Are marine nematodes hyperdiverse? A metagenomic solution.

海洋线虫是否高度多样化？

• 批准号: NE/E001505/1
• 负责人: Simon Creer
• 金额: $ 9.64万
• 依托单位: Bangor University
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2006
• 资助国家: 英国
• 起止时间: 2006 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=NE%2FE001505%2F1
• 关键词: marine; nematodes; hyperdiverse; metagenomic; solution.

A fundamental question in science is how many species are there on earth. The number of taxa that have currently been assigned as species is approximately 1.5 million, although the total number has been estimated at between 10 and 100 million. Thus, a huge deficit exists in our general knowledge of species diversity, but also, there is an extreme negative correlation between taxon body size and the number of species described. Current taxonomical knowledge is heavily biased towards larger taxa and, although the majority of the larger and popular fauna and flora have been described, other important groups such as nematodes have been neglected. Nematodes are the most abundant multicellular organisms on earth and they are found in all habitats, but notably in marine sediments where they can make up between 50-90% of the multicellular fauna. Nematodes are ecologically important in marine sediment ecosystem processes and comprise the majority of the productive and saprophytic trophic base upon which macroorganisms rely. Despite their pivotal role in ecosystem functioning, a current estimate of global nematode diversity (c. 1 million species) remains a matter of conjecture. This massive knowledge gap is the result of the small size and the apparent morphological similarity of nematodes that cause problems in species identification. Also, the laborious procedure of nematode identification can take orders of magnitude more specialist's time to assign individuals to species compared to taxonomists working with larger taxa. Accordingly, in the past few years there has been a noticeable move towards the establishment of a system of species identification using molecular DNA 'barcodes'. The simple concept relies on amplifying and sequencing a standard short DNA sequence in the unknown specimen, and comparing this to a reference library of sequences from identified species. Recent research effort has highlighted the efficiency of adopting a molecular operational taxonomic unit (MOTU) scheme for soil organisms. The MOTUs do not have any formal correlation with published species descriptions, but correlations can be achieved with existing databases, or future classifications in an approach that has been termed 'reverse taxonomy. Molecular identification strategies have caused considerable debate between molecular ecologists and traditional taxonomists. However, with a potential deficit of 960,000 unnamed species, the sheer magnitude of the task means that it is highly unlikely that formal classification of all nematode species will be achieved using classical morphological-based taxonomy alone. MOTU studies to date have studied diversity via sequencing molecular barcodes from a limited number of organisms obtained from environmental samples. However, molecular diversity accumulation curves suggest that there are more undiscovered species present in the meiobenthos. A new technology has been developed very recently called Massively Parallel Sequencing (MPS). MPS is capable of generating 25 million bases of DNA data in a four hour period, which is approximately 100 times faster than current sequencing technology. This project aims to harness this novel analytical power to estimate the actual molecular (and subsequent species) diversity present at different spatial scales throughout littoral communities of UK nematodes and extrapolate this information to estimates of regional and global species richness. The utilization of MPS to quantify nematode molecular biodiversity would represent a major advance towards identifying a crucial biological component of the earth's ecosystems. Furthermore, the project will serve as a template for the use of MPS in assessing the extant biodiversity in any meoi- or microfaunal or floral sample / an application that will be universally applicable to any taxon or hypothesis pertaining to the role of biodiversity in ecosystem functioning.

科学中的一个基本问题是地球上有多少物种。目前已被指定为物种的分类群数量约为150万，尽管总数估计在1000万至1亿之间。因此，我们对物种多样性的一般知识存在着巨大的不足，但分类单元的体型大小与所描述的物种数量之间也存在着极端的负相关。目前的分类学知识严重偏向较大的分类群，尽管大多数较大和受欢迎的动植物已被描述，但其他重要的类群，如线虫，已被忽视。线虫是地球上最丰富的多细胞生物，它们在所有栖息地都有发现，但值得注意的是，它们在海洋沉积物中占多细胞动物总数的50%-90%。线虫在海洋沉积物生态系统过程中具有重要的生态意义，并构成了大型生物赖以生存的大部分生产性和腐生营养基础。尽管它们在生态系统功能中起着关键作用，但目前对全球线虫多样性(约100万种)的估计仍然是一种猜测。这种巨大的知识差距是由于线虫的小尺寸和明显的形态相似造成的，这给物种鉴定带来了问题。此外，与处理较大分类群的分类学家相比，繁琐的线虫鉴定程序可能需要更多专家的时间来将个体分配到物种上。因此，在过去的几年里，在建立使用分子DNA条形码的物种识别系统方面取得了明显的进展。这个简单的概念依赖于对未知样本中的标准短DNA序列进行扩增和测序，并将其与已识别物种的序列参考库进行比较。最近的研究工作强调了对土壤生物采用分子操作分类单位(MOTU)方案的效率。Motus与已发表的物种描述没有任何正式的相关性，但可以与现有的数据库或未来的分类实现相关性，这种方法被称为“反向分类法”。分子识别策略在分子生态学家和传统分类学家之间引起了相当大的争论。然而，由于潜在的96万个未命名物种的不足，这项任务的巨大规模意味着，仅使用经典的基于形态的分类学来实现对所有线虫物种的正式分类是非常不可能的。到目前为止，MOTU的研究已经通过对从环境样本中获得的有限数量的生物进行分子条形码测序来研究多样性。然而，分子多样性积累曲线表明，小型底栖动物中存在更多未被发现的物种。最近开发了一种新技术，称为大规模并行测序(MPS)。MPS能够在四小时内产生2500万个碱基的DNA数据，这大约比目前的测序技术快100倍。该项目旨在利用这一新的分析能力来估计英国沿海线虫群落在不同空间尺度上存在的实际分子(和随后的物种)多样性，并将这些信息外推到区域和全球物种丰富度的估计中。利用MPS来量化线虫分子生物多样性将是在确定地球生态系统的一个重要生物组成部分方面取得的重大进展。此外，该项目将作为MPS用于评估任何小型或微型动物或花卉样本中现存生物多样性的模板，这一应用将普遍适用于任何关于生物多样性在生态系统功能中的作用的分类或假说。

项目成果

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

Sequencing our way towards understanding global eukaryotic biodiversity.

• DOI: 10.1016/j.tree.2011.11.010
• 发表时间: 2012-04
• 期刊: Trends in ecology & evolution
• 影响因子: 16.8
• 作者: Bik HM;Porazinska DL;Creer S;Caporaso JG;Knight R;Thomas WK
• 通讯作者: Thomas WK