Are marine nematodes hyperdiverse? A metagenomic solution.

科学中的一个基本问题是地球上有多少物种。虽然总数量估计在1000万到1亿之间，但目前被指定为物种的分类群数量约为150万。因此，我们对物种多样性的一般认识存在巨大的缺陷，而且分类单元体大小与描述的物种数量之间存在极端的负相关关系。目前的分类知识严重偏向于较大的分类群，尽管大多数较大和常见的动植物群已经被描述，但其他重要的类群，如线虫，却被忽视了。线虫是地球上数量最多的多细胞生物，它们在所有栖息地都能找到，尤其是在海洋沉积物中，它们占多细胞动物群的50-90%。线虫在海洋沉积物生态系统过程中具有重要的生态学意义，并构成了大型生物所依赖的大部分生产性和腐生性营养基础。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）的估计仍然是一个猜测问题。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性导致物种鉴定的问题。此外，与研究更大的分类群的分类学家相比，鉴定线虫这一费力的过程所花费的时间要多得多。因此，在过去几年中，利用分子DNA“条形码”建立物种识别系统取得了显著进展。这个简单的概念依赖于扩增和测序未知标本中的标准短DNA序列，并将其与已识别物种的序列参考库进行比较。近年来的研究表明，采用分子操作分类单元（MOTU）方案对土壤生物是有效的。motu与已发表的物种描述没有任何正式的相关性，但相关性可以与现有数据库或未来的分类方法实现，这种方法被称为“反向分类学”。分子鉴定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，由于存在96万个未命名物种的潜在缺口，这项任务的绝对规模意味着，仅使用基于形态学的经典分类学对所有线虫物种进行正式分类是极不可能的。迄今为止，MOTU研究通过对从环境样本中获得的有限数量的生物体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，在小底栖动物中存在更多未被发现的物种。最近发展了一项新技术，称为大规模并行测序（MPS）。MPS能够在4小时内生成2500万个DNA碱基数据，比目前的测序技术快大约100倍。该项目旨在利用这种新的分析能力来估计英国线虫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对线虫分子生物多样性进行量化，将是在确定地球生态系统的关键生物成分方面取得的重大进展。此外，该项目将作为使用MPS评估任何大型或微型动物或植物样本中现存生物多样性的模板/一个应用程序，将普遍适用于任何分类单元或有关生物多样性在生态系统功能中的作用的假设。

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.