Habitat-Associated Phylogenetic Community Patterns of Microbial Ammonia Oxidizers

Microorganisms mediating ammonia oxidation play a fundamental role in the connection between biological nitrogen fixation and anaerobic nitrogen losses. Bacteria and Archaea ammonia oxidizers (AOB and AOA, respectively) have colonized similar habitats worldwide. Ammonia oxidation is the rate-limiting step in nitrification, and the ammonia monooxygenase (Amo) is the key enzyme involved. The molecular ecology of this process has been extensively explored by surveying the gene of the subunit A of the Amo (amoA gene). In the present study, we explored the phylogenetic community ecology of AOB and AOA, analyzing 5776 amoA gene sequences from >300 isolation sources, and clustering habitats by environmental ontologies. As a whole, phylogenetic richness was larger in AOA than in AOB, and sediments contained the highest phylogenetic richness whereas marine plankton the lowest. We also observed that freshwater ammonia oxidizers were phylogenetically richer than their marine counterparts. AOA communities were more dissimilar to each other than those of AOB, and consistent monophyletic lineages were observed for sediments, soils, and marine plankton in AOA but not in AOB. The diversification patterns showed a more constant cladogenesis through time for AOB whereas AOA apparently experienced two fast diversification events separated by a long steady-state episode. The diversification rate (γ statistic) for most of the habitats indicated γ_AOA > γ_AOB. Soil and sediment experienced earlier bursts of diversification whereas habitats usually eutrophic and rich in ammonium such as wastewater and sludge showed accelerated diversification rates towards the present. Overall, this work shows for the first time a global picture of the phylogenetic community structure of both AOB and AOA assemblages following the strictest analytical standards, and provides an ecological view on the differential evolutionary paths experienced by widespread ammonia-oxidizing microorganisms. The emerged picture of AOB and AOA distribution in different habitats provides a new view to understand the ecophysiology of ammonia oxidizers on Earth.     

Dynamics of ammonia-oxidizing communities in barley-planted bulk soil and rhizosphere following nitrate and ammonium fertilizer amendment

Oxidation of ammonia by nitrifying microorganisms is a major pathway that fertilizer nitrogen (N) may take upon application to agricultural soils, but the relative roles of bacterial (AOB) vs. archaeal (AOA) ammonia oxidizers are controversial. We explored the effects of various forms of mineral N fertilizer on the AOB and AOA community dynamics in two different soils planted with barley. Ammonia oxidizers were monitored via real-time PCR and terminal restriction fragment length polymorphism analysis of bacterial and archaeal amoA genes following the addition of either [NH?]?SO?, NH?NO? or KNO?. AOB and AOA communities were also studied specifically in the rhizospheres of two different barley varieties upon [NH?]?SO? vs. KNO? addition. AOB changed in community composition and increased in abundance upon ammonium amendment in bulk soil and rhizosphere, with changes in bacterial amoA copy numbers lagging behind relative to changes in soil ammonium. In both soils, only T-RFs corresponding to phylotypes related to Nitrosospira clade 3a underwent significant community changes. Increases in AOB abundance were generally stronger in the bulk soil than in the rhizosphere, implying significant ammonia uptake by plant roots. AOA underwent shifts in the community composition over time and fluctuated in abundance in all treatments irrespective of ammonia availability. AOB were thus considered as the main agents responsible for fertilizer ammonium oxidation, while the functions of AOA in soil N cycling remain unresolved.     

Nitrous oxide production by ammonia oxidizers: Physiological diversity,niche differentiation and potential mitigation strategies

Oxidation of ammonia to nitrite by bacteria and archaea is responsible for global emissions of nitrous oxide directly and indirectly through provision of nitrite and, after further oxidation, nitrate to denitrifiers. Their contributions to increasing N₂O emissions are greatest in terrestrial environments, due to the dramatic and continuing increases in use of ammonia‐based fertilizers, which have been driven by requirement for increased food production, but which also provide a source of energy for ammonia oxidizers (AO), leading to an imbalance in the terrestrial nitrogen cycle. Direct N₂O production by AO results from several metabolic processes, sometimes combined with abiotic reactions. Physiological characteristics, including mechanisms for N₂O production, vary within and between ammonia‐oxidizing archaea (AOA) and bacteria (AOB) and comammox bacteria and N₂O yield of AOB is higher than in the other two groups. There is also strong evidence for niche differentiation between AOA and AOB with respect to environmental conditions in natural and engineered environments. In particular, AOA are favored by low soil pH and AOA and AOB are, respectively, favored by low rates of ammonium supply, equivalent to application of slow‐release fertilizer, or high rates of supply, equivalent to addition of high concentrations of inorganic ammonium or urea. These differences between AOA and AOB provide the potential for better fertilization strategies that could both increase fertilizer use efficiency and reduce N₂O emissions from agricultural soils. This article reviews research on the biochemistry, physiology and ecology of AO and discusses the consequences for AO communities subjected to different agricultural practices and the ways in which this knowledge, coupled with improved methods for characterizing communities, might lead to improved fertilizer use efficiency and mitigation of N₂O emissions.     

