Perfil taxonômico e funcional microbiano em ambientes aquáticos

Tese (doutorado)—Universidade de Brasília, Instituto de Ciências Biológicas, Departamento de Biologia Celular, Programa de Pós-Graduação em Biologia Microbiana, 2016.A mensuração da diversidade microbiana é um dos maiores desafios do campo microbiológico, principalmente por problemas metodológicos. Com o avanço de novas metodologias foi possível observar que a diversidade de microrganismos era maior do que se pensava, assim, possibilitando o estudo desse conjunto de microrganismos. O estudo dos genomas de diversos microrganismos contidos em um dado ambiente é denominado de metagenômica. A metagenômica pode ser utilizada para o estudo de diversos tipos de ambientes, como solo, ar, corpo humano, intestino de cupim, entre outros. Dentro dos ambientes estudados pela metagenômica, o ambiente aquático vem sendo alvo de diversos estudos. Apesar de apresentar diversos estudos descrevendo diferentes profundidades e até mesmo diferentes hábitats (esponja, corais por exemplo), ainda existem inúmeros hábitats no ambiente marinho que ainda não possuem estudos focados sobre a microbiota. Diferente do ambiente marinho, trabalhos focados na descrição da microbiota de água doce são escassos. Além disso, apesar de toda sua importância ecológica, diversos desses corpos d’água estão sendo perturbados por atividades antropogênicas, levando à alteração da microbiota. Alguns trabalhos focaram na detecção de biossensores capazes de detectar impactos antropogênicos no meio ambiente. O objetivo de presente trabalho foi contribuir na descrição da comunidade microbiana em ambientes aquáticos. Para atingir essa meta foram realizados dois estudos, o primeiro estudo foi realizar a análise taxonômica e funcional da comunidade bacteriana do rio Paraguaçú na estação de chuva e seca, além de avaliar o efeito de proteção do Parque Nacional da Chapada Diamantina (PNCD) sobre a qualidade da água e da diversidade da microbiota do rio Paraguaçú. Outro estudo realizado foi o primeiro trabalho metagenômico focado em poças de maré. Esse trabalho deu enfoque na descrição do perfil taxonômico e funcional da microbiota das poças de maré situados em Ocean Beach, San Diego, CA, EUA. Ambos ambientes trabalhados possuem um grande potencial biotecnológico e se apresentaram como fundamentais na determinação do perfil da microbiota encontrada. No rio Paraguaçú foi possível observar uma predominância de genes relacionados à degradação de pesticidas (como o Benzoato), enquanto nas poças de maré foi possível observar uma maior abundância de genes relacionados à tolerância a ambientes com alta concentração salina. Novos estudos devem ser realizados para ambos ambientes buscando elucidar melhor os processos que ocorrem nesses ambientes.Determining the true diversity in a microbial community is one of the biggest challenges in microbiology. The development of new techniques has revealed a higher microbial diversity than what was previously thought and provided a new way to study these organisms. Metagenomics, the study of microbial DNA recovered from specific environments, allows the study of microbial communities in soil, air, human body, and termite gut. Among the environments studied using this approach, water is one of the most important. Each of the two types of water environments (seawater and freshwater) has a specific microbial community. Although previous studies have described microbial communities in different water layers and habitats (e.g. sponge, coral), the microbial communities of several seawater habitats have not been studied, and studies describing microbial communities in freshwater environments are rare. Moreover, ecologically important freshwater environments are being disturbed by anthropogenic activity, which can change the microbial profile. Previous studies have focused on identifying biosensors that can detect anthropogenic impacts on the environment. The aim of this work was to characterize the microbial communities in two water environments, and this objective was developed in two separate studies. The first described taxonomic and functional analyses of the bacterial community in the Paraguaçú River during both wet and dry seasons. Additionally, we evaluated the protective effect of Parque Nacional da Chapada Diamantina (PNCD) on water quality and microbial diversity in this river. The second study was the first metagenomic study of tide pools, in which we described the taxonomic and functional profiles of microbial communities in tide pools at Ocean Beach, San Diego, CA, USA. Both studies describe environments with great biotechnological potential and showed themselves as fundamental factors shaping the microbial communities. For example, in the Paraguaçú River we observed a high abundance of genes encoding enzymes capable of degrading pesticides such as emamectin benzoate, whereas tide pools showed a high abundance of halotolerance genes. Further studies are needed to elucidate processes in both environments

