Document of bibliographic reference 287672

BibliographicReference record

Type

Bibliographic resource

Type of document

Journal article

BibLvlCode

AS

Title

Next-generation environmental diversity surveys of Foraminifera: preparing the future

Abstract

Foraminifera are commonly defined as marine testate protists, and their diversity is mainly assessed on the basis of the morphology of their agglutinated or mineralized tests. Diversity surveys based on environmental DNA (eDNA) have dramatically changed this view by revealing an unexpected diversity of naked and organic-walled lineages as well as detecting foraminiferal lineages in soil and freshwater environments. Moreover, single-cell analyses have allowed discrimination among genetically distinctive types within almost every described morphospecies. In view of these studies, the foraminiferal diversity appeared to be largely underestimated, but its accurate estimation was impeded by the low speed and coverage of a cloning-based eDNA approach. With the advent of high-throughput sequencing (HTS) technologies, these limitations disappeared in favor of exhaustive descriptions of foraminiferal diversity in numerous samples. Yet, the biases and errors identified in early HTS studies raised some questions about the accuracy of HTS data and their biological interpretation. Among the most controversial issues affecting the reliability of HTS diversity estimates are (1) the impact of technical and biological biases, (2) the sensitivity and specificity of taxonomic sequence assignment, (3) the ability to distinguish rare species, and (4) the quantitative interpretation of HTS data. Here, we document the lessons learned from previous HTS surveys and present the current advances and applications focusing on foraminiferal eDNA. We discuss the problems associated with HTS approaches and predict the future trends and avenues that hold promises for surveying foraminiferal diversity accurately and efficiently.

WebOfScience code

https://www.webofscience.com/wos/woscc/full-record/WOS:000345447800002

Bibliographic citation

Pawlowski, J.; Lejzerowicz, F.; Esling, P. (2014). Next-generation environmental diversity surveys of Foraminifera: preparing the future. Biol. Bull. 227(2): 93-106. https://dx.doi.org/10.1086/bblv227n2p93

Topic

Marine

Is peer reviewed

true

Access rights

open access

Is accessible for free

true