Microbial mats are prokaryotic communities that are thought to represent the present-day analogues of the first ecosystems on Earth. Their study reveals microbial strategies for survival under a broad range of environments. The aim of this work was the application of new techniques and combination of existing ones to give an integrated vision of the structure and physiology, and also characterize less-known microbial populations involved in important processes in the mat. As a result of this study, we can conclude that the application of the "Signature Lipid Biomarker approach" in microbial mat samples has proved to be an effective method to obtain information about physiology and composition of natural microbial assemblages. However, more studies need to be performed in order to increase the sensibility and reproducibility of these techniques, and to evaluate the model of distribution of data in mat samples.

In addition, the combination of lipid analysis and nucleic acid-based methods in microbial mats at different depths has provided useful information about the temporal dynamic of populations, their phylogenetic affiliation and physiological status. This study has revealed the importance of heterotrophic bacteria in the photosynthetic layers, the presence of green non-sulfur bacteria in several 'niches', as well as fermentative bacteria in the deepest layers. Besides, divergence analysis has showed that depth-related changes might have a greater influence than temporal changes.

Apart from that, the application of the quinone profiling method has been useful for taxonomic purposes, biomass estimation and microbial redox state. In this case, we have observed important differences in the community structure and redox status in microbial mats from different locations that were apparently very similar. In addition, we have performed a preliminarily study about the detection of intact polar lipids in mat samples that will be improved in the future because of its higher taxonomical potential. We have also detected archaeal members that might have an important role in the physiology of the system.

The mentioned approaches were also applied to microbial mat samples along a circadian cycle in order to evaluate changes as a response to daily processes. We observed a pattern of physicochemical responses of the mat that reproduces every day. During this study, we have also observed daily changes attributed to anaerobic microorganisms, and for this reason we have isolated representative members of anaerobic spore-formers.

As a result of the data obtained after the application of combined analysis in mats, we realized about the importance of the heterotrophic bacteria in the regulation of metabolic processes in the photic zone. Previous studies have investigated the heterotrophic diversity in mats, but the information about their role and the interactions with other microbial groups are still limiting. In this work, we have isolated and characterized two microbial strains involved in the metabolic interactions of the photic zone. We have demonstrated the metabolic capacities of Pseudoalteromonas sp. EBD and the relationship with cyanobacteria. On the other hand, a member of the Sphingomonas genus has been also characterized and its importance in the nutrient cycling and in the polyhydroxyalkanoate dynamics will be investigated.

Finally, we have studied the microbial diversity of sulfur-oxidizers involved in the sulfur cycle of transition zones between oxygen and sulfide. In this case, we have investigated the morphological succession in microbial 'blooms' in sulfur-rich environments to predict their reproducibility. In addition, we have applied molecular techniques that have provided important information about the composition of the 'sulfur-blooms' and have permitted the design of probes that will be applied in future studies for the detection of the observed microorganisms in mats.