Bacterial communities in temperate and polar coastal sands are seasonally stable.

Coastal sands are biocatalytic filters for dissolved and particulate organic matter of marine and terrestrial origin, thus, acting as centers of organic matter transformation. At high temporal resolution, we accessed the variability of benthic bacterial communities over two annual cycles at Helgoland (North Sea), and compared it with seasonality of communities in Isfjorden (Svalbard, 78°N) sediments, where primary production does not occur during winter. Benthic community structure remained stable in both, temperate and polar sediments on the level of cell counts and 16S rRNA-based taxonomy. Actinobacteriota of uncultured Actinomarinales and Microtrichales were a major group, with 8 ± 1% of total reads (Helgoland) and 31 ± 6% (Svalbard). Their high activity (frequency of dividing cells 28%) and in situ cell numbers of >10% of total microbes in Svalbard sediments, suggest Actinomarinales and Microtrichales as key heterotrophs for carbon mineralization. Even though Helgoland and Svalbard sampling sites showed no phytodetritus-driven changes of the benthic bacterial community structure, they harbored significantly different communities (p < 0.0001, r = 0.963). The temporal stability of benthic bacterial communities is in stark contrast to the dynamic succession typical of coastal waters, suggesting that pelagic and benthic bacterial communities respond to phytoplankton productivity very differently.

The effect of sediment grain properties and porewater flow on microbial abundance and respiration in permeable sediments.

Sandy sediments cover 50-60% of the continental shelves and are highly efficient bioreactors in which organic carbon is remineralized and inorganic nitrogen is reduced to N2. As such they seem to play an important role, buffering the open ocean from anthropogenic nitrogen inputs and likely remineralizing the vast amounts of organic matter formed in the highly productive surface waters. To date however, little is known about the interrelation between porewater transport, grain properties and microbial colonization and the consequences for remineralization rates in sandy sediments. To constrain the effect of theses factors on remineralization in silicate sands, we incubated North Sea sediments in flow-through reactors after separating into five different grain size fractions. Bulk sediment and sediment grain properties were measured along with microbial colonization and cell abundances, oxygen consumption and denitrification rates. Volumetric oxygen consumption ranged from 14 to 77 µmol O2 l-1 h-1 while nitrogen-loss via denitrification was between 3.7 and 8.4 µmol N l-1 h-1. Oxygen consumption and denitrification rates were linearly correlated to the microbial cell abundances, which ranged from 2.9 to 5.4·108 cells cm-3. We found, that cell abundance and consumption rates in sandy sediments are influenced (i) by the surface area available for microbial colonization and (ii) by the exposure of these surfaces to the solute-supplying porewater flow. While protective structures such as cracks and depressions promote microbial colonization, the oxygen demand is only met by good ventilation of these structures, which is supported by a high sphericity of the grains. Based on our results, spherical sand grains with small depressions, i.e. golf ball like structures, provide the optimal supporting mineral structure for microorganisms on continental shelves.

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

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.

Ubiquitous Gammaproteobacteria dominate dark carbon fixation in coastal sediments.

Marine sediments are the largest carbon sink on earth. Nearly half of dark carbon fixation in the oceans occurs in coastal sediments, but the microorganisms responsible are largely unknown. By integrating the 16S rRNA approach, single-cell genomics, metagenomics and transcriptomics with (14)C-carbon assimilation experiments, we show that uncultured Gammaproteobacteria account for 70-86% of dark carbon fixation in coastal sediments. First, we surveyed the bacterial 16S rRNA gene diversity of 13 tidal and sublittoral sediments across Europe and Australia to identify ubiquitous core groups of Gammaproteobacteria mainly affiliating with sulfur-oxidizing bacteria. These also accounted for a substantial fraction of the microbial community in anoxic, 490-cm-deep subsurface sediments. We then quantified dark carbon fixation by scintillography of specific microbial populations extracted and flow-sorted from sediments that were short-term incubated with (14)C-bicarbonate. We identified three distinct gammaproteobacterial clades covering diversity ranges on family to order level (the Acidiferrobacter, JTB255 and SSr clades) that made up >50% of dark carbon fixation in a tidal sediment. Consistent with these activity measurements, environmental transcripts of sulfur oxidation and carbon fixation genes mainly affiliated with those of sulfur-oxidizing Gammaproteobacteria. The co-localization of key genes of sulfur and hydrogen oxidation pathways and their expression in genomes of uncultured Gammaproteobacteria illustrates an unknown metabolic plasticity for sulfur oxidizers in marine sediments. Given their global distribution and high abundance, we propose that a stable assemblage of metabolically flexible Gammaproteobacteria drives important parts of marine carbon and sulfur cycles.