DNA sequence and taxonomic gap analyses to quantify the coverage of aquatic cyanobacteria and eukaryotic microalgae in reference databases: Results of a survey in the Alpine region

Salmaso, Nico; Vasselon, Valentin; Rimet, Frédéric; Vautier, Marine; Eleršek, Tina; Adriano, Bruno; Donati, Claudio; Moretto, Marco; Pindo, Massimo; Riccioni, Giulia; Stefani, E.; Capelli, Camilla; Lepori, Fabio; Kurmayer, Rainer; Mischke, Ute; Klemenčić, Aleksandra Krivograd; Novak, Katarina; Greco, C.; Franzini, Giorgio; Fusato, Giampaolo; Giacomazzi, Federica; Lea, A. H.; Menegon, Silvia; Macor, Arianna; Virgilio, Damiano; Zanut, Elisa; Zorza, Raffaella; Buzzi, Fabio; Domaizon, Isabelle

doi:10.1016/j.scitotenv.2022.155175

Cited by 25 publications

(15 citation statements)

References 115 publications

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“…Most sequences in the databases belong to planktic cyanobacteria and there are much fewer sources to obtain the information about benthic microorganisms from. Research recently published by Salmaso et al (2022) on a coverage of 16S rRNA sequences from environments of considerably well-studied alpine lakes and rivers showed that 30% of planktic and 60% of biofilm sequences had no close match in public databases. Comparing microscopic identifications with molecular data the authors found the gap even larger.…”

Section: Discussionmentioning

confidence: 99%

Salinity matters the most: How environmental factors shape the diversity and structure of cyanobacterial mat communities in high altitude arid ecosystems

et al. 2023

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IntroductionMicrobial mats are complex communities of benthic microorganisms that occur at the soil-water interphase in lakes’ shores, streams, and ponds. In the cold, mountainous desert of Eastern Pamir (Tajikistan), where scarce water bodies are influenced by extreme environmental conditions, photosynthetic cyanobacteria form diverse mats. The mats are characterized by different morphology and thickness. Their habitats exhibit a wide range of conditions; from oligosaline to hypersaline, oligotrophic to hypertrophic, and from cold ponds to hot springs. The aim of the present study was to reveal the taxonomic composition and structure of these mats and to examine which environmental factors influence them.MethodsFifty-one mats were collected from small water bodies around Bulunkul, Karakul, and Rangkul Lakes in 2015 and 2017. The physical and chemical properties of the water were measured in situ, while the concentration of nutrients was analyzed ex-situ. To reveal the taxonomic composition of the mats, the hypervariable V3-V4 region of the 16S rRNA gene was examined using NGS technology.ResultsThe results of bioinformatic analyses were compared with microscopic observations. They showed that Cyanobacteria was the dominant phylum, constituting on average 35% of bacterial ASVs, followed by Proteobacteria (28%), Bacteroidota (11%), and Firmicutes (9%). Synechococcales, Oscillatoriales, and Nostocales orders prevailed in Oxyphotobacteria, with a low contribution of Chroococcales, Gloeobacterales, and Chroococcidiopsidales. Occasionally the non-photosynthetic Vampirivibrionia (Melainabacteria) and Sericytochromatia from sister clades to Oxyphotobacteria were noted in the samples. Moreover, there was a high percentage of unidentified cyanobacterial sequences, as well as the recently described Hillbrichtia pamiria gen. et sp. nov., present in one of the samples. Salinity, followed by Na and K concentrations, correlated positively with the composition and structure of Oxyphotobacteria on different taxonomic levels and the abundance of all bacterial ASVs.DiscussionThe study suggests that the investigated communities possibly host more novel and endemic species. Among the environmental factors, salinity influenced the Oxyphotobacteria communities the most. Overall, the microenvironmental factors, i.e. the conditions in each of the reservoirs seemed to have a larger impact on the diversity of microbial mats in Pamir than the “subregional” factors, related to altitude, mean annual air temperature and distance between these subregions.

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Section: Discussionmentioning

confidence: 99%

Salinity matters the most: How environmental factors shape the diversity and structure of cyanobacterial mat communities in high altitude arid ecosystems

et al. 2023

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“…The results from this study support a much earlier introduction of these sub‐tropical species to South Center and perhaps other north temperate lakes in the region, indicating that it was abundant going back to the 1990's with the first detectable DNA in sediment sections dated to c. 1950. In terms of the identification of exotic species via sed DNA, it must be noted that 16S rRNA is insufficient to obtain a precise taxonomic assignment of cyanobacteria at the species level due to the relatively short sequences (~300 bp) used here (Salmaso et al, 2022). However, the lack of other closely‐related native species (e.g., no other species of the genus Raphidiopsis are known to be native to Minnesota) and the confirmation of its presence in contemporary water samples from this lake via light microscopy (Heiskary et al, 2016) independently corroborate this taxonomic identification.…”

