闽江河口区淡水和半咸水潮汐沼泽湿地土壤产甲烷菌多样性

为认识盐度对河口潮汐沼泽湿地土壤产甲烷菌的影响,应用PCR-RFLP技术及测序分析对闽江河口区淡水-半咸水盐度梯度上分布的4个短叶茳芏潮汐沼泽湿地土壤产甲烷菌群落结构进行研究。闽江河口区短叶茳芏潮汐沼泽湿地土壤产甲烷菌群落结构受盐度影响明显,位于下洋洲和塔礁洲的短叶茳芏潮汐淡水沼泽湿地土壤产甲烷菌的香农-威纳多样性指数值分别为2.81和2.65,位于蝙蝠洲和鳝鱼滩的短叶茳芏潮汐半咸水沼泽湿地土壤产甲烷菌香农-威纳多样性指数值分别仅为2.33和2.27。系统发育分析表明:短叶茳芏沼泽湿地土壤产甲烷菌类群主要有甲烷杆菌目(Methanobacteriales),包括Methanobacterium、Methanobrevibacter和Methanobacteriaceae;甲烷微菌目(Methanomicrobiales),主要有Methanoregula,以及甲烷八叠球菌目(Methanosarcinales),主要有Methanosarcina和Methanococcoides。闽江河口区短叶茳芏潮汐淡水沼泽湿地土壤主要的优势产甲烷菌有Methanoregula、Methanosarcina和Methanobacterium,而短叶茳芏潮汐半咸水沼泽湿地土壤主要的优势产甲烷菌则转化为仅以Methanoregula为主。     

模拟增温对青海湖高寒湿地产甲烷菌群落特征的影响

高寒湿地生态系统作为重要的甲烷排放源, 对全球气候变暖有着较大的贡献率。湿地的产甲烷菌群落在温室气体排放中扮演着重要角色, 探究高寒湿地产甲烷菌群落结构及多样性对温度升高的响应十分重要。以青海湖高寒湿地为研究对象, 采用高通量测序方法开展研究。基于97%的序列相似度聚类, 10个土壤样品的总OTU数量为602个, 对照与增温处理样品的特有OTU数分别为30和43。与对照相比, 增温处理并未显著改变高寒湿地产甲烷菌群落的多样性指数及目水平优势菌群(P>0.05)。高寒湿地产甲烷菌均为广古菌门, 目水平以甲烷微菌目(Methanomicrobiales, 67.35%)、八叠球菌目(Methanosarcinales, 14.14%)、甲烷杆菌目(Methanobacteriales, 10.21%)为优势菌群。Lefse分析表明, 增温后Methanomassiliicoccus相对丰度显著降低、Candidatus Methanogranum相对丰度显著升高。整体而言, 青海湖高寒湿地产甲烷菌群落组成及多样性较为稳定, 温度升高对产甲烷菌群落影响较小, Methanomassiliicoccus和Candidatus Methanogranum对温度变化较为敏感。     

模拟增温对青海湖鸟岛土壤产甲烷菌群落特征的影响

甲烷生成与产甲烷菌群落关系密切,探究温度升高对产甲烷菌群落的影响可以预测产甲烷菌群落特征对气候变暖的响应.以青海湖鸟岛为研究对象,通过高通量测序方法开展研究.结果表明,基于97％的序列相似度聚类,共得到697个操作分类单元.鸟岛土壤产甲烷菌群落以甲烷微菌目(Methanomicrobiales)、甲烷八叠球菌目(Met...     

炉渣与生物炭施加对稻田土壤碳库及微生物的影响

以福州平原稻田为实验区,在2015年早、晚稻秧苗移栽前,对稻田进行施加生物炭、炉渣、生物炭+炉渣（混施）处理,并以不施加处理作为对照。为了了解施加处理的后续效应,于2017年检测早、晚稻拔节期和成熟期土壤有机碳含量及真菌、细菌数量。结果表明：3种施加处理稻田土壤有机碳（SOC）含量均比对照组有显著提高（P < 0.05）,但溶解性有机碳（DOC）、易氧化碳（EOC）、土壤微生物量碳（MBC）含量各处理之间差异不显著（P > 0.05）。与对照组相比,各施加处理组在一定程度上提高了土壤中真菌和细菌数量,但差异不显著（P > 0.05）。细菌数量与DOC含量呈极显著负相关（P < 0.01）,与EOC含量呈显著负相关（P < 0.05）,与MBC含量呈显著正相关（P < 0.05）。真菌/细菌比值与真菌数量、DOC含量呈极显著正相关（P < 0.01）。说明炉渣和生物炭施加处理2年后,仍可提高稻田土壤的碳库稳定性,并增加土壤微生物数量。     

