有机碳氮添加对酸性森林土壤氨氧化过程的影响

以亚热带酸性森林土壤为研究对象,开展了微宇宙室内培养实验,设置了有机碳和有机氮添加处理,分析了土壤硝化活性和氨氧化古菌(Ammonia-oxidizing archaea,AOA)、氨氧化细菌(Ammonia-oxidizing bacteria,AOB)的功能基因丰度,研究了外源有机碳和有机氮对酸性森林土壤氨氧化过程的影响规律。结果表明:外源有机氮添加显著刺激了酸性森林土壤硝化活性,乙炔抑制实验表明自养氨氧化对酸性森林土壤硝化过程的贡献率90%。有机碳添加对土壤硝化活性未有显著影响,同时添加有机碳和无机铵态氮也未显著提高土壤硝化活性,而外源有机氮添加提高了土壤矿化速率并导致土壤NH3浓度升高,可能是土壤硝化活性、AOA和AOB数量显著增加的主要原因。     

A positive relationship between the abundance of ammonia oxidizing archaea and natural abundance δ15N of ecosystems

We present a significant relationship between the natural abundance isotopic composition of ecosystem pools and the abundance of a microbial gene. Natural abundance ¹⁵N of soils and soil DNA were analysed and compared with archaeal ammonia oxidizer abundance along an elevation gradient in northern Arizona and along a substrate age gradient in Hawai'i. There was a significant positive correlation between the abundance of archaeal amoA genes and natural abundance δ¹⁵N of total soil or DNA suggesting that ammonia oxidizing archaea play an important role in ecosystem N release.     

Classification of chemoautotrophic ammonia-oxidizing bacteria using pyruvate kinase genes as high resolution phylogenetic markers

Abstract

The phylogenetic relationship of β-proteobacterial ammonia-oxidizing bacteria (AOB) is mainly based on comparative sequence analyses of the genes encoding the 16S rRNA (16S rDNA) and the active site polypeptide of the ammonia monooxygenase (AmoA). However, classification of AOB with different morphotypes is not possible based solely on these markers. Pyruvate kinase (PYK), which is a key enzyme in the glycolytic pathway, functions at a primary metabolic intersection. The gene sequence of PYK is known to be a phylogenetic marker for bacteria and has been used for this purpose. The phylogenetic relationships of closely related AOB, ‘Nitrosolobus’, ‘Nitrosovibrio’ and Nitrosospira, were estimated based on pyk (PYK), a housekeeping and protein-coding gene. As a result, the pyk phylogenetic tree of the AOB showed a high resolution compared with the tree based on 16S rDNA sequences. Therefore, we conclude that analysis of the PYK gene sequences could play an important role in the in-depth classification and identification of AOB at a rank below the genus level.     

Main environmental drivers of abundance, diversity and community structure of comammox Nitrospira in paddy soils

The recently discovered complete ammonia oxidizers comammox Nitrospira contain clades A and B that can establish an independent one-step nitrification process; however, little is known about their environmental drivers or habitat distributions in agricultural soils. Previous studies on comammox Nitrospira in paddy soils have mainly focused on small-scale samples, and there is a lack of multisite research on comammox Nitrospira in paddy soils. In this study, we conducted a survey of 36 paddy soils to understand the community structure, abundance, and diversity of comammox Nitrospira and the degree to which they are affected by environmental factors at a large scale. Comammox Nitrospira were found to be widely distributed among the paddy soils. The abundance of comammox Nitrospira clade A was mostly lower than that of clade B, whereas its diversity was mostly higher than that of clade B. Correlation analysis showed that multiple factors affected (P < 0.05) the abundance of comammox Nitrospira, including soil pH, organic matter, total carbon, and total nitrogen, latitude, mean annual temperature, and mean annual precipitation. Moreover, there was a clear relationship between the comammox Nitrospira community and habitat, indicating that some amplicon sequence variants (ASVs) had a unique dominant position in specific habitats. Phylogenetic analysis showed that the ASVs of comammox Nitrospira clade A clustered with the known sequences in the paddy soils and were significantly different from the known sequences in other habitats, which may be related to the unique paddy field habitat. In contrast, comammox Nitrospira clade B showed no clear habitat dependence. These results support the wide distribution and high abundance of comammox Nitrospira in paddy soils and provide novel insights into nitrogen cycling and nutrient management in agricultural ecosystems.     

Effects of a blend of garlic oil,nitrate and fumarate on in vitro ruminal fermentation and microbial population

Although garlic oil and nitrate can effectively suppress ruminal methane (CH₄) production in vitro, the application of these compounds is associated with suppressed total volatile fatty acid (VFA) concentration. On the other hand, the effectiveness of fumarate as a ruminal CH₄ mitigating agent is variable but its application increases total VFA concentration. We therefore hypothesized that the different characteristics of the compounds can compensate for the shortcomings of the other. The objective of this study was to develop an optimal blend of garlic oil, nitrate and fumarate that can suppress in vitro ruminal CH₄ without affecting total VFA concentration. Three ruminal in vitro fermentation experiments were carried out. The first one, a one factor at a time experiment was employed to investigate the effective concentration of each of the compounds on CH₄ and VFA production by ruminal bacteria. We then applied the fractional factorial design and response surface methodology in the second experiment to determine optimal concentrations of the compounds in the blend. The optimal blending of garlic oil, fumarate and nitrate was determined to be 50 mg/l, 15 mm and 20 mm , respectively. This simulated optimal blend was verified in a 48 h in vitro batch fermentation experiment. The blend achieved the intended goal of suppressing CH₄ whilst maintaining total VFA concentration. The blend and nitrate suppressed archaea populations (p < 0.001) but did not affect the total microbial population (p = 0.945). The observed results could be explained by additive effects of the agents making up the blend. Supplementing a high concentrate diet with the blend can significantly decrease ruminal CH₄ and maintain total VFAin vitro. These findings however, need to be verified in vivo using the optimized ratio of combining the three methane inhibitors as a guide.     

