Effects of grassland controlled burning on symbiotic skin microbes in Neotropical amphibians

Climate change has led to an alarming increase in the frequency and severity of wildfires worldwide. While it is known that amphibians have physiological characteristics that make them highly susceptible to fire, the specific impacts of wildfires on their symbiotic skin bacterial communities (i.e., bacteriomes) and infection by the deadly chytrid fungus, Batrachochytrium dendrobatidis, remain poorly understood. Here, we address this research gap by evaluating the effects of fire on the amphibian skin bacteriome and the subsequent risk of chytridiomycosis. We sampled the skin bacteriome of the Neotropical species Scinax squalirostris and Boana leptolineata in fire and control plots before and after experimental burnings. Fire was linked with a marked increase in bacteriome beta dispersion, a proxy for skin microbial dysbiosis, alongside a trend of increased pathogen loads. By shedding light on the effects of fire on amphibian skin bacteriomes, this study contributes to our broader understanding of the impacts of wildfires on vulnerable vertebrate species.

Burkholderia vietnamiensis G4 as a biological agent in bioremediation processes of polycyclic aromatic hydrocarbons in sludge farms

Polycyclic aromatic hydrocarbons (PAHs) are one of the main pollutants generated by the refining and use of oil. To search bioremediation alternatives for these compounds, mainly in situ, considering the biotic and abiotic variables that affect the contaminated sites is determinant for the success of bioremediation techniques. In this study, bioremediation strategies were evaluated in situ, including biostimulation and bioaugmentation for 16 priority PAHs present in activated sludge farms. B. vietnamiensis G4 was used as a biodegradation agent for bioaugmentation tests. The analyses occurred for 12 months, and temperature and humidity were measured to verify the effects of these factors on the biodegradation. We used the technique GC-MS to evaluate and quantify the degradation of PAHs over the time of the experiment. Of the four treatments applied, bioaugmentation with quarterly application proved to be the best strategy, showing the degradation of compounds of high (34.4% annual average) and low (21.9% annual average) molecular weight. A high degradation rate for high molecular weight compounds demonstrates that this technique can be successfully applied in bioremediation of areas with compounds considered toxic and stable in nature, contributing to the mitigation of impacts generated by PAHs.

A new huriine genus and notes on morphological characters (Araneae: Salticidae: Salticinae)

Huriini Simon, 1901 currently consists of six genera and 17 species, distributed exclusively in South America. In this work, the huriine genus Guriurius Marta, Bustamante, Ruiz Rodrigues, gen. nov. is proposed with two new species herein described: Guriurius minuano Marta, Bustamante, Ruiz Rodrigues, sp. nov. (type species) and Guriurius nancyae Marta, Bustamante, Ruiz Rodrigues, sp. nov. The female of Atelurius segmentatus Simon, 1901 is described and illustrated for the first time. Scoturius dipterioides Perger Rubio, 2018 is transferred to Atelurius Simon, 1901 due to the morphological similarity of copulatory ducts of epigyne, and Hurius pisac Galiano, 1985 is transferred to Simonurius Galiano, 1988 due to the similarities in body shape and female genitalia. Simonurius campestratus (Simon, 1901) is synonymized with Simonurius quadratarius (Simon, 1901). The interpretation of genitalic characters in Huriini is discussed. In addition, we provide new distributional records for Admesturius bitaeniatus (Simon, 1901), Ad. mariaeugeniae Bustamante Scioscia, 2014, Ad. schajovskoyi Galiano, 1988, At. segmentatus Simon, 1901, Scoturius tigris Simon, 1901, Hurius aeneus (Mello-Leito, 1941), and Simonurius gladifer (Simon, 1901). Except for Urupuyu Ruiz Maddison, 2015, all huriine genera are rediagnosed in the new context of tribe and genus composition.