DGGE揭示红壤稻田以产甲烷菌为主的稳定古菌群落结构特征

尽管古菌在农田土壤生态系统物质、能量循环中的作用尚未系统揭示,但已有研究表明产甲烷古菌和氨氧化古菌等在甲烷排放、固氮等方面具有重要生态功能。本研究采用优化的变性梯度凝胶电泳(DGGE)与克隆、序列测定相结合的方法,基于古菌16S V4~V5区分析我国水稻种植最常见的红壤地区稻田古菌在水稻生长不同时期的群落结构及多样性。在采集自江西省南昌地区的稻田土壤中,共检测到2个门、4个纲及5个目的古菌。作为主要优势类群,产甲烷菌纲(Methanomicrobia)丰度达49.15%;甲烷八迭球菌目(Methanosarcinales)丰度达39.45%。而氨氧化古菌属(Nitrosotalea)丰度也达6.07%。水稻分蘖期、灌浆期及成熟期稻田土壤古菌DGGE电泳条带数量及序列高度相似,分蘖期、灌浆期香农多样性指数未检测到具有统计学意义的差异(p=0.534)。成熟期香农多样性指数略高于分蘖期(p=0.017)和灌浆期(p=0.009),分析可能主要由土壤含水显著下降导致。红壤稻田的古菌群落结构在水稻生长期内能够基本保持稳定,是稻田古菌与人类耕作活动的长期共进化造成的。产甲烷菌中的优势类群——甲烷八迭球菌在水稻土壤中究竟是以消耗乙酸还是利用氢气/二氧化碳合成甲烷或两种代谢方式转换条件等方面研究,将有助于建立红壤水稻可持续耕作及红壤稻田酸化修复等的新方法。总之,稻田等农田生态系统中古菌的生态功能研究具有重要的理论意义和潜在应用价值,应予以高度重视。     

生物质炭对水稻土团聚体微生物多样性的影响

生物质炭施用对土壤微生物群落结构的影响已有报道,但土壤团聚体粒组中微生物群落对生物质炭施用的响应的研究还相对不足。以施用玉米秸秆生物质炭两年后的水稻土为对象,采用团聚体湿筛法,通过高通量测序对土壤团聚体的微生物群落结构与多样性进行分析,结果表明:(1)与对照相比,生物质炭施用显著促进了大团聚体(2000—250μm)的形成,并提高了团聚体的稳定性。(2)不同粒径团聚体间微生物相对丰度存在显著差异。在未施生物质炭的处理(C0)中,随着团聚体粒径增大,变形菌门、子囊菌门、β-变形杆菌目、格孢腔菌目的相对丰度逐渐降低,而酸杆菌门、担子菌门、粘球菌目、类球囊霉目的相对丰度逐渐升高。(3)生物质炭施用显著改变了团聚体间的微生物群落结构。与C0处理相比,生物质炭施用处理的大团聚体中变形菌门、鞭毛菌门和β-变形杆菌目的相对丰度分别显著提高了14.37%、33.28%和33.82%;微团聚体(250—53μm)中酸杆菌门、子囊菌门和粘球菌目的相对丰度分别显著降低了20.15%、19.93%和17.66%;粉、黏粒组分(53μm)中担子菌门的相对丰度升高90.25%,而子囊菌门和鞭毛菌门的相对丰度分别降低12.15%和12.58%。由此可见,生物质炭不仅改变土壤团聚体组成和分布,同时伴随着土壤微生物群落结构的改变。     

