With its unique consortium of microorganisms from all domains of life, termite gut is considered one of the most efficient lignocellulose degrading systems in nature. Recently, host diet and taxonomy as well as gut microenvironmental conditions have emerged as main factors shaping microbial communities in termite guts. The aim of this thesis was to investigate this highly efficient lignocellulolytic system at holobiont level, with a particular focus on gut microbiome function and composition in relation to the host diet. As a starting point, we optimised a complete framework for an accurate termite gut prokaryote-oriented metatranscriptomics, which was at the basis of all subsequent sequencing assay designs and analyses performed in the course of the work. Afterwards, we characterised the compositions and functions of biomass-degrading bacterial communities in guts of plant fibre- and soil-feeding higher termites, proving the existence of functional equivalence across microbial populations from different termite hosts. We also showed that each termite is a reservoir of unique microorganisms and their accompanying genes. We further extended above approach to metagenomics and bacterial genomes reconstruction and we applied it to explore the process of biomass digestion in the different sections of the highly compartmented gut of soil feeding Labiotermes labralis. We showed that primarily cellulolytic activity of the termite host was restricted to foregut and midgut, while bacterial contribution was most pronounced in P1 and P3 hindgut compartments and included activities targeting broad range of lignocellulose components. Finally, we investigated the adaptation of a laboratory-maintained grass-feeding higher termite colony of Cortaritermes spp. to Miscanthus diet at host and symbiont levels. A natural system of a termite gut was shown to progressively change in composition to yield a consortium of microbes specialised in degradation of a specific biomass. Overall, the integrative omics approach proposed here provide a framework for a better understanding of a complex lignocellulose degradation by a higher termite gut system and pave a road towards its future bioprospecting. / Doctorat en Sciences / info:eu-repo/semantics/nonPublished

Polymerase chain reaction (PCR) is a method used in many research protocols to amplify a small amount of a short segment of DNA to millions of copies. PCR is used for many taxonomic studies, as well as for some medical diagnostic procedures. Through PCR, short DNA primers bind to the template DNA to allow the thermostable DNA polymerase to copy the DNA. Often, researchers create universal primers to target a conserved region of DNA in multiple species, for example, the 16S rRNA gene in bacteria. The problem with these universal primers is that they do not always perfectly match the target DNA. The mismatch primers can still bind to the template, but could affect the efficiency of the PCR amplification. The effect of mismatch primers on the efficiency of the amplification in PCR is the focus of this thesis. Four forward primers with various mismatch overhangs were generated and incorporated into a DNA template through an initial PCR. These primers contained the binding region complementary to the V3/V4 region of the 16S rRNA bacterial gene. Further quantitative PCR (qPCR) reactions were run on these newly-made templates using two sets of primers complementary to the 16S rRNA gene region – one with ambiguous base pairs, one with unambiguous base pairs. The qPCR amplification curves, the Cq values, and the initial concentrations of DNA products (seed values) were analyzed and compared. The results showed differences in the Cq values and seed values between the reactions containing mismatches and those not containing mismatches. Other variables including annealing temperature, addition of Illumina sequencing tails to the primers, and initial primer concentration were also tested to determine if these variables had an effect on the amplification. The results from these reactions using different variables were inconclusive.