New benzo(a)pyrene-degrading strains of the Burkholderia cepacia complex prospected from activated sludge in a petrochemical wastewater treatment plant

The prospection of bacteria that are resistant to polyaromatic hydrocarbons (PAH) of activated sludge from a Petrochemical Wastewater Treatment Plant (WWTP) allows investigating potential biodegraders of PAH. For this purpose, sludge samples were cultured with benzo(a)pyrene and/or naphthalene as carbon sources. The recovered isolates were characterized by biochemical methods and identified based on the analysis of the sequence of three genes: 16S, recA and gyrB. The isolated strains were shown to be capable of producing surfactants, which are important for compound degradation. The ability to reduce benzo(a)pyrene in vitro was tested by gas chromatography. After 20 days of experiment, the consortium that was enriched with 1 mg/L of benzo(a)pyrene was able to reduce 30% of the compound when compared to a control without bacteria. The four isolated strains that significantly reduced benzo(a)pyrene belong to the Burkholderia cepacia complex and were identified within the consortium as the species B. cenocepacia IIIa, B. vietnamiensis, B. cepacia, and B. multivorans. This finding demonstrates the biotechnological potential of the B. cepacia complex strains for use in wastewater treatment and bioremediation. Previous studies on hydrocarbon-degrading strains focused mainly on contaminated soil or marine areas. In this work, the strains were prospected from activated sludge in a WWTP and showed the potential of indigenous samples to be used in both improving treatment systems and bioremediation of areas contaminated with petrochemical waste.

Widespread Pig Farming Practice Linked to Shifts in Skin Microbiomes and Disease in Pond-Breeding Amphibians

Farming practices may reshape the structure of watersheds, water quality, and the health of aquatic organisms. Nutrient enrichment from agricultural pollution increases disease pressure in many host-pathogen systems, but the mechanisms underlying this pattern are not always resolved. For example, nutrient enrichment should strongly influence pools of aquatic environmental bacteria, which has the potential to alter microbiome composition of aquatic animals and their vulnerability to disease. However, shifts in the host microbiome have received little attention as a link between nutrient enrichment and diseases of aquatic organisms. We examined nutrient enrichment through the widespread practice of integrated pig-fish farming and its effects on microbiome composition of Brazilian amphibians and prevalence of the globally distributed amphibian skin pathogen Batrachochytrium dendrobatidis (Bd). This farming system drove surges in fecal coliform bacteria, disturbing amphibian skin bacterial communities such that hosts recruited higher proportions of Bd-facilitative bacteria and carried higher Bd prevalence. Our results highlight previously overlooked connections between global trends in land use change, microbiome dysbiosis, and wildlife disease. These interactions may be particularly important for disease management in the tropics, a region with both high biodiversity and continually intensifying anthropogenic pressures on aquatic wildlife habitats.

Differential Expression and PAH Degradation: What Burkholderia vietnamiensis G4 Can Tell Us?

Petroleum is the major energy matrix in the world whose refining generates chemical byproducts that may damage the environment. Among such waste, polycyclic aromatic hydrocarbons (PAH) are considered persistent pollutants. Sixteen of these are considered priority for remediation, and among them is benzo(a)pyrene. Amid remediation techniques, bioremediation stands out. The genus Burkholderia is amongst the microorganisms known for being capable of degrading persistent compounds; its strains are used as models to study such ability. High-throughput sequencing allows researchers to reach a wider knowledge about biodegradation by bacteria. Using transcripts and mRNA analysis, the genomic regions involved in this aptitude can be detected. To unravel these processes, we used the model B. vietnamiensis strain G4 in two experimental groups: one was exposed to benzo(a)pyrene and the other one (control) was not. Six transcriptomes were generated from each group aiming to compare gene expression and infer which genes are involved in degradation pathways. One hundred fifty-six genes were differentially expressed in the benzo(a)pyrene exposed group, from which 33% are involved in catalytic activity. Among these, the most significant genomic regions were phenylacetic acid degradation protein paaN, involved in the degradation of organic compounds to obtain energy; oxidoreductase FAD-binding subunit, related to the regulation of electrons within groups of dioxygenase enzymes with potential to cleave benzene rings; and dehydrogenase, described as accountable for phenol degradation. These data provide the basis for understanding the bioremediation of benzo(a)pyrene and the possible applications of this strain in polluted environments.

