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All issues Volume 59 (2023) Int. J. Lim., 59 (2023) 8 Full HTML
Open Access
Issue
Int. J. Lim.
Volume 59, 2023
Article Number 8
Number of page(s) 15
DOI https://doi.org/10.1051/limn/2023008
Published online 18 September 2023

© A. Canino et al., Published by EDP Sciences, 2023

Licence Creative CommonsThis is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

1 Introduction

Freshwater ecosystems are key to support human populations (Cardinale et al., 2012). Microalgae are the most abundant primary producers in these ecosystems and are used to monitor their ecological quality. For instance, phytoplankton and benthic microalgae are ecological indicators required in Europe (Water Framework Directive; European Commission, 2000) and the US (Clean Water Act; United States, 1972) to assess lake and river ecological quality.

Classically, when using microalgae to assess the ecological quality of lakes or rivers, monitoring methods require assessing the taxonomic composition of the community. For instance, phytoplankton community composition is analysed by microscopy using the Utermohl (1958) method, which is standardised at the European level (CEN, 2006). Floristic lists are established from lugol preserved samples that are set to sediment during several hours and then examined by a taxonomist expert under an inverted microscope. In addition, biomass is estimated for each species for a given sample volume. However, this method is a lengthy process based on an ever-decreasing number of taxonomic experts. Metabarcoding is an appealing approach to speed up the process, to avoid the bottleneck due to lack of experts, and to obtain more robust and accurate identifications as it was shown for some particular microalgae like diatoms (e.g. Vasselon et al., 2019).

Deciphering microalgal communities using eDNA metabarcoding is a challenge, due to their wide taxonomic diversity, ranging from prokaryotes to eukaryotes, in diverse phyla of the tree of life (Adl et al., 2019, Hug et al., 2016). Several studies have already tested the metabarcoding approach for phytoplankton, many of them using a combination of two different barcodes, one targeting the prokaryotic fraction, like the 16S rRNA gene, and the other targeting the eukaryotic fraction, like the 18S rRNA gene (e.g. Hug et al., 2016, Needham and Fuhrman, 2016, Djurhuus et al., 2017, Filker et al., 2019, Nowinski et al., 2019, Yarimizu et al., 2020, Sildever et al., 2022). These two genetic markers, 18S rRNA and 16S rRNA are well represented in reference libraries like Silva (Quast et al., 2013) and PR2 (Guillou et al., 2013). Using two different genetic markers (e.g. 16S rRNA and 18S rRNA) targeting different clades (cyanobacteria and photosynthetic eukaryotes) for a study whose objective is to analyse the composition of the entire algal community can be a major drawback, especially when one seeks to have a molecular method that could replace microscopy. Indeed, assembling the floristic lists from two different markers to get a single list is something that seems difficult to achieve, especially when it comes to respect the relative proportions of each taxon in the final floristic list. For this reason, in this study we looked for primers that amplify a single barcode that targets the entire phytoplankton community, whether prokaryotic or eukaryotic. The efficiency of a barcode relies on its ability to identify a taxon at species level (Hebert et al., 2003), which is linked to both its polymorphism and specificity. As microalgae represent a widely diverse, polyphyletic clade, the availability of primer pairs targeting the whole of it while being specific enough can be challenging. In this framework, the 18S rRNA gene, although it is widely used (e.g. Debroas et al., 2015, Capo et al., 2017, Keck et al., 2020), was not selected as it only targets the eukaryotic compartment, overlooking the prokaryotic taxa. Moreover, it has a low-resolution power for several algal clades, e.g. diatoms (Kermarrec et al., 2013), Dinoflagellates (Stern et al., 2012), generally detecting taxa at higher taxonomic levels than species level. On the other hand, 16S rRNA (Decelle et al., 2015) and 23S rRNA (Djemiel et al., 2020) genes are encoding for prokaryotic ribosomal components (small and large sub-unit, respectively) that are present in Cyanobacteria, as well as in the chloroplasts of eukaryotic photosynthetic organisms, thus potentially enabling the detection of both prokaryotic and eukaryotic phytoplankton species.

In this study, we aimed to investigate (1) if one single barcode could efficiently decipher the microalgal diversity and (2) which one would be the most appropriate for microalgal monitoring in freshwater environments. To achieve these aims, the assessment of the most suited barcodes and primer pairs was achieved with a four-step approach. (1) An in silico step was dedicated to the evaluation of different barcodes and primer pairs selected from the literature or designed for this study. This first step enabled a 1st selection based on primers and amplicon characteristics, as well as in silico amplification efficiency. (2) An in vitro test of the 1st selection of barcodes and primer pairs was carried out using a mock community composed of strains covering part of the phytoplankton diversity and introduced in equimolar proportions. This experiment enabled to check both the efficiency and specificity of the primers in lab conditions in order to make a 2nd selection. (3) The selected barcodes/primers were then tested again in vitro in order to assess their ability to assess differences of abundance, using more complex mock communities with a larger set of strains in variable DNA amplicon concentrations. (4) To complement this, the assignation power of the amplicons obtained from this 2nd selection of primers/barcodes was assessed in silico. The results of these different analyses will enable to provide advices for future use of DNA metabarcoding for phytoplankton in environmental conditions.

