Identification of anammox bacteria in a full-scale deammonification plant making use of anaerobic ammonia oxidation

The existence of anaerobic ammonia-oxidizing (anammox) bacteria was postulated in the late 1970s. Approximately 20 years later, these lithotrophic members of the nitrogen cycle were identified as deep-branching members of the planctomycetes. Recently, full-scale implementation of biological deammonification was successfully achieved in the DEMON reactor at the wastewater treatment plant in Strass, Austria. The sludge of this reactor contains red granules and brownish flocs that can be physically separated. The two fractions yielded different banding patterns in denaturing gradient gel electrophoresis of PCR products obtained with primer sets targeting the 16S rRNA genes of planctomycetes. Comparative analysis of partial sequences of almost full-length 16S rRNA gene clones obtained from the granules and flocs confirms the differences in the community composition of the two fractions. The sequences retrieved from the red granules were 93% similar to those of Candidatus Brocadia anammoxidans, a bacterium known to catalyze the anaerobic ammonia oxidation.     

16S rRNA gene and lipid biomarker evidence for anaerobic ammonium-oxidizing bacteria (anammox) in California and Nevada hot springs

Anammox, the oxidation of ammonium with nitrite to dinitrogen gas under anoxic conditions, is an important process in mesophilic environments such as wastewaters, oceans and freshwater systems, but little is known of this process at elevated temperatures. In this study, we investigated anammox in microbial mats and sediments obtained from several hot springs in California and Nevada, using geochemical and molecular microbiological methods. Anammox bacteria-specific ladderane core lipids with concentrations ranging between 0.3 and 52 ng g⁻¹ sediment were detected in five hot springs analyzed with temperatures up to 65 °C. In addition, 16S rRNA gene analysis showed the presence of genes phylogenetically related to the known anammox bacteria Candidatus Brocadia fulgida, Candidatus Brocadia anammoxidans and Candidatus Kuenenia stuttgartiensis (96.5–99.8% sequence identity) in three hot springs with temperatures up to 52 °C. Our data indicate that anammox bacteria may be able to thrive at thermophilic temperatures and thus may play a significant role in the nitrogen cycle of hot spring environments.     

Induced cooperation between marine nitrifiers and anaerobic ammonium-oxidizing bacteria by incremental exposure to oxygen

In oxygen-limited marine ecosystems cooperation between marine nitrifiers and anaerobic ammonium-oxidizing (anammox) bacteria is of importance to nitrogen cycling. Strong evidence for cooperation between anammox bacteria and nitrifiers has been provided by environmental studies but little is known about the development of such communities, the effects of environmental parameters and the physiological traits of their constituents. In this study, a marine laboratory model system was developed. Cooperation between marine nitrifiers and anammox bacteria was induced by incremental exposure of a marine anammox community dominated by Scalindua species to oxygen in a bioreactor set-up under high ammonium (40 mM influent) conditions. Changes in the activities of the relevant functional groups (anammox bacteria, aerobic ammonia oxidizers and nitrite oxidizers) were monitored by batch tests. Changes in community composition were followed by Fluorescence in situ Hybridization (FISH) and by amplification and sequencing of 16S rRNA and amoA genes. A co-culture of Scalindua sp., an aerobic ammonia-oxidizing Nitrosomonas-like species, and an aerobic (most likely Nitrospira sp.) nitrite oxidizer was obtained. Aerobic ammonia oxidizers became active immediately upon exposure to oxygen and their numbers increased 60-fold. Crenarchaea closely related to the ammonia-oxidizer Candidatus 'Nitrosopumilus maritimus' were detected in very low numbers and their contribution to nitrification was assumed negligible. Activity of anammox bacteria was not inhibited by the increased oxygen availability. The developed marine model system proved an effective tool to study the interactions between marine anammox bacteria and nitrifiers and their responses to changes in environmentally relevant conditions.     

