Microbial community shift with decabromodiphenyl ether (BDE 209) in sediments of the Pearl River estuary, China

To compare the effect of decabromodiphenyl ether (BDE 209) on microbial community from the Pearl River estuary, the microbial community at three in situ sites and the responses of microbial community to BDE-209 stressor were investigated. Denaturing gradient gel electrophoresis analysis of 16S rRNA gene showed that microbial community at site A2 has less diversity than sites A1 and A3. Physicochemical parameters (NH₄-N, salinity and SiO₃-Si) could significantly impact the microbial community composition in this estuary. In laboratory-incubated experiments, results indicated high concentration of BDE 209 (100 mg/kg) could increase the microbial diversity at sites A1 and A2, whereas reduced the microbial diversity at site A3. The unweighted pair group method with arithmetic means cluster analysis and principal component analysis demonstrated that the community structure changes at sites A1 and A2 were driven by the BDE 209 concentration, whereas at site A3 they depended on the incubation time. Thirty-five days after the addition of 100 mg/kg BDE 209, Firmicutes were found to be the dominant bacteria at sites A1 and A2. These data suggest the BDE 209 may have different effects on the microbial community in the Pearl River estuary.     

Novel bacteria capable of degrading phenanthrene in activated sludge revealed by stable-isotope probing coupled with high-throughput sequencing

The indigenous microorganisms responsible for degrading phenanthrene (PHE) in activated biosludge were identified using DNA-based stable isotope probing. Besides the well-known PHE degraders Burkholderia, Ralstonia, Sinobacteraceae and Arthrobacter, we for the first time linked the taxa Paraburkholderia and Kaistobacter with in situ PHE biodegradation. Analysis of PAH-RHD_α gene detected in the heavy DNA fraction of ¹³C-PHE treatment suggested the mechanisms of horizontal gene transfer or inter-species hybridisation in PAH-RHD gene spread within the microbial community. Additionally, three cultivable PHE degraders, Microbacterium sp. PHE-1, Rhodanobacter sp. PHE-2 and Rhodococcus sp. PHE-3, were isolated from the same activated biosludge. Among them, Rhodanobacter sp. PHE-2 is the first identified strain in its genus with PHE-degrading ability. However, the involvement of these strains in PHE degradation in situ was questionable, due to their limited enrichment in the heavy DNA fraction of ¹³C-PHE treatment and lack of PAH-RHD_α gene found in these isolates. Collectively, our findings provide a deeper understanding of the diversity and functions of indigenous microbes in PHE degradation.     

青藏高原察尔汗盐湖地区可培养中度嗜盐菌的群落结构与多样性

【目的】研究青海察尔汗盐湖地区的可培养中度嗜盐菌的群落结构及多样性。【方法】采用多种选择性培养基进行中度嗜盐菌的分离、培养;通过16S r RNA基因序列扩增、测定,根据序列信息,进行系统进化树构建、群落结构组成分析及多样性指数计算。【结果】从察尔汗盐湖卤水及湖泥中分离到中度嗜盐菌421株,合并重复菌株后共83株中度嗜盐菌。菌株16S rRNA基因序列信息显示,4株中度嗜盐菌为潜在的新分类单元。83株嗜盐细菌分布于3个门的6个科16个属。其中,Bacillus属、Oceanobacillus属和Halomonas属为优势属。多样性结果显示,水样中的菌株多样性高于泥样,而泥样中的菌株优势度高于水样。【结论】察尔汗盐湖中度嗜盐菌具有丰富的遗传多样性,种群种类丰富,优势菌群集中,该盐湖地区存在可分离培养的中度嗜盐菌的疑似新物种。     

Soil Type-Dependent Responses to Phenanthrene as Revealed by Determining the Diversity and Abundance of Polycyclic Aromatic Hydrocarbon Ring-Hydroxylating Dioxygenase Genes by Using a Novel PCR Detection System

