Nitrifiers Cooperate to Produce Nitrous Oxide in Plateau Wetland Sediments.

The thawing of dormant plateau permafrost emits nitrous oxide (N2O) through wetlands; however, the N2O production mechanism in plateau wetlands is still unclear. Here, we used the 15N-18O double tracer technique and metagenomic sequencing to analyze the N2O production mechanism in the Yunnan-Kweichow and Qinghai-Tibet plateau wetlands during the summer of 2020. N2O production activity was detected in all 16 sediment samples (elevation 1020-4601 m: 2.55 ± 0.42-26.38 ± 3.25 ng N g-1 d-1) and was promoted by nitrifier denitrification (ND). The key functional genes of ND (amoA, hao, and nirK) belonged to complete ammonia oxidizing (comammox) bacteria, and the key ND species was the comammox bacterium Nitrospira nitrificans. We found that the comammox bacterial species N. nitrificans and the ammonia oxidizing bacterial (AOB) species Nitrosomonas europaea cooperate to produce N2O in the plateau wetland sediments. Furthermore, we inferred that environmental factors (elevation and total organic matter (TOM)) influence the cooperation pattern via N. nitrificans, thus affecting the N2O production activity in the plateau wetland sediments. Our findings advance the mechanistic understanding of nitrifiers in biogeochemical cycles and global climate change.

Nutrient-Limited Enrichments of Nitrifiers From Soil Yield Consortia of Nitrosocosmicus-Affiliated AOA and Nitrospira-Affiliated NOB.

The discovery of ammonia-oxidizing archaea (AOA) and complete ammonia-oxidizing (comammox) bacteria widespread in terrestrial ecosystems indicates an important role of these organisms in terrestrial nitrification. Recent evidence indicated a higher ammonia affinity of comammox bacteria than of terrestrial AOA and ammonia-oxidizing bacteria (AOB), suggesting that comammox bacteria could potentially represent the most low-nutrient adapted nitrifiers in terrestrial systems. We hypothesized that a nutrient-limited enrichment strategy could exploit the differences in cellular kinetic properties and yield enrichments dominated by high affinity and high yield comammox bacteria. Using soil with a mixed community of AOA, AOB, and comammox Nitrospira, we compared performance of nutrient-limited chemostat enrichment with or without batch culture pre-enrichment in two different growth media without inhibitors or antibiotics. Monitoring of microbial community composition via 16S rRNA and amoA gene sequencing showed that batch enrichments were dominated by AOB, accompanied by low numbers of AOA and comammox Nitrospira. In contrast, nutrient-limited enrichment directly from soil, and nutrient-limited sub-cultivation of batch enrichments consistently yielded high enrichments of Nitrosocosmicus-affiliated AOA associated with multiple canonical nitrite-oxidizing Nitrospira strains, whereas AOB numbers dropped below 0.1% and comammox Nitrospira were lost completely. Our results reveal competitiveness of Nitrosocosmicus sp. under nutrient limitation, and a likely more complex or demanding ecological niche of soil comammox Nitrospira than simulated in our nutrient-limited chemostat experiments.

[Long-term Fertilization Effects on the Abundance of Complete Ammonia Oxidizing Bacteria(Comammox Nitrospira) in a Neutral Paddy Soil].

The discovery of the complete ammonia-oxidizing microbes, Comammox Nitrospira, had fundamentally changed our perspective on traditional nitrification. The microbe also played a potentially under-appreciated role in the biogeochemical N cycle and provided a new dimension for the research of nitrification. To investigate the abundance of Comammox in different ecosystems was urgently needed. In the present study, three treatments with different quantities of fertilization in a paddy soil (blank control, NPK and 1.5 NPKS) to investigate the nitrification and amoA gene abundance for nitrifying microorganisms, especially for the complete ammonia oxidizing bacteria (Comammox Nitrospira). The results showed that:① Both Comammox Clade A and Comammox Clade B were detected in all three treatments, and the abundance of Comammox Clade A were 9.0×107, 1.7×108, 7.2×108 copies·g-1 (dry soil), respectively, and for Comammox Clade B were 1.5×107, 1.2×107, 1.7×107 copies·g-1 (dry soil), respectively. ② The abundances of both ammonia-oxidizing archaea (AOA)in the three fertilizers was 1.5×107-1.2×108 copies·g-1 (dry soil), and the ammonia-oxidizing bacteria (AOB) in the three fertilizers was 2.0×105-9.3×107 copies·g-1 (dry soil), lower than the abundance of the Comammox. The ratio of Comammox to AOA was 7.2, and the ratio for Comammox to AOB was 524.4 for blank control, were greater than NPK and 1.5 NPKS treatments. ③ The ratio of Comammox Clade A to Comammox Clade B showed an increasing trend with the increase in fertilizer application, at 6.1, 14.4 and 43.1, respectively. ④ For NPK and 1.5 NPKS treatments, Comammox Clade A amoA gene copies were 1.9 and 8.0 times higher than that of the blank control treatment respectively, and the numbers for AOA significantly increased to 3.2 and 7.2 times that of the blank control. The AOB gene copy numbers increased by two orders of magnitude compared with the blank control. In addition, the nitrification potential increased with the increase in N fertilizer application; however, the effects of different fertilizer treatments on Comammox Clade B were not significant. Results indicated that Comammox was widely distributed in the neutral purple paddy soil and was higher in abundance than AOA or AOB, which implied that Comammox-especially Clade A-may contribute to the nitrification of paddy soil.