Contrasting leaf and ‘ecosystem’ CO2 and H2O exchange in Avena fatua monoculture: Growth at ambient and elevated CO2

Elevated CO₂ (ambient + 35 Pa) increased shoot dry mass production in Avena fatua by 68% at maturity. This increase in shoot biomass was paralleled by an 81% increase in average net CO₂ uptake (A) per unit of leaf area and a 65% increase in average A at the ecosystem level per unit of ground area. Elevated CO₂ also increased ecosystem A per unit of biomass. However, the products of total leaf area and light-saturated leaf A divided by the ground surface area over time appeared to lie on a single response curve for both CO₂ treatments. The approximate slope of the response suggests that the integrated light saturated capacity for leaf photosynthesis is 10-fold greater than the ecosystem rate. Ecosystem respiration (night) per unit of ground area, which includes soil and plant respiration, ranged from-20 (at day 19) to-18 (at day 40) mol m^-2 s^-1 for both elevated and ambient CO₂ Avena. Ecosystem below-ground respiration at the time of seedling emergence was -10 mol m^-2 s^-1, while that occuring after shoot removal at the termination of the experiment ranged from -5 to-6 mol m^-2 s^-1. Hence, no significant differences between elevated and ambient CO₂ treatments were found in any respiration measure on a ground area basis, though ecosystem respiration on a shoot biomass basis was clearly reduced by elevated CO₂. Significant differences existed between leaf and ecosystem water flux. In general, leaf transpiration (E) decreased over the course of the experiment, possibly in response to leaf aging, while ecosystem rates of evapotranspiration (ET) remained constant, probably because falling leaf rates were offset by an increasing total leaf biomass. Transpiration was lower in plants grown at elevated CO₂, though variation was high because of variability in leaf age and ambient light conditions and differences were not significant. In contrast, ecosystem evapotranspiration (ET) was significantly decreased by elevated CO₂ on 5 out of 8 measurement dates. Photosynthetic water use efficiencies (A/E at the leaf level, A/ET at the ecosystem level) were increased by elevated CO₂. Increases were due to both increased A at leaf and ecosystem level and decreased leaf E and ecosystem ET.     

Biophysical stratification of the Amazon basin

In field measurement programmes, stratified sampling can optimize sampling efficiency, but stratification is often undertaken subjectively, and is frequently based on a priori classification schemes such as those used for vegetation maps. In order to avoid the problems associated with a priori subjective schemes, we explore here an objective procedure, Regression Tree Analysis (RTA). RTA has previously been used in local-scale studies, but here we apply it to a very large study domain, namely the entire humid tropical zone of South America. The aim of the study was to develop an optimal sampling design in preparation for the Large Scale Biosphere-Atmosphere Experiment in Amazonia (LBA). Co-registered spatially continuous fields of rainfall, temperature, photosynthetically active radiation (PAR), the normalized difference index (NDVI), an index of surface moisture, and other independent variables were used to predict three dependent variables, annual net radiation (Rn), latent heat (LE) and net primary production (NPP). Rather than simply dividing the study area based on differing levels of the three dependent variables, empirical models were developed using RTA to indicate how the relationships between these and possible forcing variables vary across the study area. For each variable long-term seasonal indices such as annual average, monthly minimum and amplitude were used to exclude effects of temporal phase differences between the hemispheres. The resulting hierarchical models revealed variations in the interdependence of the forcing variables throughout the study area and therefore provided a basis for a stratified sampling and identifying the most important variables to be collected in LBA for the Amazon basin as a whole as well as optimizing the sampling scheme for scaling up findings from the field scale to larger areas.     

Globally significant changes in biological processes of the Amazon Basin: results of the Large-scale Biosphere–Atmosphere Experiment

