The Isolation and Characterization of Untapped Diversity of Culturable Bacteria in the Red Sea Mangrove Ecosystem

Abstract

Microorganisms are widespread in all ecosystems and play critical roles in nature. They are major players in global biogeochemical cycles that are fundamental in nutrient cycling. Molecular ecology surveys that investigate the microbial diversity of many different environments have revealed an impressive diversity of microbes in nature and have highlighted our inability to cultivate the vast majority of them in the laboratory. The improvement of our ability to grow uncultivable microbes in laboratory conditions will help us in this challenging task. Standard cultivation methods that have helped to bring to culture many relevant microorganisms in the past century are, however, characterized by limitations which hamper the isolation of novel microbes. For this reason, alternative cultivation strategies have been developed in recent decades which have allowed to expand the collection of environmentally relevant but poorly represented microbial strains. The use of such novel approaches for investigating the microbial diversity of underexplored natural ecosystems, such as sub-tropical mangrove forests, can result in the isolation, in laboratory conditions, of bacterial strains belonging to previously undescribed taxa. Mangroves are unique environments exposed to strong selection forces with respect to other marine environments, including high temperatures, salinity and oligotrophy. I hypothesize that these unique combinations of environmental features have selected microbiomes with unique characteristics. The aim of this PhD research is to explore the bacterial diversity of the Red Sea mangrove ecosystem, by applying an alternative cultivation strategy that uses oligotrophic conditions and long incubation time. I also exploited the diffusion chamber to cultivate bacterial taxa belonging to rarely isolated or even novel genera. This approach allowed me to isolate four novel bacterial taxa. Using 16S rRNA gene sequencing, the isolated bacteria were identified as one novel species and three novel genera belonging to Alpha-proteobacteria, Bacteroidetes, and Firmicutes, respectively. These isolates were further characterized and described through genomic, phylogenetic, chemotaxonomic, and phenotypic analysis to describe their ecological significance in the ecosystem of origin (i.e., mangrove sediments). This study reveals that the extreme conditions of the Red Sea mangroves have selected a unique and yet mostly untapped culturable microbiome with great potential for environmental applications.