Development of a simultaneous partial nitrification and anaerobic ammonia oxidation process in a single reactor

Up-flow oxygen-controlled biofilm reactors equipped with a non-woven fabric support were used as a single reactor system for autotrophic nitrogen removal based on a combined partial nitrification and anaerobic ammonium oxidation (anammox) reaction. The up-flow biofilm reactors were initiated as either a partial nitrifying reactor or an anammox reactor, respectively, and simultaneous partial nitrification and anammox was established by careful control of the aeration rate. The combined partial nitrification and anammox reaction was successfully developed in both biofilm reactors without additional biomass inoculation. The reactor initiated as the anammox reactor gave a slightly higher and more stable mean nitrogen removal rate of 0.35 (± 0.19) kg-N m⁻³ d⁻¹ than the reactor initiated as the partial nitrifying reactor (0.23 (± 0.16) kg-N m⁻³ d⁻¹). FISH analysis revealed that the biofilm in the reactor started as the anammox reactor were composed of anammox bacteria located in inner anoxic layers that were surrounded by surface aerobic AOB layers, whereas AOB and anammox bacteria were mixed without a distinguishable niche in the biofilm in the reactor started as the partial nitrifying reactor. However, it was difficult to efficiently maintain the stable partial nitrification owing to inefficient aeration in the reactor, which is a key to development of the combined partial nitrification and anammox reaction in a single biofilm reactor.     

Candidatus "Scalindua brodae", sp. nov., Candidatus "Scalindua wagneri", sp. nov., two new species of anaerobic ammonium oxidizing bacteria

Anaerobic ammonium oxidation (anammox) is both a promising process in wastewater treatment and a long overlooked microbial physiology that can contribute significantly to biological nitrogen cycling in the world's oceans. Anammox is mediated by a monophyletic group of bacteria that branches deeply in the Planctomycetales. Here we describe a new genus and species of anaerobic ammonium oxidizing planctomycetes, discovered in a wastewater treatment plant (wwtp) treating landfill leachate in Pitsea, UK. The biomass from this wwtp showed high anammox activity (5.0 +/- 0.5 nmol/mg protein/min) and produced hydrazine from hydroxylamine, one of the unique features of anammox bacteria. Eight new planctomycete 16S rRNA gene sequences were present in the 16S rRNA gene clone library generated from the biomass. Four of these were affiliated to known anammox 16S rRNA gene sequences, but branched much closer to the root of the planctomycete line of descent. Fluorescence in situ hybridization (FISH) with oligonucleotide probes specific for these new sequences showed that two species (belonging to the same genus) together made up > 99% of the planctomycete population which constituted 20% of the total microbial community. The identification of these organisms as typical anammox bacteria was confirmed with electron microscopy and lipid analysis. The new species, provisionally named Candidatus "Scalindua brodae" and "Scalindua wagneri" considerably extend the biodiversity of the anammox lineage on the 16S rRNA gene level, but otherwise resemble known anammox bacteria. Simultaneously, another new species of the same genus, Candidatus "Scalindua sorokinii", was detected in the water column of the Black Sea, making this genus the most widespread of all anammox bacteria described so far.     

传统泡菜中乳酸菌多样性的分析

目的分析传统泡菜中乳酸菌的多样性。方法采用生理生化学特性和16S rRNA基因序列同源性分析相结合的方法,对传统泡菜中筛得的46株菌进行鉴定。结果菌株分布于乳杆菌属、肠球菌属、葡萄球菌属和片球菌属4个属的9个种,更为重要的是在泡菜中发现有Lactobacillus namurensis和巴氏葡萄球菌的存在。结论泡菜中存在着丰富的乳酸菌。     

Characterization of culturable anaerobic bacteria from the forestomach of an eastern grey kangaroo, Macropus giganteus

