Metagenomic Insights Into the Microbial Iron Cycle of Subseafloor Habitats

Abstract

Microbial iron cycling influences the flux of major nutrients in the environment (e.g., through the adsorptive capacity of iron oxides) and includes biotically induced iron oxidation and reduction processes. The ecological extent of microbial iron cycling is not well understood, even with increased sequencing efforts, in part due to limitations in gene annotation pipelines and limitations in experimental studies linking phenotype to genotype. This is particularly true for the marine subseafloor, which remains undersampled, but represents the largest contiguous habitat on Earth. To address this limitation, we used FeGenie, a database and bioinformatics tool that identifies microbial iron cycling genes and enables the development of testable hypotheses on the biogeochemical cycling of iron. Herein, we survey the microbial iron cycle in diverse subseafloor habitats, including sediment-buried crustal aquifers, as well as surficial and deep sediments. We inferred the genetic potential for iron redox cycling in 32 of the 46 metagenomes included in our analysis, demonstrating the prevalence of these activities across underexplored subseafloor ecosystems. We show that while some processes (e.g., iron uptake and storage, siderophore transport potential, and iron gene regulation) are near-universal, others (e.g., iron reduction/oxidation, siderophore synthesis, and magnetosome formation) are dependent on local redox and nutrient status. Additionally, we detected niche-specific differences in strategies used for dissimilatory iron reduction, suggesting that geochemical constraints likely play an important role in dictating the dominant mechanisms for iron cycling. Overall, our survey advances the known distribution, magnitude, and potential ecological impact of microbe-mediated iron cycling and utilization in sub-benthic ecosystems.

Shewanella sp. T2.3D-1.1 a Novel Microorganism Sustaining the Iron Cycle in the Deep Subsurface of the Iberian Pyrite Belt

“…However, the recent discovery of microorganisms associated to hard rocks has increased the interest in the exploration of the continental subsurface and subseafloor. These studies range from the evaluation of its diversity [4,5], the study of microbial community dynamics [6] or the interaction with the environment [7,8]. An exciting feature is its isolation from light and therefore from the photosynthetic-based carbon cycle of the surface, hence this microbial communities are known as the dark biosphere [9][10][11].…”

Diversity of Iron Oxides: Mechanisms of Formation, Physical Properties and Applications

“…Fe 3 O 4 NPs can be considered as one of the most frequently used iron oxide magnetic materials and their production techniques are mostly chemical since this approach is most suitable for biomedical applications [81][82][83][84][85][86][87][88][89]. Additionally, "green" techniques, involving the use of natural plant extracts [90,91], biomimetic formation [92] or microbial mineralization [93][94][95][96][97][98], are widely used. Other commonly described forms of magnetite are its inclusion within ore samples [6,[99][100][101][102][103][104] widely used in geosciences and the external magnetite layer of metal surfaces [105][106][107][108][109], which is an important object of iron corrosion studies.…”

Microbial Catalysis for CO2Sequestration: A Geobiological Approach

“…Siderophore synthesis pathways have been identified in many organisms through both experiments and bioinformatics (Hider and Kong 2010;Garber et al 2020Garber et al , 2021. Several pathways have been expressed and further engineered in the model organism Escherichia coli, with the goal of producing siderophores as therapeutic antibiotics (Fujita and Sakai 2013;Fujita et al 2018).…”