Unveiling microbial succession dynamics on different plastic surfaces using WGCNA

Abstract

Over recent decades, marine microorganisms have increasingly adapted to plastic debris, forming distinct plastic-attached microbial communities. Despite this, the colonization and succession processes on plastic surfaces in marine environments remain poorly understood. To address this knowledge gap, we conducted a microbiome succession experiment using four common plastic polymers (PE, PP, PS, and PET), as well as glass and wood, in a temperature-controlled seawater system over a 2- to 90-day period. We employed long-read 16S rRNA metabarcoding to profile the prokaryotic microbiome's taxonomic composition at five time points throughout the experiment. By applying Weighted Gene Co-expression Network Analysis (WGCNA) to our 16S metabarcoding data, we identified unique succession signatures for 77 bacterial genera and observed polymer-specific enrichment in 39 genera. Our findings also revealed that the most significant variations in microbiome composition across surfaces occurred during the initial succession stages, with potential intra-genus relationships that are linked to surface preferences. This research advances our understanding of microbial succession dynamics on marine plastic debris and introduces a robust statistical approach for identifying succession signatures of specific bacterial taxa.

Fig 1. Diversity parameters.

(A, B) Alpha diversity indexes for richness (Chao1) and biodiversity (Shannon). (C) PCA analysis for dissimilarity among samples (ANOVA test with post hoc pairwise comparison *p <0.05, **p <0.01).

Fig 2. Shared and unique mapped species between debris, plastic (all polymers combined), and glass.

(A) Venn diagrams by time points. (B) Percent of shared species between debris and plastic and between debris and glass (averages). (C) Percent of shared and unique species between plastic and glass at each time point. * Refer to the initial debris microbiome composition (at the beginning of the experiment).

Fig 3. Relative abundance of top abundant genera.

(A) Primary experiment at 28±2 °C. (B) Second experiment at 35±2 °C. The top 6 genera of each of the plastic polymer types are represented.

Fig 4. Cluster dendrograms and module assignments.

(A) Cluster dendrogram based on the relative abundance patterns of identified bacterial species. Hierarchical clustering was performed using topology overlap measure (TOM). The colors represent the module assignments of the clusters. (B) Merged dynamic module clustering of similar eigengenes based on a merging threshold height = 0.25. (C) Module eigengenes table with module-trait corresponding correlation and significance values.

Fig 5. Examples of pivotal genera within modules.

Module membership values of the key genera–Alteromonas (A), Dokdonia (B) and Nevskia (C) are represented in the context of their associate modules: Salmon, Brown and Turquoise accordingly (left side). The corresponding gene significance (GS) charts depicting the level of correlation of the key genera to all traits (surface type and time point) are presented on the right side. Dashed line indicates significance threshold (p-value = 0.05) to trait.

Fig 6. Pseudomonas genus demonstrates succession sub-groups.

(A, B) Distribution of mapped species in modules Green (A) and Turquoise (B) by module membership and significance to the relevant trait (according to module eigengenes). Pseudomonas species are emphasized in Red. (C, D) The corresponding gene significance (GS) heat maps for Pseudomonas, depicting the level of correlation to each trait (surface types and time points).

Fig 7. Co-occurrence network of dominant plastisphere genera.

Only genera that passed the abundance filter are represented (see Methods section for details). The relative abundances of the represented genera on the different plastic polymers are shown in the pie charts in different colors: Green—PE, purple—PP, PET—orange and PS—pink. The pie chart sizes represent the general prevalence of each genus. Four identified clusters are marked with Roman letters (I-IV).