Differential contributions of ammonia oxidizers and nitrite oxidizers to nitrification in four paddy soils

Rice paddy fields are characterized by regular flooding and nitrogen fertilization, but the functional importance of aerobic ammonia oxidizers and nitrite oxidizers under unique agricultural management is poorly understood. In this study, we report the differential contributions of ammonia-oxidizing archaea (AOA), bacteria (AOB) and nitrite-oxidizing bacteria (NOB) to nitrification in four paddy soils from different geographic regions (Zi-Yang (ZY), Jiang-Du (JD), Lei-Zhou (LZ) and Jia-Xing (JX)) that are representative of the rice ecosystems in China. In urea-amended microcosms, nitrification activity varied greatly with 11.9, 9.46, 3.03 and 1.43 μg NO₃⁻-N g⁻¹ dry weight of soil per day in the ZY, JD, LZ and JX soils, respectively, over the course of a 56-day incubation period. Real-time quantitative PCR of amoA genes and pyrosequencing of 16S rRNA genes revealed significant increases in the AOA population to various extents, suggesting that their relative contributions to ammonia oxidation activity decreased from ZY to JD to LZ. The opposite trend was observed for AOB, and the JX soil stimulated only the AOB populations. DNA-based stable-isotope probing further demonstrated that active AOA numerically outcompeted their bacterial counterparts by 37.0-, 10.5- and 1.91-fold in ¹³C-DNA from ZY, JD and LZ soils, respectively, whereas AOB, but not AOA, were labeled in the JX soil during active nitrification. NOB were labeled to a much greater extent than AOA and AOB, and the addition of acetylene completely abolished the assimilation of ¹³CO₂ by nitrifying populations. Phylogenetic analysis suggested that archaeal ammonia oxidation was predominantly catalyzed by soil fosmid 29i4-related AOA within the soil group 1.1b lineage. Nitrosospira cluster 3-like AOB performed most bacterial ammonia oxidation in the ZY, LZ and JX soils, whereas the majority of the ¹³C-AOB in the JD soil was affiliated with the Nitrosomona communis lineage. The ¹³C-NOB was overwhelmingly dominated by Nitrospira rather than Nitrobacter. A significant correlation was observed between the active AOA/AOB ratio and the soil oxidation capacity, implying a greater advantage of AOA over AOB under microaerophilic conditions. These results suggest the important roles of soil physiochemical properties in determining the activities of ammonia oxidizers and nitrite oxidizers.     

亚热带米槠天然林土壤氨氧化微生物对模拟氮沉降的响应

我国亚热带地区是全球氮沉降的热点区域。氮沉降会影响氨氧化微生物的丰度和群落结构,进而改变土壤微生物驱动的养分循环。目前对新近发现的完全氨氧化菌认识不足,极大地制约了对森林土壤氨氧化微生物响应氮沉降的整体认识。本研究以福建省三明市辛口镇格氏栲自然保护区长期模拟氮沉降处理土壤为研究对象,利用实时定量PCR方法,研究氨氧化微生物(包括氨氧化细菌AOB、氨氧化古菌AOA和完全氨氧化菌comammox Nitrospira),尤其是完全氨氧化菌的amoA基因丰度。模拟氮沉降处理包括:不添加N(CK)、低氮(添加40 kg N·hm^-2·a^-1,LN)和高氮(添加80 kg N·hm^-2·a^-1,HN)。结果表明: 8年的氮添加降低了土壤pH值和有机碳含量,提高了土壤硝态氮含量。供试土壤的AOB丰度低于检测限,无法获得目的片段。高氮处理显著提高了AOA丰度,但对完全氨氧化菌clade A和clade B丰度无显著影响。两种氮添加处理均降低了完全氨氧化菌/AOA值,表明氮添加降低了完全氨氧化菌在亚热带森林土壤氨氧化微生物类群中的相对竞争力。针对完全氨氧化菌clade A和clade B的扩增都存在非特异性产物,表明针对森林土壤的高特异性和覆盖度设计引物的必要性。Clade A和clade B丰度与总氮和铵态氮含量呈显著正相关,clade B丰度还与有机碳含量呈显著正相关。总之,模拟氮沉降提高了AOA在亚热带米槠天然林土壤硝化过程中的相对重要性,这些发现可为该地区应对全球变化和氮沉降的风险评估提供理论依据。     

