Habitat structure and food resources for wildlife across successional stages in a tropical forest

Tropical forests are experiencing an increase in the proportion of secondary forests as a result of the balance between the widespread harvesting of old-growth forests and the regeneration in abandoned areas. The impacts of such a process on biodiversity are poorly known and intensely debated. Recent reviews and multi-taxa studies indicate that species replacement in wildlife assemblages is a consistent pattern, sometimes stronger than changes in diversity, with a replacement from habitat generalists to old-growth specialists being commonly observed during tropical forest regeneration. However, the ecological drivers of such compositional changes are rarely investigated, despite its importance in assessing the conservation value of secondary forests, and to support and guide management techniques for restoration. By sampling 28 sites in a continuous Atlantic forest area in Southeastern Brazil, we assessed how important aspects of habitat structure and food resources for wildlife change across successional stages, and point out hypotheses on the implications of these changes for wildlife recovery. Old-growth areas presented a more complex structure at ground level (deeper leaf litter, and higher woody debris volume) and higher fruit availability from an understorey palm, whereas vegetation connectivity, ground-dwelling arthropod biomass, and total fruit availability were higher in earlier successional stages. From these results we hypothetize that generalist species adapted to fast population growth in resource-rich environments should proliferate and dominate earlier successional stages, while species with higher competitive ability in resource-limited environments, or those that depend on resources such as palm fruits, on higher complexity at the ground level, or on open space for flying, should dominate older-growth forests. Since the identification of the drivers of wildlife recovery is crucial for restoration strategies, it is important that future work test and further develop the proposed hypotheses. We also found structural and functional differences between old-growth forests and secondary forests with more than 80 years of regeneration, suggesting that restoration strategies may be crucial to recover structural and functional aspects expected to be important for wildlife in much altered ecosystems, such as the Brazilian Atlantic forest. (C) 2012 Elsevier B.V. All rights reserved.

A model of road effect using line integrals and a test of the performance of two new road indices using the distribution of small mammals in an Atlantic Forest landscape

Effects of roads on wildlife and its habitat have been measured using metrics, such as the nearest road distance, road density, and effective mesh size. In this work we introduce two new indices: (1) Integral Road Effect (IRE), which measured the sum effects of points in a road at a fixed point in the forest; and (2) Average Value of the Infinitesimal Road Effect (AVIRE), which measured the average of the effects of roads at this point. IRE is formally defined as the line integral of a special function (the infinitesimal road effect) along the curves that model the roads, whereas AVIRE is the quotient of IRE by the length of the roads. Combining tools of ArcGIS software with a numerical algorithm, we calculated these and other road and habitat cover indices in a sample of points in a human-modified landscape in the Brazilian Atlantic Forest, where data on the abundance of two groups of small mammals (forest specialists and habitat generalists) were collected in the field. We then compared through the Akaike Information Criterion (AIC) a set of candidate regression models to explain the variation in small mammal abundance, including models with our two new road indices (AVIRE and IRE) or models with other road effect indices (nearest road distance, mesh size, and road density), and reference models (containing only habitat indices, or only the intercept without the effect of any variable). Compared to other road effect indices, AVIRE showed the best performance to explain abundance of forest specialist species, whereas the nearest road distance obtained the best performance to generalist species. AVIRE and habitat together were included in the best model for both small mammal groups, that is, higher abundance of specialist and generalist small mammals occurred where there is lower average road effect (less AVIRE) and more habitat. Moreover, AVIRE was not significantly correlated with habitat cover of specialists and generalists differing from the other road effect indices, except mesh size, which allows for separating the effect of roads from the effect of habitat on small mammal communities. We suggest that the proposed indices and GIS procedures could also be useful to describe other spatial ecological phenomena, such as edge effect in habitat fragments. (C) 2012 Elsevier B.V. All rights reserved.

Terrestrial non-volant small mammals in agro-silvicultural landscapes of Southeastern Brazil

The area covered by Eucalyptus plantations is significantly increasing in Brazil for economic reasons. However, the impact of such land use change is still unknown. In this study we evaluated the spatial-temporal distribution and abundance of terrestrial non-volant small mammals on a recently converted landscape whose matrix is formed by Eucalyptus plantations up to 3 years of age. From August 2007 to July 2009 we carried out monthly sampling campaigns over a grid of 30 sampling units, formed by pitfall traps covering both the landscape matrix of Eucalyptus plantations (n = 18) and legal conservation areas of native vegetation (n = 7) and abandoned pastures (n = 5). A total of 1640 individuals from 14 species of the orders Didelphimorphia (4 spp.) and Rodentia (10 spp.) were captured. However, only three species of rodents (Olygorysomys flavescens, Oligoryzomys nigripes and Calomy tener) represented 81.8% of the total amount. Eucalyptus plantations had a lower species richness and abundance than the abandoned pasture and the remaining fragments of native vegetation. Although the present species are predominantly generalists, there is clear distinction among environments in terms of their species composition and relative abundance, which also present a pronounced time variation. The assemblage found in this study suggests that silvicultural landscapes still have some conservation value, with species that seem to be resident at the Eucalyptus plantations. Moreover, the presence of the native and abandoned pastures patches imbibed in the Eucalyptus plantation matrix may increase the carrying capacity of such a silvicultural system and these landscapes may play a role in maintaining local biodiversity. (C) 2012 Elsevier B.V. All rights reserved.

