Ancient dispersal of the human fungal pathogen Cryptococcus gattii from the Amazon rainforest

Over the past two decades, several fungal outbreaks have occurred, including the high-profile 'Vancouver Island' and 'Pacific Northwest' outbreaks, caused by Cryptococcus gattii, which has affected hundreds of otherwise healthy humans and animals. Over the same time period, C. gattii was the cause of several additional case clusters at localities outside of the tropical and subtropical climate zones where the species normally occurs. In every case, the causative agent belongs to a previously rare genotype of C. gattii called AFLP6/VGII, but the origin of the outbreak clades remains enigmatic. Here we used phylogenetic and recombination analyses, based on AFLP and multiple MLST datasets, and coalescence gene genealogy to demonstrate that these outbreaks have arisen from a highly-recombining C. gattii population in the native rainforest of Northern Brazil. Thus the modern virulent C. gattii AFLP6/VGII outbreak lineages derived from mating events in South America and then dispersed to temperate regions where they cause serious infections in humans and animals.

AMAZON RAINFOREST COSMETICS: CHEMICAL APPROACH FOR QUALITY CONTROL

The market for natural cosmetics featuring ingredients derived from Amazon natural resources is growing worldwide. However, there is neither enough scientific basis nor quality control of these ingredients. This paper is an account of the chemical constituents and their biological activities of fourteen Amazonian species used in cosmetic industry, including açaí (Euterpe oleracea), andiroba (Carapa guianensis), bacuri (Platonia insignis), Brazil nut (Bertholletia excelsa), buriti (Mauritia vinifera or M. flexuosa), cumaru (Dipteryx odorata), cupuaçu (Theobroma grandiflorum), guarana (Paullinia cupana), mulateiro (Calycophyllum spruceanum), murumuru (Astrocaryum murumuru), patawa (Oenocarpus bataua or Jessenia bataua), pracaxi (Pentaclethra macroloba), rosewood (Aniba rosaeodora), and ucuuba (Virola sebifera). Based on the reviewed articles, we selected chemical markers for the quality control purpose and evaluated analytical methods. Even though chromatographic and spectroscopic methods are major analytical techniques in the studies of these species, molecular approaches will also be important as used in food and medicine traceability. Only a little phytochemical study is available about most of the Amazonian species and some species such as açaí and andiroba have many reports on chemical constituents, but studies on biological activities of isolated compounds and sampling with geographical variation are limited.

SPECIES RICHNESS AND ABUNDANCE OF LOW-TRUNK HERB EPIPHYTES IN RELATION TO HOST TREE SIZE AND BARK TYPE, EASTERN AMAZONIA

ABSTRACTThe composition and structure of the low-trunk epiphytic herb assembly as well as its vertical distribution were studied. DBH of host tree and bark type influence species richness and abundance in a nonlooded lowland tropical rainforest in Eastern Amazonia (1º57’36"S 51º36’55"W). A total of 37 epiphytic herb species were identified, among which 60% were Araceae. Species richness and abundance of epiphytic herbs showed tendency of positive correlation with host tree size and no relationships with bark type. Low positive correlation may be a by-product of the predominance of trees with smaller diameter in our sample rather than a reflection of neutral relationship. The absence of relationships with bark type may be partially explained by the large number of secondary, generalist, hemi-epiphytes and also may reflect the absence of suitable substrate in trees with smaller diameter.

Fungal succession on leaves of Alchornea triplinervia (Spreng.) Muell. Arg. submerged in a stream of an Atlantic Rainforest in the state of São Paulo, Brazil

