Effect of process temperature on bacterial and archaeal communities in two methanogenic bioreactors treating organic household waste

The bacterial and archaeal community structure was examined in two methanogenic anaerobic digestion processes degrading organic household waste at mesophilic (37 degrees C) and thermophilic (55 degrees C) temperatures. Analysis of bacterial clone libraries revealed a predominance of Bacteroidetes (34% of total clones) and Chloroflexi (27%) at the mesophilic temperature. In contrast, in the thermophilic clone library, the major group of clones were affiliated with Thermotogae (61%). Within the domain Archaea, the phyla Euryarchaeota and Crenarchaeota were both represented, the latter only at the mesophilic temperature. The dominating archaeons grouped with Methanospirillum and Methanosarcina species at the mesophilic and thermophilic temperature, respectively. Generally, there was a higher frequency of different sequences at the lower temperature, suggesting a higher diversity compared to the community present at the thermophilic temperature. Furthermore, it was not only the species richness that was affected by temperature, but also the phylogenetic distribution of the microbial populations.     

石油污染对土壤微生物群落多样性的影响

土壤中的微生物主要有细菌、放线菌、真菌三大类群,微生物在石油污染的土壤中发挥着维持生态平衡和生物降解的功能。文中以四川省遂宁市射洪县某废弃油井周围不同程度石油污染土壤为供试土壤,首先对各组供试土壤的基本理化性质进行测定分析;然后采用平板菌落计数法测定了供试土壤中三大类微生物数量的变化,结果表明:相比未被污染的对照土壤,石油污染的土壤中细菌、放线菌、真菌数量均减少,并且土壤中可培养微生物的数量与土壤含水量呈正相关;再采用454焦磷酸测序技术对土壤中的细菌群落多样性及变化进行16S rRNA基因分析。在所有供试的4个土壤样品中,共鉴定出不少于23 982个有效读取序列和6 123种微生物,相比于未被污染的对照土壤,石油污染土壤中细菌的种类更加丰富,主要优势门类为酸杆菌门、放线菌门、拟杆菌门、绿弯菌门、浮霉菌门和变形菌门。但不同土壤样品中优势菌群的群落结构有所差异,石油污染的土壤中,酸杆菌门、放线菌门和变形菌门的数量最多,未被石油污染的土壤中,放线菌门、拟杆菌门和变形菌门的数量最多。     

Impact of chromium-contaminated wastewaters on the microbial community of a river

The influence of chromium on the microbial community structure was analyzed in a river system subjected to long-term chromium contamination, by plating and by sequencing 16S rRNA genes cloned from DNA extracted from the river sediments. We also analyzed the influence of chromium on the ability of the microbial community to resist and reduce Cr(VI) and on its resistance to antibiotics. Shifts in the microbial community structure were analyzed by amplified ribosomal DNA restriction analysis fingerprinting. The isolates obtained were phylogenetically related to Actinobacteria, Firmicutes, Bacteroidetes and Proteobacteria, whereas Acidobacteria and Deltaproteobacteria were only revealed by clone analyses. Cr(VI)-resistant and Cr(VI)-reducing strains were isolated in all sites examined. However, each sample site had a microbial community with a different antibiotic resistance pattern. Our study seems to indicate that in this river ecosystem chromium influenced the microbial communities, altering some of their functional characteristics, such as the percentage of the microbial community able to resist or to reduce Cr(VI) and the phylogenetic groups isolated, but it did not affect the structural diversity. Furthermore, the concentration of Cr(VI) in the sediments could not be correlated with a lower number of bacteria or lower index of generic diversity, neither with the ability of the microbial community to resist or to reduce higher Cr(VI) concentrations.     

Effect of storage temperature on prokaryotic cell counts and community composition analysis from fixed and filtered seawater samples

Marine, pelagic prokaryotes commonly are visualized and enumerated by epifluorescence microscopy after staining with fluorescent, DNA-binding dyes and sample preparation and storage has a major influence on obtaining reliable estimates. However, sampling often takes place in remote locations and the recommended continuous sample storage at −20°C until further sample evaluation is often logistically challenging or infeasible. We investigated the effect of storage temperature on fixed and filtered seawater samples for subsequent enumeration of total prokaryotic cells and community composition analysis by fluorescence in situ hybridization (FISH). Prokaryotic abundance in surface seawater was not significantly different after 99 days when filters were stored either at room temperature (RT) or at −20°C. Furthermore, there was no loss in detection rates of phylotypes by FISH from filters stored at RT or −20°C for 28–30 days. We conclude that fixed and filtered seawater samples intended for total prokaryote counts or for FISH may be maintained long-term at room temperature, and this should logistically facilitate diverse studies of prokaryote ecology, biogeography, and the occurrence of human and fish/shellfish pathogens.     

