, which ultimately led to nitrification failure. The first episode caused the extinction of Nitrospira spp. from the system, resulting in chronic incomplete ammonia oxidation and nitrite accumulation. The second episode caused complete loss of nitrification activity, likely resulting from metal toxicity and the previous extinction of Nitrospira spp. from the system. These results exemplify the types of changes that can occur within the NOB guild that result in process impairment or failure, and provide one possible explanation for why nitrification is often unstable at higher dilution rates.

The phylogeny of the genus Nitrobacter based on comparative rep-PCR, 16S rRNA and nitrite oxidoreductase gene sequence analysis

Strains of Nitrobacter mediate the second step in the nitrification process by oxidizing nitrite to nitrate. The phylogenetic diversity of the genus is currently not well investigated. In this study, a rep-PCR profile and the nearly complete 16S rRNA gene sequence of 30 strains, comprising a wide physiological as well as ecological diversity and encompassing representatives of the four species, were determined. The sequence diversity of the 16S rRNA gene between different species was low, indicating the need for additional phylogenetic markers. Therefore, primers were developed for amplifying the complete nxrX gene and a 380bp fragment of the nxrB1 gene, which are both genes involved in the nitrite oxidation process. These genes confirmed the division into phylogenetic groups revealed by the 16S rRNA gene but showed a better discriminatory power. They can be a valuable additional tool for phylogenetic analysis within the genus Nitrobacter and can assist in the identification of new Nitrobacter isolates.

Selective enrichment and molecular characterization of a previously uncultured Nitrospira-like bacterium from activated sludge

Previously uncultured nitrite-oxidizing bacteria affiliated to the genus Nitrospira have for the first time been successfully enriched from activated sludge from a municipal wastewater treatment plant. During the enrichment procedure, the abundance of the Nitrospira-like bacteria increased to approximately 86% of the total bacterial population. This high degree of purification was achieved by a novel enrichment protocol, which exploits physiological features of Nitrospira-like bacteria and includes the selective repression of coexisting Nitrobacter cells and heterotrophic contaminants by application of ampicillin in a final concentration of 50 microg ml(-1). The enrichment process was monitored by electron microscopy, fluorescence in situ hybridization (FISH) with rRNA-targeted probes and fatty acid profiling. Phylogenetic analysis of 16S rRNA gene sequences revealed that the enriched bacteria represent a novel Nitrospira species closely related to uncultured Nitrospira-like bacteria previously found in wastewater treatment plants and nitrifying bioreactors. The enriched strain is provisionally classified as 'Candidatus Nitrospira defluvii'.

Competition betweenNitrospira spp. andNitrobacter spp. in nitrite-oxidizing bioreactors

In this work the question was addressed if in nitrite-oxidizing activated sludge systems the environmental competition between Nitrobacter spp. and Nitrospira spp., which only recently has been discovered to play a role in these systems, is affected by the nitrite concentrations. Two parallel chemostats were inoculated with nitrifying-activated sludge containing Nitrospira and operated under identical conditions. After addition of Nitrobacter to both chemostats, the nitrite concentration in the influent of one of the chemostats was increased such that nitrite peaks in the bulk liquid of this reactor were detected. The other chemostat served as control reactor, which always had a constant nitrite influent concentration. The relative cellular area (RCA) of Nitrospira and Nitrobacter was determined by quantitative fluorescence in situ hybridization (FISH). The nitrite perturbation stimulated the growth of Nitrobacter while in the undisturbed control chemostat Nitrospira dominated. Overall, the results of this experimental study support the hypothesis that Nitrobacter is a superior competitor when resources are abundant, while Nitrospira thrive under conditions of resource scarcity. Interestingly, the dominance of Nitrobacter over Nitrospira, caused by the elevated nitrite concentrations, could not be reverted by lowering the available nitrite concentration to the original level. One possible explanation for this result is that when Nitrobacter is present at a certain cell density it is able to inhibit the growth of Nitrospira. An alternative explanation would be that the length of the experimental period was not long enough to observe an increase of the Nitrospira population.

