Tree shape, forest structure and diversity of drosophilid community: Comparison between boreal and temperate birch forests

Some models, based on the latitudinal variation in sun angle distribution, predict that trees at high latitudes have narrowly conical crowns and constitute simple-layered forests, whereas trees at low latitudes have shallowly dome-shaped and form more structurally complex multilayered forests. There is a hypothesis that structurally complex habitats can harbor potentially more species than simple ones. In this study, we examined latitudinal correlations between tree shape, forest structure and diversity in drosophilid communities, comparing boreal and cool-temperate forests. We selected secondary birch forests with a common canopy tree species, white birch (Betula platyphylla Sukatchev), as study sites. The crown shape of white birch tended to be spherical in the cool-temperate forest, but narrowly conical in the boreal forest. The foliage structure differed between the two forests. The cool-temperate forest was characterized by a clearly two-layered structure, whereas foliage in the boreal forest was less clearly stratified, being distributed somewhat continuously from the ground to the canopy at lower densities. The structural complexity expressed by foliage height diversity was greater in the cool-temperate forest than in the boreal forest. Various measures of drosophilid diversity were higher in the cool-temperate forest than in the boreal forest, probably resulting from the impoverishment of the canopy subcommunity in the boreal forest. Thus, a physical environmental factor (i.e. the angle of solar inclination) could be a potentially important factor in structuring latitudinal patterns of sylvan animal communities through changes in plant structure at the individual and community levels.     

AFLP-derived SCARs facilitate construction of a 1.1 Mb sequence-ready map of a region that spans the Vf locus in the apple genome

The availability of high-density anchored markers is a prerequisite for reliable construction of a deep coverage BAC contig, which leads to creation of a sequence-ready map in the target chromosomal region. Unfortunately, such markers are not available for most plant species, including woody perennial plants. Here, we report on an efficient approach to build a megabase-size sequence-ready map in the apple genome for the Vf region containing apple scab resistance gene(s) by targeting AFLP-derived SCAR markers to this specific genomic region. A total of 11 AFLP-derived SCAR markers, previously tagged to the Vf locus, along with three other Vf-linked SCAR markers have been used to screen two apple genome BAC libraries. A single BAC contig which spans the Vf region at a physical distance of approximately 1,100 kb has been constructed by assembling the recovered BAC clones, followed by closure of inter-contig gaps. The contig is 4 ×deep, and provides a minimal tiling path of 16 contiguous and overlapping BAC clones, thus generating a sequence-ready map. Within the Vf region, duplication events have occurred frequently, and the Vf locus is restricted to the ca. 290 kb region covered by a minimum of three overlapping BAC clones.     

Assessment of Pollution-Induced Microbial Community Tolerance to Heavy Metals in Soil Using Ammonia-Oxidizing Bacteria and Biolog Assay

This study attempted to investigate if the tolerance of soil bacterial communities in general, and autotrophic ammonia-oxidizing bacteria (AOB) in particular, evolved as a result of prolonged exposure to metals, and could be used as an indigenous bioindicator for soil metal pollution. A soil contaminated with copper, chromium, and arsenic (CCA) was mixed with an uncontaminated garden soil (GS3) to make five test soils with different metal concentrations. A modified potential ammonium oxidation assay was used to determine the metal tolerance of the AOB community. Tolerance to Cr, Cu, and As was tested at the beginning and after up to 13 months of incubation. Compared with the reference GS3 soil, the five CCA soils showed significantly higher tolerance to Cr no matter which form of Cr (Cr³⁺, CrO₄ ^2?, or Cr₂O₇ ^2?) was tested, and the Cr tolerance correlated with the total soil Cr concentration. However, the tolerance to Cu²⁺, As³⁺, and As⁵⁺ did not differ significantly between the GS3 soil and the five CCA soils. Community level physiological profiles using Biolog microtiter plates were also used to examine the chromate tolerance of the bacterial communities extracted after six months of exposure. Our results showed that the bacterial community tolerance was altered and increased as the soil Cr concentration was increased, indicating that the culturable microbial community and the AOB community responded in a similar manner.     

Crystal structure of a thermostable lipase from Bacillus stearothermophilus P1

We describe the first lipase structure from a thermophilic organism. It shares less than 20% amino acid sequence identity with other lipases for which there are crystal structures, and shows significant insertions compared with the typical alpha/beta hydrolase canonical fold. The structure contains a zinc-binding site which is unique among all lipases with known structures, and which may play a role in enhancing thermal stability. Zinc binding is mediated by two histidine and two aspartic acid residues. These residues are present in comparable positions in the sequences of certain lipases for which there is as yet no crystal structural information, such as those from Staphylococcal species and Arabidopsis thaliana. The structure of Bacillus stearothermophilus P1 lipase provides a template for other thermostable lipases, and offers insight into mechanisms used to enhance thermal stability which may be of commercial value in engineering lipases for industrial uses.     