黄河三角洲盐碱地花生根层土壤菌群结构多样性

花生属豆科固氮作物,具较强的抗旱耐盐性,土壤微生物在盐碱土生态系统中具有重要的生态功能。以花生平作、花生/棉花间作为对象,通过16S rRNA基因克隆文库技术分析了黄河三角洲滨海盐碱地花生旺盛生长期不同含盐量盐碱地和非盐碱地0—40cm根层非培养土壤微生物群落组成及其多样性,分析了盐碱地花生根层土壤细菌群落与非盐碱地花生根层土壤细菌群落的差异,为揭示盐碱地花生根层土壤微生物的多样性以及土地利用变化与生态环境效应间的关系奠定基础。利用免培养技术直接从土壤样品提取总DNA,针对细菌基因组16S rRNA基因的V3高变区进行PCR扩增;利用焦磷酸测序的方法对V3高变区PCR产物进行高通量测序,并对测序数据进行生物信息学分析。结果表明,(1)黄河三角洲滨海盐碱土较高含盐量土壤中根层土壤微生物种类、优势种群数量和群落功能多样性较非盐碱土壤较为丰富。(2)盐碱土花生平作或花生//棉花间作两种种植方式基本不影响二者0—40cm根层土壤微生物优势类群;不同土壤类型和种植模式下,花生和棉花根层土壤中优势菌群均为变形菌门(Proteobacteria)、放线菌门(Actinobacteria)、绿弯菌门(Chloroflexi)和酸杆菌门(Acidobacteria) 4种菌群,其总丰度为80%—90%。非盐碱土壤中花生根层的酸杆菌门(Acidobacteria)丰度是盐碱土壤中的3倍以上,嗜热油菌纲(Thermoleophilia)和放线菌纲(Actinomycetales)丰度远高于各种盐碱土壤花生平作和花生//棉花间作两种植模式下的花生根层土壤;非盐碱土平作花生0—40cm土层中Rubellimicrobium、Pontibacter和Lamia细菌则显著缺失。(3)土壤类型对土壤微生物菌群类型影响较大,聚类分析表明,10个土壤样本依据土壤含盐量高低和根系分布深度聚为3类,即非盐碱土壤归为1类,盐碱土壤根系密集分布层0—20cm、20—40cm各归为1类。     

基于16S rRNA基因序列分析受砷和硫酸盐污染的土壤细菌多样性（英文稿）

为了了解普通耕地土壤(Nor-1)和受砷及硫酸盐污染土壤(Sul-1)中的细菌组成和多样性差异,对2个不同土壤样品直接提取总DNA,通过PCR扩增16S rRNA基因并建立文库,对文库克隆进行核糖体DNA扩增片段酶切分析(ARDRA)和测序,构建系统进化树。从Nor-1土壤样品中测序获得23个16S rRNA基因序列,分析序列系统发育关系表明,共包含Acidobacteria(12.3%,8/65)、Actinobacteria(3.1%,2/65)、Firmicutes(21.5%,14/65)、Nitrospira(3.1%,2/65)和Proteobacteria(60%,39/65)等5个不同细菌门。而从Sul-1土壤样品中测序获得19个16S rRNA基因序列,分析序列系统发育关系表明,共包含Firmicutes(29.5%,13/44)和Proteobacteria(70.5%,31/44)等2个不同细菌门。结果表明,受高浓度的砷和硫酸盐的影响,Sul-1土壤中细菌群落结构相较于普通耕地土壤(Nor-1)发生了明显的改变,多样性明显下降,但有大量具有较强的污染物降解能力的不动杆菌(Acinetobacter)相关序列在Sul-1土壤细菌群落中被发现。     