CARACTERIZAÇÃO DE ISOLADOS DE Trichoderma spp. DO CERRADO TOCANTINENSE E APLICAÇÃO COMO AGENTE DE CONTROLE BIOLÓGICO CONTRA O FITOPATÓGENO Sclerotinia sclerotiorum

The phytopathogen Sclerotinia sclerotiorum, which causes the disease known as white mold, affects several agro crops worldwide, its high degree of pathogenicity is associated with the formation of sclerotia that acts as a resistance and survival mechanism. Considering the need for methods that contribute to agricultural development without causing damage to the environment and the population, biological control agents are now seen as excellent artifice. Fungi of the genus Trichoderma are considered astute biocontrol agents because they have numerous mechanisms with high antagonistic potential that impair spore germination, hyphal growth, and the development of sclerotia and chlamydospores of various phytopathogens. Seeking to evaluate the efficiency of Trichoderma spp. from areas of the Cerrado of Tocantins in the biocontrol of the phytopathogen S. sclerotiorum, pairing, enzymatic and secondary metabolite production tests were carried out. Through the obtained results it was possible to conclude that the isolate Trichoderma spp. 2, from areas of the Cerrado of Tocantins, has the potential to be considered as a bio controller for the phytopathogen S. Sclerotiorum, its antagonism being more evident through the production of volatile secondary metabolites.El fitopatógeno Sclerotinia sclerotiorum, causante de la enfermedad conocida como moho blanco, afecta a muchos cultivos agrícolas a nivel mundial, su alto grado de patogenicidad está asociado a la formación de esclerocios que actúan como mecanismo de resistencia y supervivencia. Estimando la necesidad de métodos que contribuyan al desarrollo agrícola sin causar daños al medio ambiente ya la población, los agentes de control biológico son ahora vistos como un excelente artificio. Los hongos del género Trichoderma son considerados buenos agentes de biocontrol debido a que poseen numerosos mecanismos con alto potencial antagónico que impiden la germinación de esporas, el crecimiento de hifas y el desarrollo de esclerocios y clamidosporas de diversos fitopatógenos. Buscando evaluar la eficiencia de Trichoderma spp. de áreas del Cerrado de Tocantins en el biocontrol del fitopatógeno S. sclerotiorum, se realizaron pruebas de apareamiento, enzimáticas y de producción de metabolitos secundarios. A través de los resultados obtenidos se pudo concluir que el aislado Trichoderma spp. 2, procedente de áreas del Cerrado de Tocantins, tiene potencial para ser considerada como biocontroladora del fitopatógeno S. Sclerotiorum, siendo más evidente su antagonismo a través de la producción de metabolitos secundarios volátiles.O fitopatógeno Sclerotinia sclerotiorum, causador da doença conhecida como mofo-branco acomete diversas culturas agrícolas em todo o mundo, seu alto grau de patogenicidade está associado à formação de escleródios que atuam como mecanismo de resistência e sobrevivência. Considerando a necessidade de métodos que contribuam no desenvolvimento agrícola sem promover danos ao ambiente e a população, os agentes de controle biológico são hoje vistos como um excelente artifício. Fungos do gênero Trichoderma são considerados agentes de biocontrole sagazes por apresentarem inúmeros mecanismos com alto potencial antagônico que prejudicam a germinação de esporos, o crescimento das hifas e o desenvolvimento de escleródios e clamidósporo de diversos fitopatógenos. Buscando avaliar a eficiência de isolados de Trichoderma spp. provenientes de áreas do Cerrado do Tocantins no biocontrole do fitopatógeno S. sclerotiorum foram realizados testes de pareamento, enzimáticos e de produção de metabólitos secundários. Através dos resultados obtidos foi possível concluir que o isolado Trichoderma spp. 2, oriundo de áreas do Cerrado tocantinense, possui potencial para ser considerado como um biocontrolador ao fitopatógeno S. Sclerotiorum, sendo seu antagonismo mais evidente por meio da produção dos metabólitos secundários voláteis

