鄱阳湖湖泊细菌群落组成及结构——以松门山为例

于2011年5月在鄱阳湖——松门山湖区采集底泥与表层水样,分别提取了表层水体浮游和底泥微生物基因组DNA,利用454高通量测序技术对细菌的16S rRNA基因进行了序列测定,分析了湖泊底泥细菌、水体浮游细菌群落结构特征。结果显示:底泥细菌OTUs(Operational Taxonomic Units)为1454,表层水体浮游细菌OTUs为269;底泥细菌群落比表层水体更加多样化,底泥细菌的物种数大大多于表层水体。同时,底泥细菌群落与表层浮游细菌群落结构存在显著差异。物种分类显示鄱阳湖底泥细菌种类隶属于20门,228属,其中优势种群为δ-变形菌纲(Deltaproteobacteria)、β-变形菌纲(Betaproteobacteria)和疣微菌门(Verrucomicrobia);表层水体浮游细菌隶属于13门116属,优势种群为β-变形菌纲、拟杆菌门(Bacteroidetes)和放线菌门(Actinobacteria)。结果进一步揭示,无论是浮游细菌群落还是沉积物细菌群落,优势细菌种群的基因型多样性更高。     

Temporal and spatial variability in nearshore bacterioplankton communities of Lake Michigan

The spatial and temporal variability of bacterial communities were determined for the nearshore waters of Lake Michigan, an oligotrophic freshwater inland sea. A freshwater estuary and nearshore sites were compared six times during 2006 using denaturing gradient gel electrophoresis (DGGE). Bacterial composition clustered by individual site and date rather than by depth. Seven 16S rRNA gene clone libraries were constructed, yielding 2717 bacterial sequences. Spatial variability was detected among the DGGE banding patterns and supported by clone library composition. The clone libraries from deep waters and the estuary environment revealed highest overall bacterial diversity. Betaproteobacteria sequence types were the most dominant taxa, comprising 40.2–67.7% of the clone libraries. BAL 47 was the most abundant freshwater cluster of Betaproteobacteria , indicating widespread distribution of this cluster in the nearshore waters of Lake Michigan. Incertae sedis 5 and Oxalobacteraceae sequence types were prevalent in each clone library, displaying more diversity than previously described in other freshwater environments. Among the Oxalobacteraceae sequences, a globally distributed freshwater cluster was determined. The nearshore waters of Lake Michigan are a dynamic environment that experience forces similar to the coastal ocean environment and share common bacterial diversity with other freshwater habitats.     

Disentangling the relative influence of bacterioplankton phylogeny and metabolism on lysogeny in reservoirs and lagoons

Previous studies indicate that lysogeny is preponderant when environmental conditions are challenging for the bacterial communities and when their metabolism is reduced. Furthermore, it appears that lysogeny is more frequent within certain bacterial phylogenetic groups. In this comparative study from 10 freshwater reservoirs and 10 coastal lagoons, we aim to disentangle the influence of these different factors. In eight reservoirs and four lagoons, lysogeny was detected by induction assays with mitomycin C, and induction significantly modified the bacterial community composition (BCC), whereas community composition remained constant in ecosystems in which lysogeny was not observed. Among the phylogenetic groups studied, the most abundant ones were Bacteroidetes and α-proteobacteria in lagoons, and β-proteobacteria and Bacteroidetes in reservoirs. These dominant groups comprised the highest proportions of inducible lysogens. In order to unravel the effects of bacterial metabolism from phylogeny on lysogeny, we measured bacterial community physiology and the specific activities of selected phylogenetic groups. The proportion of inducible lysogens within the α- and the β-proteobacteria decreased with increasing group-specific metabolism in lagoons and reservoirs, respectively. In contrast, this relationship was not observed for the other lysogen-containing groups. Hence, both host physiology and phylogeny are critical for the establishment of lysogeny. This study illustrates the importance of lysogeny among the most abundant phylogenetic groups, and further suggests its strong structuring impact on BCC.     

