Symbiosis and microbial genomics

共生和微生物基因组学

• 批准号: RGPIN-2014-03994
• 负责人: Keeling, Patrick
• 金额: $ 5.17万
• 依托单位: University of British Columbia
• 依托单位国家: 加拿大
• 项目类别: Discovery Grants Program - Individual
• 财政年份: 2015
• 资助国家: 加拿大
• 起止时间: 2015-01-01 至 2016-12-31
• 项目状态: 已结题
• 来源: https://www.nserc-crsng.gc.ca/ase-oro/Details-Detailles_eng.asp?id=587539
• 关键词: Symbiosis; microbial; genomics

Symbiosis and genome evolution Our longterm aim is to understand the impacts of major changes like horizontal gene transfer and symbiosis on genome structure and function in microbial eukaryotes. Here, we extend our work on endosymbiosis to complex symbiotic associations between microbes in two environments that are rich in symbiotic interactions; the hindgut of wood-eating insects, and coral reefs. A. Protist-Bacteria Associations in the Termite Hindgut The hindguts of termites and the wood-eating cockroach Cryptocercus harbour a complex, host-specific community of anaerobic protists and bacteria, the composition of which is stable through time. Within this symbiotic community are also many symbioses between the microbes: 60% of hindgut bacteria live inside or on the surface of a protist. The functions of these associations are unknown, although nitrogen metabolism has been implicated in some. We will use single-cell genomics and transcriptomics to address the following questions: 1. What is the functional relationship of epibionts to host protists? Epibionts, or surface symbionts, are not as well-studied as endosymbionts, but are nonetheless common in anaerobic environments, where many protists are coated with a monolayer like a ‘filter’ between it and its environment. To examine the functional relationship between epibionts and host, we will characterize epibiont genomes and host transcriptomes from four hosts with a single epibiont species: Barbulonympha, Urinympha, Devescovina, and Staurojeonina. We will create metabolic maps for the epibionts, and identify pathways absent from host transcriptomes to test whether nitrogen metabolism is a general feature of such associations. We will also compare epibiont and endosymbiont genomes to identify any features that may functionally distinguish them. 2. Do multiple symbionts partition essential metabolic pathways? In sap-feeding insect with multiple endosymbionts, essential metabolic pathways have been partitioned between symbionts. We will test the hypothesis that this also explains epibiotic systems with multiple symbionts by sequencing epibiont genomes and host transcriptomes from Streblomastix and Calonympha. Metabolic mapping will show whether complete pathways are encoded within individual epibiont genomes or distributed among them. The symbionts of Streblomastix are of additional interest since the oxymonad host is a different lineage than most termite protists, and it is also not demonstrably cellulolytic. B. Coral-Protist Associations Coral reefs are hotspot for biodiversity and symbiotic interactions, but almost nothing is known about reef microbial eukaryotes. To develop reefs as a system to study symbiotic interactions at the genomic level, we will establish baseline information and address two specific questions: 1. Does the diversity of coral reef protist communities follow similar trends as bacteria and viruses? The characteristics of bacterial and viral communities in coral reefs have been documented, but not protists. To establish a baseline for comparisons, we will carry out protist surveys for 3 reef systems, as well as thrombolites (calcified microbial mat communities), using deep sequence tagging of the same samples used to study bacteria and viruses. We will also focus specifically on a gradient of reef degradation - from protected pristine reefs to heavily fished reefs with massive coral death. For bacteria, abundance and prevalence of heterotrophs increase over this gradient, and we will test the hypothesis that protists follow the same trends by applying the same methodology. Variation in abundance and taxonomic diversity along the gradient will be analysed and lineages specifically associated with reef degradation will be identified.

共生与基因组进化 我们的长期目标是了解微生物真核生物基因组结构和功能的主要变化，如水平基因转移和共生的影响。在这里，我们将我们的内共生研究扩展到两种环境中微生物之间复杂的共生关系，这两种环境都具有丰富的共生相互作用;食木昆虫的后肠和珊瑚礁。 A.白蚁后肠中的原生生物-细菌组合 白蚁和食木蟑螂隐尾虫的后肠内有一个复杂的、宿主特异性的厌氧原生生物和细菌群落，其组成随时间推移而稳定。在这个共生群落中，微生物之间也有许多共生关系：60%的后肠细菌生活在原生生物的内部或表面。这些协会的功能是未知的，虽然氮代谢已牵连在一些。我们将使用单细胞基因组学和转录组学来解决以下问题： 1.附着生物与宿主原生生物的功能关系是什么？外共生体或表面共生体，不像内共生体那样被充分研究，但在厌氧环境中仍然很常见，其中许多原生生物被单层包裹，就像它和环境之间的“过滤器”。为了研究表生体和宿主之间的功能关系，我们将表征表生体基因组和宿主转录组从四个主机与一个单一的表生体物种：Barbulphypha，Urinympha，Devescopyra，Staurojeonina。我们将创建代谢地图的epibiont，并确定从主机转录组不存在的途径，以测试是否氮代谢是这样的协会的一般特征。我们还将比较表生体和内共生体的基因组，以确定任何功能上可能区分它们的功能。 2.多个共生体划分基本代谢途径吗？在具有多个内共生体的取食汁液昆虫中，必需的代谢途径在共生体之间被分配。我们将测试的假设，这也解释了多个共生体的表生体系统的测序表生体基因组和主机转录组从Streblomastix和Calciumpha。代谢图谱将显示完整的途径是否编码在单个表生体基因组中或分布在它们之间。Streblomastix的共生体是额外的兴趣，因为氧化单胞菌的主机是一个不同的谱系比大多数白蚁原生生物，它也没有明显的纤维素分解。 B。珊瑚原生生物协会 珊瑚礁是生物多样性和共生相互作用的热点，但对珊瑚礁微生物真核生物几乎一无所知。为了将珊瑚礁发展成为一个在基因组水平上研究共生相互作用的系统，我们将建立基线信息并解决两个具体问题： 1.珊瑚礁原生生物群落的多样性是否遵循与细菌和病毒相似的趋势？ 珊瑚礁中的细菌和病毒群落的特征已被记录在案，但原生生物却没有。为了建立比较基准，我们将对3个珊瑚礁系统以及血栓岩（钙化微生物垫群落）进行原生生物调查，使用用于研究细菌和病毒的相同样品的深度序列标记。我们还将特别关注珊瑚礁退化的梯度-从受保护的原始珊瑚礁到大量珊瑚死亡的严重捕捞珊瑚礁。对于细菌来说，异养生物的丰度和流行率在这个梯度上增加，我们将通过应用相同的方法来测试原生生物遵循相同趋势的假设。将分析丰度和分类多样性沿着梯度的变化，并查明与珊瑚礁退化具体有关的谱系。