2 Materials and methods

2.1 Reference libraries

Two reference libraries were built for the 16S rRNA and 23S rRNA genes respectively (later simplified as 16S and 23S), collecting phytoplankton sequences from public reference libraries (Silva_138.1–; Quast et al., 2013; PhytoRef − del Campo et al., 2018; PR2–Guillou et al., 2013; μgreen-db − Djemiel et al., 2020). These reference libraries are available at the shiny application Phytool v2 (Canino et al., 2021) at the following link: https://github-carrtel.shinyapps.io/phytool_v2/.

For each barcode, a curation procedure was carried out, based on sequences similarity and taxonomic homogeneity (see details in Phytool v2, Canino et al., 2021). To enable comparisons through different barcodes (e.g. 16S vs 23S) or methods (e.g. molecular vs microscopy), Phytool v2 was also used to harmonize the taxonomy from the different public reference libraries.

2.2 Genes and primer pairs tested

Primer pairs from 16S and 23S genes were first selected regarding their ability to produce amplicons with a length that fits with the MiSeq (Illumina) technology (2*250 bp to 2*300 bp). Thus, in silico were conducted on (1) primer pairs gathered from the literature (Tab. 1), (2) new combinations of known primers and (3) newly designed primers considering phytoplankton species and clades that were sequenced since the publication of the primers given in Table 1 for 16S and 23S genes.

The methodology to design the new primers was carried out as follows for each genetic marker (16S, 23S): (1) a single sequence was kept from each species to avoid the over-representation of taxa abundant in reference libraries. (2) A random sampling without replacement was performed on all these sequences to produce multiple clusters of few sequences (e.g. 100 clusters of 10 sequences for 1000 initial sequences). (3) For each cluster, a multiple alignment was carried out with the msa package (Bodenhofer et al., 2015) using Muscle (Edgar, 2004) with default settings. (4) Conserved regions were checked and the most redundant were selected with BioPython (Cock et al., 2009). From these multiple alignments the variability of the different regions within the genes were evaluated with Shannon index based on nucleotide diversity calculated at each base position. Regions which appear to be the most redundant through the different clusters were kept as candidate regions for primers. Additionally, a special attention was given to the followings: primers length ranging from 18 to 23 base pairs; GC percentage between 40 and 60% to ensure efficient polymerisation; presence of GC in the 5 first and last nucleotides to ensure good fixation; low number of ambiguous bases; resulting amplicons size suited for MiSeq sequencing. (5) Then, candidate primers were tested for in silico PCR according to the methodology given in the following paragraph (“In silico tests”).

The selection of the primer pairs is listed in Table 1, and the corresponding oligonucleotides sequences are available in Supplementary data 1.

Table 1

Primer pairs tested in silico. Combinations not tested before this study are indicated with a star (*).

2.3 In silico tests

The in silico tests of the primers rely on the different approaches are detailed hereafter.

The main characteristics of the primers' pairs were first assessed using OligoAnalyzer (Integrated DNA Technologies OligoAnalyzer: http://scitools.idtdna.com/analyzer/Applications/OligoAnalyzer/).

The following criteria were evaluated with this tool for each pair: the mean amplicon size; the difference between forward and reverse primers mean melting temperature (ΔTm = |Tm_FORWARD − Tm_REVERSE|; the smaller the difference, the higher the PCR efficiency is supposed to be); the oligonucleotide structure of the primers and their predicted behaviour. Potential problematic structures could be: «Hairpin» (folding of the oligonucleotide on itself which is likely to occur around or above the melting temperature which would decrease its ability to fix to its target and thus inhibit the PCR amplification); «Homodimer» (one oligonucleotide is likely to hybridize with itself and produce a dimer, resulting in a reduction of the amplification efficiency); «Heterodimer» (the two oligonucleotides are likely to hybridize together).

The amplification efficiency was assessed in silico on sequences of microalgal species, allowing a maximum of 2 mismatches between the amplicon and its target sequence, following indications by Nossa et al. (2010) and Klindworth et al., (2013). This was done using pcr.seqs command from Mothur (Schloss et al., 2009). This enabled to assess the number of sequences that matched perfectly with the primer pair (no mismatches) and the number of sequences that are likely to be amplified by a standard PCR (maximum 2 mismatches allowed) out of the total number of reference sequences used from the corresponding reference library. In complement, an estimation of the resolution of each barcode was assessed by the proportion of the number of species with strictly different barcodes among the total number of species amplified in silico (maximum 2 mismatches allowed). The variability for undefined species (sp.) was not considered in this assessment.

The specificity of the primer pairs for microalgae at the expense of heterotrophic bacteria was assessed.

For 23S, an in silico PCR was conducted with candidate primer pairs using pcr.seqs (Mothur) on 183 976 sequences of 23S for heterotrophic bacteria downloaded from SILVA 138.1. For 16S, as the number of available sequences was much higher, we used a less time-consuming approach. The estimation was made using a ratio of the proportion of microalgae species amplified in silico using pcr.seqs command (Mothur, Schloss et al., 2009) out of the proportion of heterotrophic bacteria amplified in silico using RDP ProbeMatch tool (Cole et al., 2014, available at http://rdp.cme.msu.edu/probematch/search.jsp), the higher the score, the higher the specificity.

