Diversity and abundance of anammox bacterial community in the deep-ocean surface sediment from equatorial Pacific

Impact of TiO2, ZnO, and Ag nanoparticles on anammox activity in enriched river Nile sediment cultures: unveiling differential effects and environmental implications

BACKGROUND

The increasing use of nanoparticles (NPs) necessitates investigation of their impact on wastewater treatment processes, particularly anammox, a critical biological nitrogen removal pathway. This study explored the effects of short-term exposure to TiO2, ZnO, and Ag-NPs on anammox activity in enriched cultures derived from River Nile sediments.

MATERIALS AND METHODS

Anammox bacteria were identified and enriched, with activity confirmed through 16S rRNA and hydrazine oxidoreductase (hzo) gene amplification and sequencing. Activity assays demonstrated efficient ammonium removal by the enriched culture. Subsequently, the impact of different sized and concentrated NPs on anammox activity was assessed.

RESULTS

XRD analysis confirmed NP behavior within the microcosms: TiO2 transformed, ZnO partially dissolved, and Ag remained ionic. hzo gene expression served as a biomarker for anammox bacterial activity. Interestingly, 100 nm TiO2-NPs up-regulated hzo expression, potentially indicating a non-inhibitory transformed phase. Conversely, ZnO and Ag-NPs across all sizes and concentrations significantly down-regulated hzo expression, suggesting detrimental effects. Ag-NPs amended microcosms showed a significant reduction (79%) in hzo gene expression and a detrimental effect on bacterial populations. Overall, anammox activity mirrored hzo expression patterns, with TiO2 (21 and 25 nm, respectively) exhibiting the least inhibition, followed by ZnO and Ag-NPs.

CONCLUSION

This study highlights the differential effects of NPs on anammox, with the order of impact being Ag > ZnO > TiO2. These findings provide valuable insights into the potential environmental risks of NPs on anammox-mediated nitrogen cycling in freshwater ecosystems.

Diversity and Distribution of Anaerobic Ammonium Oxidation Bacteria in Hot Springs of Conghua, China

Anaerobic ammonium oxidation (anammox) is an important process of the nitrogen cycle, and the anammox bacteria have been studied in a wide variety of environments. However, the distribution, diversity, and abundance of anammox bacteria in hot springs remain enigmatic. In this study, the anammox process was firstly investigated in hot springs of Conghua, China. Anammox-like bacterial sequences that closely affiliated to “Candidatus Brocadia,” “Candidatus Kuenenia,” “Candidatus Scalindua,” “Candidatus Anammoxoglobus,” and “Candidatus Jettenia” were detected. Several operational taxonomic units (OTUs) from this study shared low sequence identities to the 16S rRNA gene of the known anammox bacteria, suggesting that they might be representing putative novel anammox bacteria. A quantitative PCR analysis of anammox-specific 16S rRNA gene confirmed that the abundance of anammox bacteria ranged from 1.60 × 10⁴ to 1.20 × 10⁷ copies L^–1. Nitrate was a key environmental factor defining the geographical distribution of the anammox bacterial community in the hot spring ecosystem. Dissolved inorganic carbon had a significant influence on anammox bacterial biodiversity. Our findings for the first time revealed that the diverse anammox bacteria, including putative novel anammox bacterial candidates, were present in Conghua hot spring, which extended the existence of anammox bacteria to the hot springs in China and expands our knowledge of the biogeography of anammox bacteria. This work filled up the research lacuna of anammox bacteria in Chinese hot spring habitat and would guide for enrichment strategies of anammox bacteria of Conghua hot springs.

Biostimulation of a marine anammox bacteria-dominated bioprocess by Co(II) to treat nitrogen-rich, saline wastewater

The biostimulation of a marine anammox bacteria (MAB)-dominated bioprocess with Co(II) was studied in a sequencing batch reactor (SBR) treating nitrogen-rich saline wastewater at 15 °C. The low Co(II) load of 0.0015 kgCo²⁺_added/(m^3.d) had little effect on the removal of nitrogen. The nitrite removal rate (NRR), ammonia removal rate (ARR), and specific anammox activity (SAA) reached 0.73 kg/(m³·d), 0.59 kg/(m³·d), and 0.23 kg/(kg·d), respectively, under the Co(II) load of 0.009 kgCo²⁺_added/(m^3.d). However, the loadings of Co(II) at 0.024-0.03 kgCo²⁺_added/(m^3.d) negatively affected the activity of MAB. Besides, the values of ΔNO₂^--N/ΔNH₄⁺-N (1.15-1.29) were lower than the theoretical ratio values (around 1.32) likely because of the marine commamox process. The removal of nitrogen from nitrogen-rich saline wastewater was achieved by the synergy between Candidatus Scalindua (27.11%) and Candidatus Kuenenia (9.55%). The nitrogen removal with Co(II) addition could be well described by a modified Logistic model.

