Integrative analyses on the ciliates Colpoda illuminate the life history evolution of soil microorganisms

作者：Haichao Li, Kun Wu, Yuan Feng, Chao Gao, Yaohai Wang, Yuanyuan Zhang, Jiao Pan, Xiaopeng Shen, Rebecca A. Zufall, Yu Zhang, Weipeng Zhang, Jin Sun, Zhiqiang Ye, Weiyi Li, Michael Lynch, Hongan Long · 发表于：mSystems · 年份：2024 · DOI：10.1128/msystems.01379-23 · 被引用次数：14 · 研究领域：Protist diversity and phylogeny、Microbial Community Ecology and Physiology、Methane Hydrates and Related Phenomena

ABSTRACT Microorganisms play a central role in sustaining soil ecosystems and agriculture, and these functions are usually associated with their complex life history. Yet, the regulation and evolution of life history have remained enigmatic and poorly understood, especially in protozoa, the third most abundant group of organisms in the soil. Here, we explore the life history of a cosmopolitan species— Colpoda steinii . Our analysis has yielded a high-quality macronuclear genome for C. steinii , with size of 155 Mbp and 37,123 protein-coding genes, as well as mean intron length of ~93 bp, longer than most other studied ciliates. Notably, we identify two possible whole-genome duplication events in C. steinii , which may account for its genome being about twice the size of C. inflata’s , another co-existing species. We further resolve the gene expression profiles in diverse life stages of C. steinii , which are also corroborated in C. inflata . During the resting cyst stage, genes associated with cell death and vacuole formation are upregulated, and translation-related genes are downregulated. While the translation-related genes are upregulated during the excystment of resting cysts. Reproductive cysts exhibit a significant reduction in cell adhesion. We also demonstrate that most genes expressed in specific life stages are under strong purifying selection. This study offers a deeper understanding of the life history evolution that underpins the extraordinary success and ecologi...