Consistency of Targeted Metatranscriptomics and Morphological Characterization of Phytoplankton Communities

Vuorio, Kristiina; Mäki, Anita; Salmi, Pauliina; Aalto, Sanni L.; Tiirola, Marja

doi:10.3389/fmicb.2020.00096

Cited by 11 publications

(2 citation statements)

References 54 publications

(57 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Their relative read abundance was therefore not directly proportional to each other. Nevertheless, general trends such as presence and absence, as well as high and low abundance are usually representative for the overall community composition [41,42]. In the future, predator-prey dynamics between U. cf.…”

Section: Discussionmentioning

confidence: 99%

Ciliate grazing on the bloom-forming microalga Gonyostomum semen

Bergman,

Lindström,

Sassenhagen

2023

Preprint

View full text Add to dashboard Cite

The freshwater raphidophyte Gonyostomum semen forms extensive summer blooms in northern European humic lakes. The development of these blooms might be facilitated by a lack of natural top-down control, as few zooplankton species are able to prey on these large algal cells (up to 100µm) that expel trichocysts upon physical stress. In this study, we describe a small ciliate species (< 17µm) that preys on G. semen by damaging the cell membrane until cytoplasm and organelles spill out. Sequencing of clonal cultures of the ciliate tentatively identified it as the prostomatid species Urotricha pseudofurcata. Grazing experiments illustrated that feeding by U. cf. pseudofurcata can significantly reduce cell concentrations of the microalga. However, differences in cell size and growth rate between two investigated ciliate strains resulted in noticeably different grazing pressure. Environmental sequencing data from five different lakes supported potential interactions between the two species. Urotricha cf. pseudofurcata might, thus, play an important role in aquatic ecosystems that are regularly dominated by G. semen, reducing the abundance of this bloom-forming microalga and enabling transfer of organic carbon to higher trophic levels.

show abstract

Section: Discussionmentioning

confidence: 99%

Ciliate grazing on the bloom-forming microalga Gonyostomum semen

Bergman,

Lindström,

Sassenhagen

2023

Preprint

View full text Add to dashboard Cite

show abstract

“…The large copy number variation of ribosomal genes and the absence of universal primers for simultaneous amplification of cyanobacterial and eukaryotic phytoplankton genes hinder the application of DNA-based molecular methods. We applied a directional randomprimed high throughput sequencing (HTS) approach (Mäki and Tiirola 2018) to analyse 16S and 18S rRNA community structures of 83 boreal lakes in Finland, Northern Europe. ‡ § § | § ‡ With the method it was possible to simultaneously amplify all groups of aquatic microorganisms in addition to cyanobacteria and eukaryotic phytoplankton.…”

mentioning

confidence: 99%

Consistency between high throughput sequencing and microscopy-based morphological characterization of phytoplankton communities

Vuorio¹,

Mäki²,

Salmi³

et al. 2021

ACA

Self Cite

View full text Add to dashboard Cite

Thus far, the phytoplankton community composition analyses, used e.g. monitoring and assessment of the ecological status of water bodies, are based on time-consuming and expertise-demanding light microscopy analyses. Currently, DNA-based molecular tools are being developed to replace microscopy-based analyses. Although most of the DNA is expected to be found in living cells, long-lasting DNA in damaged cells or soluble extracellular or relic DNA can make up a large proportion of the total DNA in water samples. DNA-based phytoplankton analysis has been shown to be affected by the huge variation in the copy number of the rRNA gene between phytoplankton species (Mäki et al. 2017). On the contrary, RNA is present only in living organisms and reflects active protein synthesis. Therefore, RNA-based methods can provide a more reliable estimate of community composition. The large copy number variation of ribosomal genes and the absence of universal primers for simultaneous amplification of cyanobacterial and eukaryotic phytoplankton genes hinder the application of DNA-based molecular methods. We applied a directional random-primed high throughput sequencing (HTS) approach (Mäki and Tiirola 2018) to analyse 16S and 18S rRNA community structures of 83 boreal lakes in Finland, Northern Europe. With the method it was possible to simultaneously amplify all groups of aquatic microorganisms in addition to cyanobacteria and eukaryotic phytoplankton. A comparison between microscopy and HTS showed that the relative phylum (Fig. 0) and class level abundances of eukaryotic phytoplankton and order level abundances of cyanobacteria were consistent between the methods, despite that the HTS method overestimated the relative abundance of cyanobacteria. However, correspondence was low at genus and species level, mainly due to the lack of reference library sequences. HTS revealed more genera and was able to differentiate cryptic genera lacking morphological characteristics, but microscopy revealed a longer list of species (Vuorio et al. 2020). The RNA-based method applied showed potential, but it is not yet able to replace microscopy, mainly due to the lack of full length 16S and 18S sequences in the reference libraries. The main advantage of the method is that it is not limited to phytoplankton, but can be applied to simultaneous investigation of the total composition of microbes, including all bacteria, protists, ciliates, rotifers and zooplankton.

show abstract

Integrating pigment and fatty acid profiles for enhanced estimation of seston community composition

Litmanen,

Perälä,

Vuorio

et al. 2024

Ecosphere

View full text Add to dashboard Cite

Climate change, nutrition pollution, and land use alterations influence the primary production of lakes. While light‐microscopy counting remains the standard for estimating phytoplankton community composition, its expense and time‐consuming nature necessitate cost‐effective alternatives for seston analysis. Furthermore, estimating the contribution of seston constituents other than primary producers, or non‐algal particles, is not possible with light‐microscopy counting. Biotracer approach using computational methods and chemotaxonomic biomarkers such as carotenoid pigments and fatty acids have been used as an alternative in seston analysis when species‐level taxonomy is not required. However, a comprehensive testing of how well carotenoid and fatty acids can be used in estimating a wide range of seston phytoplankton communities using different estimation methods is lacking. To assess the accuracy of a suite of state‐of‐the‐art biotracer‐based computational methods, namely CHEMTAX, FASTAR (Fatty Acid Source‐Tracking Algorithm in R), MixSIAR, and QFASA (Quantitative Fatty Acid Signature Analysis), lake water samples were collected in 2016, 2018, 2019, 2020, and 2021 for seston composition analysis in a boreal eutrophic lake with light‐microscopy counting serving as the reference for seston composition. Absolute errors between the biotracer‐based estimates were calculated to evaluate method performance. A small laboratory experiment to assess the reliability of estimating the contribution of non‐algal particles using the computational methods with fatty acids was also conducted. The closest alignment to light‐microscopy counting in terms of absolute error was achieved when both carotenoids and fatty acids were used together in the QFASA method. For CHEMTAX, FASTAR, and MixSIAR, using carotenoids alone produced the closest results. Additionally, the estimation methods accurately assessed the proportion of non‐algal particles in the seston when using fatty acid profiles, a capability not possible with light‐microscopy counting. Our findings demonstrate that the biotracer approach provides a viable and cost‐effective alternative to light‐microscopy counting when group‐level information of phytoplankton community composition suffices. Furthermore, we show that non‐algal particles can be effectively estimated together with phytoplankton when using fatty acids.

show abstract

Consistency of Targeted Metatranscriptomics and Morphological Characterization of Phytoplankton Communities

Cited by 11 publications

References 54 publications

Ciliate grazing on the bloom-forming microalga Gonyostomum semen

Ciliate grazing on the bloom-forming microalga Gonyostomum semen

Consistency between high throughput sequencing and microscopy-based morphological characterization of phytoplankton communities

Integrating pigment and fatty acid profiles for enhanced estimation of seston community composition

Contact Info

Product

Resources

About