A DNA mini‐barcode for marine macrophytes

Abstract

Marine macrophytes, especially macroalgae, form highly productive ecosystems, with a global net primary production of about 2 Pg C year −1 spread across 4 million km 2 in coastal areas (Duarte, 2017). Marine macrophytes export most of their net production to the global ocean and seafloor (Duarte & Cebrián, 1996;

Environmental DNA identifies marine macrophyte contributions to Blue Carbon sediments

“…Several taxa abundant in situ were not recovered in the eDNA pool. This was the case for seagrasses Thalassia hemprichii and Halophila decipiens, whose barcoding was unsuccessful with our primer (Ortega et al 2020), and for ubiquitous macroalgae that were not recovered at all (e.g., Turbinaria), or were limited to genus level despite a high species diversity in sampled locations (e.g., Laurencia spp., Caulerpa spp., and Halimeda spp.). Those missing species underline PCR bias and artifacts of using a universal primer, and could be overcome by including degenerated versions of the primer in the amplification (Kanagawa 2003;Fuller et al 2006).…”

“…Once in the lab, the five biological replicates were pooled together as a single sample in 5 mL tubes, and frozen at −80°C until eDNA extraction. All species of seagrass, mangrove, and macroalgae found in situ were collected, and a local DNA reference library was created as reported in Ortega et al (2020).…”

“…Intracellular and extracellular eDNA from the Red Sea coastal sediments and from the experiment were isolated following the method developed by Lever et al (2015). A step‐by‐step protocol of this extraction method can be found in Ortega et al (2020). eDNA was amplified in five PCR replicates of 10 μL reactions by adding 5 μL of QIAGEN Multiplex PCR Master Mix, 1 μL of 18S‐V7 forward and reverse primers (Euka02 from Guardiola et al (2015), F‐ TTTGTCTGSTTAATTSCG, R‐ CACAGACCTGTTATTGC), 1 μL of DNA template and 2 μL of PCR water.…”

“…Alternatively, metabarcoding of environmental DNA (eDNA) can identify organisms from environmental samples based on their unique DNA sequences (Hebert et al 2005), and can identify degraded marine macrophytes within sediment pools (Reef et al 2017; Ortega et al 2020). Since approximately 3% of cellular organic carbon (C org ) is DNA (Landenmark et al 2015), eDNA‐based methods also provide an approach to estimate contributions to blue carbon stocks (Ortega et al 2019).…”

Characteristics and Mutational Hotspots of Plastomes in Debregeasia (Urticaceae)

“…Theoretically, whole plastomes or nuclear genomes will provide the final solution for species identification. However, from both an economic and a practical perspective, a barcode or mini barcode is often sufficient, e.g., for Taxus (Liu et al, 2018) and macrophyte (Ortega et al, 2020) identification. In our study, the whole plastome can clearly distinguish all five Debregeasia species examined ( Figure 6A).…”