Microbial Diversity of a Brazilian Coastal Region Influenced by an Upwelling System and Anthropogenic Activity

BACKGROUND: Upwelling systems are characterised by an intense primary biomass production in the surface (warmest) water after the outcrop of the bottom (coldest) water, which is rich in nutrients. Although it is known that the microbial assemblage plays an important role in the food chain of marine systems and that the upwelling systems that occur in southwest Brazil drive the complex dynamics of the food chain, little is known about the microbial composition present in this region. METHODOLOGY/PRINCIPAL FINDINGS: We carried out a molecular survey based on SSU rRNA gene from the three domains of the phylogenetic tree of life present in a tropical upwelling region (Arraial do Cabo, Rio de Janeiro, Brazil). The aim was to analyse the horizontal and vertical variations of the microbial composition in two geographically close areas influenced by anthropogenic activity (sewage disposal/port activity) and upwelling phenomena, respectively. A lower estimated diversity of microorganisms of the three domains of the phylogenetic tree of life was found in the water of the area influenced by anthropogenic activity compared to the area influenced by upwelling phenomena. We observed a heterogenic distribution of the relative abundance of taxonomic groups, especially in the Archaea and Eukarya domains. The bacterial community was dominated by Proteobacteria, Cyanobacteria and Bacteroidetes phyla, whereas the microeukaryotic community was dominated by Metazoa, Fungi, Alveolata and Stramenopile. The estimated archaeal diversity was the lowest of the three domains and was dominated by uncharacterised marine Crenarchaeota that were most closely related to Marine Group I. CONCLUSIONS/SIGNIFICANCE: The variety of conditions and the presence of different microbial assemblages indicated that the area of Arraial do Cabo can be used as a model for detailed studies that contemplate the correlation between pollution-indicating parameters and the depletion of microbial diversity in areas close to anthropogenic activity; functional roles and geochemical processes; phylogeny of the uncharacterised diversity; and seasonal variations of the microbial assemblages

Impact of COVID-19 on cardiovascular testing in the United States versus the rest of the world

Objectives: This study sought to quantify and compare the decline in volumes of cardiovascular procedures between the United States and non-US institutions during the early phase of the coronavirus disease-2019 (COVID-19) pandemic. Background: The COVID-19 pandemic has disrupted the care of many non-COVID-19 illnesses. Reductions in diagnostic cardiovascular testing around the world have led to concerns over the implications of reduced testing for cardiovascular disease (CVD) morbidity and mortality. Methods: Data were submitted to the INCAPS-COVID (International Atomic Energy Agency Non-Invasive Cardiology Protocols Study of COVID-19), a multinational registry comprising 909 institutions in 108 countries (including 155 facilities in 40 U.S. states), assessing the impact of the COVID-19 pandemic on volumes of diagnostic cardiovascular procedures. Data were obtained for April 2020 and compared with volumes of baseline procedures from March 2019. We compared laboratory characteristics, practices, and procedure volumes between U.S. and non-U.S. facilities and between U.S. geographic regions and identified factors associated with volume reduction in the United States. Results: Reductions in the volumes of procedures in the United States were similar to those in non-U.S. facilities (68% vs. 63%, respectively; p = 0.237), although U.S. facilities reported greater reductions in invasive coronary angiography (69% vs. 53%, respectively; p < 0.001). Significantly more U.S. facilities reported increased use of telehealth and patient screening measures than non-U.S. facilities, such as temperature checks, symptom screenings, and COVID-19 testing. Reductions in volumes of procedures differed between U.S. regions, with larger declines observed in the Northeast (76%) and Midwest (74%) than in the South (62%) and West (44%). Prevalence of COVID-19, staff redeployments, outpatient centers, and urban centers were associated with greater reductions in volume in U.S. facilities in a multivariable analysis. Conclusions: We observed marked reductions in U.S. cardiovascular testing in the early phase of the pandemic and significant variability between U.S. regions. The association between reductions of volumes and COVID-19 prevalence in the United States highlighted the need for proactive efforts to maintain access to cardiovascular testing in areas most affected by outbreaks of COVID-19 infection