利迪链霉菌M01对番茄生长、青枯病发病率及根际细菌群落组成的影响

【背景】利迪链霉菌(Streptomyces lydicus)对多种作物均有较好的促生效果,且对病原真菌具有广谱抑制作用,但该菌对细菌性青枯病的防控研究较少。【目的】探究利迪链霉菌M01能否促进番茄生长并抑制番茄青枯病,以及M01对番茄生长的影响是否通过影响根际细菌群落结构实现。【方法】采用温室盆栽试验和扩增子高通量测序技术研究M01对番茄生长、青枯病发病率及根际细菌群落组成的影响。【结果】施用利迪链霉菌M01的番茄植株鲜重、干重、株高、用土壤与作物分析开发(soil and plant analyzer develotrnent, SPAD)方法测量的叶绿素浓度、根系活力和植株P含量比对照分别提高了22.7%、12.5%、16.0%、28.1%、18.4%和17.9%,其中对株高、SPAD值和植株磷含量影响显著(P<0.05)。M01处理延缓了番茄青枯病的发病时间,接种9周后发病率比对照降低了41.8%。此外,M01对番茄根际细菌群落无显著影响(门水平群落组成,P=0.4;属水平群落组成,P=0.4)。【结论】利迪链霉菌M01可促进番茄植株生长并抑制番茄青枯病,利迪链霉菌M01对番茄生长的影响并非通过调控根际细菌群落实现。     

Diversity of endophytic bacterial communities in poplar grown under field conditions

Bacterial endophytes may be important for plant health and other ecologically relevant functions of poplar trees. The composition of endophytic bacteria colonizing the aerial parts of poplar was studied using a multiphasic approach. The terminal restriction fragment length polymorphism analysis of 16S rRNA genes demonstrated the impact of different hybrid poplar clones on the endophytic community structure. Detailed analysis of endophytic bacteria using cultivation methods in combination with cloning of 16S rRNA genes amplified from plant tissue revealed a high phylogenetic diversity of endophytic bacteria with a total of 53 taxa at the genus level that included Proteobacteria, Actinobacteria, Firmicutes and Bacteroidetes. The community structure displayed clear differences in terms of the presence and relative proportions of bacterial taxa between the four poplar clones studied. The results showed that the genetic background of the hybrid poplar clones corresponded well with the endophytic community structure. Out of the 513 isolates and 209 clones identified, Actinobacteria, in particular the family Microbacteriaceae, made up the largest fraction of the isolates, whereas the clone library was dominated by Alpha- and Betaproteobacteria. The most abundant genera among the isolates were Pseudomonas and Curtobacterium, while Sphingomonas prevailed among the clones.     

Altering the balance between bacterial production and protistan bacterivory triggers shifts in freshwater bacterial community composition

Bacterivorous protists are known to induce changes in bacterial community composition (BCC). We hypothesized that changes in BCC could be related quantitatively to a measure of grazing: the ratio of bacterial mortality to growth rate. To test this hypothesis, we analyzed time-course changes in BCC, protistan grazing rate, and bacterial production from 3 in situ studies conducted in a freshwater reservoir and three laboratory studies. In the field experiments, samples were manipulated to yield different levels of protistan bacterivory and incubated in dialysis bags. Laboratory investigations were continuous cultivation studies in which different bacterivorous protists were added to bacterial communities. BCC was assessed using 4–6 different rRNA-targeted oligonucleotide probes for community analysis. Change in BCC (Δ BCC) was estimated as the sum of changes in the proportions of the two phylogenetic groups that showed the largest shifts. Analysis of a set of 22 estimates of shifts in the ratio of grazing to production rate over periods of 48–72 h and Δ BCC showed that Δ BCC was positively and tightly correlated (r ² = 0.784) with shifts in the ratio of grazing mortality to cell production. While the nature of a shift in BCC is unpredictable, the magnitude of the change can be related to changes in the balance between bacterial production and protistan grazing. This revised version was published online in August 2006 with corrections to the Cover Date.     

