Bacterial community structure correlates with decomposition parameters along a Hawaiian precipitation gradient

We analyzed soil bacterial communities with terminal restriction fragment length polymorphisms (TRFLP) along a precipitation gradient on the Hawaiian island Maui where mean annual rainfall increases from 2200 to 5050 mm. Principal component and cluster analysis of TRFLP patterns indicated there were only small differences in bacterial communities in soils receiving 2200-2750 mm of rain annually but large changes in bacterial community structure occurred as annual precipitation exceeded 2750 mm. The change in bacterial community structure correlated with several ecosystem parameters including mean annual precipitation, aboveground net primary productivity, soil redox status, litter decomposition rates, net methane flux and soil respiration. We suggest the dominant change in bacterial community structure along the gradient reflects a shift from respiratory to fermentative metabolism.     

复垦土壤细菌群落结构及其与土壤肥力的关系

为了解两淮煤矿区复垦状况及其对土壤微生物的影响机制,合理人工干预,快速有效提高复垦土壤生产力,本研究以煤矸石充填复垦土壤为研究对象,通过野外调查与采样分析,采用Illumina MiSeq 高通量测序分析土壤细菌特定基因片段V4 区域,基于非度量多维尺度分析、冗余分析、方差分析、肥力指数、回归模型方法,对矸石充填土壤不同复垦方向的土壤细菌优势群落和生物多样性进行了探索,明晰土壤细菌群落及其与土壤肥力的响应作用。研究结果表明：细菌群落组成上,不同复垦方向对细菌优势群落分布并无显著性影响,变形菌门、酸杆菌门和放线菌门菌群为主要优势菌群。土壤微生物多样性层面上,表层土壤微生物有较高的丰富度和多样性,均匀度并无显著性差异。微生物多样性在不同复垦方向不存在显著性差异,Shannon_Wiener指数介于6.19～6.85之间,Chao1指数为3131.97～4938.37,Pielou指数介于0.79～0.84之间,表中层同深层土壤的细菌群落结构具有差异性。TN、SOM、AP和AK是影响土壤细菌群落的主要肥力因子,土壤肥力质量指数与奇古菌门相对丰度呈显著正相关（P＜0.01）,同链霉菌属呈显著负相关（P＜0.05）,在一定程度上可将二者的相对丰度作为评价复垦土壤肥力状况的重要生物指标。研究成果可为两淮矿区矸石充填复垦土壤在微生物层面提高肥力质量提供理论支持。     

半纤维素分解菌群HMC的微生物群落结构及功能

为明确半纤维素分解菌群HMC（hemicellulolytic microbial consortium）的微生物群落结构及其在半纤维素降解中的潜在功能;该研究测定了其在降解半纤维素主链木聚糖及玉米芯的典型理化指标,并利用16S rDNA测序技术及生物信息学手段对其微生物群落结构及功能注释进行了宏基因组学分析。结果表明,HMC在7d内能高效降解木聚糖和玉米芯,降解率达80%,木聚糖降解产生的高值产物包括还原糖、甲酸、乳酸及乙酸,最高浓度分别为1.30、0.50、1.19与1.23 mg/mL,HMC降解玉米芯时可累积挥发性脂肪酸浓度高达3.54 mg/mL。HMC是由厚壁菌门Firmicutes的多个属的微生物组成的复合微生物菌群,宏基因组分析揭示了HMC在木聚糖降解过程中的关键碳水化合物活性酶系;HMC的半纤维素降解酶系完整,包括19个木聚糖分解及下游产物代谢相关的酶;同时涵盖了乙酸、乳酸等半纤维素关键分解产物代谢相关的通路。HMC蕴含半纤维素及玉米芯高值生物转化的潜力,该研究为深入探究半纤维素在生物降解应用中的分子机制提供了重要线索,有助于推动天然半纤维素生物降解技术的发展。     