Nitrobacter and Nitrospira genera as representatives of nitrite-oxidizing bacteria: detection, quantification and growth along the lower Seine River (France)

Pollution from agriculture and urban effluents influences the ecology and biochemical functioning of the Seine River. Nitrification dominates nitrogen transformations downstream of the effluents of the Paris wastewater treatment plant (WWTP) at Achères, treating, by activated sludge the wastewater of 6.5 million inhabitant equivalents from Paris and its suburbs, without nitrification and denitrification treatment. It discharges effluents containing large amounts of nitrogen, ammonium mostly (approximately 30 mg L(-1) N-NH(4+) L(-1)), on average 45 mg L(-1) of suspended particulate matter, high quantities of total organic carbon (approximately 30 mg C L(-1)) largely biodegradable (40%), and high concentration in total phosphorus ( approximately 3 mg Tot P L(-1)), as well as microorganisms. Ammonium, brought into the river system, is slowly nitrified in the lower Seine River and especially in the freshwater estuary. The nitrifying activities can be observed by measuring inorganic nitrogen compound concentrations and potential activities. To understand the contributions of the WWTP effluents, the upstream agricultural runoff water and the Seine tributaries, it is useful to investigate the bacterial community. Whereas ammonia oxidation has been widely studied, the second step, i.e. nitrite oxidation, is less well understood. We have previously analysed the ammonium-oxidizing bacterial (AOB) community in the Seine (Cébron, A., Berthe, T., Garnier, J., 2003. Nitrification and nitrifying bacteria in the lower Seine River and estuary (France). Appl. Environ. Microbiol. 69, 7091-7100; Cébron, A., Coci, M., Garnier, J., Laanbroek, H.J., 2004. DGGE analysis of the ammonia oxidizing bacterial community structure in the lower Seine River: impact of the Paris wastewater effluents. Appl. Environ. Microbiol. 70, 6726-6737), and focus here on the composition of the nitrite-oxidizing bacterial (NOB) community. As no general molecular probe targeting all known NOBs is currently available, we chose to target and quantify (by competitive PCR) the two genera Nitrobacter and Nitrospira assumed to be the major players in nitrite oxidation in freshwater environments. Nitrobacter species were dominant in the upstream Seine River basin but Nitrospira was the dominant NOB downstream of the WWTP. These two genera were equally represented in WWTP effluents. In the Seine River estuary, especially in the salinity gradient, the Nitrobacter proportion increases and that of Nitrospira disappears, possibly due dilution by seawater.

Moderately thermophilic nitrifying bacteria from a hot spring of the Baikal rift zone

Samples from three hot springs (Alla, Seya and Garga) located in the northeastern part of Baikal rift zone (Buryat Republic, Russia) were screened for the presence of thermophilic nitrifying bacteria. Enrichment cultures were obtained solely from the Garga spring characterized by slightly alkaline water (pH 7.9) and an outlet temperature of 75 degrees C. The enrichment cultures of the ammonia- and nitrite oxidizers grew at temperature ranges of 27-55 and 40-60 degrees C, respectively. The temperature optimum was approximately 50 degrees C for both groups and thus they can be designated as moderate thermophiles. Ammonia oxidizers were identified with classical and immunological techniques. Representatives of the genus Nitrosomonas and Nitrosospira-like bacteria with characteristic vibroid morphology were detected. The latter were characterized by an enlarged periplasmic space, which has not been previously observed in ammonia oxidizers. Electron microscopy, denaturing gradient gel electrophoresis analyses and partial 16S rRNA gene sequencing provided evidence that the nitrite oxidizers were members of the genus Nitrospira.

