Incompatibilidade vegetativa entre isolados de Bipolaris sorokiniana

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A next-generation approach to assess the cyanobacterial diversity and biogeography in the High Arctic (Svalbard)

Polar ecosystems are extremely sensitive to global climate changes and human activities. Cyanobacteria are key photosynthetic organisms in these latitudes, due to their roles in soil aggregation, nitrogen fixation, carbon cycles, and secondary metabolite production, among others. Previous works indicate that different cyanobacterial taxa/communities have different impacts on the environment, in both biogeochemical cycles and bioactive compound productions. Furthermore, the presence of biogeographical patterns in microorganisms, as found in macroorganisms, is an ongoing debate. In this study, during the 2013 MicroFun expedition, we sampled 72 locations around Svalbard including diverse biotopes such as glacial forefields, tundra soils, hot springs, soil crusts, microbial mats, wet walls, cryoconites, plankton and periphyton, in order to (1) assess the biodiversity of cyanobacteria around Svalbard, (2) verify the existence of biogeographical trends around the archipelago, and (3) compare these data with other polar (cold) areas, especially Antarctica. We used a pyrosequencing approach targeting cyanobacteria-specific 16S rRNA gene sequences to deeply study the cyanobacterial communities.BIPOLES, PYROCYAN

Past cyanobacteria biodiversity in herbarium collections: a time travel to a lost world?

A pilot study of the cyanobacterial diversity in ten herbarium samples from the Smithsonian Institution (Washington DC, USA) was carried out. The samples had been collected between 1897 and 1964 in Antarctica, Alaska, Yellowstone Park and Austrian and American glaciers. The V3-V4 portion of the 16S rRNA gene was sequenced by multiplex 454 pyrosequencing and data was analyzed using the bioinformatic pipeline of Pessi et al. (2016). We obtained 131 OTUs (threshold of 97.5% 16S rRNA similarity), of which 74 were very closely related to existing sequences in public databases. Moreover, the diversity patterns were different between samples, ruling out an homogenization due to contaminations during the handling of herbarium samples since their collection and in our laboratory. The older specimen (1898) came from a pool at 46°C in Yellowstone Park with dominant sequences of Stigonema and Leptolyngbya, that are known from these biotopes. For the Antarctic samples taken in 1948-9 from Ross Island, in 1940 from Deception Island and in 1964 from Victoria Land, the DNA could be amplified in all cases and 55 OTUs were detected. Sequences of Nostoc sp., Microcoleus sp., Phormidesmis priestleyi, Leptolyngbya sp., and Timaviella sp. were retrieved. An Alaskan river specimen from 1949 yielded mostly Nostoc sequences, as could be expected from the herbarium label. This study gives access to the cyanobacterial community composition in a period where anthropogenic and climatic pressures were still low in the remote polar regions. We will assess if it is possible to detect changes in biogeographic patterns or shifts of genotypes towards more generalist ones.HERBA: Herbaria for the preservation of cyanobacterial diversity and biogeography studies : past and futur

Contribution of cyanobacteria to the building of travertines in a calcareous stream

The ambient temperature travertine deposits of the calcareous Hoyoux River (Modave, Belgium) and several tributaries are organized and promoted by the filamentous cyanobacterium identified by its morphotype and ecological properties as Phormidium cf. incrustatum. A combination of techniques was used to study this biotope: physico-chemical parameters and CO2 measurements, Scanning and Transmission Electron Microscopy, RAMAN microspectroscopy. A molecular diversity study with pyrosequencing of the cyanobacterial 16S rRNA is in progress. A potential candidate was isolated in culture.Caractérisation des processus de fossilisation dans les roches calcaires et évolution des cyanobactéries impliquées dans la biominéralisatio

