Diversity, distribution, and expression of opsin genes in freshwater lakes
Diversity, distribution, and expression of opsin genes in freshwater lakes
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DOI：
10.1111/mec.16891
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发表时间：
2023-03-07
影响因子：
4.9
通讯作者：
McMahon, Katherine D.
中科院分区：
文献类型：
--
作者：
He, Shaomei;Linz, Alexandra M.;McMahon, Katherine D.
微生物视紫红质广泛分布在水生环境中，可能对全球海洋的光养和能量预算做出重大贡献。然而，淡水视紫红质的研究在很大程度上受到限制。在这里，我们探索了腐殖质湖和清水湖中编码 I 型视紫红质脱辅基蛋白的视蛋白基因的多样性、生态分布和表达，并具有对比的物理化学和光学特征。使用宏基因组和宏基因组组装的基因组，我们从多种类群中恢复了视蛋白基因，其中大部分预测编码绿色光吸收质子泵。回收了病毒视蛋白和新的细菌视蛋白进化枝。视蛋白基因在来自清水的类群中比来自腐殖水的类群中更频繁地出现，并且某些类群中的视蛋白具有非典型的离子泵基序，可能与这两种淡水类型的物理化学条件有关。对 33 个淡水系统表层的分析揭示了视蛋白基因丰度与湖泊溶解有机碳 (DOC) 之间呈负相关。在具有高陆地 DOC 和吸光腐殖质的腐殖水中，视蛋白基因丰度较低，并在最初几米内急剧下降，而在低 DOC 的清水湖中，沿主体水柱的丰度仍然相对较高，表明视蛋白基因分布受到湖泊光学特性和 DOC 的影响。基因表达分析证实了清水湖中基于视紫红质的光养作用的重要性，并揭示了主要门类之间不同的昼夜表达模式。总体而言，我们的分析揭示了淡水视蛋白的多样性、分布和表达模式，并表明基于视紫红质的光养作用在淡水能量预算中的重要性，特别是在清水湖泊中。
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.