Far away, so close! Integrative taxonomy reveals a new genus and species of land flatworm (Platyhelminthes: Geoplanidae) from southern South America

Land flatworms usually show low ability to disperse and high endemicity, displaying many singletons in studies on land planarian assemblages. Thus, many species have been described based on specimens sampled in a single locality and/or on a few specimens. Based on phylogenetic analyses of concatenated COI and 18S rRNA genes and morphological analyses, a new genus and species of geoplaninid land planarian is described from central–east Argentina and southern Brazil. Winsoria gen. nov. shows, among its most outstanding features, a ventral cephalic retractor muscle and a subneural muscle layer that extends throughout the anterior region of the body. In addition, characters of the reproductive system and the phylogenetic analyses support the erection of this new genus. According to molecular phylogenies,Winsoria bipatria sp. nov. is closely related to species of Luteostriata, Supramontana and Issoca, taxa that also possess a cephalic retractor muscle. Despite its disjunct distribution, phylogenetic analyses, genetic divergence and morphological features show that the allopatric populations studied herein belong to a single species. We argue that the occurrence of W. bipatria in localities separated by hundreds of kilometres and a geographical barrier should be explained by passive dispersal.

Integrative approach reveals two new species of Obama (Platyhelminthes: Tricladida) from the South-Brazilian Atlantic Forest

The genus Obama Carbayo et al., 2013 includes 38 species, being the most species-rich within Geoplaninae. Species of this genus show a similar anatomy regarding their copulatory apparatus, which may hinder species differentiation. In this study, we describe two new species, presenting a marbled colour pattern, found in two different phytophysionomies of the Atlantic Forest, namely Semi-deciduous Forest and Araucaria Forest. Both species can be distinguished from their congeners, as well from each other, by colour pattern and eye arrangement combined with characteristics of the pharynx, penis papilla and prostatic vesicle, confirmed by molecular analyses from cytochrome c oxidase subunit I gene (COI). Phylogenetic analyses suggest that both species herein studied are closely related to another species that occurs in areas of Araucaria Forest (O. maculipunctata). Results also indicate the need to use at least 600 bp of the gene COI in the definitions of interspecific divergences and for species delineation, at least for the genus Obama.

Combining morphology and molecular data to improve Drosophila paulistorum (Diptera, Drosophilidae) taxonomic status

The willistoni species subgroup has been the subject of several studies since the latter half of the past century and is considered a Neotropical model for evolutionary studies, given the many levels of reproductive isolation and different evolutionary stages occurring within them. Here we present for the first time a phylogenetic reconstruction combining morphological characters and molecular data obtained from 8 gene fragments (COI, COII, Cytb, Adh, Ddc, Hb, kl-3 and per). Some relationships were incongruent when comparing morphological and molecular data. Also, morphological data presented some unresolved polytomies, which could reflect the very recent divergence of the subgroup. The total evidence phylogenetic reconstruction presented well-supported relationships and summarized the results of all analyses. The diversification of the willistoni subgroup began about 7.3 Ma with the split of D. insularis while D.paulistorum complex has a much more recent diversification history, which began about 2.1 Ma and apparently has not completed the speciation process, since the average time to sister species separation is one million years, and some entities of the D. paulistorum complex diverge between 0.3 and 1 Ma. Based on the obtained data, we propose the categorization of the former "semispecies" of D. paulistorum as a subspecies and describe the subspecies D. paulistorum amazonian, D. paulistorum andeanbrazilian, D. paulistorum centroamerican, D. paulistorum interior, D. paulistorum orinocan and D. paulistorum transitional.

Bacterial Community of the Rice Floodwater Using Cultivation-Independent Approaches

In agricultural systems, interactions between plants and microorganisms are important to maintaining production and profitability. In this study, bacterial communities in floodwaters of rice fields were monitored during the vegetative and reproductive stages of rice plant development using 16S amplicon sequencing. The study was conducted in the south of Brazil, during the crop years 2011/12 and 2012/13. Comparative analyses showed strong differences between the communities of floodwaters associated with the two developmental stages. During the vegetative stage, 1551 operational taxonomic units (OTUs) were detected, while less than half that number (603) were identified in the reproductive stage. The higher bacterial richness observed in floodwater collected during the vegetative stage may have been favored by the higher concentration of nutrients, such as potassium, due to rhizodeposition and fertilizer application. Eighteen bacterial phyla were identified in both samples. Both communities were dominated by Gammaproteobacteria. In the vegetative stage, Alphaproteobacteria and Betaproteobacteria were more abundant and, in contrast, Bacilli and Clostridia were the more dominant classes in the reproductive stage. The major bacterial taxa identified have been previously identified as important colonizers of rice fields. The richness and composition of bacterial communities over cultivation time may contribute to the sustainability of the crop.