Bacteria dominate the ammonia-oxidizing community in a hydrothermal vent site at the Mid-Atlantic Ridge of the South Atlantic Ocean

Ammonia oxidation is the first and rate-limiting step of nitrification, which is carried out by two groups of microorganisms: ammonia-oxidizing bacteria (AOB) and the recently discovered ammonia-oxidizing archaea (AOA). In this study, diversity and abundance of AOB and AOA were investigated in five rock samples from a deep-sea hydrothermal vent site at the Mid-Atlantic Ridge (MAR) of the South Atlantic Ocean. Both bacterial and archaeal ammonia monooxygenase subunit A (amoA) gene sequences obtained in this study were closely related to the sequences retrieved from deep-sea environments, indicating that AOB and AOA in this hydrothermal vent site showed typical deep ocean features. AOA were more diverse but less abundant than AOB. The ratios of AOA/AOB amoA gene abundance ranged from 1/3893 to 1/242 in all investigate samples, indicating that bacteria may be the major members responding to the aerobic ammonia oxidation in this hydrothermal vent site. Furthermore, diversity and abundance of AOA and AOB were significantly correlated with the contents of total nitrogen and total sulfur in investigated samples, suggesting that these two environmental factors exert strong influences on distribution of ammonia oxidizers in deep-sea hydrothermal vent environment.     

Ammonia concentration determines differential growth of ammonia-oxidising archaea and bacteria in soil microcosms

The first step of nitrification, oxidation of ammonia to nitrite, is performed by both ammonia-oxidising archaea (AOA) and ammonia-oxidising bacteria (AOB) in soil, but their relative contributions to ammonia oxidation and existence in distinct ecological niches remain to be determined. To determine whether available ammonia concentration has a differential effect on AOA and AOB growth, soil microcosms were incubated for 28 days with ammonium at three concentrations: native (control), intermediate (20 μg NH₄⁺-N per gram of soil) and high (200 μg NH₄⁺-N per gram of soil). Quantitative PCR demonstrated growth of AOA at all concentrations, whereas AOB growth was prominent only at the highest concentration. Similarly, denaturing gradient gel electrophoresis (DGGE) analysis revealed changes in AOA communities at all ammonium concentrations, whereas AOB communities changed significantly only at the highest ammonium concentration. These results provide evidence that ammonia concentration contributes to the definition of distinct ecological niches of AOA and AOB in soil.     

High Abundances of Potentially Active Ammonia-Oxidizing Bacteria and Archaea in Oligotrophic,High-Altitude Lakes of the Sierra Nevada,California, USA

Nitrification plays a central role in the nitrogen cycle by determining the oxidation state of nitrogen and its subsequent bioavailability and cycling. However, relatively little is known about the underlying ecology of the microbial communities that carry out nitrification in freshwater ecosystems—and particularly within high-altitude oligotrophic lakes, where nitrogen is frequently a limiting nutrient. We quantified ammonia-oxidizing archaea (AOA) and bacteria (AOB) in 9 high-altitude lakes (2289–3160 m) in the Sierra Nevada, California, USA, in relation to spatial and biogeochemical data. Based on their ammonia monooxygenase (amoA) genes, AOB and AOA were frequently detected. AOB were present in 88% of samples and were more abundant than AOA in all samples. Both groups showed >100 fold variation in abundance between different lakes, and were also variable through time within individual lakes. Nutrient concentrations (ammonium, nitrite, nitrate, and phosphate) were generally low but also varied across and within lakes, suggestive of active internal nutrient cycling; AOB abundance was significantly correlated with phosphate (r² = 0.32, p<0.1), whereas AOA abundance was inversely correlated with lake elevation (r² = 0.43, p<0.05). We also measured low rates of ammonia oxidation—indicating that AOB, AOA, or both, may be biogeochemically active in these oligotrophic ecosystems. Our data indicate that dynamic populations of AOB and AOA are found in oligotrophic, high-altitude, freshwater lakes.     

