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

Study information

Needs review

study design

time series / longitudinal observational

Citation

PMID PubMed identifier for scientific articles.

34766210

DOI Digital object identifier for electronic documents.

10.1007/s00248-021-01914-5

URI

Authors

Sanseverino I, Pretto P, António DC, Lahm A, Facca C, Loos R, Skejo H, Beghi A, Pandolfi F, Genoni P, Lettieri T

Journal

Microbial ecology

Year

2022

Keywords:

Algal bloom, Freshwater, Lyngbya, Metagenomics, Microbial populations, Water quality

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

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Curated date: 2023/11/17

Curator: Davvve

Revision editor(s): Davvve, Imaspecial, Chloe

Subjects

Location of subjects: Italy

Host species Species from which microbiome was sampled. Contact us to have more species added.: Not specified

Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology: Space surrounding organism External to organism,Outside of body,Space surrounding organism,space surrounding organism

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: Environmental factor environment factor,Environmental factor,environmental factor

Group 0 name Corresponds to the control (unexposed) group for case-control studies: No healthy samples

Group 1 name Corresponds to the case (exposed) group for case-control studies: 2017 samples

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: 2017 samples are samples obtained from the three river depths(Meso, Secchi, and surface depth) during the cyanobacterial bloom in 2017.

Group 1 sample size Number of subjects in the case (exposed) group: 3

Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any): non

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).: relative abundances

Significance threshold p-value or FDR threshold used for differential abundance testing (if any): 0.05

Matched on Factors on which subjects have been matched on in a case-control study: Matched on: "depth" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.depth

Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment: Confounders controlled for: "depth" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.depth

Alpha Diversity

Pielou Quantifies how equal the community is numerically: decreased

Shannon Estimator of species richness and species evenness: more weight on species richness: decreased

Chao1 Abundance-based estimator of species richness: unchanged

Simpson Estimator of species richness and species evenness: more weight on species evenness: decreased

Richness Number of species: decreased

Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample: decreased

Signature 1

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Curated date: 2024/03/07

Curator: Imaspecial

Revision editor(s): Imaspecial

Source: Figure 3

Description: Taxonomic analysis at the phylum level showed that, in most of the samples, Proteobacteria was the predominant taxonomic group followed by Actinobacteriota, Cyanobacteria and Bacteroidota .

Abundance in Group 1: increased abundance in 2017 samples

NCBI	Quality Control	Links
ProteobacteriaProteobacteria

Revision editor(s): Imaspecial