减氮配施稻秆生物炭对稻田土壤养分及植株氮素吸收的影响

通过2018年早稻和晚稻田间试验,研究化学氮肥减量及配施稻秆生物炭对稻田土壤养分特性及植株氮素吸收的影响。试验包括6个处理:不施氮(CK)、常规施氮(N₁₀₀)、减氮20%(N₈₀)、减氮20%配施生物炭(N₈₀+BC)、减氮40%(N₆₀)、减氮40%配施生物炭(N₆₀+BC)。结果表明: 与常规施氮相比,单纯减氮20%和40%或配施生物炭对早晚稻不同生育期土壤pH、有机质、全氮、铵态氮、全磷、有效磷、全钾、速效钾无显著影响;减氮20%配施生物炭显著增加晚稻分蘖期的土壤阳离子交换量(CEC),而减氮40%配施生物炭则显著增加晚稻抽穗期的电导率(EC)值。与单纯减氮相比,N₈₀+BC的土壤速效钾含量在早晚稻抽穗期均显著升高,土壤pH值、全氮在晚稻成熟期显著增加;N₆₀+BC的土壤全钾含量在早稻成熟期显著升高。不同处理早稻土壤硝态氮含量随生育进程逐渐降低,与分蘖期相比,抽穗期和成熟期的常规施氮土壤硝态氮含量分别降低50.0%和71.6%,而配施生物炭处理则降低6.3%～45.5%,减氮配施生物炭显著降低了硝态氮的流失。在晚稻抽穗期,减氮配施生物炭植株吸氮量显著高于常规施氮和单纯减氮,增加幅度为34.8%～52.4%。综上,适度的减氮或配施稻秆生物炭能有效保持土壤养分,促进水稻对氮素的吸收,提高氮素利用率。     

长期施肥对黄土旱塬农田土壤微生物丰度的影响

以长武黄土高原农业生态试验站的长期定位试验为平台,通过荧光实时定量PCR (real-time PCR) 技术,研究不同施肥制度下的黄土旱塬农田土壤微生物群落丰度,揭示长期不同施肥制度对土壤微生物群落的影响规律.结果表明: 单施化肥处理细菌数量较CK裸地增加21％,古菌增加32％;化肥配施有机肥处理细菌数量增加37％,古菌数量增加36％.化肥配施有机肥处理显著增加了土壤细菌和古菌的丰度.30年长期施氮肥处理导致氨氧化细菌(AOB)的增幅达7.13倍,而氨氧化古菌(AOA)的增幅仅为0.2倍.AOB对施肥的响应程度较高,尤其是对氮肥具有较高的敏感性.与单施氮肥和氮肥混施有机肥处理相比,施磷肥处理显著增加了固氮酶铁蛋白和甲烷氧化菌含量,撂荒地的固氮酶铁蛋白、亚硝酸还原酶和甲烷氧化菌含量显著高于耕作土壤.结合土壤基本理化性质的相关性分析结果,pH、全氮和有机碳含量是影响土壤微生物群落丰度的重要因子.总之,长期施肥显著改变了黄土旱塬农田土壤各微生物丰度,不同施肥模式、耕作方式对微生物群落丰度具有显著影响.     

香蕉假茎生物炭对根际土壤细菌丰度和群落结构的影响

【目的】将香蕉假茎生物炭施加到土壤,探讨香蕉假茎生物炭对香蕉根际土壤微生物的影响。【方法】以香蕉假茎生物炭(BPB)0、1%、2%、3%的质量比与土壤均匀混合。盆栽培养3个月后分离香蕉根际土壤。采用16S rRNA高通量测序技术对根际土壤细菌群落结构和丰度进行表征。【结果】提高BPB施用量可增加土壤有机质、有效钾、有效磷含量,提高土壤pH值,但降低有效氮浓度。在1%BPB样品中获得2278个OTUs,其显示细菌群落中的最大多样性。施加3%的BPB处理土壤,拟杆菌门、疣微菌门和厚壁菌门的相对丰度显著增加;放线菌门、酸杆菌门、芽单胞菌门明显减少。主成分分析发现,1%BPB和2%BPB处理的样本之间土壤细菌群落相似。【结论】施加不同比例BPB改变了根际土壤中细菌丰度和群落结构,且高比例添加改变更加明显。     

