FLUXNET and modelling the global carbon cycle

Measurements of the net CO₂ flux between terrestrial ecosystems and the atmosphere using the eddy covariance technique have the potential to underpin our interpretation of regional CO₂ source–sink patterns, CO₂ flux responses to forcings, and predictions of the future terrestrial C balance. Information contained in FLUXNET eddy covariance data has multiple uses for the development and application of global carbon models, including evaluation/validation, calibration, process parameterization, and data assimilation. This paper reviews examples of these uses, compares global estimates of the dynamics of the global carbon cycle, and suggests ways of improving the utility of such data for global carbon modelling. Net ecosystem exchange of CO₂ (NEE) predicted by different terrestrial biosphere models compares favourably with FLUXNET observations at diurnal and seasonal timescales. However, complete model validation, particularly over the full annual cycle, requires information on the balance between assimilation and decomposition processes, information not readily available for most FLUXNET sites. Site history, when known, can greatly help constrain the model‐data comparison. Flux measurements made over four vegetation types were used to calibrate the land‐surface scheme of the Goddard Institute for Space Studies global climate model, significantly improving simulated climate and demonstrating the utility of diurnal FLUXNET data for climate modelling. Land‐surface temperatures in many regions cool due to higher canopy conductances and latent heat fluxes, and the spatial distribution of CO₂ uptake provides a significant additional constraint on the realism of simulated surface fluxes. FLUXNET data are used to calibrate a global production efficiency model (PEM). This model is forced by satellite‐measured absorbed radiation and suggests that global net primary production (NPP) increased 6.2% over 1982–1999. Good agreement is found between global trends in NPP estimated by the PEM and a dynamic global vegetation model (DGVM), and between the DGVM and estimates of global NEE derived from a global inversion of atmospheric CO₂ measurements. Combining the PEM, DGVM, and inversion results suggests that CO₂ fertilization is playing a major role in current increases in NPP, with lesser impacts from increasing N deposition and growing season length. Both the PEM and the inversion identify the Amazon basin as a key region for the current net terrestrial CO₂ uptake (i.e. 33% of global NEE), as well as its interannual variability. The inversion's global NEE estimate of −1.2 Pg [C] yr⁻¹ for 1982–1995 is compatible with the PEM‐ and DGVM‐predicted trends in NPP. There is, thus, a convergence in understanding derived from process‐based models, remote‐sensing‐based observations, and inversion of atmospheric data. Future advances in field measurement techniques, including eddy covariance (particularly concerning the problem of night‐time fluxes in dense canopies and of advection or flow distortion over complex terrain), will result in improved constraints on land‐atmosphere CO₂ fluxes and the rigorous attribution of mechanisms to the current terrestrial net CO₂ uptake and its spatial and temporal heterogeneity. Global ecosystem models play a fundamental role in linking information derived from FLUXNET measurements to atmospheric CO₂ variability. A number of recommendations concerning FLUXNET data are made, including a request for more comprehensive site data (particularly historical information), more measurements in undisturbed ecosystems, and the systematic provision of error estimates. The greatest value of current FLUXNET data for global carbon cycle modelling is in evaluating process representations, rather than in providing an unbiased estimate of net CO₂ exchange.     