油井采出液中微生物群落结构的T-RFLP分析

应用末端标记限制性片段长度多态性(Terminal Restriction Fragment Length Polymorphism,T-RFLP)和克隆文库分析,以微生物群落16SrRNA基因(16S rDNA)为目标,对大庆油田过渡带油井采出液(于2005年7月和10月取样)中的微生物群落结构进行了解析和比较。T-RFLP分析表明,2005年7月和10月油井采出液中古菌群落结构较为单一,随时间变化不大;而细菌群落结构较为复杂,不同时间群落中的优势菌有明显的差别。古菌和细菌16S rDNA片段测序和系统发育分析表明,大庆油田过渡带油井采出液古菌群落中的优势菌均为产甲烷菌;细菌群落中的优势菌则与β、γ、δ、ε变形杆菌(Proteobacteria)、拟杆菌(Bacte-roidetes)和脱铁杆菌(Deferribacteres)有较高的相似性,细菌群落中检出了大量的未培养微生物(Deep-branching lineages)。     

Application of DGGE analysis to the study of bacterial community structure in plant roots and in nonrhizosphere soil

To analyze the structure of bacterial communities in spinach roots and in the nonrhizosphere soil, we used PeR-amplified 16S rRNA gene fragments separated by denaturing gradient gel electrophoresis (DGGE). DGGE revealed a large number of band patterns, which were ascribed to various bacterial species composing each of the bacterial communities. The pattern from the roots was less complex than that from the soil. It is considered that DGGE analysis is suitable for studies of bacterial community structure in soil-plant ecosystems.     

Substrate inputs and pH as factors controlling microbial biomass, activity and community structure in an arable soil

Our aim was to determine whether the smaller biomasses generally found in low pH compared to high pH arable soils under similar management are due principally to the decreased inputs of substrate or whether some factor(s) associated with pH are also important. This was tested in a soil incubation experiment using wheat straw as substrate and soils of different pHs (8.09, 6.61, 4.65 and 4.17). Microbial biomass ninhydrin-N, and microbial community structure evaluated by phospholipid fatty acids (PLFAs), were measured at 0 (control soil only), 5, 25 and 50 days and CO₂ evolution up to 100 days. Straw addition increased biomass ninhydrin-N, CO₂ evolution and total PLFA concentrations at all soil pH values. The positive effect of straw addition on biomass ninhydrin-N was less in soils of pH 4.17 and 4.65. Similarly total PLFA concentrations were smallest at the lowest pH. This indicated that there is a direct pH effect as well as effects related to different substrate availabilities on microbial biomass and community structure. In the control soils, the fatty acids 16:1ω5, 16:1ω7c, 18:1ω7c&9t and i17:0 had significant and positive linear relationships with soil pH. In contrast, the fatty acids i15:0, a15:0, i16:0 and br17:0, 16:02OH, 18:2ω6,9, 17:0, 19:0, 17:0c9,10 and 19:0c9,10 were greatest in control soils at the lowest pHs. In soils given straw, the fatty acids 16:1ω5, 16:1ω7c, 15:0 and 18:0 had significant and positive linear relationships with pH, but the concentration of the monounsaturated 18:1ω9 PLFA decreased at the highest pHs. The PLFA profiles indicative of Gram-positive bacteria were more abundant than Gram-negative ones at the lowest pH in control soils, but in soils given straw these trends were reversed. In contrast, straw addition changed the microbial community structures least at pH 6.61. The ratio: [fungal PLFA 18:2w6,9]/[total PLFAs indicative of bacteria] indicated that fungal PLFAs were more dominant in the microbial communities of the lowest pH soil. In summary, this work shows that soil pH has marked effects on microbial biomass, community structure, and response to substrate addition.     

亚热带四种主要植被类型土壤细菌群落结构分析

应用PCR-DGGE方法分别对天目山和玲珑山的四种典型森林土壤细菌群落结构进行了研究分析。结果表明,阔叶林、杉木林、马尾松林和毛竹林在天目山土壤中的DGGE条带数分别为49、45、51和51条,在玲珑山土壤中的DGGE条带数分别为42、4i多是奥前啊2、44和48条。不同森林植被土壤DGGE带谱差异不明显,天目山和玲珑山4种森林土壤分别有31条和23条共性条带,分别占总数的61%和48%以上,然而每种林分也有各自的特征条带。相对而言,两个样地杉木林与其他三种林分的土壤细菌群落结构相似度较低,相似值分别为0.72和0.68,其土壤细菌多样性指数也明显低于其他3种林分,而毛竹林和马尾松林多样性指数则没有显著差异。同时分析两个采样区的土壤细菌DGGE发现,土壤性质对细菌群落结构的影响大于植被。     