Diversity of sediment associated Planctomycetes and its related phyla with special reference to anammox bacterial community in a high Arctic fjord

The fjords of west Spitsbergen Svalbard, Arctic Norway, are undergoing a transformation as the impact of nutrient rich warmer Atlantic water is significantly altering the primary production and subsequently the carbon pool. Members of the phylum Planctomycetes are ubiquitous in marine systems and are important in the mineralization of organic matter. Hence, the phylogenetic diversity and distribution pattern of Planctomycetes in the surface sediments of a high Arctic fjord, the Kongsfjorden were studied. Further, considering the release of ammonium as a part of mineralization, the diversity of bacterial community involved in anaerobic ammonium oxidation (anammox) was also evaluated. The highly diverse Planctomycetes community, which consisted mainly of uncultivated and uncharacterized Planctomycetes, was observed in the study area with a total of 162 OTUs. The major genera observed were Blastopirellula (13.3%), Gimesia (13%), Rhodopirellula (10%), Planctomicrobium (2%) and Thermogutta (1.6%). Functional prediction revealed the dominance of carbohydrate metabolism genes and the presence of gene clusters for production of secondary metabolites and xenobiotic degradation. Anammox bacterial sequences were detected from all the samples with a total of 52 OTUs. Most of the OTUs belonged to the genus Candidatus Scalindua and three distinct clusters were observed in the phylogenetic tree, (a) Ca. Scalindua brodae (49%), (b) Ca. Scalindua wagneri (31%) and (c) Ca. Scalindua marina (12%) based on their phylogenic distance. Our findings suggest the existence of highly diverse Planctomycetes and anammox bacterial community with regional variants in the sediments of Kongsfjorden.

Nitrogen removal performance of marine anammox bacteria treating nitrogen-rich saline wastewater under different inorganic carbon doses: High inorganic carbon tolerance and carbonate crystal formation

With different inorganic carbon (IC) doses, nitrogen removal performance of marine anammox bacteria (MAB) treating nitrogen-rich saline wastewater was investigated in a sequencing batch reactor. Ammonium removal efficiency (ARE) was above 99% at 108-3600 mg/L IC, which indicated MAB had a good tolerance to high IC dose. When IC was 108-1200 mg/L, ARE reached 90% within 2.5 h. MAB activity was greatly promoted by providing adequate IC. Besides, the maximal substrate conversion rate (3.4 kg/(m³ d)) was achieved at 180 mg/L IC. Both the modified Logistic and Boltzmann models were appropriate to describe nitrogen removal at low IC doses, while the modified Gompertz model was more accurate at high IC doses. Calcium carbonate crystal was formed on the surface of MAB granule at high IC doses, which resulted in a significant deterioration of nitrogen removal performance.

Anaerobic Ammonium Oxidation in Acidic Red Soils

Anaerobic ammonium oxidation (anammox) has been proven to be an important nitrogen removal process in terrestrial ecosystems, particularly paddy soils. However, the contribution of anammox in acidic red soils to nitrogen loss has not been well-documented to date. Here, we investigated the activity, abundance, and distribution of anammox bacteria in red soils collected from nine provinces of Southern China. High-throughput sequencing analysis showed that Candidatus Brocadia dominates the anammox bacterial community (93.03% of sequence reads). Quantification of the hydrazine synthase gene (hzsB) and anammox 16S rRNA gene indicated that the abundance of anammox bacteria ranged from 6.20 × 10⁶ to 1.81 × 10⁹ and 4.81 × 10⁶ to 4.54 × 10⁸ copies per gram of dry weight, respectively. Contributions to nitrogen removal by anammox were measured by a ¹⁵N isotope-pairing assay. Anammox rates in red soil ranged from 0.01 to 0.59 nmol N g⁻¹ h⁻¹, contributing 16.67–53.27% to N₂ production in the studied area, and the total amount of removed nitrogen by anammox was estimated at 2.33 Tg N per year in the natural red soils of southern China. Pearson correlation analyses revealed that the distribution of anammox bacteria significantly correlated with the concentration of nitrate and pH, whereas the abundance and activity of anammox bacteria were significantly influenced by the nitrate and total nitrogen concentrations. Our findings demonstrate that Candidatus Brocadia dominates anammox bacterial communities in acidic red soils and plays an important role in nitrogen loss of the red soil in Southern China.

