Rodríguez-Ramos Josué, Sadler Natalie, Zegeye Elias K, Farris Yuliya, Purvine Samuel, Couvillion Sneha, Nelson William C, Hofmockel Kirsten S
Pacific Northwest National Laboratory, Earth and Biological Sciences Directorate, Richland, Washington, USA.
mSystems. 2025 Mar 18;10(3):e0161624. doi: 10.1128/msystems.01616-24. Epub 2025 Feb 24.
Soil moisture and porosity regulate microbial metabolism by influencing factors, such as system chemistry, substrate availability, and soil connectivity. However, accurately representing the soil environment and establishing a tractable microbial community that limits confounding variables is difficult. Here, we use a reduced-complexity microbial consortium grown in a glass bead porous media amended with chitin to test the effects of moisture and a structural matrix on microbial phenotypes. Leveraging metagenomes, metatranscriptomes, metaproteomes, and metabolomes, we saw that our porous media system significantly altered microbial phenotypes compared with the liquid incubations, denoting the importance of incorporating pores and surfaces for understanding microbial phenotypes in soils. These phenotypic shifts were mainly driven by differences in expression of and , which included a significant decrease in overall chitin degradation between porous media and liquid. Our findings suggest that the success of in porous media is likely related to its ability to repurpose carbon via the glyoxylate shunt amidst a lack of chitin degradation byproducts while potentially using polyhydroxyalkanoate granules as a C source. We also identified traits expressed by and others, including motility, stress resistance, and carbon conservation, that likely influence the metabolic profiles observed across treatments. Together, these results demonstrate that porous media incubations promote structure-induced microbial phenotypes and are likely a better proxy for soil conditions than liquid culture systems. Furthermore, they emphasize that microbial phenotypes encompass not only the multi-enzyme pathways involved in metabolism but also include the complex interactions with the environment and other community members.IMPORTANCESoil moisture and porosity are critical in shaping microbial metabolism. However, accurately representing the soil environment in tractable laboratory experiments remains a challenging frontier. Through our reduced complexity microbial consortium experiment in porous media, we reveal that predicting microbial metabolism from gene-based pathways alone often falls short of capturing the intricate phenotypes driven by cellular interactions. Our findings highlight that porosity and moisture significantly affect chitin decomposition, with environmental matrix (i.e., glass beads) shifting community metabolism towards stress tolerance, reduced resource acquisition, and increased carbon conservation, ultimately invoking unique microbial strategies not evident in liquid cultures. Moreover, we find evidence that changes in moisture relate to community shifts regarding motility, transporters, and biofilm formation, which likely influence chitin degradation. Ultimately, our incubations showcase how reduced complexity communities can be informative of microbial metabolism and present a useful alternative to liquid cultures for studying soil microbial phenotypes.
土壤湿度和孔隙度通过影响系统化学、底物可用性和土壤连通性等因素来调节微生物代谢。然而,准确表征土壤环境并建立一个能够限制混杂变量的易于处理的微生物群落是困难的。在这里,我们使用在添加了几丁质的玻璃珠多孔介质中生长的低复杂性微生物群落,来测试湿度和结构基质对微生物表型的影响。利用宏基因组、宏转录组、宏蛋白质组和代谢组,我们发现与液体培养相比,我们的多孔介质系统显著改变了微生物表型,这表明纳入孔隙和表面对于理解土壤中的微生物表型很重要。这些表型变化主要由[具体基因1]和[具体基因2]的表达差异驱动,其中包括多孔介质和液体之间几丁质总体降解的显著下降。我们的研究结果表明,[微生物名称]在多孔介质中的成功可能与其在缺乏几丁质降解副产物的情况下通过乙醛酸循环重新利用碳的能力有关,同时可能使用聚羟基脂肪酸酯颗粒作为碳源。我们还确定了[微生物名称]和其他微生物表达的特征,包括运动性、抗逆性和碳守恒,这些特征可能影响不同处理中观察到的代谢谱。总之,这些结果表明,多孔介质培养促进了结构诱导的微生物表型,并且可能比液体培养系统更能代表土壤条件。此外,它们强调微生物表型不仅包括参与代谢的多酶途径,还包括与环境和其他群落成员的复杂相互作用。
重要性
土壤湿度和孔隙度对塑造微生物代谢至关重要。然而,在易于处理的实验室实验中准确表征土壤环境仍然是一个具有挑战性的前沿领域。通过我们在多孔介质中进行的低复杂性微生物群落实验,我们揭示仅从基于基因的途径预测微生物代谢往往不足以捕捉由细胞相互作用驱动的复杂表型。我们的研究结果突出表明,孔隙度和湿度显著影响几丁质分解,环境基质(即玻璃珠)使群落代谢朝着耐胁迫、减少资源获取和增加碳守恒的方向转变,最终引发了液体培养中不明显的独特微生物策略。此外,我们发现有证据表明湿度变化与群落关于运动性、转运蛋白和生物膜形成的转变有关,这可能影响几丁质降解。最终,我们的培养展示了低复杂性群落如何能够为微生物代谢提供信息,并为研究土壤微生物表型提供了一种有用的替代液体培养的方法。