Geochemical transition zone powering microbial growth in subsurface sediments

Abstract

No other environment hosts as many microbial cells as the marine sedimentary biosphere. While the majority of these cells are expected to be alive, they are speculated to be persisting in a state of maintenance without net growth due to extreme starvation. Here, we report evidence for in situ growth of anaerobic ammonium-oxidizing (anammox) bacteria in ∼80,000-y-old subsurface sediments from the Arctic Mid-Ocean Ridge. The growth is confined to the nitrate–ammonium transition zone (NATZ), a widespread geochemical transition zone where most of the upward ammonium flux from deep anoxic sediments is being consumed. In this zone the anammox bacteria abundances, assessed by quantification of marker genes, consistently displayed a four order of magnitude increase relative to adjacent layers in four cores. This subsurface cell increase coincides with a markedly higher power supply driven mainly by intensified anammox reaction rates, thereby providing a quantitative link between microbial proliferation and energy availability. The reconstructed draft genome of the dominant anammox bacterium showed an index of replication (iRep) of 1.32, suggesting that 32% of this population was actively replicating. The genome belongs to aScalinduaspecies which we nameCandidatus Scalindua sediminis, so far exclusively found in marine sediments. It has the capacity to utilize urea and cyanate and a mixotrophic lifestyle. Our results demonstrate that specific microbial groups are not only able to survive unfavorable conditions over geological timescales, but can proliferate in situ when encountering ideal conditions with significant consequences for biogeochemical nitrogen cycling.

Genomes of Thaumarchaeota from deep sea sediments reveal specific adaptations of three independently evolved lineages

“…Genomic DNA from four sediment horizons in each core was selected for metagenome sequencing, based on the published porewater geochemical data and 16S rRNA gene profiles (Fig. S1 ) [ 12 , 39 ]. In particular, sediments of 0.1 m below the sea floor (mbsf) (oxic), 10.0 mbsf (oxic), 22.0 mbsf (oxic–anoxic transition zone; OATZ), and 29.5 mbsf (anoxic–oxic transition zone) were selected from U1383E.…”

“…Detailed information about sampling sites, sampling procedure, 16S rRNA gene profiles, and porewater analysis was published in refs. [ 12 , 39 ].

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Small sinking particles control anammox rates in the Peruvian oxygen minimum zone

“…We derived carbon-based export production using a particle export to primary production ratio (pe-ratio) determined via two methods: (1) using the global empirical relationship described in ref. 77 (based on temperature and chlorophyll a) and (2) using a pe-ratio of 0.4 as described in a previous report from the Peruvian OMZ 97 . The UVP-based estimate of export of organic nitrogen out of the euphotic zone was derived for particle size classes between 128 and 2048 µm and was based on the particle flux (J) at the base of the euphotic zone and the upper boundary of the OMZ (similar to refs.…”

“…74,75 ), these encounter rates would support in situ rates between 3 and 30 nmol L −1 day −1 , which is in line with the measured rates (Table 1). It is likely that this is a conservative estimate as the encounter model assumes that anammox bacteria are not motile 76,77 , which limits encounters with sinking particles and resulting nutrient hotspots. So far, Scalindua (which are the most abundant anammox bacteria within the Peruvian OMZ 78 ) are not known to be motile, however it should be noted that for motile bacteria at the same cell numbers, encounter rates could be increased by 179-400 times (Supplementary Fig.…”

Diverse Intracellular Inclusion Types Within Magnetotactic Bacteria: Implications for Biogeochemical Cycling in Aquatic Environments

“…The oxic‐anoxic transition zone (OATZ) between oxic and anoxic environments in sediments or water columns is a critical zone for microbial redox reactions of various compounds (e.g., C, N, Fe, and S) (Brune et al., 2000; Canfield et al., 2010; Canfield & Thamdrup, 2009; Zhao et al., 2020). An aquatic OATZ generally has an opposing gradient with oxidized compounds (e.g., O 2 , NO 3 − , and Fe 3+ ) decreasing downward from the upper region and reduced compounds (e.g., S 2− , NH 4 + , and Fe 2+ ) increasing from the lower region (Flies et al., 2005; Jogler et al., 2010; Jørgensen et al., 2019; Simmons et al., 2004; Wang et al., 2013; Zhao et al., 2020). Magnetotactic bacteria (MTB) are typically gradient‐loving microorganisms that occur globally but live dominantly at or just below aquatic OATZ environments (Lefèvre & Bazylinski, 2013).…”