Tallo: A global tree allometry and crown architecture database

Data capturing multiple axes of tree size and shape, such as a tree's stem diameter, height and crown size, underpin a wide range of ecological research-from developing and testing theory on forest structure and dynamics, to estimating forest carbon stocks and their uncertainties, and integrating remote sensing imagery into forest monitoring programmes. However, these data can be surprisingly hard to come by, particularly for certain regions of the world and for specific taxonomic groups, posing a real barrier to progress in these fields. To overcome this challenge, we developed the Tallo database, a collection of 498,838 georeferenced and taxonomically standardized records of individual trees for which stem diameter, height and/or crown radius have been measured. These data were collected at 61,856 globally distributed sites, spanning all major forested and non-forested biomes. The majority of trees in the database are identified to species (88%), and collectively Tallo includes data for 5163 species distributed across 1453 genera and 187 plant families. The database is publicly archived under a CC-BY 4.0 licence and can be access from: https://doi.org/10.5281/zenodo.6637599. To demonstrate its value, here we present three case studies that highlight how the Tallo database can be used to address a range of theoretical and applied questions in ecology-from testing the predictions of metabolic scaling theory, to exploring the limits of tree allometric plasticity along environmental gradients and modelling global variation in maximum attainable tree height. In doing so, we provide a key resource for field ecologists, remote sensing researchers and the modelling community working together to better understand the role that trees play in regulating the terrestrial carbon cycle.

Slow rate of secondary forest carbon accumulation in the Guianas compared with the rest of the Neotropics

Secondary forests are a prominent component of tropical landscapes, and they constitute a major atmospheric carbon sink. Rates of carbon accumulation are usually inferred from chronosequence studies, but direct estimates of carbon accumulation based on long-term monitoring of stands are rarely reported. Recent compilations on secondary forest carbon accumulation in the Neotropics are heavily biased geographically as they do not include estimates from the Guiana Shield. We analysed the temporal trajectory of aboveground carbon accumulation and floristic composition at one 25-ha secondary forest site in French Guiana. The site was clear-cut in 1976, abandoned thereafter, and one large plot (6.25 ha) has been monitored continuously since. We used Bayesian modeling to assimilate inventory data and simulate the long-term carbon accumulation trajectory. Canopy change was monitored using two aerial lidar surveys conducted in 2009 and 2017. We compared the dynamics of this site with that of a surrounding old-growth forest. Finally, we compared our results with that from secondary forests in Costa Rica, which is one of the rare long-term monitoring programs reaching a duration comparable to our study. Twenty years after abandonment, aboveground carbon stock was 64.2 (95% credibility interval 46.4, 89.0) Mg C/ha, and this stock increased to 101.3 (78.7, 128.5) Mg C/ha 20 yr later. The time to accumulate one-half of the mean aboveground carbon stored in the nearby old-growth forest (185.6 [155.9, 200.2] Mg C/ha) was estimated at 35.0 [20.9, 55.9] yr. During the first 40 yr, the contribution of the long-lived pioneer species Xylopia nitida, Goupia glabra, and Laetia procera to the aboveground carbon stock increased continuously. Secondary forest mean-canopy height measured by lidar increased by 1.14 m in 8 yr, a canopy-height increase consistent with an aboveground carbon accumulation of 7.1 Mg C/ha (or 0.89 Mg C·ha^-1 ·yr^-1 ) during this period. Long-term AGC accumulation rate in Costa Rica was almost twice as fast as at our site in French Guiana. This may reflect higher fertility of Central American forest communities or a better adaptation of the forest tree community to intense and frequent disturbances. This finding may have important consequences for scaling-up carbon uptake estimates to continental scales.

Improving plant allometry by fusing forest models and remote sensing

Allometry determines how tree shape and function scale with each other, related through size. Allometric relationships help scale processes from the individual to the global scale and constitute a core component of vegetation models. Allometric relationships have been expected to emerge from optimisation theory, yet this does not suitably predict empirical data. Here we argue that the fusion of high-resolution data, such as those derived from airborne laser scanning, with individual-based forest modelling offers insight into how plant size contributes to large-scale biogeochemical processes. We review the challenges in allometric scaling, how they can be tackled by advances in data-model fusion, and how individual-based models can serve as data integrators for dynamic global vegetation models.

New formula and conversion factor to compute basic wood density of tree species using a global wood technology database

PREMISE OF THE STUDY

Basic wood density is an important ecological trait for woody plants. It is used to characterize species performance and fitness in community ecology and to compute tree and forest biomass in carbon cycle studies. While wood density has been historically measured at 12% moisture, it is convenient for ecological purposes to convert this measure to basic wood density, i.e., the ratio of dry mass over green volume. Basic wood density can then be used to compute tree dry biomass from living tree volume.

METHODS

Here, we derive a new exact formula to compute the basic wood density D_b from the density at moisture content w denoted D_w , the fiber saturation point S, and the volumetric shrinkage coefficient R. We estimated a new conversion factor using a global wood technology database where values to use this formula are available for 4022 trees collected in 64 countries (mostly tropical) and representing 872 species.

KEY RESULTS

We show that previous conversion factors used to convert densities at 12% moisture into basic wood densities are inconsistent. Based on theory and data, we found that basic wood density could be inferred from the density at 12% moisture using the following formula: D_b = 0.828D₁₂ . This value of 0.828 provides basic wood density estimates 4-5% smaller than values inferred from previous conversion factors.

CONCLUSIONS

This new conversion factor should be used to derive basic wood densities in global wood density databases. Its use would prevent overestimating global forest carbon stocks and allow predicting better tree species community dynamics from wood density.

