RESUMO
Soil samples from a transect from low to highly hydrocarbon-contaminated soils were collected around the Brazilian Antarctic Station Comandante Ferraz (EACF), located at King George Island, Antarctica. Quantitative PCR (qPCR) analysis of bacterial 16S rRNA genes, 16S rRNA gene (iTag), and shotgun metagenomic sequencing were used to characterize microbial community structure and the potential for petroleum degradation by indigenous microbes. Hydrocarbon contamination did not affect bacterial abundance in EACF soils (bacterial 16S rRNA gene qPCR). However, analysis of 16S rRNA gene sequences revealed a successive change in the microbial community along the pollution gradient. Microbial richness and diversity decreased with the increase of hydrocarbon concentration in EACF soils. The abundance of Cytophaga, Methyloversatilis, Polaromonas, and Williamsia was positively correlated (p-value = <.05) with the concentration of total petroleum hydrocarbons (TPH) and/or polycyclic aromatic hydrocarbons (PAH). Annotation of metagenomic data revealed that the most abundant hydrocarbon degradation pathway in EACF soils was related to alkyl derivative-PAH degradation (mainly methylnaphthalenes) via the CYP450 enzyme family. The abundance of genes related to nitrogen fixation increased in EACF soils as the concentration of hydrocarbons increased. The results obtained here are valuable for the future of bioremediation of petroleum hydrocarbon-contaminated soils in polar environments.
Assuntos
Microbiota , Petróleo , Poluentes do Solo , Regiões Antárticas , Hidrocarbonetos/análise , Petróleo/metabolismo , RNA Ribossômico 16S/genética , Solo/química , Microbiologia do Solo , Poluentes do Solo/análise , Poluentes do Solo/metabolismoRESUMO
BACKGROUND/METHODOLOGY: 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. PRINCIPAL FINDINGS: Bacteria of four phyla (12 genera) were present in both nymphs (all five stages) and adults, thus defining T. sordida's 'bacterial core': Actinobacteria (Brevibacterium, Corynebacterium, Dietzia, Gordonia, Nitriliruptor, Nocardia, Nocardiopsis, Rhodococcus, and Williamsia), Proteobacteria (Pseudomonas and Sphingobium), and Firmicutes (Staphylococcus). We found some clear differences in bacterial composition and relative abundance among development stages; overall, Firmicutes and Proteobacteria increased, but Actinobacteria decreased, through development. Finally, the bacterial microbiotas of the bugs' anterior midgut, posterior midgut, and hindgut were sharply distinct. CONCLUSIONS/SIGNIFICANCE: Our results identify the 'bacterial core set' of T. sordida and reveal important gut microbiota differences among development stages-particularly between 1st-3rd stage nymphs and adults. Further, we show that, within any given development stage, the vectors' gut cannot be regarded as a single homogeneous environment. Cultivable, non-pathogenic 'core' bacterial species may now be tested as candidates for paratransgenic control of T. cruzi transmission by T. sordida.
Assuntos
Bactérias/classificação , Microbioma Gastrointestinal , Trato Gastrointestinal/microbiologia , Triatoma/microbiologia , Animais , Brasil , Feminino , Masculino , Ninfa , RNA Bacteriano/genética , RNA Ribossômico 16S/genética , Triatoma/crescimento & desenvolvimentoRESUMO
ABSTRACT Arbuscular mycorrhizal fungi make up an important ecological niche in ecosystems, and knowledge of their diversity in extreme environments is still incipient. The objective of this work was to evaluate the density and diversity of arbuscular mycorrhizal fungi in the soil of King George Island in the South Shetland Islands archipelago, Antarctica. For that, soil and roots of Deschampsia antarctica were collected at the brazilian research station in Antarctica. The spore density, species diversity and mycorrhizal colonization in the roots were evaluated. There was a low density of spores (27.4 ± 17.7) and root mycorrhizal colonization (6 ± 5.1%), which did not present statistical difference. Four species of arbuscular mycorrhizal fungi were identified, distributed in two genera: three species of the genus Glomus (Glomus sp1, Glomus sp2 and Glomus sp3) and one of the genus Acaulospora, which was identified at species level (Acaulospora mellea). Greater soil diversity was verified with pH 5.9 and phosphorus concentration of 111 mg dm-3, occurring two species of genus Glomus and A. mellea. Based on literature data, this may be the first record of this species of Acaulospora mellea in Antarctic soils, colonizing D. antarctica plants.
Assuntos
Microbiologia do Solo , Micorrizas/classificação , Biodiversidade , Regiões AntárticasRESUMO
Arbuscular mycorrhizal fungi make up an important ecological niche in ecosystems, and knowledge of their diversity in extreme environments is still incipient. The objective of this work was to evaluate the density and diversity of arbuscular mycorrhizal fungi in the soil of King George Island in the South Shetland Islands archipelago, Antarctica. For that, soil and roots of Deschampsia antarctica were collected at the brazilian research station in Antarctica. The spore density, species diversity and mycorrhizal colonization in the roots were evaluated. There was a low density of spores (27.4 ± 17.7) and root mycorrhizal colonization (6 ± 5.1%), which did not present statistical difference. Four species of arbuscular mycorrhizal fungi were identified, distributed in two genera: three species of the genus Glomus (Glomus sp1, Glomus sp2 and Glomus sp3) and one of the genus Acaulospora, which was identified at species level (Acaulospora mellea). Greater soil diversity was verified with pH 5.9 and phosphorus concentration of 111 mg dm-3, occurring two species of genus Glomus and A. mellea. Based on literature data, this may be the first record of this species of Acaulospora mellea in Antarctic soils, colonizing D. antarctica plants.