三峡库区消落带周期性淹水-落干对硝化微生物生态过程的影响

【目的】明确三峡库区消落带周期性淹水-落干对土壤硝化过程及功能微生物的影响。【方法】在重庆段万州、丰都和长寿3个典型消落带区域,分别采集淹水-落干8次、淹水-落干5次、淹水-落干0次土壤样品,通过室内培养分析土壤硝化作用强度;利用实时荧光定量PCR研究不同淹水-落干周期土壤氨氧化古菌和细菌的数量变化规律;采用DGGE分子指纹图谱和克隆文库技术研究土壤氨氧化古菌和细菌的群落组成差异。【结果】万州、丰都和长寿3个消落带中,土壤有机质和pH含量随淹水-落干次数的增加而增加;除长寿消落带外,土壤硝化强度也随着淹水-落干次数的增加而增强;随着硝化作用的发生,氨氧化古菌和细菌数量呈上升趋势,DGGE条带数量、位置和亮度均发生明显变化;氨氧化功能基因amoA的系统发育分析表明:万州和丰都消落带氨氧化古菌均属于土壤类古菌Group 1.1b;而长寿消落带则检测到少量的海洋类古菌Group 1.1a;3个消落带的优势氨氧化细菌均属于Nitrosospira和Cluster 0类群。【结论】三峡库区独特的"冬蓄夏泄"管理方式,导致淹水-落干8次的土壤经历了周期性的淹水-落干水分胁迫,提升了土壤有机质含量和pH,增加了土壤硝化作用强度,并可能改变了土壤硝化微生物群落结构。     

长期不同施肥制度对水稻土氨氧化微生物数量和群落结构的影响

由氨氧化微生物驱动的氨氧化过程是硝化作用的限速步骤,在土壤氮素循环过程中扮演着重要角色.以湖南省宁乡县长达30 a定位试验水稻土壤为研究对象,采用荧光定量PCR和Illumina MiSeq高通量测序分析方法,以amoA基因为靶标,研究了4种施肥制度[不施肥(CK)、化肥(CF)、70%化肥+30%有机肥(CFM₁)和40%化肥+60%有机肥(CFM₂)]水稻土壤氨氧化微生物的数量和群落结构变化.结果表明: 不同施肥处理氨氧化古菌(AOA)和氨氧化细菌(AOB) amoA基因拷贝数分别为3.09×10⁷～8.37×10⁷和1.04×10⁷～7.03×10⁷ copies·g^-1干土.施肥显著提高了AOA和AOB数量,但处理CFM₂中AOB数量与CK差异不显著.有机肥配施比例对AOB群落α多样性指数的影响强于AOA,处理CFM₁中AOA群落的多样性指数(Shannon)和AOB群落的丰富度指数(ACE和Chao1)均显著高于CK.奇古菌门和泉古菌门是AOA群落的优势门类群,占AOA amoA基因总序列的83.4%;亚硝化螺菌属、environmental_samples_norank、Bacteria_unclassified和Nitrosomonadales_unclassified是AOB群落的优势属类群,占AOB amoA基因总序列的97.8%.维恩分析结果显示,有机肥配施比例对AOB群落操作分类单元(OTU)数量的影响强于AOA,但对各处理共有AOA和AOB amoA基因序列条数的影响均较小.冗余分析结果显示,不同施肥处理AOB群落结构差异强于AOA,且所有土壤理化性质均与AOA和AOB群落结构存在显著相关关系.综上可知:有机肥配施比例显著改变了AOA和AOB数量、多样性和群落结构,配施30%有机肥时,AOA群落的Shannon指数最高,AOB群落数量、ACE和Chao1指数均最高.研究结果可为进一步探讨农业系统中氨氧化微生物对不同施肥制度的响应机制及其在氮素转化中的作用提供科学依据.     

