模拟水位下降与刈割对高寒湿地土壤氨氧化与反硝化微生物的影响

湿地土壤是温室气体重要的源和汇,认识湿地生态系统氮循环过程有助于预测氮循环对未来气候变化的响应与反馈机制。为探讨硝化作用和反硝化作用对土壤水位变化和刈割的响应机制,依托于2013年在青藏高原东部若尔盖泥炭地南部湿地设置的野外实验,通过在样地周围挖掘不同深度的排水沟模拟水位下降,结合刈割处理,研究水位下降和刈割对泥炭地土壤氨氧化古菌(Ammonia-oxidizing archaea,AOA)、氨氧化细菌(Ammonia-oxidizing bacteria,AOB)和反硝化细菌(Denitrifying bacteria)丰度的影响。2014年7月取样分析结果表明:水位下降显著降低土壤含水量,水位下降与刈割均显著降低土壤呼吸;氨氧化及反硝化微生物功能基因丰度在各处理间无显著差异,但刈割及其与水位下降的交互作用显著影响AOA-amo A与AOB-amo A基因丰度比。刈割处理显著增加AOB-amo A基因相对丰度,但对AOA-amo A基因丰度无显著影响,揭示AOB可能在湿地土壤硝化过程中占主导地位。土壤nir S基因丰度显著高于nir K基因,表明nir S基因对水位下降及刈割的响应更为敏感。随着土壤水位的下降,刈割促进了由AOB主导的氨氧化过程,而反硝化微生物丰度的增加削减了氨氧化产物硝酸盐的积累,继而降低了土壤硝酸盐含量。     

生物炭与有机肥对菜田土壤氨氧化菌丰度的影响

通过土壤培育试验,运用定量PCR技术,研究了添加生物炭和有机肥对土壤氮营养及氨氧化古菌(AOA)和氨氧化细菌(AOB)丰度的影响。结果表明,土壤培育时间、有机肥显著增加硝态氮的含量(P0.001),促进硝化作用;生物炭通过抑制有机氮矿化作用降低硝化作用,106d时生物炭处理的硝态氮、可溶性总氮含量低于没有生物炭的处理(P0.05),并且中和了有机肥对矿化作用的促进效应。随着处理时间的延长,生物炭促进氨氧化菌群的丰度,AOA丰度的提高较AOB显著,且AOA丰度的变化与硝态氮含量的变化呈正相关。因此认为AOA是土壤中氨氧化作用的主要驱动力,且生物炭与有机肥主要对AOA的丰度产生影响。     

Effect of soil aggregate size and dicyandiamide on N2O emissions and ammonia oxidizer abundance in a grazed pasture soil

Nitrous oxide (N₂O) is a potent greenhouse gas, which is mainly produced from agricultural soils. Ammonia oxidation is the rate‐determining step in N₂O production, and the process is carried out by ammonia oxidizers, bacteria and archaea. Soil aggregate size has been shown to alter soil properties, which affect N₂O emissions and bacterial communities. However, the effect of aggregate size on temporal and total N₂O emissions and ammonia‐oxidizing bacteria (AOB) and archaea (AOA) is not fully understood. This incubation study investigated the effect of three different soil aggregate sizes on N₂O emissions and ammonia oxidizer abundance under high urine‐N concentrations and the effectiveness of a nitrification inhibitor, dicyandiamide (DCD), at reducing N₂O emissions in different aggregate soils. It was found that temporal patterns of N₂O emissions were affected by aggregate size with higher peak emissions in the large and medium aggregates. However, the total emissions were the same due to a ‘switch’ in emissions at day 66, after which smaller aggregates produced higher N₂O emissions. It is suggested that the switch was caused by an increase in aggregate disruption in the small aggregates, following the urine application, due to their higher surface area to volume ratio. AOB and AOA abundances were not significantly affected by aggregate size. DCD was effective in reducing N₂O emissions in all aggregate sizes by an average of 79%. These results suggest that similar ammonia oxidizer abundance is found in soils of different aggregate sizes, and the efficacy of DCD in reducing N₂O emissions was not affected by aggregate size of the soil.     

