Mitochondrial genome and polymorphic microsatellite markers from the abyssal sponge Plenaster craigi Lim & Wiklund, 2017: tools for understanding the impact of deep-sea mining

Gordon L J Paterson,Sergi Taboada,Helena Wiklund,Ana Riesgo,Adrian G Glover,Thomas G Dahlgren,Nathan J Kenny

doi:10.1007/s12526-017-0786-0

Abstract

The abyssal demosponge Plenaster craigi is endemic to the Clarion - Clipperton Zone (CCZ) in the NE Pacific, a region with abundant seafloor polymetallic nodules and of potential interest for mining. Plenaster craigi encrusts on these nodules and is an abundant component of the ecosystem. To assess the impact of mining operations, it is crucial to understand the genetics of this species, because its genetic diversity and connectivity across the area may be representative of other nodule-encrusting invertebrate epifauna. Here we describe and characterize 14 polymorphic microsatellite markers from this keystone species using Illumina MiSeq, tested for 75 individuals from three different areas across the CCZ, including an Area of Particular Environmental Interest (APEI-6) and two areas within the adjacent UK1 mining exploration area. The number of alleles per locus ranged from 3 to 30 (13.33 average alleles for all loci across areas). Observed and expected heterozygosity ranged from 0.909–0.048 and from 0.954–0.255, respectively. Several loci displayed significant deviation from the Hardy-Weinberg equilibrium, which appears to be common in other sponge studies. The microsatellite loci described here will be used to assess the genetic structure and connectivity on populations of the sponge across the CCZ, which will be invaluable for monitoring the impact of mining operations on its habitat. Also, we provide the annotated mitochondrial genome of P. craigi, compare its arrangement with other closely related species, and discuss the phylogenetic framework for the sponge after Maximum Likelihood and Bayesian Inference analyses using nucleotide and amino acid sequences data sets separately.

Highlights

The abyssal area between the Clarion - Clipperton Zones (CCZ) in the equatorial NE Pacific spans approximately 6 million km2, and encompasses a broad range of habitats including hills, seamounts, fracture zones, and extensive abyssal plains (Wedding et al 2013)
Due to the proven low variability of cytochrome c oxidase I (COI) across the majority of sponges studied so far (Erpenbeck et al 2006), most studies aiming to establish the molecular connectivity among sponge populations have developed microsatellite loci (e.g. Dailianis et al 2011; PérezPortela et al 2015; Riesgo et al 2016)
With the development of polymorphic microsatellites for P. craigi we provide a powerful tool to detect genetic connectivity at different scales

Summary

Introduction

The abyssal area between the Clarion - Clipperton Zones (CCZ) in the equatorial NE Pacific spans approximately 6 million km, and encompasses a broad range of habitats including hills, seamounts, fracture zones, and extensive abyssal plains (Wedding et al 2013). Mining may impact areas of the seafloor owing to direct mining disturbance (at scales of 300–600 km per year), but will disturb adjacent areas through redeposition from sediment plumes 10–100 km from the mining site (Rolinski et al 2001; Sharma et al 2001). These concerns led to the suggestion and establishment of a network of deepsea marine protected areas termed Areas of Particular Environmental Interest (APEIs) across the CCZ designed to safeguard the biodiversity and ecosystem functionality in this particular region (Wedding et al 2013). Rigorous evaluation of species’ ranges and their levels of population connectivity and turnover is needed

Methods

Results

Conclusion