Body doubles: an integrative taxonomic approach reveals new sibling species of land planarians

Records of cryptic species have continued to emerge in the scientific literature, often revealed by the use of molecular phylogenetic analyses in an integrative taxonomic approach. This study addresses a group of four striped flatworms from the genus Pasipha Ogren & Kawakatsu, showing a pale median stripe on a dark dorsal surface. Based on morphological and molecular analyses from the cytochrome c oxidase subunit I gene (COI), we establish that we are dealing with sibling species that are closely related to P. brevilineata Leal-Zanchet, Rossi & Alvarenga, 2012, a recently described species with a similar colour pattern. Thus, we describe three of the studied flatworms as new species and propose one new unconfirmed candidate species based on molecular data. In addition, sequence analysis revealed 40 nucleotide autapomorphies supporting the species studied herein. Considering anatomical and histological features, the three new species are differentiated from their congeners mainly by details of the copulatory apparatus, such as the occurrence of an epithelium of pseudostratified appearance lining the female atrium and the shape and position of the proximal portion of the prostatic vesicle.

Ancient female philopatry, asymmetric male gene flow, and synchronous population expansion support the influence of climatic oscillations on the evolution of South American sea lion (Otaria flavescens)

The South American sea lion (Otaria flavescens) is widely distributed along the southern Atlantic and Pacific coasts of South America with a history of significant commercial exploitation. We aimed to evaluate the population genetic structure and the evolutionary history of South American sea lion along its distribution by analyses of mitochondrial DNA (mtDNA) and 10 nuclear microsatellites loci. We analyzed 147 sequences of mtDNA control region and genotyped 111 individuals of South American sea lion for 10 microsatellite loci, representing six populations (Peru, Northern Chile, Southern Chile, Uruguay (Brazil), Argentina and Falkland (Malvinas) Islands) and covering the entire distribution of the species. The mtDNA phylogeny shows that haplotypes from the two oceans comprise two very divergent clades as observed in previous studies, suggesting a long period (>1 million years) of low inter-oceanic female gene flow. Bayesian analysis of bi-parental genetic diversity supports significant (but less pronounced than mitochondrial) genetic structure between Pacific and Atlantic populations, although also suggested some inter-oceanic gene flow mediated by males. Higher male migration rates were found in the intra-oceanic population comparisons, supporting very high female philopatry in the species. Demographic analyses showed that populations from both oceans went through a large population expansion ~10,000 years ago, suggesting a very similar influence of historical environmental factors, such as the last glacial cycle, on both regions. Our results support the proposition that the Pacific and Atlantic populations of the South American sea lion should be considered distinct evolutionarily significant units, with at least two managements units in each ocean.

Diversity of culturable Gram-negative bacteria isolated from irrigation water of two rice crop regions in Southern Brazil

In this study, we assessed the diversity of Gram-negative bacteria found in water used for irrigation of rice crops in two growing areas of southern Brazil. Samples were collected from the main irrigation channel and field drain area. Twenty-two bacterial species were found in Cachoeirinha and 28 in Camaquã. In both areas, the most frequent bacterial families were Enterobacteriaceae and Aeromonadaceae. Differences in microbial diversity were observed in both study areas. Thirty-five Gram-negative species were identified; however, only 15 were common in both locations. In addition, there were found pathogenic and drug-resistant species, such as Acinetobacter sp., Brucella spp., and Chryseobacterium meningosepticum. This study demonstrates the existence of a number of pathogenic species in aquatic ecosystems analyzed in three consecutive crop years, especially water used for rice production.

Trace elements concentrations in Buff-breasted Sandpiper sampled in Lagoa do Peixe National Park, Southern Brazil

Cadmium, cobalt, chromium, copper, manganese, nickel, zinc and lead concentrations were detected in feathers of Buff-breasted Sandpipers (Calidris subruficollis) captured during the non-breeding season and analyzed with relationship to body mass. Of these metals tested for, only copper levels (2.28 µg/g) were positively correlated with bird body mass. Zinc levels showed higher concentration (67.97 µg/g) than the other metals, and cadmium levels showed the lowest concentration (0.14 µg/g). Trace element concentrations were below toxicity levels for all tested chemicals and we suggest that this probably reflects that essential elements are maintained there by normal homeostatic mechanism and that no excessive environmental exposure to these elements during migration or on the wintering area is suggested by these results.

