Microbial diversity in intensively farmed lake sediment contaminated by heavy metals and identification of microbial taxa bioindicators of environmental quality

Abstract

The cumulative effects of anthropogenic stress on freshwater ecosystems are becoming increasingly evident and worrisome. In lake sediments contaminated by heavy metals, the composition and structure of microbial communities can change and affect nutrient transformation and biogeochemical cycling of sediments. In this study, bacterial and archaeal communities of lake sediments under fish pressure contaminated with heavy metals were investigated by the Illumina MiSeq platform. Despite the similar content of most of the heavy metals in the lagoon sediments, we found that their microbial communities were different in diversity and composition. This difference would be determined by the resilience or tolerance of the microbial communities to the heavy metal enrichment gradient. Thirty-two different phyla and 66 different microbial classes were identified in sediment from the three lagoons studied. The highest percentages of contribution in the differentiation of microbial communities were presented by the classes Alphaproteobacteria (19.08%), Cyanophyceae (14.96%), Betaproteobacteria (9.01%) y Actinobacteria (7.55%). The bacteria that predominated in sediments with high levels of Cd and As were Deltaproteobacteria, Actinobacteria, Coriobacteriia, Nitrososphaeria and Acidobacteria (Pomacocha), Alphaproteobacteria, Chitinophagia, Nitrospira and Clostridia (Tipicocha) and Betaproteobacteria (Tranca Grande). Finally, the results allow us to expand the current knowledge of microbial diversity in lake sediments contaminated with heavy metals and to identify bioindicators taxa of environmental quality that can be used in the monitoring and control of heavy metal contamination.

DL-TODA: A Deep Learning Tool for Omics Data Analysis

“…Likewise, in the cropland soil metagenomes, a higher proportion of Clostridia and Coriobacteriia was identified by DL-TODA compared to Centrifuge or Kraken2. The abundance of Clostridia and Coriobacteriia, as predicted by DL-TODA, aligns well with prior studies of diverse agricultural related soil types [ 34 , 35 , 36 ]. Due to the lack of ground truth data, it is difficult to fully assess the accuracy of different tools on the metagenomes.…”

Exploring the diversity and structural response of sediment-associated microbiota communities to environmental pollution at the siangshan wetland in Taiwan using environmental DNA metagenomic approach

“…Other important phyla observed in this study are, Actinobacterota, Planctomycetota, Acidobacteriota, Gemmatimonadota, Myxococcota, and Halobacteriota (Archaea) as the most abundant. All the abundant microbial phyla obtained in this study have been documented previously in other metal-contaminated environments, such as sediments (Lee et al, 2021;Rajeev et al, 2021;Yi et al, 2021;Custodio et al, 2022), iron tailing pond (Li et al, 2021), mining soils (Cao et al, 2017;Hemmat-Jou et al, 2018;Liu et al, 2021a), paddy soils (Tseng et al, 2021), arid loess region (Zeng et al, 2020), and electric waste soils (Jiang et al, 2019), this suggests that these phyla are associated with metal-polluted sediment.…”

Preliminary study of shark microbiota at a unique mix-species shark aggregation site, in the Eastern Mediterranean Sea

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