Copy of Sequencing the meiofaunal metagenome of the marine/freshwater interface in key estuarine ecosystems

主要河口生态系统海洋/淡水界面小型动物宏基因组测序的副本

• 批准号: NE/F001290/1
• 负责人: Simon Creer
• 金额: $ 4.55万
• 依托单位: Natural History Museum
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2008
• 资助国家: 英国
• 起止时间: 2008 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=NE%2FF001290%2F1
• 关键词: Copy; Sequencing; meiofaunal; metagenome; marine

Estuaries are key transitional habitats that are significantly affected by local and global human activities (ie they are main centres of habitation, industrialization, pollution and recreation). Estuaries are typically considered to be low biodiversity systems; probably due to the presence of low alpha diversity of macrofauna. In contrast, meiofaunal diversity (animals smaller than 45um, dominated by nematodes) is substantial, with most estuaries estimated to be inhabited by approximately 200 species of nematodes, with numbers ranging from a staggering 106-108 animals/m2, contributing to between 50-90% of the metazoan faunal species richness (the total numbers of species present). Meiofaunal biodiversity plays a very important role in sediment ecosystem processes, contributing to the regulation of carbon, nitrogen, and sulphur cycling, water column processes, pollutant distribution, secondary production, food chain processes, and stability of sediments. Meiofauna are clearly key components of ecosystem functioning, but studying meiofaunal communities using standard morphological approaches requires highly-skilled taxonomists and is incredibly time consuming. Not only does this restrict the analysis of meaningful sample sizes in ecological studies, but the small size and morphological similarities of different species of meiofaunal organisms have led to severe doubts regarding the reliability of morphological taxonomic approaches. As a result of these constraints, combinations of morphological approaches and new molecular genetic methods are being developed for nematode biodiversity assessments. Perhaps the most exciting development in this field is the potential to apply massively parallel sequencing (MPS), to elucidate the molecular community composition of microbial, or meiofaunal samples. This brand new technology has the ability to simultaneously sequence hundreds of thousands of short strands of DNA (in four hours), that can be used as species identification tags. To date, this has never been possible using standard cloning and sequencing methods and MPS also represents incredible value for money, with each sequence in this type of application costing less than 5p. The availability of MPS technology, in addition to recent significant advances in the knowledge of the phylogenetic and ecological relationships of nematode taxa, now offers a molecular and bioinformatic framework that can be used to accurately characterise meiofaunal biodiversity in real time. Such advances allow hypotheses to be developed and tested to elucidate relationships between meiofaunal biodiversity and biotic/abiotic processes. Moreover, these methods will facilitate the development of hydrodynamic models that can be used to predict the spatial and temporal composition of meiofaunal communities according to the relationships between flow rates and sediment composition. The current proposal seeks to create novel biodiversity genome sequence resources for ecologically important estuarine species throughout a range of substrate types in estuarine ecosystems characterized by ongoing (Mersey) and recovering (Thames) industrial and municipal pollutant regimes. The data will be used to address biotic- and abiotic-focused ecological hypotheses, and will generate a predicted c. 320,000 novel sequence reads, effectively characterizing a significant component of the UK's estuarine meiofauna, thus providing a platform for understanding ecosystem functioning in marine sediments. These data can then be combined with complimentary datasets derived from sandy sediments and be used to develop cost-effective, time-saving, DNA chip-based meiofaunal community identification tools (e.g. for biomonitoring and ecotoxicology studies), thus, driving forward research (academic and commercial) into biodiversity-ecosystem functioning in marine sediments.