Structural and sequence diversity of the transposon Galileo in the Drosophila willistoni genome

Background

Galileo is one of three members of the P superfamily of DNA transposons. It was originally discovered in Drosophila buzzatii, in which three segregating chromosomal inversions were shown to have been generated by ectopic recombination between Galileo copies. Subsequently, Galileo was identified in six of 12 sequenced Drosophila genomes, indicating its widespread distribution within this genus. Galileo is strikingly abundant in Drosophila willistoni, a neotropical species that is highly polymorphic for chromosomal inversions, suggesting a role for this transposon in the evolution of its genome.

Results

We carried out a detailed characterization of all Galileo copies present in the D. willistoni genome. A total of 191 copies, including 133 with two terminal inverted repeats (TIRs), were classified according to structure in six groups. The TIRs exhibited remarkable variation in their length and structure compared to the most complete copy. Three copies showed extended TIRs due to internal tandem repeats, the insertion of other transposable elements (TEs), or the incorporation of non-TIR sequences into the TIRs. Phylogenetic analyses of the transposase (TPase)-encoding and TIR segments yielded two divergent clades, which we termed Galileo subfamilies V and W. Target-site duplications (TSDs) in D. willistoni Galileo copies were 7- or 8-bp in length, with the consensus sequence GTATTAC. Analysis of the region around the TSDs revealed a target site motif (TSM) with a 15-bp palindrome that may give rise to a stem-loop secondary structure.

Conclusions

There is a remarkable abundance and diversity of Galileo copies in the D. willistoni genome, although no functional copies were found. The TIRs in particular have a dynamic structure and extend in different ways, but their ends (required for transposition) are more conserved than the rest of the element. The D. willistoni genome harbors two Galileo subfamilies (V and W) that diverged ~9 million years ago and may have descended from an ancestral element in the genome. Galileo shows a significant insertion preference for a 15-bp palindromic TSM.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-792) contains supplementary material, which is available to authorized users.

Implementation of the sludge biotic index in a petrochemical WWTP in Brazil: improving operational control with traditional methods

Microbiological analysis of activated sludge is an important tool for monitoring wastewater treatment plants (WWTP). The utilization of the sludge biotic index (SBI) provides helpful information in examining the quality of biological treatment process and has been tested for several different systems. Although its utilization has been increasing, it is still not widespread, especially in Brazil. Also, its applicability has been considered limited for some particular systems. Thus, it becomes important to evaluate the relations among operational and biological parameters of each WWTP in order to characterize the system and its variations. In this work, microscopic analysis were performed once a week for 1 year (n = 54) and the results were compared to the physicochemical, operational parameters and efficiency of the plant along the period. The four seasons were comprised and analyzed, as we cannot neglect the influence of environmental changes in this subtropical region. Not only had we found a strong influence of the evaluated parameters on the structure of the biological community but there is also a good correspondence of SBI with the performance of the WWTP. More importantly, including microscopic analysis in the operational routine made it possible to notice even the slightest changes in the biological community that were not enough to diminish the SBI classification of the sludge, but were satisfactorily informative to show in advance to operators when to take corrective actions about an increase of COD and BOD in the influent and when it was necessary to discard the exceeding sludge.

Reevaluating the infection status by the Wolbachia endosymbiont in Drosophila Neotropical species from the willistoni subgroup