Soil acidobacterial 16S rRNA gene sequences reveal subgroup level differences between savanna-like cerrado and atlantic forest brazilian biomes

16S rRNA sequences from the phylum Acidobacteria have been commonly reported from soil microbial communities, including those from the Brazilian Savanna (Cerrado) and the Atlantic Forest biomes, two biomes that present contrasting characteristics of soil and vegetation. Using 16S rRNA sequences, the present work aimed to study acidobacterial diversity and distribution in soils of Cerrado savanna and two Atlantic forest sites. PCA and phylogenetic reconstruction showed that the acidobacterial communities found in “Mata de galeria” forest soil samples from the Cerrado biome have a tendency to separate from the other Cerrado vegetation microbial communities in the direction of those found in the Atlantic Forest, which is correlated with a high abundance of Acidobacteria subgroup 2 (GP2). Environmental conditions seem to promote a negative correlation between GP2 and subgroup 1 (GP1) abundance. Also GP2 is negatively correlated to pH, but positively correlated to high Al3+ concentrations. The Cerrado soil showed the lowest Acidobacteria richness and diversity indexes of OTUs at the species and subgroups levels when compared to Atlantic Forest soils. These results suggest specificity of acidobacterial subgroups to soils of different biomes and are a starting point to understand their ecological roles, a topic that needs to be further explored

Diversity, distribution and ecology of fungal community present in Antarctic lake sediments uncovered by DNA metabarcoding

We assessed fungal diversity in sediments obtained from four lakes in the South Shetland Islands and James Ross Island, Antarctica, using DNA metabarcoding. We detected 218 amplicon sequence variants (ASVs) dominated by the phyla Ascomycota, Basidiomycota, Mortierellomycota, Mucoromycota and Chytridiomycota. In addition, the rare phyla Aphelidiomycota, Basidiobolomycota, Blastocladiomycota, Monoblepharomycota, Rozellomycota and Zoopagomycota as well as fungal-like Straminopila belonging to the phyla Bacillariophyta and Oomycota were detected. The fungal assemblages were dominated by unknown fungal taxa (Fungal sp. 1 and Fungal sp. 2), followed by Talaromyces rubicundus and Dactylonectria anthuriicola. In general, they displayed high diversity, richness and moderate dominance. Sequences representing saprophytic, pathogenic and symbiotic fungi were detected, including the phytopathogenic fungus D. anthuriicola that was abundant, in the relatively young Soto Lake on Deception Island. The lake sediments studied contained the DNA of rich, diverse and complex fungal communities, including both fungi commonly reported in Antarctica and other taxa considered to be rare. However, as the study was based on the use of environmental DNA, which does not unequivocally confirm the presence of active or viable organisms, further studies using other approaches such as shotgun sequencing are required to elucidate the ecology of fungi in these Antarctic lake sediments

Microbial community profile and water quality in a protected area of the caatinga biome

The Caatinga is a semi-arid biome in northeast Brazil. The Paraguaçú River is located in the Caatinga biome, and part of its course is protected by the National Park of Chapada Diamantina (PNCD). In this study we evaluated the effect of PNCD protection on the water quality and microbial community diversity of this river by analyzing water samples obtained from points located inside and outside the PNCD in both wet and dry seasons. Results of water quality analysis showed higher levels of silicate, ammonia, particulate organic carbon, and nitrite in samples from the unprotected area compared with those from protected areas. Pyrosequencing of the 16S rRNA genes revealed that Burkholderiales was abundant in samples from all three sites during both seasons and was represented primarily by the genus Polynucleobacter and members of the Comamonadaceae family (e.g., genus Limnohabitans). During the dry season, the unprotected area showed a higher abundance of Flavobacterium sp. and Arthrobacter sp., which are frequently associated with the presence and/or degradation of arsenic and pesticide compounds. In addition, genes that appear to be related to agricultural impacts on the environment, as well as those involved in arsenic and cadmium resistance, copper homeostasis, and propanediol utilization, were detected in the unprotected areas by metagenomic sequencing. Although PNCD protection improves water quality, agricultural activities around the park may affect water quality within the park and may account for the presence of bacteria capable of pesticide degradation and assimilation, evidencing possible anthropogenic impacts on the Caatinga