Mimicking the oxygen minimum zones: stimulating interaction of aerobic archaeal and anaerobic bacterial ammonia oxidizers in a laboratory‐scale model system

In marine oxygen minimum zones (OMZs), ammonia‐oxidizing archaea (AOA) rather than marine ammonia‐oxidizing bacteria (AOB) may provide nitrite to anaerobic ammonium‐oxidizing (anammox) bacteria. Here we demonstrate the cooperation between marine anammox bacteria and nitrifiers in a laboratory‐scale model system under oxygen limitation. A bioreactor containing ‘Candidatus Scalindua profunda’ marine anammox bacteria was supplemented with AOA (Nitrosopumilus maritimus strain SCM1) cells and limited amounts of oxygen. In this way a stable mixed culture of AOA, and anammox bacteria was established within 200 days while also a substantial amount of endogenous AOB were enriched. ‘Ca. Scalindua profunda’ and putative AOB and AOA morphologies were visualized by transmission electron microscopy and a C₁₈ anammox [3]‐ladderane fatty acid was highly abundant in the oxygen‐limited culture. The rapid oxygen consumption by AOA and AOB ensured that anammox activity was not affected. High expression of AOA, AOB and anammox genes encoding for ammonium transport proteins was observed, likely caused by the increased competition for ammonium. The competition between AOA and AOB was found to be strongly related to the residual ammonium concentration based on amoA gene copy numbers. The abundance of archaeal amoA copy numbers increased markedly when the ammonium concentration was below 30 μM finally resulting in almost equal abundance of AOA and AOB amoA copy numbers. Massive parallel sequencing of mRNA and activity analyses further corroborated equal abundance of AOA and AOB. PTIO addition, inhibiting AOA activity, was employed to determine the relative contribution of AOB versus AOA to ammonium oxidation. The present study provides the first direct evidence for cooperation of archaeal ammonia oxidation with anammox bacteria by provision of nitrite and consumption of oxygen.     

长期施用猪粪对红壤完全氨氧化菌基因丰度的影响

完全氨氧化菌(comammox Nitrospira)的发现对硝化微生物的研究提出了新的挑战。大量研究表明完全氨氧化菌在陆地生态系统中广泛分布,但其在农田土壤中的分布规律及其对长期施用粪肥的响应尚不清楚。研究了长期施用猪粪对农田红壤完全氨氧化菌、氨氧化古菌(AOA)和氨氧化细菌(AOB)功能基因(amoA)丰度的影响,及其与土壤净硝化速率的关系。结果表明：与不施肥的对照处理相比,猪粪施用显著提高土壤有机质和养分含量,且随着猪粪的施用量增加而增加。同时,施用中量和高量猪粪显著提升土壤净硝化速率,增幅分别达到317%和416%。所有处理中,完全氨氧化菌丰度以进化枝A为主,进化枝B丰度极低,大多为非特异性扩增产物,但进化枝A的amoA丰度均低于氨氧化古菌和氨氧化细菌。长期施用高量猪粪显著提升进化枝A的amoA基因丰度,表明存在喜好富营养环境的完全氨氧化菌,而有效磷是最主要的影响因子。相关性分析表明,进化枝A的amoA丰度与净硝化速率呈显著正相关(P<0.01),而氨氧化古菌和氨氧化细菌则没有,表明进化枝A可能在长期施用粪肥的农田红壤硝化过程中发挥重要功能。综上所述,长期施用粪肥显著提高...     

Interactions between Thaumarchaea,Nitrospira and methanotrophs modulate autotrophic nitrification in volcanic grassland soil

Ammonium/ammonia is the sole energy substrate of ammonia oxidizers, and is also an essential nitrogen source for other microorganisms. Ammonia oxidizers therefore must compete with other soil microorganisms such as methane-oxidizing bacteria (MOB) in terrestrial ecosystems when ammonium concentrations are limiting. Here we report on the interactions between nitrifying communities dominated by ammonia-oxidizing archaea (AOA) and Nitrospira-like nitrite-oxidizing bacteria (NOB), and communities of MOB in controlled microcosm experiments with two levels of ammonium and methane availability. We observed strong stimulatory effects of elevated ammonium concentration on the processes of nitrification and methane oxidation as well as on the abundances of autotrophically growing nitrifiers. However, the key players in nitrification and methane oxidation, identified by stable-isotope labeling using ¹³CO₂ and ¹³CH₄, were the same under both ammonium levels, namely type 1.1a AOA, sublineage I and II Nitrospira-like NOB and Methylomicrobium-/Methylosarcina-like MOB, respectively. Ammonia-oxidizing bacteria were nearly absent, and ammonia oxidation could almost exclusively be attributed to AOA. Interestingly, although AOA functional gene abundance increased 10-fold during incubation, there was very limited evidence of autotrophic growth, suggesting a partly mixotrophic lifestyle. Furthermore, autotrophic growth of AOA and NOB was inhibited by active MOB at both ammonium levels. Our results suggest the existence of a previously overlooked competition for nitrogen between nitrifiers and methane oxidizers in soil, thus linking two of the most important biogeochemical cycles in nature.     

