中国主要矿区油页岩可培养细菌的分离与鉴定

【目的】研究油页岩本源环境中可培养细菌多样性,对于发掘利用尚未开发的油页岩细菌资源具有重要意义。【方法】以野外采集的吉林桦甸、广东茂名和辽宁抚顺3个中国主要矿区的油页岩作为研究对象,采用稀释平板培养法,以营养琼脂培养基对油页岩中的细菌进行分离纯化,并对分离菌株进行基于16S rRNA基因的序列测定和系统发育分析。【结果】3个矿区共鉴定出10属,其中抚顺矿的9个操作分类单元(Operational taxonomic units,OTUs)属于Pantoea、Brevibacillus、Paenibacillus、Microbacterium、Arthrobacter、Pseudomonas和Bacillus菌属;茂名矿的5个OTUs属于Bacillus和Sinomona菌属,桦甸矿的5个OTUs属于Staphylococcus、Acinetobacter、Bacillus和Arthrobacter菌属。【结论】3个矿区可培养细菌群落组成均较简单,且在门的分类层次上相似,即均具有厚壁菌门和放线菌门,抚顺矿和桦甸矿还存在部分变形菌门细菌。在属的分类层次上,各矿区差异较大。     

Sexual selection explains more functional variation in the mammalian major histocompatibility complex than parasitism

Understanding drivers of genetic diversity at the major histocompatibility complex (MHC) is vitally important for predicting how vertebrate immune defence might respond to future selection pressures and for preserving immunogenetic diversity in declining populations. Parasite-mediated selection is believed to be the major selective force generating MHC polymorphism, and while MHC-based mating preferences also exist for multiple species including humans, the general importance of mate choice is debated. To investigate the contributions of parasitism and sexual selection in explaining among-species variation in MHC diversity, we applied comparative methods and meta-analysis across 112 mammal species, including carnivores, bats, primates, rodents and ungulates. We tested whether MHC diversity increased with parasite richness and relative testes size (as an indicator of the potential for mate choice), while controlling for phylogenetic autocorrelation, neutral mutation rate and confounding ecological variables. We found that MHC nucleotide diversity increased with parasite richness for bats and ungulates but decreased with parasite richness for carnivores. By contrast, nucleotide diversity increased with relative testes size for all taxa. This study provides support for both parasite-mediated and sexual selection in shaping functional MHC polymorphism across mammals, and importantly, suggests that sexual selection could have a more general role than previously thought.     

Genetic variation in pathogenic bacteria

In contrast to textbook ideas of pure cultures and defined strains, genetic variation is a fact of life in the microbial world. It not only allows pathogens to establish themselves in their chosen host, but also allows them to resist that host's subsequent attempts to evict them. Here we review some of the mechanisms that bring about this variation, and some of the functional consequences that result from it.     

椰子织蛾幼虫肠道细菌的初步分离鉴定及功能分析

[目的] 研究椰子织蛾幼虫肠道微生物的种类和功能,以揭示其消化利用寄主老叶的机制。[方法] 采用传统微生物分离培养技术分离培养肠道细菌,用16S rRNA基因序列分析的方法鉴定菌株,采用透明圈染色法对所得菌株进行功能性验证。[结果] 基因序列检测对比鉴定得到9种可培养细菌菌株,主要属于变形菌门和厚壁菌门以及放线菌门;功能性验证结果表明,伯克霍尔德氏菌、解淀粉芽孢杆菌、贝莱斯芽孢杆菌、蜡样芽孢杆菌菌株具有纤维素降解酶,寒气玫瑰单胞菌、解淀粉芽孢杆菌含木聚糖降解酶。[结论] 椰子织蛾肠道中存在可培养的具有降解纤维素及木聚糖能力的细菌,这些细菌可能有助于椰子织蛾取食消化椰子等老叶,研究所获得的肠道微生物菌株也为后续研究该虫与环境的关系及相关菌株应用于农业、能源、环保价值的探索提供帮助。     

