Marine heterotrophic alveolates: a genomic and morphometric single cell approach.

海洋异养肺泡:基因组和形态测量单细胞方法。

基本信息

项目摘要

Microbial eukaryotes (protists) apparently account for the majority of eukaryotic species, but comparably few taxa have been taxonomically investigated from both morphological and molecular criteria, as there are only limited sequence data. The gap between known and unknown microbial eukaryotes is even higher for heterotrophs, because most descriptions and nucleic acid based investigations depend upon laboratory cultures and heterotrophs tend to be more difficult to cultivate than autotrophs. Newly developed single cell methods, such as single cell PCR, enable classification without cultivation, but most nucleic acid based studies still rely almost entirely on published sequences, rendering unknown species invisible as poorly or completely unassigned sequences. Furthermore, data about heterotrophs is almost completely lacking from the new field of metatranscriptomics. The need for an extensive annotation of new sequences and correct taxonomic classification of the respective heterotrophic species is therefore evident. In this study, we will focus on marine heterotrophic protists, i.e. alveolates, since at times they represent the major component of planktonic biomass, transferring biological matter to higher trophic levels, and may play key functional roles in marine ecosystems. We will conduct a winter and summer field study in Greenland and a cruise around Spitzbergen to study the successional processes of heterotrophic communities and the differences in their biodiversity during annual shifts. The goal of collecting comprehensive data for completing databases will be reached with the development of a toolbox integrating microscopy, single cell multiplex PCR, single cell transcriptomics and meta-analysis of the collected environmental samples. With single cell PCR and sequencing of ribosomal DNA (SSU, LSU and ITS), we will obtain sequences for classification or identification of species and will identify cryptic species. Higher sequence resolution will be achieved with ITS2 rRNA secondary structure modeling and compensatory base change (CBC). Light microscopic analysis will serve to find established and new morphological classification features congruent with sequence data. Additionally, the organisms will be photographed and/or filmed and fixed for archiving. For selected understudied species, single cell transcriptomics will be utilized to develop new classification markers and to fill major gaps in metatranscriptomic databases. Meta-analyses of abiotic and biotic environmental data will complete the dataset of the species to offer additional biogeographical information. Existing databases will be supplied with the collected comprehensive data after thorough revision and nomenclatural analysis. The new toolbox will facilitate future identification and the data obtained will substantially enrich existing databases, thereby yielding a more comprehensive view of diversity of microbial eukaryotes and their functional role in marine ecosystems.
微生物真核生物(原生生物)显然占真核生物种类的大多数,但由于只有有限的序列数据,从形态学和分子标准上进行分类研究的分类群相对较少。对于异养生物来说,已知和未知的真核微生物之间的差距甚至更大,因为大多数描述和基于核酸的研究都依赖于实验室培养,而异养生物往往比自养生物更难培养。新开发的单细胞方法,如单细胞PCR,可以在没有培养的情况下进行分类,但大多数基于核酸的研究仍然几乎完全依赖于已发表的序列,使得未知物种作为不良或完全未分配的序列而不可见。此外,关于异养的数据几乎完全缺乏新领域的亚转录组学。因此,有必要对新序列进行广泛的注释,并对各自异养物种进行正确的分类。在本研究中,我们将重点关注海洋异养原生生物,即肺泡藻,因为它们有时代表浮游生物生物量的主要组成部分,将生物物质转移到更高的营养水平,并可能在海洋生态系统中发挥关键功能作用。我们将在格陵兰岛进行冬季和夏季的实地考察,并在斯匹茨卑尔根岛周围进行巡航,研究异养群落的演替过程及其生物多样性在年变化中的差异。通过开发集显微镜、单细胞多重PCR、单细胞转录组学和收集的环境样本的荟萃分析为一体的工具箱,将达到收集全面数据以完成数据库的目标。通过单细胞PCR和核糖体DNA测序(SSU, LSU和ITS),我们将获得用于物种分类或鉴定的序列,并将鉴定隐种。利用ITS2 rRNA二级结构建模和代偿性碱基变化(CBC)可以获得更高的序列分辨率。光镜分析将有助于发现与序列数据一致的已建立的和新的形态分类特征。此外,生物将被拍照和/或拍摄并固定存档。对于选定的未充分研究的物种,单细胞转录组学将用于开发新的分类标记,并填补亚转录组学数据库的主要空白。非生物和生物环境数据的荟萃分析将完善物种数据集,提供额外的生物地理信息。在经过彻底修订和命名分析后,将向现有数据库提供收集到的全面数据。新的工具箱将有助于未来的鉴定,所获得的数据将大大丰富现有数据库,从而对微生物真核生物的多样性及其在海洋生态系统中的功能作用产生更全面的看法。

