莱斯大学开发出能够看穿土壤的气体传感器
导读：莱斯大学的研究人员已经开发出一种能够“看穿”土壤的气体生物传感器，能够让科研人员追踪土壤中微生物群落的行为。
莱斯大学的研究人员已经开发出一种能够“看穿”土壤的气体生物传感器，能够让科研人员追踪土壤中微生物群落的行为。
发表在美国化学学会期刊《环境科学和技术》的论文中，莱斯研究团队使用释放出卤代甲烷气体的基因工程细菌，在实验室监测土壤样本中微生物的基因表达。
利用合成生物技术对该细菌进行基因编辑使其释放出气体，当细菌通过基因水平转移进行DNA交换时（基因水平转移在生物进化过程中有着独特的作用，生物通过这个过程无需亲子关系就能够分享遗传性状），这种气体能够发出报告。这种生物传感器能够让研究人员实时监控这个过程，无需时时刻刻盯住土壤样本。
莱斯大学的研究人员希望他们的技术对于有着同样研究目的的环境科学家有所帮助，他们利用荧光报告蛋白追踪生物系统中的蛋白质表达和其它过程。
这项工作是由莱斯大学实验室的生物地球化学家卡洛琳马谢洛，生物化学家乔纳森西尔伯格，微生物学家乔治班尼特和莱斯大学研究生论文主要作者Hsiao-Ying (谢利) Cheng共同承担的，是W.M.凯克基金会100万美元资助项目中首个产品，一种气体微生物传感器。
“本文介绍了一种新的工具，用于研究微生物如何在环境中进行遗传物质的交换，”地球学教授马谢洛说。
“我们关注这个问题是因为，水平基因转移过程控制了对人类来说很多重要的事情，或者是好的方面，根瘤菌如何交换它们所需的基因来固氮和支持植物生长，或者是坏的方面，细菌如何在土壤中交换耐抗生素，”她说。“在过去，在真实的土壤中建立这种动态过程模型，以及研究水平基因交换在不同土壤类型中如何变化，是非常具有挑战性的工作。我们创造了一套新的工具实现了我们的研究目标。”
研究人员预计，科学家将在实验室中使用气体生物传感器来研究农业中的氮固定，污水处理中的抗生素交换，营养素缺乏的条件下的基因转移以及土壤中基因表达与温室气体释放之间的关系。
“还有其他的技术会以这项技术为参考，”生物化学和细胞生物学副教授西尔伯格说。使用气体的想法让我们对基因编码有了深层次的了解。但是，我们在一些技术细节上还需进一步的提升。”
他说释放和传感卤代甲烷气体代表了一个简单的概念证明。“现在，我们想利用合成生物技术，通过创造更加复杂的遗传程序，获取其他类型生物学现象的细节信息，”西尔伯格说。
他们预计将会很快进行农业土壤样本的测试，通过有效的灌溉和施肥，帮助作物的生长进行微调。“农业如何在没有浪费的情况下，达到效率的提升？很多人都提到了这一点，解决的办法有很多，”他说。“我们正在开发高科技工具，让我们通过了解生物学现象的机制来做出可靠的预测。对这些工具的改进和提升是一件耗时的工作。”
研究人员强调，这些工具都是用于实验室环境中的土壤研究。一旦获得研究结果，这些合成的微生物就被破坏了。
当它们与另一种微生物进行DNA转移时，将被编辑的大肠杆菌添加入释放气体之后，莱斯实验室在位于密歇根的国家科学基金会的凯洛格生物站长期生态研究基地测试土壤样本。从气体中发出的信号是实验室的检测极限10000倍。
与绿色荧光蛋白不同，气体传感器在缺氧和贫氧条件下也是有效的，绿色荧光蛋白必须在有氧条件下工作。可以预料的是，报告蛋白可用于多种土壤微生物，其中的一部分目前正在进行测试，班尼特说。
“英文原文”
Gas sensors 'see' through soil to analyze microbial interactions
RiceUniversityresearchers have developed gas biosensors to "see" into soil and allow them to follow the behavior of the microbial communities within.
In a study in the American Chemical Society's journal Environmental Science and Technology, the Rice team described using genetically engineered bacteria that release methyl halide gases to monitor microbial gene expression in soilsamples in the lab.
The bacteria are programmed using synthetic biology to release gas to report when they exchange DNA through horizontal gene transfer, the process by which organisms share genetic traits without a parent-to-child relationship. The biosensors allow researchers to monitor such processes in real time without having to actually see into or disturb a lab soil sample.
The Rice researchers expect their technique will serve the same purpose for environmental scientists that fluorescent reporter proteins serve for biochemists who track protein expression and other processes in biological systems.
The work by the Rice labs of biogeochemist Caroline Masiello, biochemist Jonathan Silberg, microbiologist George Bennett and lead author Hsiao-Ying (Shelly) Cheng, a Rice graduate student, is the first product of a $1 million grant by the W.M. Keck Foundation to develop gas-releasing microbial sensors.
"This paper describes a new tool to study how microbes trade genetic material in the environment," said Masiello, a professor of Earth science.
"We care about this because the process of horizontal gene transfer controls a lot of things that are important to humans either because they're good—it's how rhizobia trade the genes they need to fix nitrogen and support plant growth—or they're bad—it's how bacteria trade antibiotic resistance in soils," she said. "It's been much more challenging in the past to construct models of this dynamic process in real soils and to study how horizontal gene exchange varies across soil types. We've created a new set of tools that makes that possible."
The researchers expect scientists will use gas biosensors in the lab to study nitrogen fixing in agriculture, antibiotic exchange in wastewater treatment, gene transfer in conditions where nutrients are scarce and the relationship between gene expression in soil and the release of greenhouse gases.
"There are other technologies that will build on this," said Silberg, an associate professor of biochemistry and cell biology. "The idea of using gases opens up most anything that's genetically encoded. However, we do need to improve technologies for some of the subtler kinds of questions."
He said releasing and sensing methyl halide gas represented an easy proof of concept. "Now we want higher-resolution information about other types of biological events by creating more sophisticated genetic programs using synthetic biology," Silberg said.
They expect they will soon be able to test agricultural soil samples to help fine-tune crop growth through more efficient watering and fertilizer use. "How can agriculture get this extra level of efficiency without the waste? Lots of people are coming to that, and there are lots of ways to do it," he said. "We're trying to build high-tech tools that allow us to understand mechanisms to make reliable predictions. That's the long game with these tools."
The researchers emphasized that these are tools for soil studies within lab environments. The synthetic microbes are destroyed once the results are obtained.
The Rice lab tested soil samplesfrom the National Science Foundation's Kellogg Biological Station Long-Term Ecological Research Site in Michigan after adding Escherichia coli bacteria programmed to release gas upon transfer of their DNA to another microbe. Signals from the gas were up to 10,000 times the lab's detection limit.
The gas sensors were effective in anoxic—or oxygen-depleted—conditions, unlike green fluorescent protein, which requires oxygen to work. It is anticipated the reporter proteins can be used in many kinds of soil microbes, and some are currently being tested, Bennett said.