Metagenomic Analysis of Upwelling-Affected Brazilian Coastal Seawater Reveals Sequence Domains of Type I PKS and Modular NRPS

Submitted by sandra infurna ([email protected]) on 2016-04-18T12:55:02Z No. of bitstreams: 1 rafael_cuadrat_etal_IOC_2015.pdf: 1349645 bytes, checksum: 1e9e4c31b62514366f2804feff5831d0 (MD5)Approved for entry into archive by sandra infurna ([email protected]) on 2016-04-18T13:08:57Z (GMT) No. of bitstreams: 1 rafael_cuadrat_etal_IOC_2015.pdf: 1349645 bytes, checksum: 1e9e4c31b62514366f2804feff5831d0 (MD5)Made available in DSpace on 2016-04-18T13:08:57Z (GMT). No. of bitstreams: 1 rafael_cuadrat_etal_IOC_2015.pdf: 1349645 bytes, checksum: 1e9e4c31b62514366f2804feff5831d0 (MD5) Previous issue date: 2015Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Biologia Computacional e Sistemas. Rio de Janeiro, RJ, Brasil / Leibniz-Institute of Freshwater Ecology and Inland Fisheries. Stechlin, Germany / Berlin Center for Genomics in Biodiversity Research. Berlin, Germany.Universidade Federal de São João del-Rei. Laboratório de Microbiologia Molecular. Sete Lagoas, MG, Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Biologia Computacional e Sistemas. Rio de Janeiro, RJ, Brasil.Marine environments harbor a wide range of microorganisms from the three domains of life. These microorganisms have great potential to enable discovery of new enzymes and bioactive compounds for industrial use. However, only ~1% of microorganisms from the environment can currently be identified through cultured isolates, limiting the discovery of new compounds. To overcome this limitation, a metagenomics approach has been widely adopted for biodiversity studies on samples from marine environments. In this study, we screened metagenomes in order to estimate the potential for new natural compound synthesis mediated by diversity in the Polyketide Synthase (PKS) and Nonribosomal Peptide Synthetase (NRPS) genes. The samples were collected from the Praia dos Anjos (Angel’s Beach) surface water—Arraial do Cabo (Rio de Janeiro state, Brazil), an environment affected by upwelling. In order to evaluate the potential for screening natural products in Arraial do Cabo samples, we used KS (keto-synthase) and C (condensation) domains (from PKS and NRPS, respectively) to build Hidden Markov Models (HMM) models. From both samples, a total of 84 KS and 46 C novel domain sequences were obtained, showing the potential of this environment for the discovery of new genes of biotechnological interest. These domains were classified by phylogenetic analysis and this was the first study conducted to screen PKS and NRPS genes in an upwelling affected sample

Field-collected Triatoma sordida from central Brazil display high microbiota diversity that varies with regard to developmental stage and intestinal segmentation

Submitted by Sandra Infurna ([email protected]) on 2019-02-20T13:22:57Z No. of bitstreams: 1 joanal_oliveira_etal_IOC_2018.pdf: 4332655 bytes, checksum: 721bf55a3109259b063a5eafd883da51 (MD5)Approved for entry into archive by Sandra Infurna ([email protected]) on 2019-02-20T13:34:55Z (GMT) No. of bitstreams: 1 joanal_oliveira_etal_IOC_2018.pdf: 4332655 bytes, checksum: 721bf55a3109259b063a5eafd883da51 (MD5)Made available in DSpace on 2019-02-20T13:34:55Z (GMT). No. of bitstreams: 1 joanal_oliveira_etal_IOC_2018.pdf: 4332655 bytes, checksum: 721bf55a3109259b063a5eafd883da51 (MD5) Previous issue date: 2018Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Epidemiologia e Sistemática Molecular. Rio de Janeiro, RJ, Brasil / Universidade Federal do Rio de Janeiro. Instituto de Biofísica Carlos Chagas Filho. Laboratório de Bioquímica de Insetos e Parasitos. Rio de Janeiro, RJ, Brasil.Universidade Federal de São João del-Rei. Departamento de Ciências Exatas e Biológicas. Campus de Sete Lagoas. Sete Lagoas, MG, BrasilUniversidade de Brasília. Faculdade de Medicina. Laboratório de Parasitologia Médica e Biologia de Vetores. Brasília, DF, Brasil.Universidade Federal do Rio de Janeiro. Instituto de Biofísica Carlos Chagas Filho. Laboratório de Bioquímica de Insetos e Parasitos. Rio de Janeiro, RJ, Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Epidemiologia e Sistemática Molecular. Rio de Janeiro, RJ, Brasil / Instituto Nacional de Ciência e Tecnologia em Entomologia Molecular. Rio de Janeiro, RJ, Brasil.Triatomine bugs are the vectors of Trypanosoma cruzi, the agent of Chagas disease. Vector control has for decades relied upon insecticide spraying, but insecticide resistance has recently emerged in several triatomine populations. One alternative strategy to reduce T. cruzi transmission is paratransgenesis, whereby symbiotic bacteria are genetically engineered to produce T. cruzi-killing proteins in the vector's gut. This approach requires in-depth knowledge of the vectors' natural gut microbiota. Here, we use metagenomics (16S rRNA 454 pyrosequencing) to describe the gut microbiota of field-caught Triatoma sordida-likely the most common peridomestic triatomine in Brazil. For large nymphs (4th and 5th stage) and adults, we also studied separately the three main digestive-tract segments-anterior midgut, posterior midgut, and hindgut

