Comparative metagenomics insight into the microbial structures of the Lemna dumpsite, an open dumpsite, and a non-dumpsite soil ecosystem

Abstract

Open dumpsites remain the solid disposal method of choice in various Nigerian cities and towns. Dumpsite soil ecosystems hold dynamic microbial communities that are still poorly described. This study is aimed at comparing the microbial communities of an open dumpsite soil popularly called Lemna dumpsite located in Calabar, Cross River State, Nigeria, with those of a control soil in addition to their physicochemical properties. Deciphering the effects of waste disposal on soil microbial communities, which is crucial for developing sustainable waste management practices and protecting soil health form the importance of the study. Composite samples were evaluated for physicochemistry using standard protocols, while microbial communities were assessed using metagenomics on the Illumina Miseq platform. The result of the physicochemical analysis showed significant differences between the control (CSS) and dumpsite soil (DSS) (p < 0.05). The pH of the DSS was lower than that of the CSS with values that were 6.5 ± 0.21 and 7.40 ± 0.02, respectively. On the other hand, the concentrations of electrical conductivity (EC), total hydrocarbon content (THC), total moisture and total organic carbon (TOC) for the DSS were higher than that of the CSS with values that were 34.3 ± 0.28 µ/Scm^-1, 3.04 ± 0.25 mg/kg, 0.76 ± 0.22 % and 5.0 ± 0.21 % for DSS and 15.60 ± 0.26 µ/Scm-1, 0.95 ± 0.22 mg/kg, 0.71 ± 0.23 %, and 4.50 ± 0.24 % for the CSS, respectively. Similarly, the concentrations of Pb, Ni, Cd and Co were higher in DSS than CSS with values that were 1.00 ± 0.02, 0.02 ± 0.01, 0.17 ± 0.02, 0.33 ± 0.03 mg/kg for DSS and BDL, 0.01 ± 0.0, 0.03 ± 0.01 and BDL mg/kg, for the CSS respectively for Pb, Ni, Cd and Co. Metagenomics revealed differences in both samples from kingdom to species level; however, overall, DSS had more abundance than the CSS. The top two most abundant kingdoms were bacteria and protozoa in both samples, with abundance rates of 98.9 and 1.01 %, and 98.26 and 0.08 % for DSS and CSS, respectively. At phyla level in the DSS, proteobacteria (42.4 %) followed by unknown (41.66 %) were the top two phyla while for CSS, it as unknown taxa with an abundance of 83.74 % followed by actinobacteria (7.36 %). Diverse classes and orders were also observed in both groups. In the DSS, medically important species with high public health significance were detected and these were Clostridium, Enterococcus and Pseudomonas species while the CSS was dominated by biotechnologically important species such as Streptomyces. Overall, our findings indicate a need for proper management of waste.