Nitrifier Gene Abundance and Diversity in Sediments Impacted by Acid Mine Drainage

Abstract

Extremely acidic and metal-rich acid mine drainage (AMD) waters can have severe toxicological effects on aquatic ecosystems. AMD has been shown to completely halt nitrification, which plays an important role in transferring nitrogen to higher organisms and in mitigating nitrogen pollution. We evaluated the gene abundance and diversity of nitrifying microbes in AMD-impacted sediments: ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), and nitrite-oxidizing bacteria (NOB). Samples were collected from the Iron Springs Mining District (Ophir, CO, United States) during early and late summer in 2013 and 2014. Many of the sites were characterized by low pH (<5) and high metal concentrations. Sequence analyses revealed AOA genes related to Nitrososphaera, Nitrosotalea, and Nitrosoarchaeum; AOB genes related to Nitrosomonas and Nitrosospira; and NOB genes related to Nitrospira. The overall abundance of AOA, AOB and NOB was examined using quantitative PCR (qPCR) amplification of the amoA and nxrB functional genes and 16S rRNA genes. Gene copy numbers ranged from 3.2 × 104 – 4.9 × 107 archaeal amoA copies ∗ μg DNA-1, 1.5 × 103 – 5.3 × 105 AOB 16S rRNA copies ∗ μg DNA-1, and 1.3 × 106 – 7.7 × 107 Nitrospira nxrB copies ∗ μg DNA-1. Overall, Nitrospira nxrB genes were found to be more abundant than AOB 16S rRNA and archaeal amoA genes in most of the sample sites across 2013 and 2014. AOB 16S rRNA and Nitrospira nxrB genes were quantified in sediments with pH as low as 3.2, and AOA amoA genes were quantified in sediments as low as 3.5. Though pH varied across all sites (pH 3.2–8.3), pH was not strongly correlated to the overall community structure or relative abundance of individual OTUs for any gene (based on CCA and Spearman correlations). pH was positivity correlated to the total abundance (qPCR) of AOB 16S rRNA genes, but not for any other genes. Metals were not correlated to the overall nitrifier community composition or abundance, but were correlated to the relative abundances of several individual OTUs. These findings extend our understanding of the distribution of nitrifying microbes in AMD-impacted systems and provide a platform for further research.

Does universal 16S rRNA gene amplicon sequencing of environmental communities provide an accurate description of nitrifying guilds?

“…Taken together, our results provide the first systematic validation of the use of universal approaches for quantification and composition estimation of nitrifying guilds, as done by several authors (Rughöft et al, 2016;Ramanathan et al 2017;Meerbergen et al, 2017;Saarenheimo et al 2017). Overall, the 16S rRNA gene based universal amplicon sequencing of environmental communities can be efficiently used as substitute to more narrow targeted approaches for:…”

Functional diversity and abundance of nitrogen cycle-related genes in paddy soil

“…Among the studied nitrifying genes, namely, nxrB and amoA, the abundance of nxrB was two-times higher than that of amoA. Similar results were reported by Ramanathan et al [31], in their study on nitrifier gene abundance in a sediment affected by acid mine drainage. Among various genes used in this study, namely, nifH, amoA, nxrB, hzsA, nirK, nirS, nosZ1, and nosZ2, the abundance of nxrB and nirS was relatively higher than that of the others, whereas the abundance of hzsA was found to be relatively lower.…”

Functional Characterization and Diversity of Ammonia-Oxidizing Microorganisms in Streams South of the Dabie Mountains, China

“…Nevertheless, our findings indicated the presence of some adapted species related to the Nitrosotalea cluster that can resist a comparably acidic pH (>6.5). Furthermore, our findings imply that, regarding the physiologic adaptation of microbial guilds to environmental pressure [36][37][38], most of the OTUs found in the sampling sites (more neutral pH) were correlated with sequences of freshwater [39][40][41]. Out of the AOB genes (Supplementary Figure S1), 61 sequences were collected, and these sequences were clustered into three OTUs.…”

“…Despite the pH, AOA and AOB abundance was high (3.92E+8 to 3.60E+8 gene copies per µg DNA extract) at site S4, with pH as low as 6.5. Due to consequent decreased pH in the bioavailability of nitrogen, acidic environments might preference AOA dominance over AOB because of their significant correlation with ammonia [41,61]. Various results of the comparative abundance of AOB and AOA have been reported in streams.…”