Tree species diversity in a seasonally-dry forest: the case of the Pinkaití site, in the Kayapó Indigenous Area, Southeastern limits of the Amazon

This study investigates patterns of forest structure and tree species diversity in an anthropogenic palm grove and undisturbed areas at the seasonally-dry Pinkaití research station, in the Kayapó Indigenous Area. This site, managed by the Conservation International do Brasil, is the most southeastern site floristically surveyed in the Amazon until now. The secondary and a nearby undisturbed forest were sampled in a group of 52 floristic plots of 0.0625-ha (25x25-m) where all trees with DBH > 10 cm were measured and identified. The analyses were complemented with other two floristic plots of 1-ha (10x1000-m). The present study has shown that the Pinkaití, like other seasonally-dry forests, have great heterogeneity in forest structure and composition, associated with biotic characteristics of the most important tree species, natural disturbance and history of land-use. The palm grove, moderately dominated by the arborescent palm Attalea maripa (Aubl.) Mart., presented high tree species diversity and was floristically similar to undisturbed forests at the study site. It is discussed the importance of large arborescent palms for the seasonally-dry Amazon forests regeneration.

Exploring TM image texture and its relationships with biomass estimation in Rondônia, Brazilian Amazon

Many texture measures have been developed and used for improving land-cover classification accuracy, but rarely has research examined the role of textures in improving the performance of aboveground biomass estimations. The relationship between texture and biomass is poorly understood. This paper used Landsat Thematic Mapper (TM) data to explore relationships between TM image textures and aboveground biomass in Rondônia, Brazilian Amazon. Eight grey level co-occurrence matrix (GLCM) based texture measures (i.e., mean, variance, homogeneity, contrast, dissimilarity, entropy, second moment, and correlation), associated with seven different window sizes (5x5, 7x7, 9x9, 11x11, 15x15, 19x19, and 25x25), and five TM bands (TM 2, 3, 4, 5, and 7) were analyzed. Pearson's correlation coefficient was used to analyze texture and biomass relationships. This research indicates that most textures are weakly correlated with successional vegetation biomass, but some textures are significantly correlated with mature forest biomass. In contrast, TM spectral signatures are significantly correlated with successional vegetation biomass, but weakly correlated with mature forest biomass. Our findings imply that textures may be critical in improving mature forest biomass estimation, but relatively less important for successional vegetation biomass estimation.

Close relationship between diameters at 30cm height and at breast height (DBH)

This paper proposes the establishment of a second diameter measuring standard at 30cm shoot extension ('diam30') as input variable for allometric biomass estimation of small and mid-sized plant shoots. This diameter standard is better suited than the diameter at breast height (DBH, i.e. diameter at 1.30m shoot extension) for adequate characterization of plant dimensions in low bushy vegetation or in primary forest undergrowth. The relationships between both diameter standards are established based on a dataset of 8645 tree, liana and palm shoots in secondary and primary forests of central Amazonia (ranging from 1-150mm dbh). Dbh can be predicted from the diam(30) with high precision, the error introduced by diameter transformation is only 2-3% for trees and palms, and 5% for lianas. This is well acceptable for most field study purposes. Relationships deviate slightly from linearity and differ between growth forms. Relationships were markedly similar for different vegetation types (low secondary regrowth vs. primary forests), soils, and selected genera or species. This points to a general validity and applicability of diameter transformations for other field studies. This study provides researchers with a tool for the allometric estimation of biomass in low or structurally heterogeneous vegetation. Rather than applying a uniform diameter standard, the measuring position which best represents the respective plant can be decided on shoot-by-shoot. Plant diameters measured at 30cm height can be transformed to dbh for subsequent allometric biomass estimation. We recommend the use of these diameter transformations only for plants extending well beyond the theoretical minimum shoot length (i.e., >2m height). This study also prepares the ground for the comparability and compatability of future allometric equations specifically developed for small- to mid-sized vegetation components (i.e., bushes, undergrowth) which are based on the diam(30) measuring standard.

Outcrossing rate of Couratari multiflora (J.Smith) Eyma (Lecythidaceae), a low-density tropical tree species from a central Amazonian rainforest

A multilocus mixed-mating model was used to evaluate the mating system of a population of Couratari multiflora, an emergent tree species found in low densities (1 individual/10 ha) in lowland forests of central Amazonia. We surveyed and observed phenologically 41 trees in an area of 400 ha. From these, only four mother trees were analyzed here because few of them set fruits, which also suffered high predation. No difference was observed between the population multilocus outcrossing rate (t mp = 0.953 ± 0.040) and the average single locus rate (t sp = 0.968 ± 0.132). The four mother trees were highly outcrossed (t m ~ 1). Two out of five loci showed departures from the Hardy-Weinberg Equilibrium (HWE) expectations, and the same results occurred with the mixed-mating model. Besides the low number of trees analyzed, the proportion of loci in HWE suggests random mating in the population. However, the pollen pool was heterogeneous among families, probably due to both the small sample number and the flowering of trees at different times of the flowering season. Reproductive phenology of the population and the results presented here suggest, at least for part of the population, a long-distance pollen movement, around 1,000 m.

