RUI: Biodiversity of testate (shelled) amoebae in New England bogs and fens

RUI：新英格兰沼泽和沼泽中有遗嘱（带壳）变形虫的生物多样性

• 批准号: 1651908
• 负责人: Laura Katz
• 金额: $ 40.9万
• 依托单位: Smith College
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2017
• 资助国家: 美国
• 起止时间: 2017-06-01 至 2023-05-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1651908&HistoricalAwards=false
• 关键词: RUI; Biodiversity; testate; shelled; amoebae

We live on a microbial planet: microbes have inhabited the Earth for more than 3 billion years and comprise most of life on Earth in terms of number, biomass and biodiversity. We still know very little about the biodiversity of microbes, though extending our knowledge has the potential to advance the national interest in relation to ecosystem health. This project focuses on one group of microbes, namely the testate (shelled) amoebae, which are abundant and top predators in New England bogs and fens. Testate amoebae have a rich history of classification based on the shape and composition of their tests (shells); yet these traits have been shown to be misleading in relation to their identification, because there are many cryptic species. Hence, this research project relies on molecular tools to explore their biodiversity across time and space. Such studies are important given that testate amoebae serve as markers for changing climates and are abundant in threatened wetland habitats like bogs and fens. Beyond scientific discovery, this research project will train a group of undergraduate women plus a postdoctoral fellow on the biodiversity of microorganisms. Testate amoebae have been used as bioindicators in both paleoecological and contemporary studies, and some taxa are argued to be top predators in Sphagnum dominated habitats. This research project will illuminate the diversity of testate amoebae from bogs and fens within New England and across seasons. Comparison of morphological and phylogenetic species, defined initially based on two molecular markers and then by multilocus delineation through transcriptome analyses, will allow exploration of the biodiversity of this clade. The work will probe the ecological factors that drive the distribution of testate amoebae by assessing fine (local) and larger (New England) scale variation. Patterns among community members will also be characterized using high-throughput sequencing of target regions in the genome, which allows detection of rare community members. This research will generate images of testate amoebae, gene sequence data, alignments, phylogenies, and transcriptomes (i.e. expressed genes) from a poorly studied clade of eukaryotes, all of which will be made available to the community. Students and postdoctoral fellows working on this project will develop expertise in microbial diversity, microscopy, and analyses of high throughput sequencing data. Participant recruitment will aim to broaden participation from underrepresented minorities.

我们生活在一个微生物星球上：微生物已经在地球上居住了30多亿年，就数量、生物量和生物多样性而言，它们构成了地球上的大部分生命。我们对微生物的生物多样性仍然知之甚少，尽管扩大我们的知识有可能促进与生态系统健康有关的国家利益。这个项目的重点是一组微生物，即有遗嘱（带壳）变形虫，这是丰富的和顶级捕食者在新英格兰沼泽和沼泽。有壳变形虫有着丰富的分类历史，基于其测试（壳）的形状和组成;然而，这些特征已被证明与其识别有关，因为有许多神秘的物种。因此，该研究项目依赖于分子工具来探索它们在时间和空间上的生物多样性。这些研究是重要的，因为有遗嘱的变形虫作为气候变化的标志，并在沼泽和沼泽等受威胁的湿地栖息地丰富。除了科学发现之外，该研究项目还将培训一批本科生妇女和一名博士后研究员，研究微生物的生物多样性。有壳变形虫在古生态学和现代研究中都被用作生物指示物，一些类群被认为是泥炭藓占主导地位的栖息地的顶级捕食者。 这个研究项目将阐明新英格兰内沼泽和沼泽以及跨季节的有遗嘱阿米巴的多样性。 形态和系统发育的物种，最初定义的基础上两个分子标记，然后通过转录组分析的多位点划定比较，将允许探索这个分支的生物多样性。 这项工作将探讨生态因素，推动分布的有遗嘱的变形虫通过评估罚款（当地）和更大的（新英格兰）规模的变化。 群落成员之间的模式也将使用基因组中目标区域的高通量测序来表征，这允许检测稀有的群落成员。 这项研究将产生的图像，有遗嘱的变形虫，基因序列数据，比对，基因组，和转录组（即表达的基因）从一个研究不足的真核生物分支，所有这些都将提供给社区。 参与该项目的学生和博士后研究员将发展微生物多样性、显微镜和高通量测序数据分析方面的专业知识。 参与者的招募将旨在扩大代表性不足的少数群体的参与。

项目成果

The concept of the hologenome, an epigenetic phenomenon, challenges aspects of the modern evolutionary synthesis

全基因组的概念是一种表观遗传现象，对现代进化综合的各个方面提出了挑战

• DOI: 10.1002/jez.b.22915
• 发表时间: 2019
• 期刊: Journal of Experimental Zoology Part B: Molecular and Developmental Evolution
• 作者: Collens, Adena;Kelley, Emma;Katz, Laura A.
• 通讯作者: Katz, Laura A.

Phylogenomics of the Epigenetic Toolkit Reveals Punctate Retention of Genes across Eukaryotes

• DOI: 10.1093/gbe/evaa198
• 发表时间: 2020-12-01
• 期刊: GENOME BIOLOGY AND EVOLUTION
• 影响因子: 3.3
• 作者: Weiner, Agnes K. M.;Ceron-Romero, Mario A.;Katz, Laura A.
• 通讯作者: Katz, Laura A.

Opinion: Genetic Conflict With Mobile Elements Drives Eukaryotic Genome Evolution, and Perhaps Also Eukaryogenesis

• DOI: 10.1093/jhered/esaa060
• 发表时间: 2021-01-01
• 期刊: JOURNAL OF HEREDITY
• 影响因子: 3.1
• 作者: Collens, Adena B.;Katz, Laura A.
• 通讯作者: Katz, Laura A.

High Diversity of Testate Amoebae (Amoebozoa, Arcellinida) Detected by HTS Analyses in a New England Fen using Newly Designed Taxon‐specific Primers

使用新设计的分类单元特异性引物，通过 HTS 分析在新英格兰沼泽中检测到有遗嘱变形虫（Amoebozoa、Arcellinida）的高度多样性

• DOI: 10.1111/jeu.12794
• 发表时间: 2020
• 期刊: Journal of Eukaryotic Microbiology
• 影响因子: 2.2
• 作者: Ruggiero, Alistaire;Grattepanche, Jean‐David;Weiner, Agnes K. M.;Katz, Laura A.
• 通讯作者: Katz, Laura A.

PhyloToL: A Taxon/Gene-Rich Phylogenomic Pipeline to Explore Genome Evolution of Diverse Eukaryotes

• DOI: 10.1093/molbev/msz103
• 发表时间: 2019-08-01
• 期刊: MOLECULAR BIOLOGY AND EVOLUTION
• 影响因子: 10.7
• 作者: Ceron-Romero, Mario A.;Maurer-Alcala, Xyrus X.;Katz, L. A.
• 通讯作者: Katz, L. A.