秸秆还田对黑土亚表层微生物群落结构的影响特征及原因分析

为明确切碎秸秆与秸秆颗粒对黑土亚表层土壤微生物群落结构的影响效应,从而评价不同秸秆还田方式对亚表层的培肥效果,该研究于2016—2018年在东北黑土区进行一次性玉米秸秆深埋还田试验,设置切碎秸秆低量(QS1)、切碎秸秆高量(QS5)、秸秆颗粒低量(KL1)与秸秆颗粒高量(KL5)4种秸秆还田处理,并与秸秆不还田(CK)进行对比,于每年玉米收获季对土壤理化指标及微生物菌群结构进行监测。结果表明,1)秸秆还田第1年,切碎秸秆处理显著提高土壤总磷脂脂肪酸含量及真菌摩尔百分数,其高量处理较CK最高增加71.0%和120.5%,而秸秆颗粒处理对细菌、革兰氏阳性菌和革兰氏阴性菌的摩尔百分数增幅更显著,其高量处理最高增加41.6%、29.7%和26.3%;还田第2年高量处理显著提高各菌群磷脂脂肪酸含量,且切碎高量处理的真菌摩尔百分数含量显著高于颗粒高量处理21.0%;还田第3年仅高量处理下的菌群结构有显著分异。2)还田初期切碎秸秆处理显著提高真菌:细菌比值,而低量还田则对革兰氏阳性菌和革兰氏阴性菌比有提高,随还田时间的增加,高量还田比值提高更显著,利于长期维持生态系统稳定性。3)秸秆高量还田可显著改...     

土壤微生物群落结构对凋落物组成变化的响应

凋落物分解是陆地生态系统养分循环的关键过程,明确凋落物多样性如何影响土壤微生物群落构成和多度,继而潜在地改变凋落物分解的微生物学机制有助于认识生物多样性和森林生态系统功能的关系。通过小盆模拟试验,应用磷脂脂肪酸谱图的方法研究了我国南方红壤丘陵区典型物种马尾松和湿地松的凋落物分别与白栎和青冈的凋落物混合,与单一针叶凋落物分解时相比,针阔混合凋落物分解过程中土壤微生物群落结构的变化,结果显示:(1)针阔混合凋落物分解时土壤微生物群落磷脂脂肪酸(Phospholipidfatty acids,PLFA)总量低于单一针叶处理,细菌和放线菌的相对多度高于单一针叶处理,真菌则相反,群落真菌/细菌低于单一针叶处理,土壤微生物生物量的差异主要来自于真菌;(2)主成分分析表明:针阔混合凋落物分解与单一针叶凋落物分解的土壤微生物群落结构差异显著,两个时期(分解9个月和18个月)主成分一分别可以解释65.74%和89.63%的变异,第一主成分主要包括18∶2ω6,9、18∶1ω9c、17∶0和10Me18∶0等磷脂脂肪酸;(3)土壤微生物群落结构受凋落物初始C/N和木质素/N调控,土壤微生物群落细菌的相对多度与凋落物初始C/N和木质素/N显著负相关,真菌则与凋落物初始C/N和木质素/N显著正相关,群落真菌/细菌与凋落物初始C/N和木质素/N显著正相关。针阔凋落物混合分解通过改变凋落物C/N和木质素/N,提供了对分解者更为有利的微环境。     

Bacterial communities from soil sediments of a mountain oasis in northern Oman

Paleoecological records of a 20 meter deep profile near an oasis settlement in northern Oman have yielded a chronosequence providing insights into relationships between vegetation, the environment and development of human settlements in this area over a period of time spanning 19,000 years. In conjunction with analysis of the chemical and physical properties of this profile, we hypothesized that bacterial community structures associated with this chronosequence may also constitute a part of the biogeochemical record of the climate history that has been preserved at this site. To examine this hypothesis, we studied the composition of the community as revealed by profiling of 16S rRNA genes at 1 meter intervals along the entire profile. The results of our study show distinct changes in bacterial communities with increasing depth that correspond with differences in the climatic record as indicated by the occurrence of micro-charcoal particles. Sequencing of 16S rRNA genes proved the presence of Acidobacteria, Actinobacteria, Proteobacteria, Gemmatimonadetes, Chloroflexi and representatives from the candidate divisions SPAM, NC10, and OP10. Differences in the communities support the hypothesis that the bacterial species compositions in the sediment reflect properties of the organic matter and vegetation at the time they were deposited.     

