Microbial life on a sand grain: from bulk sediment to single grains

Abstract

Globally, marine surface sediments constitute a habitat for estimated 1.7 × 1028 prokaryotes. For benthic microbial community analysis, usually, several grams of sediment are processed. In this study, we made the step from bulk sediments to single sand grains to address the microbial community directly in its micro-habitat: the individual bacterial diversity on 17 sand grains was analyzed by 16S ribosomal RNA gene sequencing and visualized on sand grains using catalyzed reporter deposition fluorescence in situ hybridization. In all, 104–105 cells were present on grains from 202 to 635 μm diameter. Colonization was patchy, with exposed areas largely devoid of any epi-growth (mean cell–cell distance 4.5±5.9 μm) and protected areas more densely populated (0.5±0.7 μm). Mean cell–cell distances were 100-fold shorter compared with the water column. In general, growth occurred in monolayers. Each sand grain harbors a highly diverse bacterial community as shown by several thousand species-level operational taxonomic units (OTU)0.97. Only 4–8 single grains are needed to cover 50% of OTU0.97 richness found in bulk sediment. Although bacterial communities differed between sand grains, a core community accounting for >50% of all cells was present on each sand grain. The communities between sediment grains are more similar than between soil macroaggregates.

Iron to Gas: Versatile Multiport Flow-Column Revealed Extremely High Corrosion Potential by Methanogen-Induced Microbiologically Influenced Corrosion (Mi-MIC)

“…Compared to glass beads, sand grains are more textured and denser, allowing enhanced microbial attachment. Furthermore, sand grains enhances the growth of microorganisms, it has been found that each sand grain can habit 10 5 cells (Probandt et al, 2018) with only 0.5 µm between each cell (Probandt et al, 2018). Sand grains can shield microorganism from mechanical sheer stress, while providing necessary porosity for substrate availability (Probandt et al, 2018).…”

Spatial structure increases the benefits of antibiotic production in Streptomyces griseus

“…Streptomycetes in soil live on soil grains where overall cell densities are anticipated to be heterogenous and patchy (Probandt et al, 2018). One of the challenges to understanding the role of antibiotics in nature is that their estimated concentrations in bulk soil are extremely small.…”

“…Microscopic analysis of sand grains from marine sediments revealed that colonization is highly uneven, with protected areas on individual grains being more densely populated than exposed areas (Probandt et al, 2018). Because the fitness of S. griseus scales with density, the colonization density in nature will undoubtedly influence the benefits of antibiotic production.…”

In situgrowth of anammox bacteria in subseafloor sediments

“…Apparently, their cellular metabolic rates are lower than the required metabolic level (10 4 -10 5 protons per second) for the rotation of a single bacterial flagellum in E. coli 17 , suggesting that these anammox bacteria do not have enough metabolic activity to fuel the flagellar rotation. Instead, we speculate the function of the flagella of anammox bacteria in the subsurface are more likely facilitating their adhesion onto particle surfaces 18 , as the majority of microbial cells in marine sediments are particle-attached 19 . This could provide them a protection in unfavorable conditions like the oxic zone where they could hide in anoxic microniches.…”