Abstract

The discovery of complete ammonia oxidizers, comammox Nitrospira, represents a breakthrough in the history of nitrification research. Nitrospira inopinata, which was obtained from an aquatic ecosystem, is the only pure comammox bacterial isolate reported so far. Ammonia oxidation kinetics of N. inopinata indicated that they prefer an oligotrophic lifestyle and may directly compete with ammonia-oxidizing archaea (AOA), but representatives of comammox Nitrospira from terrestrial ecosystems are lacking. Current studies demonstrate that the functionally dominant comammox Nitrospira in terrestrial ecosystems are separated from most sequences obtained from aquatic and engineering systems. Clades A and B of comammox Nitrospira seemingly have different ecological preferences in soils, possibly due to their different ammonium uptake systems. Analyses of the evolutionary history indicate that some genes of comammox Nitrospira involved in ammonia oxidation could be laterally transferred from β-ammonia-oxidizing bacteria (AOB). Some comammox Nitrospira species may have similar ecological preferences with AOB and be functionally active in the niches where nitrification was previously considered to be dominated by AOB. Taken together, this review summarizes the recent findings of the biogeographical distribution and ecological preference of comammox Nitrospira in large-scale soil surveys, the responses of comammox Nitrospira to nitrogen application in soil, and the putative mechanisms underpinning the ecological niche of terrestrial comammox Nitrospira. These studies from terrestrial ecosystems suggest that comammox Nitrospira are not strictly oligotrophic but both oligotrophic and copiotrophic with a broader ecological niche breadth. Comammox Nitrospira in terrestrial ecosystems are abundant and active in both oligotrophic and copiotrophic environments. These findings have profoundly expanded our knowledge of the environmental niches of comammox Nitrospira and their relative contribution to nitrification in soils.

摘要

完全氨氧化剂 comammox Nitrospira的发现代表了硝化研究史上的突破。从水生生态系统中获得的Nitrospira inopinata是迄今为止报道的唯一一种纯 comammox 细菌分离物。N. inopinata的氨氧化动力学表明它们更喜欢贫营养的生活方式，并可能直接与氨氧化古细菌 (AOA) 竞争，但缺乏来自陆地生态系统的 comammox Nitrospira的代表。目前的研究表明，功能上占主导地位的 comammox Nitrospira在陆地生态系统中，从水生和工程系统中获得的大多数序列是分开的。comammox Nitrospira的进化枝 A 和 B似乎在土壤中具有不同的生态偏好，这可能是由于它们不同的铵吸收系统。进化史分析表明，参与氨氧化的 comammox Nitrospira的一些基因可以从 β-氨氧化细菌 (AOB) 横向转移。一些comammox Nitrospira物种可能与 AOB 具有相似的生态偏好，并且在以前被认为由 AOB 主导硝化作用的生态位中具有功能活性。总之，这篇综述总结了在大规模土壤调查中 comammox Nitrospira的生物地理分布和生态偏好的最新发现，comammox Nitrospira对土壤中施氮的响应，以及支持陆地 comammox Nitrospira生态位的推定机制。这些来自陆地生态系统的研究表明，comammox Nitrospira并非严格意义上的寡养，而是兼具寡养和富养性，具有更广泛的生态位宽度。Comammox Nitrospira在陆地生态系统中，它们在贫营养和富营养环境中都很丰富且活跃。这些发现极大地扩展了我们对 comammox Nitrospira的环境生态位及其对土壤硝化作用的相对贡献的认识。