Bacterial community structure and microbial activity in different soils amended with biogas residues and cattle slurry

Anaerobic digestion of organic materials generates residues of differing chemical composition compared to undigested animal manures, which may affect the soil microbial ecosystem differently when used as fertilizers. This study investigated the effects of two biogas residues (BR-A and BR-B) and cattle slurry (CS) applied at rates corresponding to 70 kg NH₄⁺-N ha⁻¹ on bacterial community structure and microbial activity in three soils of different texture (a sandy, a clay and an organic clay soil). 16S rRNA genes were targeted in PCR reactions and bacterial community profiles visualized using terminal restriction fragment length polymorphism. General microbial activity was measured as basal respiration (B-resp), substrate-induced respiration (SIR), specific growth rate (μ_SIR), metabolic quotient (qCO₂) and nitrogen mineralization capacity (NMC). Non-metric multidimensional scaling analysis visualized shifts in bacterial community structure related to microbial functions. There were significant differences in bacterial community structure after 120 days of incubation (+20 °C at 70% of WHC) between non-amended (control) and amended soils, especially in the sandy soil, where CS caused a more pronounced shift than biogas residues. Terminal-restriction fragment (TRF) 307, the predominant peak in CS-amended sandy soil, was identified as possibly Bacillus or Streptococcus. TRF 226, the dominant peak in organic soil amended with BR-B, was classified as Rhodopseudomonas. B-resp significantly increased and SIR decreased in all amendments to organic soil compared with the control, potentially indicating decreased efficiency of heterotrophic microorganisms to convert organic carbon into microbial biomass. This was also reflected in an elevated qCO₂ in the organic soil. The μ_SIR level was higher in the sandy soil amended with BR-A than with BR-B or CS, indicating a shift toward species capable of rapidly utilizing glucose. NMC was significantly elevated in the clay and organic soils amended with BR-A and BR-B and in the sandy soil amended with BR-B and CS. Thus, biogas residues and cattle slurry had different effects on the bacterial community structure and microbial activity in the three soils. However, the effects of biogas residues on microbial activities were comparable in magnitude to those of cattle slurry and the bacterial community structure was less affected. Therefore, we do not see any reason not to recommend using biogas residues as fertilizers based on the results presented.     

Changes in the soil microbial community structure with latitude in eastern China, based on phospholipid fatty acid analysis

Phospholipid fatty acid (PLFA) profiles were measured in soils from 14 sites in eastern China representing typical geographic zones of varying latitude from north (47.4°N) to south (21.4°N). Amounts of soil microbial biomass, measured as total amounts of PLFAs, showed no regular trend with latitude, but were positively correlated with soil organic carbon content, the concentration of humic acid and amorphous iron oxide. Soil microbial community structure showed some biogeographical distribution trends and was separated into three groups in a cluster analysis and principal coordinate analysis of log transformed PLFA concentrations (mol%). Soils in the first group came from northern China with medium mean annual temperature (1.2–15.7 °C) and rainfall (550–1021 mm). Soils in the second group originated from southern China with a relatively higher mean annual temperature (15.7–21.2 °C) and rainfall (1021–1690 mm). Soils clustered in the third group originated from the most southerly region. The northern soils contained relatively more bacteria and Gram-negative PLFAs, while the southern soils had more fungi and pressure indexed PLFAs. These differences in soil microbial community structure were largely explained by soil pH, while other site and soil characteristics were less important.     

