Garber Arkadiy I, Cohen Ashley B, Nealson Kenneth H, Ramírez Gustavo A, Barco Roman A, Enzingmüller-Bleyl Tristan C, Gehringer Michelle M, Merino Nancy
School of Life Sciences, Arizona State University, Tempe, AZ, United States.
School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, United States.
Front Microbiol. 2021 Sep 3;12:667944. doi: 10.3389/fmicb.2021.667944. eCollection 2021.
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.
微生物铁循环影响环境中主要营养物质的通量（例如，通过氧化铁的吸附能力），并包括生物诱导的铁氧化和还原过程。即使测序工作有所增加，微生物铁循环的生态范围仍未得到很好的理解，部分原因是基因注释流程存在局限性，以及将表型与基因型联系起来的实验研究存在局限性。对于海洋海底以下区域而言尤其如此，该区域的采样仍然不足，但却是地球上最大的连续栖息地。为了解决这一局限性，我们使用了FeGenie，这是一个数据库和生物信息学工具，可识别微生物铁循环基因，并能够就铁的生物地球化学循环提出可检验的假设。在此，我们调查了不同海底以下栖息地中的微生物铁循环，包括沉积物掩埋的地壳含水层以及表层和深层沉积物。我们推断了分析中包含的46个宏基因组中32个的铁氧化还原循环的遗传潜力，证明了这些活动在未充分探索的海底以下生态系统中的普遍性。我们表明，虽然某些过程（例如，铁的吸收和储存、铁载体转运潜力以及铁基因调控）几乎是普遍存在的，但其他过程（例如，铁还原/氧化、铁载体合成和磁小体形成）则取决于局部氧化还原和营养状况。此外，我们检测到异化铁还原所采用策略的生态位特异性差异，这表明地球化学限制可能在决定铁循环的主导机制方面发挥重要作用。总体而言，我们的调查推进了对微生物介导的铁循环及其在底栖以下生态系统中的利用的已知分布、规模和潜在生态影响的认识。
