C-DEBI Newsletter – April 15, 2020

mSystems
Selection Is a Significant Driver of Gene Gain and Loss in the Pangenome of the Bacterial Genus Sulfurovum in Geographically Distinct Deep-Sea Hydrothermal Vents – NEW!
Alief Moulana, Rika E. Anderson*, Caroline S. Fortunato, Julie A. Huber*
*C-DEBI Contribution 525

Microbial genomes have highly variable gene content, and the evolutionary history of microbial populations is shaped by gene gain and loss mediated by horizontal gene transfer and selection. To evaluate the influence of selection on gene content variation in hydrothermal vent microbial populations, we examined 22 metagenome-assembled genomes (MAGs) (70 to 97% complete) from the ubiquitous vent Epsilonbacteraeota genus Sulfurovum that were recovered from two deep-sea hydrothermal vent regions, Axial Seamount in the northeastern Pacific Ocean (13 MAGs) and the Mid-Cayman Rise in the Caribbean Sea (9 MAGs). Genes involved in housekeeping functions were highly conserved across Sulfurovum lineages. However, genes involved in environment-specific functions, and in particular phosphate regulation, were found mostly in Sulfurovum genomes from the Mid-Cayman Rise in the low-phosphate Atlantic Ocean environment, suggesting that nutrient limitation is an important selective pressure for these bacteria. Furthermore, genes that were rare within the pangenome were more likely to undergo positive selection than genes that were highly conserved in the pangenome, and they also appeared to have experienced gene-specific sweeps. Our results suggest that selection is a significant driver of gene gain and loss for dominant microbial lineages in hydrothermal vents and highlight the importance of factors like nutrient limitation in driving microbial adaptation and evolution.

Communications Biology
Deep microbial proliferation at the basalt interface in 33.5–104 million-year-old oceanic crust – NEW!
Yohey Suzuki, Seiya Yamashita, Mariko Kouduka, Yutaro Ao, Hiroki Mukai, Satoshi Mitsunobu, Hiroyuki Kagi, Steven D’Hondt*, Fumio Inagaki, Yuki Morono, Tatsuhiko Hoshino, Naotaka Tomioka, Motoo Ito
*C-DEBI Contribution 526

The upper oceanic crust is mainly composed of basaltic lava that constitutes one of the largest habitable zones on Earth. However, the nature of deep microbial life in oceanic crust remains poorly understood, especially where old cold basaltic rock interacts with seawater beneath sediment. Here we show that microbial cells are densely concentrated in Fe-rich smectite on fracture surfaces and veins in 33.5- and 104-million-year-old (Ma) subseafloor basaltic rock. The Fe-rich smectite is locally enriched in organic carbon. Nanoscale solid characterizations reveal the organic carbon to be microbial cells within the Fe-rich smectite, with cell densities locally exceeding 10¹⁰ cells/cm³. Dominance of heterotrophic bacteria indicated by analyses of DNA sequences and lipids supports the importance of organic matter as carbon and energy sources in subseafloor basalt. Given the prominence of basaltic lava on Earth and Mars, microbial life could be habitable where subsurface basaltic rocks interact with liquid water.

Frontiers in Marine Science
Dissolved Inorganic Carbon Pump in Methane-Charged Shallow Marine Sediments: State of the Art and New Model Perspectives – NEW!
Sajjad A. Akam, Richard B. Coffin, Hussain A. N. Abdulla and Timothy W. Lyons

Methane transport from subsurface reservoirs to shallow marine sediment is characterized by unique biogeochemical interactions significant for ocean chemistry. Sulfate-Methane Transition Zone (SMTZ) is an important diagenetic front in the sediment column that quantitatively consumes the diffusive methane fluxes from deep methanogenic sources toward shallow marine sediments via sulfate-driven anaerobic oxidation of methane (AOM). Recent global compilation from diffusion-controlled marine settings suggests methane from below and sulfate from above fluxing into the SMTZ at an estimated rate of 3.8 and 5.3 Tmol year^–1, respectively, and wider estimate for methane flux ranges from 1 to 19 Tmol year^–1. AOM converts the methane carbon to dissolved inorganic carbon (DIC) at the SMTZ. Organoclastic sulfate reduction (OSR) and deep-DIC fluxes from methanogenic zones contribute additional DIC to the shallow sediments. Here, we provide a quantification of 8.7 Tmol year^–1 DIC entering the methane-charged shallow sediments due to AOM, OSR, and the deep-DIC flux (range 6.4–10.2 Tmol year^–1). Of this total DIC pool, an estimated 6.5 Tmol year^–1 flows toward the water column (range: 3.2–9.2 Tmol year^–1), and 1.7 Tmol year^–1 enters the authigenic carbonate phases (range: 0.6–3.6 Tmol year^–1). This summary highlights that carbonate authigenesis in settings dominated by diffusive methane fluxes is a significant component of marine carbon burial, comparable to ∼15% of carbonate accumulation on continental shelves and in the abyssal ocean, respectively. Further, the DIC outflux through the SMTZ is comparable to ∼20% of global riverine DIC flux to oceans. This DIC outflux will contribute alkalinity or CO₂ in different proportions to the water column, depending on the rates of authigenic carbonate precipitation and sulfide oxidation and will significantly impact ocean chemistry and potentially atmospheric CO₂. Settings with substantial carbonate precipitation and sulfide oxidation at present are contributing CO₂ and thus to ocean acidification. Our synthesis emphasizes the importance of SMTZ as not only a methane sink but also an important diagenetic front for global DIC cycling. We further underscore the need to incorporate a DIC pump in methane-charged shallow marine sediments to models for coastal and geologic carbon cycling.
 

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