Microbial Genome Sequencing: Genome Sequencing of a Nitrogen-Fixing Bacterial Endophyte

20世纪50年代至70年代的绿色革命预示着作物产量的大幅增加，主要是通过使用氮肥。 然而，氮肥在经济上和环境上都是昂贵的。 氮肥是农业中最高的农场成本之一。 大量的化石燃料用于生产这些肥料，成本不断增加。 此外，施用于土壤的大部分固定氮从未被植物吸收并渗入地下水，污染了美国许多农村地区的大部分饮用水。为了消除对氮肥的需求，需要发现可以为农业中的重要草（如小麦和玉米）提供固定氮的细菌。 近年来，一些固氮细菌已经从生长所需的氮很少的禾本科植物中分离出来。 固氮细菌已经被研究了100多年，它们从大气中捕获N2，并将其转化为植物可以利用的氮的形式。在Triplett实验室分离的一种细菌已经被广泛研究，并且能够侵入许多植物的内部而不会引起疾病症状。这种菌株之所以能大量进入植物体内，可能是因为它要么避开了植物防御机制，要么未能诱导植物防御机制，而植物防御机制可以阻止其他细菌进入植物。 事实上，这种菌株，肺炎克雷伯氏菌342（Kp342），实际上促进植物生长。 在小麦（但不是其他禾本科植物）中，Kp342实际上为植物提供固定氮，并且在没有任何氮肥的情况下培养时可以缓解缺氮症状。 为了进一步提高Kp342菌株为小麦、玉米、水稻和其他禾本科植物提供氮的能力，需要对Kp342的代谢和调节回路有更多的基础知识。 了解更多关于这种菌株的最彻底和有效的方法是通过确定这种生物体的整个基因组序列。 一旦序列已知，它将被仔细检查，以发现这种生物体中的每一个基因。 基因组研究所和佛罗里达大学将对Kp342进行完整的基因组测序。 随着Kp342中每个基因的发现，将在培训和推广方面做出重大努力。 将在佛罗里达大学为本科生和研究生建立一个夏季讲习班，学生将学习比较固氮细菌、细菌内生菌和克雷伯氏菌菌株的基因组。 将开展一项重要的推广工作，以制定一个全国性的基因组科学课程，供对科学和技术感兴趣的美国青年使用。

The green revolution of the 1950s-1970s heralded large increases in crop yields largely through the use of nitrogen fertilizers. However, nitrogen fertilization is expensive economically and environmentally. Nitrogen fertilization is one of the highest on-farm costs in agriculture. A significant amount of fossil fuel is used to produce these fertilizers at an ever-increasing cost. In addition, much of the fixed nitrogen applied to soils is never taken up by the plants and leaches into ground water, contaminating much of the drinking water in many rural areas of the United States. To eliminate the need for nitrogen fertilization, bacteria need to be discovered that can provide fixed nitrogen to important grasses in agriculture such as wheat and corn. In recent years, several nitrogen-fixing bacteria have been isolated from lines of grasses that require very little nitrogen for growth. Nitrogen-fixing bacteria have been studied for over 100 years and they capture N2 from the atmosphere and convert it to a form of nitrogen that can be used by plants.One of the bacteria isolated in the Triplett laboratory has been studied extensively and is capable of invading the interior of many plants without causing disease symptoms. This strain probably enters plants in such high numbers because it either eludes, or fails to induce, plant defense mechanisms that would prevent other bacteria from entering the plant. In fact, this strain, Klebsiella pneumoniae 342 (Kp342), actually enhances plant growth. In wheat (but not other grasses), Kp342 actually provides fixed nitrogen to plants and can relieve N-deficiency symptoms when cultured in the absence of any nitrogen fertilizer. More basic knowledge of Kp342's metabolism and regulatory circuits is needed in order to further improve this strain's ability to provide nitrogen to wheat, corn, rice, and other grasses. The most thorough and effective way to learn more about this strain is through determining the entire genome sequence of this organism. Once the sequence is known, it will be examined carefully to discover every gene in this organism. The Institute for Genomic Research and the University of Florida will perform complete genome sequencing of Kp342. With the discovery of every gene in Kp342 will come a significant effort in training and outreach. A summer workshop will be established for undergraduate and graduate students at the University of Florida where students will learn to compare the genomes of nitrogen fixing bacteria, bacterial endophytes, and Klebsiella strains. A significant outreach effort will be done to develop a national curriculum in genome science that will be available to the youth in America who are interested in science and technology.