Comparing microscopy and DNA metabarcoding techniques for identifying cyanobacteria assemblages across hundreds of lakes

MacKeigan, Paul W.; Garner, Rebecca E.; Monchamp, Marie‐Ève; Walsh, David A.; Onana, Vera E.; Kraemer, Susanne A.; Pick, Frances R.; Beisner, Beatrix E.; Agbeti, Michael D.; Costa, Naíla Barbosa da; Shapiro, Ben; Gregory‐Eaves, Irene

doi:10.1016/j.hal.2022.102187

Cited by 38 publications

(22 citation statements)

References 84 publications

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“…Microscopy and molecular tools have been found to identify the same predominant taxa of cyanobacteria, with the exception of pico-cyanobacteria which are underestimated by microscopy ( MacKeigan et al, 2022 ). Here, molecular tools allowed detection of Synechococcus as one of the dominant genera of cyanobacteria in Lake Erie’s watershed, along with Microcystis , Planktothrix , and Aphanizomenon , which were already identified in Lake Erie using microscopy ( Millie et al, 2009 ; Chaffin et al, 2011 ; Allinger and Reavie, 2013 ; Davis et al, 2015 ).…”

Section: Discussionmentioning

confidence: 99%

Spatio-temporal connectivity of the aquatic microbiome associated with cyanobacterial blooms along a Great Lake riverine-lacustrine continuum

Crèvecoeur

Edge²,

Watson³

et al. 2023

Front. Microbiol.

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Lake Erie is subject to recurring events of cyanobacterial harmful algal blooms (cHABs), but measures of nutrients and total phytoplankton biomass seem to be poor predictors of cHABs when taken individually. A more integrated approach at the watershed scale may improve our understanding of the conditions that lead to bloom formation, such as assessing the physico-chemical and biological factors that influence the lake microbial community, as well as identifying the linkages between Lake Erie and the surrounding watershed. Within the scope of the Government of Canada’s Genomics Research and Development Initiative (GRDI) Ecobiomics project, we used high-throughput sequencing of the 16S rRNA gene to characterize the spatio-temporal variability of the aquatic microbiome in the Thames River–Lake St. Clair-Detroit River–Lake Erie aquatic corridor. We found that the aquatic microbiome was structured along the flow path and influenced mainly by higher nutrient concentrations in the Thames River, and higher temperature and pH downstream in Lake St. Clair and Lake Erie. The same dominant bacterial phyla were detected along the water continuum, changing only in relative abundance. At finer taxonomical level, however, there was a clear shift in the cyanobacterial community, with Planktothrix dominating in the Thames River and Microcystis and Synechococcus in Lake St. Clair and Lake Erie. Mantel correlations highlighted the importance of geographic distance in shaping the microbial community structure. The fact that a high proportion of microbial sequences found in the Western Basin of Lake Erie were also identified in the Thames River, indicated a high degree of connectivity and dispersal within the system, where mass effect induced by passive transport play an important role in microbial community assembly. Nevertheless, some cyanobacterial amplicon sequence variants (ASVs) related to Microcystis, representing less than 0.1% of relative abundance in the upstream Thames River, became dominant in Lake St. Clair and Erie, suggesting selection of those ASVs based on the lake conditions. Their extremely low relative abundances in the Thames suggest additional sources are likely to contribute to the rapid development of summer and fall blooms in the Western Basin of Lake Erie. Collectively, these results, which can be applied to other watersheds, improve our understanding of the factors influencing aquatic microbial community assembly and provide new perspectives on how to better understand the occurrence of cHABs in Lake Erie and elsewhere.

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Section: Discussionmentioning

confidence: 99%

Spatio-temporal connectivity of the aquatic microbiome associated with cyanobacterial blooms along a Great Lake riverine-lacustrine continuum

Crèvecoeur

Edge²,

Watson³

et al. 2023

Front. Microbiol.

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“…It is also possible that some cyanobacteria sequences are wrongly assigned as Cyanobium in the SILVA database, leading to an over-representation of this genus in our results. Given their small size and difficulties with identifying them, it is also highly likely they are commonly overlooked in traditional light microscopy analysis of lake samples 80 . A study of cyanobacterial diversity in 143 New Zealand lakes identified an equally high number of operational taxonomic units and associated sequence reads of picocyanobacteria and suggested that this group has been overlooked in most limnological studies in this country 81 .…”

Section: Discussionmentioning

confidence: 99%

Using metabarcoding and droplet digital PCR to investigate drivers of historical shifts in cyanobacteria from six contrasting lakes

Picard

Pochon

Atalah

et al. 2022

Sci Rep

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The frequency and intensity of cyanobacterial blooms is increasing worldwide. Multiple factors are implicated, most of which are anthropogenic. New Zealand provides a useful location to study the impacts of human settlement on lake ecosystems. The first humans (Polynesians) arrived about 750 years ago. Following their settlement, there were marked landscape modifications which intensified after European settlement about 150 years ago. The aims of this study were to reconstruct cyanobacterial communities in six lakes over the last 1000 years and explore key drivers of change. Cyanobacterial environmental DNA was extracted from sediment cores and analysed using metabarcoding and droplet digital PCR. Cyanobacteria, including potentially toxic or bloom forming species, were already present in these lakes prior to human arrival, however their overall abundance was low. Total cyanobacteria abundance and richness increased in all lakes after European settlement but was very pronounced in four lakes, where bloom-forming taxa became dominant. These shifts occurred concomitant with land-use change. The catchment of one deteriorated lake is only moderately modified, thus the introduction of non-native fish is posited as the key factor driving this change. The paleolimnological approach used in this study has enabled new insights into timing and potential causes of changes in cyanobacterial communities.

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“…Phosphorus was found to be an important predictor of littoral protist diversity in European lakes ( 44 ) and of long-term microeukaryote community turnover evidenced from paleolimnological trends ( 19 ). Interactions between protists and Cyanobacteria likely also play a role in determining protist assemblages in hypereutrophic lakes, especially as Cyanobacteria of the genus Microcystis were found to be associated with high-nutrient conditions across LakePulse sites ( 72 ).…”

Section: Discussionmentioning

confidence: 99%

Protist Diversity and Metabolic Strategy in Freshwater Lakes Are Shaped by Trophic State and Watershed Land Use on a Continental Scale

et al. 2022

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Comparing microscopy and DNA metabarcoding techniques for identifying cyanobacteria assemblages across hundreds of lakes

Cited by 38 publications

References 84 publications

Spatio-temporal connectivity of the aquatic microbiome associated with cyanobacterial blooms along a Great Lake riverine-lacustrine continuum

Spatio-temporal connectivity of the aquatic microbiome associated with cyanobacterial blooms along a Great Lake riverine-lacustrine continuum

Using metabarcoding and droplet digital PCR to investigate drivers of historical shifts in cyanobacteria from six contrasting lakes

Protist Diversity and Metabolic Strategy in Freshwater Lakes Are Shaped by Trophic State and Watershed Land Use on a Continental Scale

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