In complement, the in silico amplicons were re-assigned using their corresponding reference library to evaluate the number of correct re-assignments. This was investigated for each taxonomic rank using two assignation methods: the DADA2 function assignTaxonomy (with a boostrap value of 80) and the Mothur function classify.seqs (with the same boostrap value and 10,000 iterations).

Based on all these tests, we performed a 1st selection of the most efficient primer pairs.

2.4 In vitro experiments

2.4.1 Mock communities

The primer' pairs resulting from the in silico selection step, were compared in two in vitro experiments with mock communities composed of a mix of DNA from known pure algal cultures from the TCC culture collection (Rimet et al., 2018a). Two mock communities (Mock 1 and Mock 2) were designed to cover a large taxonomic diversity of phytoplankton, including species from Eubacteria, Plantae and Chromista kingdoms (Tab. 2)

Mock 1 was made as an equimolar mix of DNA from 10 different microalgal strains (Tab. 2). DNA extractions were performed on 2 mL of each TCC strain culture following the GenElute protocol in Kermarrec et al. (2013). DNA concentrations were quantified using a NanoDrop spectrophotometer (Thermo Scientific) and dilutions were made to prepare aliquots with a similar DNA concentration of 5 ng μL−1. Then PCRs were carried out in triplicates (Tab. 3).

Mock 2 was made from a larger taxonomic basis, including 18 microalgal strains (Tab. 2) at various DNA concentrations to mimic environmental conditions and to evaluate how these variations can be assessed by the different primer pairs. To reduce bias that could raise from the TCC non-axenic strains (e.g. potential presence of DNA from non-target microorganisms, as associated bacteria), Mock 2 was made as a mixture of amplicons from each of the 18 strains. Moreover, in anticipation of later routine implementation, an automated DNA extraction method was compared to GenElute DNA extraction used for Mock 1 (Kermarrec et al., 2013). This automated DNA extraction was performed using the MagnetaPure 32 automated system (Dutscher) and the NucleoMag Microbiome extraction kit (Macherey-Nagel) following the manufacturer's instructions. DNA extract from each culture was then amplified by PCR, 2 μL of the amplification product was controlled on agarose gel (1%), and the remaining volume of amplicon (23 μL) was purified using Illustra GFX PCR DNA kit (Cytiva). DNA concentrations of the purified amplicons were measured with Qubit 4 Fluorometer (Invitrogen) in order to build three types of mock communities with controlled amplicon concentrations (Supplementary data 2). Mock 2a was an «equimolar» mix (20 ng) of the DNA amplicon from each species. Mock 2b was a linear «gradient» mix with DNA quantities ranging from 5 to 50 ng of DNA amplicon. Mock 2c was an «exponential» mix with two highly-represented species (50 ng), 8 low-concentration species (1 ng) and 8 species mimicking rare ones (0.1 ng). Finally, with two DNA extraction methods, two primer pairs and three types of mock, 12 mock samples were prepared for Mock 2.

Table 2

Microalgal strains used to create mock communities Mock 1 and Mock 2.

Table 3

PCR program used to amplify the different barcodes.

2.4.2 First in vitro metabarcoding experiment

This in vitro experiment was conducted on the primer pairs selected from the in silico test. Their ability to detect species along a wide taxonomic diversity and their amplification efficiency were tested performing metabarcoding on Mock 1. First, the selected primer pairs were used to amplify Mock 1, second, amplicons were sequenced, and then, the obtained community composition was compared to the expected composition of Mock 1. To that aim, Illumina libraries were prepared in a dual-step PCR approach. Briefly, forward and reverse primers were tailed with the 5'-TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG-3' and the 5'-GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG-3' overhanging adapters to proceed to the first PCR step (PCR1) where Mock 1 was amplified in triplicates in a final volume of 25 μL using 5 μL of each forward and reverse tailed primers (1 μM), 12.5 μL of 2× KAPA HiFi HotStart Ready Mix (Roche), and 2.5 μL of DNA template of Mock 1 (5 ng μL⁻1). The PCR program is given in Table 3. A common and optimal melting temperature of 58 °C was selected for all primer pairs.

Three replicates of PCR were carried out and sequenced separately. PCR products were then checked on an agarose gel and sent to the sequencing platform (PGTB, France) using sealed plates (Thermo Scientific sealed with PCR Seal 4TITUDE). Since all amplicons from the different primer pairs are close in length (see Tab. 1), not exceeding 50 bp differences, they were all gathered on the same sequencing run. The PGTB platform performed a second PCR (PCR2) amplification using the purified PCR1 amplicons as template and the Illumina-tailed primers to add dual-index specific to the samples. The final pool corresponding to an equimolar mix of all the PCR2 dual-indexed amplicons was sequenced using a NanoMiseq (Illumina) run with kit v2 (2*250 bp).

2.4.3 Second in vitro metabarcoding experiment

This experiment was conducted on the primer pairs selected from the 1st in vitro metabarcoding experiment. Their ability to detect species among a wider and different taxonomic diversity, a higher richness, even when species proportions are unequal, and their amplification efficiency were tested using the different samples of Mock 2. Following the same dual-step PCR approach as in the first experiment, the primer pairs were used to amplified Mock 2a, 2b and 2c. In that experiment, the final pool was sequenced at the PGTB platform using a MiSeq (Illumina) with kit v3 (2*250 bp) in order to get a higher sequencing depth than the 1st experiment to better unravel rare species.

