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J Environ Manage ; 256: 109894, 2020 Feb 15.
Artigo em Inglês | MEDLINE | ID: mdl-31989973


Despite the wide variety of variables commonly employed to measure the success of rehabilitation, the assessment and subsequent definition of indicators of environmental rehabilitation status are not simple tasks. The main challenges are comparing rehabilitated sites with target ecosystems as well as integrating individual environmental and eventually collinear variables into a single tractable measure for the state of a system before effective indicators that track rehabilitation may be modeled. Furthermore, a consensus is lacking regarding which and how many variables need to be surveyed for a reliable estimation of rehabilitation status. Here, we propose a multivariate ordination to integrate variables related to ecological processes, vegetation structure, and community diversity into a single estimation of rehabilitation status. As a case, we employed a curated set of 32 environmental variables retrieved from nonrevegetated, rehabilitating and reference sites associated with iron ore mines from the Urucum Massif, Mato Grosso do Sul, Brazil. By integrating this set of environmental variables into a single estimation of rehabilitation status, the proposed multivariate approach is straightforward and able to adequately address collinearity among variables. The proposed methodology allows for the identification of biases towards single variables, surveys or analyses, which is necessary to rank environmental variables regarding their importance to the assessment. Furthermore, we show that bootstrapping permitted the detection of the minimum number of environmental variables necessary to achieve reliable estimations of the rehabilitation status. Finally, we show that the proposed variable integration enables the definition of case-specific environmental indicators for more rapid assessments of mineland rehabilitation. Thus, the proposed multivariate ordination represents a powerful tool to facilitate the diagnosis of rehabilitating sites worldwide provided that sufficient environmental variables related to ecological processes, diversity and vegetation structure are gathered from nonrehabilitated, rehabilitating and reference study sites. By identifying deviations from predicted rehabilitation trajectories and providing assessments for environmental agencies, this proposed multivariate ordination increases the effectiveness of (mineland) rehabilitation.

Ecologia , Ecossistema , Brasil , Emprego , Monitoramento Ambiental , Mineração
Front Microbiol ; 10: 2003, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31555238


During the last decades it has become increasingly clear that the microbes that live on and in humans are critical for health. The communities they form, termed microbiomes, are involved in fundamental processes such as the maturation and constant regulation of the immune system. Additionally, they constitute a strong defense barrier to invading pathogens, and are also intricately linked to nutrition. The parameters that affect the establishment and maintenance of these microbial communities are diverse, and include the genetic background, mode of birth, nutrition, hygiene, and host lifestyle in general. Here, we describe the characterization of the gut microbiome of individuals living in the Amazon, and the comparison of these microbial communities to those found in individuals from an urban, industrialized setting. Our results showed striking differences in microbial communities from these two types of populations. Additionally, we used high-throughput metabolomics to study the chemical ecology of the gut environment and found significant metabolic changes between the two populations. Although we cannot point out a single cause for the microbial and metabolic changes observed between Amazonian and urban individuals, they are likely to include dietary differences as well as diverse patterns of environmental exposure. To our knowledge, this is the first description of gut microbial and metabolic profiles in Amazonian populations, and it provides a starting point for thorough characterizations of the impact of individual environmental conditions on the human microbiome and metabolome.

Proc Natl Acad Sci U S A ; 116(30): 15106-15115, 2019 Jul 23.
Artigo em Inglês | MEDLINE | ID: mdl-31270239