The Amazon River, its huge basin, and the changes in biological processes that are rapidly occurring in this region are unquestionably of global significance. Hence, Global Change Biology is delighted to host a special thematic issue devoted to the Large‐scale Biosphere–Atmosphere Experiment in Amazônia (LBA), which is a multinational, interdisciplinary research program led by Brazil. The goal of LBA is no less modest than its subject: to understand how Amazônia functions as a regional entity in the Earth system and how these functions are changing as a result of ongoing changes in land use. This compilation of 26 papers resulting from LBA‐related research covers a broad range of topics: forest stocks of carbon (C) and nitrogen (N); fluxes of greenhouse gases and volatile organic compounds from vegetation, soils and wetlands; mapping and modeling land‐use change, fire risk, and soil properties; measuring changes caused by logging, pasturing and cultivating; and new research approaches in meteorology to estimate nocturnal fluxes of C from forests and pastures. Some important new synthesis can be derived from these and other studies. The aboveground biomass of intact Amazonian forests appears to be a sink for atmospheric carbon dioxide (CO₂), while the wetlands and soils are a net source of atmospheric methane (CH₄) and nitrous oxide (N₂O), respectively. Land‐use change has, so far, had only a minor effect on basin‐wide emissions of CH₄ and N₂O, but the net effect of deforestation and reforestation appears to be a significant net release of CO₂ to the atmosphere. The sum of the 100‐year global warming potentials (GWP) of these annual sources and sinks of CH₄, N₂O, and CO₂ indicate that the Amazonian forest–river system currently may be nearly balanced in terms of the net GWP of these biogenic atmospheric gases. Of course, large uncertainties remain for these estimates, but the papers published here demonstrate tremendous progress, and also large remaining hurdles, in narrowing these uncertainties in our understanding of how Amazônia functions as a regional entity in the Earth system.     

Bacterial transposons are co-transferred with T-DNA to rice chromosomes during Agrobacterium-mediated transformation

Agrobacterium tumefaciens is widely utilized for delivering a foreign gene into a plant's genome. We found the bacterial transposon Tn5393 in transgenic rice plants. Analysis of the flanking sequences of the transferred-DNA (T-DNA) identified that a portion of the Tn5393 sequence was present immediately next to the end of the T-DNA. Because this transposon was present in A. tumefaciens strain LBA4404, but not in EHA105 and GV3101, our findings indicated that Tn5393 was transferred from LBA4404 into the rice genome during the transformation process. We also noted that another bacterial transposon, Tn5563, is present in transgenic plants. Analyses of 331 transgenic lines revealed that 26.0% carried Tn5393 and 2.1% contained Tn5563. In most of the lines, an intact transposon was integrated into the T-DNA and transferred to the rice chromosome. More than one copy of T-DNA was introduced into the plants, often at a single locus. This resulted in T-DNA repeats of normal and transposon-carrying TDNA that generated deletions of a portion of the T-DNA, joining the T-DNA end to the bacterial transposon. Based on these data, we suggest that one should carefully select the appropriate Agrobacterium strain to avoid undesirable transformation of such sequences.     

Probing recalcitrant problems in polyclad evolution and systematics with novel mitochondrial genome resources

For their apparent morphological simplicity, the Platyhelminthes or “flatworms” are a diverse clade found in a broad range of habitats. Their body plans have however made them difficult to robustly classify. Molecular evidence is only beginning to uncover the true evolutionary history of this clade. Here we present nine novel mitochondrial genomes from the still undersampled orders Polycladida and Rhabdocoela, assembled from short Illumina reads. In particular we present for the first time in the literature the mitochondrial sequence of a Rhabdocoel, Bothromesostoma personatum (Typhloplanidae, Mesostominae). The novel mitochondrial genomes examined generally contained the 36 genes expected in the Platyhelminthes, with all possessing 12 of the 13 protein-coding genes normally found in metazoan mitochondrial genomes (ATP8 being absent from all Platyhelminth mtDNA sequenced to date), along with two ribosomal RNA genes. The majority presented possess 22 transfer RNA genes, and a single tRNA gene was absent from two of the nine assembled genomes. By comparison of mitochondrial gene order and phylogenetic analysis of the protein coding and ribosomal RNA genes contained within these sequences with those of previously sequenced species we are able to gain a firm molecular phylogeny for the inter-relationships within this clade.Our phylogenetic reconstructions, using both nucleotide and amino acid sequences under several models and both Bayesian and Maximum Likelihood methods, strongly support the monophyly of Polycladida, and the monophyly of Acotylea and Cotylea within that clade. They also allow us to speculate on the early emergence of Macrostomida, the monophyly of a “Turbellarian-like” clade, the placement of Rhabditophora, and that of Platyhelminthes relative to the Lophotrochozoa (=Spiralia). The data presented here therefore represent a significant advance in our understanding of platyhelminth phylogeny, and will form the basis of a range of future research in the still-disputed classifications within this taxon.     