Enhanced performance and kinetics of marine anammox bacteria (MAB) treating nitrogen-rich saline wastewater with Mn(II) and Ni(II) addition

A sequencing batch reactor (SBR) was used to study nitrogen removal performance of marine anammox bacteria (MAB) with Mn(II) and Ni(II) addition. The reactor was operated at 25 ± 0.5 °C with influent pH of 7.5 ± 0.1. Optimal ammonium removal efficiencies (AREs) were 93.95% and 93.18% with 0.05 mM Mn(II) and 0.025 mM Ni(II), respectively. Both Mn(II) and Ni(II) played key roles in treating nitrogen-rich saline wastewater. However, the effect resulting from Ni(II) was far stronger than Mn(II). With optimal Ni(II) addition (0.025 mM), maximal nitrogen removal rate (NRR) and specific anammox activity (SAA) increased by 14.64% and 57.88%, respectively. Modified Boltzmann model was appropriate to describe nitrogen removal at low Mn(II) and Ni(II) concentrations while remodified Logistic model could be used at high Mn(II) and Ni(II) concentrations. Mn(II) and Ni(II) dosage should be controlled within 0.075 mM to achieve good nitrogen removal in nitrogen-rich saline wastewater treatment.

Comparative analysis of two 16S rRNA gene-based PCR primer sets provides insight into the diversity distribution patterns of anammox bacteria in different environments

Due to the high divergence among 16S rRNA genes of anammox bacteria, different diversity pattern of the community could be resulted from using different primer set. In this study, the efficiencies and specificities of two commonly used sets, Amx368F/Amx820R and Brod541F/Amx820R, were evaluated by exploring the diversity characteristics of anammox bacteria in sediments from marine, estuary, and freshwater wetland. Statistical analysis indicated that the base mispairing rate between bases on 16S rRNA gene sequences retrieved by Amx368F/Amx820R and their corresponding ones on primer Brod541F was quite high, suggesting the different efficiency and specificity of Amx368F/Amx820R and Brod541F/Amx820R. Further experimental results demonstrated that multiple genera of anammox bacteria, including Ca. Scalindua, Ca. Brocadia, and Ca. Kuenenia, were able to be detected by Amx368F/Amx820R, but only Ca. Scalindua could be retrieved by Brod541F/Amx820R. Moreover, the phylogenetic clusters of Ca. Scalindua by Amx368F/Amx820R were different completely from those by Brod541F/Amx820R, presenting a significant complementary effect. By joint application of these two primer sets, the diversity distribution patterns of anammox bacteria in different environments were analyzed. Almost all retrieved sequences from marine sediments belonged to Ca. Scalindua. Sequences from freshwater wetland were affiliated to Ca. Brocadia and two new clusters, while high diversity of anammox bacteria was found in estuary, including Ca. Scalindua, Ca. Brocadia, and Ca. Kuenenia, corresponding to the river-sea intersection environmental feature. In total, these two prime sets have different characteristic for anammox bacteria detecting from environmental samples, and their combined application could achieve better diversity display of anammox community.