稻鱼共生系统的土壤产甲烷和甲烷氧化微生物群落

稻鱼共生对稻田甲烷(CH₄)排放产生明显影响，但稻鱼共生是否影响与CH₄排放相关的产甲烷菌和甲烷氧化菌仍有待阐明。本研究以全球重要农业文化遗产——青田稻鱼系统为例，通过田间试验，比较研究了水稻单作系统(RM)、无饲料投放的稻鱼共生系统(RFN)和有饲料投放的稻鱼共生系统(RFF)水稻和田鱼的产量、土壤碳氮磷含量以及产甲烷和甲烷氧化微生物的特征。结果表明，RFF的水稻产量和土壤碳氮增量均显著高于RM。荧光定量PCR分析表明，稻鱼共生(RFN和RFF)的产甲烷菌和甲烷氧化菌丰度显著高于RM,且RFF的产甲烷菌丰度显著高于RFN。Illumina Miseq测序分析表明，稻鱼共生显著影响产甲烷菌群落结构，但对甲烷氧化菌群落结构的影响不显著；对于不同代谢类型的产甲烷菌，稻鱼共生(RFN和RFF)氢营养型产甲烷菌的丰度显著高于RM,且RFF的乙酸营养型产甲烷菌丰度显著高于RFN;对于不同代谢类型的甲烷氧化菌，RFN和RFF对类型Ⅰ的甲烷氧化菌丰度影响均不显著；RFF中类型Ⅱ的甲烷氧化菌丰度显著高于RM和RFN。可见，稻鱼共生可明显影响产甲烷菌和甲烷氧化...     

人肠道梭菌和甲烷马赛球菌协同代谢甜菜碱和胆碱产甲烷研究

【目的】根据人肠道富含胆碱和甜菜碱,同时肠道微生物组中具有裂解胆碱和还原甜菜碱产三甲胺的细菌,以及利用三甲胺产甲烷的古菌,本研究探讨肠道细菌与古菌协同代谢甜菜碱和胆碱产甲烷的可能性。【方法】调查不同年龄段人群粪便中的16S rRNA基因多样性,分析肠道中古菌的菌群组成;利用定量PCR(quantitativePCR,qPCR)定量甲烷马赛球菌(Methanomassiliicoccus)特异的甲醇甲基转移酶基因mtaB和甲烷八叠球菌(Methanosarcina)及细菌的16SrRNA基因拷贝数,分析肠道中甲基营养型产甲烷古菌及总细菌的含量;宏基因组组装基因组(metagenome-assembled genomes, MAGs)分析携带甜菜碱还原酶基因grdH和胆碱裂解酶基因cutC的细菌组成。从粪便中分离代谢甜菜碱及胆碱产生三甲胺的细菌,并与分离自人肠道的甲烷马赛球菌构建共培养物,测定其协同转化甜菜碱和胆碱产甲烷的能力。【结果】年轻人粪便中含有甲烷杆菌科(Methanobacteriaceae,82.16%)的甲烷短杆菌属(Methanobrevibacter,49.18%)和甲烷...     

Diversity and Structure of the Methanogenic Community in Anoxic Rice Paddy Soil Microcosms as Examined by Cultivation and Direct 16S rRNA Gene Sequence Retrieval

A dual approach consisting of cultivation and molecular retrieval of partial archaeal 16S rRNA genes was carried out to characterize the diversity and structure of the methanogenic community inhabiting the anoxic bulk soil of flooded rice microcosms. The molecular approach identified four groups of known methanogens. Three environmental sequences clustered with Methanobacterium bryantii and Methanobacterium formicicum, six were closely related but not identical to those of strains of Methanosaeta concilii, two grouped with members of the genus Methanosarcina, and two were related to the methanogenic endosymbiont of Plagiopyla nasuta. The cultivation approach via most-probable-number counts with a subsample of the same soil as an inoculum yielded cell numbers of up to 10⁷ per g of dry soil for the H₂-CO₂-utilizing methanogens and of up to 10⁶ for the acetate-utilizing methanogens. Strain VeH52, isolated from the terminal positive dilution on H₂-CO₂, grouped within the phylogenetic radiation characterized by M. bryantii and M. formicicum and the environmental sequences of the Methanobacterium-like group. A consortium of two distinct methanogens grew in the terminal positive culture on acetate. These two organisms showed absolute 16S rRNA gene identities with environmental sequences of the novel Methanosaeta-like group and the Methanobacterium-like group. Methanosarcina spp. were identified only in the less-dilute levels of the same dilution series on acetate. These data correlate well with acetate concentrations of about 11 μM in the pore water of this rice paddy soil. These concentrations are too low for the growth of known Methanosarcina spp. but are at the acetate utilization threshold of Methanosaeta spp. Thus, our data indicated Methanosaeta spp. and Methanobacterium spp. to be the dominant methanogenic groups in the anoxic rice soil, whereas Methanosarcina spp. appeared to be less abundant.     