Bootstrapping phylogenies inferred from rearrangement data

ABSTRACT: Large-scale sequencing of genomes has enabled the inference of phylogenies based on the evolution of genomic architecture, under such events as rearrangements, duplications, and losses. Many evolutionary models and associated algorithms have been designed over the last few years and have found use in comparative genomics and phylogenetic inference. However, the assessment of phylogenies built from such data has not been properly addressed to date. The standard method used in sequence-based phylogenetic inference is the bootstrap, but it relies on a large number of homologous characters that can be resampled; yet in the case of rearrangements, the entire genome is a single character. Alternatives such as the jackknife suffer from the same problem, while likelihood tests cannot be applied in the absence of well established probabilistic models. We present a new approach to the assessment of distance-based phylogenetic inference from whole-genome data; our approach combines features of the jackknife and the bootstrap and remains nonparametric. For each feature of our method, we give an equivalent feature in the sequence-based framework; we also present the results of extensive experimental testing, in both sequence-based and genome-based frameworks. Through the feature-by-feature comparison and the experimental results, we show that our bootstrapping approach is on par with the classic phylogenetic bootstrap used in sequence-based reconstruction, and we establish the clear superiority of the classic bootstrap for sequence data and of our corresponding new approach for rearrangement data over proposed variants. Finally, we test our approach on a small dataset of mammalian genomes, verifying that the support values match current thinking about the respective branches. Our method is the first to provide a standard of assessment to match that of the classic phylogenetic bootstrap for aligned sequences. Its support values follow a similar scale and its receiver-operating characteristics are nearly identical, indicating that it provides similar levels of sensitivity and specificity. Thus our assessment method makes it possible to conduct phylogenetic analyses on whole genomes with the same degree of confidence as for analyses on aligned sequences. Extensions to search-based inference methods such as maximum parsimony and maximum likelihood are possible, but remain to be thoroughly tested.     

Leaf Stripe and Stem Rot Caused by Burkholderia gladioli,a New Maize Disease in Mexico

A disease in maize plants, not previously observed, appeared in 2003–2004 in Cosoleacaque, Tlalixcoyan and Paso de Ovejas counties, in the state of Veracruz, Mexico. Initial symptoms on leaves were small white‐yellow watery spots, which coalesced into dry necrotic stripes 0.3 wide and up to 8 cm long. Reddening sometimes developed on these leaves. Stems developed a rot in the crown. The flag leaf became rot and necrotic at the base, rolled inwards and dried out. Necrosis developed at the base of the corn ears and their growth was inhibited. These symptoms were initially observed in Asgrow‐7573 commercial maize plantings. A bacterium characterized by white colonies, gram negative, aerobic, rod‐shape, opaque, round colonies with entire margins on casaaminoacid peptone and glucose media was consistently isolated from diseased maize plants. On King’s Medium B, the isolates produced yellow, non‐mucoid colonies, with the majority of the strains secreting a diffusible yellow pigment into the media. The bacterium identity was confirmed by PCR amplification and sequencing of 16S and 23S genes rDNA fragments. The bacterium was identified as Burkholderia gladioli. Its pathogenicity on maize plants in Mexico is a new record.     

Genetic polymorphisms of CYP2C8, CYP2C9 and CYP2C19 in Ecuadorian Mestizo and Spaniard populations: a comparative study

This study was designed to investigate the potential differences between Spaniards and Ecuadorian Mestizo people regarding CYP2C8, CYP2C9, and CYP2C19 genetic polymorphisms. DNA from 282 Spaniard and 297 Ecuadorian subjects were analyzed by either a previously reported pyrosequencing method (CY2C8*3, CYP2C9*2, CYP2C9*3, CYP2C19*2 and CYP2C19*3) or a nested PCR technique (CYP2C19*17). Whereas CYP2C19*17 allele distribution was higher in Ecuadorians than in Spaniards (P < 0.001) and the frequency of CYP2C19*3 was similar in these two populations (P > 0.05), the other allelic variants were detected at significantly lower frequencies in Ecuadorians than in Spaniards (P < 0.05). According to the diplotype distributions, the prevalence of the presumed CYP2C9 and CYP2C8 extensive metabolizers was higher in Ecuadorians than in Spaniards (P < 0.05). Individuals genotyped CYP2C19*1/*17 and *17/*17 who were considered as ultrarapid metabolizers were overrepresented in Ecuadorians in relation to Spaniards (P < 0.001). By contrast, among Ecuadorians no poor metabolizers (PMs) of either CYP2C8 or CYP2C9 were found and only two individuals were CYP2C19 PMs. These data are compatible with a higher CYP2C8, CYP2C9, and CYP2C19 activity in Mestizo Ecuadorians as opposed to Spaniards, which could imply differences in dosage requirements for drugs metabolized by these cytochromes and should also be considered in allele-disease association studies.     