Genera-specific immunofluorescence labeling of ammonia oxidizers with polyclonal antibodies recognizing both subunits of the ammonia monooxygenase

Polyclonal antibodies that recognize the two subunits AmoA and AmoB of the ammonia monooxygenase (AMO) were applied to identify ammonia-oxidizing bacteria by immunofluorescence (IF) labeling in pure, mixed, and enriched cultures. The antibodies against the AmoA were produced using a synthetic peptide of the AmoA of Nitrosomonas eutropha, whereas the antibodies against the AmoB had been developed previously is against the whole B-subunit of the AMO [Pinck et al. (2001) Appl Environ Microbiol 67:118-124]. Using IF labeling, the AmoA antibodies were specific for the detection of all species of the genus Nitrosomonas. In contrast, the antiserum against AmoB labeled all genera of ammonia oxidizers of the beta-subclass of Proteobacteria (Nitrosomonas, Nitrosospira, Nitrosolobus, and Nitrosovibrio). The fluorescence signals of the AmoA antibodies were spread all over the cells, whereas the signals of the AmoB antibodies were associated with the cytoplasmic membranes. The specificity of the reactions of the antisera with ammonia oxidizers were proven in pure and mixed cultures, and the characteristic IF labeling and the morphology of the cells enabled their identification at the genus level. The genus-specific IF labeling could be used to identify ammonia oxidizers enriched from various habitats. In enrichment cultures of natural sandstone, cells of the genera Nitrosomonas, Nitrosovibrio, and Nitrosospira were detected. Members of the genus Nitrosovibrio and Nitrosolobus were most prominent in enriched garden soil samples, whereas members of the genus Nitrosomonas dominated in enriched activated sludge. The antibodies caused only slight background fluorescence on sandstone and soil particles compared to oligonucleotide probes, which could not be used to detect ammonia oxidizers on these materials because of strong nonspecific fluorescence.

Detection methods for the expression of the dissimilatory copper-containing nitrite reductase gene (DnirK) in environmental samples

In situ assays, based on monoclonal antibodies (mAbs), were developed to study the microbial expression of the bacterial dissimilatory copper-containing nitrite reductase gene (DnirK), one of the key enzymes involved in denitrification, in different ecosystems. With a combination of an anti-DnirK mAb and phylogenetic oligonucleotide probes, it is possible to bring structural and functional aspects of microbial communities together. To perform a double labelling, yielding a high signal strength for both the oligonucleotide and the antibody, cells have to be labelled with the oligonucleotide first followed by immunostaining. When the labelling sequence was changed, the accessibility for the oligonucleotide was reduced if high amounts of DnirK were expressed. Using flow cytometry, it was possible to sort bacterial cells, which were stained by the antibody, from nonlabelled cells. This technique provides means for a detailed analysis of populations, which express DnirK genes in the environment, including structural aspects of a community and detailed promoter studies. Using the immunostaining approach, it was possible to identify bacteria, which have the DnirK system expressed, in samples from a wastewater sewage treatment plant as well as in samples from the rhizosphere of wheat roots. Furthermore, expression studies using an Ochrobactrum anthropi strain were carried out to investigate the correlation between N(2)O production rates and DnirK expression in batch cultures, which had been shifted from aerobic to anaerobic conditions. As expected, expression of DnirK was the highest during periods with the greatest synthesis rates for N(2)O. However, the amount of expressed enzyme was not reduced in the cells, although the N(2)O production rates dropped in the cultures 12 h after the shift from aerobic to anaerobic conditions.

Use of polyclonal antibodies to detect and quantify the NOR protein of nitrite oxidizers in complex environments

In the approaches or models which aim to understand and/or predict how the functioning of ecosystems may be affected by perturbations or disturbances, little attention is generally given to microorganisms. Even when they are taken into account as indicators, variables which are poorly informative about the changes in the microbial functioning (microbial biomass or diversity or total number of microorganisms) are often used. To be able to estimate, in complex environments, the quantity of enzymes involved in key ecosystem processes may constitute a useful complementary tool. Here, we describe an immunological method for detecting and quantifying, in complex environments, the nitrite oxidoreductase (NOR), responsible for the oxidation of nitrite to nitrate. The alpha-catalytic subunit of the enzyme was purified from Nitrobacter hamburgensis and used for the production of polyclonal antibodies. These antibodies were used to detect and quantify the NOR by a chemifluorescence technique on Western blots after separation of total proteins from pure cultures and soil samples. They recognized the alpha-NOR of all the Nitrobacter species described to date, but no reaction was observed with members of other nitrite-oxidizing genera. The detection threshold and reproducibility of the proposed method were evaluated. The feasibility of its use to quantify NOR in a soil was tested.