18S rDNA sequences from microeukaryotes reveal oil indicators in mangrove sediment.

BACKGROUND: Microeukaryotes are an effective indicator of the presence of environmental contaminants. However, the characterisation of these organisms by conventional tools is often inefficient, and recent molecular studies have revealed a great diversity of microeukaryotes. The full extent of this diversity is unknown, and therefore, the distribution, ecological role and responses to anthropogenic effects of microeukaryotes are rather obscure. The majority of oil from oceanic oil spills (e.g., the May 2010 accident in the Gulf of Mexico) converges on coastal ecosystems such as mangroves, which are threatened with worldwide disappearance, highlighting the need for efficient tools to indicate the presence of oil in these environments. However, no studies have used molecular methods to assess the effects of oil contamination in mangrove sediment on microeukaryotes as a group. METHODOLOGY/PRINCIPAL FINDINGS: We evaluated the population dynamics and the prevailing 18S rDNA phylotypes of microeukaryotes in mangrove sediment microcosms with and without oil contamination, using PCR/DGGE and clone libraries. We found that microeukaryotes are useful for monitoring oil contamination in mangroves. Our clone library analysis revealed a decrease in both diversity and species richness after contamination. The phylogenetic group that showed the greatest sensitivity to oil was the Nematoda. After contamination, a large increase in the abundance of the groups Bacillariophyta (diatoms) and Biosoecida was detected. The oil-contaminated samples were almost entirely dominated by organisms related to Bacillariophyta sp. and Cafeteria minima, which indicates that these groups are possible targets for biomonitoring oil in mangroves. The DGGE fingerprints also indicated shifts in microeukaryote profiles; specific band sequencing indicated the appearance of Bacillariophyta sp. only in contaminated samples and Nematoda only in non-contaminated sediment. CONCLUSIONS/SIGNIFICANCE: We believe that the microeukaryotic targets indicated by our work will be of great applicability in biomonitoring hydrocarbons in mangroves under oil contamination risk or during recovery strategies

Evaluation of soil bioremediation techniques in an aged diesel spill at the Antarctic Peninsula

Many areas on the Antarctic continent already suffer from the direct and indirect influences of human activities. The main cause of contamination is petroleum hydrocarbons because this compound is used as a source of energy at the many research stations around the continent. Thus, the current study aims to evaluate treatments for bioremediation (biostimulation, bioaugmentation, and bioaugmentation + biostimulation) using soils from around the Brazilian Antarctic Station "Comandante Ferraz" (EACF), King George Island, Antarctic Peninsula. The experiment lasted for 45 days, and at the end of this period, chemical and molecular analyses were performed. Those analyses included the quantification of carbon and nitrogen, denaturing gradient gel electrophoresis (DGGE) analysis (with gradient denaturation), real-time PCR, and quantification of total hydrocarbons and polyaromatics. Molecular tests evaluated changes in the profile and quantity of the rrs genes of archaea and bacteria and also the alkB gene. The influence of the treatments tested was directly related to the type of soil used. The work confirmed that despite the extreme conditions found in Antarctic soils, the bacterial strains degraded hydrocarbons and bioremediation treatments directly influenced the microbial communities present in these soils even in short periods. Although the majority of the previous studies demonstrate that the addition of fertilizer seems to be most effective at promoting bioremediation, our results show that for some conditions, autochthonous bioaugmentation (ABA) treatment is indicated. This work highlights the importance of understanding the processes of recovery of contaminated environments in polar regions because time is crucial to the soil recovery and to choosing the appropriate treatment