花生种子相关促生菌分离鉴定及功能评价

【背景】利用微生物促进植物健康生长是农业可持续发展的重要方向之一,而种子相关的促生菌可在植物生命周期早期与植物相互作用,对植物健康生长具有重要意义。【目的】发掘与利用种子相关促生菌的前提是筛选获得促生菌菌种资源,验证其益生能力,为其进一步应用与机理研究提供依据与支持。【方法】以花生种子为研究对象,从种子表面及种子内部分离纯化多株菌,测定菌株的固氮、解磷、解钾、吲哚乙酸合成和铁载体合成等促生能力,并验证菌株对常见植物病原菌的生长抑制特性;通过16S rRNA基因序列进行系统发育分析,确定分类地位;通过生物膜形成能力及根际定殖能力测定菌株在植物根际的生存能力;最后通过催芽及盆栽试验测定菌株对花生种子发芽及幼苗生长的影响。【结果】从花生种子表面、种子内和胚根内分离筛选到41株菌,均有吲哚乙酸合成能力,其中35株有固氮能力,2株有铁载体分泌能力,14株有植物病原菌生长抑制能力。各选一株为代表的菌株,即PS3、PE5和PR5,经16S rRNA基因序列比对分析鉴定为芽孢杆菌属(Bacillus)。PS3、PE5和PR5均可在MSgg液体培养基表面形成褶皱较强的生物膜,也可在花生根际形成有效定殖。催芽试验结果表明经过促生菌浸种后花生种子萌发率明显提高,在第2天时,PS5将发芽率由14.17%提高至38.33%,PE5发芽率提高至30.83%,PR5发芽率提高至39.17%。三株菌能够明显促进花生幼苗生长,PS5对花生幼苗苗高、根长、鲜重和干重分别提高21.82%、22.20%、37.11%和35.64%,PE5分别提高17.45%、18.93%、26.10%和21.18%,PR5分别提高23.11%、23.92%、38.66%和37.47%。【结论】筛选获得的花生种子相关促生菌,具有促进植物生长的潜力,明显促进种子萌发及幼苗生长,是良好的促生菌生物资源,具有较好的应用潜力。     

On the variation explained by ordination and constrained ordination axes

Abstract. Total inertia (TI), the sum of eigenvalues for all ordination axes, is often used as a measure of total variation in a data set. By use of simulated data sets, I demonstrate that lack-of-fit of data to the response model implicit in any eigenvector ordination method results in polynomial distortion ordination axes, with eigenvalues that normally contribute 30–70% to TI (depending on data set properties). The amount of compositional variation extracted on ecologically interpretable ordination axes (structure axes) is thus underestimated by the eigenvalue-to-total-inertia ratio. I recommend that the current use of total inertia as a measure of compositional variation is discontinued. Eigenvalues of structure axes can, however, be used with some caution to indicate their relative importance. I also demonstrate that when the total inertia is partitioned on different sets of explanatory variables and unexplained variation by use of (partial) constrained ordination, (35) 50–85% of the variation ‘unexplained’ by the supplied explanatory variables represents lack-of-fit of data to model. Thus, the common interpretation of ‘unexplained variation’ as random variation (‘noise’) or coenoclinal variation caused by unmeasured explanatory variables, is generally inappropriate. I recommend a change of focus from the variation-explained-to-total inertia ratio and ‘unexplained’ variation to relative amounts of variation explained by different sets of explanatory variables.     

HLA-DP and HLA-DO genes in presumptive HLA-identical siblings: structural and functional identification of allelic variation

We analyzed HLA class II genomic polymorphisms in three families in which bone marrow transplantation was performed between individuals presumed to be HLA identical, but in which unexplained mixed lymphocyte culture reactivity was observed. These families were characterized by classical HLA serology, MLC, and DP typing. In each family, a pair of "HLA-identical" siblings demonstrated a small proliferative response in bidirectional MLC. Southern blotting analysis performed with cDNA probes for DQ alpha, DP alpha, and DP beta identified DP genomic differences in each case. Hybridization of Bgl II-digested genomic DNA with a DP alpha cDNA probe revealed three prominent polymorphic fragments (7.7, 5.8, and 3.7 kb), which discriminated between presumptive identical siblings and indicated crossover events within HLA. Similarly, hybridization of SstI-digested genomic DNA with a DP beta cDNA probe, although resulting in a more complex pattern, identified DP genomic disparity between the presumed HLA identical siblings. Hybridization of SstI-digested DNA from two families with evidence of DP recombination was performed by using an oligonucleotide probe specific for the newly described HLA class II gene DO beta. Two major polymorphic fragments, at 6.2 and 3.3 kb, segregated in these families and localized the crossovers flanking the DO beta gene between the DQ and DP loci. The contribution of the antigenic differences marked by these HLA DP and DO DNA polymorphisms to allorecognition in MLR and in graft-vs-host disease are discussed.     