Assuntos
Biodiversidade , Micorrizas/classificação , Microbiologia do Solo , Regiões AntárticasRESUMO
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.
Assuntos
Metagenômica , Peptídeo Sintases/genética , Policetídeo Sintases/genética , Água do Mar/microbiologia , Microbiologia da Água , Biologia Computacional , Conjuntos de Dados como Assunto , FilogeniaRESUMO
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.
Assuntos
Archaea/crescimento & desenvolvimento , Bactérias/crescimento & desenvolvimento , Amônia/análise , Archaea/classificação , Archaea/genética , Bactérias/classificação , Bactérias/genética , Brasil , Eletroforese em Gel de Gradiente Desnaturante , Análise de Componente Principal , Água do Mar/microbiologia , TemperaturaRESUMO
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.
Assuntos
Poluição Ambiental , Gasolina , Poluentes do Solo/metabolismo , Regiões Antárticas , Archaea/classificação , Archaea/genética , Archaea/isolamento & purificação , Bactérias/classificação , Bactérias/genética , Bactérias/isolamento & purificação , Biodegradação Ambiental , Biota , Carbono/análise , Eletroforese em Gel de Gradiente Desnaturante , Hidrocarbonetos/análise , Nitrogênio/análise , Reação em Cadeia da Polimerase em Tempo Real , Solo/química , Microbiologia do SoloRESUMO
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.
Assuntos
Biodiversidade , Biomassa , Ecossistema , Água do Mar/microbiologia , Poluição da Água/efeitos adversos , Brasil , Cadeia Alimentar , RNA Ribossômico/análiseRESUMO
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.
Assuntos
Monitoramento Ambiental/métodos , Eucariotos/isolamento & purificação , Sedimentos Geológicos/química , Petróleo/análise , Poluição Química da Água/análise , Sequência de Bases , DNA Ribossômico/genética , Eucariotos/classificação , Eucariotos/genética , Dados de Sequência Molecular , RNA Ribossômico 18S/genéticaRESUMO
The Antarctic is a pristine environment that contributes to the maintenance of the global climate equilibrium. The harsh conditions of this habitat are fundamental to selecting those organisms able to survive in such an extreme habitat and able to support the relatively simple ecosystems. The DNA of the microbial community associated with the rhizospheres of Deschampsia antarctica Desv (Poaceae) and Colobanthus quitensis (Kunth) BartI (Caryophyllaceae), the only two native vascular plants that are found in Antarctic ecosystems, was evaluated using a 16S rRNA multiplex 454 pyrosequencing approach. This analysis revealed similar patterns of bacterial diversity between the two plant species from different locations, arguing against the hypothesis that there would be differences between the rhizosphere communities of different plants. Furthermore, the phylum distribution presented a peculiar pattern, with a bacterial community structure different from those reported of many other soils. Firmicutes was the most abundant phylum in almost all the analyzed samples, and there were high levels of anaerobic representatives. Also, some phyla that are dominant in most temperate and tropical soils, such as Acidobacteria, were rarely found in the analyzed samples. Analyzing all the sample libraries together, the predominant genera found were Bifidobacterium (phylum Actinobacteria), Arcobacter (phylum Proteobacteria) and Faecalibacterium (phylum Firmicutes). To the best of our knowledge, this is the first major bacterial sequencing effort of this kind of soil, and it revealed more than expected diversity within these rhizospheres of both maritime Antarctica vascular plants in Admiralty Bay, King George Island, which is part of the South Shetlands archipelago.
Assuntos
Bactérias/isolamento & purificação , Biodiversidade , Caryophyllaceae/microbiologia , Poaceae/microbiologia , Microbiologia do Solo , Regiões Antárticas , Bactérias/classificação , Bactérias/genética , DNA Bacteriano/genética , DNA Ribossômico/genética , Dados de Sequência Molecular , Filogenia , Raízes de Plantas/microbiologia , RNA Ribossômico 16S/genética , Solo/análiseRESUMO
ProtozoaDB (http://www.biowebdb.org/protozoadb) is being developed to initially host both genomics and post-genomics data from Plasmodium falciparum, Entamoeba histolytica, Trypanosoma brucei, T. cruzi and Leishmania major, but will hopefully host other protozoan species as more genomes are sequenced. It is based on the Genomics Unified Schema and offers a modern Web-based interface for user-friendly data visualization and exploration. This database is not intended to duplicate other similar efforts such as GeneDB, PlasmoDB, TcruziDB or even TDRtargets, but to be complementary by providing further analyses with emphasis on distant similarities (HMM-based) and phylogeny-based annotations including orthology analysis. ProtozoaDB will be progressively linked to the above-mentioned databases, focusing in performing a multi-source dynamic combination of information through advanced interoperable Web tools such as Web services. Also, to provide Web services will allow third-party software to retrieve and use data from ProtozoaDB in automated pipelines (workflows) or other interoperable Web technologies, promoting better information reuse and integration. We also expect ProtozoaDB to catalyze the development of local and regional bioinformatics capabilities (research and training), and therefore promote/enhance scientific advancement in developing countries.