In situ analysis of sulfur species in sulfur globules produced from thiosulfate by Thermoanaerobacter sulfurigignens and Thermoanaerobacterium thermosulfurigenes

The Firmicutes Thermoanaerobacter sulfurigignens and Thermoanaerobacterium thermosulfurigenes convert thiosulfate, forming sulfur globules inside and outside cells. X-ray absorption near-edge structure analysis revealed that the sulfur consisted mainly of sulfur chains with organic end groups similar to sulfur formed in purple sulfur bacteria, suggesting the possibility that the process of sulfur globule formation by bacteria is an ancient feature.     

Natural Competence and the Evolution of DNA Uptake Specificity

Many bacteria are naturally competent, able to actively transport environmental DNA fragments across their cell envelope and into their cytoplasm. Because incoming DNA fragments can recombine with and replace homologous segments of the chromosome, competence provides cells with a potent mechanism of horizontal gene transfer as well as access to the nutrients in extracellular DNA. This review starts with an introductory overview of competence and continues with a detailed consideration of the DNA uptake specificity of competent proteobacteria in the Pasteurellaceae and Neisseriaceae. Species in these distantly related families exhibit strong preferences for genomic DNA from close relatives, a self-specificity arising from the combined effects of biases in the uptake machinery and genomic overrepresentation of the sequences this machinery prefers. Other competent species tested lack obvious uptake bias or uptake sequences, suggesting that strong convergent evolutionary forces have acted on these two families. Recent results show that uptake sequences have multiple “dialects,” with clades within each family preferring distinct sequence variants and having corresponding variants enriched in their genomes. Although the genomic consensus uptake sequences are 12 and 29 to 34 bp, uptake assays have found that only central cores of 3 to 4 bp, conserved across dialects, are crucial for uptake. The other bases, which differ between dialects, make weaker individual contributions but have important cooperative interactions. Together, these results make predictions about the mechanism of DNA uptake across the outer membrane, supporting a model for the evolutionary accumulation and stability of uptake sequences and suggesting that uptake biases may be more widespread than currently thought.     

Vector Competence in West African Aedes aegypti Is Flavivirus Species and Genotype Dependent

Background

Vector competence of Aedes aegypti mosquitoes is a quantitative genetic trait that varies among geographic locations and among different flavivirus species and genotypes within species. The subspecies Ae. aegypti formosus, found mostly in sub-Saharan Africa, is considered to be refractory to both dengue (DENV) and yellow fever viruses (YFV) compared to the more globally distributed Ae. aegypti aegypti. Within Senegal, vector competence varies with collection site and DENV-2 viral isolate, but knowledge about the interaction of West African Ae. aegypti with different flaviviruses is lacking. The current study utilizes low passage isolates of dengue-2 (DENV-2-75505 sylvatic genotype) and yellow fever (YFV BA-55 -West African Genotype I, or YFV DAK 1279-West African Genotype II) from West Africa and field derived Ae. aegypti collected throughout Senegal to determine whether vector competence is flavivirus or virus genotype dependent.

Methodology/Principal Findings

Eight collections of 20–30 mosquitoes from different sites were fed a bloodmeal containing either DENV-2 or either isolate of YFV. Midgut and disseminated infection phenotypes were determined 14 days post infection. Collections varied significantly in the rate and intensity of midgut and disseminated infection among the three viruses.

Conclusions/Significance

Overall, vector competence was dependent upon both viral and vector strains. Importantly, contrary to previous studies, sylvatic collections of Ae. aegypti showed high levels of disseminated infection for local isolates of both DENV-2 and YFV.     

