Symbiosis and microbial genomics

共生与基因组进化*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，我们将我们关于内共生的工作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.白蚁后肠中的原生细菌协会*白蚁和以木头为食的蟑螂的后肠含有一个复杂的、宿主特有的厌氧原生动物和细菌群落，其组成随着时间的推移是稳定的。在这个共生群落中还有许多微生物之间的共生：60%的后肠细菌生活在原生动物的内部或表面。这些关联的功能尚不清楚，尽管一些关联与氮代谢有关。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.表面生物体与宿主原生生物之间的功能关系是什么？表面共生体或表面共生体没有内共生体研究得那么深入，但在厌氧环境中仍然很常见，在厌氧环境中，许多原生动物在它与环境之间覆盖着一层像过滤器一样的单分子层。为了研究表生生物和寄主之间的功能关系，我们将研究具有单一表生生物物种的四个寄主的表生生物基因组和寄主转录本：羽毛虫属、尿囊藻属、德维科夫纳属和Staurojeonina属。我们将创建表生微生物的代谢图，并确定宿主转录本中没有的途径，以测试氮代谢是否是这种关联的一般特征。我们还将比较表生生物和内共生生物的基因组，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汁性昆虫中，重要的代谢途径已在共生体之间分配。我们将通过对Streblomastix和Calonympha的表生细菌基因组和寄主转录本进行测序来检验这一假设，即这也解释了具有多个共生体的共生系统。代谢图谱将显示完整的途径是在单个表观生物基因组中编码的，还是分布在它们之间的。由于加氧单胞菌是与大多数白蚁原生生物不同的谱系，而且它也不能明显地分解纤维素，所以链霉菌的共生体引起了人们的额外兴趣。**B.珊瑚-原生生物协会：珊瑚礁是生物多样性和共生互动的热点，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经被记录在案，但没有原生生物。为了建立比较基准，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本的深层序列标签。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捕捞、珊瑚大量死亡的珊瑚礁。对于细菌，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检验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梯度的变化，并查明与珊瑚礁退化具体相关的谱系。

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.