云南热带户用沼气池的原核生物群落结构研究

【目的】揭示云南热带农村户用沼气池中的原核生物(细菌和古菌)的群落结构特征。【方法】采用16S r RNA基因克隆文库技术对云南(北)热带代表性气候区的户用沼气池中的原核生物(细菌和古菌)多样性进行研究。【结果】得到细菌330条有效序列,划分为108个OTUs,文库覆盖度为81.5%;古菌有效序列185条,划分为17个OTUs,文库覆盖度为97.8%。通过Gen Bank数据库进行相似性比对与系统发育分析,结果表明:大部分细菌为未知细菌(Unclassified bacteria,占24.19%),优势细菌类群归属拟杆菌门(Bacteroidetes,占23.58%)、绿弯菌门(Chloroflexi,占21.46%)、厚壁菌门(Firmicutes,占13.91%)和变形菌门(Proteobacteria,占8.74%);古菌主要的优势类群为乙酸盐营养型的甲烷八叠球菌目(Methanosarcinales)的鬃毛甲烷菌属(Methanosaeta,占76.75%);此外还检测到少量未培养的泉古菌门细菌(Crenarchaeota,占9.19%)。【结论】云南(北)热带代表性气候区的农村户用沼气池中的微生物种类十分丰富,不同微生物种类的丰度存在明显差异,并存在明显优势种群,且细菌比古菌具有更丰富的多样性。     

山西左云县采煤区人工湿地冬季沉积物细菌群落多样性

【背景】人工湿地处理煤炭矿井废水效果显著,而关于人工湿地沉积物的细菌群落结构和特征研究较少。【目的】阐明人工湿地净化采煤区废水的效应和细菌群落结构及特征。【方法】对山西省左云县采煤区人工湿地不同采样点水质进行监测,利用高通量测序技术对人工湿地沉积物中细菌16S rRNA基因V3-V4区进行测序,分析沉积物中细菌群落组成。【结果】采煤区废水流经人工湿地后水质得到有效改善,其中生化需氧量(Biochemical oxygen demand,BOD5)、化学需氧量(Chemical oxygen demand,CODCr)、总氮(Total nitrogen,TN)、总磷(Total phosphorus,TP)去除率分别达到76.2%、93.4%、73.4%和99.3%;测序共获得2 832个操作分类单元(Operational taxonomic units,OTUs),共753个属,分布于51个门的150个纲;4个采样点中优势菌门为变形菌门(Proteobacteria,50%-64.7%)和拟杆菌门(Bacteroidetes,15.8%-21.2%),变形菌门中优势菌纲为β-变形菌纲和γ-变形菌纲,其中M1、M2、M3中富含氨氮氧化细菌的β-变形菌纲和γ-变形菌纲丰度最高;M4沉积物细菌OTU最多,多样性最高;沉积物特有优势菌属Sulfurimonas、Sulfuricurvum的相对丰度与NH4+-N的含量显著负相关,Azoarcus菌属相对丰度与TN存在显著正相关,Novosphingobium菌属相对丰度与TP含量存在显著正相关。【结论】煤矿废水流经人工湿地可得到有效的净化,细菌多样性在人工湿地生态功能中起到了决定作用。     

不同养殖场林麝肠道微生物组成和功能的差异

肠道疾病是养殖林麝(Moschus berezovskii)常见疾病。动物肠道微生物伴随宿主进化并与胃肠道构成了复杂的微生态系统。为探究不同饲养环境对圈养林麝肠道微生物组成和功能的影响,本研究对采自国内5个不同养殖场的215份粪便样品进行了16S rRNA基因高通量测序,对比分析不同养殖场林麝肠道微生物组成、多样性和功能的差异。结果显示,厚壁菌门和拟杆菌门是未喂食复合益生菌的祁连县养殖场林麝肠道菌群的绝对优势菌门,而喂食复合益生菌的甘肃两当县和陕西凤县的4家养殖场林麝肠道菌群的绝对优势菌门为厚壁菌门和变形菌门。不同养殖场林麝肠道菌群组成、优势菌门、优势菌属、潜在致病菌、代谢及疾病相关功能均有显著差异。祁连县养殖场林麝肠道微生物的α多样性和疾病相关功能表达量显著低于其他养殖场,并以肠型2为主,其主导菌为厚壁菌门、UCG-005和拟杆菌属;两当县和凤县的4家养殖场林麝肠道菌群潜在致病菌相对丰度较低。本研究推测食物组成差异可能是导致不同养殖场林麝肠道微生物差异的主要因素,复合益生菌的使用可能是导致α多样性和潜在致病菌下降的重要因素。该结果可为林麝的人工养殖和有效管理提供科学依据,也对人工饲养...     