Ammonia-oxidizing bacteria: a model for molecular microbial ecology

The eutrophication of many ecosystems in recent decades has led to an increased interest in the ecology of nitrogen transformation. Chemolitho-autotrophic ammonia-oxidizing bacteria are responsible for the rate-limiting step of nitrification in a wide variety of environments, making them important in the global cycling of nitrogen. These organisms are unique in their ability to use the conversion of ammonia to nitrite as their sole energy source. Because of the importance of this functional group of bacteria, understanding of their ecology and physiology has become a subject of intense research over recent years. The monophyletic nature of these bacteria in terrestrial environments has facilitated molecular biological approaches in studying their ecology, and progress in this field has been rapid. The ammonia-oxidizing bacteria of the beta-subclass Proteobacteria have become somewhat of a model system within molecular microbial ecology, and this chapter reviews recent progress in our knowledge of their distribution, diversity, and ecology.

Fatty acid profiles of nitrite-oxidizing bacteria reflect their phylogenetic heterogeneity

The fatty acid profiles of all described species of the nitrite-oxidizing genera Nitrobacter, Nitrococcus, Nitrospina and Nitrospira were analyzed. The four genera had distinct profiles, which can be used for the differentiation and allocation of new isolates to these genera. The genus Nitrobacter is characterized by vaccenic acid as the main compound with up to 92% of the fatty acids and the absence of hydroxy fatty acids. The genus Nitrococcus showed cis-9-hexadecenoic acid, hexadecanoic acid and vaccenic acid as main parts. Small amounts of 3-hydroxy-dodecanoic acid were detected. The genus Nitrospina possessed tetradecanoic acid and cis-9-hcxadecenoic acid as main compounds, also 3-hydroxy-hexadecanoic acid was detected for this genus. The genus Nitrospira showed a pattern with more variations among the two described species. These organisms are characterized by the cis-7 and cis-11-isomers of hexadecenoic acid. For Nitrospira moscoviensis a specific new fatty acid was found, which represented the major constituent in the fatty acid profiles of autotrophically grown cultures. It was identified as 11-methyl-hexadecanoic acid. Since this compound is not known for other bacterial taxa, it represents a potential lipid marker for the detection of Nitrospira moscoviensis relatives in enrichment cultures and environmental samples. A cluster analysis of the fatty acid profiles is in accordance with 16S rRNA sequence-based phylogeny of the nitrite-oxidizing bacteria.

Polyclonal antibodies recognizing the AmoB protein of ammonia oxidizers of the beta-subclass of the class Proteobacteria

A 41-kDa protein of Nitrosomonas eutropha was purified, and the N-terminal amino acid sequence was found to be nearly identical with the sequence of AmoB, a subunit of ammonia monooxygenase. This protein was used to develop polyclonal antibodies, which were highly specific for the detection of the four genera of ammonia oxidizers of the beta-subclass of Proteobacteria (Nitrosomonas, including Nitrosococcus mobilis, which belongs phylogenetically to Nitrosomonas; Nitrosospira; Nitrosolobus; and Nitrosovibrio). In contrast, the antibodies did not react with ammonia oxidizers affiliated with the gamma-subclass of Proteobacteria (Nitrosococcus oceani and Nitrosococcus halophilus). Moreover, methane oxidizers (Methylococcus capsulatus, Methylocystis parvus, and Methylomonas methanica) containing the related particulate methane monooxygenase were not detected. Quantitative immunoblot analysis revealed that total cell protein of N. eutropha consisted of approximately 6% AmoB, when cells were grown using standard conditions (mineral medium containing 10 mM ammonium). This AmoB amount was shown to depend on the ammonium concentration in the medium. About 14% AmoB of total protein was found when N. eutropha was grown with 1 mM ammonium, whereas 4% AmoB was detected when 100 mM ammonium were used. In addition, the cellular amount of AmoB was influenced by the absence of the substrate. Cells starved for more than 2 months contained nearly twice as much AmoB as actively growing cells, although these cells possessed low ammonia-oxidizing activity. AmoB was always present and could even be detected in cells of Nitrosomonas after 1 year of ammonia starvation.