Comparison of Relative and Absolute Abundance and Biomass of Freshwater Phytoplankton Taxa Using Metabarcoding and Microscopy DOI Creative Commons
И. С. Михайлов, Yurij Bukin, Alena Firsova

et al.

Ecology and Evolution, Journal Year: 2025, Volume and Issue: 15(3)

Published: March 1, 2025

Phytoplankton is the basis of food web and an indicator environmental change in aquatic ecosystems. assessment uses microscopy, which estimates composition, absolute abundance biomass taxa, metabarcoding, high richness diversity, relative taxa. Problems remain with consistency results from these two methods quantification metabarcoding. Using 18S rRNA metabarcoding microscopy we compared or phytoplankton taxa (class genus/species) south basin Lake Baikal spring over 3 years. Absolute abundance/biomass estimated by was obtained combining abundances amplicon sequence variants (ASV produced error-correcting method) derived V8-V9 region gene sequencing (primers were used that accurately represented mean different microalgae) total class-specific light microscopy. Many Spearman correlations found between (non- clr-transformed) abundances/biomasses same classes genus/species. Correlation coefficients higher values than values. Correlations abundance/biomass, both methods, Bacillariophyceae, Coscinodiscophyceae, Mediophyceae, Chrysophyceae, Cryptophyceae, Chlorophyceae, but not Dinophyceae Trebouxiophyceae. dominant species ASVs diatoms (Ulnaria, Aulacoseira, Stephanodiscus), Chrysophyceae (Dinobryon), Cryptophyceae (Cryptomonas). Thus, dynamics revealed. combination improve accuracy metabarcoding-based ecological assessment.

Language: Английский

Composition and spatial-temporal dynamics of phytoplankton community shaped by environmental selection and interactions in the Jiaozhou Bay DOI
Shuya Liu,

Zongmei Cui,

Yongfang Zhao

et al.

Water Research, Journal Year: 2022, Volume and Issue: 218, P. 118488 - 118488

Published: April 22, 2022

Language: Английский

Citations

59
metaPR2: A database of eukaryotic 18S rRNA metabarcodes with an emphasis on protists DOI Creative Commons
Daniel Vaulot, Clarence Wei Hung Sim, Denise Rui Ying Ong

et al.

Molecular Ecology Resources, Journal Year: 2022, Volume and Issue: 22(8), P. 3188 - 3201

Published: June 28, 2022

In recent years, metabarcoding has become the method of choice for investigating composition and assembly microbial eukaryotic communities. The number environmental data sets published increased very rapidly. Although unprocessed sequence files are often publicly available, processed data, in particular clustered sequences, rarely available a usable format. Clustered sequences reported as operational taxonomic units (OTUs) with different similarity levels or more recently amplicon variants (ASVs). This hampers comparative studies between environments sets, example examining biogeographical patterns specific groups/species, well analysing genetic microdiversity within these groups. Here, we present newly-assembled database 18S rRNA metabarcodes that annotated PR2 reference database. database, called metaPR2 , contains 41 corresponding to than 4000 samples 90,000 ASVs. which is accessible through both web-based interface (https://shiny.metapr2.org) an R package, should prove useful all researchers working on protist diversity variety systems.

Language: Английский

Citations

54
Extreme environments offer an unprecedented opportunity to understand microbial eukaryotic ecology, evolution, and genome biology DOI Creative Commons
Hannah Rappaport, Angela Oliverio

Nature Communications, Journal Year: 2023, Volume and Issue: 14(1)

Published: Aug. 16, 2023

Abstract Research in extreme environments has substantially expanded our understanding of the ecology and evolution life on Earth, but a major group organisms been largely overlooked: microbial eukaryotes (i.e., protists). In this Perspective, we summarize data from over 80 studies protists identify focal lineages that are significant interest for further study, including clades within Echinamoebida, Heterolobosea, Radiolaria, Haptophyta, Oomycota, Cryptophyta. We argue prime sampling targets to fill gaps eukaryotic tree increase ecology, metabolism, genome architecture, life.

Language: Английский

Citations

28
Mind the gap - The need to integrate novel plankton methods alongside ongoing long-term monitoring DOI Creative Commons
Matthew M. Holland, Luis Felipe Artigas, Angus Atkinson

et al.

Ocean & Coastal Management, Journal Year: 2025, Volume and Issue: unknown, P. 107542 - 107542

Published: Jan. 1, 2025

Language: Английский

Citations

1
Comparing eDNA and eRNA Sampling Methodologies From Pond Environments DOI Creative Commons
Katarzyna Janik-Papis, Dawid Krawczyk, Monika Baranowska

et al.

