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. 2024 Jun;16(3):e13272.
doi: 10.1111/1758-2229.13272.

Metagenomic analysis of microbial consortia native to the Amazon, Highlands, and Galapagos regions of Ecuador with potential for wastewater remediation

Juan José Guadalupe  1 , Miguel Pazmiño-Vela  1 , Gabriela Pozo  1 , Wendy Vernaza  2 , Valeria Ochoa-Herrera  2   3 , Maria de Lourdes Torres  1 , Andres F Torres  1
Affiliations

Metagenomic analysis of microbial consortia native to the Amazon, Highlands, and Galapagos regions of Ecuador with potential for wastewater remediation

Juan José Guadalupe et al. Environ Microbiol Rep. 2024 Jun.

Abstract

Native microbial consortia have been proposed for biological wastewater treatment, but their diversity and function remain poorly understood. This study investigated three native microalgae-bacteria consortia collected from the Amazon, Highlands, and Galapagos regions of Ecuador to assess their metagenomes and wastewater remediation potential. The consortia were evaluated for 12 days under light (LC) and continuous dark conditions (CDC) to measure their capacity for nutrient and organic matter removal from synthetic wastewater (SWW). Overall, all three consortia demonstrated higher nutrient removal efficiencies under LC than CDC, with the Amazon and Galapagos consortia outperforming the Highlands consortium in nutrient removal capabilities. Despite differences in α- and β-diversity, microbial species diversity within and between consortia did not directly correlate with their nutrient removal capabilities. However, all three consortia were enriched with core taxonomic groups associated with wastewater remediation activities. Our analyses further revealed higher abundances for nutrient removing microorganisms in the Amazon and Galapagos consortia compared with the Highland consortium. Finally, this study also uncovered the contribution of novel microbial groups that enhance wastewater bioremediation processes. These groups have not previously been reported as part of the core microbial groups commonly found in wastewater communities, thereby highlighting the potential of investigating microbial consortia isolated from ecosystems of megadiverse countries like Ecuador.

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Conflict of interest statement

The authors declare that there is no conflict of interest.

Figures

FIGURE 1
FIGURE 1
Map of Ecuador indicating the sampling sites for each of three microalgae–bacteria consortia native to the (A) Amazon, (B) Highlands, and (C) Galapagos regions of Ecuador. The map was generated using ArcGIS Pro 3.2.
FIGURE 2
FIGURE 2
Nutrient removal patterns for (A) ammonium (NH4 +), (B) phosphate (PO4 3−), and (C) soluble COD for three microalgae‐bacteria consortia from the Ecuadorian Amazon, Highlands, and Galapagos regions incubated in SWW under light (LC) and continuous dark (CDC) conditions. All batch bioassays were carried out in duplicate. Results show means and error bars indicate ± standard deviation of duplicate measures.
FIGURE 3
FIGURE 3
Percent relative abundance of the most represented taxa (phylum level) for three microalgae–bacteria consortia from the Ecuadorian Amazon, Highlands, and Galapagos regions incubated in SWW under light (LC) and continuous dark (CDC) conditions.
FIGURE 4
FIGURE 4
Histogram showing linear discriminant analysis (LDA) scores for the most abundant taxonomic groups (genus level) in three microalgae–bacteria consortia from the Ecuadorian Amazon, Highlands, and Galapagos regions incubated in SWW under light (LC) and continuous dark (CDC) conditions. Significance was tested by Kruskal–Wallis test (α < 0.05) and log LDA score (>2.0). Asterisks (*) highlight microbial taxa commonly found in wastewater communities (Dueholm et al., ; Wu et al., 2019).
FIGURE 5
FIGURE 5
Principal coordinate analyses of Bray–Curtis beta‐diversity showing the effects of geographic origin (Location) and light conditions (Treatments) on the microbial community structure of three microalgae–bacteria consortia from the Ecuadorian Amazon, Highlands, and Galapagos regions incubated in SWW under light (LC) and continuous dark (CDC) conditions.
FIGURE 6
FIGURE 6
Heatmap showing the relative abundance for the two most dominant KEGG pathway identifiers (KP IDs) associated with nitrogen metabolism (i.e., ammonium metabolism and nitrogen fixation) for three Ecuadorian microalgae–bacteria consortia from the Ecuadorian Amazon, Highlands, and Galapagos regions incubated in SWW under light (LC) and continuous dark (CDC) conditions. Transcripts per million (TPM) refers to the number of genes from each KEGG pathway per million genes in the metagenome.
FIGURE 7
FIGURE 7
Heatmaps showing the raw abundance (counts) of the KP IDs collapsed into metabolic functions at a first‐order (based on the annotation according to the KEGG database) of three microalgae–bacteria consortia from the Ecuadorian Amazon, Highlands, and Galapagos regions incubated in SWW under light conditions (LC). Each heatmap is related to a specific nutrient or compound removed: (A) COD, (B) Phosphate (PO4 3−), and (C) Ammonium (NH4 +).
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