Variation in Soil Methane Release or Uptake Responses to Biochar Amendment: A Separate Meta-analysis

Agricultural soils play an important role in the atmospheric methane (CH₄) budget, where paddy soils can contribute significant CH₄ to atmosphere whereas upland soils may act as a source or sink of atmospheric CH₄, dependent on soil water conditions. Biochar amendments have effects on soil CH₄ production or oxidation processes in individual experiments, but the causative mechanisms are yet to be fully elucidated. To synthesize the response of soil CH₄ release or uptake to biochar amendment, we performed a meta-analysis using data from 61 peer-reviewed papers with 222 updated paired measurements. When averaged across all studies, biochar amendment significantly decreased CH₄ release rates by 12% for paddy soils and 72% for upland soils, and CH₄ uptake rates by 84% for upland soils. Neither soil CH₄ release nor uptake responses to biochar amendment were significant in field soils. Nitrogen (N) fertilizer application would weaken the response of soil CH₄ release or uptake to biochar amendment. Biochar-incurred decreases in soil CH₄ release and uptake rates were the largest in medium-textured soils or neutral-pH soils. Soil CH₄ release or uptake responses to biochar were also significantly altered by biochar characteristics, such as feedstock source, C/N ratio, pH, and pyrolysis temperature. The results of this synthesis suggest that the role of biochar in soil CH₄ mitigation potential might have been exaggerated, particularly in fields when biochar is applied in combination with N fertilizer.     

Methanosarcina as the dominant aceticlastic methanogens during mesophilic anaerobic digestion of putrescible waste

Taking into account isotope ¹³C value a mathematical model was developed to describe the dynamics of methanogenic population during mesophilic anaerobic digestion of putrescible solid waste and waste imitating Chinese municipal solid waste. Three groups of methanogens were considered in the model including unified hydrogenotrophic methanogens and two aceticlastic methanogens Methanosaeta sp. and Methanosarcina sp. It was assumed that Methanosaeta sp. and Methanosarcina sp. are inhibited by high volatile fatty acids concentration. The total organic and inorganic carbon concentrations, methane production, methane and carbon dioxide partial pressures as well as the isotope ¹³C incorporation in PSW and CMSW were used for the model calibration and validation. The model showed that in spite of the high initial biomass concentration of Methanosaeta sp. Methanosarcina sp. became the dominant aceticlastic methanogens in the system. This prediction was confirmed by FISH. It is concluded that Methanosarcina sp. forming multicellular aggregates may resist to inhibition by volatile fatty acids (VFAs) because a slow diffusion rate of the acids limits the VFA concentrations inside the Methanosarcina sp. aggregates.     

Soil amendment with biochar and manure alters wood stake decomposition and fungal community composition

Biochar and manure can be used for sustainable land management. However, little is known about how soil amendments might affect surface and belowground microbial processes and subsequent wood decomposition. In a split-split-split plot design, we amended soil with two rates of manure (whole plot; 0 and 9 Mg ha⁻¹) and biochar (split plot; 0 and 10 Mg ha⁻¹). Wood stakes of three species (hybrid poplar, triploid Populus tomentosa Carr.; aspen, Populus tremuloides Michx.; and pine, Pinus taeda L.) were placed in two positions (horizontally on the soil surface, and inserted vertically in the mineral soil), which served as a substrate for fungal growth. In 3 years, the decomposition rate (density loss), moisture content, and fungal community (via high-throughput sequencing methods) of stakes were evaluated. Results indicated that biochar and/or manure increased the wood stake decomposition rates, moisture content, and operational taxonomic unit abundance. However, the richness and diversity of fungi were dependent on wood stake position (surface > mineral), species (pine > the two Populus), and sample dates. This study highlights that soil amendment with biochar and/or manure can alter the fungal community, which in turn can enhance an important soil process (i.e., decomposition).     

