Symbiosis and microbial genomics

我们的长期目标是了解水平基因转移和共生等重大变化对微生物真核生物基因组结构和功能的影响。在这里，我们将我们对内共生的工作扩展到微生物在两种富含共生相互作用的环境中复杂的共生关联；食木昆虫的后肠和珊瑚礁。白蚁后肠中原生生物与细菌的关联白蚁和食木蟑螂隐尾虫的后肠中有一个复杂的、宿主特有的厌氧原生生物和细菌群落，其组成随着时间的推移是稳定的。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。这些关联的功能尚不清楚，尽管氮代谢已涉及一些。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。表观生物与宿主原生生物的功能关系是什么？表面共生体，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，在厌氧环境中，许多原生生物被一层单层覆盖，就像它和环境之间的“过滤器”一样。为了研究外生体与宿主之间的功能关系，我们将对四种宿主的外生体基因组和宿主转录组进行特征分析：Barbulonympha， Urinympha， Devescovina和Staurojeonina。我们将创建表观生物的代谢图谱，并确定宿主转录组中缺失的途径，以测试氮代谢是否是此类关联的一般特征。我们还将比较表观生物和内共生基因组，以确定可能在功能上区分它们的任何特征。2. 多个共生体是否划分了必要的代谢途径？在具有多个内共生体的食液昆虫中，重要的代谢途径在共生体之间被划分。我们将通过对Streblomastix和Calonympha的表观生物基因组和宿主转录组测序来验证这一假设，即这也解释了具有多个共生体的表观生物系统。代谢图谱将显示完整的通路是在单个表观生物基因组内编码还是分布在它们之间。Streblomastix的共生体是额外的兴趣，因为oxymonad宿主与大多数白蚁原生生物不同，而且它也没有明显的纤维素分解能力。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。为了将珊瑚礁作为一个系统来研究基因组水平上的共生相互作用，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？珊瑚礁中细菌和病毒群落的特征已经被记录下来，但原生生物却没有。为了建立比较基线，我们将对3个珊瑚礁系统以及血栓（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过度捕捞珊瑚礁。对于细菌来说，异养生物的丰度和流行度在这个梯度上增加，我们将通过应用相同的方法来检验原生生物遵循相同趋势的假设。将分析沿梯度的丰度和分类多样性的变化，并确定与珊瑚礁退化特别相关的谱系。

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.