Leaves of Alchornea triplinervia (Spreng.) Muell. Arg. were submerged in a stream in an Atlantic Rainforest in São Paulo state, Brazil, from July/1988 to June/1989 and from July/1989 to May/1990. Fungi were isolated by the leaf disks washing technique followed by plating on culture media and also by using baiting techniques (using substrates with chitin, keratin and cellulose), what resulted on 565 fungal registers corresponding to 81 taxa. The most common species found during this study of the fungal succession were Trichoderma viride Pers. ex S.F. Gray and Fusarium oxysporum Schlecht emend. Snyd. & Hans. (23 registers), Penicillium hirsutum Dierckx (21 registers), Fusarium solani (Mart.) Appel & Wollenw. emend. Snyd. & Hans. (17), followed by 14 registers of: Cylindrocladium scoparium Morgan, Triscelophorus monosporus Ingold and Polychytrium aggregatum Ajello. Although the monthly obtained mycota had been composed by species of different taxonomic groups, the fungal succession was defined by the initial presence of typical terrestrial leaf inhabiting fungi (mostly Deuteromycotina), followed by species of Mastigomycotina and Zygomycotina. Combining culture methods and baiting techniques, it was possible to verify the presence of terrestrial fungi on the decomposition of submerged leaves and the importance of zoosporic fungi in the fungal succession. This is the first paper about the fungal succession on the decomposition of leaves submerged in a lotic ecosystem in Brazil.

Spatial distribution and preferential substrate of Neoregelia johannis (Carriére) L.B. Smith (Bromeliaceae) in a disturbed area of Atlantic Rainforest at Ilha Grande, RJ, Brazil

In bromeliad populations, amount of light and available substrates influence individuals spatial organization. In Atlantic Rainforest of Ilha Grande, the heliophylous bromeliad Neoregelia johannis is a large and abundant species. In this forest, it would be expected that N. johannis would occupy stable substrates, as large trunks, large branches, rock boulders or ground, with high sunlight, enough for the bromeliad survivor. In the present work, we analyzed the distribution and most used substrates of N. johannis in secondary forest. We analyzed the frequency of reproductive modes (sexual and vegetative) used by the bromeliad shoots, registering if the shoots were originated from seeds or by vegetative reproduction. The results indicated an aggregated distribution pattern (Ip = 0.052). The preferred substrate was boulders (91%), whereas tree trunks (6%) and the ground (3%) were rarely used. Small and fragile substrates are unstable to support large adults of this species, which may explain the predominant pattern of establishment over boulders within the secondary forest, as the presence of this substrate also results in more opened canopy cover. Approximately 50% of young individuals entered the population by vegetative reproduction. We conclude that the preferential habit and the aggregated distribution of N. johannis are due to the conjunction of preferred substrate with higher amount of light resulting from breaks in tree canopy over areas with rock blocks, and high frequency of recruitment by vegetative reproduction.

Community structure of vascular plants in treefall gaps and fire-disturbed habitats in the Atlantic rainforest, southern Bahia, Brazil

The effects of disturbances on plant community structure in tropical forests have been widely investigated. However, a majority of these studies examined only woody species, principally trees, whereas the effects of disturbances on the whole assemblage of vascular plants remain largely unexplored. At the present study, all vascular plants < 5m tall were surveyed in four habitats: natural treefall gaps, burned forest, and their adjacent understorey. The burned area differed from the other habitats in terms of species composition. However, species richness and plant density did not differ between burned area and the adjacent understorey, which is in accordance to the succession model that predict a rapid recovery of species richness, but with a different species composition in areas under moderate disturbance. The treefall gaps and the two areas of understorey did not differ among themselves in terms of the number of individuals, number of species, nor in species composition. The absence of differences between the vegetation in treefall gaps and in understorey areas seems to be in agreement with the current idea that the species present in treefall gaps are directly related to the vegetation composition before gap formation. Only minimal differences were observed between the analyses that considered only tree species and those that considered all growth habits. This suggests that the same processes acting on tree species (the best studied group of plants in tropical forests) are also acting on the whole assemblage of vascular plants in these communities.