The Cyanobacterial Biota of Polar Regions: a Molecular Approach

Cyanobacteria are major components of Polar ecosystems. They comprise a considerable amount of the total biomass, are the main primary producers, and play important roles in the initial development of terrestrial and aquatic habitats. Although the cyanobacterial diversity in the Polar Regions has been well studied, research has been mostly limited to traditional methods such as microscopy, culturing, and Sanger-based molecular ecology approaches. High-troughput sequencing (HTS) has revolutionized our knowledge of microbial diversity and distribution, but a thorough investigation of polar cyanobacterial communities using HTS has not yet been performed. As a result, knowledge of the distributional patterns of polar cyanobacterial communities and the mechanisms underlying their structure is fragmentary. In this thesis, we applied the HTS approach to investigate the diversity and distributional patterns of cyanobacteria in a range of polar habitats. The main goals were: 1. To evaluate the use of HTS as a tool for assessing the cyanobacterial diversity in polar environments, including an assessment of different bioinformatics pipelines and the improvement represented by HTS in comparison to traditional methods; 2. To assess the spatial patterns of cyanobacterial communities across polar environments and the environmental factors shaping cyanobacterial community composition; 3. Tho study the successional dynamics of cyanobacterial communities following the colonization of recently deglaciated habitats. Due to its higher analytical depth, HTS was proven a valuable tool for the study of the cyanobacterial biota of Polar Regions. Nevertheless, the analysis of artificial communities highlighted the importance of strict bioinformatics control of HTS reads, as PCR and sequencing errors might bias the observed structure of the communities. Given the strict bioinformatics workflow applied, our results suggest a previously undetected polar cyanobacterial rare biosphere. On one side, the HTS approach revealed that microbial mat and biological soil crust (BSCs) across different Antarctic and Svalbard (High Arctic) regions are somewhat homogeneous, being dominated by filamentous cyanobacteria from the orders Pseudanabaenales and Oscillatoriales. At the phylotype level (97.5% similarity threshold), on the other hand, cyanobacterial communities were highly variable along environmental gradients within and between habitats. A study of benthic mat communities in Antarctic lakes revealed cyanobacterial communities highly structured by lake conductivity, and comparable compositions in lakes from distant Antarctic regions. In a study of BSC communities in four nunataks and mountain ridges in the Sør Rondane Mountains (Dronning Maud Land), highly dissimilar communities were observed between locations. Finally, two studies of BSC communities in Petunia Bay (Svalbard) revealed a marked, linear cyanobacterial community turnover along gradients of soil development. Altogether, the results obtained in the present thesis show that HTS is a powerful yet underused tool for the study of cyanobacterial diversity, not only in Polar Regions, but also on a global scale. This can be attributed to the very high sequencing depth achieved by HTS, which provides more robust assessments of community turnover and with a stronger statistical support than Sanger- based molecular ecology approaches