Mechanisms of fluconazole resistance in Candida albicans isolates from Japanese AIDS patients

Four Candida albicans isolates, TIMM 3163, TIMM 3164, TIMM 3165 and TIMM 3166, with reduced fluconazole susceptibility were obtained from three AIDS patients in Japan, and the mechanisms of their drug resistance were studied. All isolates showed lower levels of intracellular accumulation of fluconazole than ATCC 10231, a susceptible control strain of C. albicans. Increased amounts of CDR1 and CDR2 mRNA encoding putative ATP binding cassette (ABC) transporters were associated with the azole resistance of all TIMM isolates, apart from TIMM 3164. In addition, increased Cdr1p levels were immunodetected in the cell membrane fractions of all the TIMM strains except for TIMM 3164. Gene amplification was not responsible for CDR1 overexpression and there were no significant differences in the mRNA levels of CDR3 or CDR4 (ABC transporters) in the azole-susceptible and -resistant cells. CaMDR1 (a major facilitator superfamily) gene expression was not observed in any of the resistant isolates or the control strain. These results suggest that energy-dependent drug efflux associated with increased expression of CDR1 and CDR2 is involved in the fluconazole resistance mechanisms in two of the four isolates, TIMM 3165 and TIMM 3166. TIMM 3164 demonstrated energy-dependent drug efflux without overexpression of CDR1-4 or CaMDR1, indicating that some other pump may be operating. Despite showing low levels of drug efflux and overexpression of CDR1 and CDR2, efflux in TIMM 3163 was not energy dependent, suggesting that the expressed Cdr1p non-functional Cdr1p and that other resistance mechanisms may operate in this strain.

Specific chromosome alterations in fluconazole-resistant mutants of Candida albicans

The exposure of Candida albicans to fluconazole resulted in the nondisjunction of two specific chromosomes in 17 drug-resistant mutants, each obtained by an independent mutational event. The chromosomal changes occurred at high frequencies and were related to the duration of the drug exposure. The loss of one homologue of chromosome 4 occurred after incubation on a fluconazole medium for 7 days. A second change, the gain of one copy of chromosome 3, was observed after exposure for 35 or 40 days. We found that the mRNA levels of ERG11, CDR1, CDR2, and MDR1, the candidate fluconazole resistance genes, remained either the same or were diminished. The lack of overexpression of putative drug pumps or the drug target indicated that some other mechanism(s) may be operating. The fluconazole resistance phenotype, electrophoretic karyotypes, and transcript levels of mutants were stable after growth for 112 generations in the absence of fluconazole. This is the first report to demonstrate that resistance to fluconazole can be dependent on chromosomal nondisjunction. Furthermore, we suggest that a low-level resistance to fluconazole arising during the early stages of clinical treatment may occur by this mechanism. These results support our earlier hypothesis that changes in C. albicans chromosome number is a common means to control a resource of potentially beneficial genes that are related to important cellular functions.

Drug pumping mechanisms in Candida albicans

Multiple drug resistance is becoming a major problem in the treatment of AIDS patients with oropharyngeal candidosis. Candida albicans strains isolated from candidosis patients who do not respond to fluconazole therapy often show azole drug resistance which usually correlates with the expression of C. albicans CDR1, CDR2 or BENr genes, encoding potential drug efflux pumps. The objective of this study was to develop a yeast secretory vesicle transport assay and use this system to study the pumping function of Cdr1 and Benr. The C. albicans CDR1 and BEN r genes were cloned separately into plasmid pVT101-U, to form plasmids pKY1011 and pKN5001 respectively. Plasmids pVT101-U, pKY1011 and pKN5001 were transformed into Saccharomyces cerevisiae SY1, a sec6-4 mutant with a temperature-sensitive mutation in the secretory pathway. SY1 cells transformed with pKY1011 or pKN5001, were more resistant to fluconazole (MICs in both cases 64 microg/ml) than SY1 cells (MIC 32 microg/ml). In addition, cells transformed with pKY1011 were more resistant to cycloheximide (MIC 16 microg/ml) than SY1 cells (MIC 2 microg/ml). Intact secretory vesicles were isolated from SY1 cells expressing Cdr1 and these vesicles accumulated fluconazole in a time dependent manner. These experiments demonstrated that S. cerevisiae secretory vesicles can be used to examine the mechanism of fluconazole transport by putative C. albicans membrane pumps.

A new in-cage treatment system for control of northern fowl mites on laying hens

Commercially available plastic and other types of flexible tubing were tested to determine their relative permeability to an emulsifiable concentrate (EC) of permethrin acaricide. Bioassays employing northern fowl mites, Ornithonyssus sylviarum (Canestrini and Fanzago), indicated that .3 mg permethrin/cm2 surface area penetrated vinyl plastic tubing that had been filled with 42.5% active ingredient EC for 14 days. Vinyl tubing circuits were installed in wire poultry cages, either in the form of suspended loops or woven through the rear cage wall, and permethrin EC was introduced by means of a small pump. Significant reductions in northern fowl mite populations on hens caged therein were apparent after 48 days posttreatment. This approach has merit as a long-term, labor-economical form of mite control on caged poultry.

Comparative efficacy of plastic strips impregnated with permethrin and permethrin dust for northern fowl mite control on caged laying hens

Established populations of northern fowl mites, Ornitonyssus sylviarum (Canestrini and Fanzago), on caged laying hens were effectively controlled within 77 days by application of two plastic strips impregnated with permethrin per cage. Such strips contained 9.6% active ingredient (wt/wt), were ca. 20.5-cm long, and were affixed to the top cage wires. Use of only one strip per cage resulted in less control, approximating that obtained with .25% permethrin dust. Egg mass, expressed as gram egg per hen per day, was significantly greater in all treated groups.