NOx and O3 above a tropical rainforest: an analysis with a global and box model

A cross-platform field campaign, OP3, was conducted in the state of Sabah in Malaysian Borneo between April and July of 2008. Among the suite of observations recorded, the campaign included measurements of NOx and O3 – crucial outputs of any model chemistry mechanism. We describe the measurements of these species made from both the ground site and aircraft. We then use the output from two resolutions of the chemistry transport model p-TOMCAT to illustrate the ability of a global model chemical mechanism to capture the chemistry at the rainforest site. The basic model performance is good for NOx and poor for ozone. A box model containing the same chemical mechanism is used to explore the results of the global model in more depth and make comparisons between the two. Without some parameterization of the nighttime boundary layer – free troposphere mixing (i.e. the use of a dilution parameter), the box model does not reproduce the observations, pointing to the importance of adequately representing physical processes for comparisons with surface measurements. We conclude with a discussion of box model budget calculations of chemical reaction fluxes, deposition and mixing, and compare these results to output from p-TOMCAT. These show the same chemical mechanism behaves similarly in both models, but that emissions and advection play particularly strong roles in influencing the comparison to surface measurements.

Differentiation between Neotropical rainforest, dry forest and savannah ecosystems by their modern pollen spectra and implications for the fossil pollen record

Accurate differentiation between tropical forest and savannah ecosystems in the fossil pollen record is hampered by the combination of: i) poor taxonomic resolution in pollen identification, and ii) the high species diversity of many lowland tropical families, i.e. with many different growth forms living in numerous environmental settings. These barriers to interpreting the fossil record hinder our understanding of the past distributions of different Neotropical ecosystems and consequently cloud our knowledge of past climatic, biodiversity and carbon storage patterns. Modern pollen studies facilitate an improved understanding of how ecosystems are represented by the pollen their plants produce and therefore aid interpretation of fossil pollen records. To understand how to differentiate ecosystems palynologically, it is essential that a consistent sampling method is used across ecosystems. However, to date, modern pollen studies from tropical South America have employed a variety of methodologies (e.g. pollen traps, moss polsters, soil samples). In this paper, we present the first modern pollen study from the Neotropics to examine the modern pollen rain from moist evergreen tropical forest (METF), semi-deciduous dry tropical forest (SDTF) and wooded savannah (cerradão) using a consistent sampling methodology (pollen traps). Pollen rain was sampled annually in September for the years 1999–2001 from within permanent vegetation study plots in, or near, the Noel Kempff Mercado National Park (NKMNP), Bolivia. Comparison of the modern pollen rain within these plots with detailed floristic inventories allowed estimates of the relative pollen productivity and dispersal for individual taxa to be made (% pollen/% vegetation or ‘p/v’). The applicability of these data to interpreting fossil records from lake sediments was then explored by comparison with pollen assemblages obtained from five lake surface samples.

Classification of seed storage behaviour of 67 Amazonian tree species

Information was collated on the seed storage behaviour of 67 tree species native to the Amazon rainforest of Brazil; 38 appeared to show orthodox, 23 recalcitrant and six intermediate seed storage behaviour. A double-criteria key based on thousand-seed weight and seed moisture content at shedding to estimate likely seed storage behaviour, developed previously, showed good agreement with the above classifications. The key can aid seed storage behaviour identification considerably.

Microhabitat Selection of three Forest Understory Birds in the Brazilian Atlantic Rainforest

When assessing fragmentation effects on species, not only habitat preferences on the landscape scale, but also microhabitat selection is an important factor to consider, as microhabitat is also affected by habitat disturbance, but nevertheless essential for species for foraging, nesting and sheltering. In the Atlantic Rainforest of Brazil we examined microhabitat selection of six Pyriglena leucoptera (white-shouldered fire-eye), 10 Sclerurus scansor (rufous-breasted leaftosser), and 30 Chiroxiphia caudata (blue manakin). We radio-tracked the individuals between May 2004 and February 2005 to gain home ranges based on individual fixed kernels. Vegetation structures in core plots and fringe plots were compared. In C. caudata, we additionally assessed the influence of behavioural traits on microhabitat selection. Further, we compared microhabitat structures in the fragmented forest with those in the contiguous, and contrasted the results with the birds` preferences. Pyriglena leucoptera preferred liana tangles that were more common in the fragmented forest, whereas S. scansor preferred woody debris, open forest floor (up to 0.5 m), and a thin closed leaf litter cover which all occurred significantly more often in the contiguous forest. Significant differences were detected in C. caudata for vegetation densities in the different strata; the distance of core plots to the nearest lek site was significantly influenced by sex and age. However, core sites of C. caudata in fragmented and contiguous forests showed no significant differences in structure. Exploring microhabitat selection and behavior may greatly support the understanding of habitat selection of species and their susceptibility to fragmentation on the landscape scale.