动物系统发育和大规模测序:进展和问题

Phylogenomics, the inference of phylogenetic trees using genome-scale data, is becoming the rule for resolving difficult parts of the tree of life. Its promise resides in the large amount of information available, which should eliminate stochastic error. However, systematic error, which is due to limitations of reconstruction methods, is becoming more apparent. We will illustrate, using animal phylogeny as a case study, the three most efficient approaches to avoid the pitfalls of phylogenomics (1) using a dense taxon sampling, (2) using probabilistic methods with complex models of sequence evolution that more accurately detect multiple substitutions, and (3) removing the fastest evolving part of the data (e.g., species and positions). The analysis of a dataset of 55 animal species and 102 proteins (25712 amino acid positions) shows that standard site-homogeneous model inference is sensitive to long-branch attraction artifact, whereas the site-heterogeneous CAT model is less so. The latter model correctly locates three very fast evolving species, the appendicularian tunicate Oikopleura, the acoel Convoluta and the myxozoan Buddenbrockia. Overall, the resulting tree is in excellent agreement with the new animal phylogeny, confirming that "simple" organisms like platyhelminths and nematodes are not necessarily of basal emergence. This further emphasizes the importance of secondary simplification in animals, and for organismal evolution in general.     

Etr1-1 Gene Expression Alters Regeneration Patterns in Transgenic Lettuce Stimulating Root Formation

We have evaluated the transformation efficiency of two lettuce (Lactuca sativa L.) cultivars, LE126 and Seagreen, using Agrobacterium tumefaciens-mediated gene transfer. Six-day-old cotyledons were co-cultivated with Agrobacterium cultures carrying binary vectors with two different genetic constructs. The first construct contained the β-glucuronidase gene (GUS) under the control of the cauliflower mosaic virus 35S promoter (CaMV 35S), while the second construct contained the ethylene mutant receptor etr1-1, which confers ethylene insensitivity, under the control of a leaf senescence-specific promoter (sag12). Tissues co-cultivated with the GUS construct showed strong regeneration potential with over 90% of explants developing callus masses and 85% of the calli developing shoots. Histochemical GUS assays showed that 85.7% of the plants recovered were transgenic. Very different results were observed when cotyledon explants were co-cultivated with Agrobacteria carrying the etr1-1 gene. There was a dramatic effect on the regeneration properties of the cultured explants with root formation taking place directly from the cotyledon tissue in 34% of the explants and no callus or shoots observed initially. Eventually callus formed in 10% of cotyledons and some organogenic shoots were obtained (2.86%). These results indicate that the ethylene insensitivity conferred by the etr1-1 gene alters the normal pattern of regeneration in lettuce cotyledons, inhibiting the formation of shoots and stimulating root formation during regeneration.     

Binary vectors for efficient transformation of rice

We constructed binary vectors that were designed for transfer and expression of a gene into rice chromosomes. The binary vectors contained the hygromycin-resistance gene for selection of transformants and multiple-cloning sites within the transfer DNA. In addition, vectors were designed to express foreign genes using four kinds of promoters. We also report a procedure for efficient transformation of rice plants using scutellum-derived calli and theAgrobacterium strain LBA4404.     

The land–atmosphere water flux in the tropics

Tropical vegetation is a major source of global land surface evapotranspiration, and can thus play a major role in global hydrological cycles and global atmospheric circulation. Accurate prediction of tropical evapotranspiration is critical to our understanding of these processes under changing climate. We examined the controls on evapotranspiration in tropical vegetation at 21 pan-tropical eddy covariance sites, conducted a comprehensive and systematic evaluation of 13 evapotranspiration models at these sites, and assessed the ability to scale up model estimates of evapotranspiration for the test region of Amazonia. Net radiation was the strongest determinant of evapotranspiration (mean evaporative fraction was 0.72) and explained 87% of the variance in monthly evapotranspiration across the sites. Vapor pressure deficit was the strongest residual predictor (14%), followed by normalized difference vegetation index (9%), precipitation (6%) and wind speed (4%). The radiation-based evapotranspiration models performed best overall for three reasons: (1) the vegetation was largely decoupled from atmospheric turbulent transfer (calculated from Ω decoupling factor), especially at the wetter sites; (2) the resistance-based models were hindered by difficulty in consistently characterizing canopy (and stomatal) resistance in the highly diverse vegetation; (3) the temperature-based models inadequately captured the variability in tropical evapotranspiration. We evaluated the potential to predict regional evapotranspiration for one test region: Amazonia. We estimated an Amazonia-wide evapotranspiration of 1370 mm yr⁻¹, but this value is dependent on assumptions about energy balance closure for the tropical eddy covariance sites; a lower value (1096 mm yr⁻¹) is considered in discussion on the use of flux data to validate and interpolate models.