Bacterial Diversity and Community Structure of a Municipal Solid Waste Landfill: A Source of Lignocellulolytic Potential

Abstract

Omics have given rise to research on sparsely studied microbial communities such as the landfill, lignocellulolytic microorganisms and enzymes. The bacterial diversity of Municipal Solid Waste sediments was determined using the illumina MiSeq system after DNA extraction and Polymerase chain reactions. Data analysis was used to determine the community's richness, diversity, and correlation with environmental factors. Physicochemical studies revealed sites with mesophilic and thermophilic temperature ranges and a mixture of acidic and alkaline pH values. Temperature and moisture content showed the highest correlation with the bacteria community. The bacterial analysis of the community DNA revealed 357,030 effective sequences and 1891 operational taxonomic units (OTUs) assigned. Forty phyla were found, with the dominant phyla Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidota, while Aerococcus, Stenotrophomonas, and Sporosarcina were the dominant species. PICRUSt provided insight on community's metabolic function, which was narrowed down to search for lignocellulolytic enzymes' function. Cellulase, xylanase, esterase, and peroxidase were gene functions inferred from the data. This article reports on the first phylogenetic analysis of the Pulau Burung landfill bacterial community. These results will help to improve the understanding of organisms dominant in the landfill and the corresponding enzymes that contribute to lignocellulose breakdown.

Keywords: bacteria; biodiversity; landfill; lignocellulolytic bacteria; lignocellulolytic enzyme; lignocellulose biomass; metagenomics.

Figure 1

Location of study sites and layout of the sampling points in Pulau Burung Landfill, Penang, Malaysia. (Top right—Map of Malaysia; Top left—Map of Penang; Bottom—Study area detailing the sampling points in the landfill.

Figure 2

Principal coordinates analysis (PCoA) of the bacterial community structure showing plot based on the similarity coefficients of bacterial communities. Points closer to one another in ordination space indicate a closer similarity than those farther apart. Axes 1 and 2 represent principal components 1 and 2, 45.1% and 39.6% of the total variations, respectively.

Figure 3

Observing similarities among the samples. The Venn diagram showing the number of shared and unique OTUs between the libraries of bacterial 16S rRNA genes on sediment samples A to D.

Figure 4

Composition of the bacterial community in MSW sediments from the landfill at the phylum level.

Figure 5

Composition of bacteria in MSW sediments from the Pulau Burung landfill at the class level.

Figure 6

Heatmap of bacterial distribution of from the four samples at the genus level. Row represents the relative percentage of each bacterial genus, and column stands for different samples. The relative abundance for each bacterial genus was depicted by color intensity with the legend indicated at the top of the figure.

Figure 7

Correlation analysis showing relationship between (a) the bacterial community and the physicochemical properties (b), the distribution of the top genus observed in the bacterial community.

Figure 7

Correlation analysis showing relationship between (a) the bacterial community and the physicochemical properties (b), the distribution of the top genus observed in the bacterial community.

Figure 8

Summary of prediction of lignocellulolytic enzyme gene functions, as seen in Samples A–D. (a) Ligninolytic family of enzymes, showing their function inference at each site. (b) Cellulolytic enzymes inferred in the different samples. Bars represent standard errors. Different letters over columns indicate significant differences between various samples.