Section: Discussionmentioning

confidence: 99%

Sedimentary DNA and pigments show increasing abundance and toxicity of cyanoHABs during the Anthropocene

et al. 2023

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Cyanobacterial harmful algal blooms (cyanoHABs) are assumed to be increasing in abundance and toxicity, but comprehensive analysis of change through time is limited, in part, because some key taxa (e.g., Microcystis) leave ambiguous evidence of historical abundance and toxicity. Sedimentary DNA (sedDNA) can allow the reconstruction of the cyanobacteria community as well as the frequency of genes specific to cyanotoxin production, enabling us to determine which taxa are present and their potential for toxin‐production. Using a combination of droplet digital polymerase chain reaction (ddPCR) and high‐throughput sequencing (HTS), we quantified the abundance of cyanobacterial genes of known function and changes in cyanobacteria taxa from sedDNA over the last century in nine lakes along a gradient of lake size, depth and trophic state in Minnesota, U.S.A. Using ddPCR, we quantified genes associated with microcystin toxin‐producing potential (mcyE), total cyanobacteria (CYA, 16S rRNA) and the genus Microcystis (MICR, 16S rRNA). Using HTS on a subset of lakes, we investigated how the abundance of this toxin‐producing gene covaried with the cyanobacteria community composition. We also compared ddPCR and HTS data to fossil pigments, a well‐established palaeolimnological method used to track changes in primary producers over time. Our results showed a significant correlation between MICR and the quantity of mcyE gene and cyanobacterial taxa with known toxin‐production potential. The abundance of both genes likewise increased concomitantly through time. Community analyses of HTS data showed significant change in cyanobacterial communities commencing c. 1950 when major land‐use change in this region led to increased lake productivity, and c. 1990 when Dolichospermum and Microcystis genera increased in abundance, and the subtropical exotic cyanobacteria Raphidiopsis raciborskii and Sphaerospermopsis aphanizomenoides became abundant. Cyanobacteria pigment data reflected these changes only in deeper lakes, suggesting issues related to benthic production or biomarker preservation in shallower systems. This study provides evidence for historical development of increasingly toxic cyanoHABs across a diverse set of lakes and illustrates how sedDNA may help link changes in the cyanobacteria community to the expression of potentially toxic genes.

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“…In contrast, only sparse fits to the available reference sequences were for the Ulvophyceae and Xanthophyceae, demonstrating that they exhibit the most extensive still-unknown species diversity yet to be studied. Inadequacy of taxonomic coverage is a significant obstacle in the metabarcoding approach impairing its appropriate use for the species rank ( Machado-de-Lima et al, 2019 ; Salmaso et al, 2022 ). Metabarcoding will remain one of the principal methods for community analyses, although a future shift toward PCR-free metagenomics and transcriptomic approaches can be expected ( Salmaso et al, 2022 ).…”

Section: Discussionmentioning

confidence: 99%

Unrecognized diversity and distribution of soil algae from Maritime Antarctica (Fildes Peninsula, King George Island)

et al. 2023

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IntroductionEukaryotic algae in the top few centimeters of fellfield soils of ice-free Maritime Antarctica have many important effects on their habitat, such as being significant drivers of organic matter input into the soils and reducing the impact of wind erosion by soil aggregate formation. To better understand the diversity and distribution of Antarctic terrestrial algae, we performed a pilot study on the surface soils of Meseta, an ice-free plateau mountain crest of Fildes Peninsula, King George Island, being hardly influenced by the marine realm and anthropogenic disturbances. It is openly exposed to microbial colonization from outside Antarctica and connected to the much harsher and dryer ice-free zones of the continental Antarctic. A temperate reference site under mild land use, SchF, was included to further test for the Meseta algae distribution in a contrasting environment.MethodsWe employed a paired-end metabarcoding analysis based on amplicons of the highly variable nuclear-encoded ITS2 rDNA region, complemented by a clone library approach. It targeted the four algal classes, Chlorophyceae, Trebouxiophyceae, Ulvophyceae, and Xanthophyceae, representing key groups of cold-adapted soil algae.ResultsA surprisingly high diversity of 830 algal OTUs was revealed, assigned to 58 genera in the four targeted algal classes. Members of the green algal class Trebouxiophyceae predominated in the soil algae communities. The major part of the algal biodiversity, 86.1% of all algal OTUs, could not be identified at the species level due to insufficient representation in reference sequence databases. The classes Ulvophyceae and Xanthophyceae exhibited the most unknown species diversity. About 9% of the Meseta algae species diversity was shared with that of the temperate reference site in Germany.DiscussionIn the small portion of algal OTUs for which their distribution could be assessed, the entire ITS2 sequence identity with references shows that the soil algae likely have a wide distribution beyond the Polar regions. They probably originated from soil algae propagule banks in far southern regions, transported by aeolian transport over long distances. The dynamics and severity of environmental conditions at the soil surface, determined by high wind currents, and the soil algae’s high adaptability to harsh environmental conditions may account for the high similarity of soil algal communities between the northern and southern parts of the Meseta.

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DNA sequence and taxonomic gap analyses to quantify the coverage of aquatic cyanobacteria and eukaryotic microalgae in reference databases: Results of a survey in the Alpine region

Cited by 25 publications

References 115 publications

Salinity matters the most: How environmental factors shape the diversity and structure of cyanobacterial mat communities in high altitude arid ecosystems

Salinity matters the most: How environmental factors shape the diversity and structure of cyanobacterial mat communities in high altitude arid ecosystems

Sedimentary DNA and pigments show increasing abundance and toxicity of cyanoHABs during the Anthropocene

Unrecognized diversity and distribution of soil algae from Maritime Antarctica (Fildes Peninsula, King George Island)

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