Assessment of marine benthic diatom communities: insights from a combined morphological–metabarcoding approach in Mediterranean shallow coastal waters

Pérez-Burillo, Javier; Valoti, Greta; Witkowski, Andrzej; Prado, Patricia; Mann, David G.; Trobajo, Rosa

doi:10.1016/j.marpolbul.2021.113183

Cited by 18 publications

(8 citation statements)

References 91 publications

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“…Typical contaminants found in our cultures were heterotrophic flagellated or amoeboid protists and green algae. Particular attention was paid to heterotrophic chrysophytes, whose DNA is amplified by diatom-specific primers (Pérez-Burillo et al, 2022). Whenever con-taminations were detected, single diatom cells were once again isolated.…”

Section: Isolation Of Cells and Removal Of Contaminantsmentioning

confidence: 99%

Exploring diatom diversity through cultures - a case study from the Bow River, Canada

et al. 2022

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Diatom cultures can help answer taxonomic, biogeographic and ecological questions on a local and global scale. Unialgal cultures are derived from a single cell and provide abundant material for morphological and molecular analyses. The link between the historic morphological species concept and the molecular data is becoming increasingly important with the use of eDNA metabarcoding. Additionally, cultures provide insights into the life cycle of diatoms and thereby complement taxonomy and species ecology. In this study, we present an approach to extract benthic diatoms from an environmental sample to generate unialgal cultures. We explored diatom diversity in preserved assemblages and by culturing as many different taxa as possible from benthic freshwater samples taken on the same day from the Bow River in Calgary, Canada. With both methods we found a total of 221 different benthic diatom taxa, of which 182 were identified in the preserved diatom assemblages. Interestingly, an additional 39 taxa only appeared in the cultures. In total 129 strains were cultivated representing 71 different taxa. This study includes pictures of living cells demonstrating the additional merits of unialgal cultures, as they provide information on plastid details, auxospores and endosymbionts. Both, the identification of the diatom assemblages and the generation and identification of strains provide the foundation for additional water quality assessment tools, taxonomic insights and molecular references libraries.

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Section: Isolation Of Cells and Removal Of Contaminantsmentioning

confidence: 99%

Exploring diatom diversity through cultures - a case study from the Bow River, Canada

et al. 2022

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“…Furthermore, DNA sequences are crucially needed as references for DNA metabarcoding studies to investigate diatom biodiversity in environmental samples. This technique has proved to be a reliable method for studying species diversity and has shown to be a valuable addition to light microscope-based identifications (Kermarrec et al 2014;Zimmermann et al 2015;Mora et al 2019;Pérez-Burillo et al 2022).…”

Section: Introductionmentioning

confidence: 99%

Molecular phylogenetics coupled with morphological analyses of Arctic and Antarctic strains place Chamaepinnularia (Bacillariophyta) within the Sellaphoraceae

Schimani¹,

Abarca²,

Zimmermann³

et al. 2024

Fottea

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The diatom genus Chamaepinnularia was first published by Lange-Bertalot et Krammer in 1996 to accommodate several small species previously included within Navicula and Pinnularia. Despite its morphological similarity to those two genera, the family-level classification of Chamaepinnularia has been considered incertae sedis since its description almost three decades ago. We provide the first molecular characterisation (18S and rbcL) of the genus based on cultured polar strains and investigated its phylogenetic placement. Molecular data are complemented with observations on living cells, as well as detailed examination of oxidized material with light microscopy and scanning electron microscopy. The 12 investigated strains were morphologically identified as three taxa: two already described species (C. gerlachei, C. krookii) and one here newly described (C. australis sp. nov.). These species formed three separate, well-supported branches in the phylogeny. Our analyses placed Chamaepinnularia as a sister group to members of the Sellaphoraceae for which sequence data exist (i.e. Sellaphora, Fallacia, Rossia and Diprora). Based on the presence of hymenate areolae, a single Hshaped plastid with girdle appressed plates and the results of the phylogenetic trees, we propose the inclusion of Chamaepinnularia within the family Sellaphoraceae, which altogether form a supported monophyletic group.

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“…DNA metabarcoding methods have proven useful to investigate diversity of microbial communities and have been used for exploring biogeographic trends (Antich et al., 2022 ; Pitz et al., 2020 ; Šupraha et al., 2022 ). Advantages of metabarcoding over the traditional light microscopy methods for identifying and quantifying algal communities include cost, reproducibility (Kermarrec et al., 2013 ), detection of species that may be overlooked in morphological assessments due to their small size or rarity (Pérez‐Burillo et al., 2022 ), clear identification of some groups of microbes (especially when reproductive structures are lacking), and an increasing lack of taxonomists available for this work (Kahlert et al., 2012 ). Metabarcoding studies have found higher diversity than detected with morphological methods in studies of cyanobacteria (e.g., Li et al., 2019 ) and diatoms (e.g., Zimmermann et al., 2015 ).…”

Section: Introductionmentioning

confidence: 99%

Metabarcoding reveals unique microbial mat communities and evidence of biogeographic influence in low‐oxygen, high‐sulfur sinkholes and springs

Fray,

McGovern,

Casamatta

et al. 2024

Ecology and Evolution

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High‐sulfur, low‐oxygen environments formed by underwater sinkholes and springs create unique habitats populated by microbial mat communities. To explore the diversity and biogeography of these mats, samples were collected from three sites in Alpena, Michigan, one site in Monroe, Michigan, and one site in Palm Coast, Florida. Our study investigated previously undescribed eukaryotic diversity in these habitats and further explored their bacterial communities. Mat samples and water parameters were collected from sulfur spring sites during the spring, summer, and fall of 2022. Cyanobacteria and diatoms were cultured from mat subsamples to create a culture‐based DNA reference library. Remaining mat samples were used for metabarcoding of the 16S and rbcL regions to explore bacterial and diatom diversity, respectively. Analyses of water chemistry, alpha diversity, and beta diversity articulated a range of high‐sulfur, low‐oxygen habitats, each with distinct microbial communities. Conductivity, pH, dissolved oxygen, temperature, sulfate, and chloride had significant influences on community composition but did not describe the differences between communities well. Chloride concentration had the strongest correlation with microbial community structure. Mantel tests revealed that biogeography contributed to differences between communities as well. Our results provide novel information on microbial mat composition and present evidence that both local conditions and biogeography influence these unique communities.

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Assessment of marine benthic diatom communities: insights from a combined morphological–metabarcoding approach in Mediterranean shallow coastal waters

Cited by 18 publications

References 91 publications

Exploring diatom diversity through cultures - a case study from the Bow River, Canada

Exploring diatom diversity through cultures - a case study from the Bow River, Canada

Molecular phylogenetics coupled with morphological analyses of Arctic and Antarctic strains place Chamaepinnularia (Bacillariophyta) within the Sellaphoraceae

Metabarcoding reveals unique microbial mat communities and evidence of biogeographic influence in low‐oxygen, high‐sulfur sinkholes and springs

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