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

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

The production of nitric oxide by marine ammonia‐oxidizing archaea and inhibition of archaeal ammonia oxidation by a nitric oxide scavenger

Nitrification is a critical process for the balance of reduced and oxidized nitrogen pools in nature, linking mineralization to the nitrogen loss processes of denitrification and anammox. Recent studies indicate a significant contribution of ammonia‐oxidizing archaea (AOA) to nitrification. However, quantification of the relative contributions of AOA and ammonia‐oxidizing bacteria (AOB) to in situ ammonia oxidation remains challenging. We show here the production of nitric oxide (NO) by Nitrosopumilus maritimus SCM1. Activity of SCM1 was always associated with the release of NO with quasi‐steady state concentrations between 0.05 and 0.08 μM. NO production and metabolic activity were inhibited by the nitrogen free radical scavenger 2‐phenyl‐4,4,5,5,‐tetramethylimidazoline‐1‐oxyl‐3‐oxide (PTIO). Comparison of marine and terrestrial AOB strains with SCM1 and the recently isolated marine AOA strain HCA1 demonstrated a differential sensitivity of AOB and AOA to PTIO and allylthiourea (ATU). Similar to the investigated AOA strains, bulk water column nitrification at coastal and open ocean sites with sub‐micromolar ammonia/ammonium concentrations was inhibited by PTIO and insensitive to ATU. These experiments support predictions from kinetic, molecular and biogeochemical studies, indicating that marine nitrification at low ammonia/ammonium concentrations is largely driven by archaea and suggest an important role of NO in the archaeal metabolism.     

Ammonia Oxidizers in a Pilot-Scale Multilayer Rapid Infiltration System for Domestic Wastewater Treatment

A pilot-scale multilayer rapid infiltration system (MRIS) for domestic wastewater treatment was established and efficient removal of ammonia and chemical oxygen demand (COD) was achieved in this study. The microbial community composition and abundance of ammonia oxidizers were investigated. Efficient biofilms of ammonia oxidizers in the stationary phase (packing material) was formed successfully in the MRIS without special inoculation. DGGE and phylogenetic analyses revealed that proteobacteria dominated in the MRIS. Relative abundance of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) showed contrary tendency. In the flowing phase (water effluent), AOA diversity was significantly correlated with the concentration of dissolve oxygen (DO), NO₃-N and NH₃-N. AOB abundance was significantly correlated with the concentration of DO and chemical oxygen demand (COD). NH₃-N and COD were identified as the key factors to shape AOB community structure, while no variable significantly correlated with that of AOA. AOA might play an important role in the MRIS. This study could reveal key environmental factors affecting the community composition and abundance of ammonia oxidizers in the MRIS.     

Population ecology of nitrifying Archaea and Bacteria in the Southern California Bight

Marine Crenarchaeota are among the most abundant microbial groups in the ocean, and although relatively little is currently known about their biogeochemical roles in marine ecosystems, recognition that Crenarchaeota posses ammonia monooxygenase (amoA) genes and may act as ammonia‐oxidizing archaea (AOA) offers another means of probing the ecology of these microorganisms. Here we use a time series approach combining quantification of archaeal and bacterial ammonia oxidizers with bacterial community fingerprints and biogeochemistry, to explore the population and community ecology of nitrification. At multiple depths (150, 500 and 890 m) in the Southern California Bight sampled monthly from 2003 to 2006, AOA were enumerated via quantitative PCR of archaeal amoA and marine group 1 Crenarchaeota 16S rRNA genes. Based on amoA genes, AOA were highly variable in time – a consistent feature of marine Crenarchaeota– however, average values were similar at different depths and ranged from 2.20 to 2.76 × 10⁴amoA copies ml^?1. Archaeal amoA genes were correlated with Crenarchaeota 16S rRNA genes (r² = 0.79) and the slope of this relationship was 1.02, demonstrating that the majority of marine group 1 Crenarchaeota present over the dates and depths sampled possessed amoA. Two AOA clades were specifically quantified and compared with betaproteobacterial ammonia‐oxidizing bacteria (β‐AOB) amoA genes at 150 m; these AOA groups were found to strongly co‐vary in time (r² = 0.70, P < 0.001) whereas AOA : β‐AOB ratios ranged from 13 to 5630. Increases in the AOA : β‐AOB ratio correlated with the accumulation of nitrite (r² = 0.87, P < 0.001), and may be indicative of differences in substrate affinities and activities leading to periodic decoupling between ammonia and nitrite oxidation. These data capture a dynamic nitrogen cycle in which multiple microbial groups appear to be active participants.     

