Putative Mixotrophic Nitrifying-Denitrifying Gammaproteobacteria Implicated in Nitrogen Cycling Within the Ammonia/Oxygen Transition Zone of an Oil Sands Pit Lake

Abstract

Anthropogenically-impacted environments offer the opportunity to discover novel microbial species and metabolisms, which may be undetectable in natural systems. Here, a combined metagenomic and geochemical study in Base Mine Lake, Alberta, Canada, which is the only oil sands end pit lake to date, revealed that nitrification was performed by members from Nitrosomonadaceae, Chloroflexi and unclassified Gammaproteobacteria “MBAE14.” While Nitrosomonadaceae and Chloroflexi groups were relatively abundant in the upper oxygenated zones, MBAE14 dominated the hypoxic hypolimnetic zones (approximately 30% of total microbial communities); MBAE14 was not detected in the underlying anoxic tailings. Replication rate analyses indicate that MBAE14 grew in metalimnetic and hypolimnetic water cap regions, most actively at the metalimnetic, ammonia/oxygen transition zone consistent with it putatively conducting nitrification. Detailed genomic analyses of MBAE14 evidenced both ammonia oxidation and denitrification into dinitrogen capabilities. However, the absence of known CO2-fixation genes suggests a heterotrophic denitrifying metabolism. Functional marker genes of ammonia oxidation (amo and hao) in the MBAE14 genome are homologous with those conserved in autotrophic nitrifiers, but not with those of known heterotrophic nitrifiers. We propose that this novel MBAE14 inhabits the specific ammonia-rich, oxygen and labile organic matter-limited conditions occurring in Base Mine Lake which selectively favors mixotrophic coupled nitrifier denitrification metabolism. Our results highlight the opportunities to better constrain biogeochemical cycles from the application of metagenomics to engineered systems associated with extractive resource sectors.

Active Anaerobic Archaeal Methanotrophs in Recently Emerged Cold Seeps of Northern South China Sea

“…Both Dehalococcoidia and JG30-KF-CM66 are affiliated to Chloroflexi. Meanwhile, the former contains the genes associated with degradation of various organic matter such as fatty acids and aromatic compounds (Wasmund et al, 2014) and the latter contains genes related to nitrite oxidoreduction (Mori et al, 2019). Gemmatimonadetes can be involved in polyphosphate accumulation and carotenoid production in soil (Zhang H. et al, 2003;Takaichi et al, 2010).…”

Large freshwater phages with the potential to augment aerobic methane oxidation

“…The Base Mine Lake is characterized by high concentrations of dissolved methane and ammonia (up to 253 μM and 73.5 μM, respectively; Fig. 1a and see also Supplementary Table 1 ), especially in the hypolimnetic zone (the lower layer of water in a thermally stratified lake) and at the tailings–water interface, reflecting mobilization of these reductants from the underlying tailings 21 , 22 . Stable isotope analysis (d 13 C, d 2 H) of pore water methane from within the tailings indicated that the methane was produced via fermentation by indigenous methanogenic archaea 23 .…”

Seasonal dynamics of prokaryotes and their associations with diatoms in the Southern Ocean as revealed by an autonomous sampler

“…Among the well‐known ammonia oxidizers, Nitrosopumilus and Nitrospina were present at low relative abundances during the first two time points (<4% of total abundance), and they accounted for <1% during the remaining season. Pseudomonadaceae and Nitrincolaceae contain genes for nitrite oxidoreductase (Mori et al ., 2019), mediating the transformation from nitrite to nitrate. Genes for nitrite reductase, nitric oxide reductase and nitrous oxide reductase are further present in Nitrincolaceae (Mori et al ., 2019) indicating their potential to reduce nitrite to nitrous oxide (N 2 O) and dinitrogen (N 2 ).…”