Aquatic Conservation Marine and Freshwater Ecosystems, Journal Year: 2025, Volume and Issue: 35(2)

Published: Feb. 1, 2025

ABSTRACT Molecular traces are increasingly being applied to assess the presence of species and communities. Studies on environmental DNA (eDNA) have, a large extent, become common practice in detection, but less studies have compared biodiversity estimations with more temporary RNA (eRNA). This study compares metabarcoding results from pond water obtained both molecule types by sequencing V4 region 18S rRNA marker. Water was collected two depths, 20 80 cm, filtered sequentially through filter porosities, 0.45 0.22 μm. Each cut half before fixation either 96% ETOH or RNAlater. The showed no differences between fixatives for molecule. Overall, estimates eDNA significantly overperformed eRNA, likely due higher concentrations terrestrial sources. Comparisons depths variation only, increasing levels found at upper layer. Both pore sizes captured distinctive compositions taxa, where about 30% diversity uniquely identified second, finer filter. Taken together, these findings imply that choice molecular marker, depth size affects pond.

Language: Английский

Citations

1
Microalgal biorefineries in sustainable biofuel production and other high-value products DOI Creative Commons

Swapnamoy Dutta,

Sampriti Kataki, Ishita Banerjee

et al.

New Biotechnology, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 1, 2025

Language: Английский

Citations

1
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 DOI
Nico Salmaso, Valentin Vasselon, Frédéric Rimet

et al.

The Science of The Total Environment, Journal Year: 2022, Volume and Issue: 834, P. 155175 - 155175

Published: April 12, 2022

Language: Английский

Citations

31
Groundwater environmental DNA metabarcoding reveals hidden diversity and reflects land‐use and geology DOI Creative Commons
Marjorie Couton,

Samuel Hürlemann,

Angela Studer

et al.

Molecular Ecology, Journal Year: 2023, Volume and Issue: 32(13), P. 3497 - 3512

Published: April 17, 2023

Abstract Despite being the most important source of liquid freshwater on planet, groundwater is severely threatened by climate change, agriculture, or industrial mining. It thus extensively monitored for pollutants and declines in quantity. The organisms living groundwater, however, are rarely target surveillance programmes little known about fauna inhabiting underground habitats. difficulties accessing lack expertise, apparent scarcity these challenge sampling prohibit adequate knowledge fauna. Environmental DNA (eDNA) metabarcoding provides an approach to overcome limitations but largely unexplored. Here, we sampled water 20 communal spring catchment boxes used drinking provisioning Switzerland, with a high level replication at both filtration amplification steps. We sequenced portion COI mitochondrial gene, which resulted 4917 ASVs, yet only 3% reads could be assigned species, genus, family more than 90% identity. Careful evaluation unassigned corroborated that sequences were true belonging mostly diverse eukaryotic groups, not present reference databases. Principal component analyses showed strong correlation community composition surface land‐use (agriculture vs. forest) geology (fissured rock unconsolidated sediment). While incomplete databases limit assignment taxa eDNA metabarcoding, taxonomy‐free approaches can reveal large hidden diversity couple it major drivers, revealing their imprint chemical biological properties groundwater.

Language: Английский

Citations

17
The global genetic diversity of planktonic foraminifera reveals the structure of cryptic speciation in plankton DOI Creative Commons
Raphaël Morard, Kate Darling, Agnes K. M. Weiner

et al.

Biological reviews/Biological reviews of the Cambridge Philosophical Society, Journal Year: 2024, Volume and Issue: 99(4), P. 1218 - 1241

Published: Feb. 13, 2024

ABSTRACT The nature and extent of diversity in the plankton has fascinated scientists for over a century. Initially, discovery many new species remarkably uniform unstructured pelagic environment appeared to challenge concept ecological niches. Later, it became obvious that only fraction had been formally described, because assemblages are dominated by understudied eukaryotic lineages with small size lack clearly distinguishable morphological features. high confirmed comprehensive metabarcoding surveys, but interpretation underlying molecular taxonomies is hindered insufficient integration genetic taxonomy observations. Here we use planktonic foraminifera as study model reveal full their investigate geographical patterns distribution. To this end, assembled global data set ~7600 ribosomal DNA sequences obtained from morphologically characterised individual foraminifera, established robust taxonomic framework observed diversity, used query covering ~1700 samples ~2.48 billion reads. This allowed us extract assign 1 million reads, enabling characterisation structure group across ~1100 oceanic stations worldwide. Our sampling revealed existence of, at most, 94 distinct operational units (MOTUs) level divergence indicative biological species. doubles number described identified Furthermore, allocation morphospecies uneven. Only 16 disguise evolutionarily significant proportion show increases poleward. Finally, observe MOTUs have narrower geographic distribution than some cases belonging same (cryptic species) different environmental preferences. Overall, our analysis reveals even light sampling, modest finite. However, cryptic diversification decoupled diversification, hinting mechanisms acting levels divergence.

Language: Английский

Citations

8
The high molecular diversity in Noctiluca scintillans is dominated by intra-genomic variations revealed by single cell high-throughput sequencing of 18S rDNA V4 DOI

Kuiyan Liu,

Xianliang Huang,

Xiangxiang Ding

et al.

Harmful Algae, Journal Year: 2024, Volume and Issue: 132, P. 102568 - 102568

Published: Jan. 6, 2024

Language: Английский

Citations

6