Rasmussen Anna N, Tolar Bradley B, Bargar John R, Boye Kristin, Francis Christopher A
Department of Earth System Science, Stanford University, Stanford, California, USA.
Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California, USA.
Environ Microbiol. 2025 Mar;27(3):e70060. doi: 10.1111/1462-2920.70060.
Riparian floodplains are important regions for biogeochemical cycling, including nitrogen. Here, we present MAGs from nitrifying microorganisms, including ammonia-oxidising archaea (AOA) and comammox bacteria from Slate River (SR) floodplain sediments (Crested Butte, CO, US). Additionally, we explore MAGs from potential nitrite-oxidising bacteria (NOB) from the Nitrospirales. AOA diversity in SR is lower than observed in other western US floodplain sediments and Nitrosotalea-like lineages such as the genus TA-20 are the dominant AOA. No ammonia-oxidising bacteria (AOB) MAGs were recovered. Microorganisms from the Palsa-1315 genus (clade B comammox) are the most abundant ammonia-oxidizers in SR floodplain sediments. Established NOB are conspicuously absent; however, we recovered MAGs from uncultured lineages of the NS-4 family (Nitrospirales) and Nitrospiraceae that we propose as putative NOB. Nitrite oxidation may be carried out by organisms sister to established Nitrospira NOB lineages based on the genomic content of uncultured Nitrospirales clades. Nitrifier MAGs recovered from SR floodplain sediments harbour genes for using alternative sources of ammonia, such as urea, cyanate, biuret, triuret and nitriles. The SR floodplain therefore appears to be a low ammonia flux environment that selects for oligotrophic nitrifiers.
河岸洪泛区是生物地球化学循环的重要区域，包括氮循环。在此，我们展示了来自硝化微生物的宏基因组，包括来自美国科罗拉多州克里斯特德比特的斯莱特河（SR）洪泛区沉积物中的氨氧化古菌（AOA）和完全氨氧化细菌。此外，我们还探索了来自硝化螺旋菌门潜在亚硝酸盐氧化细菌（NOB）的宏基因组。SR中的AOA多样性低于美国西部其他洪泛区沉积物中观察到的多样性，并且诸如TA-20属的类硝化螺旋菌属谱系是主要的AOA。未获得氨氧化细菌（AOB）的宏基因组。来自帕尔萨-1315属（B类完全氨氧化菌）的微生物是SR洪泛区沉积物中最丰富的氨氧化菌。明显缺乏已确定的NOB；然而，我们从NS-4家族（硝化螺旋菌门）和硝化螺菌科未培养谱系中获得了宏基因组，我们将其作为假定的NOB。根据未培养的硝化螺旋菌门分支的基因组内容，亚硝酸盐氧化可能由已确定的硝化螺菌属NOB谱系的姐妹生物进行。从SR洪泛区沉积物中获得的硝化菌宏基因组含有利用替代氨源（如尿素、氰酸盐、缩二脲、三聚脲和腈）的基因。因此，SR洪泛区似乎是一个低氨通量环境，选择了贫营养型硝化菌。