Tree communities of white-sand and terra-firme forests of the upper Rio Negro

The high tree diversity and vast extent of Amazonian forests challenge our understanding of how tree species abundance and composition varies across this region. Information about these parameters, usually obtained from tree inventories plots, is essential for revealing patterns of tree diversity. Numerous tree inventories plots have been established in Amazonia, yet, tree species composition and diversity of white-sand and terra-firme forests of the upper Rio Negro still remain poorly understood. Here, we present data from eight new one-hectare tree inventories plots established in the upper Rio Negro; four of which were located in white-sand forests and four in terra-firme forests. Overall, we registered 4703 trees > 10 cm of diameter at breast height. These trees belong to 49 families, 215 genera, and 603 species. We found that tree communities of terra-firme and white-sand forests in the upper Rio Negro significantly differ from each other in their species composition. Tree communities of white-sand forests show a higher floristic similarity and lower diversity than those of terra-firme forests. We argue that mechanisms driving differences between tree communities of white-sand and terra-firme forests are related to habitat size, which ultimately influences large-scale and long-term evolutionary processes.

Biological and morphometric aspects and rearing of Syssphinx molina (Cramer) (Lepidoptera: Saturniidae), a defoliator of parica tree

The objective of this research was to describe the biological and morphometric aspects of the parica tree defoliator, Syssphinx molina (Cramer), and make recommendations about the insect rearing. The life cycle was 62.9 days with mean periods for the egg, larval, pre-pupal and pupal stages of 5.6, 31.1, 2.2 and 16.6 days respectively. The pupal viability was 60.5% for females and 48.6% for males. The sexual ratio was 0.5 with mean production of 182.3 ± 2.2 eggs per female and egg viability of 24.3%. The mean longevity was 7.9 ± 2 and 8.1 ± 3 days for females and males respectively. Other parameters were also observed and compared with description of other Saturniidae species.

Yield of essential oil and safrole content based on fresh and dry biomass of long pepper in the Brazilian Amazon

Long pepper (Piper hispidinervum) is an Amazonian species of commercial interest due to the production of safrole. Drying long pepper biomass to extract safrole is a time consuming and costly process that can also result in the contamination of the material by microorganisms. The objective of this study was to analyze the yield of essential oil and safrole content of fresh and dried biomass of long pepper accessions maintained in the Active Germoplasm Bank of Embrapa Acre, in the state of Acre, Brazil, aiming at selecting genotypes with best performance on fresh biomass to recommend to the breeding program of the species. Yield of essential oil and safrole content were assessed in 15 long pepper accessions. The essential oil extraction was performed by hydrodistillation and analyzed by gas chromatography. A joint analysis of experiments was performed and the means of essential oil yield and safrole content for each biomass were compared by Student's t-test. There was variability in the essential oil yield and safrole content. There was no difference between the types of biomass for oil yield; however to the safrole content there was difference. Populations 9, 10, 12 and 15 had values of oil yield between 4.1 and 5.3%, and safrole content between 87.2 and 94.3%. The drying process does not interfere in oil productivity. These populations have potential for selection to the long pepper breeding program using oil extraction in the fresh biomass

Updated List and identification key of 219 tree species of white sand forests of the Allpahuayo Mishana National Reserve, Loreto, Peru

White sand forests, although low in nutrients, are characterized not only by several endemic species of plants but also by several monodominant species. In general, plants in this forest have noticeably thin stems. The aim of this work was to elaborate a parallel dichotomous key for the identification of Angiosperm tree species occurring on white sand forests at the Allpahuayo Mishana National Reserve, Loreto, Peru. We compiled a list of species from several publications in order to have the most comprehensive list of species that occur on white sand forest. We found 219 species of Angiosperm, the more abundant species were Pachira brevipes (26.27%), Caraipa utilis (17.90%), Dicymbe uaiparuensis (13.27%), Dendropanax umbellatus (3.28%), Sloanea spathulata (2.52%), Ternstroemia klugiana (2.30%), Haploclathra cordata (2.28%), Parkia igneiflora (1.20%), Emmotum floribundum (1.06%), Ravenia biramosa (1.04%) among others. Most species of white sand forests can be distinguished using characteristics of stems, branches and leaves. This key is very useful for the development of floristic inventories and related projects on white sand forests from Allpahuayo Mishana National Reserve.

