Metagenomics in Polluted Aquatic Environments

Metagenomics is defined as the culture-independent genomic analysis of biological assemblages providing access to the whole set of genes and genomes from a sample. It encompasses a variety of techniques that are based on (i) total DNA extraction from samples followed by PCR amplification of specific genes, (ii) library construction or amplification and sequencing of the whole genetic material. These methodologies have successfully been applied in studies of composition, dynamics, and functions of microbial communities in a variety of ecosystems including those subjected to anthropogenic modifications (Gilbert & Dupont, 2011). Culture independent methods allow the analysis of a set of metabolic genes from microbial communities, which can be used to determine how environmental conditions such as pollution can shape community composition and the diversity of genes associated with biogeochemical cycles such as those of carbon, nitrogen, and phosphorus (Singh et al., 2009). This approach is also useful for the discovery of novel environmental microorganisms and genes, with important applications for biotechnology, medicine, and bioremediation (Cardoso et al., 2011). This applicability has resulted in a recent sharp increase in studies focusing in the metagenomic analysis of polluted sites. Their aim is to characterize microbial communities from a diverse set of environments such as freshwater, marine sediments, open ocean, pelagic ecosystems, soil, and host-associated communities. An example of these initiatives is the Global Ocean Sampling Expedition (GOS), which assessed the genetic diversity of marine microbial communities around the Earth. Since 2003, an enormous amount of data has been generated by GOS helping scientists to reveal the microbial diversity and also allowing them to better understand microbial phylogeny and ecology (Gilbert & Dupont, 2011)

Lower lip squamous cell carcinoma in patients with photosensitive disorders : analysis of cases treated at the Brazilian National Cancer Institute (INCA) from 1999 to 2012

Lower lip squamous cell carcinoma (LLSCC) is a common malignancy of the head and neck, being mainly a consequence of a chronic exposure to ultraviolet (UV) light solar radiation. Here, we evaluated the clinicopathological profile of patients with photosensitive disorders (xeroderma pigmentosum, lupus erythematosus and albinism) that developed LLSCC. Data from patients who had a diagnosed LLSCC with a prior xeroderma pigmentosum, lupus erythematosus or albinism diagnosis that were treated at INCA from 1999 to 2012 were collected from patients? medical records (n=16). The control group was composed of 68 patients with LLSCC without a medical history of photosensitivity. The clinicopathological data of this study population were collected and the association between these variables was analyzed by Fisher?s exact test. Survival curves were constructed using the Kaplan?Meier method and compared by log-rank test. All statistical analyses were performed using SPSS statistics package. The mean age of patients in the photosensitive and non-photosensitive groups was 42 years and 67 years, respectively (p<0.0001). A previous history of malignant diseases was more common in the photosensitive group (p=0.001). In both groups, most tumors showed a pathological stage I/II disease. Overall and cancer-specific survival were not statistically different. However, disease-free interval showed a significant difference (p=0.01) between the photosensitive and non-photosensitive patients. Photosensitive patients presented LLSCC at earlier age but it usually was not the primary tumor in these patients. Furthermore, a more aggressive pathological behavior was not seen when compared with tumors from non-photosensitive patients. The disease-free interval was lower in photosensitive patients, as expected

Gut Bacterial Communities in the Giant Land Snail Achatina fulica and Their Modification by Sugarcane-Based Diet

The invasive land snail Achatina fulica is one of the most damaging agricultural pests worldwide representing a potentially serious threat to natural ecosystems and human health. This species is known to carry parasites and harbors a dense and metabolically active microbial community; however, little is known about its diversity and composition. Here, we assessed for the first time the complexity of bacterial communities occurring in the digestive tracts of field-collected snails (FC) by using culture-independent molecular analysis. Crop and intestinal bacteria in FC were then compared to those from groups of snails that were reared in the laboratory (RL) on a sugarcane-based diet. Most of the sequences recovered were novel and related to those reported for herbivorous gut. Changes in the relative abundance of Bacteroidetes and Firmicutes were observed when the snails were fed a high-sugar diet, suggesting that the snail gut microbiota can influence the energy balance equation. Furthermore, this study represents a first step in gaining a better understanding of land snail gut microbiota and shows that this is a complex holobiont system containing diverse, abundant and active microbial communities

Environmental Shaping of Sponge Associated Archaeal Communities

Archaea are ubiquitous symbionts of marine sponges but their ecological roles and the influence of environmental factors on these associations are still poorly understood.We compared the diversity and composition of archaea associated with seawater and with the sponges Hymeniacidon heliophila, Paraleucilla magna and Petromica citrina in two distinct environments: Guanabara Bay, a highly impacted estuary in Rio de Janeiro, Brazil, and the nearby Cagarras Archipelago. For this we used metagenomic analyses of 16S rRNA and ammonia monooxygenase (amoA) gene libraries. Hymeniacidon heliophila was more abundant inside the bay, while P. magna was more abundant outside and P. citrina was only recorded at the Cagarras Archipelago. Principal Component Analysis plots (PCA) generated using pairwise unweighted UniFrac distances showed that the archaeal community structure of inner bay seawater and sponges was different from that of coastal Cagarras Archipelago. Rarefaction analyses showed that inner bay archaeaoplankton were more diverse than those from the Cagarras Archipelago. Only members of Crenarchaeota were found in sponge libraries, while in seawater both Crenarchaeota and Euryarchaeota were observed. Although most amoA archaeal genes detected in this study seem to be novel, some clones were affiliated to known ammonia oxidizers such as Nitrosopumilus maritimus and Cenarchaeum symbiosum.The composition and diversity of archaeal communities associated with pollution-tolerant sponge species can change in a range of few kilometers, probably influenced by eutrophication. The presence of archaeal amoA genes in Porifera suggests that Archaea are involved in the nitrogen cycle within the sponge holobiont, possibly increasing its resistance to anthropogenic impacts. The higher diversity of Crenarchaeota in the polluted area suggests that some marine sponges are able to change the composition of their associated archaeal communities, thereby improving their fitness in impacted environments