Episodic Selection and the Maintenance of Competence and Natural Transformation in Bacillus subtilis

We present a new hypothesis for the selective pressures responsible for maintaining natural competence and transformation. Our hypothesis is based in part on the observation that in Bacillus subtilis, where transformation is widespread, competence is associated with periods of nongrowth in otherwise growing populations. As postulated for the phenomenon of persistence, the short-term fitness cost associated with the production of transiently nongrowing bacteria can be compensated for and the capacity to produce these competent cells can be favored due to episodes where the population encounters conditions that kill dividing bacteria. With the aid of a mathematical model, we demonstrate that under realistic conditions this “episodic selection” for transiently nongrowing (persisting) bacteria can maintain competence for the uptake and expression of exogenous DNA transformation. We also show that these conditions for maintaining competence are dramatically augmented even by rare episodes where selection favors transformants. Using experimental populations of B. subtilis and antibiotic-mediated episodic selection, we test and provide support for the validity of the assumptions behind this model and the predictions generated from our analysis of its properties. We discuss the potential generality of episodic selection for the maintenance of competence in other naturally transforming species of bacteria and critically evaluate other hypotheses for the maintenance (and evolution) of competence and their relationship to this hypothesis.     

一株厌氧嗜热杆菌生长及发酵特性的初步研究

论文对筛选并鉴定为Thermoanaerobacterium saccharolyticum菌株的生长、底物利用情况、产物生成以及酒精耐受性进行了研究。结果表明,该菌在以甘露糖、葡萄糖和木糖为碳源时生长较好,同时能够较好的利用木聚糖和木薯淀粉;最适底物浓度为15g/L;不同的葡萄糖:木糖比例对其生长无显著影响;能耐受的培养基最高初始酒精浓度为3%(V/V)。在5g/L的木聚糖、木糖和木薯淀粉培养基中发酵60h后,产物主要有乙醇、乳酸和乙酸,乙醇产量分别为0.824、0.867和0.916g/L。     

新疆喀纳斯自然保护区藓类植物物种多样性与区系调查

从1995～2009年,作者对新疆喀纳斯自然保护区藓类植物进行了全面的调查、采集、鉴定,分析研究。结果表明,该自然保护区藓类植物共有37科113属253种（含1变种）,优势科主要体现寒、温带地区分布类型,该区藓类植物生境的多样性可以从物种多样性,如曲尾藓科、木灵藓科、泥炭藓科、紫萼藓科、丛藓科等的广泛分布反映出来。通过与该区相邻的6个地区的物种丰富度系数比较,该自然保护区综合系数S i排第三位,说明此区藓类植物物种多样性丰富,这与本区的水分条件有很大关系。藓类植物区系成分以北温带成分为绝对优势,占总种数的83.33%;东亚成分占总种数的5.10%;东亚-北美成分占总种数的4.17%,各区系成分交汇。主成分分析和聚类分析表明,喀纳斯自然保护区藓类植物区系与新疆东部天山、内蒙古大青山、吉林长白山、河北木兰围场藓类植物区系关系较接近,与贵州梵净山、云南鸡足山藓类植物区系关系疏远,体现了我国北方藓类植物分布特征。     

陕西周至老县城自然保护区天然林物种组成及主要种群生态位

采用样方法对陕西周至老县城自然保护区森林植物群落进行调查,运用生态位宽度(B)、生态位重叠值(L)及生态位相似比例(C)指标对主要乔木种群的生态位特征进行测定与分析,探讨植物种群在群落中的地位和作用以及彼此间的竞争关系。结果表明:(1)经调查老县城自然保护区共记录到植物物种243种,隶属于64科159属;分为3个植被型、9个群系。(2)主要乔木种群中,华山松和锐齿槲栎的生态位宽度较大,其Bi、Ba值分别为0.654、0.699和0.534、0.460;短柄枹栎和兴山榆的生态位宽度较小,其Bi、Ba值分别为0.064、0.023和0.049、0.016。(3)白桦和太白杨、糙皮桦和山杨种对的生态位重叠值和生态位相似性比例均较大,其Lij、Lji分别为0.108、0.114和0.089、0.128,Cij分别为0.939和0.744。优势种间的生态位重叠值和生态位相似比例总体较小,表明在现阶段群落演替中,植物对环境资源的竞争不激烈,物种空间异质性低。     