AIM: To determine the culturable biodiversity of anaerobic bacteria isolated from the forestomach contents of an eastern grey kangaroo, Macropus giganteus, using phenotypic characterization and 16S rDNA sequence analysis. METHODS AND RESULTS: Bacteria from forestomach contents of an eastern grey kangaroo were isolated using anaerobic media containing milled curly Mitchell grass (Astrebla lappacea). DNA was extracted and the 16S rDNA sequenced for phylogenetic analysis. Forty bacterial isolates were obtained and placed in 17 groups based on phenotypic characteristics and restriction enzyme digestion of 16S rDNA PCR products. DNA sequencing revealed that the 17 groups comprised five known species (Clostridium butyricum, Streptococcus bovis, Clostridium sporogenes, Clostridium paraputrificum and Enterococcus avium) and 12 groups apparently representing new species, all within the phylum Firmicutes. CONCLUSIONS: Foregut contents from Australian macropod marsupials contain a microbial ecosystem with a novel bacterial biodiversity comprising a high percentage of previously unrecognized species. SIGNIFICANCE AND IMPACT OF THE STUDY: This study adds to knowledge of Australia's unique biodiversity, which may provide a future bioresource of genetic information and bacterial species of benefit to agriculture.     

抑黄曲霉乳酸菌的筛选及菌种鉴定

目的筛选具有抑制黄曲霉(Aspergillus flavus)生长的乳酸菌。方法以各地泡菜、实验室自制泡菜、豆浆渣以及新鲜猪肠、鸡肠道内容物为材料,采用牛津杯法筛选所需菌株。对筛选出的菌株进行生理生化及16S rRNA基因序列同源性分析。结果分离得到756株乳酸菌,其中有6株菌株对黄曲霉的生长有明显的抑制作用。结论实验获得的6株产酸菌,3株为植物乳杆菌(Lactobacillus plantarum),2株为消化乳杆菌(L.alimentari-us),1株为亚利桑那乳杆菌(L.arizonenensis)。     

Effects of ammonium and nitrite on communities and populations of ammonia-oxidizing bacteria in laboratory-scale continuous-flow reactors

This study investigated the effects of ammonium and nitrite on ammonia-oxidizing bacteria (AOB) from an activated sludge process in laboratory-scale continuous-flow reactors. AOB communities were analyzed using specific PCR followed by denaturing gel gradient electrophoresis, cloning and sequencing of the 16S rRNA gene, and AOB populations were quantified using real-time PCR. To study the effect of ammonium, activated sludge from a sewage treatment system was enriched in four reactors receiving inorganic medium containing four different ammonium concentrations (2, 5, 10 and 30 mM NH(4) (+)-N). One of several sequence types of the Nitrosomonas oligotropha cluster predominated in the reactors with lower ammonium loads (2, 5 and 10 mM NH(4) (+)-N), whereas Nitrosomonas europaea was the dominant AOB in the reactor with the highest ammonium load (30 mM NH(4) (+)-N). The effect of nitrite was studied by enriching the enriched culture possessing both N. oligotropha and N. europaea in four reactors receiving 10-mM-ammonium inorganic medium containing four different nitrite concentrations (0, 2, 12 and 22 mM NO(2) (-)-N). Nitrosomonas oligotropha comprised the majority of AOB populations in the reactors without nitrite accumulation (0 and 2 mM NO(2) (-)-N), whereas N. europaea was in the majority in the 12- and 22-mM NO(2) (-)-N reactors, in which nitrite concentrations were 2.1-5.7 mM (30-80 mg N L(-1)).     

