Connecting environmental and evolutionary microbiology for the development of new agrobiotechnological tools.
Connecting environmental and evolutionary microbiology for the development of new agrobiotechnological tools.
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DOI：
10.1111/1462-2920.16197
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发表时间：
2023-01
影响因子：
5.1
通讯作者：
Espinosa-Urgel, Manuel
中科院分区：
文献类型：
--
作者：
Espinosa-Urgel, Manuel
我们都熟悉Theodosius Dobzhansky的名言：“生物学中没有什么是有意义的，除非从进化的角度来看”，这实际上是他在《美国生物教师》（Dobzhansky, 1973）上发表的一篇短文的标题。用这个书名，他揭示了一个连我们生物学家有时也会回避的基本事实：生命意味着进化。基因变化为任何形式的进化提供了所需的多样性，而环境将“决定”这些变化是否成功。多布赞斯基认为进化是一个过程，生命倾向于填补所有可用的生态位。微生物似乎决心要证明他是对的；事实上，在我们的星球上，真正空缺的生态位似乎很少见，因为即使在条件对其他形式的生命来说过于极端的环境中，也不断发现细菌定植的证据（Merino等人，2019）。如果生命是进化，微生物生命可以被认为是快车道上的进化。在有利的生长条件下，细菌种群在很短的时间内复制，这一事实已被利用来研究实验室条件下的进化。除了早期关于细菌突变和选择的开创性工作（Atwood et al., 1951; Lederberg & Lederberg, 1952），也许最著名的例子之一是Richard Lenski于1988年开始的长期进化实验（LTEE）：将大肠杆菌在规定的培养基中培养过夜，然后每天将（每个群体的1%）转移到新鲜培养基中，并定期保存每种培养物的冷冻保存样本（Lenski et al., 1991）。它们允许进行详细的表型和基因分析，并充当中间“营地”，如果出现问题，可以从那里重新开始实验，而不必从头开始（就像电子游戏的“保存”按钮）。LTEE由Lenski集团维护了34年，最近转移到德克萨斯大学（奥斯汀）的Jeffrey Barrick实验室，已经达到了75,000代以上，并且已经成为有关适应特定生长条件的动态和可重复性的相关见解的来源（Lenski, 2017）。在实验室条件下研究细菌进化的其他方法包括，大肠杆菌对饥饿和静止期的长期适应（Finkel & Kolter, 1999），这导致选择接管亲代种群的特定突变体（Zinser & Kolter, 2004）；或在空气-液体界面上培养荧光假单胞菌，其中营养和氧气梯度导致表型和遗传分化，这是适应性辐射的结果（Rainey & Travisano, 1998）。适应性辐射也发生在恶臭假单胞菌的长期生物膜种群中（Yousef-Coronado和Espinosa-Urgel，未发表）。Van den Bergh及其同事对进一步的例子和实验设置进行了很好的回顾（Van den Bergh et al., 2018）。尽管有一些明显的限制，例如使用单一物种培养和相当特定和控制良好的环境条件（另一方面，这些限制是确保可重复性和得出适当结论所必需的），所有这些
We all are familiar with Theodosius Dobzhansky’s famous sentence:‘Nothing in biology makes sense except in the light of evolution’, which is actually the title of a short essay he published in The American Biology Teacher (Dobzhansky, 1973). With that title, he was exposing a fundamental truth that even us biologists sometimes tend to obviate: Life means evolution. Genetic changes provide the diversity required for any form of evolution to take place, while the environment will ‘decide’if those changes are successful or not. Dobzhansky viewed evolution as a process by which life tends to fill all available ecological niches. Microorganisms seem determined to prove him right; in fact, truly vacant ecological niches appear to be rare on our planet, as evidences of bacterial colonization keep being found even in environments where conditions are too extreme for other forms of life (Merino et al., 2019). If life is evolution, microbial life can be considered evolution on the fast lane. Under favourable growth conditions, a bacterial population duplicates in a very short time, a fact that has been exploited to study evolution under laboratory conditions. Besides the early, pioneering work on mutations and selection in bacteria (Atwood et al., 1951; Lederberg & Lederberg, 1952), perhaps one of the best-known examples is that of the long-term evolution experiment (LTEE) started in 1988 by Richard Lenski: parallel batch cultures of Escherichia coli grown overnight in defined medium and then transferred (1% of each population) to fresh medium every day, with periodical storage of cryopreserved samples of each culture (Lenski et al., 1991). These allow detailed phenotypic and genetic analysis and serve as intermediate ‘camps’ from where the experiment can be resumed if something goes wrong, without having to start all over (pretty much as the ‘save’button of a videogame). The LTEE, maintained for 34 years by the Lenski group and recently transferred to Jeffrey Barrick’s lab at the University of Texas (Austin), has reached over 75,000 generations, and has been a source of relevant insights regarding the dynamics and repeatability of adaptation to particular growth conditions (Lenski, 2017). Additional approaches to study bacterial evolution in laboratory conditions include, among others, long-term adaptation of Escherichia coli to starvation and stationary phase (Finkel & Kolter, 1999), which results in the selection of specific mutants that take over the parental population (Zinser & Kolter, 2004); or static cultures of Pseudomonas fluorescens on the air-liquid interface, where nutrient and oxygen gradients lead to phenotypic and genetic differentiation as the result of adaptive radiation (Rainey & Travisano, 1998). Adaptive radiation also takes place in long-term biofilm populations of Pseudomonas putida (Yousef-Coronado and Espinosa-Urgel, unpublished). Further examples and experimental setups have been nicely reviewed by Van den Bergh and coworkers (Van den Bergh et al., 2018). Despite some obvious limitations, such as the use of single-species cultures and the rather specific and well-controlled environmental conditions (limitations which on the other hand are necessary to ensure reproducibility and to extract proper conclusions), all these
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影响因子：
5.6
作者：
Mavrodi DV;Mavrodi OV;Elbourne LDH;Tetu S;Bonsall RF;Parejko J;Yang M;Paulsen IT;Weller DM;Thomashow LS
通讯作者：
Thomashow LS
影响因子：
64.5
作者：
Salazar, Guillem;Paoli, Lucas;Wincker, Patrick
通讯作者：
Wincker, Patrick
影响因子：
2.9
作者：
LENSKI, RE;ROSE, MR;TADLER, SC
通讯作者：
TADLER, SC
DOI：
10.1073/pnas.37.3.146
发表时间：
1951-01-01
影响因子：
11.1
作者：
ATWOOD, KC;SCHNEIDER, LK;RYAN, FJ
通讯作者：
RYAN, FJ
DOI：
10.1073/pnas.0307195101
发表时间：
2004-05-25
影响因子：
11.1
作者：
MacLean, RC;Bell, G;Rainey, PB
通讯作者：
Rainey, PB