Predicting the distribution of forest tree species using topographic variables and vegetation index in eastern Acre, Brazil

Species distribution modeling has relevant implications for the studies of biodiversity, decision making about conservation and knowledge about ecological requirements of the species. The aim of this study was to evaluate if the use of forest inventories can improve the estimation of occurrence probability, identify the limits of the potential distribution and habitat preference of a group of timber tree species. The environmental predictor variables were: elevation, slope, aspect, normalized difference vegetation index (NDVI) and height above the nearest drainage (HAND). To estimate the distribution of species we used the maximum entropy method (Maxent). In comparison with a random distribution, using topographic variables and vegetation index as features, the Maxent method predicted with an average accuracy of 86% the geographical distribution of studied species. The altitude and NDVI were the most important variables. There were limitations to the interpolation of the models for non-sampled locations and that are outside of the elevation gradient associated with the occurrence data in approximately 7% of the basin area. Ceiba pentandra (samaúma), Castilla ulei (caucho) and Hura crepitans (assacu) is more likely to occur in nearby water course areas. Clarisia racemosa (guariúba), Amburana acreana (cerejeira), Aspidosperma macrocarpon (pereiro), Apuleia leiocarpa (cumaru cetim), Aspidosperma parvifolium (amarelão) and Astronium lecointei (aroeira) can also occur in upland forest and well drained soils. This modeling approach has potential for application on other tropical species still less studied, especially those that are under pressure from logging.

Fine time scaling of purifying selection on human nonsynonymous mtDNA mutations based on the worldwide population tree and mother-child pairs

A high-resolution mtDNA phylogenetic tree allowed us to look backward in time to investigate purifying selection. Purifying selection was very strong in the last 2,500 years, continuously eliminating pathogenic mutations back until the end of the Younger Dryas (∼11,000 years ago), when a large population expansion likely relaxed selection pressure. This was preceded by a phase of stable selection until another relaxation occurred in the out-of-Africa migration. Demography and selection are closely related: expansions led to relaxation of selection and higher pathogenicity mutations significantly decreased the growth of descendants. The only detectible positive selection was the recurrence of highly pathogenic nonsynonymous mutations (m.3394T>C-m.3397A>G-m.3398T>C) at interior branches of the tree, preventing the formation of a dinucleotide STR (TATATA) in the MT-ND1 gene. At the most recent time scale in 124 mother-children transmissions, purifying selection was detectable through the loss of mtDNA variants with high predicted pathogenicity. A few haplogroup-defining sites were also heteroplasmic, agreeing with a significant propensity in 349 positions in the phylogenetic tree to revert back to the ancestral variant. This nonrandom mutation property explains the observation of heteroplasmic mutations at some haplogroup-defining sites in sequencing datasets, which may not indicate poor quality as has been claimed.

Floristic and structure of an Amazonian primary forest and a chronosequence of secondary succession

ABSTRACT The analysis of changes in species composition and vegetation structure in chronosequences improves knowledge on the regeneration patterns following land abandonment in the Amazon. Here, the objective was to perform floristic-structural analysis in mature forests (with/without timber exploitation) and secondary successions (initial, intermediate and advanced vegetation regrowth) in the Tapajós region. The regrowth age and plot locations were determined using Landsat-5/Thematic Mapper images (1984-2012). For floristic analysis, we determined the sample sufficiency and the Shannon-Weaver (H'), Pielou evenness (J), Value of Importance (VI) and Fisher's alpha (α) indices. We applied the Non-metric Multidimensional Scaling (NMDS) for similarity ordination. For structural analysis, the diameter at the breast height (DBH), total tree height (Ht), basal area (BA) and the aboveground biomass (AGB) were obtained. We inspected the differences in floristic-structural attributes using Tukey and Kolmogorov-Smirnov tests. The results showed an increase in the H', J and α indices from initial regrowth to mature forests of the order of 47%, 33% and 91%, respectively. The advanced regrowth had more species in common with the intermediate stage than with the mature forest. Statistically significant differences between initial and intermediate stages (p<0.05) were observed for DBH, BA and Ht. The recovery of carbon stocks showed an AGB variation from 14.97 t ha-1 (initial regrowth) to 321.47 t ha-1 (mature forests). In addition to AGB, Ht was also important to discriminate the typologies.