A novel PCR primer system that targets a wide range of polycyclic aromatic hydrocarbon ring-hydroxylating dioxygenase (PAH-RHD_α) genes of both Gram-positive and Gram-negative bacteria was developed and used to study their abundance and diversity in two different soils in response to phenanthrene spiking. The specificities and target ranges of the primers predicted in silico were confirmed experimentally by cloning and sequencing of PAH-RHD_α gene amplicons from soil DNA. Cloning and sequencing showed the dominance of phnAc genes in the contaminated Luvisol. In contrast, high diversity of PAH-RHD_α genes of Gram-positive and Gram-negative bacteria was observed in the phenanthrene-spiked Cambisol. Quantitative real-time PCR based on the same primers revealed that 63 days after phenanthrene spiking, PAH-RHD_α genes were 1 order of magnitude more abundant in the Luvisol than in the Cambisol, while they were not detected in both control soils. In conclusion, sequence analysis of the amplicons obtained confirmed the specificity of the novel primer system and revealed a soil type-dependent response of PAH-RHD_α gene-carrying soil bacteria to phenanthrene spiking.Polycyclic aromatic hydrocarbons (PAHs) are hydrophobic compounds composed of two or more fused aromatic rings. Although PAHs are ubiquitous in the environment (from natural oil seeps, brush fires, and plant derivatives), anthropogenic activities, such as disposal of coal-processing waste, mining accidents, petroleum wastes, and vehicle exhaust, have drastically increased their occurrence in the environment. The fate of PAHs in soil is of great interest due to their potential for bioaccumulation, persistence, transport, and toxicity. Microbe-driven aerobic degradation of PAHs is well documented (15-17). The diversity of PAH-degrading genes in soils is assumed to be huge, but the extent of diversity and how it is influenced by different soil types or their history and type of pollution are not yet fully explored. Knowledge of the genes coding for dioxygenase enzymes that catalyze the primary step of PAH degradation by incorporating molecular oxygen into the aromatic nucleus is an essential prerequisite to unraveling the contributions of microbial population networks to transformation, assimilation, and degradation of organic chemicals in soil. Recently, the complete genomes of several PAH-degrading bacteria became available and allowed new insights into degradative pathways (6, 18, 36). Organic pollutants also serve as nutrients for those microbes that have the appropriate genetic makeup to utilize them, resulting in their increased metabolic activity and abundance (4, 14). In the last decade, impressive progress was seen in techniques that allow cultivation-independent analysis of microbial communities and thus overcome the most severe limitations in studying microbial communities in natural habitats, namely, that only a rather small portion of microbes are accessible to standard cultivation conditions (1, 29). For more than a decade, cultivation-independent approaches have also been employed to unravel the responses of microbial communities in soils and sediments to PAH pollution. In all these studies, PCR amplification of PAH-degrading gene fragments from nucleic acids directly extracted from environmental samples was used to explore the abundance and diversity of PAH ring-hydroxylating dioxygenase (PAH-RHD_α) genes (4, 8, 9, 13, 14, 22, 34, 37). Despite the known biases of PCR amplification from mixed templates, these techniques allow highly sensitive and specific detection even from minute amounts of nucleic acids. In order to select suitable primer systems, previously published primer systems were analyzed for their ranges of target sequences. The existing primer systems were found to have limitations, as they often target only a rather narrow range of sequences, e.g., nahAc- or phnAc-type sequences (21, 34) or only PAH-RHD_α genes from Gram-negative bacteria (3, 13). In other studies, two-primer systems were used to target PAH-RHD_α genes of both Gram-positive and Gram-negative bacteria (4, 37). Only one primer system targeting the Rieske gene fragment was described that amplified a small fragment from PAH-RHD_α genes from both Gram-negative and Gram-positive bacteria (24). However, the amplicon size was only 78 bp and the primer might also target genes coding for dioxygenases that attack nonpolar aromatic compounds, such as benzene, toluene, and xylene. Therefore, this work aimed to design an improved primer system that targets PAH-RHD_α genes from both Gram-positive and Gram-negative bacteria and provides larger amplicon sizes. The novel primer system was tested in silico and validated by sequencing cloned PAH-RHD_α genes amplified from total-community (TC) DNA and was used in endpoint and quantitative real-time PCR (qPCR) formats. The primer system was also applied to study the responses of soil microbial communities in two different soils (a Cambisol and a Luvisol representing typical arable soils in Central Europe with different texture compositions) to artificial phenanthrene pollution.     

