Do trace gas oxidising bacteria help build soil on volcanic rock?

背景了解土壤是如何形成的是恢复退化土壤的关键。世界上80%的土壤是火山成因的，这些土壤是最肥沃的。火山作用是陆地形成的主要过程，是研究土壤形成的模式系统。熔岩凝固后，微生物通过从光或化学物质的氧化中获取能量来殖民它。此前，Hernandez检查了智利Llaima火山上遵循时间序列路径的细菌(即不同年龄的土壤)的多样性，并发现一类特定的细菌(Ktedonbacterales)主导着新形成的土壤1。人们对克氏杆菌知之甚少，但它们含有编码酶的基因，使它们能够利用H2和CO气体生长2。埃尔南德斯和其他人对火山土的研究表明，在火山土序列2、3、4、5、6的头几十年里，CH4、H2和消耗CO的微生物占主导地位。大气中的这些微量气体为细菌提供能量和碳源，这些细菌定居在火山岩上，并将这些底物转化为生物量，从而将有机碳转化为有机碳，从而对火山岩上的土壤形成做出了重大贡献。假设最重要的假设是，一氧化碳氧化微生物及其消耗其他气体(例如H2)的能力，在产生启动土壤形成的有机物方面发挥了关键作用。目的1)确定微量气体和消耗它们的微生物在火山土发育中的作用。2)确定居住在火山土中的微量气体代谢微生物，特别是克氏杆菌的共同代谢途径。工作包WP-1。土壤培养和群落概况(0-1.5年级)学生将使用与培养无关的方法描述微生物群落，解决以下问题：i)早期火山沉积中的一氧化碳氧化能力最大吗？二)早期火山沉积中微生物群落的(其他)重要碳和能源来源是什么？这名学生将参加智利的采样活动，准备微型宇宙孵化，并学习跨学科技术，包括定量聚合酶链式反应、气相色谱测量、DNA猎枪测序和生物信息学。交付成果：1)沿连续梯度的CO氧化速率。2)连续鉴定细菌及其功能集团，在高质量的微生物生态学期刊上发表论文。细菌分离和鉴定(0.8-3.0年级)：学生将评估火山沉积物中微生物群落的潜力，解决以下问题：i)克氏杆菌是否能够氧化CO和H2？Ii)这些环境中还有哪些细菌能够氧化一氧化碳？三)其他主要碳和能源来源是如何处理的？这位博士生将学习依赖于培养的技术，包括细菌的浓缩和分离、基因组测序、气相色谱测量和生物信息学。交付成果：1)成功地从火山土壤中分离出细菌，并确定了菌株和基因表达网络的特征。2)这些菌株潜在的CO、H2和CH4氧化速率和动力学参数，导致在环境微生物学期刊上发表高质量的文章。

BackgroundUnderstanding how soil establishes is crucial to be able to restore degraded soil. 80% of the world's soils are of volcanic origin, and these are among the most fertile. Volcanism is a primary process of land formation serving as model system to study soil formation. After lava solidifies, microbes colonise it by obtaining energy from light or from oxidation of chemicals. Previously, Hernandez examined the diversity of bacteria following a chrono-sequence path (i.e. soils of different ages) on Llaima volcano, Chile and discovered that a specific class of bacteria (Ktedonobacterales), dominated newly-formed soil1. Very little is known about Ktedonobacterales, but they contain genes encoding for enzymes that enable them to grow using H2 and CO gases2. Hernandez's work on volcanic soils, and that of others, has shown a dominance of CH4, H2 and CO-consuming microbes in the first decades of volcanic soil succession2,3,4,5,6. These trace gases in the atmosphere provide energy and carbon sources for bacteria that colonise volcanic rocks and convert these substrates into biomass and hence organic carbon, which in turn make a substantial contribution to soil formation on volcanic rocks.HypothesisThe overarching hypothesis is that CO-oxidising microorganisms, and their ability to consume other gases (e.g. H2), play a key role in producing organic matter that initiates soil formation. Objectives1) To determine the role of trace gases and the microbes that consume them in the development of volcanic soils. 2) To determine the metabolic pathways common to trace-gas metabolising microbes, particularly Ktedonobacterales, inhabiting volcanic soils.Work PackagesWP-1. Soil incubations and community profiling (years 0-1.5)The student will characterise the microbial community using cultivation-independent methods addressing the questions: i) Is CO-oxidation capacity greatest in early volcanic deposits? ii) What are the (other) important carbon and energy sources for the microbial community in early volcanic deposits? The student will join sampling campaigns in Chile, prepare microcosms incubations and learn interdisciplinary techniques including qPCR, gas-chromatography measurements, DNA shotgun sequencing and bioinformatics. Deliverables: 1) CO oxidation rates along successional gradients. 2) Identify bacteria and their functional guilds along succession, leading to publications in high quality microbial ecology journals.WP-2. Bacterial isolation and characterisation (years 0.8-3.0): The student will assess the potential of microbial communities in volcanic deposits, addressing the questions: i) Are Ktedonobacterales able to oxidise CO and H2? ii) Which other bacteria from these environments are able to oxidise CO? iii) How are other primary sources of carbon and energy processed? The PhD student will learn cultivation-dependent techniques including enrichment and isolation of bacteria, genome sequencing, gas-chromatography measurements, and bioinformatics. Deliverables: 1) Successful isolation of bacteria from volcanic soils and characterisation of isolates and gene expression networks. 2) Potential CO, H2 and CH4 oxidation rates and kinetic parameters in these isolates, leading to high quality publications in environmental microbiology journals.