Selective enrichment and metagenomic analysis of three novel comammox Nitrospira in a urine-fed membrane bioreactor

Jiyun Li,Jianhua Guo,Ge Bai,Tao Liu,Chengwen Wang,Jie Li,Mike S M Jetten,Min Zheng,Zheng-Shuang Hua,Sebastian Lücker

doi:10.1038/s43705-021-00005-3

Abstract

The discovery of complete ammonia-oxidizing (comammox) Nitrospira has added an important new process to the microbial nitrogen cycle. While comammox Nitrospira have been detected in various ecosystems, only few studies have achieved their enrichment over other canonical nitrifiers. Here, we obtained a selective enrichment of comammox Nitrospira in a urine-fed membrane bioreactor in less than 200 days. By using 16S rRNA gene amplicon sequencing and quantitative PCR of the functional marker gene amoA, we observed a dominance (up to 30% relative abundance) of comammox Nitrospira over ammonia-oxidizing bacteria and archaea. Furthermore, the complete genomes of three new clade A comammox Nitrospira were recovered by metagenomics. These three strains were divergent from previously reported comammox species according to comparative genome and amoA-based analyses. In addition to the key genes for ammonia and nitrite oxidation, the three recovered genomes contained a complete urea utilization pathway. Our findings suggest that the urea present in the urine media played a significant role in the selective enrichment of these novel comammox Nitrospira, and support the diversity and versatility of their metabolism.

Highlights

Nitrification, an essential part of the global microbial nitrogen cycle, was for a long time assumed to be a two-step process catalyzed by distinct guilds of chemolithoautotrophic microorganisms.[1]
These kinetics were recently corroborated in a highly enriched culture that was dominated by a novel comammox Nitrospira, which surprisingly was partly inhibited by very low ammonium concentrations (>25 μM) in the media.[9]
Unlike any of the previous enrichments of comammox Nitrospira,[5,6] oxygen in this reactor was supplied in excess to maintain the dissolved oxygen (DO) concentration above 4 mg O2 L−1

Summary

INTRODUCTION

Nitrification, an essential part of the global microbial nitrogen cycle, was for a long time assumed to be a two-step process catalyzed by distinct guilds of chemolithoautotrophic microorganisms.[1]. Comammox Nitrospira has been widely detected in various natural and engineered systems, such as drinking water production and distribution systems,[10,11,12,13] agricultural soils,[14,15] and wastewater treatment processes.[16,17,18] In these aforementioned investigations, comammox Nitrospira nearly always cooccur with other nitrifiers, with whom they compete for the same substrates (mainly ammonia and oxygen) As mentioned above, their kinetic properties indicate that highly oligotrophic habitats and systems favoring slow growth are preferred niches facilitating the dominance of comammox Nitrospira.[8] to date there are only very few enriched comammox Nitrospira cultures, and only one pure culture available,[5,6,8] all of which were obtained after intensive cultivation efforts.

1234567890();,: MATERIALS AND METHODS

RESULTS

DISCUSSION