Potential PCR amplification bias in identifying complex ecological patterns: Higher species compositional homogeneity revealed in smaller-size coral reef zooplankton by metatranscriptomics.

PCR-based high-throughput sequencing has permitted comprehensive resolution analyses of zooplankton diversity dynamics. However, significant methodological issues still surround analyses of complex bulk community samples, not least as in prevailing PCR-based approaches. Marine drifting animals-zooplankton-play essential ecological roles in the pelagic ecosystem, transferring energy and elements to higher trophic levels, such as fishes, cetaceans and others. In the present study, we collected 48 size-fractionated zooplankton samples in the vicinity of a coral reef island with environmental gradients. To investigate the spatiotemporal dynamics of zooplankton diversity patterns and the effect of PCR amplification biases across these complex communities, we first took metatranscriptomics approach. Comprehensive computational analyses revealed a clear pattern of higher/lower homogeneity in smaller/larger zooplankton compositions across samples respectively. Our study thus suggests changes in the role of dispersal across the sizes. Next, we applied in silico PCR to the metatranscriptomics datasets, in order to estimate the extent of PCR amplification bias. Irrespective of stringency criteria, we observed clear separations of size fraction sample clusters in both metatranscriptomics and in silico datasets. In contrast, the pattern-smaller-fractioned communities had higher compositional homogeneity than larger ones-was observed in the metatranscriptomics data but not in the in silico datasets. To investigate this discrepancy further, we analysed the mismatches of widely used mitochondrial CO1 primers and identified priming site mismatches likely driving PCR-based biases. Our results suggest the use of metatranscriptomics or, although less ideal, redesigning the CO1 primers is necessary to circumvent these issues.

Diversity and Ecology of Lobophora Species Associated with Coral Reef Systems in the Western Gulf of Thailand, including the Description of Two New Species.

The brown macroalgal genus Lobophora plays important ecological roles in many marine ecosystems. This group has received much attention over the past decade, and a considerable number of new species have been identified globally. However, our knowledge of the genus diversity and ecology along south-east Asian coasts are still limited. Given the growing body of research that uses a combination of molecular and morphological data to identify cryptic species, this study investigates the diversity of Lobophora in the western Gulf of Thailand using morphological and molecular data, as well as their interactions with scleractinian corals. A total of 36 Lobophora specimens were collected from 15 sites in the western Gulf of Thailand and used for molecular and morphological analyses. One mitochondrial (cox3) and two chloroplast (psbA and rbcL) genes were amplified and sequenced for molecular phylogenetic analyses. Based primarily on phylogenetic evidence, two new species were formally described, L. chumphonensis sp. nov. and L. thailandensis sp. nov. Additionally, L. lamourouxii was newly recorded from Thailand. Two new lineages of Lobophora obscura were identified, L. obscura12 and L. obscura13. Among the Lobophora species identified, three were found in interaction with corals, the most notable of which was the massive coral Porites. Lobophora chumphonensis sp. nov. only interacted with Porites by growing on bare coral skeleton between Porites colonies. Furthermore, L. obscura13 was observed under the branching coral Pocillopora. Our findings revealed that Lobophora presented both effects and absence of effects on coral. A thorough understanding of Lobophora diversity and ecology is essential for ongoing and future research on coral-macroalgal ecological relationships.