2.4.4 Bioinformatic analyses

Primers were checked and removed from demultiplexed FASTQ reads using Cutadapt v3.5 (Martin, 2011). Only reads with no error in primer sequences were kept (max-n 0). Next steps for the read quality filtering, merging and determination of Amplicon Sequence Variants (ASVs) were done using the DADA2 package v1.20 (Callahan et al., 2016) on R v4.1 (R Core Team, 2018). Briefly, reads were filtered using the function filterAndTrim with parameters set as default (i.e. maxEE = c(2,2), truncQ = 2, maxN = 0) and by only keeping the first 220 and 200 bases for the forward and reverse sequences respectively, due to their expected lower quality at the end of the read (Schirmer et al., 2015). Reads were then merged with default parameters of mergePairs function, and chimera were detected de novo and removed using the function removeBimeraDenovo with the consensus method. Sequences were then size-filtered by keeping sequences with a size comprised between 245 and 270 bp, to avoid aspecific ASVs. Taxonomic assignment of each ASV was done with the RDP (Ribosomal Database Project) naive Bayesian classifier (Wang et al., 2007) implemented in DADA2, using Phytool v2 database (Canino et al., 2021) as a reference. In parallel, a blast search of each ASV sequence was done on the same database as well as against all NCBI nucleotide database using blast 2.13 (Altschul et al., 2009). The combination of these three taxonomic assignations permitted an efficient recovery of almost all species that compose the Mock 2 community.

Bioinformatic pipelines are available at https://github.com/Github-Carrtel/2023_Canino_MBMG

2.4.5 Taxonomic assignation test of in silico amplicons

To assess the efficiency of the barcodes amplified by the selected primer pairs, taxonomic assignation was processed for the amplicons obtained in silico. To this end, 16S sequences were downloaded from the Phytool v2 reference library and cut in order to keep only the short portions corresponding to the barcodes amplified by the primers (in silico amplicons). These in silico amplicons were then reassigned to the Phytool v2 reference library using DADA2 (command assignTaxonomy, minBoot = 75) and Mothur (command classify.seqs, same bootstrap value 75 and 10,000 iterations).

3 Results

3.1 In silico evaluation of the primer pairs

Primer pairs in silico evaluations are given in Table 4. The 16S reference library used for this step gathered 8479 sequences, representing 1 675 species, and the 23S reference library gathered 1995 sequences, representing 913 species. For both 16S and 23S, these sequences covered all microalgal phyla (Bacillariophyta, Charophyta, Chlorophyta, Chromista, Cryptophyta, Cyanobacteria, Glaucophyta, Haptophyta, Miozoa, Ochrophyta, Prasinodermatophyta, Rhodophyta).

Based on these results, a primer selection was carried out. For 16S, all tested primers presented high resolution and were able to amplify a high number of targeted taxa according to in silico PCR results. The primer pair CYA359F/CYA781Rd (targeting v3-v4 region) was selected based on its low ΔTm, high specificity (43.64) for phytoplankton and high proportion of amplified targets. Despite its low specificity (4.4), a second primer pair (ECLA16S_F1/ECLA16S_R1) was selected for 16S, as it targets a different variable region (v5-v6) and presented good characteristics (low ΔTm, no structure warning and a higher number of amplified targets). For 23S, all primer pairs showed satisfactory results in the in silico investigations among which three pairs (p23SrV_f1/p23SrV_r1, A23SrV_F1/A23SrV_R1 and A23SrV_F2/A23SrV_R2) showed comparable results in terms of amplification efficiency and resolution power. The primer pair p23SrV_f1/p23SrV_r1 was selected as it showed a higher specificity to phytoplankton organisms and had already been widely used in former environmental studies. In addition, we selected ECLA23S_F1/ECLA23S_R1 and ECLA23S_F2/ECLA23S_R2 due to their high number of perfect matches with target sequences (in silico PCR output of 1727 and 1672 respectively), good specificity toward microalgae organisms, combined to high resolution. At the end, two primer pairs for 16S and three for 23S were kept for further in vitro lab test.

In order to avoid amplification issues in PCR1 due to the addition of adapters to the primers, as required by the sequencing facility (for them to add Illumina adapters in a PCR2 step), complementary in silico investigations were performed prior to the in vitro evaluation steps. Checking the behaviour of the five selected pairs to which the adapters were added, no major issue was observed (Tab. 5), except some heterodimer structures which were more likely to occur for some pairs. However, since homodimers which may reduce amplification efficiency were not suspected to occur, all five pairs were kept for following in vitro tests.

Table 4

Results of in silico tests for the 16S and 23S primers. ΔTm: melting temperature difference between forward and reverse. Oligonucleotide structure warnings: warnings obtained with OligoAnalyzer. In silico PCR output: number of sequences that perfectly match with primers (in brackets) followed by the number of sequences likely to be amplified out of the total number of reference sequences. Estimated resolution: percentage of species with strictly different barcodes (in brackets are given the exact numbers of species with different barcodes out of the total number of species). Estimated specificity: for 16S it is the proportion of phytoplankton species out of the proportion of heterotrophic bacteria amplified in silico; for 23S it is given as the result of in silico PCR done on heterotrophic bacteria sequences (i.e. « in silico PCR output »).

