Cyanoseq: A database of cyanobacterial 16S rRNA gene sequences with curated taxonomy

Journal of Phycology, Journal Year: 2023, Volume and Issue: 59(3), P. 470 - 480

Published: April 7, 2023

Abstract Cyanobacteria are photosynthetic bacteria that occupy various habitats across the globe, playing critical roles in many of Earth's biogeochemical cycles both aquatic and terrestrial systems. Despite their well‐known significance, taxonomy remains problematic is subject much research. Taxonomic issues have consequently led to inaccurate curation within known reference databases, ultimately leading taxonomic assignment during diversity studies. Recent advances sequencing technologies increased our ability characterize understand microbial communities, generation thousands sequences require assignment. We herein propose CyanoSeq ( https://zenodo.org/record/7569105 ), a database cyanobacterial 16S rRNA gene with curated taxonomy. The based on current state taxonomy, ranks from domain genus level. Files provided for use common naive Bayes classifiers, such as those included DADA2 or QIIME2 platform. Additionally, FASTA files creation de novo phylogenetic trees (near) full‐length determine relationship strains and/or ASV/OTUs. currently consists 5410 along 123 Chloroplast, Bacterial, Vampirovibrionia (formally Melainabacteria) sequences.

Language: Английский

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A genome catalogue of lake bacterial diversity and its drivers at continental scale

Nature Microbiology, Journal Year: 2023, Volume and Issue: 8(10), P. 1920 - 1934

Published: July 31, 2023

Language: Английский

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Environmental drivers of taxonomic and functional variation in zooplankton diversity and composition in freshwater lakes across Canadian continental watersheds

Limnology and Oceanography, Journal Year: 2022, Volume and Issue: 67(5), P. 1081 - 1097

Published: March 11, 2022

ABSTRACT Canada is home to more lakes than any other nation, but there a fragmented and limited understanding of the ecological status these water bodies. Zooplankton are excellent bioindicators lake health, given their central food web position. To date, many studies have investigated effect individual stressors on zooplankton communities, mediated through changes in quality (e.g., macronutrients, temperature, or chemicals). Increasingly, act simultaneously lakes, often over extended periods time. As part NSERC Canadian Lake Pulse Network project, pelagic were sampled 624 across Canada, spanning six continental drainage basins. We evaluated 40+ environmental variables diversity community composition, considering both taxonomic functional approaches. also tested specific hypotheses relationships between communities conditions, including eutrophication, calcium, chloride, fish predation. found that morphometry among most important predictors diversity, while metrics critical explaining variation composition. Our results reveal significant heterogeneity with contrasting effects drivers watersheds, highlighting response models cannot be assumed apply universally.

Language: Английский

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Genetic Markers for Metabarcoding of Freshwater Microalgae: Review

Biology, Journal Year: 2023, Volume and Issue: 12(7), P. 1038 - 1038

Published: July 22, 2023

The metabarcoding methods for studying the diversity of freshwater microalgae and routine biomonitoring are actively used in modern research. A lot experience has been accumulated already, many methodological questions have solved (such as influence time sample conservation, DNA extraction bioinformatical processing). reproducibility method tested confirmed. However, one main problems-choosing a genetic marker study-still lacks clear answer. We analyzed 70 publications found out that studies on eukaryotic use 12 markers (different nuclear regions 18S ITS plastids

Language: Английский

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

Frontiers in Microbiology, Journal Year: 2023, Volume and Issue: 14

Published: Feb. 9, 2023

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

Language: Английский

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Microcystin concentrations and congener composition in relation to environmental variables across 440 north-temperate and boreal lakes

The Science of The Total Environment, Journal Year: 2023, Volume and Issue: 884, P. 163811 - 163811