In-feed administered sub-therapeutic chlortetracycline alters community composition and structure but not the abundance of community resistance determinants in the fecal flora of the rat

The impact of continuous sub-therapeutic chlortetracycline on community structure, composition and abundance of tetracycline resistance genes in the rat fecal community was investigated. Rats were fed a standard diet containing chlortetracycline at 15 μg g⁻¹ diet for 28 days, followed by 30 μg g⁻¹ diet to completion of the study on day-56. These levels are similar to those administered to swine during the grow-out phase. Sub-therapeutic chlortetracycline affected the fecal community as determined through change in the cultivable anaerobic community and through molecular-based analyses including denaturing gradient gel electrophoresis profiles of the variable 2–3 region community 16S rRNA genes over time and through comparative sequence analysis of 16S rRNA gene community libraries. Significant decreases in fecal phylotype diversity occurred in response to sub-therapeutic chlortetracycline, although total bacterial output remained constant over the entire feeding trial. Chlortetracycline at 15 μg g⁻¹ diet resulted in significant change in community composition, but only modest change to the fecal community structure in terms of the distribution of individual phylotypes among the major fecal lineages. Chlortetracycline at 30 μg g⁻¹ diet significantly altered the distribution of phylotypes among the major fecal lineages shifting the overall community such that Gram-negative phylotypes aligning within the phylum Bacteroidetes became the dominant lineage (>60% of total community). While chlortetracycline impacted both fecal community structure and composition, there was no significant effect on the abundance of community tetracycline resistance genes [tet(Q), tet(W), tet(O)] or on the emergence of a new putative tetracycline resistance gene identified within the fecal community. While sub-therapeutic chlortetracycline provides sufficient selective pressure to significantly alter the fecal community, the primary outcome appears to be the development of a community which may have a higher inherent tolerance to sub-therapeutic levels of chlortetracycline rather than an overgrowth of the tetracycline resistant bacteria already present within the community.     

淹水培养过程中水稻土细菌丰度与群落结构变化

水稻土是非常复杂又典型的生态系统, 分析淹水培养过程中水稻土细菌的丰度和群落结构变化规律, 可以客观反映水稻土中细菌群落结构信息, 为深入探讨水稻土细菌微生物对稻田的影响和在生态系统中的作用(营养元素转换、重金属还原与抑制甲烷生成过程等)提供实验基础与理论依据。作者采用淹水非种植水稻土微环境模式系统, 提取水稻土淹水培养1 h和1、5、10、20、30、40、60 d后的微生物总DNA, 利用Real-time PCR和PCR-DGGE (denaturing gradient gel electrophoresis)技术检测了淹水培养过程中细菌丰度与群落结构的变化。结果表明: 淹水水稻土中细菌的丰度在1 d时最大, 并在40 d到达第二个峰值, 说明淹水过程改变了细菌的丰度。基于16S rRNA基因V3区的DGGE图谱分析显示, 淹水过程中细菌的群落结构发生了演替性变化: r-策略生存的细菌仅存在于淹水初期; k-策略生存的细菌存在于淹水后期; r-和k-策略共生存的细菌存在于整个淹水过程中, 淹水后期k-策略的细菌占据优势。淹水培养过程中优势种群多样性指数大体呈现先上升后减小的趋势。主成分分析(PCA)将淹水处理过程分成几类不同的生境, 反映出中、后期细菌群落结构较为稳定; 测序结果表明, 32个优势条带所代表的细菌分别属于厚壁菌门、绿弯菌门、拟杆菌门、变形菌门和酸杆菌门, 且与来自不同地域的水稻土、其他类型土壤、活性污泥以及湖泊沉积物等生态系统的细菌关系密切。     

云冈石窟石质文物表面及周边岩石样品中微生物群落分析

【目的】通过对云冈石窟石质文物表面及云冈石窟周边岩石样品中微生物的研究,建立可用于快速检测石质文物中微生物的方法。【方法】选取云冈石窟石质样品和云冈石窟周边岩石样品作为研究对象,应用PCR-DGGE技术对样品中的微生物群落结构进行了分析研究。【结果】根据系统发育树聚类分析,可以得出云冈石窟中检测出的微生物主要分为四大类群:γ-变形菌纲、鞘脂杆菌门、α-变形菌纲和放线菌纲;根据GenBank数据库中的序列比对结果,可以知道云冈石窟周边类似岩石样品中的微生物主要属于γ-变形菌纲、厚壁菌门和α-变形菌纲等。【结论】本实验成功检测出云冈石窟石质样品表面及云冈石窟周边岩石样品中的微生物类群,为云冈石窟的保护工作提供了有力依据,同时也证明了DEEG和分子克隆技术相结合的方法是检测石质文物中微生物群落结构的一种可操作性强、快速、准确的检测手段。     

Effect of temperature on composition of the methanotrophic community in rice field and forest soil