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.     

氨氧化菌及其在中国池塘养殖水质调控过程中的应用

氨氮是池塘养殖尾水治理过程中需着重考虑的一种污染物,池塘养殖环境氨氮氧化去除主要依赖氨氧化细菌、氨氧化古菌和厌氧氨氧化菌。本研究介绍了在自然界中已发现的几种氨氧化菌的氮素代谢机理,并结合池塘生态系统特征,着重从温度、pH、溶解氧、附着基质和光照角度,阐释氨氧化菌对池塘养殖水体的生态调控机制。基于氨氧化菌附着生活习性,现已研发出多种异位池塘养殖水质净化技术,在一定程度上,这些技术能发挥净水效果,但普遍存在占地面积大,造价高、效率低等问题。目前,中国池塘养殖水体处理领域,在氨氧化微生物菌剂和高效微生物反应器应用及研发方面比较薄弱。建议未来强化池塘低温高效氨氧化菌株筛选和富集培养研究,促进结构紧凑型水处理微生物反应器研发,丰富淡水池塘养殖尾水氨氮去除手段。     

不同温度下尿素对水稻土甲烷产生及相关古菌群落的影响

水稻田是大气甲烷的重要排放源。尿素氮肥施用是提升水稻产量和品质的重要措施,但其对稻田土壤中产甲烷古菌的影响规律仍不清楚。通过模拟水稻生长季节可能的田间温度变化,本文对水稻土进行施加尿素（400 mg N/kgdry soil）与未施加尿素（0 mg N/kgdry soil）两个处理,并在15℃、25℃、37℃以及50℃四个温度下进行为期100d的厌氧培养,定期测定了培养过程中产甲烷累积量以及土壤理化因子pH、铵氮以及有机碳的变化。并运用基于16S rRNA基因的T-RFLP（末端限制性片段多态性分析）技术分析了产甲烷过程中古菌群落结构随时间的变化情况。结果表明,在中低温范围内（15℃-37℃）,尿素对水稻土产甲烷有抑制作用,但在50℃高温下尿素对水稻土产甲烷量没有显著影响。尿素可能通过改变产甲烷古菌群落结构来影响产甲烷,在15℃-37℃范围内,尿素降低了水稻土产甲烷古菌群落的稳定性,增大了其在不同时间的差异性;而在50℃高温时,尿素对水稻土产甲烷古菌稳定性和差异性的影响不明显。不同温度下,尿素均降低了甲烷八叠球菌（Methanosarcinaceae）的丰度,且随着温度的变化,尿素对水稻土产甲烷机制的改变可能没有影响。     

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.     

Uptake of milk with and without solid feed during the monogastric phase: Effect on fibrolytic and methanogenic microorganisms in the gastrointestinal tract of calves

Microbial communities are affected by diet and play a role in the successful transition from milk to a solid diet. The response of microorganisms in the gastrointestinal tract of Holstein bull calves to the uptake of milk with solid feed (control treatment; CT), or milk without solid feed (milk‐only treatment; MT) during the first 3 weeks of life was investigated. Samples were collected from the rumen (fluid and tissue), abomasum (fluid), cecum (fluid and tissue) and feces at 7, 14 and 20 days of age. Calf weight was higher on days 14 and 20 in the MT than the CT. In the rumen at 14 days, the fibrolytic bacteria Fibrobacter succinogenes and Prevotella ruminicola increased in the CT and Ruminococcus flavefaciens increased in the MT. This suggests that R. flavefaciens is not strictly fibrolytic and that it might use milk as a substrate or other microbial species might supply a substrate. Diet affected methanogens, but this may have been due to an indirect effect via an association with Geobacter spp. or other syntrophic partners. The treatments also affected microorganisms in the abomasum, cecum and feces. Our results contribute to an understanding of diet, microbes in the gastrointestinal tract and weaning.