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Novel diversity within marine Mamiellophyceae (Chlorophyta) unveiled by metabarcoding.

ABSTRACT: Mamiellophyceae (unicellular green algae) are a key phytoplankton group in coastal waters. Although extensively studied over the last 20 years, the overall oceanic distribution of the major species/clades is still poorly known. To address this problem, we analyzed the 2014 Ocean Sampling Day (OSD) metabarcoding dataset providing sequences from the V4 hypervariable region of the 18S rRNA gene for 157 samples collected at 143 mostly coastal stations. Mamiellophyceae were found at nearly all OSD stations and represented 55% of the green microalgae (Chlorophyta) reads. We performed phylogenetic analyses of unique OSD metabarcodes (amplicon single variants, ASVs) and GenBank reference sequences from cultures and from the environment, focusing on the four most represented genera: Ostreococcus (45% of the Mamiellophyceae reads), Micromonas (34%), Bathycoccus (10%) and Mantoniella (8.7%). These analyses uncovered novel diversity within each genus except Bathycoccus. In Ostreococcus, a new clade (E) was the second most represented clade after Ostreococcus "lucimarinus". Micromonas could be separated into nine clades, exceeding the six species and candidate species already described. Finally, we found two new environmental clades within Mantoniella. Each Mamiellophyceae clade had a specific distribution in the OSD dataset suggesting that they are adapted to different ecological niches.

SUBMITTER: Tragin M

PROVIDER: S-EPMC6435750 | biostudies-literature | 2019 Mar

REPOSITORIES: biostudies-literature

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Novel diversity within marine Mamiellophyceae (Chlorophyta) unveiled by metabarcoding.

Tragin Margot M Vaulot Daniel D

Scientific reports 20190326 1

Mamiellophyceae (unicellular green algae) are a key phytoplankton group in coastal waters. Although extensively studied over the last 20 years, the overall oceanic distribution of the major species/clades is still poorly known. To address this problem, we analyzed the 2014 Ocean Sampling Day (OSD) metabarcoding dataset providing sequences from the V4 hypervariable region of the 18S rRNA gene for 157 samples collected at 143 mostly coastal stations. Mamiellophyceae were found at nearly all OSD st ...[more]

PMID: 30914730

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Project description:DNA metabarcoding is used to generate species composition data for entire communities. However, sequencing errors in high-throughput sequencing instruments are fairly common, usually requiring reads to be clustered into operational taxonomic units (OTUs), losing information on intraspecific diversity in the process. While Cytochrome c oxidase subunit I (COI) haplotype information is limited in resolving intraspecific diversity it is nevertheless often useful e.g. in a phylogeographic context, helping to formulate hypotheses on taxon distribution and dispersal.This study combines sequence denoising strategies, normally applied in microbial research, with additional abundance-based filtering to extract haplotype information from freshwater macroinvertebrate metabarcoding datasets. This novel approach was added to the R package "JAMP" and can be applied to COI amplicon datasets. We tested our haplotyping method by sequencing (i) a single-species mock community composed of 31 individuals with 15 different haplotypes spanning three orders of magnitude in biomass and (ii) 18 monitoring samples each amplified with four different primer sets and two PCR replicates.We detected all 15 haplotypes of the single specimens in the mock community with relaxed filtering and denoising settings. However, up to 480 additional unexpected haplotypes remained in both replicates. Rigorous filtering removes most unexpected haplotypes, but also can discard expected haplotypes mainly from the small specimens. In the monitoring samples, the different primer sets detected 177-200 OTUs, each containing an average of 2.40-3.30 haplotypes per OTU. The derived intraspecific diversity data showed population structures that were consistent between replicates and similar between primer pairs but resolution depended on the primer length. A closer look at abundant taxa in the dataset revealed various population genetic patterns, e.g. the stonefly Taeniopteryx nebulosa and the caddisfly Hydropsyche pellucidula showed a distinct north-south cline with respect to haplotype distribution, while the beetle Oulimnius tuberculatus and the isopod Asellus aquaticus displayed no clear population pattern but differed in genetic diversity.We developed a strategy to infer intraspecific genetic diversity from bulk invertebrate metabarcoding data. It needs to be stressed that at this point this metabarcoding-informed haplotyping is not capable of capturing the full diversity present in such samples, due to variation in specimen size, primer bias and loss of sequence variants with low abundance. Nevertheless, for a high number of species intraspecific diversity was recovered, identifying potentially isolated populations and taxa for further more detailed phylogeographic investigation. While we are currently lacking large-scale metabarcoding datasets to fully take advantage of our new approach, metabarcoding-informed haplotyping holds great promise for biomonitoring efforts that not only seek information about species diversity but also underlying genetic diversity.

Dataset Information

Novel diversity within marine Mamiellophyceae (Chlorophyta) unveiled by metabarcoding.

Publications

Novel diversity within marine Mamiellophyceae (Chlorophyta) unveiled by metabarcoding.

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