Metagenomics Analysis to Investigate the Microbial Communities and Their Functional Profile During Cyanobacterial Blooms in Lake Varese

From BugSigDB
Needs review
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI
Authors
Andrea Beghi, Armin Lahm, Chiara Facca, Diana Conduto António, Franca Pandolfi, Helle Skejo, Isabella Sanseverino, Pietro Genoni & Teresa Lettieri, Robert Loos
Journal
Microbiology of Aquatic Systems
Year
2022
Pages:
18
First page:
850
Keywords:
Toxic cyanobacterial blooms represent a natural phenomenon caused by a mass proliferation of photosynthetic prokaryotic microorganisms in water environments. Bloom events have been increasingly reported worldwide and their occurrence can pose serious threats to aquatic organisms and human health. In this study, we assessed the microbial composition, with a focus on Cyanobacteria, in Lake Varese, a eutrophic lake located in northern Italy. Water samples were collected and used for obtaining a 16S-based taxonomic profile and performing a shotgun sequencing analysis. The phyla found to exhibit the greatest relative abundance in the lake included Proteobacteria, Cyanobacteria, Actinobacteriota and Bacteroidota. In the epilimnion and at 2.5 × Secchi depth, Cyanobacteria were found to be more abundant compared to the low levels detected at greater depths. The blooms appear to be dominated mainly by the species Lyngbya robusta, and a specific functional profile was identified, suggesting that distinct metabolic processes characterized the bacterial population along the water column. Finally, analysis of the shotgun data also indicated the presence of a large and diverse phage population.

Experiment 1


incomplete

Curated date: 2024/03/14

Curator: Omojokunoluwatomisin

Revision editor(s): Omojokunoluwatomisin, Victoria

Subjects

Location of subjects
Italy
Host species Species from which microbiome was sampled. Contact us to have more species added.
Not specified


Lab analysis

Sequencing type
16S
16S variable region One or more hypervariable region(s) of the bacterial 16S gene
V3-V4
Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
Illumina

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
raw counts
Statistical test
DESeq2
Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
0.05
MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
No