Riverine Bacterial Communities Reveal Environmental Disturbance Signatures within the Betaproteobacteria and Verrucomicrobia

Abstract

Riverine bacterial communities play an essential role in the biogeochemical coupling of terrestrial and marine environments, transforming elements and organic matter in their journey from land to sea. However, precisely due to the fact that rivers receive significant terrestrial input, the distinction between resident freshwater taxa vs. land-derived microbes can often become ambiguous. Furthermore, ecosystem perturbations could introduce allochthonous microbial groups and reshape riverine bacterial communities. Using full- and partial-length 16S ribosomal RNA gene sequences, we analyzed the composition of bacterial communities in the Tar River of North Carolina from November 2010 to November 2011, during which a natural perturbation occurred: the inundation of the lower reaches of an otherwise drought-stricken river associated with Hurricane Irene, which passed over eastern North Carolina in late August 2011. This event provided the opportunity to examine the microbiological, hydrological, and geochemical impacts of a disturbance, defined here as the large freshwater influx into the Tar River, superimposed on seasonal changes or other ecosystem variability independent of the hurricane. Our findings demonstrate that downstream communities are more taxonomically diverse and temporally variable than their upstream counterparts. More importantly, pre- vs. post-disturbance taxonomic comparison of the freshwater-dominant Betaproteobacteria class and the phylum Verrucomicrobia reveal a disturbance signature of previously undetected taxa of diverse origins. We use known traits of closely-related taxa to interpret the ecological function of disturbance-associated bacteria, and hypothesize that carbon cycling was enhanced post-disturbance in the Tar River, likely due to the flux of organic carbon into the system associated with the large freshwater pulse. Our analyses demonstrate the importance of geochemical and hydrological alterations in structuring bacterial communities, and illustrate the response of temperate riverine bacteria on fine taxonomic scales to a disturbance.

Keywords: 16S rRNA gene; Betaproteobacteria; Verrucomicrobia; bacterial community; river.

Figure 1

Tar River Watershed showing the upstream and downstream sampling sites, T1 and T6, respectively. The inset shows the location of the Tar-Pamlico watershed within North Carolina.

Figure 2

Physical, chemical, and biological parameters from the Tar River at Stn. T1 (upstream) and Stn. T6 (downstream). The diamond in the maximum gauge height plot represents the water level (2.30 m, source: USGS) immediately after the landfall of Hurricane Irene (indicated by the vertical dashed line) on August 27, 2011. DOC, cell counts, and bacterial production data are from a separate study (Bullock, 2014).

Figure 3

Tar River clone libraries from November 2010 to November 2011. Actinobacteria is in dark gray, Betaproteobacteria is in light gray, and Verrucomicrobia is in white. “Others” include Armatimonadetes, Chlorobium, Chloroflexi, Spirochaetae as well as candidate phyla OD1, OP3, OP11, TM6, and TM7.

Figure 4

Non-metric Multidimensional Scaling (NMDS). Bray-Curtis dissimilarity index was used to calculate the dissimilarity matrix for bacterial community composition at an OTU cutoff of 0.05.

Figure 5

Relative contributions of families within the Betaproteobacteria (A) as well as genera and unassigned phylotypes within Comamonadaceae (B). The identification of the different families, genera and well-defined clusters in Betaproteobacteria was based on constructed phylogenetic trees shown in Figure S2A (families) and Figure S2B (genera and other clusters), their annotation following published taxonomies of betaproteobacterial families and genera. “Un. Phylotype” refers to the Unassigned phylogtypes found within Comamonadaceae.

Figure 6

Phylogeny of subdivisions of the phylum Verrucomicrobia. Individual well-defined clusters are identified in the tree. Wherever possible, each identification includes a class and genus name; otherwise, a descriptive name is given to each cluster. “verI” refers to a freshwater lineage within Subdivision 2 as classified by Newton et al. (2011). Clones in bold type font are the Tar River clones; cultured species are italicized. The rapid bootstrap analysis feature of the Maximum Likelihood algorithm was used. The tree is rooted by Lentisphaera araneosa (AY3490428) and Victivallis vadensis (AY049713).