Marine biotechnology in Brazil : recent developments and its potential for innovation

Marine biotechnology is an emerging field in Brazil and includes the exploration of marine microbial products, aquaculture, omics, isolation of biologically active compounds, identification of biosynthetic gene clusters from symbiotic microorganisms, investigation of invertebrate diseases caused by potentially pathogenic marine microbes, and development of antifouling compounds. Furthermore, the field also encompasses description of new biological niches, current threats, preservation strategies as well as its biotechnological potential. Finally, it is important to depict some of the major approaches and tools being employed to such end. To address the challenges of marine biotechnology, the Brazilian government, through the Ministry of Science, Technology, Innovation, and Communication, has established the National Research Network in Marine Biotechnology (BiotecMar) (www.biotecmar.sage.coppe.ufrj.br). Its main objective is to harness marine biodiversity and develop the marine bioeconomy through innovative research

Caracterização molecular, filogênica e enzimática de isolados de Trichoderma spp

Made available in DSpace on 2014-07-29T15:16:32Z (GMT). No. of bitstreams: 1 LOPES FAC Dissertacao.pdf: 1587334 bytes, checksum: 1fcac951d597992ec49231a64f8eff03 (MD5) Previous issue date: 2012-02-24Devido aos efeitos danosos causados ao meio ambiemte e à procura por métodos mais eficientes, o uso de agrodefensivos vem sendo gradualmente substituído pelo uso de agentes de controle biológico. A utilização do gênero Trichoderma tem sido satisfatória no controle de vários fitopatógenos em diversas culturas agrícolas por meio da competição por nutrientes, produção de antibióticos e do micoparasitismo. Esse gênero possui sua taxonomia bastante discutida, porém com o advento de técnicas moleculares o problema da identificação da espécie do isolado estudado vem sendo resolvido. Os objetivos desse trabalho foram identificar isolados de Trichoderma spp. provenientes de diversas espécies cultivadas, além de visualizar as relações filogenéticas, e realizar a avaliação da atividade específica de enzimas hidrolíticas frente aos fitopatógenos Fusarium solani, Fusarium oxysporum, Rhizoctonia solani e Sclerotinia sclerotiorum. Dentro os 100 isolados, 96 isolados foram identficados, sendo 43 isolados da espécie T. harzianum, 33 isolados de T. asperellum, 6 isolados de T. tomentosum, 5 isolados de T. koningiopsis, 4 isolados de T. erinaceum, 2 isolados de T. ghanense, 1 isolado de T. virens, 1 isolado de T. brevicompactum e 1 isolado de T. hamatum. Quatro isolados não foram identificados por nenhuma ferramenta molecular ou por análise filogenética. No estudo feito com as enzimas em F. oxysporum, todas as correlações apresentadas entre as atividades específicas são significativas, possuíam valores elevados de coeficiente de Pearson e positivos. Em F. solani, os resultados foram bastante semelhantes aos encontrados em F. oxysporum. Na indução com parede celular de R. solani, foram observadas correlações entre enzimas que desempenham papel fundamental no processo de micoparasitismo. Em S. sclerotiorum, foram observadas correlações entre enzimas envolvidas no processo de micoparasitismo. Os isolados T. asperellum 356/01, que obteve destaque em todas as enzimas estudadas em parede celular de F. oxysporum, T. asperellum 40T/03 e T. harzianum 100T/01, se destacando em praticamente todas as enzimas em F. solani, Trichoderma spp. 55/03, que apresentou as maiores atividades em Fosfatase ácida e Proteases em parede celular de R. solani, e o isolado T. erinaceum 17/06, possuindo atividades expressivas em NAGase nas paredes celulares de F. solani e R. solani e em β-1,3-glicanase na parede celular de R. solani, são alguns organismos que possuem um grande potencial para um futuro uso biotecnológico. Todos esses resultados levantados propiciam um melhor entendimento do mecanismo de micoparasitismo do gênero Trichoderma frente a fitopatógenos de grande importânci