污水处理系统中厌氧氨氧化菌分布及影响因素

基于厌氧氨氧化的污水生物脱氮工艺近年来发展迅速,污水处理系统中厌氧氨氧化菌的分布和多样性成为了重要的研究方向。目前,在污水处理系统中曾检测出多种厌氧氨氧化(Anaerobic ammonium oxidation,Anammox)菌,最常被检测出的是待定布罗卡地菌Candidate Brocadia和待定斯图加特库氏菌Candidate Kuenenia的Anammox菌,并且研究发现单一生境下往往只存在一种类型的Anammox菌,但是影响Anammox菌分布和多样性的因素与机制目前仍不明确。系统总结了污水处理系统中,不同工艺形式和运行条件下的Anammox菌分布情况,归纳分析了关键因素对Anammox菌分布的影响,包括底物浓度和微生物比生长速率、污泥性质与微生物生境、多重因素的联合作用和影响等。在此基础上,阐述了Anammox菌分布机制研究的工程意义,并对该领域的研究方向和思路进行了展望。     

一株海水异养硝化-好氧反硝化菌系统发育及脱氮特性

【目的】确定一株分离自海水的异养硝化-好氧反硝化菌的系统发育地位并探索其脱氮特性和机理,以期为解释异养硝化-好氧反硝化机理以及改进海水养殖及废水的生物脱氮工艺提供理论依据。【方法】通过形态观察、生理生化实验和16S rRNA基因序列分析,鉴定该菌株;通过测定菌株在不同无机氮源降解测试液中的生长和脱氮效率,分析其异养硝化和好氧反硝化性能。【结果】经鉴定该菌株属于盐单胞菌属(Halomonas);最适生长条件为盐度3%、pH 8.5、温度28℃、碳氮比10:1,在盐度为15%的培养液中仍能生长;可以同时去除氨氮、亚硝酸氮和硝酸氮,24 h时对NH4+-N、NO2--N、和NO3--N的去除率可分别达到98.29%、99.07%、96.48%,3种形态无机氮同时存在时,会优先利用NH4+-N,且总无机氮去除率较单一存在时更高,说明该菌株可实现同步硝化反硝化。【结论】该分离自海水的异养硝化-好氧反硝化菌属于盐单胞菌属(Halomonas),在高盐环境中仍能生长,同时具有高效的异养硝化和好氧反硝化能力,能够独立完成脱氮的全部过程。     

Phylogenetic relationships among Rhacophorinae (Rhacophoridae, Anura, Amphibia), with an emphasis on the Chinese species

The partial nucleotide sequence of mitochondrial 12S and 16S rRNA genes was determined for 23 Chinese species of Rhacophoridae (Amphibia: Anura), representing four of the eight recognized genera. Using Buergeriinae as the outgroup, phylogenetic analyses (maximum parsimony, maximum likelihood, and Bayesian inference) were performed in combination with already published mitochondrial 12S and 16S sequences of Rhacophorinae frogs. In all cases, Philautus romeri Smith, 1953 is recovered as the sister taxon to all other Rhacophorinae, although the support values are weak. Chirixalus doriae Boulenger, 1893 is closer to Chiromantis [ Chiromantis rufescens (Günther, 1868) and Chiromantis xerampelina Peters, 1854] than to Chirixalus vittatus (Boulenger, 1887). The clade { Philautus odontotarsus Ye & Fei, 1993, [ Philautus idiootocus (Kuramoto & Wang, 1987), Kurixalus eiffingeri (Boettger, 1895)]} is recovered with strong support. The monophyly of Theloderma and Rhacophorus rhodopus Liu & Hu, 1959 is not supported. It is suggested that Philautus albopunctatus Liu & Hu, 1962 should be placed into the synonymy of Theloderma asperum (Boulenger, 1886), and that Philautus rhododiscus Liu & Hu, 1962 should be assigned to Theloderma , so as to correct the paraphyly. Additionally, the monophyly of ' Aquixalus ' is not supported, and this requires further examination. Results also indicate that the Rhacophorus leucomystax (Gravenhorst, 1829)/ Rhacophorus megacephalus (Hallowell, 1861) complex needs further revision. Studies employing broader sampling and more molecular markers will be needed to resolve the deep relationships within the subfamily Rhacophorinae.  © 2008 The Linnean Society of London, Zoological Journal of the Linnean Society, 2008, 153 , 733–749.     