项目成果

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Dr. Uwe John其他文献

Dr. Uwe John的其他文献

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{{ truncateString('Dr. Uwe John', 18)}}的其他基金

Exploring the adaptive within- and between bloom dynamics of heterogenic dinoflagellate population of the toxigenic Alexandrium ostenfeldii in field and laboratory experiments.
在田间和实验室实验中探索产毒奥氏亚历山大藻异质甲藻种群的水华内和水华之间的适应性动态。
  • 批准号:
    257505798
  • 财政年份:
    2014
  • 资助金额:
    --
  • 项目类别:
    Priority Programmes

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NSF PRFB FY 2022: Identifying a Novel Green Fluorescent Small Molecule in a Heterotrophic Dinoflagellate
NSF PRFB 2022 财年:鉴定异养甲藻中的新型绿色荧光小分子
  • 批准号:
    2208914
  • 财政年份:
    2023
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    --
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    Fellowship Award
Collaborative Research: How iron states impact temperature sensitivity of heterotrophic respiration in humid tropical soils
合作研究:铁态如何影响潮湿热带土壤异养呼吸的温度敏感性
  • 批准号:
    2241390
  • 财政年份:
    2023
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    --
  • 项目类别:
    Standard Grant
Collaborative Research: How iron states impact temperature sensitivity of heterotrophic respiration in humid tropical soils
合作研究:铁态如何影响潮湿热带土壤异养呼吸的温度敏感性
  • 批准号:
    2241389
  • 财政年份:
    2023
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MSA: Self-organizing principles for upscaling ecosystem water and heterotrophic carbon fluxes
MSA:扩大生态系统水和异养碳通量的自组织原理
  • 批准号:
    2213630
  • 财政年份:
    2022
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    --
  • 项目类别:
    Standard Grant
"Invisible interaction" between heterotrophic bacteria and other organisms in marine ecosystem
异养细菌与海洋生态系统其他生物的“看不见的相互作用”
  • 批准号:
    22H02422
  • 财政年份:
    2022
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    --
  • 项目类别:
    Grant-in-Aid for Scientific Research (B)
Transitions: Metagenomics of aquatic biofilms: evaluating linkages between autotrophic and heterotrophic microbial diversity and function
转变:水生生物膜的宏基因组学:评估自养和异养微生物多样性和功能之间的联系
  • 批准号:
    2153767
  • 财政年份:
    2022
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    --
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    Standard Grant
Comparative genomic and functional approaches for investigating biology and evolution of heterotrophic plants
研究异养植物生物学和进化的比较基因组和功能方法
  • 批准号:
    RGPIN-2021-02689
  • 财政年份:
    2022
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Improving the performance and efficiency of heterotrophic carbon fixation through strain engineering and membrane-based CO2 delivery
通过菌株工程和基于膜的二氧化碳输送提高异养碳固定的性能和效率
  • 批准号:
    2148629
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    2022
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Mapping heterotrophic functions to microbial population structures in wastewater resource recovery processes for optimization and prediction of antimicrobial resistance dissemination.
将异养功能映射到废水资源回收过程中的微生物种群结构,以优化和预测抗菌药物耐药性传播。
  • 批准号:
    RGPIN-2022-04203
  • 财政年份:
    2022
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    --
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    Discovery Grants Program - Individual
Heterotrophic microorganisms in Arctic hydrothermal sediments - the ecological roles and impact of their CAZymes repertoire
北极热液沉积物中的异养微生物 - 其 CAZymes 库的生态作用和影响
  • 批准号:
    467458523
  • 财政年份:
    2021
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  • 项目类别:
    WBP Fellowship
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