Effects of polycyclic aromatic hydrocarbons on microbial community structure and PAH ring hydroxylating dioxygenase gene abundance in soil

Development of successful bioremediation strategies for environments contaminated with recalcitrant pollutants requires in-depth knowledge of the microorganisms and microbial processes involved in degradation. The response of soil microbial communities to three polycyclic aromatic hydrocarbons, phenanthrene (3-ring), fluoranthene (4-ring) and benzo(a)pyrene (5-ring), was examined. Profiles of bacterial, archaeal and fungal communities were generated using molecular fingerprinting techniques (TRFLP, ARISA) and multivariate statistical tools were employed to interpret the effect of PAHs on community dynamics and composition. The extent and rate of PAH removal was directly related to the chemical structure, with the 5-ring PAH benzo(a)pyrene degraded more slowly than phenathrene or fluoranthene. Bacterial, archaeal and fungal communities were all significantly affected by PAH amendment, time and their interaction. Based on analysis of clone libraries, Actinobacteria appeared to dominate in fluoranthene amended soil, although they also represented a significant portion of the diversity in phenanthrene amended and unamended soils. In addition there appeared to be more γ-Proteobacteria and less Bacteroidetes in soil amended with either PAH compared to the control. The soil bacterial community clearly possessed the potential to degrade PAHs as evidenced by the abundance of PAH ring hydroxylating (PAH-RHDα) genes from both gram negative (GN) and gram positive (GP) bacteria in PAH-amended and control soils. Although the dioxygenase gene from GP bacteria was less abundant in soil than the gene associated with GN bacteria, significant (p < 0.001) increases in the abundance of the GP PAH-RHDα gene were observed during phenanthrene and fluoranthene degradation, whereas there was no significant difference in the abundance of the GN PAH-RHDα gene during the course of the experiment. Few studies to-date have examined the effect of pollutants on more than one microbial community in soil. The current study provides information on the response of soil bacterial, archaeal and fungal communities during the degradation of three priority pollutants and contributes to a knowledge base that can inform the development of effective bioremediation strategies for contaminated sites.     

Indigenous oil-degrading bacteria in crude oil-contaminated seawater of the Yellow sea,China

Indigenous oil-degrading bacteria play an important role in efficient remediation of polluted marine environments. In this study, we investigated the diversity and abundance of indigenous oil-degrading bacteria and functional genes in crude oil-contaminated seawater of the Dalian coast. The gene copy number bacterial 16S rRNA in total were determined to be about 10¹⁰ copies L^?1 in contaminated seawater and 10⁹ copies L^?1 in uncontaminated seawater. Bacteria of Alcanivorax, Marinobacter, Novosphingobium, Rhodococcus, and Pseudoalteromonas were found to be predominant oil-degrading bacteria in the polluted seawater in situ. In addition, bacteria belonging to Algoriphagus, Aestuariibacter, Celeribacter, Fabibacter, Zobellia, Tenacibaculum, Citreicella, Roseivirga, Winogradskyella, Thioclava, Polaribacter, and Pelagibaca were confirmed to be the first time as an oil-degrading bacterium. The indigenous functional enzymes, including AlkB or polycyclic aromatic hydrocarbons ring-hydroxylating dioxygenases α (PAH-RHDα) coding genes from Gram-positive (GP) and Gram-negative bacteria (GN), were revealed and quite diverse. About 10¹⁰ to 10¹¹ copies L^?1 for the expression of alkB genes were recovered and showed that the two-thirds of all the AlkB sequences were closely related to widely distributed Alcanivorax and Marinobacter isolates. About 10⁹ copies L^?1 seawater for the expression of RHDαGN genes in contaminated seawater and showed that almost all RHDαGN sequences were closely related to an uncultured bacterium; however, RHDαGP genes represented only about 10⁵ copies L^?1 seawater for the expression of genes in contaminated seawater, and the naphthalene dioxygenase sequences from Rhodococcus and Mycobacterium species were most abundant. Together, their data provide evidence that there exists an active aerobic microbial community indigenous to the coastal area of the Yellow sea that is capable of degrading petroleum hydrocarbons.     