云南松林次生演替阶段土壤细菌群落的变化

土壤细菌多样性是维持森林生态系统功能的关键因子,森林演替是影响其动态变化的重要因素.研究云南松林不同演替阶段土壤细菌群落结构及其多样性的变化规律,有助于深入理解森林生态系统恢复过程的驱动机制.本研究以云南省永仁县皆伐后形成的针叶林、针阔混交林和常绿阔叶林为对象,基于Illumina Hiseq高通量测序技术,分析森林演...     

Rhizosphere bacterial community composition responds to arbuscular mycorrhiza, but not to reductions in microbial activity induced by foliar cutting

Differences in bacterial community composition (BCC) between bulk and rhizosphere soil and between rhizospheres of different plant species are assumed to be strongly governed by quantitative and qualitative rhizodeposit differences. However, data on the relationship between rhizodeposit amounts and BCC are lacking. Other soil microorganisms, e.g. arbuscular mycorrhizal fungi (AMF), may also influence BCC. We simulated foliar herbivory (cutting) to reduce belowground carbon allocation and rhizodeposition of pea plants grown either with or without AMF. This reduced soil respiration, rhizosphere microbial biomass and bacteriovorous protozoan abundance, whereas none of these were affected by AMF. After labelling plants with (13)CO(2), root and rhizosphere soil (13)C enrichment of cut plants were reduced to a higher extent (24-46%) than shoot (13)C enrichment (10-24%). AMF did not affect (13)C enrichment. Despite these clear indications of reduced rhizosphere carbon-input, denaturing gradient gel electrophoresis (DGGE) of 16S rRNA genes PCR-amplified targeting DNA and RNA from rhizosphere soil did not reveal any effects of cutting on banding patterns. In contrast, AMF induced consistent differences in both DNA- and RNA-based DGGE profiles. These results show that a reduction in rhizosphere microbial activity is not necessarily accompanied by changes in BCC, whereas AMF presence inhibits proliferation of some bacterial taxa while stimulating others.     

水稻种子的细菌含量和群落结构及其影响因素分析

【目的】种子是植物微生物群代际传递的重要途径,但种子携带的微生物群落尚缺乏系统的研究。本研究以水稻种子为模型,定量分析种子的细菌含量、测定种子的细菌群落结构、探究地域与品种对细菌含量及群落结构的影响和鉴定水稻种子的核心菌群。【方法】选取18个水稻品种,每个品种分别来自中国海南和天津2个地域,共36组样本。每组样本包含5或10个DNA样本,每个DNA样本由3粒种子提取的总DNA构成。使用细菌特异性16S rDNA介导的荧光定量PCR技术测定种子的细菌含量,并分析影响因素;使用16S rDNA扩增子测序技术测定种子的细菌群落结构,并用生物信息学方法分析了影响因素和核心菌群。【结果】本研究测定了1 080粒水稻种子的细菌含量,发现经过表面除菌的水稻种子内部存在共栖细菌,平均每克种子的细菌含量为1.53×10⁶。水稻品种对种子的细菌含量有显著影响,而地域无影响。测定180个扩增子文库的细菌群落结构,发现水稻种子的菌群与水稻植株有相似之处,均以变形菌门为主要的细菌门类;地域对水稻种子的细菌群落结构有重要影响,不同地域的水稻种子在主坐标分析(principal co-ordinate analysis, PCoA)中有明显分离;而粳稻和籼稻之间无显著差异。还发现水稻种子存在核心菌群,且相对丰度高达总菌群的85.56%。【结论】本研究系统地揭示了水稻种子的细菌含量、群落结构及其影响因素,为利用种传微生物促进水稻健康提供了数据和方法支持。     