Landscape perception by forest understory birds in the Atlantic Rainforest: black-and-white versus shades of grey

Even among forest specialists, species-specific responses to anthropogenic forest fragmentation may vary considerably. Some appear to be confined to forest interiors, and perceive a fragmented landscape as a mosaic of suitable fragments and hostile matrix. Others, however, are able to make use of matrix habitats and perceive the landscape in shades of grey rather than black-and-white. We analysed data of 42 Chiroxiphia caudata (Blue Manakin), 10 Pyriglena leucoptera (White-shouldered Fire-eye) and 19 Sclerurus scansor (Rufous-breasted Leaftosser) radio-tracked in the Atlantic Rainforest of Brazil between 2003 and 2005. We illustrate how habitat preferences may determine how species respond to or perceive the landscape structure. We compared available with used habitat to develop a species-specific preference index for each of six habitat classes. All three species preferred old forest, but relative use of other classes differed significantly. S. scansor perceived great contrast between old forest and matrix, whereas the other two species perceived greater habitat continuity. For conservation planning, our study offers three important messages: (1) some forest specialist species are able to persist in highly fragmented landscapes; (2) some forest species may be able to make use of different anthropogenic habitat types to various degrees; whereas (3) others are restricted to the remaining forest fragments. Our study suggests species most confined to forest interiors to be considered as potential umbrella species for landscape-scale conservation planning.

Seed dispersal and predation in the endemic Atlantic rainforest palm Astrocaryum aculeatissimum across a gradient of seed disperser abundance

Tropical forests have been subject to intense hunting of medium and large frugivores that are important in dispersing large-seeded species. It has been hypothesized that in areas with extinction or low abundance of medium and large-bodied animals the density of small rodents may increase. Therefore, this increment in the density of small rodents may compensate for the absence or low abundance of medium and large frugivores on seed removal and seed dispersal. Here, we fill up this gap in the literature by determining if seed removal, seed dispersal, and seed predation by small rodents (spiny rats, Trinomys inheringi and squirrels, Sciurus ingrami) are maintained in defaunated areas. We accessed seed removal, seed dispersal, seed predation, and seedling recruitment of an endemic Atlantic rainforest palm, Astrocaryum aculeatissimum, in a gradient of abundance of agoutis. We found that seed removal, scatter hoarding, and seed predation increase with the abundance of agoutis. In contrast, the proportion of dispersed but non-cached seeds decreased with the abundance of agoutis. We did not find any effect of the abundance of agoutis on seed dispersal distance, but we did find a positive trend on the density of seedlings. We concluded that small rodents do not compensate the low abundance of agoutis on seed removal, scatter hoarding, and seed predation of this palm tree. Moreover, areas in which agoutis are already extinct did not present any seed removal or scatter hoarding, not even by small rodents. This study emphasizes both the importance of agoutis in dispersing seeds of A. aculeatissimum and the collapse in seed dispersal of this palm in areas where agoutis are already extinct.

Forest structure in a mosaic of rainforest sites: The effect of fragmentation and recovery after clear cut

