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Rhizomorphs are hair- or wire-like melanized structures with structural differentiation analogous to plant roots that help fungi spread over an area and find food resources. Some species of multiple groups of the Ascomycota and the Basidiomycota produce different types of rhizomorphs. In the Agaricales, the structures are largely found in Marasmiineae, particularly in the Omphalotaceae, Marasmiaceae, and Physalacriaceae. Many rhizomorph-forming species spread over the forest floor (ground level), while others form aerial litter-trapping rhizomorph systems that hang on living branches of the forest understorey. Here, we describe three new species that form aerial systems, two in Marasmius and one in Pusillomyces, all of which inhabit areas of the Amazon rainforest in Amazonas State, Brazil. Support for these new species is based on evidence derived from morphological and molecular phylogenetic analyses using nuclear ribosomal internal transcribed spacer region (nrITS) and nuclear ribosomal large subunit (nrLSU) markers. Marasmius foliauceps sp. nov., with a pileipellis made up of Rotalis-type broom cells, is different from all other species described to date and branched along with species of the monophyletic Marasmius sect. Marasmius subsect. Marasmius, being conspecific with specimens from Guyana. Also different from all other described Marasmius species, Marasmius arachnotropus sp. nov. has a pileipellis mostly composed of Siccus-type but in transition to Rotalis-type broom cells and branched along with species of the Marasmius crinis-equi species complex. Pusillomyces cuieirasensis is morphologically very similar to Pusillomyces manuripioides to which it is sister, but it has a non-umbonate pileus and smaller basidiospores. They all form aerial litter-trapping rhizomorph systems that mimic spider webs, particularly those hanging on the understorey. Whether made of mycelia or silk, such webs serve to capture food. The aerial rhizomorph-forming 'spider fungi' make up a guild with hidden species diversity in tropical systems. [ABSTRACT FROM AUTHOR]

In the search for new strains of edible mushrooms in the Brazilian Amazon Forest, we found Lentinula specimens different from Lentinula raphanica. These were described morphologically and evaluated phylogenetically within the Lentinula clade. The mating system was determined, and interbreeding compatibility with L. raphanica was verified. The basidiomata have a cinnamon or deep orange to fulvous brown, moist to dry pileus, occasionally with whitish scales; crowded whitish cream lamellae; and an eccentric to lateral stipe. The typical, predominant basidiospores are 4.4-7.2 µm in length. Endogenous, elongate (7.8-14 µm) basidiospores were also found in some specimens. The long spores seem rare and occasional, but nonetheless a novelty for the group. Basidia are homogeneous in size, cheilocystidia are pyriform or bulboid, and caulocystidia are long and spheropedunculate. The hyphae of the pileipellis are pigment-encrusted. The characteristics match those of Agaricus ixodes originally described from Guyana, currently a synonym of Lentinula boryana. In the phylogenetic trees, such taxon appears distinct from L. boryana and sister to L. raphanica with strong support. This unique lineage was confirmed to be reproductively isolated from sympatric L. raphanica strains. Lentinula ixodes comb. nov. is the second species of the genus reported in the Amazon Forest. [ABSTRACT FROM AUTHOR]

A new luminescent lignicolous fungal species, Mycena cristinae sp. nov., is proposed from the Central Amazon forest. This is unique and supported by morphological evaluation along with LSU- and ITS-based phylogenetic analyses. The basidiomata have mostly fuscous olivaceous brown pileus, adnate to subdecurrent and distant lamellae, and stipe with slightly bulbous base (basal mycelium absent). It also has inamyloid and/or weakly amyloid basidiospores, ramose cheilocystidia and a pileipellis composed of an aerated tangle of slender, diverticulate hyphae forming a coralloid pellicle overlaying the hypodermium. The luminescence is evident in the basidiomata (especially the stipe) and in the mycelium on the substrate. The LSU phylogenetic trees reveal that M. cristinae is sister to M. coralliformis within the Mycenaceae clade. In the ITS trees, it forms a unique lineage grouping with undetermined Mycena taxa. Morphological data support M. cristinae as a different species compared to previously described taxa. [ABSTRACT FROM AUTHOR]

Despite the reduction in the prevalence of soil-transmitted helminthiases in many regions of the world, morbidity rates remain high in some rural regions. The Kato–Katz technique is a simple, inexpensive and field-applicable tool commonly used for the diagnosis and worm-burden characterization of these infections. Molecular studies have revolutionized our understanding of the epidemiology and evolutionary genetics of parasites. In this study we recovered helminthic DNA from Kato–Katz slides (n = 93) prepared in 2011 in the Brazilian Amazon. We achieved DNA recovery by polymerase chain reaction (PCR) in 84% of cases for Ascaris sp. and 75% of cases for hookworms. The sequencing confirmed the specific species of the amplicons. The slides stored for a few years could be analysed using this methodology, allowing access to DNA from a large collection of samples. We must consider the Kato–Katz thick smears as a source of helminth DNA. This can significantly reduce logistical difficulties in the field in terms of obtaining, preserving, transporting and initial processing of samples. [ABSTRACT FROM AUTHOR]