Salamanders and lungfishes are the only sarcopterygians (lobe-finned vertebrates) capable of paired appendage regeneration, regardless of the amputation level. Among actinopterygians (ray-finned fishes), regeneration after amputation at the fin endoskeleton has only been demonstrated in polypterid fishes (Cladistia). Whether this ability evolved independently in sarcopterygians and actinopterygians or has a common origin remains unknown. Here we combine fin regeneration assays and comparative RNA-sequencing (RNA-seq) analysis of Polypterus and axolotl blastemas to provide support for a common origin of paired appendage regeneration in Osteichthyes (bony vertebrates). We show that, in addition to polypterids, regeneration after fin endoskeleton amputation occurs in extant representatives of 2 other nonteleost actinopterygians: the American paddlefish (Chondrostei) and the spotted gar (Holostei). Furthermore, we assessed regeneration in 4 teleost species and show that, with the exception of the blue gourami (Anabantidae), 3 species were capable of regenerating fins after endoskeleton amputation: the white convict and the oscar (Cichlidae), and the goldfish (Cyprinidae). Our comparative RNA-seq analysis of regenerating blastemas of axolotl and Polypterus reveals the activation of common genetic pathways and expression profiles, consistent with a shared genetic program of appendage regeneration. Comparison of RNA-seq data from early Polypterus blastema to single-cell RNA-seq data from axolotl limb bud and limb regeneration stages shows that Polypterus and axolotl share a regeneration-specific genetic program. Collectively, our findings support a deep evolutionary origin of paired appendage regeneration in Osteichthyes and provide an evolutionary framework for studies on the genetic basis of appendage regeneration.

Sci Data ; 6: 190008, 2019 02 12.
Artigo em Inglês | MEDLINE | ID: mdl-30747914


Microorganisms are useful environmental indicators, able to deliver essential insights to processes regarding mine land rehabilitation. To compare microbial communities from a chronosequence of mine land rehabilitation to pre-disturbance levels from references sites covered by native vegetation, we sampled non-rehabilitated, rehabilitating and reference study sites from the Urucum Massif, Southwestern Brazil. From each study site, three composed soil samples were collected for chemical, physical, and metagenomics analysis. We used a paired-end library sequencing technology (NextSeq 500 Illumina); the reads were assembled using MEGAHIT. Coding DNA sequences (CDS) were identified using Kaiju in combination with non-redundant NCBI BLAST reference sequences containing archaea, bacteria, and viruses. Additionally, a functional classification was performed by EMG v2.3.2. Here, we provide the raw data and assembly (reads and contigs), followed by initial functional and taxonomic analysis, as a base-line for further studies of this kind. Further investigation is needed to fully understand the mechanisms of environmental rehabilitation in tropical regions, inspiring further researchers to explore this collection for hypothesis testing.

Monitoramento Ambiental/métodos , Metagenômica/métodos , Microbiota , Microbiologia do Solo , Archaea/genética , Bactérias/genética , Brasil , Sequenciamento de Nucleotídeos em Larga Escala , Ferro , Microbiota/genética , Mineração , Vírus/genética
PLoS One ; 13(8): e0201417, 2018.
Artigo em Inglês | MEDLINE | ID: mdl-30089144


Isoetes are ancient quillworts members of the only genus of the order Isoetales. The genus is slow evolving but is resilient, and widespread worldwide. Two recently described species occur in the Eastern Brazilian Amazon, Isoetes serracarajensis and Isoetes cangae. They are found in the ironstone grasslands known as Canga. While I. serracarajensis is present mostly in seasonal water bodies, I. cangae is known to occur in a single permanent lake at the South mountain range. In this work, we undertake an extensive morphological, physiological and genetic characterization of both species to establish species boundaries and better understand the morphological and genetic features of these two species. Our results indicate that the morphological differentiation of the species is subtle and requires a quantitative assessment of morphological elements of the megaspore for diagnosis. We did not detect differences in microspore output, but morphological peculiarities may establish a reproductive barrier. Additionally, genetic analysis using DNA barcodes and whole chloroplast genomes indicate that although the plants are genetically very similar both approaches provide diagnostic characters. There was no indication of population structuring I. serracarajensis. These results set the basis for a deeper understanding of the evolution of the Isoetes genus.

