Spatial distribution of sediment bacterial communities from São Francisco River headwaters is influenced by human land-use activities and seasonal climate shifts

Abstract

Riverbed sediments are dynamic freshwater environments colonized by a great diversity of microorganisms which play important roles in supporting freshwater ecosystem by performing a vast array of metabolic functions. Recent evidence generated by HTS approaches has revealed that the structure of sediment microbial communities is influenced by natural seasonal variations in water such as temperature or streamflow as well by disturbances caused by local human activities. Here, a spatiotemporal analysis of sediment microbial distribution from São Francisco River headwaters section was conducted using Illumina 16S rRNA-V4 region amplicon sequencing in order to accomplish three major goals: (i) to investigate whether the diversity and composition of bacterial communities accessed in riverbed sediments vary in response to distinct land-use activities; (ii) to estimate whether the diversity patterns vary between the dry and wet seasons; and (iii) to evaluate whether the diversity of bacterial metabolic functions, predicted by PICRUSt2 approach, varies similarly to the estimated taxonomic diversity. Our findings revealed that bacterial communities in the sediment show differences in diversity and taxonomic composition according to the anthropic activities performed in the local environment. However, the patterns in which this taxonomic diversity is spatially structured show differences between the dry and wet seasons. On the other hand, the most changes in predicted bacterial metabolic functions were verified between sediment samples accessed in portions of the river located in protected and unprotected areas. Our findings contributed with new evidence about the impact of typical land-use practices conducted in countryside landscapes from developing countries on riverbed bacterial communities, both in their taxonomic and functional structure.

Keywords: 16S rDNA; Bacterial communities; Land-use; River; Sediment.

Figure 1

Schematic diagram of study design and sampling. Study design (A); São Francisco River headwaters placed at Canastra Ridge region (B); Google Earth images from sampled zones: spring (C), urban (D), tourism + rural (E); collection sites: spring (F), urban (G), rural (H)

Figure 2

Taxonomic alpha-diversity indices of the sediment samples from the four land-use zones organized by season

Figure 3

Principal coordinate analysis (PCoA) plots of the dissimilarity (UniFrac-weighted matrices) in bacterial community composition by dry and wet seasons

Figure 4

Relative abundances of dominant phyla in sediment communities from each sampling site organized by season

Figure 5

Heatmap diagram of dominant family abundances from each sediment sample organized by season

Figure 6

Relative abundance of predicted metabolic functions classified by secondary level of KEGG pathway hierarchy and organized by season. Functional groups with less than < 1% relative abundance were not included

Figure 7

KO diversity and composition comparisons between adjacent zones, structured by secondary level of KEGG pathway hierarchy and organized by season

Figure 8

KO diversity and composition comparisons between wet and dry samples for each land-use zone structured by secondary level of KEGG pathway hierarchy and organized by season