Genetic diversity of Couratari multiflora and Couratari guianensis (Lecythidaceae): consequences of two types of rarity in central Amazonia

We quantified the within-population genetic variation of Couratari multiflora and C. guianensis, two tree species found in terra firme forests of central Amazonia. Both species have some ecological features in common, but they differ in population abundance across their geographic ranges. While C. multiflora has been found only in low-density populations in all sites studied to date, C. guianensis is relatively common in some sites and very scarce in others. In a 400-ha plot, we found 41 and 29 adults of C. multiflora and C. guianensis, respectively. Twenty-two saplings of C. guianensis and 103 seedlings of C. multiflora were also examined. The mean expected heterozygosities (H_em) of seedlings and adults of C. multiflora were 0.431 and 0.436, and the mean fixation indices (F_m), 0.114 and 0.176, respectively. For C. guianensis, saplings and adults presented H_em equal to 0.425 and 0.429, and the F_m were 0.393 and 0.527, respectively. These low-density populations of two congeneric species did not differ in terms of genetic diversity, but rather they differed in terms of mean observed heterozygosity (H_om), and therefore F_m. The species with variable population density had lower H_om and greater F_m relative to the species that is always found in low-density.     

Glucose transport in a methylotrophic yeast Hansenula polymorpha

Glucose transport was studied in a methylotrophic yeast Hansenula polymorpha . Two kinetically different glucose transport systems were revealed in cells grown under different growth conditions. Glucose-repressed cells exhibited a low-affinity transport system ( K _m for glucose 1.75 mM) while glucose-derepressed and ethanol-grown cells had a high-affinity transport system ( K _m for glucose 0.05–0.06 mM). The high- and low-affinity transport systems differed in substrate specificity, sensitivity to pH, dinitrophenol and protonophore carbonyl cyanide- m -chlorophenyl-hydrazone. The kinetic rearrangement of the glucose transport system in response to altered growth conditions was dependent on de novo protein synthesis.     

Carbons from choline present in the phospholipids of Pseudomonas aeruginosa

The phospholipid composition of Pseudomonas aeruginosa grown in a mineral medium with choline as the carbon source was: phosphatidylethanolamine, 71.6±1.4%; phosphatidylglycerol, 11.8±0.4%; diphosphatidylglycerol, 0.8±0.4%; phosphatidic acid, 2.4±0.6%; lysophosphatidylethanolamine, 1.6±0.3%; phosphatidylcholine 7.9±0.3%; lysophosphatidylcholine, 3.9±0.7%. The molar ratio between the acidic and the neutral phospholipids was 0.18. Radiolabeling experiments with [methyl-¹⁴C]choline or [1,2-¹⁴C]choline carried out in cell suspension from bacteria that were grown in the presence of choline as the sole carbon source demonstrated that the carbons of the N-methyl groups of choline contributed to the synthesis of fatty acids while the carbons comprising the backbone of choline were used for the synthesis of glycerol.     

湘西地区猕猴桃溃疡病病原菌分离及其全基因组分析

通过了解湘西地区猕猴桃溃疡病致病菌分类地位和基因类型,初步探讨其致病的分子机理。采用纯培养法分离猕猴桃溃疡病菌;基于16S～23S rRNA基因内转录间隔序列进行病原菌的系统发育分析;通过基因组测序和生物信息学分析解析其致病的分子机理。从“米良1号”和“红阳”猕猴桃感病枝条中分离获得5株溃疡病菌,编号为L211、L212、L321、L322、L323;通过形态特征和16S～23S rRNA基因内转录间隔序列分析,鉴定5株细菌均为丁香假单胞菌猕猴桃致病变种(Pseudomonas syringae pv.actinidae,Psa)。以菌株L211为代表进行体外猕猴桃枝条接种实验表明能引起典型溃疡病症状。通过菌株L211的全基因组测序和生物信息学分析,获得5 741条基因数目,长5 412 072 bp;基因功能注释发现菌株L211携带121种毒力因子、71个植物互作因子和77个耐药基因;同时,基因组单核苷酸多态性分析发现病原菌L211为基因Ⅲ型Psa。引起湘西地区猕猴桃溃疡病的病原菌是丁香假单胞菌猕猴桃致病变种基因Ⅲ型,与国内外报道的引起猕猴桃溃疡病大流行的致病菌一致。猕猴桃溃疡病发病...     