The Neotropical hylid genus Sphaenorhynchus includes 15 species of small, greenish treefrogs widespread in the Amazon and Orinoco basins, and in the Atlantic Forest of Brazil. Although some studies have addressed the phylogenetic relationships of the genus with other hylids using a few exemplar species, its internal relationships remain poorly understood. In order to test its monophyly and the relationships among its species, we performed a total evidence phylogenetic analysis of sequences of three mitochondrial and three nuclear genes, and 193 phenotypic characters from all species of Sphaenorhynchus. Our results support the monophyly of Sphaenorhynchus with molecular and phenotypic evidence, with S. pauloalvini as the earliest diverging taxon, followed by S. carneus, as the sister taxon of all remaining species of the genus. We recognize three species groups in Sphaenorhynchus (the S. lacteus, S. planicola and S. platycephalus groups), to facilitate its taxonomic study; only three species (S. carneus, S. pauloalvini and S. prasinus) remain unassigned to any group. Sequence data were not available for only two species (S. bromelicola and S. palustris) for which we scored phenotypic data; wildcard behaviour was detected only in S. bromelicola nested inside the S. platycephalus group. On the basis of the resulting phylogenetic hypothesis, we discuss the evolution of oviposition site and a number of phenotypic characters that could be associated with heterochronic events in the evolutionary history of this group. [ABSTRACT FROM AUTHOR]

Species of the Amazonian jumping spider genus Soesiladeepakius Makhan are confirmed as non-salticoids. Sequences of nuclear (28S, Actin) and mitochondrial (16S through NADH dehydrogenase subunit I, '16S-ND1') gene regions, analysed under parsimony and maximum likelihood, placed the genus within the lapsiines, closely related to Galianora Maddison. Additionally, six new species of this genus are herein described, namely Soesiladeepakius lyra sp. nov., Soesiladeepakius retroversus sp. nov., Soesiladeepakius arthrostylus sp. nov., Soesiladeepakius gasnieri sp. nov., Soesiladeepakius biarmatus sp. nov., and Soesiladeepakius uncinatus sp. nov., all from the Amazon region in Brazil. To test the monophyly of Soesiladeepakius within lapsiines, a cladistic analysis was carried out using a data matrix comprising 24 morphological characters scored for 12 taxa. The analysis resulted in two equally parsimonious trees of 29 steps. One of these trees is used to discuss the relationships among the species of Soesiladeepakius and character evolution. © 2012 The Linnean Society of London, Zoological Journal of the Linnean Society, 2012, 165, 274-295. [ABSTRACT FROM AUTHOR]

The genus Synechococcus is widespread in aquatic environments and is known to be abundant in the Tucuruí Hydroelectric Power Station (HPS) reservoir, in eastern Brazilian Amazonia. However, little is known about this man-made water body's planktonic community. The diversity and phylogeny of the Synechococcus group present in the Tucuruí HPS reservoir were analysed using a culture-independent approach, by amplifying three different loci: the rpoC1 gene, the 16S-23S rRNA-internal transcribed spacer (ITS) and the cpcBA-IGS operon and comparing them to the 16S rRNA gene. The phenograms inferred independently using the three markers indicate the presence of at least six Synechococcus groups in the reservoir. The results also demonstrate a high level of microdiversity in the reservoir. The rpoC1 gene was unable to resolve the most recent branches and is therefore not suggested for studies at the Cyanobacteria genus level. The ITS sequences obtained permitted the modelling of the secondary structure of the RNA of the segment containing the two transfer RNAs and a variable stem region, which was a useful complementary tool in diversity studies of the group. The cpcBA genes have good phylogenetic signal and resolution throughout several taxonomic levels, allowing for correlation between the sequence and pigmentation physiology. However, the choice of molecular markers for phylogenetic analysis of cyanobacteria should be made carefully to maximize the phylogenetic signal. [ABSTRACT FROM PUBLISHER]

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Many of the most virulent emerging infectious diseases in humans, e.g., AIDS and Ebola, are zoonotic, having shifted from wildlife populations. Critical questions for predicting disease emergence are: (1) what determines when and where a disease will first cross from one species to another, and (2) which factors facilitate emergence after a successful host shift. In wild primates, infectious diseases most often are shared between species that are closely related and inhabit the same geographic region. Therefore, humans may be most vulnerable to diseases from the great apes, which include chimpanzees and gorillas, because these species represent our closest relatives. Geographic overlap may provide the opportunity for cross-species transmission, but successful infection and establishment will be determined by the biology of both the host and pathogen. We extrapolate the evolutionary relationship between pathogen sharing and divergence time between primate species to generate “hotspot” maps, highlighting regions where the risk of disease transfer between wild primates and from wild primates to humans is greatest. We find that central Africa and Amazonia are hotspots for cross-species transmission events between wild primates, due to a high diversity of closely related primate species. Hotspots of host shifts to humans will be most likely in the forests of central and west Africa, where humans come into frequent contact with their wild primate relatives. These areas also are likely to sustain a novel epidemic due to their rapidly growing human populations, close proximity to apes, and population centers with high density and contact rates among individuals. [ABSTRACT FROM AUTHOR]