Evaluation of geostatistical techniques to estimate the spatial distribution of aboveground biomass in the Amazon rainforest using high-resolution remote sensing data

ABSTRACT The spatial distribution of forest biomass in the Amazon is heterogeneous with a temporal and spatial variation, especially in relation to the different vegetation types of this biome. Biomass estimated in this region varies significantly depending on the applied approach and the data set used for modeling it. In this context, this study aimed to evaluate three different geostatistical techniques to estimate the spatial distribution of aboveground biomass (AGB). The selected techniques were: 1) ordinary least-squares regression (OLS), 2) geographically weighted regression (GWR) and, 3) geographically weighted regression - kriging (GWR-K). These techniques were applied to the same field dataset, using the same environmental variables derived from cartographic information and high-resolution remote sensing data (RapidEye). This study was developed in the Amazon rainforest from Sucumbíos - Ecuador. The results of this study showed that the GWR-K, a hybrid technique, provided statistically satisfactory estimates with the lowest prediction error compared to the other two techniques. Furthermore, we observed that 75% of the AGB was explained by the combination of remote sensing data and environmental variables, where the forest types are the most important variable for estimating AGB. It should be noted that while the use of high-resolution images significantly improves the estimation of the spatial distribution of AGB, the processing of this information requires high computational demand.

Development of computational and experimental methods for biomass composition and evaluation of its impact in genome-scale models prediction

The use of genome-scale metabolic models has been rapidly increasing in fields such as metabolic engineering. An important part of a metabolic model is the biomass equation since this reaction will ultimately determine the predictive capacity of the model in terms of essentiality and flux distributions. Thus, in order to obtain a reliable metabolic model the biomass precursors and their coefficients must be as precise as possible. Ideally, determination of the biomass composition would be performed experimentally, but when no experimental data are available this is established by approximation to closely related organisms. Computational methods however, can extract some information from the genome such as amino acid and nucleotide compositions. The main objectives of this study were to compare the biomass composition of several organisms and to evaluate how biomass precursor coefficients affected the predictability of several genome-scale metabolic models by comparing predictions with experimental data in literature. For that, the biomass macromolecular composition was experimentally determined and the amino acid composition was both experimentally and computationally estimated for several organisms. Sensitivity analysis studies were also performed with the Escherichia coli iAF1260 metabolic model concerning specific growth rates and flux distributions. The results obtained suggest that the macromolecular composition is conserved among related organisms. Contrasting, experimental data for amino acid composition seem to have no similarities for related organisms. It was also observed that the impact of macromolecular composition on specific growth rates and flux distributions is larger than the impact of amino acid composition, even when data from closely related organisms are used.

An efficient Azorean thermophilic consortium for lignocellulosic biomass degradation

[Excerpt] Lignocellulosic plant biomass is being envisioned by biorefinery industry as an alternative to current petroleum platform because of the large scale availability, low cost and environmentally benign production. The industrial bioprocessing designed to transform lignocellulosic biomass into biofuels are harsh and the enzymatic reactions may be severely compromised reducing the production of fermentable sugars from lignocellulosic biomass. Thermophilic bacteria consortium are a potential source of cellulases and hemicellulases adapted to extreme environmental conditions, which can be exploited as a new source for the development of more robust enzymatic cocktails. (...)

Tapping the wealth of microbial data in high-throughput metabolic model reconstruction

Genome-scale metabolic models are valuable tools in the metabolic engineering process, based on the ability of these models to integrate diverse sources of data to produce global predictions of organism behavior. At the most basic level, these models require only a genome sequence to construct, and once built, they may be used to predict essential genes, culture conditions, pathway utilization, and the modifications required to enhance a desired organism behavior. In this chapter, we address two key challenges associated with the reconstruction of metabolic models: (a) leveraging existing knowledge of microbiology, biochemistry, and available omics data to produce the best possible model; and (b) applying available tools and data to automate the reconstruction process. We consider these challenges as we progress through the model reconstruction process, beginning with genome assembly, and culminating in the integration of constraints to capture the impact of transcriptional regulation. We divide the reconstruction process into ten distinct steps: (1) genome assembly from sequenced reads; (2) automated structural and functional annotation; (3) phylogenetic tree-based curation of genome annotations; (4) assembly and standardization of biochemistry database; (5) genome-scale metabolic reconstruction; (6) generation of core metabolic model; (7) generation of biomass composition reaction; (8) completion of draft metabolic model; (9) curation of metabolic model; and (10) integration of regulatory constraints. Each of these ten steps is documented in detail.