革兰氏阳性菌自然感受态生理机制的研究进展

自然感受态是指菌体在自然生长过程中吸附、摄取和内化外源DNA的生理状态。大部分细菌具有相似的DNA摄取机制,该机制主要由两部分组成:外源DNA在多种感受蛋白的共同作用下被核酸酶降解为单链DNA进入细胞,然后单链DNA在Dpr A、Ssb B和Rec A等蛋白的保护下整合到受体染色体上。目前对变形链球菌自然感受的调控系统研究较为广泛,拟以变形链球菌为例,结合其他细菌介绍自然感受的研究进展。Com X是变形链球菌的感受核心调控因子,可以激活多种后期感受基因的转录,这些后期感受基因对外源DNA的摄取发挥着重要作用。以变形链球菌的com X为核心,梳理总结了Com DE、ComRS、HdrRM、BsrRM和RcrRPQ等系统对com X的调控机理,分析了Com X稳定性及其对后期感受基因的调控,阐述了自然感受与生物膜形成、耐酸性和细菌素合成等毒力因子的内在联系,在此基础上展望了自然感受未来可能的研究方向。     

Differences in Cellular Immune Competence Explain Parasitoid Resistance for Two Coleopteran Species

The immune defence of an organism is evolving continuously, causing counteradaptations in interacting species, which in turn affect other ecological and evolutionary processes. Until recently comparative studies of species interactions and immunity, combining information from both ecological and immunological fields, have been rare. The cellular immune defense in insects, mainly mediated by circulating hemocytes, has been studied primarily in Lepidoptera and Diptera, whereas corresponding information about coleopteran species is still scarce. In the study presented here, we used two closely related chrysomelids, Galerucella pusilla and G. calmariensis (Coleoptera), both attacked by the same parasitoid, Asecodes parviclava (Hymenoptera). In order to investigate the structure of the immune system in Galerucella and to detect possible differences between the two species, we combined ecological studies with controlled parasitism experiments, followed by an investigation of the cell composition in the larval hemolymph. We found a striking difference in parasitism rate between the species, as well as in the level of successful immune response (i.e. encapsulation and melanisation of parasitoid eggs), with G. pusilla showing a much more potent immune defense than G. calmariensis. These differences were linked to differences in the larval cell composition, where hemocyte subsets in both naïve and parasitised individuals differed significantly between the species. In particular, the hemocytes shown to be active in the encapsulation process; phagocytes, lamellocytes and granulocytes, differ between the species, indicating that the cell composition reflects the ability to defend against the parasitoid.     

An Analysis of Fish Species Richness in Natural Lakes

There is a growing recognition of the need to conserve biodiversity that has been conceptualised in the Convention of Biological Diversity. Maintenance of fish species richness is particularly important, because habitat degradation in inland waters continues to accelerate on a global scale. Here we develop empirical models for predicting fish species richness in natural lakes in various geographical regions of the world. In tropical lakes where fish biodiversity is richer than in temperate lakes, fish species richness can be predicted by a few variables such as lake area and altitude. Low fish species richness in most temperate lakes might be due to the effect of glaciation on colonisation and speciation of fishes. In US, Canadian and northern European lakes, lake acidification is one of the important factors influencing fish species richness. Although limnological characteristics influence fish species richness in temperate lakes, lake area and altitude have greater predictive power. This is in contrast to fish species richness in rivers, which can be reliably predicted by basin area. In the power curves, which describe the relationship between fish species richness and habitat size in lakes and rivers, the exponent is always greater in tropical regions than in temperate regions. Because fish biodiversity is greater in the tropics threats to fish biodiversity through habitat degradation are greater than those in temperate inland waters.     

