Ammonia-oxidizing communities in agricultural soil incubated with organic waste residues

The impact of organic compounds present in different kinds of organic fertilizers, i.e., anaerobically digested household waste, composted organic household waste, swine manure, and cow manure, on microbial communities in arable soil was investigated using microcosms. Soil was amended with dried residues or organic extracts of the residues and incubated for 12 weeks at 25°C. The microbial community composition was investigated by phospholipid fatty acid (PLFA) analysis, and the community of ammonia-oxidizing bacteria (AOB) was assessed by denaturing gradient gel electrophoresis (DGGE) of 16S rDNA fragments, followed by sequencing. All dried residues increased the AOB activity, determined as potential ammonia oxidation, whereas the organic extracts from the thermophilically digested waste and the swine manure caused a decreased potential activity. However, no differences in the DGGE banding patterns were detected, and the same AOB sequences were present in all samples treated with the residue extracts. Moreover, the PLFA composition showed that none of the residue additions affected the overall microbial community structure in the soil. We conclude that the AOB community composition was not affected by the organic compounds in the fertilizers, although the activity in some cases was.     

农田土壤好氧氨氧化和甲烷氧化交互作用机制的研究进展

从农田土壤生态系统中硝化和甲烷氧化的研究意义、氨氧化和甲烷氧化的功能微生物演替规律,以及二者交互作用机制三个方面综述了现阶段取得的主要研究成果,并进一步阐述了土壤碳氮元素生物地球化学循环机制研究的科学问题和面临的挑战。未来研究应充分利用学科交叉,结合宏观结果和土壤微观动态过程,揭示土壤中不可培养微生物代谢能力及其在土壤生物地球化学循环中的重要作用,逐步实现对土壤生态过程的预测和调控。     

Lipids of Prokaryotic Origin at the Base of Marine Food Webs

In particular niches of the marine environment, such as abyssal trenches, icy waters and hot vents, the base of the food web is composed of bacteria and archaea that have developed strategies to survive and thrive under the most extreme conditions. Some of these organisms are considered “extremophiles” and modulate the fatty acid composition of their phospholipids to maintain the adequate fluidity of the cellular membrane under cold/hot temperatures, elevated pressure, high/low salinity and pH. Bacterial cells are even able to produce polyunsaturated fatty acids, contrarily to what was considered until the 1990s, helping the regulation of the membrane fluidity triggered by temperature and pressure and providing protection from oxidative stress. In marine ecosystems, bacteria may either act as a sink of carbon, contribute to nutrient recycling to photo-autotrophs or bacterial organic matter may be transferred to other trophic links in aquatic food webs. The present work aims to provide a comprehensive review on lipid production in bacteria and archaea and to discuss how their lipids, of both heterotrophic and chemoautotrophic origin, contribute to marine food webs.     

Weaning methods affect ruminal methanogenic archaea composition and diversity in Holstein calves

The objective of the present study was to examine the effect of different weaning methods on the ruminal methanogenic archaea composition and diversity in Holstein calves.Thirty-six newborn Holstein bull calves were assigned to 1 of 3 treatments:(1)conventional weaning(d 56)and fed a high proportion of solid feed(CWS);(2)conventional weaning(d 56)and fed a high proportion of liquid feed(CWL);(3)early weaning(d 42)and fed with a high proportion of solid feed(EWS).High-throughput sequencing of the methyl coenzyme M reductase(mcr A)gene,which encodes theα-subunit of methyl coenzyme M reductase-the enzyme that catalyzes the final step in methanogenesis was used to determine the composition and diversity of rumen methanogens.No significant difference(P0.05)was observed for operational taxonomic units(OTUs)or richness indices,but diversity indices increased(P0.05)for calves fed high dietary solids.Predominant families across the three treatments were Methanobacteriaceae,Thermoplasmataceae and Methanomassiliicoccaceae.Calves in the EWS treatment had a higher(P0.05)relative abundance of Methanobrevibacter sp.strain AbM4 and Methanosphaera stadtmanae,while calves in the CWL treatment had a higher(P0.05)abundance of Methanosphaera sp.strain SM9.A positive(P0.05)relationship was identified between butyrate and Methanobrevibacter sp.strain AbM4.In conclusion,the composition and diversity of methanogens in the rumen of Holstein calves varied under the different weaning methods.This study identified a positive relationship between butyrate and Methanobrevibacter sp.strain AbM4,potentially reflecting correlations between ruminal fermentation variables and methanogenesis function.These in-depth analyses provide further understanding of weaning methods for intensified production systems.     

模拟氮沉降对贝加尔针茅草原土壤氮转化微生物的影响

草地土壤是温室气体重要的源和汇,认识草地生态系统氮转化过程有助于预测氮循环对未来氮沉降增加的响应与反馈机制。依托于2010年在内蒙古贝加尔针茅草原设置的长期模拟氮沉降增加的氮添加试验,共设置了8个氮添加水平(0、15、30、50、100、150、200、300 kg N·hm~(-2)·a~(-1))。应用荧光定量PCR方法,研究氮转化功能基因丰度对不同氮添加水平的响应。2015年8月取样分析结果表明:固氮微生物(nifH)基因丰度随着氮添加水平的升高,表现为先升高后降低的趋势。低于200 kg N·hm~(-2)·a~(-1)硝酸铵处理有利于固氮菌生长。低氮添加(N15、N30和N50)对氨氧化细菌(AOB-amoA)和氨氧化古菌(AOA-amoA)基因丰度无显著影响。高氮添加(N100、N150、N200和N300)显著提高了AOB基因丰度,降低了AOA基因丰度。高氮添加(N150、N200和N300)显著降低了nirK基因丰度。随着氮添加量的增加,高氮添加促进了AOB主导的氨氧化过程,而反硝化微生物丰度的减少提高了氨氧化产物硝酸盐的积累,继而提高了土壤硝酸盐含量。     

