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：微生物已经居住了地球超过30亿年，并且在人数，生物量和生物多样性方面占了地球上的大部分生命。我们仍然对微生物的生物多样性知之甚少，尽管扩展我们的知识有可能提高国家与生态系统健康有关的利益。该项目侧重于一组微生物，即遗嘱（壳）变形虫，它们在新英格兰沼泽和羊毛中很丰富和顶级捕食者。根据其测试的形状和组成（壳），遗嘱遗嘱的变形虫具有丰富的分类史；然而，这些特征已被证明与它们的识别有关，因为有许多隐秘的物种。因此，该研究项目依靠分子工具来探索其在时间和空间之间的生物多样性。考虑到遗嘱变形虫是变化气候的标志，并且在受威胁的湿地栖息地（如沼泽和羊毛）中富裕，因此这项研究很重要。除了科学发现之外，该研究项目还将培训一群本科女性以及有关微生物生物多样性的博士后研究员。在古生态学和当代研究中，遗嘱认证的变形虫已被用作生物指导者，并且某些分类单元被认为是泥炭主导的栖息地中的顶级捕食者。 该研究项目将阐明新英格兰和整个季节内沼泽和羊毛的遗嘱遗嘱变态性多样性。 最初基于两个分子标记，然后通过转录组分析来定义的形态和系统发育物种的比较，将允许探索该进枝的生物多样性。 这项工作将通过评估罚款（本地）和较大（新英格兰）的量表变化来探测驱动遗嘱变态分布的生态因素。 社区成员之间的模式还将使用基因组中目标区域的高通量测序进行表征，该测序允许检测稀有社区成员。 这项研究将产生遗嘱认证的图像，基因序列数据，比对，系统发育和转录组（即表达的基因），这些图像是从研究不足的真核生物进化枝中产生的，所有这些基因都将提供给社区。 从事该项目的学生和博士后研究员将在微生物多样性，显微镜和高通量测序数据的分析方面发展专业知识。 参与者的招聘将旨在扩大代表性不足的少数民族的参与。

项目成果

Illuminating the first bacteria

• DOI: 10.1126/science.abh2814
• 发表时间: 2021-05-07
• 期刊: SCIENCE
• 影响因子: 56.9
• 作者: Katz, Laura A.

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.