珠江口沉积物来源链霉菌SCSIO 40020中bafilomycins的鉴定及其生物合成基因簇的异源表达

【目的】从珠江口沉积物来源的菌株SCSIO40020中分离bafilomycins,并对其生物合成基因簇进行克隆和异源表达研究。【方法】通过分析菌株SCSIO 40020的16S rRNA基因序列并构建系统发育树以鉴定菌种,以柱层析法和制备色谱法对次级代谢产物进行分离纯化,借助波谱学手段完成单体化合物的结构鉴定,采用生物信息学分析定位bafilomycins的生物合成基因簇,通过筛选菌株SCSIO 40020基因组的细菌人工染色体文库和接合转移将bafilomycins生物合成基因簇导入3种链霉菌进行异源表达,利用高效液相色谱检测异源表达菌株的发酵产物。【结果】菌株SCSIO 40020被鉴定为链霉菌属菌株,从其发酵产物中分离鉴定了2个单体化合物bafilomycinsA1和D。克隆了链霉菌SCSIO40020中bafilomycins的生物合成基因簇并推导了其生物合成途径,在3种链霉菌中表达产生了bafilomycins。【结论】从珠江口环境中获得了一株产生bafilomycins的链霉菌SCSIO 40020,成功建立了该菌株次级代谢产物生物合成基因簇的异源表达体系,并首次在链霉菌...     

基于数据库分析不同类型生境中厌氧氨氧化细菌的多样性分布特征

【目的】厌氧氨氧化过程是一种能在厌氧条件下氧化NH4+同时还原NO2–或者NO3–生成N2的过程,是氮素循环过程的重要途径之一。厌氧氨氧化过程由厌氧氨氧化细菌催化完成,目前通过分子生物学的手段已证实了厌氧氨氧化细菌存在于多种类型的生境中,本文对厌氧氨氧化细菌在不同类型生境中的多样性分布规律进行了系统分析。【方法】基于NCBI数据库中厌氧氨氧化细菌的16SrRNA基因序列,利用Mothur分析平台系统分析了厌氧氨氧化细菌在不同生境中的多样性分布规律和特征。【结果】分析表明,海洋环境中Ca. Scalindua属的厌氧氨氧化细菌占绝对主导;淡水和农业土壤中Ca. Brocadia属的厌氧氨氧化细菌占优势;工程系统中普遍存在Ca. Brocadia和Ca. Kuenenia属的厌氧氨氧化细菌;而湿地和河口环境中厌氧氨氧化细菌多样性最高,Ca. Scalindua、Ca. Brocadia和Ca. Kuenenia属的厌氧氨氧化细菌均有较高的相对丰度,显示出了陆地与海洋交汇的显著特征。【结论】本研究系统展示了不同的生境中厌氧氨氧化细菌的多样性群落结构生境分布特征,表明环境特征差异直接影响了厌氧氨氧化细菌的种群分布和系统演化。     

