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

了解土壤如何形成对于能够恢复退化的土壤至关重要。世界上80%的土壤是火山土壤，这些土壤是最肥沃的土壤之一。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得能量来定居。此前，Hernandez在智利的Llaima火山上研究了细菌的多样性（即不同年龄的土壤），发现一种特殊的细菌（Ktedonobacterales）在新形成的土壤中占主导地位。人们对Ktedonobacterales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。Hernandez和其他人对火山土壤的研究表明，在火山土壤演替的前几十年，CH4、H2和co消耗微生物占主导地位2,3,4,5,6。大气中的这些微量气体为细菌提供了能量和碳源，细菌在火山岩中定居，并将这些基质转化为生物质，从而转化为有机碳，这反过来又对火山岩上的土壤形成做出了重大贡献。最重要的假设是，co氧化微生物及其消耗其他气体（如H2）的能力，在产生引发土壤形成的有机物中起着关键作用。目的1)确定微量气体及其消耗微生物在火山土发育过程中的作用。2)确定居住在火山土壤中的微量气体代谢微生物（特别是Ktedonobacterales）的代谢途径。PackagesWP-1工作。土壤培养和群落分析（0-1.5年级）学生将使用与培养无关的方法来描述微生物群落的特征，解决以下问题：i)早期火山沉积物的co氧化能力最大吗？ii)早期火山沉积物中微生物群落的重要碳和能量来源是什么？该学生将参加在智利的采样活动，准备微生物孵化，并学习跨学科技术，包括qPCR，气相色谱测量，DNA霰弹枪测序和生物信息学。成果：1)CO氧化速率沿连续梯度。2)在演替过程中鉴定出细菌及其功能行会，并在高质量的微生物生态学期刊上发表论文。细菌分离和表征（0.8-3.0年）：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) Ktedonobacterales是否能够氧化CO和H2？ii)这些环境中的其他哪些细菌能够氧化CO？其他主要的碳和能源来源是如何加工的？博士生将学习与培养相关的技术，包括细菌的富集和分离、基因组测序、气相色谱测量和生物信息学。成果：1)从火山土壤中成功分离细菌，并鉴定分离物和基因表达网络。2)这些菌株潜在的CO、H2和CH4氧化速率和动力学参数，在环境微生物学期刊上发表了高质量的论文。

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.