Next-generation sequencing and metabarcoding to understand the ecology of benthic foraminiferal community in the Bering Sea

Abstract

The sedimentary archives from the Bering Sea can provide excellent records of the global climate shift. However, paleoclimatic studies from the Bering Sea are limited due to the lack of well calibrated proxies. Various characteristics of foraminifera are frequently used as paleoclimatic and paleoceanographic proxies. A precise understanding of the ecology of foraminiferal species is required to use it as proxy. Here, we use next-generation sequencing and metabarcoding to understand the ecology of benthic foraminiferal community in the Bering Sea. The total genomic deoxyribonucleic acid (DNA) was extracted from 11 surface sediment samples collected from the Bering Sea. The foraminiferal small sub unit (SSU) rDNA was amplified with foraminiferal-specific primers. A total of 2,170,762 effective tags and 1046 operational taxonomic unit (OTUs) were obtained after next-generation sequencing, strict quality control, and data processing. The results showed that the station BR07 had the highest number of OTUs. The highest foraminiferal Margalef index and Shannon-Wiener index were obtained at BR06. Rotaliida accounted for the highest proportion, followed by Textulariida and Monothalamida, with the lowest proportion of Miliolida. From the principal component analysis (PCA), Leptohalysis scottii, Stainforthiidae_X sp., and Rectuvigerina phlegeri were found to be the more important species in the Bering Sea. Based on the redundancy analysis (RDA) and Spearman correlation analysis, we found that the grain size and water depth exhibited significant control on foraminiferal community. The foraminiferal reads were positively correlated with the grain size, whereas the Shannon-Wiener index was negatively correlated with it. The water depth was positively correlated with OTUs, Leptohalysis scottii, and Rectuvigerina phlegeri. The clustering analysis showed that Bering Sea stations cluster together with Yellow Sea stations of similar water depth. The water depth was a bigger factor for foraminiferal community than the geographical distance.