Código de Barras de DNA Taxonômico , Genoma de Cloroplastos , Lycopodiaceae , Lycopodiaceae/classificação , Lycopodiaceae/genética , Lycopodiaceae/crescimento & desenvolvimento , América do Sul
Res Rep Trop Med ; 8: 17-20, 2017.
Artigo em Inglês | MEDLINE | ID: mdl-30050341


Introduction: Lysinibacillus sphaericus is a highly effective and specific bioinsecticide used for the control of Culicidae larvae. Objective: This study aimed to identify and characterize L. sphaericus strains isolated from Culex quinquefasciatus larvae in Brazil. Methods: C. quinquefasciatus larvae were collected from streams in the urban area of São Paulo state. L. sphaericus strains were identified through cytomorphology, biochemical, and physiological analyses. Qualitative bioassays were performed to evaluate the toxicity of the strains against C. quinquefasciatus. The crystal compound protein pattern of L. sphaericus strains was analyzed by sodium dodecyl sulfate polyacrylamide gel electrophoresis. Five reference strains were used as standards in all tests performed. Repetitive extragenic palindromic elements-polymerase chain reaction (REP-PCR) was utilized in an attempt to differentiate pathogenic and nonpathogenic isolates. Results: Twenty-one strains were isolated. Only one presented toxic activity against C. quinquefasciatus. REP-PCR results identified 23 patterns among the 26 strains used in the study, and the fragment analysis showed low similarity (16%) between L. sphaericus isolates and the five reference strains. Conclusion: Comparison of strains isolated in this study using REP-PCR showed a low similarity to other strains, demonstrating the high intraspecific variability for L. sphaericus.

Int J Food Microbiol ; 147(1): 12-6, 2011 May 14.
Artigo em Inglês | MEDLINE | ID: mdl-21440319


Bacillus cereus is an ever-present problem. It is widely distributed in several environments such as soil and plants and is commonly isolated from food and additives. In this study we analyzed 97 foodborne B. cereus sensu stricto strains isolated in Brazil in the 1980's, 1990's and 2000's in order to investigate the genetic diversity (assessed by Rep-PCR), antimicrobial resistance and toxigenic profiles (presence of hblA, hblC and hblD; nheA, nheB and nheC as well as cytK, ces and entFM genes) of such strains. The majority of the strains (79, 81.4%) were ß-hemolytic. The NHE complex was found in 82 strains (84.5%) and HBL complex was found in 61 (62.9%) strains. All strains were negative to ces. The cytK-2 gene was found in 44 (45.4%) strains. The predominant toxigenic pattern was type I (32, 33%) which included strains positive for all toxin genes but ces. Computer assisted cluster analysis of Rep-PCR profiles showed a high genetic diversity. Seven major clusters comprising two or more strains were found and cluster 1 was predominant (ten strains, nine of them showing 100% similarity). This cluster included strains isolated in the 1980's and the 1990's. Cluster analysis of Rep-PCR profiles based on decade of isolation, source, hemolytic pattern, toxigenic and antibiotic resistance patterns revealed a similar clustering pattern as found in the analysis including all strains. The inability to observe a predominant band pattern when Rep-PCR cluster analysis was based on decade of isolation suggests that this diversity has been maintained over time. All strains were susceptible to gentamicin. We detected resistance to tetracycline (11 strains showing intermediate resistance and nine completely resistant strains), clindamycin (ten intermediate strains) and vancomycin (one strain). Clindamycin resistance showed statistical association with strains isolated in 2000's. The predominant resistance pattern was type A (72, 72.2%) which included strains susceptible to all drugs tested. Our results suggest that the majority of the strains present in several types of food in Brazil pose a potential risk to cause food poisoning due to the high prevalence of toxin genes found in these strains. However, additional studies involving cytotoxicity tests and affiliation of these strains to phylogenetic groups based on molecular data would be useful to better evaluate this potential and could provide a more accurate indication of the risk.

Bacillus cereus/genética , Contaminação de Alimentos/análise , Microbiologia de Alimentos , Variação Genética , Antibacterianos/farmacologia , Bacillus cereus/classificação , Bacillus cereus/efeitos dos fármacos , Bacillus cereus/isolamento & purificação , Brasil , Análise por Conglomerados , DNA Bacteriano/genética , Farmacorresistência Bacteriana , Enterotoxinas/genética , Doenças Transmitidas por Alimentos , Testes de Sensibilidade Microbiana , Reação em Cadeia da Polimerase/métodos
J Invertebr Pathol ; 107(1): 11-5, 2011 May.
Artigo em Inglês | MEDLINE | ID: mdl-21241705