稻鳝种养模式对土壤氨氧化微生物群落多样性和结构的影响

为深入了解稻鳝种养模式对土壤氮循环关键微生物的影响,本研究采用Illumina MiSeq高通量测序系统,分析了稻鳝种养模式下氨氧化微生物[氨氧化古菌（AOA）、氨氧化细菌（AOB）和完全氨氧化微生物（Comammox）]的群落结构和多样性,以明确该模式对土壤氨氧化微生物群落的影响机制。试验设置两个处理（常规稻田处理和稻鳝种养处理）,分别在处理小区的中心区域和沟渠边缘区域取样,即：常规稻田中心区域（CCS）、常规稻田沟渠边缘区域（CMS）、稻鳝种养处理中心区域（ICS）和稻鳝种养处理沟渠边缘区域（IMS）。结果表明：与常规稻田处理相比,稻鳝种养模式显著降低了土壤pH,减少了稻田中心区域和边缘区域间有机质和总氮的含量差异,增加了土壤硝化势;相较于常规稻田处理,稻鳝种养模式显著提高了 AOA、Comammox Clade-A和Comammox Clade-B的丰富度,显著降低了 AOB的丰富度;同时,IMS显著提高了 AOA的群落多样性,但降低了 AOB的群落多样性;土壤pH、有机质和速效氮是影响氨氧化微生物的关键环境因子（P<0.05）;AOA和Comammox促进了土壤硝化速率,而AOB反之;稻鳝种养模式改变了氨氧化微生物群落的结构,并增强了氨氧化微生物之间的信息交流,使其内部连接更加紧密。研究表明,稻鳝种养模式通过改变土壤环境因子,特别是土壤pH、有机质和速效氮,显著影响了土壤氨氧化微生物群落的组成、结构和多样性,增强了氨氧化微生物之间的相互作用,对土壤氮循环关键微生物产生了重要影响。     

Application of the consortia of nitrifying archaea and bacteria for fish transportation may be beneficial for fish trading and aquaculture

The growing popularity of the aquarium trade is greatly increasing the demand for many ornamental fish. While shipping technology has made the worldwide transportation of ornamental fish possible, a significant portion of the fish caught for the aquarium trade perish in transport before being sold to hobbyists. One of the major causes of fish death in transport is ammonia building up to toxic levels in the shipping bags. In order to solve this problem, we investigated the effectiveness of using nitrifying consortia in reducing the ammonia build‐up in marine fish bags during transport. A pre‐activated nitrifying consortium was effective in safely maintaining low ammonia levels during a three‐day experiment. We found that both ammonium chloride and urea can activate nitrifying consortia. Activation of nitrifiers by urea is not only novel but also beneficial due to being less harmful to fish in comparison with ammonia. We also discovered that unexpectedly one nitrifying consortium examined mainly contained ammonia‐oxidizing archaea. The confirmation of the concept of the use of activated nitrifying consortia and the usefulness of nitrifying archaea for fish transportation may be beneficial for the fish trading and aquaculture.     

Low soil C:N ratio results in accumulation and leaching of nitrite and nitrate in agricultural soils under heavy rainfall

Nitrate (NO^-₃) and nitrite (NO₂^-) leaching threatens groundwater quality.Soil C:N ratio,i.e.,the ratio of soil organic carbon to total nitrogen,affects mineralization,nitrification,and denitrification;however,its mechanism for driving soil NO^-₃ and NO^-₂ accumulation and leaching remains unclear.Here,a field investigation in a fluvo-aquic soil and a soil column experiment were performed to explore the relation...     

pH regulates key players of nitrification in paddy soils

Increasing lines of evidence have suggested the functional importance of ammonia-oxidizing archaea (AOA) rather than bacteria (AOB) for nitrification in upland soils with low pH. However, it remains unclear whether niche specialization of AOA and AOB occurs in rice paddy wetlands constrained by oxygen availability. Using DNA-based stable isotope probing, we conclude that AOA dominated nitrification activity in acidic paddy soils (pH 5.6) while AOB dominated in alkaline soils (pH 8.2). Nitrification activity was stimulated by urea fertilization and accompanied by a significant increase of AOA in acid soils and AOB in alkaline soils. DNA-based stable isotope probing indicated significant assimilation of ¹³CO₂ for AOA only in acidic paddy soil, while AOB was the solely responsible for ammonia oxidation in the alkaline paddy soil. Phylogenetic analysis further indicated that AOA members within the soil group 1.1b lineage dominated nitrification in acid soils. Ammonia oxidation in the alkaline soil was catalyzed by Nitrosospira cluster 3-like AOB, suggesting that the physiological diversity of AOA is more complicated than previously thought, and soil pH plays important roles in shaping the community structures of ammonia oxidizers in paddy field.