Unexpected Foraminiferal Diversity Revealed by Small‐subunit rDNA Analysis of Antarctic Sediment

Abstract

Studies of benthic Foraminifera typically rely on the morphological identification of dried specimens. This approach can introduce sampling bias against small, delicate, or morphologically ambiguous forms. To overcome this limitation, we extracted total DNA from sediment followed by PCR using group- and species-specific primers. Phylogenetic analyses revealed that approximately ninety percent of the PCR products represented previously undescribed sequence types that group with undersampled members of the allogromiid Foraminifera. We also used a modification of this technique to track individual species in sediment fractions too fine for normal morphological identification, and to confirm species placement of morphologically ambiguous foraminiferans. We were able to identify the DNA of several large foraminiferal species in fine fractions in a seasonally-dependent manner, indicating that in some seasons the majority of the standing stock of these species exists as gametes/juveniles. The approach outlined here represents a powerful strategy for exploring the total diversity of benthic foraminiferal communities.

Widespread intra-specific genetic homogeneity of coastal Antarctic benthic foraminifera

“…Numerous genetic studies revealed cryptic species within planktonic (e.g., de Vargas et al 1999;Darling and Wade 2008), rotaliid (e.g., Holzmann 2000), and monothalamous foraminifera (e.g., Habura et al 2004;Pawlowski et al 2008). Similarly, high hidden diversity within Antarctic planktonic Neogloboquadrina pachyderma sinistral (Darling et al 2004) as well as among monothalamids was revealed using a single-cell sequencing approach (Pawlowski et al 2002b) and by probing environmental DNA (eDNA) extracted from coastal or deep Southern Ocean sediments (Habura et al 2004;Lejzerowicz et al 2014).…”

“…Similarly, high hidden diversity within Antarctic planktonic Neogloboquadrina pachyderma sinistral (Darling et al 2004) as well as among monothalamids was revealed using a single-cell sequencing approach (Pawlowski et al 2002b) and by probing environmental DNA (eDNA) extracted from coastal or deep Southern Ocean sediments (Habura et al 2004;Lejzerowicz et al 2014). In this study, we tested genetic similarity of common benthic foraminifera from very distant coastal areas of West Antarctica.…”

“…A broad distribution of some Antarctic morphospecies was suggested by some early foraminiferal workers (e.g., Earland 1934) and more recently confirmed by Mikhalevich (2004), who concluded that the majority of foraminiferal morphospecies on the Antarctic shelf have circumpolar distributions. The idea is based, however, exclusively on morphological studies, which have been shown to underestimate the true foraminiferal diversity revealed in many cases by genetic data (e.g., de Vargas et al 1999;Holzmann 2000;Pawlowski et al 2002bPawlowski et al , 2008Habura et al 2004).…”

A New Allogromiid Foraminifer from Coastal Georgia, USA: The Case for an Unusual Form of Chloroplast Sequestration

“…Representatives are known from marginal marine settings to the deep sea, and in selected freshwater settings and terrestrial soils [3]. Molecular studies [4][5] have shown that the biodiversity of allogromiids is considerably higher than that recognized using traditional collecting methods, and as a result we know little about the adaptations and modes of life of this group.The many mudflats associated with the expansive salt marshes of coastal Georgia host an interesting array of mostly undescribed allogromiids in addition to other foraminiferal taxa. Among the new allogromiids is a small (<200 µm) translucent monothlamous species (Fig.…”

“…Representatives are known from marginal marine settings to the deep sea, and in selected freshwater settings and terrestrial soils [3]. Molecular studies [4][5] have shown that the biodiversity of allogromiids is considerably higher than that recognized using traditional collecting methods, and as a result we know little about the adaptations and modes of life of this group.…”