A variety of human-induced disturbances such as forest fragmentation and recovery after deforestation for pasture or agricultural activities have resulted in a complex landscape mosaic in the Una region of northeastern Brazil. Using a set of vegetation descriptors, we investigated the main structural changes observed in forest categories that comprise the major components of the regional landscape and searched for potential key descriptors that could be used to discriminate among different forest categories. We assessed the forest structure of five habitat categories defined as (I) interiors and (2) edges of large fragments of old-growth forest (>1000 ha), (3) interiors and (4) edges of small forest fragments (<100 ha), and (5) early secondary forests. Forest descriptors used here were: frequency of herbaceous lianas and woody climbers, number of standing dead trees, number of fallen trunks, litter depth, number of pioneer plants (early secondary and shade-intolerant species), vertical foliage stratification profile and distribution Of trees in different diameter classes. Edges and interiors of forest fragments were significantly different only in the number of standing dead trees. Secondary forests and edges of fragments showed differences in litter depth, fallen trunks and number of pioneer trees, and secondary forests were significantly different from fragment interiors in the number of standing dead trees and the number of pioneer trees. Horizontal and vertical structure evaluated via ordination analysis showed that fragment interiors, compared to secondary forests, were characterized by a greater number of medium (25-35 cm) and large (35-50 cm) trees and smaller numbers of thin trees (5-10 cm). There was great heterogeneity at the edges of small and large fragments, as these sites were distributed along almost the entire gradient. Most interiors of large and small fragments presented higher values of foliage densities at higher strata ( 15-20 m and at 20-25 m height), and lower densities at 1-5 m. All secondary forests and some fragment edge sites showed an opposite tendency. A discriminant function highlighted differences among forest categories, with transects of large fragment interiors and secondary forests representing two extremes along a disturbance gradient determined by foliage structure (densities at 15-20 m and 20-25 m), with the edges of both large and small fragments and the interiors of small fragments scattered across the gradient. The major underlying processes determining patterns of forest disturbance in the study region are discussed, highlighting the importance of forest fragments, independently of its size, as forests recovery after clear cut show a greatly distinct structure, with profound implications on fauna movements. (C) 2009 Elsevier BY. All rights reserved.

Using gap-crossing capacity to evaluate functional connectivity of two Atlantic rainforest birds and their response to fragmentation

One of the main consequences of habitat loss and fragmentation is the increase in patch isolation and the consequent decrease in landscape connectivity. In this context, species persistence depends on their responses to this new landscape configuration, particularly on their capacity to move through the interhabitat matrix. Here, we aimed first to determine gap-crossing probabilities related to different gap widths for two forest birds (Thamnophilus caerulescens, Thamnophilidae, and Basileuterus culicivorus, Parulidae) from the Brazilian Atlantic rainforest. These values were defined with a playback technique and then used in analyses based on graph theory to determine functional connections among forest patches. Both species were capable of crossing forest gaps between patches, and these movements were related to gap width. The probability of crossing 40 m gaps was 50% for both species. This probability falls to 10% when the gaps are 60 m (for B. culicivorus) or 80 m (for T caerulescens). Actually, birds responded to stimulation about two times more distant inside forest trials (control) than in gap-crossing trials. Models that included gap-crossing capacity improved the explanatory power of species abundance variation in comparison to strictly structural models based merely on patch area and distance measurements. These results highlighted that even very simple functional connectivity measurements related to gap-crossing capacity can improve the understanding of the effect of habitat fragmentation on bird occurrence and abundance.

Movements of neotropical understory passerines affected by anthropogenic forest edges in the Brazilian Atlantic rainforest

Edge effects are suggested to have great impact on the persistence of species in fragmented landscapes. We tested edge avoidance by forest understory passerines in the Brazilian Atlantic Rainforest and also compared their mobility and movement patterns in contiguous and fragmented landscapes to assess whether movements would increase in the fragmented landscape. Between 2003 and 2005, 96 Chiroxiphia caudata, 38 Pyriglena leucoptera and 27 Sclerurus scansor were radio-tracked. The most strictly forest species C. caudata and S scansor avoided forest edges while P leucoptera showed affinities for the edge Both sensitive species showed larger mean step length and maximal observed daily distance in the fragmented forest versus the unfragmented forest. P. leucoptera did not show any significant difference. There were no significant differences in proportional daily home range use for any of the three species. Our results suggested that fragmentation and the consequent increase in edge areas do influence movement behavior of sensitive forest understory birds that avoided the use of edges and increased the speed and distance they covered daily. For the most restricted forest species, it would be advisable to protect larger patches of forest instead of many small or medium fragments connected by narrow corridors. However, by comparing our data with that obtained earlier, we concluded that movement behavior of resident birds differs from that of dispersing birds and might not allow to infer functional connectivity or landscape-scale sensitivity to fragmentation; a fact that should be taken into consideration when suggesting conservation strategies. (c) 2008 Elsevier Ltd. All rights reserved.