Diversity hotspot and unique community structure of foraminifera in the world’s deepest marine blue hole – Sansha Yongle Blue Hole

Abstract

Marine blue holes are precious geological heritages with high scientific research values. Their physical and chemical characteristics are unique because of the steep-walled structure and isolated water column which create isolated ecosystems in geographically restricted areas. The Sansha Yongle Blue Hole (SYBH) is the world's deepest marine blue hole. Here, we generated the first DNA metabarcoding dataset from SYBH sediment focusing on foraminifera, a group of protists that have colonized various marine environments. We collected sediment samples from SYBH along a depth gradient to characterize the foraminiferal diversity and compared them with the foraminiferal diversity of the costal Jiaozhou Bay (JZB) and the abyssal Northwest Pacific Ocean (NWP). We amplified the SSU rDNA of foraminifera and sequenced them with high-throughput sequencing. The results showed that the foraminiferal assemblages in SYBH were vertically structured in response to the abiotic gradients and diversity was higher than in JZB and NWP. This study illustrates the capacity of foraminifera to colonize hostile environments and shows that blue holes are natural laboratories to explore physiological innovation associated with anoxia.

Mitochondrial Cytochrome Oxidase Subunit 1: A Promising Molecular Marker for Species Identification in Foraminifera

“…Metabarcoding methods have been used to identify foraminiferal community composition in water (Morard et al, 2018) and sediment samples (Frontalini et al, 2020;Li et al, 2020;Cavaliere et al, 2021). A recent study, however, unraveled extreme variations in the number of SSU rRNA gene copies in the genome of planktonic foraminifera (Milivojević et al, 2021).…”

Newly designed foraminifera primers identify habitat‐specific lineages through metabarcoding analyses

“…And to a lesser extent among Tubothalamea (Figure 4). Comparison of our primer set with the primers commonly used in foraminiferal metabarcoding studies (Pawlowski et al, 2014;Li et al, 2020;and Cordier et al, 2019) showed similar outcomes (Figure S1). The lack of Tubothalamea taxa detected using our primers could be due to one or a combination of the following reasons: (1) an absence of this lineage in our samples, (2) challenges in lysing these cells, and/or (3) a lack of ability of our primer to amplify this lineage.…”

“…We developed foraminifera‐specific primers to target ~250–300 bp of hypervariable regions of the SSU‐rDNA, aiming for amplicon analyses of community samples, adding to the primers developed by other groups (Cordier et al, 2019; Lejzerowicz et al, 2013; Li et al, 2020; Pawlowski et al, 2002, 2014). Our primer enabled us to characterize and compare foraminiferal diversity across the different habitats including marine, brackish, and freshwater/soil habitats (Figures 3 and 4).…”

“…For in silico tests of our primer sets, we used the PR2 database web version (Vaulot et al, 2020) accessed on 3/13/2021 that included 28 Tubothalamea, 5 monothalamids, 65 Globothalamea, and 4 other foraminiferal species (Figure ). We also compared our primer's performance with foraminifera‐specific primers previously developed from Pawlowski et al (2014), Li et al (2020) and Cordier et al (2019).…”

“…We designed two sets of primers to add to the existing sets in the literature (Cordier et al, 2019;Li et al, 2020;Pawlowski et al, 2014). While both of our newly designed primer pairs amplified foraminiferal DNA, only one set (18F and 19R) consistently amplified community samples (see Table S3 for details).…”