Microscale spatial distributions of microbes in marine intertidal sediments and photosynthetic microbial mats

Marine sedimentary habitats generally have their highest microbial activity in the top few centimeters. Where light reaches the surface sediments, benthic oxygenic photoautotrophs composed of cyanobacteria and eukaryotic microalgae (such as diatoms) dominate. In situations with a low grazing pressure like intertidal flats, this leads to permanently vertically laminated microbial communities (photosynthetic microbial mats). Although the importance of collecting samples at the scale relevant for microbial activity in sedimentary habitats has been acknowledged, this aspect is still virtually unstudied. The main focus in this thesis concerns, therefore, microscale (μm to mm) spatial distributions of key players in photosynthetic microbial mats, i.e. viruses, prokaryotes and oxygenic photoautotrophs. Initially, two methods were developed; to extract and count viruses from microbial mats, and to discriminate in a non-intrusive manner the different photoautotrophic groups. Application showed strong vertical and horizontal microscale heterogeneity in the distributions of these microbes, both in intertidal sediment (Scotland) and photosynthetic microbial mats (Netherlands). Moreover, I studied the effect mortality agents, such as viruses and fungi, may have on microscale spatial and temporal distributions of key members of the microbial mats and sediment. High viral abundances in the microbial mats indicated that viruses could be a significant structuring factor. Fungi clearly affected the spatial distribution of oxygenic photoautotrophs by degrading benthic cyanobacteria and diatoms in ring-like shapes during summer and autumn. Based on these findings I recommend more research on microscale distributions and underlying mortality processes to improve our understanding of species diversity, succession and biogeochemical cycling in microbial mats.