太湖有机聚集体上附着细菌群落结构与动态的T-RFLP分析

有机聚集体(organic aggregates),是指由浮游动(植)物的残体、粪便颗粒及各种有机碎屑、活的自养及异养微生物以及无机颗粒等由于物理的、化学的或生物的作用聚集而成的颗粒物。人们对水生态系统中有机聚集体的认识始于20世纪50年代的海洋学研究。细菌是有机聚集体最重要的组成部分之一。有机聚集体在水体中物质与能量循环中的作用很大程度上是靠附着其上的异养细菌而起作用的。目前,有机聚集体的概念在水生态系统中已被广泛接受,由于其独特的物理、化学及生物组成,以及复杂的形成、转化过程,使其在水生态系统中具有重要的生态学作用。然而,有关浅水湖泊中有机聚集体上细菌群落的研究目前尚未见报道。近年来,基于DNA多聚酶链式反应(PCR)的末端限制性片段长度多态性(T-RFLP)技术是一种新兴的研究微生物多态性的分子生物学方法。该技术由于具有快捷、高分辨率、高通量和不依赖于培养等优点而被广泛应用于微生物群落结构的时空演替研究。本研究采用T-RFLP技术,研究了太湖梁溪河入湖河口(Site A)和贡湖湾(Site B)2006年6月至2007年5月一年间有机聚集体上附着细菌群落组成的时空变化规律。T-RFLP分析检测到这两个采样点共有187个独特的末端限制性片段(T-RFs),月平均T-RFs分别42.7和44.9。t 检验显示它们没有显著性差异(P>0.05)。虽然河口的营养盐浓度要显著高于贡湖湾(P<0.01),T-RFLP 结果表明,太湖中营养盐的浓度已经不是有机聚集体上附着细菌多样性的限制因子。聚类分析显示,除了春季外,河口和贡湖湾有机聚集体上细菌群落结构有明显的不同。在T-RFLP分析附着细菌群落组成及季节变化的基础上,采用多元统计方法研究环境因子与附着细菌群落组成变化的相关性。典型对应分析(CCA)结果表明诸多环境因子中,DIP、DIN 和水温与有机聚集体上细菌群落结构的变化具有显著的相关性 (P<0.05)。     

Copper affects biofilm inductiveness to larval settlement of the serpulid polychaete Hydroides elegans (Haswell)

Copper (Cu) contamination is a potential threat to the marine environment due to the use of Cu-based antifouling paints. Cu stress on larval settlement of the polychaete Hydroides elegans was investigated, and this was linked to Cu stress on biofilms and on the biofilm development process. The inductiveness of young biofilms was more easily altered by Cu stress than that of old biofilms, indicating the relative vulnerability of young biofilms. This might result from changes in bacterial survival, the bacterial community composition and the chemical profiles of young biofilms. Cu also affected biofilm development and the chemical high performance liquid chromatograph fingerprint profile. The results indicate that Cu affected larval settlement mainly through its effect on the process of biofilm development in the marine environment, and the chemical profile was crucial to biofilm inductiveness. It is strongly recommended that the effects of environmentally toxic substances on biofilms are evaluated in ecotoxicity bioassays using larval settlement of invertebrates as the end point.     

Soil parent material is a key determinant of the bacterial community structure in arable soils

The bacterial community composition in soil and rhizosphere taken from arable field sites, differing in soil parent material and soil texture, was analyzed using terminal restriction fragment length polymorphism (T-RFLP) of 16S rRNA genes. Nine sandy to silty soils from North-East Germany could clearly be distinguished from each other, with a relatively low heterogeneity in the community structure within the field replicates. There was a relationship between the soil parent material, i.e. different glacial and aeolian sediments, and the clustering of the profiles from different sites. A site-specific grouping of T-RFLP profiles was also found for the rhizosphere samples of the same field sites that were planted with potatoes. The branching of the rhizosphere profiles corresponded partly with the soil parent material, whereas the effect of the plant genotype was negligible. Selected terminal restriction fragments differing in their relative abundance within the nine soils were analyzed based on the cloning of the 16S rRNA genes of one soil sample. A high phylogenetic diversity observed to include Acidobacteria, Betaproteobacteria, Bacteroidetes, Verrucomicrobia, and Gemmatimonadetes. The assignment of three out of the seven selected terminal restriction fragments to members of Acidobacteria suggested that this group seems to participate frequently in the shifting of community structures that result from soil property changes.