Published: April 29, 2023

Understanding the environmental conditions and taxa that promote occurrence of cyanobacterial toxins is imperative for effective management lake ecosystems. Herein, we modeled total microcystin presence concentrations with a broad suite predictors cyanobacteria community data collected across 440 Canadian lakes using standardized methods. We also conducted focused analysis targeting 14 congeners 190 lakes, to examine how abiotic biotic factors influence their relative proportions. Microcystins were detected in 30 % highest occurring most eutrophic located ecozones central Canada. The two commonly MC-LR (61 lakes) MC-LA (37 lakes), while 11 others more sporadically waterbodies. Congener diversity peaked Canada where biomass was highest. Using zero-altered hurdle model, probability detecting best explained by increasing Microcystis biomass, Daphnia cyclopoid soluble reactive phosphorus, pH wind. Microcystin increased other less dominant taxa, as well copepod dissolved inorganic carbon water temperature. Collectively, these models accounted 34 70 variability, respectively. Based on multiple factor congeners, data, zooplankton found abundance varied according trophic state related combination genera biomasses variables.

Language: Английский

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Assessing the relevance of DNA metabarcoding compared to morphological identification for lake phytoplankton monitoring

The Science of The Total Environment, Journal Year: 2024, Volume and Issue: 914, P. 169774 - 169774

Published: Jan. 11, 2024

Language: Английский

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Cyanobacterial Algal Bloom Monitoring: Molecular Methods and Technologies for Freshwater Ecosystems

Microorganisms, Journal Year: 2023, Volume and Issue: 11(4), P. 851 - 851

Published: March 27, 2023

Cyanobacteria (blue-green algae) can accumulate to form harmful algal blooms (HABs) on the surface of freshwater ecosystems under eutrophic conditions. Extensive HAB events threaten local wildlife, public health, and utilization recreational waters. For detection/quantification cyanobacteria cyanotoxins, both United States Environmental Protection Agency (USEPA) Health Canada increasingly indicate that molecular methods be useful. However, each detection method has specific advantages limitations for monitoring HABs in water ecosystems. Rapidly developing modern technologies, including satellite imaging, biosensors, machine learning/artificial intelligence, integrated with standard/conventional overcome associated traditional cyanobacterial methodology. We examine advances cell lysis methodology conventional/modern methods, imaging techniques, polymerase chain reaction (PCR)/DNA sequencing, enzyme-linked immunosorbent assays (ELISA), mass spectrometry, remote sensing, learning/AI-based prediction models. This review focuses specifically methodologies likely employed ecosystems, especially Great Lakes region North America.

Language: Английский

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Spatiotemporal diversity and community structure of cyanobacteria and associated bacteria in the large shallow subtropical Lake Okeechobee (Florida, United States)

Frontiers in Microbiology, Journal Year: 2023, Volume and Issue: 14

Published: Aug. 30, 2023

Lake Okeechobee is a large eutrophic, shallow, subtropical lake in south Florida, United States. Due to decades of nutrient loading and phosphorus rich sediments, the eutrophic frequently experiences cyanobacterial harmful algal blooms (cyanoHABs). In past, surveys phytoplankton community structure have been conducted by morphological studies, whereas molecular based studies seldom employed. With increased frequency cyanoHABs (e.g., 2016 2018 Microcystis-dominated blooms), it imperative determine diversity taxa that exist within limnological parameters drive bloom-forming genera. A spatiotemporal study was over course 1 year characterize (cyano)bacterial structure, using 16S rRNA metabarcoding, with coincident collection nutrients, water temperature, major ions), cyanotoxins. The objectives this were elucidate trends identify drivers examine cyanobacteria-bacterial relationships lake. Results indicated communities significantly different between wet dry season, but not periods nitrogen limitation co-nutrient limitation. Throughout year, primarily dominated picocyanobacterium Cyanobium. genera Cuspidothrix, Dolichospermum, Microcystis, Raphidiopsis highly abundant throughout had disparate requirements niches Anatoxin-a, microcystins, nodularins detected across both seasons. There no correlated (cyano)bacteria shared common cyanobacteria Raphidiopsis. This first its kind use methods assess These data greatly improve our understanding physiochemical which may Okeechobee.

Language: Английский

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Molecular quantification of herbs (Herb-Q): a pyrosequencing-based approach and its application in Pinellia ternata

Chinese Journal of Natural Medicines, Journal Year: 2024, Volume and Issue: 22(7), P. 663 - 672

Published: July 1, 2024

Language: Английский

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