As soluções convencionais de tratamento biológico de corantes azo são baseadas em processos anaeróbio-aeróbios ocorrendo em unidades distintas. Este estudo avaliou o uso da aeração intermitente para a descoloração do Direct Black 22 (DB22) e biodegradação simultânea de subprodutos tóxicos no mesmo compartimento reacional. Os microrganismos utilizados foram obtidos de florestas tropicais e previamente adaptados a concentrações crescentes de DB22 (10-32,5 mg.L-1) em meio de cultivo. Os efeitos da concentração inicial de glicose (1 – 2 – 3 g.L-1) e aeração intermitente (0 – 4 – 8 h.d-1) sobre a descoloração, constante de descoloração e remoção de demanda química de oxigênio (DQO) foram investigados por planejamento fatorial e análise de superfície de resposta. Os testes foram conduzidos com água residuária (AR) que simulava a composição dos efluentes de lavanderias têxteis do agreste pernambucano. Os resultados demonstraram que a descoloração no longo prazo não foi inibida para ciclos de aeração de até 4 h.d-1, embora menores velocidades de remoção de cor tenham sido obtidas nestas condições. Os efeitos negativos da aeração foram significativamente reduzidos pelo aumento da concentração de glicose na AR. Ademais, a remoção de DQO foi potencializada com o aumento da frequência de aeração. Após descoloração do DB22 nos ensaios não aerados, verificou-se a formação de picos de absorbância relacionados à presença de aminas aromáticas ou outros intermediários da descoloração redutiva; o que não ocorreu nos experimentos aerados. Estes fatores resultaram em menor toxicidade à Daphnia magna em experimento modelo com nível intermediário de aeração. O sequenciamento do gene 16S rRNA na plataforma Illumina HiSeq revelou a presença de gêneros de bactérias conhecidos por produzirem enzimas envolvidas na biodegradação do azo. Observou-se, ainda, uma correlação positiva entre diversidade microbiana e eficiência de descoloração. Os resultados sugerem que a estratégia de aeração intermitente, corretamente implementada, pode melhorar a performance do tratamento biológico de efluentes têxteis que contém azo-corantes. / Conventional technologies for biological treatment of azo dyes are based on anaerobic-aerobic processes taking place into distinct units. This study evaluated the use of intermittent aeration strategy for decolorization of the Direct Black 22 (DB22) and simultaneous biodegradation of metabolites. Microorganisms were obtained from tropical forests and previously acclimated to increasing concentrations of DB22 (10-32.5 mg.L-1) in growth medium. Effects of initial glucose concentration (1 – 2 – 3 g.L-1) and intermittent aeration (0 – 4 – 8 cycles.d-1) on response variables decolorization, decolorization rate, and removal of chemical oxygen demand (COD) were investigated using factorial design and response surface analysis. Tests were conducted using a wastewater that simulated the composition of textile laundry effluents from a region with harsh climate in the state of Pernambuco, known as agreste pernambucano. Results showed long-term decolorization was not impaired for up to 4 cycles.d-1 of aeration, although a decrease in color removal velocities was observed in these experiments. Negative impacts of aeration were significantly reduced by increasing initial glucose concentration. Moreover, COD removal was enhanced with increased aerations levels. After DB22 degradation in non-aerated batches, the formation of absorbance peaks associated with aromatic amines and other byproducts of reductive decolorization was observed; which did not occur in the aerated experiments. These resulted in lower toxicity to Daphnia magna in model experiment using intermediate level of aeration. 16S rRNA gene sequencing on the Illumina HiSeq platform revealed the presence of several bacteria known to produce enzymes involved in azo compounds degradation. Furthermore, a positive correlation between microbial diversity and decolorization efficiency was observed. Results suggest intermittent aeration strategy can enhance biological treatment of textile effluents containing azo dyes when correctly implemented.

We investigated the effects of substrate (cellulose or starch) and different clay contents on the production of microbial extracellular polymeric substances (EPS) and concomitant development of stable soil aggregates. Soils were incubated with different amounts of montmorillonite (+ 0.1%, + 1%, + 10%) both with and without two substrates of contrasting quality (starch and cellulose). Microbial respiration (CO2), biomass carbon (C), EPS-protein, and EPS-polysaccharide were determined over the experimental period. The diversity and compositional shifts of microbial communities (bacteria/archaea) were analysed by sequencing 16S rRNA gene fragments amplified from soil DNA. Soil aggregate size distribution was determined and geometric mean diameter calculated for aggregate formation. Aggregate stabilities were compared among 1–2-mm size fraction. Starch amendment supported a faster increase than cellulose in both respiration and microbial biomass. Microbial community structure and composition differed depending on the C substrate added. However, clay addition had a more pronounced effect on alpha diversity compared to the addition of starch or cellulose. Substrate addition resulted in an increased EPS concentration only if combined with clay addition. At high clay addition, starch resulted in higher EPS concentrations than cellulose. Where additional substrate was not provided, EPS-protein was only weakly correlated with aggregate formation and stability. The relationship became stronger with addition of substrate. Labile organic C thus clearly plays a role in aggregate formation, but increasing clay content was found to enhance aggregate stability and additionally resulted in the development of distinct microbial communities and increased EPS production.