高含氮稻田深层土壤的氨氧化古菌和厌氧氨氧化菌共存及对氮循环影响

随着海洋生态系统中的厌氧氨氧化反应和氨氧化古菌的发现,自然生态系统的氮循环过程被重新认识,但是目前尚无在陆地深层的相关报道。结合同位素示踪与分子生物学技术探索了稻田深层土壤中anammox与AOA的存在及特性。结果表明,在沼渣处理废水浇灌的高含氮稻田深层土壤中,anammox与AOA共存。通过构建克隆文库发现,此土壤中厌氧氨氧化菌的生物多样性相对较低,35个克隆序列只分为4个独立操作单元(OTU),代表序列与Genebank数据库中已探明的厌氧氨氧化菌Candidatus 'Kuenenia stuttgartiensis’的同源性超过95%;对氨氧化古菌的分析发现,20个克隆子共得到5个OTU,其与基因库中土壤/沉积物进化分支关系最近,序列的同源性部分超过98%。同位素示踪的初步结果表明,anammox产生的氮气占此土壤总氮气生成量的24.1%-29.8%。AOA与anammox的共存为anammox反应的广泛存在与发生提供了新思路。     

Origin,causes and effects of increased nitrite concentrations in aquatic environments

Literature frequently mentions increasednitrite concentrations along with itsinhibitory effect towards bacteria and aquaticlife. Nitrite accumulation has been studied fordecades, and although numerous causal factorshave already been commented on in literature,the mechanism of nitrite accumulation is notalways clear. From the broad range ofparameters and environmental factors reviewedin this paper, it is obvious that the causesand consequences of nitrite accumulation arenot yet completely understood. Among others,pH, dissolved oxygen, volatile fatty acids,phosphate and reactor operation have been foundto play a role in nitrite accumulation, whichresults from differential inhibition ordisruption of the linkage of the differentsteps in both nitrification anddenitrification. In the case of nitrification, thisdifferential inhibition could lead to thedisplacement or unlinking of the ammoniaoxidisers and nitrite oxidisers. In this paper,the idea is formulated that the nitrifierpopulation forms a role model for the totalmicrobial community. Increased nitriteconcentrations would in this aspect not onlysignal a disruption of nitrifiers, but possiblyalso of the total configuration of themicrobial community.     

Community structures and activities of nitrifying and denitrifying bacteria in industrial wastewater-treating biofilms

The bacterial community structure, in situ spatial distributions and activities of nitrifying and denitrifying bacteria in biofilms treating industrial wastewater were investigated by combination of the 16S rRNA gene clone analysis, fluorescence in situ hybridization (FISH) and microelectrodes. These results were compared with the nitrogen removal capacity of the industrial wastewater treatment plant (IWTP). Both nitrification and denitrification occurred in the primary denitrification (PD) tank and denitrification occurred in the secondary denitrification (SD) tank. In contrast, nitrification and denitrification rates were very low in the nitrification (N) tank. 16S rRNA gene clone sequence analysis revealed that the bacteria affiliated with Alphaproteobacteria, followed by Betaproteobacteria, were numerically important microbial groups in three tanks. The many clones affiliated with Alphaproteobacteria were closely related to the denitrifying bacteria (e.g., Hyphomicrobium spp., Rhodopseudomonas palustris, and Rhodobacter spp.). In addition, Methylophilus leisingeri affiliated with Betaproteobacteria, which favorably utilized methanol, was detected only in the SD-tank to which methanol was added. Nitrosomonas europaea and Nitrosomonas marina were detected as the ammonia-oxidizing bacteria affiliated with Betaproteobacteria throughout this plant, although the dominant species of them was different among three tanks. Nitrifying bacteria were mainly detected in the upper parts of the PD-biofilm whereas their populations were low in the upper parts of the N-biofilm. The presence of denitrifying bacteria affiliated with Hyphomicrobium spp. in SD- and N-biofilms was verified by FISH analysis. Microelectrode measurements showed that the nitrifying bacteria present in the N- and PD-biofilms were active and the bacteria present in the SD-biofilm could denitrify.     

