Harrison Kaitlin, Rapp Josephine Z, Jaffe Alexander L, Deming Jody W, Young Jodi
School of Oceanography, University of Washington, Seattle, Washington, USA.
Astrobiology Program, University of Washington, Seattle, Washington, USA.
Appl Environ Microbiol. 2025 Jun 18;91(6):e0060425. doi: 10.1128/aem.00604-25. Epub 2025 May 30.
The act of fixing inorganic carbon into the biosphere is largely facilitated by one enzyme, Rubisco. Beyond well-studied plants and cyanobacteria, many bacteria use Rubisco for chemolithoautotrophy in extreme environments on Earth. Here, we characterized the diversity of autotrophic pathways and chemolithoautotrophic Rubiscos from two distinct subzero, hypersaline Arctic environments: 40-kyr relic marine brines encased within permafrost (cryopeg brines) and first-year sea ice. The Calvin-Benson-Bassham (CBB) cycle was widely found in both environments, although with different predominant Rubisco forms. From cryopeg brine, reconstructions of metagenome-assembled genomes (MAGs) uncovered four MAGs with the potential for chemolithoautotrophy, of which the CBB-containing genus was most abundant. A broader survey of genomes from diverse environments identified a core complement of three Rubisco forms (II, IAc, IAq) with a complex pattern of gain and loss, with form II constitutively present in genomes from subzero environments. Using representative kinetic data, we modeled carboxylation rates of Rubisco forms II, IAc, and IAq across CO, O, and temperature conditions. We found that form II outcompetes form I at low O, but cold temperatures minimize this advantage. Inspection of form II from genomes from cold environments identified signals of potential thermal adaptation due to key amino acid substitutions, which resulted in a more exposed active site. We argue that subzero form II from warrants further study as it may have unique kinetics or thermal stability. This work can help address the limits of autotrophic functionality in extreme environments on Earth and other planetary bodies.Autotrophy, or the fixation of inorganic carbon to biomass, is a key factor in life's ability to thrive on Earth. Research on autotrophy has focused on plants and algae, but many bacteria are also autotrophic and can survive and thrive under more extreme conditions. These bacteria are a window to past autotrophy on Earth, as well as potential autotrophy in extreme environments elsewhere in the universe. Our study focused on dark, cold, saline environments, which are likely to be found on Enceladus and Europa, as well as in the Martian subsurface. We found evidence for potential cold adaptation in a key autotrophic enzyme, Rubisco, which could expand the known boundaries of autotrophy in rapidly disappearing icy environments on Earth. We also present a novel model framework that can be used to probe the limits of autotrophy not only on Earth but also on key astrobiological targets like Enceladus and Europa.
无机碳固定到生物圈的过程很大程度上由一种酶——核酮糖-1,5-二磷酸羧化酶/加氧酶（Rubisco）推动。除了经过充分研究的植物和蓝细菌外，许多细菌在地球的极端环境中利用Rubisco进行化能无机自养。在这里，我们描述了来自北极两个不同的零下高盐环境中自养途径和化能无机自养Rubisco的多样性：包裹在永久冻土中的4万年残留海洋卤水（低温盐水）和第一年的海冰。卡尔文-本森-巴斯姆（CBB）循环在这两个环境中都广泛存在，尽管主要的Rubisco形式不同。从低温盐水中，宏基因组组装基因组（MAGs）的重建发现了四个具有化能无机自养潜力的MAGs，其中含有CBB的属最为丰富。对来自不同环境的基因组进行更广泛的调查，确定了三种Rubisco形式（II、IAc、IAq）的核心互补体，其获得和丧失模式复杂，II型在零下环境的基因组中持续存在。利用代表性的动力学数据我们模拟了Rubisco II、IAc和IAq形式在不同二氧化碳、氧气和温度条件下的羧化速率。我们发现，在低氧条件下，II型比I型更具竞争力，但低温会使这种优势最小化。对来自寒冷环境的基因组中的II型进行检查，发现了由于关键氨基酸取代而产生的潜在热适应信号，这导致活性位点更加暴露。我们认为，来自低温盐水的零下II型值得进一步研究，因为它可能具有独特的动力学或热稳定性。这项工作有助于解决地球和其他行星体极端环境中自养功能的限制问题。自养，即将无机碳固定为生物量，是生命在地球上繁荣发展能力的一个关键因素。对自养的研究主要集中在植物和藻类上，但许多细菌也是自养型的，并且能够在更极端的条件下生存和繁衍。这些细菌是了解地球过去自养情况以及宇宙其他地方极端环境中潜在自养情况的一个窗口。我们的研究聚焦于黑暗、寒冷且含盐的环境，这些环境可能存在于土卫二和木卫二上，以及火星地下。我们在一种关键的自养酶Rubisco中发现了潜在冷适应的证据，这可能会扩大地球上迅速消失的冰冻环境中已知的自养边界。我们还提出了一个新的模型框架，该框架不仅可用于探究地球上自养的极限，还可用于探测土卫二和木卫二等关键天体生物学目标上自养的极限。