Biogeography of anaerobic ammonia-oxidizing (anammox) bacteria

Anaerobic ammonia-oxidizing (anammox) bacteria are able to oxidize ammonia and reduce nitrite to produce N₂ gas. After being discovered in a wastewater treatment plant (WWTP), anammox bacteria were subsequently characterized in natural environments, including marine, estuary, freshwater, and terrestrial habitats. Although anammox bacteria play an important role in removing fixed N from both engineered and natural ecosystems, broad scale anammox bacterial distributions have not yet been summarized. The objectives of this study were to explore global distributions and diversity of anammox bacteria and to identify factors that influence their biogeography. Over 6000 anammox 16S rRNA gene sequences from the public database were analyzed in this current study. Data ordinations indicated that salinity was an important factor governing anammox bacterial distributions, with distinct populations inhabiting natural and engineered ecosystems. Gene phylogenies and rarefaction analysis demonstrated that freshwater environments and the marine water column harbored the highest and the lowest diversity of anammox bacteria, respectively. Co-occurrence network analysis indicated that Ca. Scalindua strongly connected with other Ca. Scalindua taxa, whereas Ca. Brocadia co-occurred with taxa from both known and unknown anammox genera. Our survey provides a better understanding of ecological factors affecting anammox bacterial distributions and provides a comprehensive baseline for understanding the relationships among anammox communities in global environments.

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

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

A comparison of two 16S rRNA gene-based PCR primer sets in unraveling anammox bacteria from different environmental samples

Two 16S rRNA gene-based PCR primer sets (Brod541F/Amx820R and A438f/A684r) for detecting anammox bacteria were compared using sediments from Mai Po wetlands (MP), the South China Sea (SCS), a freshwater reservoir (R2), and sludge granules from a wastewater treatment plant (A2). By comparing their ability in profiling anammox bacteria, the recovered diversity, community structure, and abundance of anammox bacteria among all these diverse samples indicated that A438f/A684r performed better than Brod541F/Amx820R in retrieving anammox bacteria from these different environmental samples. Five Scalindua subclusters (zhenghei-I, SCS-I, SCS-III, arabica, and brodae) dominated in SCS whereas two Scalindua subclusters (zhenghei-II and wagneri) and one cluster of Kuenenia dominated in MP. R2 showed a higher diversity of anammox bacteria with two new retrieved clusters (R2-New-1 and R2-New-2), which deserves further detailed study. The dominance of Brocadia in sample A2 was supported by both of the primer sets used. Results collectively indicate strongly niche-specific community structures of anammox bacteria in different environments, and A438f/A684r is highly recommended for screening anammox bacteria from various environments when dealing with a collection of samples with diverse physiochemical characteristics.

Diversity and spatial distribution of hydrazine oxidoreductase (hzo) gene in the oxygen minimum zone off Costa Rica

Anaerobic ammonia oxidation (anammox) as an important nitrogen loss pathway has been reported in marine oxygen minimum zones (OMZs), but the community composition and spatial distribution of anammox bacteria in the eastern tropical North Pacific (ETNP) OMZ are poorly determined. In this study, anammox bacterial communities in the OMZ off Costa Rica (CRD-OMZ) were analyzed based on both hydrazine oxidoreductase (hzo) genes and their transcripts assigned to cluster 1 and 2. The anammox communities revealed by hzo genes and proteins in CRD-OMZ showed a low diversity. Gene quantification results showed that hzo gene abundances peaked in the upper OMZs, associated with the peaks of nitrite concentration. Nitrite and oxygen concentrations may therefore colimit the distribution of anammox bacteria in this area. Furthermore, transcriptional activity of anammox bacteria was confirmed by obtaining abundant hzo mRNA transcripts through qRT-PCR. A novel hzo cluster 2x clade was identified by the phylogenetic analysis and these novel sequences were abundant and widely distributed in this environment. Our study demonstrated that both cluster 1 and 2 anammox bacteria play an active role in the CRD-OMZ, and the cluster 1 abundance and transcriptional activity were higher than cluster 2 in both free-living and particle-attached fractions at both gene and transcriptional levels.

Presence and diversity of anammox bacteria in cold hydrocarbon-rich seeps and hydrothermal vent sediments of the Guaymas Basin

