Second-generation environmental sequencing unmasks marine metazoan biodiversity

Abstract

Biodiversity is of crucial importance for ecosystem functioning, sustainability and resilience, but the magnitude and organization of marine diversity at a range of spatial and taxonomic scales are undefined. In this paper, we use second-generation sequencing to unmask putatively diverse marine metazoan biodiversity in a Scottish temperate benthic ecosystem. We show that remarkable differences in diversity occurred at microgeographical scales and refute currently accepted ecological and taxonomic paradigms of meiofaunal identity, rank abundance and concomitant understanding of trophic dynamics. Richness estimates from the current benchmarked Operational Clustering of Taxonomic Units from Parallel UltraSequencing analyses are broadly aligned with those derived from morphological assessments. However, the slope of taxon rarefaction curves for many phyla remains incomplete, suggesting that the true alpha diversity is likely to exceed current perceptions. The approaches provide a rapid, objective and cost-effective taxonomic framework for exploring links between ecosystem structure and function of all hitherto intractable, but ecologically important, communities.

Phylogeny, phylogeography, phylobetadiversity and the molecular analysis of biological communities

“…[41]), protists (e.g. [70,71]) and marine meiofaunal elements [42,43] coding genes for nuclear ribosomal RNA (rRNA) have been employed for amplicon HTP sequencing. Again, it is their ubiquity and the fact that rRNA contains highly conserved regions that span more variable regions that have made them the marker of choice for amplicon HTP sequencing.…”

“…While there have been some efforts to apply this approach to cryptic and complex eukaryote systems (e.g. [42,43]), the potential utility of this approach has not been fully explored. What follows is an examination of recent molecular insights into the mesofaunal component of one of the most complex and poorly studied habitats of terrestrial ecosystems-soils [44].…”

The widely used small subunit 18S rDNA molecule greatly underestimates true diversity in biodiversity surveys of the meiofauna

“…The use of eDNA surveys can potentially make species delimitation more efficient and cost-effective (3). Current meiofaunal eDNA surveys rely mainly on the nuclear small subunit 18S rDNA gene (10,15,16). Cytochrome c oxidase subunit I (COI) mtDNA, although used for global barcoding initiatives (i.e., Consortium for the Barcode of Life, www.barcodeoflife.org, and the International Barcode of Life project, www.ibol.org), is less widely used for eDNA.…”

An introduction to and a reflection on the “ecogenomics promise”

“…In less than a decade metagenomics has fundamentally changed our view of life in the ocean (Doney et al 2004) and in other aquatic domains (Hofmann et al 2005), and it continues to do so (Fuhrman 2009;Fonseca et al 2010). Many researchers and environmental decision makers today agree that knowledge on microbial abundance, diversity and dynamics is required to develop a functional view of the ocean.…”

“…Impressive amounts of data are collected by research groups interested in knowing ''who is out there?'' (which, when single marker genes are used, can be referred to as ''metagenetics' ' -Fonseca et al 2010) and ''who is doing what where?''. Despite the fact that the third research direction -relevant for nature mining -can be the main focus of metagenomics projects in each phase of a project (even already from the start), until today this direction is often left untouched or only present in the discussion section of the respective articles.…”