Evidence for a Growth Zone for Deep-Subsurface Microbial Clades in Near-Surface Anoxic Sediments

Abstract

Global marine sediments harbor a large and highly diverse microbial biosphere, but the mechanism by which this biosphere is established during sediment burial is largely unknown. During burial in marine sediments, concentrations of easily-metabolized organic compounds and total microbial cell abundance decrease. However, it is unknown whether some microbial clades increase with depth. We show total population increases in 38 microbial families over 3 cm of sediment depth in the upper 7.5 cm of White Oak River (WOR) estuary sediments. Clades that increased with depth were more often associated with one or more of the following: anaerobes, uncultured, or common in deep marine sediments relative to those that decreased. Maximum doubling times (in situ steady state growth rates could be faster to balance cell decay) were estimated as 2-25 years by combining sedimentation rate with either quantitative PCR (qPCR) or the product of the Fraction Read Abundance of 16S rRNA genes and total Cell counts (FRAxC). Doubling times were within an order of magnitude of each other in two adjacent cores, as well as in two laboratory enrichments of Cape Lookout Bight (CLB), NC, sediments (average difference of 28 ± 19%). qPCR and FRAxC in sediment cores and laboratory enrichments produced similar doubling times for key deep subsurface uncultured clades Bathyarchaeota (8.7 ± 1.9 years) and Thermoprofundales/MBG-D (4.1 ± 0.7 years). We conclude that common deep subsurface microbial clades experience a narrow zone of growth in shallow sediments, offering an opportunity for selection of long-term subsistence traits after resuspension events. Significance statement: Many studies show that the uncultured microbes that dominate global marine sediments do not actually increase in population size as they are buried in marine sediments – rather they exist in a sort of prolonged torpor for thousands of years. This is because, although studies have shown biomass turnover in these clades, no evidence has ever been found that that deeper sediments have larger populations for specific clades than shallower layers. We discovered that they actually do increase population sizes during burial, but only in the upper few centimeters. This suggests that marine sediments may be a vast repository of mostly non-growing microbes with a thin and relatively rapid area of cell abundance increase in the upper 10 centimeters, offering a chance for subsurface organisms to undergo natural selection.

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“…We further investigated present day environmental drivers and main evolutionary forces shaping the composition of prokaryotic communities populating the seafloor. In addition to the longitudinal structuration of communities, we confirm a systematic vertical stratification also reported at different depth scales in previous studies (Durbin and Teske, 2011;Orcutt et al, 2011;Jochum et al, 2017;Petro et al, 2019;Lloyd et al, 2020). We took advantage of the longitudinal extent of our dataset to investigate what processes might be at play in the assembly of microbial communities in and just below the bioturbation zone.…”

“…When comparing three adjacent sites (<10 km apart), we found that site-specific ASVs only marginally contributed to the total community (<1.8%, Figure 5D), whereas horizon-specific biomarkers, considered here as proxies for environmental filtering, were predominant (36.9-45.6% of reads). This finding is in line with the hypothesis of a strong environmental influence raised in previous work (Petro et al, 2017(Petro et al, , 2019Starnawski et al, 2017;Kirkpatrick et al, 2019;Marshall et al, 2019;Lloyd et al, 2020), even within the first decimeters of sediment. The observations from Petro et al (2019) on the depth of influence of the bioturbation zone are also in line with the detection of macrofauna in a parallel metabarcoding study on these Mediterranean and Atlantic samples.…”

“…The important link between sediment horizon and community richness and composition was evident from the sample ordinations (Figure 4D), taxonomic composition (Supplementary Figure 2A), alpha-diversity patterns (Supplementary Figure 2B), and PERMANOVA analysis (F = 5.11, p = 0.001). The clearest changes in relative abundance were observed for Acidobacteria, Chloroflexi, and Bathyarchaeia, which all became more abundant deeper below the seafloor (Bienhold et al, 2016;Hoshino et al, 2020;Jørgensen et al, 2020;Lloyd et al, 2020;Vuillemin et al, 2020). In contrast, Desulfobacterota showed first an increase in relative abundance, before decreasing in deeper horizons of the upper bathyal zone, a pattern also described by Lloyd et al, 2020.…”

“…The clearest changes in relative abundance were observed for Acidobacteria, Chloroflexi, and Bathyarchaeia, which all became more abundant deeper below the seafloor (Bienhold et al, 2016;Hoshino et al, 2020;Jørgensen et al, 2020;Lloyd et al, 2020;Vuillemin et al, 2020). In contrast, Desulfobacterota showed first an increase in relative abundance, before decreasing in deeper horizons of the upper bathyal zone, a pattern also described by Lloyd et al, 2020. Recently, Petro et al (2017, 2019 invoked selection of subsurface microorganisms locally from the surface community during burial as an important process driving subsurface community assembly.…”

Novel Microbial Groups Drive Productivity in an Archean Iron Formation

“…Due to the isolation from the surface, time scales for surface derived water or carbon can range from years to hundreds of millions of years (Lippmann et al, 2003;Lin et al, 2006;Holland et al, 2013). Thus, it stands to reason that deep microbial systems operate on time scales that are counter to what we observe in the lab or at the surface, i.e., growth rates in the lab range from minutes to weeks, while subsurface may see growth on the order of years to decades (Hoehler and Jørgensen, 2013;Xie et al, 2013;Onstott et al, 2014;Trembath-Reichert et al, 2017;Lloyd et al, 2020). As a whole, the subsurface is highly populated with microorganisms.…”