Table 5

Results of in silico tests for the 16S and 23S primers including adapters from the sequencing platform: ΔTm is the melting temperature difference between forward and reverse; Oligonucleotide structure warnings.

3.2 In vitro tests results

3.2.1 In vitro experiment with Mock 1

Table 6 shows the detection results of the five primer pairs for each of the 10 microalgal strains in Mock 1. In some cases, the taxonomic assignation of ASV with DADA2 matched correctly with the target species, while in others it did not. In such cases, the taxonomic assignation was completed manually by recognizing the highest taxonomical rank at which the target species belongs based on DADA2 and Blast results (Tab. 6). Finally, all control-species could be detected with the three 23S primer pairs, while 3 species remained undetected with the 16S primer pairs.

Complementary, an overview of the percentage of ASV and reads assigned to control-species in Mock 1 for each primer pair is presented in Figures 1a and 1b. These results assess the primers specificity for microalgae. The CYA359F/CYA781Rd pair has a very good specificity to microalgae since no ASV were matching other organism but microalgae. This was not the case for ECLA16S_F1/ ECLA16S_R1 which had a low specificity to microalgae since only 27% of the reads, corresponding to 23% of the ASV, matched to microalgae. Good efficiency was observed for 23S, with 75% of the ASV assigned to target species for ECLA23S_F1/ECLA23S_R1, and slightly less for ECLA23S_F2/ECLA23S_R2 and p23SrV_f1/p23SrV_r1 (52%). The specificities were high when considering the number of reads: 96% for ECLA23S_F1/ECLA23S_R1 and ECLA23S_F2/ECLA23S_R2, and 93% for p23SrV_f1/p23SrV_r1. The non-target organisms which were detected with 16S and 23S primer pairs were heterotrophic bacteria (e.g. alphaproteobacteria, betaproteobacteria, uncultured bacteria, Pseudomonadales).

Based on these results, one primer pair was selected for each barcode for further evaluation. For 16S, CYA359F/CYA781Rd outperformed the specificity and efficiency of the other tested pair. For 23S, all three primer pairs showed quite similar results in this first in vitro test. However, ECLA23S_F1/ECLA23S_R1 was selected based on its slightly better in silico performance, with 1727 sequences that perfectly match with primers (Tab. 3).

Table 6

Detection of the 10 different control-species in Mock 1 with 16S and 23S primers. x: ASV assigned to the target species with DADA2; *: ASV manually assigned to the target species using Blast, nd: not detected.

thumbnail Fig. 1

Percentage of ASV (a) and reads (b) assigned to control-species in Mock 1. Grey bars give the average percentage of ASV (or reads) with the number of ASV (or reads) written inside. Black dots give the percentage of ASV (or reads) assigned to control-species for the three replicates taken separately.

3.2.2 in vitro experiment with Mock 2

The metabarcoding results for the two selected primer pairs on Mock 2 communities (2a: equimolar; 2b: gradient; and 2c: exponential) are presented in Figure 2.

Among the 18 control-species of the Mock 2a sample (Fig. 2), all species were detected with 23S while the Chlorophyceae Haematococcus lacustris could not be detected with 16S. Although some deviation from the expected proportion can be observed for 23S (Cosmarium regnellii and Planktothrix rubescens with GenElute DNA extraction; Pandorina morum with the Automate DNA extraction), the equimolar proportion is well represented by read numbers. For 16S, proportions were more variable, with an often-higher number of reads when DNA was extracted with the automate.

When considering Mock 2b (gradient concentration, Fig. 2), with DNA Automate extraction, the correlation between DNA concentrations and the number of reads obtained for control-species was higher for the 23S primer pair (R2 = 0.88) than for the 16S one (R2 = 0.73). With the GenElute extraction, the tendency was reversed (R2 = 0.61 for 23S; R2 = 0.77 for 16S). However, all correlations were high and significant.

When considering Mock 2c (Fig. 2) all species could be detected with 23S primer pairs, whatever their initial DNA concentration, and the exponential proportions were well represented by read numbers. For 16S primer pairs, in addition to H. lacustris, two species present at the lowest DNA concentration (0.1 μg L−1) could not be detected (Mougeotia sp. and Zygnema sp.). The two species at the highest concentration (50 μg L−1) were represented by 84.3% of the reads for 23S and 93.6% for 16S, while their DNA was expected to represent 91.2% of the DNA mix. The nine species at the medium concentration (1 μg L−1) were represented by 13.0% of the reads for 23S and 5.6% for 16S, while their DNA was expected to represent 8.2% of the DNA mix.

thumbnail Fig. 2

Metabarcoding results for the 16S primer pair CYA359F/CYA781Rd (left) and for the 23S primer pair ECLA23S_F1/ECLA23S_R1 (right) on Mock 2a, 2b, and 2c for DNA extracted with automate (dark grey) and with GenElute (light grey). Mock 2a: number of reads obtained per control-species. Mock 2b: number of reads obtained per amplicon DNA initial concentration. Mock 2c: box-plot of the number of reads obtained per amplicon DNA initial concentration.