Nitrogen fixing bacterial diversity in a tropical estuarine sediments

Microorganisms play a significant role in biogeochemical cycles, especially in the benthic and pelagic ecosystems. Role of environmental parameters in regulating the diversity, distribution and physiology of these microorganisms in tropical marine environment is not well understood. In this study, we have identified dinitrogen (N₂) fixing bacterial communities in the sediments by constructing clone libraries of nitrogenase (nifH) gene from four different stations in the Cochin estuary, along the southeastern Arabian Sea. N₂ fixing bacterial clones revealed that over 20 putative diazotrophs belong to alpha-, beta-, gamma-, delta- and epsilon- proteobacteria and firmicutes. Predominant genera among these were Bradyrhizobium sp. (α-proteobacteria), Dechloromonas sp. (β-proteobacteria); Azotobactor sp., Teredinibacter sp., Methylobacter sp., Rheinheimera sp. and Marinobacterium sp. (γ-proteobacteria); Desulfobacter sp., Desulfobulbus sp. and Desulfovibrio sp. (δ -proteobacteria); Arcobacter sp. and Sulfurospirillum sp. (ε-proteobacteria). Nostoc sp. was solely identified among the cyanobacterial phylotype. Nitrogen fixing Sulfate reducing bacteria (SRBs) such as Desulfobulbus sp., Desulfovibrio sp., Desulfuromonas sp., Desulfosporosinus sp., Desulfobacter sp., were also observed in the study. Most of the bacterial nifH sequences revealed that the identities of N₂ fixing bacteria were less than 95% similar to that available in the GenBank database, which suggested that the sequences were of novel N₂ fixing microorganisms. Shannon-Weiner diversity index of nifH gene ranged from 2.95 to 3.61, indicating an inflated diversity of N₂ fixing bacteria. Canonical correspondence analysis (CCA) implied positive correlation among nifH diversity, N₂ fixation rate and other environmental variables.     

九龙江河口区nirS型反硝化细菌多样性及系统发育学分析

【目的】结合16S rRNA基因克隆文库和nirS基因克隆文库的分析,揭示九龙江河口区nirS型反硝化细菌多样性。【方法】选取九龙江河口区一富营养化采样点,分别采集水样及沉积物样品,进行理化因子的测定并提取细菌总DNA。以水样DNA构建16S rRNA基因克隆文库,以沉积物DNA构建nirS基因克隆文库,分析微生物群落结构的多样性并构建系统发育树。【结果】从16S rRNA基因克隆文库中获得86条有效序列,按97%的序列相似性划分为53个OTU,分别属于Proteobacteria门、Planctomycetes门、Bacteroidetes门、Actinobacteria门、Firmicutes门和Chloroflexi门。其中属于Proteobacteria门OTU的克隆子占克隆数的62.9%,是最优势的类群,分属于Alphaproteobacteria、Betaproteobacteria、Gammaproteobacteria和Deltaproteobacteria纲等。从nirS基因克隆文库中获得190条有效序列,翻译为氨基酸序列后,按82%的序列相似性划分为60个OTU,并定位到属的水平。其中Proteobacteria门是最优势的类群,占文库克隆子总数的71.6%,包括Alphaproteobacteria纲(5.8%)、Betaproteobacteria纲(49.0%)和Gammaproteobacteria纲(16.9%)。nirS基因克隆文库中丰度最高的OTU与GenBank中的一株可培养反硝化菌Thauera sp. R-26906具有100%的序列相似性。【结论】九龙江河口区的微生物以及亚硝酸盐还原酶基因(nirS)具有丰富的多样性。大部分NirS序列在GenBank中的最相似序列来源于河口、海湾等相似的环境。     

典型生境巨菌草根内生固氮菌的群落多样性

【目的】探究不同生境巨菌草内生固氮菌群落组成多样性及其分异规律。【方法】采用高通量测序固氮酶nif H标靶基因方法,研究了我国6个典型地区的巨菌草内生固氮菌群,包括福建闽侯县、新疆墨玉县、内蒙古阿拉善左旗、青海贵德县、甘肃安定区、海南那大镇,结合地理气候因子统计,分析了固氮菌多样性的环境驱动机制。【结果】共获得64122条nif H基因的有效序列,640个OTUs,归属于6个门、10个纲、17个目、24个科、33个属和39个种。不同地区巨菌草中优势内生固氮菌群的种类和丰度存在较大的差异。在门水平上,福州闽侯县、甘肃安定区、新疆墨玉县、内蒙古阿拉善左旗和青海贵德县5个地区的优势菌门均为变形菌门,海南那大镇的优势菌门为变形菌门和蓝藻菌门;属水平上,不同地区巨菌草最优势内生固氮菌类群分别为:福州闽侯县(变形菌门中未定属,80.56%);新疆墨玉县(变形菌门中未定属,33.14%);内蒙古阿拉善左旗(变形菌门中未定属,76.23%);甘肃安定区(α-变形菌纲中的未定属,53.78%);海南那大镇(变形菌门中未定属,38.37%);青海贵德县(变形菌门中未定属,46.12%)。Alpha多样性和Beta多样性分析表明,不同地区巨菌草内生固氮菌群落的多样性存在较大的差异,海南那大镇样本中巨菌草各类内生固氮菌群的多样性及丰富度最高,福建闽侯县样本中巨菌草各类内生固氮菌群的多样性及丰富度最低。典范对应分析(CCA)结果表明,年均降雨量和年均气温是影响巨菌草内生固氮菌群变化的主要因素,其次是土壤有机质、土壤全氮和土壤p H。【结论】不同地区巨菌草内生固氮菌群落的组成及丰度存在着较大的差异,海南那大镇巨菌草内生固氮菌群的种类及相对丰度较高,本研究可为巨菌草内生固氮菌群的资源开发及其固氮微生物肥料的菌种选育和生产应用提供理论支持。     