Temperature change affects methane consumption in soil. However, there is no information on possible temperature control of methanotrophic bacterial populations. Therefore, we studied CH(4) consumption and populations of methanotrophs in an upland forest soil and a rice field soil incubated at different temperatures between 5 and 45 degrees C for up to 40 days. Potential methane consumption was measured at 4% CH(4). The temporal progress of CH(4) consumption indicated growth of methanotrophs. Both soils showed maximum CH(4) consumption at 25-35 degrees C, but no activity at >40 degrees C. In forest soil CH(4) was also consumed at 5 degrees C, but in rice soil only at 15 degrees C. Methanotroph populations were assessed by terminal restriction fragment length polymorphism (T-RFLP) targeting particulate methane monooxygenase (pmoA) genes. Eight T-RFs with relative abundance >1% were retrieved from both forest and rice soil. The individual T-RFs were tentatively assigned to different methanotrophic populations (e.g. Methylococcus/Methylocaldum, Methylomicrobium, Methylobacter, Methylocystis/Methylosinus) according to published sequence data. Two T-RFs were assigned to ammonium monooxygenase (amoA) gene sequences. Statistical tests showed that temperature affected the relative abundance of most T-RFs. Furthermore, the relative abundance of individual T-RFs differed between the two soils, and also exhibited different temperature dependence. We conclude that temperature can be an important factor regulating the community composition of methanotrophs in soil.     

Influence of bicarbonate,sulfate, and electron donors on biological reduction of uranium and microbial community composition

A microcosm study was performed to investigate the effect of ethanol and acetate on uranium(VI) biological reduction and microbial community changes under various geochemical conditions. Each microcosm contained an uranium-contaminated sediment (up to 2.8 g U/kg) suspended in buffer with bicarbonate at concentrations of either 1 or 40 mM and sulfate at either 1.1 or 3.2 mM. Ethanol or acetate was used as an electron donor. Results indicate that ethanol yielded in significantly higher U(VI) reduction rates than acetate. A low bicarbonate concentration (1 mM) was favored for U(VI) bioreduction to occur in sediments, but high concentrations of bicarbonate (40 mM) and sulfate (3.2 mM) decreased the reduction rates of U(VI). Microbial communities were dominated by species from the Geothrix genus and Proteobacteria phylum in all microcosms. However, species in the Geobacteraceae family capable of reducing U(VI) were significantly enriched by ethanol and acetate in low-bicarbonate buffer. Ethanol increased the population of unclassified Desulfuromonales, while acetate increased the population of Desulfovibrio. Additionally, species in the Geobacteraceae family were not enriched in high-bicarbonate buffer, but the Geothrix and the unclassified Betaproteobacteria species were enriched. This study concludes that ethanol could be a better electron donor than acetate for reducing U(VI) under given experimental conditions, and electron donor and groundwater geochemistry alter microbial communities responsible for U(VI) reduction.     

温带荒漠生物土壤结皮微生物群落结构与功能演替研究综述

生物土壤结皮(biological soil crusts,BSC)在荒漠植被的恢复及稳定性维持方面发挥了重要作用,被誉为“荒漠生态系统工程师”。BSC微生物群落是其发挥功能的主要成分,参与了BSC的形成、土壤性状的改善、土壤团聚体的稳定及植被的发育等过程。由于技术方法的限制,以往对BSC微生物群落发育如何调控荒漠植被稳定性的机理尚不清楚。近年来,随着土壤微生物组学技术的快速发展,BSC微生物群落组成及其功能的研究取得了较大进展,关于BSC微生物群落对荒漠生态系统贡献的认识日渐清晰。本文总结了温带荒漠BSC演替过程中微生物不同类群细菌、真菌、古菌群落的组成结构及参与碳氮循环的潜在功能变化,并对影响微生物群落结构和功能的土壤因素进行了剖析,阐释了BSC微生物群落与土壤功能性状相互作用及协同演替的模式,厘清了BSC促进荒漠土壤改善的机理,为温带荒漠植被恢复及荒漠生态系统对全球贡献的理解提供了依据。     

基于NGS方法评估不同保存条件对粪便样本中菌群含量的影响

目的 评估粪便样本的不同保存条件对肠道微生态研究结果的影响.方法 设计相关实验,比较7种不同的保存方法,基于高通量测序技术比对不同时间、不同贮存温度对粪便样本DNA质量、菌群多样性及病原菌检出等结果之间的差异.结果 证实了对于粪便样本采集仍建议采取即刻提取核酸或-20℃保存的方法.同时比较多种保存方法后发现,采用不同样...