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Background: Guerrero Negro microbial mat is one of the best studied microbial mat ecosystems; however, the vertical functional organization has been less well studied. In this study, the microbial ecology, environmentally relevant adaptations and the potential evolutionary interlinking of the responsible genes between bacterial, archaeal and viral lineages in Guerrero Negro (GN) microbial mat were investigated using metagenomic sequencing across a vertical transect at millimeter scale. Through metagenomics, the current study provides a taxonomic description of the vertical taxonomic organization as well as a functional organization delineated between bacteria, archaea, eukarya and viruses in a GN microbial mat – revealing new insights into the ecology of these communities. Results: The community composition based on the number of unique genes recovered (n) and coverages (c) comprised bacteria (98.06 / 98.71 % n/c), archaea (1.82 / 1.19 % n/c), eukarya (0.07 / 0.07 % n/c) and viruses (0.05 / 0.03 % n/c). The greatest coverages of genes of bacteria and eukarya were detected in first layers, while the highest coverages of genes of archaea and viruses were found in deeper layers. Many genes potentially related to adaptation to the local environment (e.g., UV radiation, multidrug resistance, oxidative stress, and heavy metals) were detected. Those genes were found in bacterial, archaeal and viral lineages totalling 3255, 44, and 1 genes, respectively. We employed phylogenetics in order to investigate the evolutionary histories of genes with similar functional annotations that were taxonomically classified as coming from bacteria, archaea and viruses. Conclusions: A gene-focused analysis of bacteria, archaea, eukarya, and viruses showed a vertical partitioning of the community, both in taxonomic affinity and function. The presence of genes potentially involved in adaptation to environmental conditions may have implications and resilience to stress conditions. Phylogenetic analyses showed an interlinking between domains, where genes taxonomically classified as archaea and viruses formed clades suggesting they were phylogenetically relatively closely related to genes present in bacteria lineages – potentially indicating horizontal gene transfer in GN mat.

Some microscopic organisms grow together to build structures known as microbial mats. These mats are formed from several layers with different colors, and their structure depends on environmental conditions such as sunlight, humidity, and available food. Microbial mats are found in oceans, lakes, and coastal lagoons, as well as in extreme environments like deserts, polar regions, and hot springs. The study of fossils indicates that microbial mats were a common form of life on early Earth, and they have persisted on our planet ever since! Therefore, the study of modern mats helps us to understand microbial life in the past, and how they might help to regulate the Earth’s climate. Scientists believe that microbial mats can prosper on rocky planets like Earth, so they are studying mats in different terrestrial environments to help them to recognize evidence indicating the presence of mats on other worlds.