Microbial community assembly and evolution in subseafloor sediment

Abstract

Bacterial and archaeal communities inhabiting the subsurface seabed live under strong energy limitation and have growth rates that are orders of magnitude slower than laboratory-grown cultures. It is not understood how subsurface microbial communities are assembled and whether populations undergo adaptive evolution or accumulate mutations as a result of impaired DNA repair under such energy-limited conditions. Here we use amplicon sequencing to explore changes of microbial communities during burial and isolation from the surface to the >5,000-y-old subsurface of marine sediment and identify a small core set of mostly uncultured bacteria and archaea that is present throughout the sediment column. These persisting populations constitute a small fraction of the entire community at the surface but become predominant in the subsurface. We followed patterns of genome diversity with depth in four dominant lineages of the persisting populations by mapping metagenomic sequence reads onto single-cell genomes. Nucleotide sequence diversity was uniformly low and did not change with age and depth of the sediment. Likewise, there was no detectable change in mutation rates and efficacy of selection. Our results indicate that subsurface microbial communities predominantly assemble by selective survival of taxa able to persist under extreme energy limitation.acteria and archaea inhabiting the subsurface seabed account for more than half of all microbial cells in the oceans (1, 2). The subsurface communities are cut off from fresh detrital organic matter deposited on the sea floor. The energy available for cellular maintenance and growth decreases rapidly with depth and age of the sediment (3-5). As a consequence, the microbial abundance and cell-specific metabolic rates decrease by orders of magnitude already within the top few meters of sediment (3, 6-8). However, even hundreds of meters below the seafloor sediments are populated by microbes that actively turn over their biomass (3,8). The growth characteristics of these microbial populations are unlike anything studied in pure culture as estimates suggest that the generation times of subsurface cells are tens to hundreds of years (3,7,8). As a model for how these deep biosphere communities are assembled, it was suggested that the microbes found in the subsurface seabed represent descendants of surface communities that were buried in the past (9-12). So far this model has not been tested systematically. Furthermore, it is not known if subsurface microorganisms during the burial evolve unique genetic traits conferring adaptation to this environment (13). Studies of adaptation and evolution in freeliving microorganisms reported high genetic heterogeneity and rapid evolutionary change within natural populations. However, these studies have focused on dynamic or mixed environments with large population sizes and rapid growth, e.g., biofilms or planktonic communities (14-16) that are very different from the subsurface seabed environment.According to "Drake's rule" (17), DNA-based or...

Microbial community assembly in marine sediments

“…These OTUs make up a small subset of the total OTU richness but comprise a significant portion of the total microbial community. Patterns of persisting OTUs mirror the results by Starnawski et al (2017), suggesting that environmental selection shapes subsurface communities on a global scale. OTUs classified as Atribacteria and Dehalococcoidia are among the most dominant persisters at all 3 analyzed sites.…”

Necromass as a Limited Source of Energy for Microorganisms in Marine Sediments

“…Interestingly, the observed decline in cell death rate with depth (Figures and ) is suggestive that microbial populations in older, deeper sediments are relatively stable. This could be indicative of dormancy (i.e., transition to a state of low activity) (Stolpovsky et al, ), adaptation to extreme energy limitation, and lower power utilization (Lever et al, ; Starnawski et al, ), and/or that maintenance power demand is provided by one or more other reactions, including the oxidation of radiolytic H 2 (D'Hondt et al, ). Based on our thermodynamic modeling and an assumed reaction rate of H 2 oxidation of 1 pM H 2 per cm 3 per year, radiolytic H 2 provides a steady source of power to the microbial community at SPG and becomes the principal electron donor in SPG sediment at depths greater than ~17 m (equivalent to ~18 million years).…”

The bacterial community structure and functional profile in the heavy metal contaminated paddy soils, surrounding a nonferrous smelter in South Korea

“…In fact, the As‐resistant Bacillus strains have been shown to reduce As(V) to As(III) (Ruta et al., ). In order to delineate the importance of different evolutionary processes (lateral gene transfer, selective survival of heavy metal resistant populations, accumulation adaptive mutations) in mediating the response of a soil microbial community to heavy metal contamination, amplicon‐based sequencing should be combined with single‐cell, gene, and genome‐centric metagenomic sequencing (Hemme et al., ; Starnawski et al., ).…”