Testing the Performance of Fourteen Native Tropical Tree Species in Two Abandoned Pastures of the Lacandon Rainforest Region of Chiapas, Mexico

The rainforest of Mexico has been degraded and severely fragmented, and urgently require restoration. However, the practice of restoration has been limited by the lack of species-specific data on survival and growth responses to local environmental variation. This study explores the differential performance of 14 wet tropical early-, mid- or late-successional tree species that were grown in two abandoned pastures with contrasting land-use histories. After 18 months, seedling survival and growth of at least 7 of the 14 tree species studied were significantly higher in the site with a much longer history of land use (site 2). Saplings of the three early-successional species showed exceptional growth rates. However, differences in performance were noted in relation to the differential soil properties between the experimental sites. Mid-successional species generally showed slow growth rates but high seedling survival, whereas late-successional species exhibited poor seedling survival at both the study sites. Stepwise linear regressions revealed that the species integrated response index combining survivorship and growth measurements, was influenced mostly by differences in soil pH between the two abandoned pastures. Our results suggest that local environmental variation among abandoned pastures of contrasting land-use histories influences sapling survival and growth. Furthermore, the similarity of responses among species with the same successional status allowed us to make some preliminary site and species-specific silvicultural recommendations. Future field experiments should extend the number of species and the range of environmental conditions to identify site generalists or more narrowly adapted species, that we would call sensitive.

Analysis of 16S rRNA and mxaF genes revealing insights into Methylobacterium niche-specific plant association

The genus Methylobacterium comprises pink-pigmented facultative methylotrophic (PPFM) bacteria, known to be an important plant-associated bacterial group. Species of this group, described as plant-nodulating, have the dual capacity of producing cytokinin and enzymes, such as pectinase and cellulase, involved in systemic resistance induction and nitrogen fixation under specific plant environmental conditions. The aim hereby was to evaluate the phylogenetic distribution of Methylobacterium spp. isolates from different host plants. Thus, a comparative analysis between sequences from structural (16S rRNA) and functional mxaF (which codifies for a subunit of the enzyme methanol dehydrogenase) ubiquitous genes, was undertaken. Notably, some Methylobacterium spp. isolates are generalists through colonizing more than one host plant, whereas others are exclusively found in certain specific plant-species. Congruency between phylogeny and specific host inhabitance was higher in the mxaF gene than in the 16S rRNA, a possible indication of function-based selection in this niche. Therefore, in a first stage, plant colonization by Methylobacterium spp. could represent generalist behavior, possibly related to microbial competition and adaptation to a plant environment. Otherwise, niche-specific colonization is apparently impelled by the host plant.

Taxonomic and Functional Microbial Signatures of the Endemic Marine Sponge Arenosclera brasiliensis

The endemic marine sponge Arenosclera brasiliensis (Porifera, Demospongiae, Haplosclerida) is a known source of secondary metabolites such as arenosclerins A-C. In the present study, we established the composition of the A. brasiliensis microbiome and the metabolic pathways associated with this community. We used 454 shotgun pyrosequencing to generate approximately 640,000 high-quality sponge-derived sequences (similar to 150 Mb). Clustering analysis including sponge, seawater and twenty-three other metagenomes derived from marine animal microbiomes shows that A. brasiliensis contains a specific microbiome. Fourteen bacterial phyla (including Proteobacteria, Cyanobacteria, Actinobacteria, Bacteroidetes, Firmicutes and Cloroflexi) were consistently found in the A. brasiliensis metagenomes. The A. brasiliensis microbiome is enriched for Betaproteobacteria (e.g., Burkholderia) and Gammaproteobacteria (e.g., Pseudomonas and Alteromonas) compared with the surrounding planktonic microbial communities. Functional analysis based on Rapid Annotation using Subsystem Technology (RAST) indicated that the A. brasiliensis microbiome is enriched for sequences associated with membrane transport and one-carbon metabolism. In addition, there was an overrepresentation of sequences associated with aerobic and anaerobic metabolism as well as the synthesis and degradation of secondary metabolites. This study represents the first analysis of sponge-associated microbial communities via shotgun pyrosequencing, a strategy commonly applied in similar analyses in other marine invertebrate hosts, such as corals and algae. We demonstrate that A. brasiliensis has a unique microbiome that is distinct from that of the surrounding planktonic microbes and from other marine organisms, indicating a species-specific microbiome.