Transformation of Leuconostoc carnosum 4010 and Evidence for Natural Competence of the Organism

Plasmid transformation in Leuconostoc carnosum 4010 was analyzed. A successful transformation protocol for L. carnosum was established by modifying an existing protocol for Lactococcus lactis. Several parameters, including the number of generations that the cells had grown at the time of harvest, glycine concentration, the time of incubation for phenotypic expression, and the electrical field strength, were investigated and proved to have influence on the transformation frequency. Electrocompetence was found to be transient and to peak in the early exponential growth phase. Optimized conditions resulted in transformation frequencies of up to 6.7 × 10⁵ transformants per microgram of plasmid DNA. A total of five plasmids in L. carnosum were successfully introduced and maintained. Interestingly, we discovered that DNA uptake was of a frequency of 3 × 10⁻⁶ to 19 × 10⁻⁶ transformants per CFU in the absence of an applied electrical field. We concluded that L. carnosum is naturally competent.     

Edges in Agricultural Landscapes: Species Interactions and Movement of Natural Enemies

Agricultural landscapes can be characterized as a mosaic of habitat patches interspersed with hostile matrix, or as a gradient of patches ranging from suitable to unsuitable for different species. Arthropods moving through these landscapes encounter a range of edges, with different permeability. Patches of native vegetation in these landscapes may support natural enemies of crop pests by providing alternate hosts for parasitic wasps and/or acting as a source for predatory insects. We test this by quantifying species interactions and measuring movement across different edge-types. A high diversity of parasitoid species used hosts in the native vegetation patches, however we recorded few instances of the same parasitoid species using hosts in both the native vegetation and the crop (canola). However, we did find overall greater densities of parasitoids moving from native vegetation into the crop. Of the parasitoid groups examined, parasitoids of aphids (Braconidae: Aphidiinae) frequently moved from native vegetation into canola. In contrast, parasitoids of caterpillars (Braconidae: Microgastrinae) moved commonly from cereal fields into canola. Late season samples showed both aphids and parasitoids moving frequently out of native vegetation, in contrast predators moved less commonly from native vegetation (across the whole season). The season-long net advantage or disadvantage of native vegetation for pest control services is therefore difficult to evaluate. It appears that the different edge-types alter movement patterns of natural enemies more so than herbivorous pest species, and this may impact pest control services.     

云冷杉天然林乔木树种组成及物种多样性对择伐强度的动态响应

以吉林省长白山金沟岭林场云冷杉天然林为研究对象,定量分析不同择伐强度(对照0%、弱度择伐20.6%、中度择伐29.9%和重度择伐41.6%)下其乔木层树种组成及物种多样性的动态变化规律。结果显示:采伐后经10年恢复,择伐对原有林分结构影响不大,其中弱度和中度择伐仍能保持择伐前以冷杉占优势、红松和云杉占亚优势的物种结构,重度择伐使林分结构略有改变,但不明显;相比择伐前,择伐后经10年恢复的样地α多样性指数均有所增加,优势度指数均有不同程度的降低,其中弱度择伐样地的物种丰富度指数、多样性指数及均匀度指数的增加量和优势度指数的减少量均最大,说明弱度择伐有利于改善林分物种多样性状况,使林分物种更为丰富。本研究结果表明采取弱度择伐的方式更有利于维持林分物种结构及物种多样性,有利于云冷杉天然林的可持续经营和发展。     

Cysteine reactivity in Thermoanaerobacter brockii alcohol dehydrogenase.