空气环境中几种细菌检测与16S rRNA测序鉴定

采集空气环境微生物,根据菌落和革兰氏染色特征,分离5株细菌。提取分离株DNA,采用设计的16SrRNA引物扩增DNA片段;纯化PCR产物,进行测序反应并再纯化,上机读序。拼接与校对DNA序列,在NCBI网站进行Blast,鉴定细菌型别。5株菌株分别是表皮葡萄球菌、头状葡萄球菌、施氏假单胞菌、溶血葡萄球菌和大肠杆菌;其中溶血葡萄球菌是致病菌,其他4株是条件致病菌。这提示,应警惕空气环境中致病菌的感染。     

A comparison of ammonia-oxidiser populations in eutrophic and oligotrophic basins of a large freshwater lake

A combination of PCR amplification and oligonucleotide probing was used to investigate the populations of ammonia-oxidisers of the -Proteobacteria in the eutrophic and oligotrophic basins of Lake Windermere, a large temperate lake in the English Lake District. Numbers of ammonia-oxidisers (MPN) in the Windermere lakewater were low (< 100 cells ml^–1) throughout the year with the exception of peaks in August, which coincided with stratification, and November in the South Basin where overturn may have introduced ammonia-oxidising bacteria into the water column. Sediment samples contained larger populations of ammonia oxidisers, usually ca. 10⁴ per g. dry weight, which remained relatively constant throughout the seasonal cycle in both Basins. DNA was recovered from lakewater and sediment samples and Nitrosospiraand N. europaea-eutrophalineage16S rRNA genes amplified in a nested PCR reaction, with confirmation of identity by oligonucleotide hybridisation. Nitrosospira 16S rDNA was readily detected in all samples and therefore found to be ubiquitous. In contrast, nitrosomonad DNA of the N. europaea-eutropha lineage could only be detected in the oligotrophic North Basin. Enrichment cultures of lakewater samples only exhibited nitrification at low (0.67 mM) and medium (5 mM) ammonium concentrations, whilst sediment enrichments nitrified at all concentrations tested including high (12.5 mM) ammonium medium. These data suggest that ammonia-oxidiser populations may be physiologically distinguished between lakewater and sediment, and that species distribution in a single lake is non-uniform.     

Factors Affecting Nitrous Oxide Production: A Comparison of Biological Nitrogen Removal Processes with Partial and Complete Nitrification

Nitrous oxide (N₂O) emission from biological nitrogen removal (BNR) processes has recently received more research attention. In this study, two lab-scale BNR systems were used to investigate the effects of various operating parameters including the carbon to nitrogen (C/N) ratio, ammonia loading, and the hydraulic retention time on N₂O production. The first system was operated in a conventional BNR mode known as the Ludzack–Ettinger (LE) process, consisting of complete denitrification and nitrification reactors, while the second one was operated in a shortcut BNR (SBNR) mode employing partial nitrification and shortcut denitrification, which requires less oxygen and carbon sources. As the C/N ratio was decreased, a significant increase in N₂O production was observed only in the anoxic reactor of the LE process, indicating that N₂O was released as an intermediate of the denitrification reaction under the carbon-limited condition. However, the SBNR process did not produce significant N₂O even at the lowest C/N ratio of 0.5. When the SBNR process was subjected to increasing concentrations of ammonia, N₂O production from the aerobic reactor was rapidly increased. Furthermore, the increasing production of N₂O was observed mostly in the aerobic reactor of the SBNR process with a decline in hydraulic retention time. These experimental findings indicated that the increase in N₂O production was closely related to the accumulation of free ammonia, which was caused by an abrupt increase of the ammonium loading. Consequently, the partial nitrification was more susceptible to shock loading conditions, resulting in a high production of N₂O, although the SBNR process was more efficient with respect to nitrogen removals as well as carbon and oxygen requirements.