河口是关键的过渡性栖息地，受到当地和全球人类活动的重大影响(即，它们是主要的居住、工业化、污染和娱乐中心)。河口通常被认为是低生物多样性系统；可能是由于大型动物的低阿尔法多样性的存在。相比之下，小型底栖动物(小于45um的动物，以线虫为主)的多样性很大，大多数河口估计居住着大约200种线虫，其数量从惊人的106-108只/m2不等，占后生动物物种丰富度的50%-90%(存在的物种总数)。小型动物生物多样性在沉积物生态系统过程中起着非常重要的作用，有助于调节碳、氮、硫的循环、水柱过程、污染物分配、次生生产、食物链过程和沉积物的稳定性。小型动物显然是生态系统功能的关键组成部分，但使用标准的形态方法研究小型动物群落需要高技能的分类学家，而且非常耗时。这不仅限制了生态学研究中有意义的样本量的分析，而且小型底栖动物不同物种的小尺寸和形态相似导致了对形态分类学方法的可靠性的严重怀疑。由于这些限制，正在开发形态方法和新的分子遗传学方法相结合的方法来评估线虫生物多样性。也许该领域最令人兴奋的发展是应用大规模并行测序(MPS)来阐明微生物或小型动物样本的分子群落组成。这项全新的技术有能力同时对数十万条DNA短链进行测序(在四个小时内)，这些DNA可以用作物种识别标签。到目前为止，使用标准的克隆和测序方法这是不可能的，MPS也代表着难以置信的金钱价值，这种类型的应用程序中的每个序列成本不到5便士。MPS技术的可获得性，加上最近在线虫分类群系统发育和生态关系知识方面的重大进展，现在提供了一个分子和生物信息学框架，可以用来准确地实时描述小型动物的生物多样性。这些进展使得可以开发和检验假说，以阐明小型底栖动物生物多样性和生物/非生物过程之间的关系。此外，这些方法将促进水动力学模型的发展，这些模型可用于根据流速与沉积物组成之间的关系来预测小型底栖动物群落的时空组成。目前的提案旨在通过河口生态系统的一系列底物类型，为具有生态重要性的河口物种创造新的生物多样性基因组序列资源，这些生态系统的特点是正在进行的(Mersey)和正在恢复(Thames)的工业和市政污染物制度。这些数据将用于解决以生物和非生物为重点的生态假说，并将产生预计约32万个新的序列读数，有效地表征英国河口小型底栖动物的一个重要组成部分，从而为了解海洋沉积物中的生态系统功能提供一个平台。然后，这些数据可以与来自沙质沉积物的免费数据集相结合，用于开发具有成本效益、节省时间、基于DNA芯片的小型动物群落识别工具(例如，用于生物监测和生态毒理学研究)，从而推动对海洋沉积物中生物多样性-生态系统功能的研究(学术和商业)。

项目成果

A critique of Rossberg et al.: Noise obscures the genetic signal of meiobiotal ecospecies in ecogenomic datasets.

对 Rossberg 等人的批评：噪声掩盖了生态基因组数据集中的减生物生态种的遗传信号。

• DOI: 10.1098/rspb.2013.3076
• 发表时间: 2014
• 期刊: Proceedings. Biological sciences
• 作者: Morgan MJ

Introduction to Marine Genomics

海洋基因组学简介

• DOI: 10.1007/978-90-481-8639-6_1
• 发表时间: 2010
• 作者: Carvalho G

Marine Benthic Nematode Molecular Protocol Handbook (Nematode Barcoding)

海洋底栖线虫分子方案手册（线虫条形码）

• 发表时间: 2011
• 作者: Creer, S.

Metagenetic analysis of patterns of distribution and diversity of marine meiobenthic eukaryotes

• DOI: 10.1111/geb.12223
• 发表时间: 2014-11-01
• 期刊: GLOBAL ECOLOGY AND BIOGEOGRAPHY
• 影响因子: 6.4
• 作者: Fonseca, Vera G.;Carvalho, Gary R.;Creer, Simon
• 通讯作者: Creer, Simon

Isolation of marine meiofauna from sandy sediments: from decanting to DNA extraction.

从沙质沉积物中分离海洋小型动物：从倾析到 DNA 提取。

• DOI: 10.1038/nprot.2010.157
• 发表时间: 2011
• 期刊: Protocol Exchange
• 作者: Fonseca V