FTIR Spectroscopic Study of Biogenic Mn-Oxide Formation by Pseudomonas putida GB-1

Biomineralization in heterogeneous aqueous systems results from a complex association between pre-existing surfaces, bacterial cells, extracellular biomacromolecules, and neoformed precipitates. Fourier transform infrared (FTIR) spectroscopy was used in several complementary sample introduction modes (attenuated total reflectance [ATR], diffuse reflectance [DRIFT], and transmission) to investigate the processes of cell adhesion, biofilm growth, and biological Mn-oxidation by Pseudomonas putida strain GB-1. Distinct differences in the adhesive properties of GB-1 were observed upon Mn oxidation. No adhesion to the ZnSe crystal surface was observed for planktonic GB-1 cells coated with biogenic MnO _x , whereas cell adhesion was extensive and a GB-1 biofilm was readily grown on ZnSe, CdTe, and Ge crystals prior to Mn-oxidation. IR peak intensity ratios reveal changes in biomolecular (carbohydrate, phosphate, and protein) composition during biologically catalyzed Mn-oxidation. In situ monitoring via ATR-FTIR of an active GB-1 biofilm and DRIFT data revealed an increase in extracellular protein (amide I and II) during Mn(II) oxidation, whereas transmission mode measurements suggest an overall increase in carbohydrate and phosphate moieties. The FTIR spectrum of biogenic Mn oxide comprises Mn-O stretching vibrations characteristic of various known Mn oxides (e.g., “acid” birnessite, romanechite, todorokite), but it is not identical to known synthetic solids, possibly because of solid-phase incorporation of biomolecular constituents. The results suggest that, when biogenic MnO _x accumulates on the surfaces of planktonic cells, adhesion of the bacteria to other negatively charged surfaces is hindered via blocking of surficial proteins.     

Pine species determine fungal microbiome composition in a common garden experiment

The factors shaping the composition of microbial communities in trees remain poorly understood. We evaluated whether the core and satellite fungal communities in five pine species (Pinus radiata, Pinus pinaster, Pinus sylvestris, Pinus nigra, and Pinus uncinata) were shaped by the host species identity. Because the trees had earlier been inoculated with a fungal pathogen (Fusarium circinatum), we also explored the possibilities to detect its presence and potential co-occurrence networks. We found interspecific variation in the fungal community composition and abundance among the different tree species and the existence of a core microbiome that was independent of the host species. The presence of F. circinatum was confirmed in some samples through qPCR but the pathogen did not co-occur with a specific fungal community. The results highlight the importance of host species as a determinant of microbiome assembly in common environments.     

宁夏云雾山典型草原灌丛化过程中植被和土壤演变特征

干旱半干旱区灌木、半灌木等木本植物的分布面积持续增加(灌丛化)显著改变了原有植被景观及生态过程,但缺乏对长期封育过程中灌木物种取代草本物种进而影响草地群落组成、结构和功能的研究。为揭示长期封育措施下典型草原灌丛化特征及地上/地下植物群落的响应规律,研究通过对宁夏云雾山典型草原同一封育草地不同时间(2010年、2016年、2021年)植物群落(物种重要值、丰富度、多样性和生物量)和土壤特性(土壤容重、土壤水分及储水量、养分、pH)的定点观测,探讨了长期封育过程中灌木物种矮脚锦鸡儿(Caragana brachypoda)驱动的植被和土壤特性变化。结果表明,(1)灌木矮脚锦鸡儿已经取代草本植物成为封育草地的优势种,群落中灌木生物量、总生物量以及盖度、高度显著增加,但对植物密度的影响较小;(2)灌丛化过程中草地群落Patrick丰富度指数、Simpson优势度指数和Shannon-Wiener多样性指数显著降低,而Pielou均匀度指数显著增加;(3)灌丛化引起土壤深层(60-100 cm)容重显著增大,土层储水量随土层深度的增加呈先减少后增加的趋势;(4)灌丛化使得土壤有机碳含量在浅层(0...     

喀斯特峰丛洼地不同退耕模式土壤微生物多样性

利用变性梯度凝胶电泳和Biolog_Eco生态培养平板技术,调查了喀斯特自然退耕(NT,撂荒)、人工种植经济林(CM,木豆-板栗)、免耕(PI,牧草-任豆)和传统耕作(MB,玉米-大豆)4种退耕模式下的土壤微生物遗传分类和土壤细菌代谢功能多样性.结果表明:退耕模式显著影响了土壤微生物群落结构和细菌代谢模式, 其中真菌群落更依赖于退耕模式,而细菌群落对季节变迁更敏感;短时期(6～7年)不同退耕模式下土壤中细菌遗传分类多样性没有显著性差异(P>0.05),经济林与牧草地土壤真菌遗传分类多样性显著高于撂荒和传统耕作地(P<0.05);免耕牧草地土壤细菌代谢功能多样性显著低于其他模式(P<0.05).因此,真菌遗传多样性和细菌代谢多样性较细菌遗传多样性对退耕模式响应更敏感;土壤细菌群落对季节的变化比真菌敏感;木豆 板栗经济林对维持土壤微生物遗传和细菌代谢功能多样性具有优势,是较好的退耕模式.