Abstract
Ammonia-oxidizing archaea (AOA) are widely distributed on the earth and play a significant role in the global nitrogen cycle. Although dozens of AOA strains were obtained in the last 13 years, it is still necessary to obtain more AOA strains for the entire exploration of their ecology, physiology, and underlying biochemistry in different environments. In this study, we designed a two-step strategy for the rapid enrichment of Nitrosocosmicus–like AOA from soils. Firstly, combination of kanamycin and ampicillin was chosen as the selective stress for bacteria and quartz sands were used as the attachment of AOA cells during the first step cultivation; only after 40–75 days cultivation, AOA enrichments with abundance >20% were obtained. Secondly, combination of ciprofloxacin and azithromycin was chosen as the selective stress for the following cultivation; it is able to penetrate the biofilms and kill the bacterial cells inside the aggregate, contributing to the AOA enrichments reached high abundances (90%) only after one-time cultivation. Basing on this strategy, three AOA strains were obtained from agricultural soils only after 90–150 days cultivation. Phylogenetic analysis suggested these AOA belong to the soil group I.1b Thaumarchaeota and are closely related to the genus Nitrosocosmicus. In general, AOA enrichment or isolation is very difficult and time-consuming (an average of 2–3 years). Here, we provide a new strategy for the rapid enrichment of high abundance of Nitrosocosmicus-like AOA from soil, which gives a new solution to the AOA enrichment and cultivation in a short period.
Highlights
Autotrophic aerobic ammonia oxidation is the primary step in oxidizing ammonia to nitrate and is central to the global nitrogen cycle (Kowalchuk and Stephen, 2001)
To find a suitable antibiotic for suppressing bacterial growth at the beginning of Ammonia-oxidizing archaea (AOA) enrichment, the nitrite that produced in ammonia oxidation was used as the evaluation index for antibiotic selection
The ammonia-oxidizing rate and nitrite-producing rate always remained at stable levels, which indicated that the AOA enrichment cultivation reached a stable phase
Summary
Autotrophic aerobic ammonia oxidation is the primary step in oxidizing ammonia to nitrate and is central to the global nitrogen cycle (Kowalchuk and Stephen, 2001). AOA appear to be adapted to life under nutrient limitation (Horak et al, 2013; Shiozaki et al, 2016), which suggests that they have a significantly broader habitat range than the characterized AOB They appear to be the dominant archaeal clade in soil (generally comprising 1–5% of all prokaryotes) (Ochsenreiter et al, 2003; Lehtovirta et al, 2009; Tago et al, 2015), the marine system (comprising 20–40% of all marine bacterioplankton) (Karner et al, 2001; Church et al, 2003), and geothermal habitats (Zhang et al, 2008; Dodsworth et al, 2011)
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