轮作模式对冬小麦土壤氨氧化微生物群落多样性和组成的影响

农田温室气体减排已成为农业绿色发展的重要内容,驱动温室气体氧化亚氮(N₂O)产生的氨氧化微生物受到了研究者们的广泛关注。为探究轮作模式对土壤氨氧化微生物群落的影响,基于田间定位试验,研究了夏红小豆-冬小麦、夏绿豆-冬小麦、夏花生-冬小麦、夏大豆-冬小麦和夏玉米-冬小麦5种轮作模式中冬小麦根际和非根际土壤氨氧化古菌(AOA)和氨氧化细菌(AOB)的群落组成和多样性变化特征。结果表明:与夏玉米-冬小麦模式相比,豆禾轮作模式增加了根际土中有机碳和硝态氮含量,以及非根际土中全氮和铵态氮含量。豆禾轮作模式降低了非根际土壤中AOA群落的ACE指数和Chao1指数,并显著降低根际土中AOB群落的ACE指数和Chao1指数(P<0.05)。豆禾轮作显著增加AOA群落中泉古菌门(Crenarchaeota)和AOB群落中变形菌门(Proteobacteria)某些类群的相对丰度(P<0.05)。根际土中豆禾轮作模式与麦玉模式的AOA群落结构发生明显分离,而非根际土中豆禾轮作模式与麦玉模式的AOB群落发生分离(P<0.05)。研究结果表明:豆禾轮作种植改变了AOA和AOB的群落结构和多样性,土壤pH值和速效氮含量是驱动AOA和AOB群落结构变化的重要因子,且根际与非根际土壤中氨氧化微生物存在生态位分离。     

Ammonia-oxidizing archaea have more important role than ammonia-oxidizing bacteria in ammonia oxidation of strongly acidic soils

Increasing evidence demonstrated the involvement of ammonia-oxidizing archaea (AOA) in the global nitrogen cycle, but the relative contributions of AOA and ammonia-oxidizing bacteria (AOB) to ammonia oxidation are still in debate. Previous studies suggest that AOA would be more adapted to ammonia-limited oligotrophic conditions, which seems to be favored by protonation of ammonia, turning into ammonium in low-pH environments. Here, we investigated the autotrophic nitrification activity of AOA and AOB in five strongly acidic soils (pH<4.50) during microcosm incubation for 30 days. Significantly positive correlations between nitrate concentration and amoA gene abundance of AOA, but not of AOB, were observed during the active nitrification. ¹³CO₂-DNA-stable isotope probing results showed significant assimilation of ¹³C-labeled carbon source into the amoA gene of AOA, but not of AOB, in one of the selected soil samples. High levels of thaumarchaeal amoA gene abundance were observed during the active nitrification, coupled with increasing intensity of two denaturing gradient gel electrophoresis bands for specific thaumarchaeal community. Addition of the nitrification inhibitor dicyandiamide (DCD) completely inhibited the nitrification activity and CO₂ fixation by AOA, accompanied by decreasing thaumarchaeal amoA gene abundance. Bacterial amoA gene abundance decreased in all microcosms irrespective of DCD addition, and mostly showed no correlation with nitrate concentrations. Phylogenetic analysis of thaumarchaeal amoA gene and 16S rRNA gene revealed active ¹³CO₂-labeled AOA belonged to groups 1.1a-associated and 1.1b. Taken together, these results provided strong evidence that AOA have a more important role than AOB in autotrophic ammonia oxidation in strongly acidic soils.