Evolution of marine roseobacters at different timescales

Ph.D.Roseobacters are known ecological generalists equipped with tremendous metabolic capabilities and various ecological roles. However, the timing and evolutionary underpinnings of Roseobacter ecological diversification are still under active discussion. In this thesis, molecular evolutionary approaches were addressed to gain insights into these questions from different timescales of resolution.First, we developed a fossil-independent approach to understand the evolutionary timescale of marine roseobacters. This approach is based on the spontaneous mutation rate determined for a model Roseobacter strain using a mutation accumulation experiment, among the first for a marine bacterium, and growth rates typical for the taxon in the ocean. This analysis first gives estimates of evolutionary time for closely related taxa, and subsequently extrapolates the timing estimates for more divergent lineages by leveraging the molecular clock approach. Using the calculated mutation rate of 1.39×10-10 per base per generation, we implement a “mutation-rate clock” approach to date the evolution of roseobacters by assuming a constant mutation rate along their evolutionary history. This approach gives an estimated date of Roseobacter genome expansion in good agreement with an earlier fossil-based estimate of approximately 250 million years ago and is consistent with a hypothesis of a correlated evolutionary history between roseobacters and marine eukaryotic phytoplankton groups.In the second part, we reported a nearly complete genome co-assembly of the Roseobacter DC5-80-3 Antarctic phylotype, and compare it to the available genomes of the other phylotype from ocean regions where iron is more accessible but phosphorus and nitrogen are less. The Antarctic phylotype exclusively contains an operon structure consisting of a dicitrate transporter fecBCDE and an upstream regulator binding site likely for iron uptake, whereas the other phylotype consistently carry a high-affinity phosphate pst transporter and the phoB-phoR regulatory system, a high-affinity ammonium amtB transporter, urea and taurine utilization systems. Moreover, the Antarctic phylotype uses proteorhodopsin to acquire light, whereas the other uses bacteriochlorophyll-a and the sulfur-oxidizing sox cluster for energy acquisition. This is potentially an iron-saving strategy for the Antarctic phylotype because only the latter two pathways have iron-requiring cytochromes. Therefore, the two DC5-80-3 phylotypes, while diverging by only 1.1% in their 16S rRNA genes, have evolved systematic differences in metabolism to support their distinct ecologies.On the third part, we developed a simple but powerful population genomic approach that allows for the identification of a subset of genes subject to homologous recombination with evolutionarily distant relatives, and would show that acquisition of novel alleles of existing genes is an equally important mechanism as the acquisition of new functions through lateral gene transfer. For all phylogenetically diverse marine bacterial lineages examined, the identified genes encode metabolic functions that match well with the key ecological features of these bacteria.玫瑰桿菌是一類生理代謝功能極其多樣並具備重要生態功能的微生物類群。它們在海洋中分佈廣泛且丰度較高，在海洋碳、硫循環和全球氣候調節中發揮著不可忽視的作用。然而，如何從進化的角度來解釋其生理及生態多樣性（包括何時及遵循何種機制進化而來）仍在學界的積極討論之中。本研究將運用分子進化方法，嘗試從不同時間尺度來探究玫瑰桿菌的進化機制及其相應的生態意義。首先，我們開發了一種獨立於化石的方法來估計海洋玫瑰桿菌的進化時間表。該方法通過突變積累實驗以獲得模式菌株的自發突變率。這在目前是僅有的兩種海洋菌株自發突變數據之一。菌株的生長速率則取之於該類群在自然海洋環境中的生長速率。該分析從近緣菌株出發，通過分子鐘的方法將由近緣菌株推導獲得的進化速率推廣至整個進化樹，從而推測出更大時間尺度（以百萬年計）上的菌株分化歷史信息。我們假定在玫瑰桿菌的進化過程當中，其自發突變率恆定，且可由我們實驗獲得的自發突變率1.39×10-10（以每位點每代為單位）作為近似估計。對於早期玫瑰桿菌基因組擴增發生的時間點，這種基於分子鐘理論的“突變率時鐘”方法給出的結論與前期基於化石的推斷一致。即，該事件發生於距今2.5億年前。從而進一步支持了玫瑰桿菌和浮游植物之間的協同進化的假設。在第二部分中，我們通過比較基因組學研究發現，玫瑰桿菌DC5-80-3類群所包括的兩種來自不同海域的種系型具備不同的生理代謝特徵。其中，南大洋種系型獨有一組與鐵元素攝取相關的操縱子結構（fecBCDE以及上游的調節子），而另一種系型則富含與氮磷攝取及代謝相關的基因。此外，在能量獲取途徑上二者亦有不同，南大洋種系型通過proteorhodopsin利用光能（無需含鐵的細胞色素參與），而另一種系型則利用細菌葉綠素-a和硫氧化sox來獲取能量（需要含鐵的細胞色素參與）。這與二者的生存環境相吻合。眾所周知，南大洋海域缺鐵但是富含氮磷營養物質，而分離出另一種系型的海域則缺氮磷但鐵則相對較易獲得。兩種種系型的基因組均體現出最大程度獲取稀缺資源的代謝潛力。由此，我們可以斷定，這兩種在16S 核糖體RNA相似度上僅差異1.1%的種系型，已經進化成為適應不同生態環境的生態型。第三部分，我們提出了一種簡單而有效的群體基因組學方法，用於鑒定由同源重組引入新的等位基因這一進化手段對於環境適應的意義。由該方法檢測出的基因均具備與被研究的海洋細菌種群的生態功能相匹配的基因功能。因此，與基因水平轉移類似，基於同源重組的等位基因交換提供了細菌微環境適應性的新機制。Sun, Ying.Thesis Ph.D. Chinese University of Hong Kong 2018.Includes bibliographical references (leaves 184-200).Abstracts also in Chinese.Title from PDF title page (viewed on 2 June, 2021)