Microbial diversity and hydrocarbon depletion in low and high diesel-polluted soil samples from Keller Peninsula, South Shetland Islands

The bioremediation of Antarctic soils is a challenge due to the harsh conditions found in this environment. To characterize better the effect of total petroleum hydrocarbon (TPH) concentrations on bacterial, archaeal and microeukaryotic communities in low (LC) and high (HC) hydrocarbon- contaminated soil samples from the Maritime Antarctic clone libraries (small-subunit rRNA genes) were constructed. The results showed that a high concentration of hydrocarbons resulted in a decrease in bacterial and eukaryotic diversity; however, no effect of the TPH concentration was observed for the archaeal community. The HC soil samples demonstrated a high relative abundance of bacterial operational taxonomic units (OTUs) affiliated with unclassified group TM7 and eukaryotic OTUs affiliated with unclassified fungi from Pezizomycotina subphyla. Chemical analyses of the LC and HC soil samples revealed the presence of negligible amounts of nitrogen, thereby justifying the use of biostimulation to remediate these Antarctic soils. Microcosm experiments showed that the application of fertilizers led to an increase of up to 27.8% in the TPH degradation values. The data presented here constitute the first step towards developing the best method to deploy bioremediation in Antarctic soils and provide information to indicate an appropriate action plan for immediate use in the case of new accidents

Bacterial and Archaeal Communities Variability Associated with Upwelling and Anthropogenic Pressures in the Protection Area of Arraial do Cabo (Cabo Frio region - RJ)