The Transcriptome of Lutzomyia longipalpis (Diptera: Psychodidae) Male Reproductive Organs

BACKGROUND: It has been suggested that genes involved in the reproductive biology of insect disease vectors are potential targets for future alternative methods of control. Little is known about the molecular biology of reproduction in phlebotomine sand flies and there is no information available concerning genes that are expressed in male reproductive organs of Lutzomyia longipalpis, the main vector of American visceral leishmaniasis and a species complex. METHODS/PRINCIPAL FINDINGS: We generated 2678 high quality ESTs ("Expressed Sequence Tags") of L. longipalpis male reproductive organs that were grouped in 1391 non-redundant sequences (1136 singlets and 255 clusters). BLAST analysis revealed that only 57% of these sequences share similarity with a L. longipalpis female EST database. Although no more than 36% of the non-redundant sequences showed similarity to protein sequences deposited in databases, more than half of them presented the best-match hits with mosquito genes. Gene ontology analysis identified subsets of genes involved in biological processes such as protein biosynthesis and DNA replication, which are probably associated with spermatogenesis. A number of non-redundant sequences were also identified as putative male reproductive gland proteins (mRGPs), also known as male accessory gland protein genes (Acps). CONCLUSIONS: The transcriptome analysis of L. longipalpis male reproductive organs is one step further in the study of the molecular basis of the reproductive biology of this important species complex. It has allowed the identification of genes potentially involved in spermatogenesis as well as putative mRGPs sequences, which have been studied in many insect species because of their effects on female post-mating behavior and physiology and their potential role in sexual selection and speciation. These data open a number of new avenues for further research in the molecular and evolutionary reproductive biology of sand flies

Data from: Influence of salinity on bacterioplankton communities from the Brazilian rain forest to the coastal Atlantic Ocean

BACKGROUND: Planktonic bacteria are recognized as important drivers of biogeochemical processes in all aquatic ecosystems, however, the taxa that make up these communities are poorly known. The aim of this study was to investigate bacterial communities in aquatic ecosystems at Ilha Grande, Rio de Janeiro, Brazil, a preserved insular environment of the Atlantic rain forest and how they correlate with a salinity gradient going from terrestrial aquatic habitats to the coastal Atlantic Ocean. METHODOLOGY/PRINCIPAL FINDINGS: We analyzed chemical and microbiological parameters of water samples and constructed 16S rRNA gene libraries of free living bacteria obtained at three marine (two coastal and one offshore) and three freshwater (water spring, river, and mangrove) environments. A total of 836 sequences were analyzed by MOTHUR, yielding 269 freshwater and 219 marine operational taxonomic units (OTUs) grouped at 97% stringency. Richness and diversity indexes indicated that freshwater environments were the most diverse, especially the water spring. The main bacterial group in freshwater environments was Betaproteobacteria (43.5%), whereas Cyanobacteria (30.5%), Alphaproteobacteria (25.5%), and Gammaproteobacteria (26.3%) dominated the marine ones. Venn diagram showed no overlap between marine and freshwater OTUs at 97% stringency. LIBSHUFF statistics and PCA analysis revealed marked differences between the freshwater and marine libraries suggesting the importance of salinity as a driver of community composition in this habitat. The phylogenetic analysis of marine and freshwater libraries showed that the differences in community composition are consistent. CONCLUSIONS/SIGNIFICANCE: Our data supports the notion that a divergent evolutionary scenario is driving community composition in the studied habitats. This work also improves the comprehension of microbial community dynamics in tropical waters and how they are structured in relation to physicochemical parameters. Furthermore, this paper reveals for the first time the pristine bacterioplankton communities in a tropical island at the South Atlantic Ocean

Rhizoniera Griessinger 1971

Subgenus &lt;i&gt;Rhizoniera&lt;/i&gt; Griessinger, 1971 &lt;p&gt; &lt;b&gt;Definition.&lt;/b&gt; Chalinidae with an anisotropic, ladder-like choanosomal skeleton consisting of uni- multispicular ascending primary lines, connected by irregular unispicular secondary lines. Ectosomal skeleton usually absent; if present, consisting only of some vaguely strewn tangentially orientated oxeas. Spongin moderate to absent. Megascleres usually slender oxeas with acerated points. No microscleres (emmended from de Weerdt, 2002). Type species: &lt;i&gt;Reniera rhizophora&lt;/i&gt; Vacelet, 1969.&lt;/p&gt;Published as part of &lt;i&gt;Muricy, Guilherme, Esteves, Eduardo L., Monteiro, Leandro C., Rodrigues, Beatriz Roma &amp; Albano, Rodolpho M., 2015, A new species of Haliclona (Demospongiae: Haplosclerida: Chalinidae) from southeastern Brazil and the first record of Haliclona vansoesti from the Brazilian coast, pp. 536-550 in Zootaxa 3925 (4)&lt;/i&gt; on page 539, DOI: 10.11646/zootaxa.3925.4.3, &lt;a href="http://zenodo.org/record/232629"&gt;http://zenodo.org/record/232629&lt;/a&gt