The free cysteine residues in the extremely thermophilic Thermoanaerobacter brockii alcohol dehydrogenase (TBADH) were characterized using selective chemical modification with the stable nitroxyl biradical bis(1-oxy-2,2,5,5-tetramethyl-3-imidazoline-4-yl)disulfide, via a thiol-disulfide exchange reaction and with 2[14C]iodoacetic acid, via S-alkylation. The respective reactions were monitored by electron paramagenetic resonance (EPR) and by the incorporation of the radioactive label. In native TBADH, the rapid modification of one cysteine residue per subunit by the biradical and the concomitant loss of catalytic activity was reversed by DTT. NADP protected the enzyme from both modification and inactivation by the biradical. RPLC fingerprint analysis of reduced and S-carboxymethylated lysyl peptides from the radioactive alkylated enzyme identified Cys 203 as the readily modified residue. A second cysteine residue was rapidly modified with both modification reagents when the catalytic zinc was removed from the enzyme by o-phenanthroline. This cysteine residue, which could serve as a putative ligand to the active-site zinc atom, was identified as Cys 37 in RPLC. The EPR data suggested a distance of < or 10 A between Cys 37 and Cys 203. Although Cys 283 and Cys 295 were buried within the protein core and were not accessible for chemical modification, the two residues were oxidized to cystine when TBADH was heated at 75 degrees C, forming a disulfide bridge that was not present in the native enzyme, without affecting either enzymatic activity or thermal stability. The status of these cysteine residues was verified by site directed mutagenesis.     

Competence of Genetic Transformation correlated with the Occurrence of Fimbriae in Three Bacterial Species

THE involvement of bacterial fimbriae (pili) in some cases of phage infection and in bacterial conjugation has been known or presumed for some years¹. Studies in our laboratories show that fimbriae are also associated with genetic transformation in several bacterial species.     

Variable Incidence of Spiroplasma Infections in Natural Populations of Drosophila Species

Spiroplasma is widespread as a heritable bacterial symbiont in insects and some other invertebrates, in which it sometimes acts as a male-killer and causes female-biased sex ratios in hosts. Besides Wolbachia, it is the only heritable bacterium known from Drosophila, having been found in 16 of over 200 Drosophila species screened, based on samples of one or few individuals per species. To assess the extent to which Spiroplasma infection varies within and among species of Drosophila, intensive sampling consisting of 50–281 individuals per species was conducted for natural populations of 19 Drosophila species. Infection rates varied among species and among populations of the same species, and 12 of 19 species tested negative for all individuals. Spiroplasma infection never was fixed, and the highest infection rates were 60% in certain populations of D. hydei and 85% in certain populations of D. mojavensis. In infected species, infection rates were similar for males and females, indicating that these Spiroplasma infections do not confer a strong male-killing effect. These findings suggest that Spiroplasma has other effects on hosts that allow it to persist, and that environmental or host variation affects transmission or persistence leading to differences among populations in infection frequencies.     

Natural Occurrence of Pepino mosaic virus in Lycopersicon Species in Central and Southern Peru

Pepino mosaic virus (PepMV), a potexvirus first described in 1980 from pepino ( Solanum muricatum ) plants cultivated in Peru, was isolated from diseased tomato plants in the Netherlands in 1999, and is now the cause of an emerging tomato disease in Europe. In a survey of central and southern Peru, 65 wild and four cultivated populations of Lycopersicon , as well as six populations of other species of Solanaceae , were tested for the presence of PepMV and six other viruses. Of the Lycopersicon population sampled, 23 (35.4%) reacted positively in double antibody sandwich (DAS)-enzyme-linked immunosorbent assay (ELISA) with antisera to PepMV. DAS-ELISA tests for PepMV of other solanaceous species were negative, except for one sample of pepino ( Solanum muricatum ). Mechanical inoculation of susceptible Lycopersicon esculentum cv. NE-1 plants with crude sap extracts of 20 of these samples confirmed that 15 of them (from the Departments of Apurimac, Arequipa and Moquegua) were infected with PepMV; these inoculated plants were also DAS-ELISA positive and, in most cases, developed symptoms. Thirteen of the infective extracts were obtained from plants of wild Lycopersicon species (three L. chilense , three L. chmielewskii , two L. parviflorum and five L. peruvianum ) and one each from the cultivated species L. esculentum and S. muricatum . The wild Lycopersicon species are newly reported natural hosts of PepMV. Tests for the other six viruses were negative, except that two samples contained Tomato mosaic virus . Thus, PepMV occurs in Lycopersicon species in central and southern Peru, even in isolated wild populations. These results indicate that the virus is not new to the region and has an efficient mechanism of natural transmission.