长期施肥对双季稻田甲烷排放和关键功能微生物的影响

研究不同施肥措施对双季稻田甲烷(CH_4)排放特征的影响及其微生物学机理,对合理利用及评价不同施肥模式对水稻生长的影响具有重要意义。以长期施肥定位试验田为平台,采用静态箱-气相色谱法对施用化肥(MF:mineral fertilizer alone)、秸秆还田配施化肥(RF:rice residues plus mineral fertilizer)、30%有机肥配施70%化肥(LOM:30%organic matter plus 70%mineral fertilizer)、60%有机肥配施40%化肥(HOM:60%organic matter plus 40%mineral fertilizer)和无肥(CK:without fertilizer)条件下双季稻田CH_4排放及其微生物学机理进行了分析。结果表明,早稻和晚稻生长期,不同施肥处理稻田CH_4排放通量均显著高于CK,表现为HOMLOMRFMFCK。各处理间CH_4总排放量差异达显著水平,其大小顺序与排放通量趋势一致,以HOM处理为最高,比CK处理增加105.56%,其次是LOM和RF处理,分别比CK处理增加72.97%和54.17%。关键功能土壤微生物测定结果表明,早稻和晚稻各个主要生育时期,各处理稻田土壤产甲烷古菌的数量变化范围为(3.18—81.07)×10~3cfu/g,土壤甲烷氧化细菌的数量变化范围为(24.82—379.72)×10~3cfu/g。稻田土壤产甲烷古菌和甲烷氧化细菌数量大小顺序为HOMLOMRFMFCK,各施肥处理均显著高于CK;HOM、LOM、RF处理显著高于MF、CK处理。双季稻田CH_4排放与稻田土壤产甲烷古菌、甲烷氧化细菌数量变化关系密切。采用有机无机肥配施促进了双季稻田生态系统CH_4的排放和关键功能微生物的数量。     

Rice to Vegetables: Short- Versus Long-Term Impact of Land-Use Change on the Indigenous Soil Microbial Community

Land-use change is known to have a significant effect on the indigenous soil microbial community, but it is unknown if there are any general trends regarding how this effect varies over time. Here, we describe a comparative analysis of microbial communities from three adjacent agricultural fields: one-century-old paddy field (OP) and two vegetable fields (new vegetable field (NV) and old vegetable field (OV)) that were established on traditional paddy fields 10 and 100 years ago, respectively. Soil chemical and physical analysis showed that both vegetable fields were more nutrient rich than the paddy field in terms of organic C, total N, total P, and available K. The vegetable fields possessed relatively higher abundance of culturable bacteria, fungi, and specific groups of bacteria (Actinomyces, nitrifying bacteria, and cellulose-decomposing bacteria) but lower levels of microbial biomass C and N. Notably, the decrease of biomass was further confirmed by analysis of seven additional soils in chronosequence sampled from the same area. Next we examined the metabolic diversity of the microbial community using the EcoPlate^TM system from Biolog Inc. (Hayward, CA, USA). The utilization patterns of 31 unique C substrates (i.e., community-level physiological profile) showed that microorganisms in vegetable soil and paddy soil prefer to use different C substrates (polymeric compounds for NV and OV soils, phenolic acids for OP soil). Principal component analysis and the average well color development data showed that the NV is metabolically more distinct from the OV and OP. The effect was likely attributable to the elevated soil pH in NV soil. Furthermore, we assessed the diversity of soil bacterial populations using the cultivation-independent technology of amplified ribosomal DNA restriction analysis (ARDRA). Results showed that levels of bacterial diversity in OP and NV soils were similar (Shannon’s diversity index H = 4.83 and 4.79, respectively), whereas bacteria in OV soil have the lowest score of diversity (H = 3.48). The low level of bacterial diversity in OV soil was supported by sequencing of ten randomly selected 16S rDNA clones from each of the three rDNA libraries. Phylogenetic analysis showed that all the ten OV clones belonged to Proteobacteria with eight in the gamma-subdivision and two in the alpha-subdivision. In contrast, the ten clones from NV and OP soils were classified into four and eight bacterial classes or unclassified groups, respectively. Taken together, our data suggest that land-use change from rice to vegetables resulted in a decrease of bacterial diversity and soil biomass despite an increase in the abundance of culturable microorganisms and, moreover, the decrease of bacterial diversity occurred during long-term rather than short-term vegetable cultivation.