The aim of this study was to investigate the naturally occurring bacteria from Culicidae larvae found in São Paulo state between 2006 and 2008 from the Tiete Ecological Park in the municipality of Caraguatatuba. Bacterial strains were obtained after surface sterilization of larvae followed by thermal treatment and incubation in bacteriological media under laboratory conditions. Identification was determined using cytomorphology, biochemical and physiological tests. Strains were characterized by qualitative evaluation of biological activity against Culicidae larvae, comparing protein profiles obtained by electrophoresis of crystal protoxins, electrophoresis of Lysinibacillus sphaericus isoenzymes, detection of the L(2) fraction of Hemolytic BL enterotoxin and amplification of DNA using Multiplex-PCR to detect HBL, NHE, CytK, BceT and EntFM enterotoxins. The results obtained in this study demonstrated that the endosymbiotic bacterial diversity belonging to Bacillus and related genera associated with Culicidae larvae is limited to a number of species that does not vary throughout the seasons.

Bacillus/isolamento & purificação , Culicidae/microbiologia , Animais , Bacillus/classificação , Brasil , Larva
Ciênc. rural ; 39(4): 1045-1050, jul. 2009. graf, tab
Artigo em Português | LILACS-Express | ID: lil-519133


Com objetivo de avaliar o efeito do lodo de esgoto na formação e qualidades de tapetes de grama, foi instalado, em Itapetininga, São Paulo (SP), o experimento utilizando grama Zoysia japonica Steud., conhecida como esmeralda. O delineamento experimental utilizado foi o de blocos ao acaso em parcelas subdivididas, com quatro repetições, sendo as parcelas principais constituídas de cinco doses de lodo (0, 10, 20, 30 e 40Mg ha-1, base seca), mais um tratamento com NPK, de acordo com as necessidades da cultura e as subparcelas com dois sistemas de manejo (com e sem o uso de escarificador utilizado para romper uma camada superficial compactada). Utilizou-se o lodo da Estação de Tratamento de Esgoto de Jundiaí, SP. As doses de lodo aplicadas correspondem às doses de 100, 200, 300 e 400kg ha-1 de nitrogênio. Após 165 dias da aplicação do lodo de esgoto, a dose de 31Mg ha-1 permitiu o fechamento completo (100% da taxa de cobertura do solo) e a maior resistência dos tapetes de grama. O mesmo resultado foi encontrado quando utilizou-se a adubação química. A testemunha e as parcelas que receberam 10Mg ha-1 de lodo não formaram tapete. O lodo de esgoto aplicado em superfície promoveu redução da massa dos tapetes de grama esmeralda. O uso do escarificador reduziu a resistência dos tapetes de grama esmeralda. Os valores de metais pesados encontrados no lodo de esgoto estavam abaixo do limite estabelecido pelas normas que regulamenta a utilização do lodo de esgoto na agricultura.

Aiming to evaluate sewage sludge effect in the grass sod qualitiy and formation it was installed in Itapetininha - SP one experiment using Zoysia japonica Steud. The experimental design adopted was randomized blocks with split plot design, with four replications, the main plots consisting of five doses of sludge (0, 10, 20, 30 and 40Mg ha-1, a dry basis), another treatment with NPK, according to the requirement of the culture, and subplots with two management systems (with and without chisel use, to break a compacted surface layer). The sludge used came from "Estação de Tratamento de Esgoto de Jundiaí/SP". The doses of sludge applied correspond to the doses of 100, 200, 300 and 400kg ha-1 of nitrogen. 165 days after sewage sludge application, the dose of 31Mg ha-1 allowed the complete closing (100% of soil cover rate) and greater resistance of the zoysiagrass sod. The same results were found when chemical fertilization was used. The control and the plots that received 10Mg ha-1 of sludge did not formed sod. The sewage sludge applied to surface promoted reduction of zoysiagrass sod mass. The use of surface chisel reduced the strength of zoysiagrass sod. The heavy metals values found in sewage sludge were below the limit set by the rules governing the sewage sludge use in agriculture.