3.2.3 Resolutive power of in silico amplicons

Results of the taxonomic assignation of in silico amplicons are given in Table 7 for the CYA359F/CYA781Rd and ECLA23S_F1/ECLA23S_R1 primer pairs on 16S and 23S reference libraries, respectively. Whatever the command used for taxonomic assignation (i.e. assignTaxonomy in DADA2 and classify.seqs in Mothur), results were rather similar. The percentages of amplicons correctly assigned from Kingdom to Family levels were comparable for both primer pairs. However, at lower taxonomic levels (Genus and Species levels), assigned percentages were higher for the 23S primer pair than for the 16S one.

Table 7

Percentages of in silico amplicons correctly assigned with Mothur and DADA2 from Kingdom to species levels: for CYA359F/CYA781Rd primer pair with the 16S reference library; for ECLA23S_F1/ECLA23S_R1 primer pair with the 23S reference library.

4 Discussion

This study followed a four-step approach with successive steps of primer pair evaluation done either in silico or in vitro using, respectively curated reference libraries and mock communities. This approach allowed us to converge to a small subset of primer pairs with good efficiency. The first in silico evaluation allowed to successfully select a subset of five primer pairs that well amplified mock samples in following in vitro steps. The first in vitro step, enabled to retain only two primer pairs being efficient to amplify most of the species in the simplified community of Mock 1, before focusing on the Mock 2 samples. Those more complex Mock 2 samples allowed to test the 2 primer pairs on a larger taxonomical diversity and to evaluate their ability to reveal relative abundances. Finally, the last in silico step aimed at evaluating de taxonomic resolution of the two primer pairs on their respective reference libraries, thus exploring a larger microalgal diversity than in the mock communities. This four-step approach appears to be time- and cost-efficient by minimizing wetlab and sequencing efforts on five and two pairs (out of 13), at steps 2 (Mock 1) and 3 (Mock 2) respectively.

4.1 Advantages and disadvantages of the tested barcodes and primer pairs

4.1.1 Amplification efficiency and specificity to phytoplankton

The five primer pairs selected from the in silico tests all showed good amplification potential and high specificities to eukaryotic and prokaryotic microalgae (cyanobacteria). However, one of them, the ECLA16S_F1/ECLA16S_R1 pair, showed a lower specificity in Mock 1. This mock community was made prior PCR amplification, as a pool of DNA extracted from strains that were non-axenic cultures and may thus include DNA from both target and non-target taxa. The lower specificity of this pair to eubacteria revealed the presence of heterotrophic bacteria (e.g. Proteobacteria, Pseudomonadales) associated to the algal strains and which DNA was thus co-extracted. In parallel, this revealed the good specificity of the four other pairs tested on Mock 1. For the two finally selected primer pairs (CYA359F/CYA781Rd, ECLA23S_F1/ECLA23S_R1 respectively for 16S and 23S), the proportion of sequences that could be amplified in silico was very high (84% and 90% for 16S and 23S, respectively). The good amplification efficiency evaluated in silico was confirmed in vitro with 70% and 100% of the 10 species of Mock 1 detected by 16S and 23S pairs, respectively. This trend was similar for Mock 2, with 83% and 100% of the 18 species, for 16S and 23S pairs respectively. Although both selected pairs (CYA359F/CYA781R, ECLA23S_F1/ECLA23S_R1) showed good efficiency to amplify phytoplankton taxa, it is notable that the 23S barcode on the v5 region performed systematically better than the 16S one, detecting more species from the mocks. Finally, we warn the future users of these primers who would like to work specifically on microalgae, that the specificity of these primers was tested against heterotrophic bacteria, a group that can be dominant in plankton or aquatic biofilm samples. If samples would contain significant biomass of higher plant tissues (Pinus, Solanum ...) alongside algae, then these higher plant tissues would be co-amplified with algae (further tests on Primer-Blast tool in NCBI for ECLA23S_F1/ECLA23S_R1 showed good affinity to higher plants alongside microalgae).

4.1.2 Taxonomic resolution

From the last in silico step, the 23S pair clearly appears to be the most resolutive with ∼90% of the in silico amplicons obtained from the reference library that could be assigned to genus level, and ∼80% to species level. The 16S pair performed less well (77% and 55% respectively for genus and species level, respectively).

4.1.3 Capacity to assess relative abundances

For Mock 1, it was not possible to assess the ability of tested pairs to assess the relative abundance of the target taxa. Indeed, although it was made of equimolar DNA quantities, the DNA quantification was not a good proxy since DNA came from both the target strains and non-target associated microorganisms (e.g. heterotrophic bacteria) present in the cultures. From the in vitro test on Mock 2a (equimolar) and Mock 2b (gradient) it was possible to evaluate the potential of the barcodes and pairs for assessing taxa relative abundances. When DNA from all species were present in equimolar proportions (Mock 2a), the number of reads obtained was similar for all species with the 23S pair, while it was more variable from one species to the other with 16S. When the proportion between taxa was unequal (Mock 2b), the DNA quantities introduced in the mock and the number of reads were significantly correlated. Relative abundances were better assessed with the 23S pair than with the 16S one. Finally, Mock 2c (exponential) enabled to assess the ability for detecting low-abundant taxa (e.g. taxa at a DNA concentration 500 times lower than others). For 16S, three out of the 7 less abundant taxa could not be detected. The 23S pair performed better as all taxa were detected. As in environmental communities, taxa are often present in unequal proportions, the 23S barcode appears to be more promising to decipher microalgae (eukaryotic algae and cyanobacteria) assemblages. Moreover, when the ultimate goal of metabarcoding is ecological quality assessment, presence-absence data are often not sufficient (e.g. IPLAC index − Laplace-Treyture et Feret, 2016). Thus, the 23S pair shows good potential to both identify phytoplankton taxa and assess their relative abundances.

