Geospatial distribution of viromes in tropical freshwater ecosystems

Abstract

This study seeks to understand the general distribution of virome abundance and diversity in tropical freshwater ecosystems in Singapore and the geospatial distribution of the virome under different landuse patterns. Correlations between diversity, environmental parameters and land use patterns were analyzed and significant correlations were highlighted. Overall, the majority (65.5%) of the annotated virome belonged to bacteriophages. The percentage of Caudovirales was higher in reservoirs whereas the percentages of Dicistroviridae, Microviridae and Circoviridae were higher in tributaries. Reservoirs showed a higher Shannon-index virome diversity compared to upstream tributaries. Land use (urbanized, agriculture and parkland areas) influenced the characteristics of the virome distribution pattern. Dicistroviridae and Microviridae were enriched in urbanized tributaries while Mimiviridae, Phycodnaviridae, Siphoviridae and Podoviridae were enriched in parkland reservoirs. Several sequences closely related to the emerging zoonotic virus, cyclovirus, and the human-related virus (human picobirnavirus), were also detected. In addition, the relative abundance of PMMoV (pepper mild mottle virus) sequences was significantly correlated with RT-qPCR measurements (0.588 < r < 0.879, p < 0.05). This study shows that spatial factors (e.g., reservoirs/tributaries, land use) are the main drivers of the viral community structure in tropical freshwater ecosystems.

Keywords: Diversity; Freshwater ecosystems; Geospatial distribution; Human-related viruses; Land use; Virome.

Graphical abstract

Fig. 1

Relative abundance of taxonomic assignment of virome based on family level using Absolute Reads matrix from Metavir2 pipeline. (Abbreviations: NA, not assigned sequences).

Fig. 2

Taxonomic percentage of annotated sequences in Metavir2 at (A) Sites 1, 2 and 4 in both reservoirs and their tributaries (B) Sites 1–7 in reservoirs in Jan, Apr 2015 based on absolute reads matrix. "R" and "T" stand for Reservoir and Tributary, respectively.

Fig. 3

PCoA analysis of (A) Metagenome (<0.22μm), (B) Virsorter Cat 1, Cat 2 phages in samples from different land use, (C) Metagenome (<0.22μm), (D) Virsorter Cat 1, Cat 2 phages in samples in all sites (labels in plot means R: Reservoir, T: Tributary), (E) 16s rRNA gene amplicon sequencing distinguished by Phylum level and (F) 16s rRNA gene amplicon sequencing distinguished by OTU level based on Bray-Curtis similarity index. In (A), individual viral family (only dominant viral families (>0.1% of all the virome) are selected) contributing to variation were determined by Spearman rank correlation (R > 0.4) to the first two PCO axis and are represented by vectors and in (E), individual bacteria phylum contributing to variation were determined by Spearman rank correlation (R > 0.7) to the first two PCO axis and are represented by vectors.

Fig. 4

Heatmap of human-related virus across all the sampling points (log(RPKM+1)). Note: Samples from reservoirs and tributaries are on the left and right part of the dashed line, respectively.