Investigating aerial diversity of non-fungal eukaryotes across a 40º latitudinal transect using DNA metabarcoding

The high number of bipolar and widespread bryophyte and microbial taxa in the Antarctic flora suggests the effective Long-Distance Dispersal (LDD) of spores and other propagules from lower latitudes and even the Northern Hemisphere to Antarctica and the sub-Antarctic regions. However, few studies have attempted to document the transfer mechanisms by which potential newcomers may arrive in Antarctica. Commonly suggested or assumed mechanisms include transport in air currents, adventitious transfer with migrating or vagrant birds, and with human assistance. In this study, we investigated the biodiversity present in the air along a 40° latitudinal transect, from the port city of Rio de Janeiro, Brazil (ca. 22°S) to Comandante Ferraz Station on King George Island (South Shetland Islands, ca. 62°S), maritime Antarctica, to shed light on the potential role of LDD in species distribution. Air samples were collected in October 2021 on the Brazilian polar support vessel Ary Rongel using air filters with membranes of 0.22 μm. Total DNA was extracted from the filters and the Internal Transcribed Spacer (ITS2) DNA sequence was used for metabarcoding. A total of 53 non-fungal taxa representing three kingdoms (most abundantly Viridiplantae) and six phyla (most abundantly Bryophyta and Magnoliophyta) were assigned from the sequences found. Aerial biodiversity was greater closer to the coast and generally decreased with increasing latitude, although a small increase was apparent in the South Shetland Islands. The taxa assigned are generally present in coastal biomes, although a small proportion of the assignments represented taxa of more distant origin, supporting the occurrence of LDD in the air column

Biochemical and metabolic profiles of Trichoderma strains isolated from common bean crops in the Brazilian Cerrado, and potential antagonism against Sclerotinia sclerotiorum

Some species of Trichoderma have successfully been used in the commercial biological control of fungal pathogens, e.g., Sclerotinia sclerotiorum, an economically important pathogen of common beans (Phaseolus vulgaris L.). The objectives of the present study were (1) to provide molecular characterization of Trichoderma strains isolated from the Brazilian Cerrado; (2) to assess the metabolic profile of each strain by means of Biolog FF Microplates; and (3) to evaluate the ability of each strain to antagonize S. sclerotiorum via the production of cell wall-degrading enzymes (CWDEs), volatile antibiotics, and dual-culture tests. Among 21 isolates, we identified 42.86 % as Trichoderma asperellum, 33.33 % as Trichoderma harzianum, 14.29 % as Trichoderma tomentosum, 4.76 % as Trichoderma koningiopsis, and 4.76 % as Trichoderma erinaceum. Trichoderma asperellum showed the highest CWDE activity. However, no species secreted a specific group of CWDEs. Trichoderma asperellum 364/01, T. asperellum 483/02, and T. asperellum 356/02 exhibited high and medium specific activities for key enzymes in the mycoparasitic process, but a low capacity for antagonism. We observed no significant correlation between CWDE and antagonism, or between metabolic profile and antagonism. The diversity of Trichoderma species, and in particular of T. harzianum, was clearly reflected in their metabolic profiles. Our findings indicate that the selection of Trichoderma candidates for biological control should be based primarily on the environmental fitness of competitive isolates and the target pathogen. (C) 2012 The British Mycological Society. Published by Elsevier Ltd. All rights reserved.FINEP (Research and Projects Financing)National Council for Scientific and Technological Development (CNPq) [FINEP/CT-AGRO/01.07.0551.00/Ref. 0845/07]CAPESFAPEGOFUNAPE [proc. 20081026700108]State of Sao Paulo Research Foundation (FAPESP) [proc. 2010/15683-8