Seasonal variation in the nitrogenase activity of aPanicum maximum var.trichoglume pasture and identification of associated bacteria

Summary The influence of seasonal variation on nitrogenase (N₂-ase) activity of undisturbed soil-plant cores ofPanicum maximum var.trichoglume was measured using the C₂H₂ reduction assay. The largest N₂-ase activity in the field, 14.7 g N ha⁻¹ day⁻¹, occurred in spring when soil moisture was high, soil temperature was low and nitrogenous fertiliser influence was at a minimum. The potential N₂-ase activity of the cores, measured under controlled conditions, reached a maximum of 27.2 g N ha⁻¹ day⁻¹ and averaged 26.3 g N ha⁻¹ day⁻¹ over the 14 month sampling period. N₂-ase activity was positively correlated (P=0.05) with field soil moisture and negatively correlated with field soil temperature (r=0.59 and −0.78 respectively). Multiple regression showed that 69% of the variation of N₂-ase activity in the field was associated with the combined effects of soil moisture and soil temperature. Nitrogen fixing bacteria were isolated from the roots ofP. maximum and based upon morphology, biochemical tests and fluorescent antibody reaction, were found to be closely related toAzospirillum lipoferum.     

一株粗糙脉孢菌的分离、鉴定及其基因组变异和功能分析

【背景】粗糙脉孢菌LY03是从武平传统"红菌豆腐"中分离得到的主要发酵菌株。【目的】研究粗糙脉孢菌LY03菌株的基因组信息,揭示武平传统"红菌豆腐"发酵特性。【方法】采用形态学观察、ITS鉴定、重测序及框架图测序对所分离的LY03菌株进行鉴定和基因组信息解析。【结果】武平传统"红菌豆腐"中分离得到的主要发酵菌株LY03确定为粗糙脉孢菌,将其在中国普通微生物菌种保藏管理中心进行专利保藏,保藏号为CGMCC3.19233。LY03菌株比对到参考基因组上的总Read数目为95.85%,测序对应深度的位点占全基因组76.13%;各变异类型在内含子区域均无变异,主要变异存在于基因组的外显子区域,具体变异数量为:单核苷酸多态性位点(single nucleotide polymorphism,SNP)位点变异总数203128个、插入缺失(insertion/deletion,In Del)突变总和26859个、拷贝数变异(copy number variation,CNV)增加和减少的拷贝总数1 039个、结构变异(structure variation,SV)注释的变异总数777个;LY03菌株...     

Plant chemical traits define functional and phylogenetic axes of plant biodiversity

To determine which types of plant traits might better explain ecosystem functioning and plant evolutionary histories, we compiled 42 traits for each of 15 perennial species in a biodiversity experiment. We used every possible combination of three traits to cluster species. Across these 11,480 combinations, clusters generated using tissue %Ca, %N and %K best mapped onto phylogeny. Moreover, for the 15 best combinations of three traits, 82% of traits were chemical, 16% morphological and 2% metabolic. The diversity-dependence of ecosystem productivity was better explained by the %Ca, %N and %K clusters: compared to adding a new species at random, adding a species from an absent cluster/clade better-explained gains in productivity. Species number impacted productivity only when all clusters were present. Our results suggest that tissue elemental chemistry might be more phylogenetically conserved and more strongly related to ecosystem functioning than commonly measured morphological and physiological traits, a possibility that merits exploration.     