Study of microbial consortia on the degradation of cellulose

A biomassa lignocelulósica é a fonte de energia renovável mais abundante no planeta, sendo fonte de açúcares que podem ser fermentados para a obtenção de etanol. No entanto, devido a sua alta recalcitrância, poucos microrganismos conseguem hidrolisar a celulose com alta eficiência. Na natureza, esta degradação é realizada por diferentes espécies de microrganismos atuando de modo sinérgico. O objetivo principal deste trabalho é verificar a degradação de celulose por consórcios microbianos. Vinte e sete microrganismos isolados do manguezal da Estação Ecológica de Carijós (Florianópolis, Brasil), foram agrupados em comunidades e cultivados utilizando como substratos bagaço de cana-de-açúcar, celobiose e carboximetilcelulose. Após o período de incubação, a geração de açúcares fermentáveis foi avaliada utilizando-se o método do ácido 3,5-dinitrosalicílico, assim como a formação de biofilme na biomassa lignocelulósica através de microscopia eletrônica de varredura. Para as comunidades crescidas em carboximetilcelulose, também foi determinada a atividade das enzimas celulolíticas, pelo método do papel filtro. As comunidades não demonstraram muita eficiência na degradação do bagaço de cana-de-açúcar e carboximetilcelulose, possivelmente devido à alta recalcitrância destes substratos. Por outro lado, as comunidades demonstraram capacidade de degradação de celobiose, acumulando uma quantidade de açúcar equivalente a até cerca de 60% do valor inicial. Os resultados relativos à atividade enzimática não foram conclusivos e novos experimentos serão realizados. Os experimentos apontaram a comunidade J e os isolados JAG02, JAG02BA e JAG06A como candidatos a novos estudos, envolvendo consórcios com um menor número de isolados.The lignocellulosic biomass is the main source of renewable energy available on the planet, providing sugars that can be fermented to produce ethanol. However, due to its high recalcitrance, few microorganisms are able to hydrolyse cellulose with high yields. In nature, this degradation is realized by different species of microorganisms acting synergistically. The main objective of this study is to verify degradation of cellulose by microbial consortium. Twenty seven microorganisms isolated from the Carijós Ecological Station’s mangrove (Florianópolis, Brazil), were grouped in communities and cultivated using sugarcane bagasse, cellobiose and carboxymethylcellulose as substrates. After the incubation period, release of fermentable sugars was evaluated using the 3,5-dinitrosalicilic acid assay, as well as the biofilm formation over the lignocellulosic biomass by scanning electron microscopy. For the communities grown on carboxymethylcellulose, activity of cellulolytic enzymes was also determined, using the filter papel assay. The communities did not release high yields of fermentable sugars derivated from the degradation of sugarcane bagasse and carboxymethylcellulose, probably due to the high recalcitrance of these substrates. However, the communities were able to degrade cellobiose, generating sugar on the quantity equivalent to 60% of the initial value. Results relative to the enzymatic activity were not conclusive and new experiments should be made. The experiments pointed community J and the isolates JAG02, JAG02BA e JAG06A as candidates to new studies, using consortia with fewer isolates

Diversidade microbiana na Ilha Rei George (Península Antártica) e prospecção de enzimas queratinolíticas

O estudo da diversidade microbiana no continente antártico é fundamental para entender os processos que moldam a distribuição microbiana em ambientes naturais, e contribui para entender os efeitos decorrentes de mudanças climáticas na biodiversidade do planeta. Em adição, microrganismos adaptados a baixas temperaturas apresentam enorme potencial para aplicação em diversos processos industriais. Este trabalho teve como objetivos avaliar a diversidade funcional e genética de comunidades microbianas de solos da Ilha Rei George (Península Antártica), e realizar a prospecção de enzimas queratinolíticas ativas em baixas temperaturas. A análise da diversidade funcional mostrou que as comunidades microbianas são formadas por uma alta diversidade de grupos funcionais (H’ = 2.14-3.30), distribuídas heterogeneamente no ambiente. Similarmente, a análise da diversidade genética mostrou a presença de comunidades microbianas altamente diversas (H’ = 5.33-6.24), formadas majoritariamente por membros dos filos Proteobacteria, Bacteroidetes e Euryarchaeota. Finalmente, em um pequeno rastreamento de 120 isolados, cinco apresentaram atividade queratinolítica, dentre eles uma possível nova espécie de Pedobacter, mostrando o alto potencial biotecnológico de microrganismos antárticos.The study of microbial diversity in the Antarctic continent is vital to understand the processes which shape microbial distribution in natural environments, and contributes to understand the impacts of climate change on Earth’s biodiversity. Furthermore, cold-adapted microorganisms present high potential for application in several industrial processes. The objectives of this study were to evaluate the functional and genetic diversity of soil microbial communities of King George Island, Antarctic Peninsula, and prospect for cold-active keratinolytic enzymes. The analysis of functional diversity showed that microbial communities are composed of a high diversity of functional groups (H’ = 2.14-3.30), heterogeneously distributed in the environment. Similarly, the analysis of genetic diversity showed the presence of highly diverse microbial communities (H’ = 5.33- 6.24), composed mostly by members of the Proteobacteria, Bacteroidetes and Euryarchaeota phyla. Finally, through a small screening of 120 isolates, five showed keratinolytic activity, among them a putative novel species of Pedobacter, showing the high biotechnological potential of Antarctic microorganisms

Incompatibilidade vegetativa entre isolados de Bipolaris sorokiniana

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