4.1.4 Completeness of reference libraries

The reference libraries used in this study have contrasted completeness depending on the barcode with 8 479 sequences for 16S and about four-time less for 23S (1 995 sequences). Although the 16S reference library had more sequences, most of them (nearly 3/4) are Cyanobacteria, while eukaryotic microalgae are poorly referenced. For 23S, more eukaryotic species (nearly 1/3) were represented proportionally. Reference libraries are clearly a pitfall of these two gene makers (16S, 23S), compared to others like 18S. The operationalisation of the metabarcoding approach for biomonitoring phytoplankton communities will not be possible without completing reference libraries as shown for other aquatic organisms (Weigand et al., 2019).

4.2 A single barcode to decipher phytoplankton communities?

This study aimed at finding a single barcode to decipher microalgal assemblages in their entirety, especially to get simultaneously eubacteria and eukaryotic microalgae. Although the eukaryotic primers of 18S are largely used and advised for phytoplankton surveys (Jerney et al., 2022), they do not allow cyanobacteria detection (e.g. Wang et al., 2022), which requires the use of a complementary barcode (e.g. 16S). A single barcode ideally fitted to phytoplankton biomonitoring must meet several criteria: (1) not exclude any microalgal phyla or families, (2) be specific enough in excluding as much as possible non-microalgal diversity, (3) offer a high taxonomic resolution, (4) provide accurate taxa proportions in final inventories.

In our study, we wanted to ensure that taxa from most of the phyla could be amplified. All tested pairs for 16S and 23S did amplify both prokaryotic and eukaryotic algae. However, some taxa could not be detected by 16S although they were present in the tested mock communities. For 16S, all cyanobacteria could be well amplified, while two Chlorophyceae and one Eustigmatophyceae could not. 23S appears as the most efficient to amplify the whole microalgal diversity, without excluding any of the tested families. Moreover, 23S primers were specific enough to microalgae taxa, as only a limited number of reads of non-target taxa were obtained (4% of reads matched to heterotrophic bacteria). Obtaining a high taxonomic resolution is also important in order to get a good ecological quality assessment. Indeed, bioassessment metrics generally require identification of taxa at species (or genus) level as it is the case for several phytoplankton biomonitoring indices (e.g. IPLAC in Laplace-Treyture & Feret 2016, Brettum Index in Dokulil et al., 2005). Although the 23S reference library is far from complete, it seems to provide a high enough taxonomic resolution from phyla to species level. The in silico evaluation toward the reference library is encouraging and bodes well for good resolution in environmental samples. Finally, mock communities with gradient and exponential proportions have shown the promising ability of 16S and, even better, of 23S to assess relative abundances and to detect rare taxa. However, as Mock 2 samples were made from DNA of purified amplicons, this still needs to be confirmed on DNA from environmental samples.

All these results point to 23S v5 having the potential to be a good gene marker to decipher microalgal and cyanobacterial diversity. Several primer pairs were tested in silico and in vitro for amplifying this v5 region. After the first selection step, three pairs amplifying this region were explored, two of them being designed in this study and the third one proposed by Sherwood and Presting (2007). With Mock 1 community, all three presented good potential which was not surprising as forward and reverse primers were all designed from the same gene region, with only little nucleotide changes from one to the other. Indeed, this region was also the one explored by Yoon et al. (2016) and Kang et al. (2018). Only slight advantages led us to select the ECLA23S_F1/ECLA23S_R1 pair, which performed also well with the more complex and uneven Mock 2 community samples.

5 Conclusion and perspectives

DNA metabarcoding is a powerful tool that can enhance freshwater ecosystem monitoring programs (Pawlowski et al., 2018). Here, we focused on the first of the five important steps managers and researchers should consider when developing eDNA monitoring program (as suggested by Gold et al., 2022): “select genes and primers to target taxa”. After the in silico and in vitro tests carried out in this study, evaluating the performance of the selected 23S primer pair on environmental samples is now mandatory. Even if several environmental samples were studied with success (Craine et al., 2018; Brown et al., 2022) using Sherwood & Presting (2007) primers, which are close to the 23S selected pair (ECLA23S_F1/ECLA23S_R1), it will be necessary to confirm our in silico and in vitro results on environmental samples from lake ecosystems.

Actually, if this 23S primer pair is to be part of the biomonitoring toolbox for lake ecosystems, it has to prove its potential to decipher a large phytoplankton biodiversity at a precise taxonomic level and to provide acceptable relative abundances of taxa, in order to accurately feed the biomonitoring metrics. This potential could be evaluated with samples originating from lakes in a large range of climatic, geological and trophic conditions. Challenging the 23S metabarcoding approach will still require to get in parallel microscopy data and 16S metabarcoding data. This will ensure that no species are missed and that no phyla or families are under or over-represented in the taxonomic inventories as shown in the study of Brown et al. (2022) where diatoms were over-represented in 23S metabarcoding relative to microscopy. The comparison of all three approaches (microscopy, 16S, 23S) in environmental samples for diversity assessment, taxonomic identification and quantification, will strengthen conclusions.