覆盖作物对猕猴桃园土壤氨氧化微生物丰度和群落结构的影响

[目的]果园行间播种覆盖作物有利于改善土壤理化性状,改变氮循环过程中的氨氧化微生物群落结构.因此,我们分析不同覆盖作物下猕猴桃园土壤氨氧化微生物的群落结构和基因丰度,以探究其与土壤硝化作用的关系.[方法]选择湖北十堰的一个5年生猕猴桃果园进行了种植多年生覆盖作物试验,供试覆盖作物有白三叶草(Trifolium repe...     

芦苇秸秆厌氧联产氢气甲烷过程中细菌群落演替规律

基于PCR-DGGE技术研究芦苇秸秆氢气-甲烷厌氧联产过程中,细菌微生物群落结构特征和演替规律。结果表明,厌氧联产过程中细菌群落结构分布存在明显的阶段性差异。产氢阶段初期,细菌群落相似性较小,随着厌氧联产的进行,细菌种类逐渐增多并在产氢高峰期保持稳定,群落相似性较高,戴斯系数(Cs)为83.6%(第12、24小时,泳道H3和H4)。产甲烷高峰期Cs值达到87.4%(第210、258小时,泳道M6,M7),群落结构稳定,产甲烷末期Cs值降低至51.5%(第210、432小时,泳道M6,M9)。序列分析表明,Enterobacter aerogenes产气肠杆菌是具有高效产氢潜力的兼性厌氧细菌,Sedimentibacter产氢产乙酸菌是产氢阶段的优势微生物。Clostridium thermocellum嗜热纤维素菌是厌氧联产过程的优势微生物,具有降解纤维素功能,对芦苇秸秆的能源化利用起到重要作用。     

Direct and indirect influence of arbuscular mycorrhizal fungi on abundance and community structure of ammonia oxidizing bacteria and archaea in soil microcosms

Both arbuscular mycorrhizal (AM) fungi and ammonia oxidizers are important soil microbial groups in regulating soil N cycling. However, knowledge of their interactions, especially the direct influences of AM fungi on ammonia oxidizers is very limited to date. In the present study, a controlled microcosm experiment was established to examine the effects of AM fungi and N supply level on the abundance and community structure of ammonia oxidizing bacteria (AOB) and archaea (AOA) in the rhizosphere of alfalfa plants (Medicago sativa L.) inoculated with AM fungus Glomus intraradices. Effects were studied using combined approaches of quantitative polymerase chain reaction (qPCR) and terminal-restriction fragment length polymorphism (T-RFLP). The results showed that inoculation with AM fungi significantly increased the plant dry weights, total N and P uptake. Concomitantly, AM fungi significantly decreased the amoA gene copy numbers of AOA and AOB in the root compartment (RC) but not in the hyphal compartment (HC). Moreover, AM fungi induced some changes in AOA community structure in HC and RC, while only marginal variations in AOA composition were observed to respond to N supply level in HC. Neither RC nor HC showed significant differences in AOB composition irrespective of experimental treatments. The experimental results suggested that AM fungi could directly shape AOA composition, but more likely exerted indirect influences on AOA and AOB abundance via the plant pathway. In general, AM fungi may play an important role in mediating ammonia oxidizers, but the AOA community appeared to be more sensitive than the AOB community to AM fungi.     

连作对再植枸杞根际细菌群落多样性和群落结构的影响研究

受枸杞道地产区土地资源等因素限制,连作障碍已成为影响枸杞产业发展的重要原因之一,导致严重的经济损失.研究连作条件下枸杞农田土壤生态系统微生物群落的演替规律对枸杞产业的可持续发展具有重要的理论意义.以宁夏银川市南梁农场连作多年的枸杞地为研究对象,利用Illumina MiSeq测序技术分析了连作对再植枸杞根际/非根际细菌群落的影响.结果表明,连作地显著抑制再植枸杞苗地径的增加,且其土壤pH较对照样地显著降低(p<0.05).测序结果证实,与对照样地相比,连作地再植枸杞根际土壤细菌物种数显著降低(p<0.05),细菌群落α多样性下降(p>0.05).主坐标分析表明,连作和对照样地间枸杞非根际细菌群落结构无明显差异,但连作显著改变再植枸杞根际细菌的群落结构.对细菌群落丰度的统计分析发现,连作地枸杞根际浮霉菌门、非根际假单胞菌门的相对丰度较对照样地显著降低(p<0.05).此外,冗余分析结果表明:枸杞园土壤pH和有效磷含量是影响枸杞非根际土壤细菌群落结构变化的主要因素,分别解释了41.8%和35.4%的群落结构变化(p<0.05),其他土壤因子无统计学意义,但土壤理化因子对再植枸杞根际细菌群落结构变化的影响均未达显著水平.这些结果证实连作能够显著抑制再植枸杞生长、影响再植枸杞根际细菌群落结构和多样性,干扰枸杞与土壤细菌群落间的互作关系.这些研究结果将为解析枸杞连作障碍机制提供理论基础.     