Submitted by sandra infurna ([email protected]) on 2016-03-03T15:16:24Z No. of bitstreams: 1 alberto_davila_etal_IOC_2015.pdf: 521977 bytes, checksum: ebf6d810fd5d1f1a0e1c42ee84127ee6 (MD5)Approved for entry into archive by sandra infurna ([email protected]) on 2016-03-03T15:32:44Z (GMT) No. of bitstreams: 1 alberto_davila_etal_IOC_2015.pdf: 521977 bytes, checksum: ebf6d810fd5d1f1a0e1c42ee84127ee6 (MD5)Made available in DSpace on 2016-03-03T15:32:44Z (GMT). No. of bitstreams: 1 alberto_davila_etal_IOC_2015.pdf: 521977 bytes, checksum: ebf6d810fd5d1f1a0e1c42ee84127ee6 (MD5) Previous issue date: 2015Instituto de Ciências do Marz Almirante Paulo Moreira. Arraial do Cabo, RJ, Brasil / Universidade Federal do Rio de Janeiro. Centro de Ciências da Saúde. Instituto de Biofísica Carlos Chagas Filho. Rio de Janeiro, RJ, Brasil.Universidade do Estado do Rio de Janeiro. Faculdade de Formação de Professores. Departamento de Ciências. Laboratório de Microbiologia. São Gonçalo, RJ, Brasil.Universidade Federal de São João del-Rei. Departamento de Ciências Exatas e Biológica. Laboratório de Microbiologia Molecular. Sete Lagoas, MG, Brasil / Universidade Federal do Rio de Janeiro. Centro de Ciências da Saúde. Instituto de Microbiologia Paulo de Góes, Laboratório de Ecologia Microbiana Molecular. Rio de Janeiro, RJ, Brasil.Universidade Federal do Rio de Janeiro. Centro de Ciências da Saúde. Instituto de Microbiologia Paulo de Góes, Laboratório de Ecologia Microbiana Molecular. Rio de Janeiro, RJ, Brasil Centro de Ciências da Saúde. Instituto de Microbiologia Paulo de Góes, Laboratório de Ecologia Microbiana Molecular. Rio de Janeiro, RJ, Brasil.Universidade Federal do Rio de Janeiro. COPPE. Centro de Tecnologia. Instituto Alberto Luiz Coimbra de Pós-Graduação e Pesquisa em Engenharia. Núcleo de Transferência de Tecnologia. Programa de Engenharia Civil. Rio de Janeiro, RJ, Brasil.Universidade Federal do Rio de Janeiro. Centro de Ciências da Saúde. Instituto de Biofísica Carlos Chagas Filho. Rio de Janeiro, RJ, Brasil.Universidade Federal do Rio de Janeiro. Centro de Ciências da Saúde. Instituto de Microbiologia Paulo de Góes, Laboratório de Ecologia Microbiana Molecular. Rio de Janeiro, RJ, Brasil Centro de Ciências da Saúde. Instituto de Microbiologia Paulo de Góes, Laboratório de Ecologia Microbiana Molecular. Rio de Janeiro, RJ, Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Biologia Computacional e Sistemas. Rio de Janeiro, RJ, Brasil.Universidade Federal do Rio de Janeiro. Centro de Ciências da Saúde. Instituto de Microbiologia Paulo de Góes, Laboratório de Ecologia Microbiana Molecular. Rio de Janeiro, RJ, Brasil Centro de Ciências da Saúde. Instituto de Microbiologia Paulo de Góes, Laboratório de Ecologia Microbiana Molecular. Rio de Janeiro, RJ, Brasil.Os sistemas de ressurgência possuem uma grande diversidade de microrganismos pelágicos e sua composição e atividade são determinadas por fatores como a temperatura e a concentração de nutrientes. A técnica de Electroforese em Gel por Gradiente Desnaturante (EGGD) foi utilizada para verificar a variabilidade genética espacial e temporal de Bacteria e Archea em duas estações na costa da região de Arraial do Cabo; uma com maior pressão da ressurgência, e a outra sobre pressão antropogênica. Além disso, as variáveis bióticas e abióticas foram medidas nas águas superficiais e de fundo de outras três estações situadas entre essas estações. Seis amostragens foram realizadas durante um ano e representaram adequadamente os diferentes graus de ressurgência e de pressões antropogênicas no sistema. A Análise por Componente Principal (ACP) mostrou uma correlação negativa entre a concentrações de amônia e de fósforo e a produção secundária procariótica e o total de bactérias heterotróficas. A ACP também mostrou uma correlação negativa entre a temperatura e a abundância de células procarióticas. As composições de Bacteria e Archaea foram variáveis, assim como as condições oceanográficas, e a ressurgência teve uma pressão regional enquanto a pressão antropogênica foi pontual. Sugerimos que as medidas de produção secundária procariótica esteve associada à atividade de ambas Bacteria e Archaea, e que a disponibilidade de substrato e a temperatura determinam a ciclagem de nutrientes.Upwelling systems contain a high diversity of pelagic microorganisms and their composition and activity are defined by factors like temperature and nutrient concentration. Denaturing gradient gel electrophoresis (DGGE) technique was used to verify the spatial and temporal genetic variability of Bacteria and Archaea in two stations of the Arraial do Cabo coastal region, one under upwelling pressure and another under anthropogenic pressure. In addition, biotic and abiotic variables were measured in surface and deep waters from three other stations between these stations. Six samplings were done during a year and adequately represented the degrees of upwelling and anthropogenic pressures to the system. Principal Component Analysis (PCA) showed negative correlations between the concentrations of ammonia and phosphorous with prokaryotic secondary production and the total heterotrophic bacteria. PCA also showed negative correlation between temperature and the abundance of prokaryotic cells. Bacterial and archaeal compositions were changeable as were the oceanographic conditions, and upwelling had a regional pressure while anthropogenic pressure was punctual. We suggest that the measurement of prokaryotic secondary production was associated with both Bacteria and Archaea activities, and that substrate availability and temperature determine nutrients cycling