Effects of Silver Nanoparticles on Soil Ammonia-Oxidizing Microorganisms Under Temperatures of 25 and 5℃

The excellent bactericidal performance of silver nanoparticles (Ag NPs) has led to their wide applications, resulting in increasing concerns about their potential environmental impacts. This study evaluated the influences of different concentrations of Ag NPs (0, 1, 10, and 100 μg g^-1 dry soil) on the ammonia-oxidizing microorganisms in soil at cultivation temperatures of 25 and 5℃ for 37 d. The results showed that 1 μg g^-1 dry soil of Ag NPs had no acute effects on the ammonia-oxidizing microorganisms. However, 10 and 100 μg g^-1 dry soil of Ag NPs levels were found to significantly inhibit the activities of soil nitrification, with a decrease of 69.89% and 94.55%, respectively, at 25℃ and 61.65% and 83.79%, respectively, at 5℃ compared to the control (0 μg g^-1 dry soil of Ag NPs). These levels of Ag NPs also obviously decreased soil urease activity from about 380.47 ±0.07 (at 5℃) and 529.76 ±13.44 (at 25℃) mg N g^-1 dry soil d^-1 to 61.70 ±2.97 and 68.29 ±8.22 mg N g^-1 dry soil d^-1, respectively, after 37 d of cultivation. Quantitative polymerase chain reaction showed the abundance of ammonia-oxidizing archaea and bacteria. For the same exposure time, the effects of Ag NPs on the activities of ammonia-oxidizing microorganisms and urease decreased with decreasing temperature. The threshold concentration of Ag NPs that induced negative effects on ammonia-oxidizing microorganisms was higher at 5℃ than at 25℃. Therefore, the temperature has a major impact on the toxicity of Ag NPs to ammonia-oxidizing microorganisms and on the urease activity, with toxicity being reduced with decreasing temperature.     

土壤亚硝酸气体(HONO)排放过程及其驱动机制

气态亚硝酸(HONO)是大气中氢氧自由基(OH·)的重要来源,直接影响到大气氧化能力和空气质量。通过比较外场测定和模型计算的HONO浓度,发现白天时存在未知的大气HONO来源。研究表明,土壤可以向大气中排放HONO。其机理可能是土壤亚硝态氮和氢离子的化学平衡作用;或土壤夜间吸附和白天解吸附的动态物理化学过程;或氨氧化细菌等微生物的直接排放;也可能是硝化过程中产生的羟胺,在土壤颗粒物等表面的化学反应。因此,土壤HONO排放通量与土壤亚硝态氮浓度、pH、氨氧化细菌丰度、土壤矿物、土壤湿度及C/N值等相关。目前对于土壤HONO排放的研究尚在起步阶段,国内亦少见相关成果报道。本文综述了土壤HONO排放的研究背景、探讨了土壤HONO排放的机理及影响因素,以期为减少氮素损失、提高氮肥利用率、评估氮肥的环境效应及城市空气质量等提供理论依据和科学指导。     

转cry1Ab和epsps基因玉米C0030.3.5对土壤古菌丰度和多样性的影响

为探讨转基因玉米的生态安全问题,2015年分别于玉米拔节期、抽雄期、乳熟期和完熟期采集土壤样品,并采用荧光定量PCR(Quantitative real-time PCR,q PCR)和末端限制性片段长度多态性分析(Terminal restriction fragment length polymorphism,TRFLP)技术,研究了转cry1Ab和epsps基因玉米C0030.3.5种植对土壤古菌丰度和多样性的影响。结果表明:转cry1Ab和epsps基因玉米C0030.3.5(TM)和受体玉米DBN318(PM)的根际土和非根际土古菌数量为1.41×10~9~4.04×10~9copies·g~(-1)土,随生长时期的推进均呈现先升高后降低的变化趋势,同一生长时期和土壤样品采集区域,2种玉米古菌16S rRNA基因丰度间无显著差异。T-RFLP分析共获得15种不同长度的T-RFs,其中89 bp和184 bp片段为优势种群,同一生长时期和土壤样品采集区域每种优势种群在TM和PM间均无显著差异。土壤古菌Shannon指数除PM非根际土呈现先降低后升高的变化趋势外,其他均表现为先降低后升高再降低;TM和PM根际土古菌Evenness指数的变化趋势均为先降低后升高,而非根际土古菌Evenness指数表现为先降低后升高再降低。同一生长时期和土壤样品采集区域TM和PM的Shannon指数间及Evenness指数间差异均不显著。冗余分析(Redundancy analysis,RDA)显示土壤总氮和硝态氮含量对古菌群落结构有显著影响。主成分分析(Principal component analysis,PCA)表明,TM和PM土壤古菌群落在根际土和非根际土中均未发生明显分离,说明TM和PM土壤古菌群落组成无显著差异。上述结果表明:转cry1Ab和epsps基因玉米C0030.3.5土壤古菌丰度和群落结构组成与受体玉米DBN318无显著差异,古菌丰度和多样性主要受生长时期的影响,受土壤样品采集区域的影响不显著,土壤总氮和硝态氮是调控土壤古菌群落变化的关键因子。