Infections by the endosymbiotic bacterium Wolbachia developed a rapid global expansion within Old World Drosophila species, ultimately infecting also Neotropical species. In this sense, screenings are necessary to characterize new variants of Wolbachia or new hosts, and also in order to map the dynamics of already known infections. In this paper, we performed a double screening approach that combined Dot-blot and PCR techniques in order to reevaluate the infection status by Wolbachia in species from the willistoni subgroup of Drosophila. Genomic DNA from isofemale lines descendent from females collected in the Amazonian Rainforest (n=91) were submitted to Dot-blot, and were positive for Wolbachia, producing a gradient of hybridization signals, suggesting different infection levels, which was further confirmed through quantitative PCR. Samples with a strong signal in the Dot-blot easily amplified in the wsp-PCR, unlike most of the samples with a medium to weak signal. It was possible to molecularly characterize three Drosophila equinoxialis isofemale lines that were found to be infected in a low density by a wMel-like Wolbachia strain, which was also verified in a laboratory line of Drosophila paulistorum Amazonian. We also found Drosophila tropicalis to be infected with the wAu strain and a Drosophila paulistorum Andean-Brazilian semispecies laboratory line to be infected with a wAu-like Wolbachia. Moreover, we observed that all Drosophila willistoni samples tested with the VNTR-141 marker harbor the same Wolbachia variant, wWil, either in populations from the South or the North of Brazil. Horizontal transfer events involving species of Old World immigrants and Neotropical species of the willistoni subgroup are discussed.

Courtship behavior of Zaprionus indianus (Gupta) (Diptera: Drosophilidae) from populations colonizing South America

We describe for the first time the sexual behavior and the courtship song of males of the African fly Zaprionus indianus (Gupta), a recent invader of South America. The male courtship song is formed by monocyclic pulses and the courtship behavior is simple when compared to that of species of Drosophila. Two interpulse interval (IPI) distributions were observed: pre-mounting and mounting. No significant difference was observed between the pre-mounting IPIs of males that descended from three geographical populations from South America. We also observed the songs produced by females and the homosexual behavior exhibited by males. A sequence of bursts is produced by females as a refusal signal against males, while males emit a characteristic song that identifies sex genus, which differs from the courtship song. The short courtship and mating latencies recorded reveal vigorous males and receptive females, respectively.

Wolbachia pipientis is associated with different mitochondrial haplotypes in natural populations of Drosophila willistoni

The prevalence of the endosymbiont Wolbachia pipientis and its effects on mitochondrial genetic diversity were analyzed in natural populations of Drosophila willistoni, a neotropical species recently infected. Total infection rate was 55% and no evidence was found that the Wolbachia infection decreased the diversity of mtDNA. Wolbachia was seen to be associated with different mitochondria, suggesting multiple horizontal transmission events and/or transmission paternal leakage of mitochondrial and/or Wolbachia. These hypotheses are evaluated in the context of the present study and other research.

Chromosomal evolution of sibling species of the Drosophila willistoni group. I. Chromosomal arm IIR (Muller's element B)

The phylogenetic relationships among nine entities of Drosophila belonging to the D. willistoni subgroup were investigated by establishing the homologous chromosomal segments of IIR chromosome, Muller's element B (equivalent to chromosome 2L of D. melanogaster). The sibling species of the D. willistoni group investigated include D. willistoni, D. tropicalis tropicalis, D. tropicalis cubana, D. equinoxialis, D. insularis and four semispecies of the D. paulistorum complex. The phylogenetic relationships were based on the existence of segments in different triads of species, which could only be produced by overlapping inversions. Polytene banding similarity maps and break points of inversions between species are presented. The implications of the chromosomal data for the phylogeny of the species and comparisons with molecular data are discussed. The aim of this study is to produce phylogenetic trees depicting accurately the sequence of natural events that have occurred in the evolution of these sibling species.

Two decades of colonization of the urban environment of Porto Alegre, southern Brazil, by Drosophila paulistorum (Diptera, Drosophilidae)

Drosophila paulistorum Dobzhansky & Pavan, 1949 had initially been considered absent in anthropogenically disturbed environments, but in 1985 the detection of the species in Porto Alegre city, southern Brazil, suggested its potential to colonize new habitats and laid the foundations for ecologic studies on this species' populations. This study followed the variations in D. paulistorum populations in this town almost 20 years after its first local record. Drosophilid specimens were collected in sites with different urbanization grades and the results point to the expressive decline in D. paulistorum populations in Porto Alegre. This decline may be linked to urban growth and to naturally driven population decline, as imputed to climatic changes like variations in maximum and minimum temperatures as a consequence of a global climate warming. Also, the recent introduction of exotic species Zaprionus indianus Gupta, 1970 seems to play a role in this scenario, changing the interactions between native species.