Composition and Patterns of Taxa Assemblages in the Western Channel Assessed by 18S Sequencing, Microscopy and Flow Cytometry

Abstract

Plankton monitoring by microscopy offers a long-term ecological perspective of plankton communities, but different detection approaches are uniquely biased. Genetic identification of marine plankton has become standard but is still not used in routine monitoring. This study assesses the value that genetic methods bring to microscopic and flow cytometry monitoring methods in the Western (English) Channel. An 18S high throughput sequencing (HTS) diversity survey of plankton taxa was performed on samples collected from an automated Water and Microplankton Sampler (WaMS) deployed on the Continuous Plankton Recorder platform (CPR) from 2011–2012. The 18S-HTS survey of WaMS samples detected contrasting but complementary taxa assemblages to that of microscopic surveys, mostly composed of smaller or naked or thin-walled plankton taxa, with most phytoplankton being under 10 µm but most taxa in the survey being mixotrophic or heterotrophic but picking up rare phytoplankton. In comparison with microscopic phytoplankton counts from the CPR survey and Western Channel Observatory station L4, only 8–12 taxonomic families were common to all three surveys, most of them dinoflagellates, with a bias towards larger diatoms and dinoflagellate taxa in microscopy surveys. Additional quantitative real-time PCR detection of two potentially harmful taxa, the pelagophyte, Aureococcus anophagefferens and four Pseudo-nitzschia from 2011–2013. This confirmed the elevated growth of A. anophagefferens in the Western Channel in the summer of 2011 and the early appearance of Pseudo-nitzschia delicatissima in that year. Individual species’ occurrence or abundance was different from their genera or other same-sized groups. Smaller phytoplankton measured by flow cytometry had distinct seasonality in the mid-Atlantic compared to coastal regions.

Single-cell trait diversity explains niche and fitness differences in aquatic microbial communities

“…Sequencing library preparation and DNA amplicon sequencing were performed by MR DNA (Molecular Research LP, Shallowater, TX) using a modified bTEFAP® library preparation protocol 73 and sequencing on an Illumina MiSeq platform with a minimum of 20,000 reads per sample and read lengths of 2×300 bp. The 16S sequencing library was prepared with Bact341F: 5’-CCTACGGGNGGCWGCAG-3’ and Bact785R:5’-GACTACHVGGGTATCTAATCC-3’ 74 , and the 18S sequencing library was prepared with euk516f:GGAGGGCAAGTCTGGT and euk1055r:CGGCCATGCACCACC 75 . A mock bacterial community was sequenced as a positive control (BEI Resources, Genomic DNA from Microbial Mock Community B, staggered, high Concentration, v5.2H, for Whole Genome Shotgun Sequencing, HM-277D).…”

“…-CCTACGGGNGGCWGCAG-3' and Bact785R:5'-GACTACHVGGGTATCTAATCC-3' 74 , and the 18S sequencing library was prepared with euk516f:GGAGGGCAAGTCTGGT and euk1055r:CGGCCATGCACCACC75 . A mock bacterial community was sequenced as a positive control (BEI Resources, Genomic DNA from Microbial Mock Community B, staggered, high Concentration, v5.2H, for Whole Genome Shotgun Sequencing, HM-277D).…”

Mapping Selected Emergent Marine Toxin-Producing Organisms Using Historical Samples with Two Methods (Biosensors and Real-Time PCR): A Comparison of Resolution

“…The 277 bp LSU rDNA product was purified and used directly as a standard in HRM-qRT-PCR assays. DNA copy number calculation was quantified from the standard as described by Stern [20], and a dilution series was prepared, ranging between 1 × 10 3 and 1 × 10 8 copies in 4 µL volume. DNA standards, genomic P. delicatissima DNA (positive control), were run alongside experimental CPR DNA samples in duplicate at 1:10 and 1:100 dilutions in HRM-qRT-PCR reactions.…”

A novel fluoro-electrochemical technique for classifying diverse marine nanophytoplankton

“…Where cytometry falls short is at being able to fully characterise ecologically relevant components of the nanophytoplankton fraction; only coccolithophores (detectable due to their unique light scattering) and cryptophytes (due to their phycoerythrin content) can be discriminated from other nanoeukaryotes (Tarran et al 2006;Tarran and Bruun 2015). Thus, in order to obtain a true representation of the species present in the nanophytoplankton fraction, previous studies have often complemented microscope taxonomy and cytometry analyses with genetics-based interpretations (Balzano et al 2012;Leblanc et al 2018;Piwosz 2019;Bolaños et al 2020;Stern et al 2023), which generally only provide a value for relative abundances.…”