We analysed 1040 individual trees, located in 62 plots across the Amazon Basin for leaf mass per unit area (MA), foliar carbon isotopic composition (δ 13C) and leaf level concentrations of C, N, P, Ca, Mg, K and Al. All trees were identified to the species level with the dataset containing 58 families, 236 genera and 508 species, distributed across a wide range of soil types and precipitation regimes. Some foliar characteristics such as MA, [C], [N] and [Mg] emerge as highly constrained by the taxonomic affiliation of tree species, but with others such as [P], [K], [Ca] and δ 13C also strongly influenced by site growing conditions. By removing the environmental contribution to trait variation, we find that intrinsic values of most trait pairs coordinate, although different species (characterised by different trait suites) are found at discrete locations along a common axis of coordination. Species that tend to occupy higher fertility soils are characterised by a lower MA and have a higher intrinsic [N], [P], [K], [Mg] and δ 13C than their lower fertility counterparts. Despite this consistency, different scaling patterns were observed between low and high fertility sites. Inter-relationships are thus substantially modified by growth environment. Analysing the environmental component of trait variation, we found soil fertility to be the most important predictor, influencing all leaf nutrient concentrations and δ 13C and reducing MA. Mean annual temperature was negatively associated with leaf level [N], [P] and [K] concentrations. Total annual precipitation positively influences MA, [C] and δ 13C, but with a negative impact on [Mg]. These results provide a first basis for understanding the relationship between the physiological functioning and distribution of tree species across Amazonia. [ABSTRACT FROM AUTHOR]

Analysis of the phylogenetic relationships among trypanosomes from vertebrates and invertebrates disclosed a new lineage of trypanosomes circulating among anurans and sand flies that share the same ecotopes in Brazilian Amazonia. This assemblage of closely related trypanosomes was determined by comparing whole SSU rDNA sequences of anuran trypanosomes from the Brazilian biomes of Amazonia, the Pantanal, and the Atlantic Forest and from Europe, North America, and Africa, and from trypanosomes of sand flies from Amazonia. Phylogenetic trees based on maximum likelihood and parsimony corroborated the positioning of all new anuran trypanosomes in the aquatic clade but did not support the monophyly of anuran trypanosomes. However, all analyses always supported four major clades (An01-04) of anuran trypanosomes. Clade An04 is composed of trypanosomes from exotic anurans. Isolates in clades An01 and An02 were from Brazilian frogs and toads captured in the three biomes studied, Amazonia, the Pantanal and the Atlantic Forest. Clade An01 contains mostly isolates from Hylidae whereas clade An02 comprises mostly isolates from Bufonidae; and clade An03 contains trypanosomes from sand flies and anurans of Bufonidae, Leptodactylidae, and Leiuperidae exclusively from Amazonia. To our knowledge, this is the first study describing morphological and growth features, and molecular phylogenetic affiliation of trypanosomes from anurans and phlebotomines, incriminating these flies as invertebrate hosts and probably also as important vectors of Amazonian terrestrial anuran trypanosomes. [ABSTRACT FROM AUTHOR]

Abstract  Efforts to clarify the affinities of the torós or brush-tailed rats (Isothrix) and document the radiation of these distinctive echimyids have been limited. The discovery of a new Andean species prompted a reanalysis of Isothrix and its relatives. Prior morphological analyses of skulls, mandibles, teeth, and external characters permitted robust diagnosis but offered little resolution of within- or between-group relationships. Analyses of mitochondrial cytochrome b sequences (798 bp), which are available for numerous echimyids, confirm the monophyly of recognized genera, including Isothrix, and resolve a number of interspecific relationships. Strikingly, the Andean toró (Isothrix barbarabrownae) is consistently recovered as sister to the remaining species. These are allied into three clades: I. sinnamariensis + I. pagurus in the lower Amazon Basin and Guianan Shield, I. orinoci + I. negrensis in the Rio Negro and Río Orinoco drainages, and I. bistriata across much of the western and southern Amazon Basin. However, the addition of a new basal taxon does not aid in identifying the sister taxon of Isothrix. These relationships are confirmed in combined analyses of cyt-b with sequence variation in the mitochondrial control region (D-loop; 450 bp) and in the nuclear RAG1 gene (1,072 bp). Analyses identify the Andes, or proto-Andes, as an important theater for the group’s evolution and may offer an explanation for the luxuriant fur of this genus. However, neither the biogeographic history of Isothrix nor the remarkable pelage evolution of the Echimyidae can be understood until the deeper nodes within the arboreal spiny rats (Echimyinae) are more fully resolved. [ABSTRACT FROM AUTHOR]