Hydrothermally active sediments are highly productive, chemosynthetic areas which are characterized by the rapid turnover of particulate organic matter under extreme conditions in which ammonia is liberated. These systems might be suitable habitats for anaerobic ammonium oxidizing (anammox) bacteria but this has not been investigated in detail. Here we report the diversity and abundance of anammox bacteria in sediments that seep cold hydrocarbon-rich fluids and hydrothermal vent areas of the Guaymas Basin in the Cortés Sea using the unique functional anammox marker gene, hydrazine synthase (hzsA). All clones retrieved were closely associated to the “Candidatus Scalindua” genus. Phylogenetic analysis revealed two distinct clusters of hzsA sequences (Ca. Scalindua hzsA cluster I and II). Comparison of individual sequences from both clusters showed that several of these sequences had a similarity as low as 76% on nucleotide level. Based on the analysis of this phylomarker, a very high interspecies diversity within the marine anammox group is apparent. Absolute numbers of anammox bacteria in the sediments samples were determined by amplification of a 257 bp fragment of the hszA gene in a qPCR assay. The results indicate that numbers of anammox bacteria are generally higher in cold hydrocarbon-rich sediments compared to the vent areas and the reference zone. Ladderanes, lipids unique to anammox bacteria were also detected in several of the sediment samples corroborating the hzsA analysis. Due to the high concentrations of reduced sulfur compounds and its potential impact on the cycling of nitrogen we aimed to get an indication about the key players in the oxidation of sulfide in the Guaymas Basin sediments using the alpha subunit of the adenosine-5′-phosphosulfate (APS) reductase (aprA). Amplification of the aprA gene revealed a high number of gammaproteobacterial aprA genes covering the two sulfur-oxidizing bacteria aprA lineages as well as sulfate-reducers.

Bacterial polycyclic aromatic hydrocarbon ring-hydroxylating dioxygenases in the sediments from the Pearl River estuary, China

Bacterial community compositions were characterized using denaturing gradient gel electrophoresis analysis of bacterial 16S rRNA gene in the sediments of the Pearl River estuary. Sequencing analyses of the excised bands indicated that Gram-negative bacteria, especially Gammaproteobacteria, were dominant in the Pearl River estuary. The diversity of polycyclic aromatic hydrocarbon ring-hydroxylating dioxygenase (PAH-RHD) gene in this estuary was then assessed by clone library analysis. The phylogenetic analyses showed that all PAH-RHD gene sequences of Gram-negative bacteria (PAH-RHD[GN]) were closely related to the nagAc gene described for Ralstonia sp. U2 or nahAc gene for Pseudomonas sp. 9816-4, while the PAH-RHD gene sequences of Gram-positive bacteria (PAH-RHD[GP]) at sampling site A1 showed high sequence similarity to the nidA gene from Mycobacterium species. Meanwhile, molecular diversity of the two functional genes was higher at the upstream of this region, while lower at the downstream. Redundancy analysis indicated that environmental factors, such as NH₄--N, ∑PAHs, pH, SiO₃--Si, and water depth, affected the distribution of the PAH-RHD[GN] gene in the Pearl River estuary.

Evaluating primers for profiling anaerobic ammonia oxidizing bacteria within freshwater environments

Anaerobic ammonia oxidizing (anammox) bacteria play an important role in transforming ammonium to nitrogen gas and contribute to fixed nitrogen losses in freshwater environments. Understanding the diversity and abundance of anammox bacteria requires reliable molecular tools, and these are not yet well established for these important Planctomycetes. To help validate PCR primers for the detection of anammox bacteria within freshwater ecosystems, we analyzed representative positive controls and selected samples from Grand River and groundwater sites, both from Ontario, Canada. The objectives of this study were to identify a suitable anammox denaturing gradient gel electrophoresis (DGGE) fingerprint method by using GC-clamp modifications to existing primers, and to verify the specificity of anammox-specific primers used for DGGE, cloning and qPCR methods. Six primer combinations were tested from four published primer sets (i.e. A438f/A684r, Amx368f/Amx820r, An7f/An1388r, and Pla46/1392r) for both direct and nested PCR amplifications. All PCR products were run subsequently on DGGE gels to compare the resulting patterns. Two anammox-specific primer combinations were also used to generate clone libraries and quantify anammox bacterial 16S rRNA genes with qPCR. The primer set A438f/A684r was highly specific to anammox bacteria, provided reliable DGGE fingerprints and generated a high proportion of anammox-related clones. A second primer set (Amx368f/Amx820r) was anammox specific, based on clone library analysis, but PCR products from different candidate species of anammox bacteria resolved poorly using DGGE analysis. Both DGGE and cloning results revealed that Ca. Brocadia and an uncharacterized anammox bacterial cluster represented the majority of anammox bacteria found in Grand River sediment and groundwater samples, respectively. Together, our results demonstrate that although Amx368f/Amx820r was useful for anammox-specific qPCR and clone library analysis, A438f/A684r was the most suitable primer set for multiple molecular assessments of anammox bacteria in freshwater environments.

