不同植茶年限茶树根际土壤细菌多样性及群落结构研究

运用传统培养法和高通量测序技术研究不同植茶年限(5年、10年、20年)茶树根际土壤细菌的多样性、结构和组成,并分析茶树土壤理化性质与细菌群落的相关性,为改善茶树的土壤和提高茶树产量提供参考。结果表明:两种方法均指出不同植茶年限下的根际细菌群落结构存在显著性差异,5年和10年茶树细菌多样性显著高于20年茶树细菌;培养法得出厚壁菌门(Firmicutes)和芽孢杆菌属(Bacillus)为优势门属,高通量测序技术得出酸杆菌门(Acidobacteria)、变形菌门(Proteobacteria)、拟杆菌门(Bacteroidetes)和Candidatus_Udaeobacter属为优势门属;总氮(TN)、总钾(TK)、总磷(TP)、pH是影响茶树细菌群落的关键理化因子;随着植茶年限增加,要采取措施防止土壤酸化,适当增施氮肥和磷肥。     

Are young trees suitable for climate-growth analysis? A trial with Pinus nigra in the central Apennines treeline

In the context of ecological research, tree-ring analysis often deals with short time series (< 30 years). Their crossdating and averaging can be difficult but crucial to use such data for ecological modelling, multivariate statistics, and climate-growth analysis. Several studies were conducted in the Central Apennines (Italy) on recent encroachment of European black pine (Pinus nigra J.F. Arnold) on treeless areas above the current forestline. Growth of young trees is mainly controlled by endogenous or microclimatic factors making usual dendrochronology methods less applicable and crossdating very difficult or even impossible. The potential ecological information deriving from tree-ring growth in short series is therefore limited by this methodological bias. The aim of this study is to test suitable methods for optimizing the use of short ring series for further analytical use. A dataset of 734 tree-ring series of young European black pines (mean cambial age 15 years) growing at high altitude in 8 sites was used in this analysis. At each site tree-ring series were divided in two groups based on inter-series correlation: the crossdated or selected series (SEL), and non-crossdated or rejected ones (REJ). The following dendrochronological parameters were calculated for SEL and REJ series: mean tree-ring width, mean sensitivity, Gini coefficient, first order autocorrelation, inter-series correlation, and Gleichläufigkeit (GLK). Two methods of pointer years analysis were tested in order to detect years with synchronous growth: i) Normalization in a moving Window (NW) and ii) the RElative growth change method (RE). The two methods were applied to the raw series varying the standard thresholds, in order to detect synchronous growth-years in SEL and REJ group. A sensitivity analysis was included to assess how the threshold choice in the analysis could affect the results obtained. The term “common” was used to indicate years with similar tree growth response. Differences in the detected number of common years within SEL and REJ were obtained using different time windows with the RE and NW methods. The 47 % of all series were classified as SEL, showing more common years than the REJ series. However, a similar result occurred considering all the series together without SEL/REJ discrimination. In general, a significant occurrence of common years could be a tool to select series to be averaged for a site mean chronology. These are preliminary but encouraging results contributing to a more efficient use of the ecological information provided by short time series from young trees.     

Phylogeography and niche modelling of the relict plant Amborella trichopoda (Amborellaceae) reveal multiple Pleistocene refugia in New Caledonia

Amborella trichopoda Baill. (Amborellaceae, Amborellales), the sole living member of the sister group to all other extant angiosperms, is endemic to New Caledonia. We addressed the intraspecific phylogeography of Amborella by investigating whether its present population genetic structure could be related to its current and past habitats. We found moderate range‐wide genetic diversity based on nuclear microsatellite data and detected four well‐differentiated, geographically distinct genetic groups using Bayesian clustering analyses. We modelled the ecological niche of Amborella based on the current climatic and environmental conditions. The predictive ability of the model was very good throughout the Central East mainland zone, but Amborella was predicted in the northern part of the island where this plant has not been reported. Furthermore, no significant barrier was detected based on habitat suitability that could explain the genetic differentiation across the area. Conversely, we found that the main genetic clusters could be related to the distribution of the suitable habitat at the last glacial maximum (LGM, c. 21 000 years BP), when Amborella experienced a dramatic 96.5% reduction in suitable area. At least two lineages survived in distinct putative refugia located in the Massif des Lèvres and in the vicinity of Mount Aoupinié. Our findings finally confirmed the importance of LGM rainforest refugia in shaping the current intra‐ and interspecific diversity in New Caledonian plants and revealed the possibility of an as yet unreported refugium. The combination of niche modelling and population genetics thereby offered novel insight into the biogeographical history of an emblematic taxon.     

