Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA.
Department of Geoscience, University of Wisconsin-Madison, Madison, Wisconsin, USA.
Mol Ecol. 2023 Jun;32(11):2798-2817. doi: 10.1111/mec.16891. Epub 2023 Mar 7.
Microbial rhodopsins are widely distributed in aquatic environments and may significantly contribute to phototrophy and energy budgets in global oceans. However, the study of freshwater rhodopsins has been largely limited. Here, we explored the diversity, ecological distribution, and expression of opsin genes that encode the apoproteins of type I rhodopsins in humic and clearwater lakes with contrasting physicochemical and optical characteristics. Using metagenomes and metagenome-assembled genomes, we recovered opsin genes from a wide range of taxa, mostly predicted to encode green light-absorbing proton pumps. Viral opsin and novel bacterial opsin clades were recovered. Opsin genes occurred more frequently in taxa from clearwater than from humic water, and opsins in some taxa have nontypical ion-pumping motifs that might be associated with physicochemical conditions of these two freshwater types. Analyses of the surface layer of 33 freshwater systems revealed an inverse correlation between opsin gene abundance and lake dissolved organic carbon (DOC). In humic water with high terrestrial DOC and light-absorbing humic substances, opsin gene abundance was low and dramatically declined within the first few meters, whereas the abundance remained relatively high along the bulk water column in clearwater lakes with low DOC, suggesting opsin gene distribution is influenced by lake optical properties and DOC. Gene expression analysis confirmed the significance of rhodopsin-based phototrophy in clearwater lakes and revealed different diel expressional patterns among major phyla. Overall, our analyses revealed freshwater opsin diversity, distribution and expression patterns, and suggested the significance of rhodopsin-based phototrophy in freshwater energy budgets, especially in clearwater lakes.
微生物视紫红质广泛分布于水生环境中，可能对全球海洋的光合作用和能量预算有重要贡献。然而，对淡水视紫红质的研究在很大程度上受到限制。在这里，我们探索了具有不同理化和光学特性的腐殖质和清水湖泊中，编码 I 型视紫红质脱辅基蛋白的 opsin 基因的多样性、生态分布和表达。通过宏基因组学和宏基因组组装基因组学，我们从广泛的分类群中回收了 opsin 基因，这些基因大多预测编码绿光吸收质子泵。回收了病毒视紫红质和新的细菌视紫红质进化枝。opsin 基因在清水物种中比在腐殖质水中更频繁出现，并且一些物种中的 opsin 具有非典型的离子泵结构基序，这些结构基序可能与这两种淡水类型的理化条件有关。对 33 个淡水系统表层的分析表明，opsin 基因丰度与湖泊溶解有机碳（DOC）之间呈负相关。在富含陆地 DOC 和吸光腐殖质的腐殖质水中，opsin 基因丰度较低，在最初几米内急剧下降，而在 DOC 较低的清水湖中，整个水柱的丰度仍然相对较高，这表明 opsin 基因的分布受到湖泊光学性质和 DOC 的影响。基因表达分析证实了视紫红质光合作用在清水湖中的重要性，并揭示了主要门类之间不同的昼夜表达模式。总的来说，我们的分析揭示了淡水视紫红质的多样性、分布和表达模式，并表明了视紫红质光合作用在淡水能量预算中的重要性，尤其是在清水湖中。