Diversity and Abundance of Nitrate Assimilation Genes in the Northern South China Sea

Marine heterotrophic microorganisms that assimilate nitrate play an important role in nitrogen and carbon cycling in the water column. The nasA gene, encoding the nitrate assimilation enzyme, was selected as a functional marker to examine the nitrate assimilation community in the South China Sea (SCS). PCR amplification, restriction fragment length polymorphism (RFLP) screening, and phylogenetic analysis of nasA gene sequences were performed to characterize in situ nitrate assimilatory bacteria. Furthermore, the effects of nutrients and other environmental factors on the genetic heterogeneity of nasA fragments from the SCS were evaluated at the surface in three stations, and at two other depths in one of these stations. The diversity indices and rarefaction curves indicated that the nasA gene was more diverse in offshore waters than in the Pearl River estuary. The phylotype rank abundance curve showed an abundant and unique RFLP pattern in all five libraries, indicating that a high diversity but low abundance of nasA existed in the study areas. Phylogenetic analysis of environmental nasA gene sequences further revealed that the nasA gene fragments came from several common aquatic microbial groups, including the Proteobacteria, Cytophaga–Flavobacteria (CF), and Cyanobacteria. In addition to the direct PCR/sequence analysis of environmental samples, we also cultured a number of nitrate assimilatory bacteria isolated from the field. Comparison of nasA genes from these isolates and from the field samples indicated the existence of horizontal nasA gene transfer. Application of real-time quantitative PCR to these nasA genes revealed a great variation in their abundance at different investigation sites and water depths.     

尖孢镰孢菌果胶裂解酶基因家族鉴定及侵染表达模式分析

【背景】番茄枯萎病是番茄生产中常见的土传真菌病害。【目的】为鉴定番茄枯萎病基因组果胶裂解酶基因家族,明确该基因家族在侵染过程表达模式。【方法】采用生物信息学方法鉴定了番茄枯萎病尖孢镰孢菌(Fusarium oxysporum f. sp. Lycopersici)基因组内PEL基因家族,并分析了基因结构、染色体定位及三级结构,同时利用荧光定量PCR分析了FoPEL1-16基因在接种番茄根系的表达情况。【结果】番茄尖孢镰孢菌基因组内PEL基因家族成员有16个。氨基酸序列长度在163-548个氨基酸,信号肽长度在16-21个氨基酸。染色体定位分析表明16个基因在染色体上分布不均,分别定位在7条染色体上。根据基因结构和保守基序分析结果 16个基因可分为4类。进化分析表明该基因家族成员可聚成4支。三级结构预测结果显示同一家族存在相似结构域。荧光定量PCR分析结果表明Fo PEL基因在侵染过程表达水平明显上升。【结论】番茄尖孢镰孢菌基因组内果胶裂解酶以基因家族形式存在,其基因结构存在差异暗示了其功能多样性;FoPEL基因在侵染过程表达明显增强,说明其参与病原菌的致病性。本研究为解析尖孢镰孢菌致病基因功能分析及寄主病原互作提供了重要理论基础。     