Alnus rubra nodulation capacity of soil under five species from harvested forest sites in coastal British Columbia

Nodulation of Alnus rubra seedlings after inoculation with soil from under A. rubra, Betula papyrifera. Rubus lacianutus, R. spectabilis, and R.ursinus on 2 recently harvested sites was compared. Nodulation capacity was low compared to other published reports, ranging from 0 to 18.9 infective units cm^-3 of soil and was significantly affected by the site and plant species. Nodulation capacity of soil under alder was significantly higher than under all other species except R. spectabilis, regardless of site. The lowest nodulation capacity was found in soil under B. papyrifera.Joint appointment with Dept. of Soil Science, Faculty of Agricultural Sciences     

Use of a novel plasmid to monitor the fate of a genetically engineered Pseudomonas putida strain

Plasmid pSI30 was constructed to increase the sensitivity of detection of a genetically engineered micro-organism (GEM) and its recombinant DNA in environmental samples. This broad host-range, mobilizable plasmid contained chlorocatechol (clc) degradative genes, antibiotic resistance genes (ampicillin and kanamycin) and a fragment of eukaryotic DNA. The clc genes encode enzymes that convert 3-chlorocatechol to maleylacetic acid permitting the host, Pseudomonas putida RC-4, to grow on 3-chlorobenzoate. This catabolic phenotype was exploited using enrichment procedures to detect RC-4(pSI30) cells, free-living in the water column or when irreversibly bound to surfaces. The eukaryotic DNA sequence provided a unique target allowing positive identification by DNA:DNA hybridization. Using the eukaryotic DNA sequence as a probe, no transfer of the plasmid to indigenous bacteria was detected. Persistence of RC-4(pSI30) and its ability to multiply upon addition of 3-chlorobenzoate were demonstrated 78 days after its addition to natural freshwater. In flow-through microcosms RC-4(pSI30), undetectable as free-living cells, was found by enrichment as irreversibly bound sessile forms. These experiments revealed the stability of pSI30 and its utility in a 'combination' detection system for tracking the survival of a GEM and its DNA in environmental samples.     

Fitness Is Strongly Influenced by Rare Mutations of Large Effect in a Microbial Mutation Accumulation Experiment

Our understanding of the evolutionary consequences of mutation relies heavily on estimates of the rate and fitness effect of spontaneous mutations generated by mutation accumulation (MA) experiments. We performed a classic MA experiment in which frequent sampling of MA lines was combined with whole genome resequencing to develop a high-resolution picture of the effect of spontaneous mutations in a hypermutator (ΔmutS) strain of the bacterium Pseudomonas aeruginosa. After ∼644 generations of mutation accumulation, MA lines had accumulated an average of 118 mutations, and we found that average fitness across all lines decayed linearly over time. Detailed analyses of the dynamics of fitness change in individual lines revealed that a large fraction of the total decay in fitness (42.3%) was attributable to the fixation of rare, highly deleterious mutations (comprising only 0.5% of fixed mutations). Furthermore, we found that at least 0.64% of mutations were beneficial and probably fixed due to positive selection. The majority of mutations that fixed (82.4%) were base substitutions and we failed to find any signatures of selection on nonsynonymous or intergenic mutations. Short indels made up a much smaller fraction of the mutations that were fixed (17.4%), but we found evidence of strong selection against indels that caused frameshift mutations in coding regions. These results help to quantify the amount of natural selection present in microbial MA experiments and demonstrate that changes in fitness are strongly influenced by rare mutations of large effect.     

Aggregation properties of cold-active lipase produced by a psychrotolerant strain of Pseudomonas palleroniana (GBPI_508)

Abstract

The present study aims to exploit microbial potential from colder region to produce lipase enzyme stable at low temperatures. A newly isolated bacterium GBPI_508 from Himalayan environment, was investigated for the production of cold-active lipase emphasizing on its aggregation properties. Plate based assays followed by quantitative production of enzyme was estimated under different culture conditions. Further characterization of partially purified enzyme was done for molecular weight determination and activity and stability under varying conditions of pH, temperature, and in presence of organic solvents, inhibitors, and metal ions. The psychrotolerant bacterium was identified as Pseudomonas palleroniana following 16S rRNA gene sequencing. Maximum lipase production by GBPI_508 was recorded in 7?days at 25?°C utilizing yeast extract as nitrogen source and olive oil as substrate in the lipase production medium. Triton X-100 (1%) in the medium as emulsifier significantly enhanced the lipase production. Lipase produced by bacterium showed aggregation which was confirmed by dynamic light scattering and native PAGE. SDS-PAGE followed by zymogram analysis of partially purified enzyme showed two active bands of ～50?kDa and ～54?kDa. Optimum activity of partially purified enzymatic preparation was recorded at 40?°C while the activity remained nearly consistent from pH 7.0 to 12.0, whereas, maximum stability was recorded at pH values 7.0 and 11.0 at 25?°C. Interestingly, lipase in the partially purified fraction retained 60% enzyme activity at 10?°C. Medium chain pNP ester (C10) was the most preferred substrate for the lipase of GBPI_508. The lipase possessed >50% residual activity when incubated with different organic solvents (25% v/v) except toluene and dichloromethane which inhibited the activity below 50%. Partially purified enzyme was also stable in the presence of metal ions and inhibitors. The study suggests applicability of GBPI_508 lipase in low temperature conditions such as cold-active detergent formulations and cold bioremediation.