Producing reliable taxonomic inventories with metabarcoding is also closely linked to the quality and completion of the reference library (Rimet et al., 2021). Being far from complete at the moment (Canino et al., 2021), the 23S reference library will first require a gap analysis (e.g. Weigand et al., 2019) to identify completion priorities. Then, 23S sequencing should be processed first on strains that may already be available in culture collections; second, with a prior strain isolation step that is unavoidable for microorganisms. In complement, Rimet et al. (2018b) suggested a more operational way using barcode sequences from metabarcoding data of natural samples as a source of primary taxonomic information for reference libraries. Thus, sampling lakes where gap-taxa are known to be present in high relative abundance would be a way to both ascertain the 23S efficiency, and complete its reference library. Finally, a fully operational and standardised reference database should follow the recommendations by Rimet et al. (2021) when building barcode reference libraries for aquatic life.

Providing tools for lake biomonitoring requires them to be well-fitted to environmental stakeholder needs in terms of production rate and ease of use (Blancher et al., 2022). Here we tested an automated DNA extraction protocol to start assessing the potential for higher throughput sample processing. Although promising, these first results show a need to improve the protocol. To be operational for professionals, the approach tested here will also require going toward standardisation. Recently, handbooks for DNA-based methods in aquatic monitoring have been released (e.g. Bruce et al., 2021; Jerney et al., 2022); inter-laboratory comparisons have been conducted (Baričević et al., 2022; Vasselon et al., 2021). Going to international standards will require next steps as done for example at the European standardisation level (CEN) for diatoms metabarcoding (e.g. phytobenthos sampling step: CEN 2018a, b).

Acknowledgements

This study was carried out in the framework of the project PhytoDOM, funded by OFB and INRAE, and developed at the Pôle R&D ECLA (ECosystèmes LAcustres).

Supplementary Material

Supplementary data 1: Sequences of the primers tested for 16S.

Supplementary data 2: DNA amplicon concentrations introduced in the three type of communities of Mock 2 (in ng/L of DNA). EQ: equimolar, GR: linear gradient, EX: exponential gradient.

Access here

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Cite this article as: Canino A, Lemonnier C, Alric B, Bouchez A, Domaizon I, Laplace-Treyture C, Rimet F 2023. Which barcode to decipher freshwater microalgal assemblages? Tests on mock communities. Int. J. Lim. 59: 8:

All Tables

Table 1

Primer pairs tested in silico. Combinations not tested before this study are indicated with a star (*).

In the text
Table 2

Microalgal strains used to create mock communities Mock 1 and Mock 2.

In the text
Table 3

PCR program used to amplify the different barcodes.

In the text
Table 4

Results of in silico tests for the 16S and 23S primers. ΔTm: melting temperature difference between forward and reverse. Oligonucleotide structure warnings: warnings obtained with OligoAnalyzer. In silico PCR output: number of sequences that perfectly match with primers (in brackets) followed by the number of sequences likely to be amplified out of the total number of reference sequences. Estimated resolution: percentage of species with strictly different barcodes (in brackets are given the exact numbers of species with different barcodes out of the total number of species). Estimated specificity: for 16S it is the proportion of phytoplankton species out of the proportion of heterotrophic bacteria amplified in silico; for 23S it is given as the result of in silico PCR done on heterotrophic bacteria sequences (i.e. « in silico PCR output »).

In the text
Table 5

Results of in silico tests for the 16S and 23S primers including adapters from the sequencing platform: ΔTm is the melting temperature difference between forward and reverse; Oligonucleotide structure warnings.

In the text
Table 6

Detection of the 10 different control-species in Mock 1 with 16S and 23S primers. x: ASV assigned to the target species with DADA2; *: ASV manually assigned to the target species using Blast, nd: not detected.

In the text
Table 7

Percentages of in silico amplicons correctly assigned with Mothur and DADA2 from Kingdom to species levels: for CYA359F/CYA781Rd primer pair with the 16S reference library; for ECLA23S_F1/ECLA23S_R1 primer pair with the 23S reference library.

In the text

All Figures

thumbnail Fig. 1

Percentage of ASV (a) and reads (b) assigned to control-species in Mock 1. Grey bars give the average percentage of ASV (or reads) with the number of ASV (or reads) written inside. Black dots give the percentage of ASV (or reads) assigned to control-species for the three replicates taken separately.
In the text
thumbnail Fig. 2

Metabarcoding results for the 16S primer pair CYA359F/CYA781Rd (left) and for the 23S primer pair ECLA23S_F1/ECLA23S_R1 (right) on Mock 2a, 2b, and 2c for DNA extracted with automate (dark grey) and with GenElute (light grey). Mock 2a: number of reads obtained per control-species. Mock 2b: number of reads obtained per amplicon DNA initial concentration. Mock 2c: box-plot of the number of reads obtained per amplicon DNA initial concentration.
In the text

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