克拉玛依油田石油污染土壤细菌群落结构与环境因子的关系

【目的】以16S rRNA为分子标记,探讨克拉玛依油田石油污染土壤中细菌群落多样性和系统发育,并分析环境因子对群落分布的影响,为生物降解石油污染物提供理论基础。【方法】在克拉玛依油田分别采集深度为5、20、50 cm的石油污染土壤样品,测定环境参数;提取石油污染土壤细菌群落基因组DNA,分别构建3个土层细菌16S rRNA基因文库,利用限制性片段长度多态性分析(Restriction fragment length polymorphisms RFLP)技术初步分群,确定各文库中的代表菌株并测定16S rRNA基因序列;利用软件Biodap计算各群落多样性和丰富度指数,以Neighbor-Joining法构建3个土层细菌的系统发育树;运用软件CANOCO 4.5结合不同样品环境因子的差异进行典型对应分析(CCA),并探讨了环境因子对细菌多样性的影响。【结果】环境参数结果表明20 cm土层总磷(TP)、总氮(TN)含量最低,50 cm含量最高;5 cm土层中有机碳(TOC)含量最高,50 cm含量最低。基于16S rRNA序列的生物多样性和物种丰富度指数表明20 cm土层生物多样性和丰富度指数较高,而50 cm土层各项指数均较低。各土层供试序列RFLP聚类分析表明,克拉玛依油田石油污染土壤细菌种群具有丰富的多样性。Neighbor-Joining构建的系统发育分析表明,石油污染土壤被分为5个类群(I–V),分别为变形菌门(Proteobacteria)、放线菌门(Actinobacteria)、厚壁菌门(Firmicute)、拟杆菌门(Bacteroidetes)、浮霉状菌门(Planctomycetes),其中群Ⅰ占78.57%,广泛分布于不同的生态环境;其中来自5 cm土层代表菌的69.23%分布于群Ⅰ。CCA分析结果显示TN、TP和TOC对大部分细菌影响较大;TOC含量对Pseudomonas影响明显。【结论】克拉玛依油田石油污染土壤细菌群落具有丰富的多样性;环境因子是影响石油污染土壤细菌群落空间分布的重要因素。     

珠江口水体浮游细菌种群多样性空间分布特征

为认识珠江口水体浮游细菌的多样性分布规律,运用聚合酶链式反应-变性梯度凝胶电泳(PCR-DGGE)和多维尺度分析(MDS)的方法,研究了春季珠江口十个站位表底水层浮游细菌种群16SrRNA基因多样性特征。研究结果表明,珠江口浮游细菌种群具有丰富的基因多样性;不同站位细菌群落结构和优势种群变化显著:大多数站位表底层细菌群落结构比较相似,河口外站位(A12,A14和C5),表底层细菌群落结构差异性较大:多样性分析表明A14,B6和C5站位底层细菌多样性大于表层。遗传发育分析表明,序列归属于变形细菌(Proteobacteria),酸杆菌(Acidobacteria),蓝细菌(Cyanobacteria),厚壁细菌(Firmicutes)和放线菌(Actinobacteria)。变形细菌(Proteobacteria)种类最多,从河口内淡水区到河口外海水区都有大量分布,是珠江口水域占优势的菌群;同时也检测到种类丰富的放线菌(Actinobacteria)的存在,也是珠江口水域的优势菌群。     

Influence of Inorganic Nitrogen Management Regime on the Diversity of Nitrite-Oxidizing Bacteria in Agricultural Grassland Soils

To assess links between the diversity of nitrite-oxidizing bacteria (NOB) in agricultural grassland soils and inorganic N fertilizer management, NOB communities in fertilized and unfertilized soils were characterized by analysis of clone libraries and denaturing gradient gel electrophoresis (DGGE) of 16S rRNA gene fragments. Previously uncharacterized Nitrospira-like sequences were isolated from both long-term-fertilized and unfertilized soils, but DGGE migration patterns indicated the presence of additional sequence types in the fertilized soils. Detailed phylogenetic analysis of Nitrospira-like sequences suggests the existence of one newly described evolutionary group and of subclusters within previously described sublineages, potentially representing different ecotypes; the new group may represent a lineage of noncharacterized Nitrospira species. Clone libraries of Nitrobacter-like sequences generated from soils under different long-term N management regimes were dominated by sequences with high similarity to the rhizoplane isolate Nitrobacter sp. strain PJN1. However, the diversity of Nitrobacter communities did not differ significantly between the two soil types. This is the first cultivation-independent study of nitrite-oxidizing bacteria in soil demonstrating that nitrogen management practices influence the diversity of this bacterial functional group.     