芦苇定居后铜尾矿细菌群落结构的变化

Soil samples were collected from both bare and vegetated mine tailings to study the changes in bacterial communities and soil chemical properties of copper mine tailings due to reed (Phragmites communis) colonization. The structures of bacterial communities were investigated using culture-independent 16S rRNA gene sequencing method. The bacterial diversity in the bare mine tailing was lower than that of the vegetated mine tailing. The former was dominated by sulfur metabolizing bacteria, whereas the latter was by nitrogen fixing bacteria. The bare mine tailing was acidic (pH = 3.78), whereas the vegetated mine tailing was near neutral (pH = 7.28). The contents of organic matter, total nitrogen, and ammonium acetate-extractable potassium in vegetated mine tailings were significantly higher than those in the bare mine tailings (P < 0.01), whereas available phosphorus and electrical conductivity were significantly lower than those in the bare mine tailings (P < 0.01). The results demonstrated that 16S rRNA gene sequencing could be successfully used to study the bacterial diversity in mine tailings. The colonization of the mine tailings by reed significantly changed the bacterial community and the chemical properties of tailings. The complex interactions between bacteria and plants deserve further investigation.     

含油污泥的堆肥处理对微生物群落结构的影响

采用堆肥方法处理含油污泥,评价堆肥处理对含油污泥中石油烃的去除效果,并采用Biolog方法和构建16SrRNA基因克隆文库的方法对处理过程中微生物碳源利用特征和微生物群落结构进行了研究。结果表明,含油污泥经过90d的堆肥处理,石油烃降解率达53.3%±9.5%,显著高于对照处理。堆肥处理可以显著促进石油烃降解,是一种处理含油污泥的有效措施。Biolog分析结果表明,堆肥处理的孔的平均颜色变化率（AWCD）显著高于对照处理,堆肥处理提高了土壤微生物代谢活性。主成分分析结果表明,对照处理和堆肥处理的微生物碳源利用特征明显不同,堆肥处理改变了含油污泥中微生物的代谢功能特征。对照处理和堆肥处理的16SrRNA基因克隆文库之间存在显著差异,对照处理的优势类群是γ-Proteobacteria,堆肥处理的优势类群是Bacteroidetes,堆肥处理显著改变了含油污泥中的微生物群落结构。Marinobacter和Alcanivorax是对照处理中的优势菌,可能与石油烃的自然降解过程有关,而Pusillimonas和Agrobacterium可能对堆肥处理中石油烃的降解起一定作用。     

Soil aggregation and bacterial community structure as affected by tillage and cover cropping in the Brazilian Cerrados

Microbial-based indicators of soil quality are believed to be more dynamic than those based on physical and chemical properties. Recent developments in molecular biology based techniques have led to rapid and reliable tools to characterize microbial community structures. We determined the effects of conventional and no-tillage in cropping systems with and without cover crops on bacterial community structure, total organic carbon (TOC) and soil aggregation. Tillage and rotation did not affect TOC from bulk soil. However, TOC was greater in the largest aggregate size class (7.98–19 mm), and had greater mean-weight diameter under no-tillage than under conventional tillage in the 0–5 cm soil layer. Soil bacterial community structure, based on denaturing gradient gel electrophoresis of polymerase chain reaction amplified DNA (PCR/DGGE) using two different genes as biomarkers, 16S rRNA and rpoB genes, indicated different populations in response to cultivation, tillage and depth, but not due to cover cropping. Soil bacterial community structure and meanweight diameter of soil aggregates indicated alterations in soil conditions due to tillage system.