Montane refugia predict population genetic structure in the Large‐blotched Ensatina salamander

Understanding the biotic consequences of Pleistocene range shifts and fragmentation remains a fundamental goal in historical biogeography and evolutionary biology. Here, we combine species distribution models (SDM) from the present and two late Quaternary time periods with multilocus genetic data (mitochondrial DNA and microsatellites) to evaluate the effect of climate‐induced habitat shifts on population genetic structure in the Large‐blotched Ensatina (Ensatina eschscholtzii klauberi), a plethodontid salamander endemic to middle and high‐elevation conifer forest in the Transverse and Peninsular Ranges of southern California and northern Baja California. A composite SDM representing the range through time predicts two disjunct refugia, one in southern California encompassing the core of the species range and the other in the Sierra San Pedro Mártir of northern Baja California at the southern limit of the species range. Based on our spatial model, we would expect a pattern of high connectivity among populations within the northern refugium and, conversely, a pattern of isolation due to long‐term persistence of the Sierra San Pedro Mártir population. Our genetic results are consistent with these predictions based on the hypothetical refugia in that (i) historical measures of population connectivity among stable areas are correlated with gene flow estimates; and (ii) there is strong geographical structure between separate refugia. These results provide evidence for the role of recent climatic change in shaping patterns of population persistence and connectivity within the Transverse and Peninsular Ranges, an evolutionary hotspot.     

Molecular evolution of two duplicated CDPK genes CPK7 and CPK12 in grass species: a case study in wheat (Triticum aestivum L.)

Gene duplication contributes to the expansion of gene families and subsequent functional diversification. Calcium-dependent protein kinases (CDPKs) are members of an important calcium sensor family involved in abiotic and biotic stress signaling in plants. We report here the molecular evolution and expression analysis of a pair of duplicated CDPK genes CPK7 and CPK12 that arose in the common ancestor of grass species. With higher nonsynonymous/synonymous ratios (dN/dS, or ω), CPK12 genes appear to diverge more rapidly than CPK7s, suggesting relaxed selection constraints on CPK12s. Sliding window analysis revealed increased dN and ω values at N-terminal regions and the calcium-binding EF hand loops. Likelihood analyses using various models in PAML 4.0 showed purifying selection on both CPK7 and CPK12 lineages. In addition to the divergence in cis-element combinations on their promoters, functional divergence of CPK7 and CPK12 genes was also observed in wheat where TaCPK7 was found to respond to drought (PEG), salt (NaCl), cold, and hydrogen peroxide (H(2)O(2)) while TaCPK12 responded only to the treatment of ABA, a feature that may complement or expand TaCPK7-mediated stress signaling networks of wheat. The contrasting expression patterns of CPK7 and CPK12 genes under stress conditions were also observed in rice, suggesting conservative functional evolution of these genes. Since no positive selection was detected between the two lineages, the divergence of CPK7 and CPK12 genes should be ascribed to subfunctionalization, rather than neofunctionalization. Thus, our work demonstrates another case of evolutionary employment of duplicated genes via subfunctionalization for better adaptation.     

Evolutionary analysis of three gibberellin oxidase genes in rice, Arabidopsis, and soybean

GAs are plant hormones that play fundamental roles in plant growth and development. GA2ox, GA3ox, and GA20ox are three key enzymes in GA biosynthesis. These enzymes belong to the 2OG-Fe (II) oxygenase superfamily and are independently encoded by different gene families. To date, genome-wide comparative analyses of GA oxidases in plant species have not been thoroughly carried out. In the present work, 61 GA oxidase family genes from rice (Oryza sativa), Arabidopsis, and soybean (Glycine max) were identified and a full study of these genes including phylogenetic tree construction, gene structure, gene family expansion and analysis of functional motifs was performed. Based on phylogeny, most of the GA oxidases were divided into four subgroups that reflected functional classifications. Intron/intron average length of GA oxidase genes in rice analysis revealed that GA oxidase genes in rice experienced substantial evolutionary divergence. Segmental duplication events were mainly found in soybean genome. However, in rice and Arabidopsis, no single expansion pattern exhibited dominance, indicating that GA oxidase genes from these species might have been subjected to a more complex evolutionary mechanism. In addition, special functional motifs were discovered in GA20ox, GA3ox, and GA2ox, which suggested that different functional motifs are associated with differences in protein function. Taken together our results suggest that GA oxidase family genes have undergone divergent evolutionary routes, especially at the monocot-dicot split, with dynamic evolution occurring in Arabidopsis thaliana and soybean.     