Diversity of bacteria and polyketide synthase associated with marine sponge Haliclona sp.

The microbial community associated with a marine sponge (Haliclona sp.) collected from Tateyama city, Japan was studied using 16S rRNA gene clone libraries. Two DNA templates were prepared using methods recommended for Gram-positive and Gram-negative bacteria in the Qiagen kit manual. From each DNA template, two 16S rRNA genes were PCR amplified, using the combination of universal bacterial primer 27f and primers 1385r and 1492r, respectively. A total of 347 clones were sequenced and compared with those available in DNA data banks. These sequences were members of ten bacterial phyla. Interestingly, more than 30 % of the clones represent novel sequences. A comparison of these sequences with sequences in a library prepared from DNA extracted from the surrounding water shows minimum DNA contamination. Taxonomically, the highest diversity was detected in the clone library prepared using a combination of primers 27f and 1492r and DNA isolated using the Gram-positive bacteria protocol. The potential of Haliclona sp.-associated bacteria to produce secondary metabolites was studied by cloning and sequencing the polyketide synthase (PKS, type 1) gene using the same DNA samples. Analysis of partial sequences derived from the sponge metagenome revealed 27 unique ketosynthase domains of PKS type I. This study suggests strongly that this Haliclona sp. plays host to diverse novel bacteria with a potential to produce novel polyketides.     

Further Analysis of Anammox Bacterial Community Structures Along an Anthropogenic Nitrogen-Input Gradient from the Riparian Sediments of the Pearl River Delta to the Deep-Ocean Sediments of the South China Sea

The community structures of anammox bacteria in sediments along an anthropogenic inorganic nitrogen input gradient were further delineated with the newly available information incorporated. Anammox bacterial 16S rRNA gene-amplified sequences retrieved from riparian sediments of the Pearl River, Mai Po coastal wetland, and the South China Sea (SCS) sediments were compiled, compared and analyzed. Results indicated that the community structures of anammox bacteria varied from the upstream of the Pearl River to deep-ocean sediment of the SCS along the anthropogenic input grandient. Mai Po wetland had the most diverse anammox bacteria, followed by the shallow SCS, deep SCS and the Pearl River. Genera of the anammox bacteria Kuenenia and Brocadia showed higher proportion in the riparian sediments of the Pearl River, while those of Kuenenia and Scalindua dominated the Mai Po coastal wetland. The Scalindua subclusters showed apparent segregation in coastal wetland (S. zhenghei-III and S. wagneri), shallow SCS (S. zhenghei-I and S3) and deep SCS (S. zhenghei-I, S2 and S. arabica). Pearson correlation analysis indicated nitrogen species [NH₄⁺ and ∑(NO₂^?+NO₃^? )] negatively correlated with the diversity indices of anammox bacteria. Canonical correspondence analysis (CCA) showed that salinity, inorganic nitrogen [NH₄+, ∑(NO₂^?+NO₃^?)], and ratio of NH₄⁺/∑(NO₂^? +NO₃^?) significantly affected the bacterial community compositions. Results collectively support that the community composition of anammox bacteria can serve as a bio-indicator to the anthropogenic terrestrial N input or pollution.     

深海热液生物共附生可培养硫氧化细菌的多样性及硫氧化特性

[背景]深海热液环境中存在大量H2S及含硫化合物,许多微生物与大型生物形成了紧密的共生体系,例如硫氧化细菌,它们利用其独特的代谢体系协助宿主更好地适应极端环境,但目前尚未对热液底栖生物共附生的硫氧化细菌进行培养鉴定和功能分析.[目的]了解深海热液生物共附生硫氧化细菌的种群特征和功能特征,筛选出深海热液生物共附生微生物中...