How to make a living from anaerobic ammonium oxidation

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

Anammox--growth physiology, cell biology, and metabolism

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

Dominance of Candidatus Scalindua species in anammox community revealed in soils with different duration of rice paddy cultivation in Northeast China

The anaerobic ammonium-oxidizing (anammox) bacteria play an important role in the oxygen-limited zone for nitrogen cycling, but their roles in agricultural ecosystems are still poorly understood. In this study, soil samples were taken from the rhizosphere and non-rhizosphere and from surface (0–5 cm) and subsurface (20–25 cm) layers with 1, 4, and 9 years of rice cultivation history on the typical albic soil of Northeast China to examine the diversity and distribution of anammox bacteria based on 16S rRNA gene and hydrazine oxidoreductase encoding gene (hzo). By comparing these soil samples, no obvious difference was observed in community composition between the rhizosphere and non-rhizosphere or the surface and subsurface layers. Surprisingly, anammox bacterial communities of these rice paddy soils were consisted of mainly Candidatus Scalindua species, which are best known to be dominant in marine and pristine environments. The highest diversity was revealed in the 4-year paddy soil based on clone library analysis. Phylogenetic analysis of 16S rRNA gene and deduced HZO from the corresponding encoding gene showed that most of the obtained clones are grouped together with Candidatus Scalindua sorokinii, Candidatus Scalindua brodae, and Candidatus Scalindua spp. of seawater. The obtained clone sequences from all samples are distributed in two subclusters that contain sequences from environmental samples only. Tentative new species were also discovered in this paddy soil. This study provides the first evidence on the existence of anammox bacteria with limited diversity in agricultural ecosystems in Northern China.

Anaerobic ammonium oxidation (anammox) in different natural ecosystems

Anammox (anaerobic ammonium oxidation), which is a reaction that oxidizes ammonium to dinitrogen gas using nitrite as the electron acceptor under anoxic conditions, was an important discovery in the nitrogen cycle. The reaction is mediated by a specialized group of planctomycete-like bacteria that were first discovered in man-made ecosystems. Subsequently, many studies have reported on the ubiquitous distribution of anammox bacteria in various natural habitats, including anoxic marine sediments and water columns, freshwater sediments and water columns, terrestrial ecosystems and some special ecosystems, such as petroleum reservoirs. Previous studies have estimated that the anammox process is responsible for 50% of the marine nitrogen loss. Recently, the anammox process was reported to account for 9–40% and 4–37% of the nitrogen loss in inland lakes and agricultural soils respectively. These findings indicate the great potential for the anammox process to occur in freshwater and terrestrial ecosystems. The distribution of different anammox bacteria and their contribution to nitrogen loss have been described in different natural habitats, demonstrating that the anammox process is strongly influenced by the local environmental conditions. The present mini-review summarizes the current knowledge of the ecological distribution of anammox bacteria, their contribution to nitrogen loss in various natural ecosystems and the effects of major influential factors on the anammox process.

Advances in methods for detection of anaerobic ammonium oxidizing (anammox) bacteria

Anaerobic ammonium oxidation (anammox), the biochemical process oxidizing ammonium into dinitrogen gas using nitrite as an electron acceptor, has only been recognized for its significant role in the global nitrogen cycle not long ago, and its ubiquitous distribution in a wide range of environments has changed our knowledge about the contributors to the global nitrogen cycle. Currently, several groups of methods are used in detection of anammox bacteria based on their physiological and biochemical characteristics, cellular chemical composition, and both 16S rRNA gene and selective functional genes as biomarkers, including hydrazine oxidoreductase and nitrite reductase encoding genes hzo and nirS, respectively. Results from these methods coupling with advances in quantitative PCR, reverse transcription of mRNA genes and stable isotope labeling have improved our understanding on the distribution, diversity, and activity of anammox bacteria in different environments both natural and engineered ones. In this review, we summarize these methods used in detection of anammox bacteria from various environments, highlight the strengths and weakness of these methods, and also discuss the new development potentials on the existing and new techniques in the future.