The structure of a truncated phosphoribosylanthranilate isomerase suggests a unified model for evolution of the (βα)8 barrel fold

The (βα)₈ barrel is one of the most common protein folds, and enzymes with this architecture display a remarkable range of catalytic activities. Many of these functions are associated with ancient metabolic pathways, and phylogenetic reconstructions suggest that the (βα)₈ barrel was one of the very first protein folds to emerge. Consequently, there is considerable interest in understanding the evolutionary processes that gave rise to this fold. In particular, much attention has been focused on the plausibility of (βα)₈ barrel evolution from homodimers of half barrels. However, we previously isolated a three-quarter-barrel-sized fragment of a (βα)₈ barrel, termed truncated phosphoribosylanthranilate isomerase (trPRAI), that is soluble and almost as thermostable as full-length N-(5′-phosphoribosyl)anthranilate isomerase (PRAI). Here, we report the NMR-derived structure of trPRAI. The subdomain is monomeric, is well ordered and adopts a native-like structure in solution. Side chains from strands β₁ (Glu3 and Lys5), β₂ (Tyr25) and β₆ (Lys122) of trPRAI repack to shield the hydrophobic core from the solvent. This result demonstrates that three-quarter barrels were viable intermediates in the evolution of the (βα)₈ barrel fold. We propose a unified model for (βα)₈ barrel evolution that combines our data, previously published work and plausible scenarios for the emergence of (initially error-prone) genetic systems. In this model, the earliest proto-cells contained diverse pools of part-barrel subdomains. Combinatorial assembly of these subdomains gave rise to many distinct lineages of (βα)₈ barrel proteins, that is, our model excludes the possibility that there was a single (βα)₈ barrel from which all present examples are descended.     

Plasmodium falciparum: worldwide sequence diversity and evolution of the malaria vaccine candidate merozoite surface protein-2 (MSP-2)

We examined patterns and putative mechanisms of sequence diversification in the merozoite surface protein-2 (MSP-2) of Plasmodium falciparum, a major dimorphic malaria vaccine candidate antigen, by analyzing 448 msp-2 alleles from all continents. We describe several nucleotide replacements, insertion and deletion events, frameshift mutations, and proliferations of repeat units that generate the extraordinary diversity found in msp-2 alleles. We discuss the role of positive selection exerted by naturally acquired type- and variant-specific immunity in maintaining the observed levels of polymorphism and suggest that this is the most likely explanation for the significant excess of nonsynonymous nucleotide replacements found in dimorphic msp-2 domains. Hybrid sequences created by meiotic recombination between alleles of different dimorphic types were observed in few (3.1%) isolates, mostly from Africa. We found no evidence for an extremely ancient origin of allelic dimorphism at the msp-2 locus, predating P. falciparum speciation, in contrast with recent findings for other surface malarial antigens.     

SINEs, evolution and genome structure in the opossum

Short INterspersed Elements (SINEs) are non-autonomous retrotransposons, usually between 100 and 500 base pairs (bp) in length, which are ubiquitous components of eukaryotic genomes. Their activity, distribution, and evolution can be highly informative on genomic structure and evolutionary processes. To determine recent activity, we amplified more than one hundred SINE1 loci in a panel of 43 M. domestica individuals derived from five diverse geographic locations. The SINE1 family has expanded recently enough that many loci were polymorphic, and the SINE1 insertion-based genetic distances among populations reflected geographic distance. Genome-wide comparisons of SINE1 densities and GC content revealed that high SINE1 density is associated with high GC content in a few long and many short spans. Young SINE1s, whether fixed or polymorphic, showed an unbiased GC content preference for insertion, indicating that the GC preference accumulates over long time periods, possibly in periodic bursts. SINE1 evolution is thus broadly similar to human Alu evolution, although it has an independent origin. High GC content adjacent to SINE1s is strongly correlated with bias towards higher AT to GC substitutions and lower GC to AT substitutions. This is consistent with biased gene conversion, and also indicates that like chickens, but unlike eutherian mammals, GC content heterogeneity (isochore structure) is reinforced by substitution processes in the M. domestica genome. Nevertheless, both high and low GC content regions are apparently headed towards lower GC content equilibria, possibly due to a relative shift to lower recombination rates in the recent Monodelphis ancestral lineage. Like eutherians, metatherian (marsupial) mammals have evolved high CpG substitution rates, but this is apparently a convergence in process rather than a shared ancestral state.