Stress responses and genetic variation in bacteria

Under stressful conditions mechanisms that increase genetic variation can bestow a selective advantage. Bacteria have several stress responses that provide ways in which mutation rates can be increased. These include the SOS response, the general stress response, the heat-shock response, and the stringent response, all of which impact the regulation of error-prone polymerases. Adaptive mutation appears to be process by which cells can respond to selective pressure specifically by producing mutations. In Escherichia coli strain FC40 adaptive mutation involves the following inducible components: (i) a recombination pathway that generates mutations; (ii) a DNA polymerase that synthesizes error-containing DNA; and (iii) stress responses that regulate cellular processes. In addition, a subpopulation of cells enters into a state of hypermutation, giving rise to about 10% of the single mutants and virtually all of the mutants with multiple mutations. These bacterial responses have implications for the development of cancer and other genetic disorders in higher organisms.     

海带发酵降解中相关海洋功能菌的分离、鉴定与筛选

目的 从海带养殖环境中筛选有效降解海带的海洋功能菌,对海带进行降解处理,提高利用率,增加海带原料价值。方法 采用以果胶或海藻酸钠为唯一碳源的选择性培养基挑选含有果胶酶、褐藻酸裂解酶的菌株;测定海带发酵液中海藻酸含量,复筛降解效果好的单菌及复合菌;16S rDNA测序对菌种进行鉴定。结果 使用含10%鲜海带的富集培养基培养48 h,其中降解效果较好的为1-2和3-10菌种的组合,其降解量为95%。结论 经上述研究选出有效的降解海带功能菌1-2和3-10,其降解海带效果较好,对海带利用率高。     

Evaluation of oxygen adaptation and identification of functional bacteria composition for anammox consortium in non-woven biological rotating contactor

In this study, the anammox consortium was found to adapt to the wastewater containing dissolved oxygen (DO), as the DO was gradually increased. Batch tests indicated the maximum aerobic ammonium oxidizing activity of the consortium was 1.38mmolNH(4)(+)-N(gVSS)(-1)day(-1), which played key roles in the oxygen consumption process; the maximum anaerobic ammonium oxidizing activity was slightly decreased after long-term oxygen exposure, but only from 21.23mmolNH(4)(+)-N(gVSS)(-1)day(-1) to 20.23mmolNH(4)(+)-N(gVSS)(-1)day(-1). Microbiological community analysis identified two strains similar to Nitrosomonas eutropha were responsible for oxygen consumption, which were able to exist in the autotrophic anaerobic condition for long periods and protect anammox bacteria Planctomycetales from the influence of oxygen. Microbiological composition analysis showed Nitrosomonas and Planctomycetales approximately accounted for 10% and 70% of the bacteria, respectively. The possibility of cultivation anammox consortium in presence of DO will lead to substantial savings of energy and resource in the industrial application.     

Seasonal variation in cell volume of epilimnetic bacteria

The relationship between bacterial cell volume and temperature was examined for field data collected over a 4-year period and through controlled chemostat incubations of aPseudomonas sp. Volumes of planktonic bacteria were found to decrease as water temperature increased. Changes in temperature accounted for 38% of the variation in average cell volume (P<0.001). Average planktobacterial cell volume fell 42% from 0.217m³ in mid-winter to 0.127m³ in mid-summer. Similar results were found for the size distribution of epibacterial cells. Controlled chemostat incubations of aPseudomonas sp. indicated that cell volume was significantly affected by temperature, growth rate, and the interaction of temperature and growth rate. The data suggest that a change in cell volume as a result of a change in temperature is an intrinsic property of planktonic bacteria.     

Computer-assisted identification of anaerobic bacteria.

A computer program was developed to identify anaerobic bacteria by using simultaneous pattern recognition via a Bayesian probabilistic model. The system is intended for use as a rapid, precise, and reproducible aid in the identification of unknown isolates. The program operates on a data base of 28 genera comprising 238 species of anaerobic bacteria that can be separated by the program. Input to the program consists of biochemical and gas chromatographic test results in binary format. The system is flexible and yields outputs of: (i) most probable species, (ii) significant test results conflicting with established data, and (iii) differential tests of significance for missing test results.