First assessment of the endoparasitic nematode fauna of four psammophilous species of Tropiduridae (Squamata: Iguania) endemic to north-eastern Brazil

Tropiduridae (Squamata: Iguania) is a lizard taxon widely distributed in the neotropics. Among its representatives, some species are classified as generalists regarding habitat usage. Others exhibit a very restricted and probably relict distribution, and are strongly associated with predominantly sandy and dry habitats. Within this rather ecologically similar than phylogenetically closely related group we examined specimens of Eurolophosaurus amathites, E. divaricatus, Tropidurus hygomi, T. psammonastes for endoparasites. In all four species examined we recorded parasitic nematodes (Nemathelminthes: Nematoda). At least three nematode species were recovered: Parapharyngodon sp., Physaloptera lutzi and Strongyluris oscari, with Ph. lutzi being the most abundant parasite encountered in all lizard species examined. In spite of the hosts' habitat specialization, these parasites are also found frequently in non-psammophilous tropidurid species as well as in other squamates. Individual species richness per lizard was low, with usually just one species parasitizing at a time. These are the first parasites registered for these tropidurids and constitute a total of six new host records.

Cellulolytic bacteria from soils in harsh environments

It is believed that the exposure of organisms to harsh climate conditions may select for differential enzymatic activities, making the surviving organisms a very promising source for bioprospecting. Soil bacteria play an important role in degradation of organic matter, which is mostly due to their ability to decompose cellulose-based materials. This work focuses on the isolation and identification of cellulolytic bacteria from soil found in two environments with stressful climate conditions (Antarctica and the Brazilian semi-arid caatinga). Cellulolytic bacteria were selected using enrichments at high and low temperatures (4 or 60A degrees C) in liquid media (trypic soy broth-TSB and minimum salt medium-MM) supplemented with cellulose (1%). Many of the isolates (119 out of 254-46.9%) displayed the ability to degrade carboxymethyl-cellulose, indicating the presence of endoglucolytic activity, while only a minority of these isolates (23 out of 254-9.1%) showed exoglucolytic activity (degradation of avicel). The obtained isolates revealed a preferential endoglucolytic activity according to the temperature of enrichments. Also, the identification of some isolates by partial sequencing of the 16S rRNA gene indicated that the Bacteroidetes (e.g., Pedobacter, Chryseobacterium and Flavobacterium) were the main phylum of cellulolytic bacteria isolated from soil in Antarctica; the Firmicutes (e.g., Bacillus) were more commonly isolated from samples from the caatinga; and Actinobacteria were found in both types of soil (e.g., Microbacterium and Arthrobacter). In conclusion, this work reports the isolation of bacteria able to degrade cellulose-based material from soil at very low or very high temperatures, a finding that should be further explored in the search for cellulolytic enzymes to be used in the bioenergy industry.

Analysis of 16S rRNA and mxaF genes reveling insights into Methylobacterium niche-specific plant association

The genus Methylobacterium comprises pink-pigmented facultative methylotrophic (PPFM) bacteria, known to be an important plant-associated bacterial group. Species of this group, described as plant-nodulating, have the dual capacity of producing cytokinin and enzymes, such as pectinase and cellulase, involved in systemic resistance induction and nitrogen fixation under specific plant environmental conditions. The aim hereby was to evaluate the phylogenetic distribution of Methylobacterium spp. isolates from different host plants. Thus, a comparative analysis between sequences from structural (16S rRNA) and functional mxaF (which codifies for a subunit of the enzyme methanol dehydrogenase) ubiquitous genes, was undertaken. Notably, some Methylobacterium spp. isolates are generalists through colonizing more than one host plant, whereas others are exclusively found in certain specific plant-species. Congruency between phylogeny and specific host inhabitance was higher in the mxaF gene than in the 16S rRNA, a possible indication of function-based selection in this niche. Therefore, in a first stage, plant colonization by Methylobacterium spp. could represent generalist behavior, possibly related to microbial competition and adaptation to a plant environment. Otherwise, niche-specific colonization is apparently impelled by the host plant.

The Evolution of Diet and Microhabitat Use in Pseudoboine Snakes

Reflecting their exceptional radiation, snakes occur in different habitats and microhabitats and are able to eat numerous types of prey. The availability of good and comprehensive phylogenies for different snake’s lineages together with natural history data provides an opportunity to explore how ecological traits diversified during their radiation. In the present study, we describe the diet and microhabitat variation (arboreal or non-arboreal) in the tribe Pseudoboini and explore how these traits evolved during the tribe’s diversification. We analyzed specimens deposited in scientific collections and gathered information on diet and microhabitat use available in the literature and provided by other researchers. We also mapped diet and microhabitat data onto a phylogeny of the tribe using the principle of parsimony. Pseudoboine snakes feed mainly on lizards and small mammals, and of the 22 species for which a minimum number of prey records was obtained, nine are diet generalists, six are lizard specialists, three are small mammal specialists, two are snake specialists, one is a lizard egg specialist, and one is a bird egg specialist. The highly diverse feeding habits of pseudoboines seem to have evolved mainly in the terminal taxa. Among those species that had enough microhabitat data (17 species), Drepanoides anomalus, Siphlophis cervinus, S. compressus, and S. pulcher frequently use the vegetation. Our results indicate that an increase in arboreality evolved several times during the diversification of the tribe, and that the Siphlophis clade seems to have maintained the high degree of arboreality from its ancestor. Species that frequently use vegetation are either lizard or lizard egg specialists, indicating that these habits might be associated in the evolution of pseudoboines.