Patterns of animal–enrichment interaction in captive brown bears

We studied the behavioral responses of three brown bears (Ursus arctos) to different types of enrichment devices to assess the predominant pattern of animal–enrichment interaction (PAI) to each type of enrichment. We assessed the bears' responses to feeding, sensory, and occupational enrichments over nine sessions. Using Pearson's correlation (r) and the coefficient of variation (CV)—we describe four models of PAIs: habituation, increasing, continuous, and fluctuating. The habituation model (r < 0 and p < 0.05; CV (%) > 0) consists of a loss of interest in the device over time and it occurred with the occupational device. The increasing model (r > 0 and p < 0.05; CV (%) > 0) consists of a sustained interest in the device over time and it was not observed for any device of this study. The continuous model (0 > r > 0 and p > 0.05; CV (%) < 100) consists of a consistent and unchanging interaction over time and it occurred with the feeding enrichments used in this study. The fluctuating PAI (0 > r > 0 and p > 0.05; CV (%) ≥ 100) consists of wide oscillations in the degree of interaction over time and we observed this pattern with sensory devices. Review of previous literature supports these classes of PAI, and suggests similar relationships between PAIs and the type of enrichment as we observed in this study.     

Seed reserve translocation and early seedling growth of eight tree species in a tropical deciduous forest in Mexico

Seed reserves play an essential role during germination and seedling establishment and are particularly important for species that grow in seasonal ecosystems with a short growing season. In this study, we examined (a) how and when the seedlings change their dependence from seed resources to external resources, (b) the lipid, nitrogen, and non-structural carbohydrate reserve translocation from seeds to seedlings over time, and (c) whether reserve translocation may be correlated to cotyledon and leaf lifespan of seedlings for eight tree species in a tropical deciduous forest in north-western Mexico. Our results showed that the cotyledon lifespan was not related to the cotyledon type (photosynthetic or reserve) and that the cotyledon biomass did not decrease significantly until germination. In six of the eight studied species, biomass allocation to the leaves was favored; lipids were the first reserve exhausted before the first leaves were totally expanded in seven of the eight study species. Species with the highest N concentration had expanded leaves and lost their cotyledons faster than species with a low N concentration. Our results suggest that tropical deciduous forest species employ different strategies to survive the dry season and re-sprout in the next growing season mediated by seed reserve concentrations, translocation patterns and subsequent biomass allocation.     

Estudio Fenológico de Cactíceas en el Enclave Seco de la Tatacoa,Colombia1

A one‐year phenological study of three columnar cacti, Stenocereus griseus (Haw.) Britton & Rose, Pilosocereus sp., Cereus hexagonus (L.) Mill., and a decumbent cactus Monvillea cf. smithiana (Britton & Rose) Backeberg., was carried out in the Andean arid region of La Tatacoa, Colombia. Pollinators and/or dispersers of the cacti species also were studied monthly, and fecal samples were collected for the identification of pollen and seeds. The flowering of all species was prolonged and showed bimodal, multimodal, or irregular patterns. Fruiting in all species also was prolonged and followed flowering with a lag of less than two months. Although there were no simple correlations between rainfall and flowering or fruiting, flower production during the dry season was higher for 5. griseus, while Pilosocereus sp. and C. hexagonus showed higher flower production during the wet season. Fruit production was also seasonal, with higher production during the wet season for 5. griseus and C. hexagonus. The patterns of flowering and fruiting in M. cf. smithiana showed no relationships with dry and wet seasons. The bats Glossophaga longirostris, Carollia perspicillata, Sturnira lilium, the birds Melanerpes rubricapillus (Picidae) and Mimus gilvus (Mimidae), and moths of the family Sphingidae, were identified as pollinators and/or fruit consumers of these cacti species.     

Complete amino acid sequence of the Aspergillus cytotoxin mitogillin

The complete amino acid sequence of the cytotoxin mitogillin has been determined by sequencing the intact chain and peptide fragments produced by cleavage at methionyl, arginyl, lysyl, and tryptophanyl residues and at one aspartic acid-proline bond. The protein consists of 149 amino acid residues with alanine at the NH2 terminus and histidine at the COOH terminus. The calculated Mr of the native mitogillin was 16 867. The native molecule presents two disulfide bridges, one between cysteine residues at positions 5 and 147 and another one between cysteine residues at positions 75 and 131. The amino acid sequence of mitogillin shows 86% homology with another cytotoxic protein called alpha-sarcin.