Surprisingly High Diversity of the Cosmopolitan, Metabolically Diverse Bacterial Family Comamonadaceae in an Appalachian (WV) Headwater Stream Impacted by Acid Mine Drainage

Abstract:

Acid mine drainage (AMD) has adversely affected thousands of miles of headwater streams in the Appalachian Mountains where surface and underground coal mining has occurred. Although AMD-impacted streams are degraded, their chemistry, hydrology and microbiology are distinct from the AMD source. Severe AMD sites have low species diversity. However, AMD-disturbed streams represent a heterogeneous environment due to overlapping chemical gradients, landscape inputs, and hydrology which could create microniches that are distinct from the undisturbed watershed and support high diversity. Family Comamonadaceae (Betaproteobacteria) is widespread in freshwater environments and soils, and displays remarkable metabolic diversity including aerobes and anaerobes, photoauto- and photoheterotrophy, denitrification, fermentation, iron reduction, hydrogen oxidation, and more. We tested the hypothesis that the chemically heterogeneous sediment of an AMD-impacted stream has high microbial diversity. The Kanawha River (WV) watershed encompasses 12,000 sq. miles and includes many surface and underground coal mines, valley fills, and acid mine drainage. Sediment samples (1-5 cm) were collected from two locations in a stream adjacent to an AMD seep (pH 3.8) near Marmet, WV. Illumina sequencing and EMP protocols were used for 16S rRNA gene diversity. Chemical analysis was done with ICP-OES and Dionex Ion Chromatography. 16S sequences totaling 174,000 paired-end reads were analyzed with QIIME. The rocky stream bottom was coated with the classic orange iron oxide and devoid of periphyton. Water pH was 7. Water and sediment chemistry varied: organic C in water (zero) and sediment (102 mg/kg); inorganic C in water (28.4 mg/L) and sediment (2.6 mg/kg); Mg in water (77.4 mg/L) and sediment (57.8 mg/kg); iron in water (0.24 mg/L) and sediment (0.07 mg/L); Ca in water (91.7 mg/L) and sediment (225.6 mg/kg). Sulfate was high in both environments (500-2200 mg/Kg). 12% of sequences represent Comamonadaceae, including 19 named genera, unnamed genera, and >2200 species (97% 16S similarity) of which 1900 are novel. In conclusion, a biologically degraded AMD headwater stream supports exceptional diversity of the metabolically flexible Comamonadaceae. Funding by USDA NIFA grant #2019-38821-29065.