Metagenomics datasets of water and sediments from eutrophication-impacted artificial lakes in South Africa

Abstract

We present metagenomes of 16 samples of water and sediment from two lakes, collected from eutrophic and non-eutrophic areas, including pooled samples enriched with phosphate and nitrate. Additionally, we assembled 167 bacterial metagenome-assembled genomes (MAGs). These MAGs were de-replicated into 83 unique genomes representing different species found in the lakes. All the MAGs exhibited >70% completeness and <10% contamination, with 79 MAGs being classified as 'nearly complete' (completeness >90%), while 54 falling within 80-90% range and 34 between 75-80% complete. The most abundant MAGs identified across all samples were Proteobacteria (n = 80), Firmicutes_A (n = 35), Firmicutes (n = 13), and Bacteriodota (n = 22). Other groups included Desulfobacteria_I (n = 2), Verrucomicrobiota (n = 4), Campylobacterota (n = 4) and Actinobacteriota (n = 6). Importantly, phylogenomic analysis identified that approximately 50.3% of the MAGs could not be classified to known species, suggesting the presence of potentially new and unknown bacteria in these lakes, warranting further in-depth investigation. This study provides valuable new dataset on the diverse and often unique microbial communities living in polluted lakes, useful in developing effective strategies to manage pollution.

Fig. 1

Sample Collection and Metagenomic Analysis. (a) Geographical location of the sample sites. (b) The sampling area within each lake. (c) Schematic representation for the metagenomic analysis conducted.

Fig. 2

Relative abundance of bacterial phyla in the lake sediment and water samples based on Kraken2/ Bracken classification.

Fig. 3

Overview of the MAGS. (a) The relationship between genomic size and N50 length among MAGs. (b) The relationship between the completeness and contamination of MAGs. (c) Boxplots compare the distribution of genomic size and GC content among MAGs at the phylum level.

Fig. 4

Taxonomic annotation and novelty of MAGs. (a) Phylogenomics-based taxonomic classification of the 167 MAGs dataset at the phylum level. The phylum Proteobacteria have been split at class level. (b) Stacked bar plot of the relative distribution of MAGs at phylum level across different samples. The top bars represent the number of MAGs in each sample. (c) Stacked bar plot for novelty quantification of 167 MAGs at different taxonomic ranks.

Fig. 5

Phylogenetic tree of bacteria at species-level MAGs (n = 167). The colors within the circle at the ends of the phylogenetic branches represent known (green) and unknown (black) species. The outer ring represents the various phyla of the MAGs as per the labels in the legend.