Anaerobic ammonium oxidizing bacteria (anammox bacteria) are contributing significantly to the nitrogen cycle and are successfully used in wastewater treatment. Due to the lack of complete genomes in the databases, little is known about the stability and variability of their genomes and how the genomes evolve in response to changing environments. Here we report the complete genome of the anammox bacterium “Candidatus Kuenenia stuttgartiensis” strain CSTR1 which was enriched planktonically in a semi-continuous stirred-tank reactor. A comparison of the genome of strain CSTR1 with the genome of “Ca. Kuenenia stuttgartiensis” MBR1 and the draft genome of KUST showed > 99% average nucleotide identity among all. Rearrangements of large genomic regions were observed, most of which were associated with transposase genes. Phylogenetic analysis suggests that strain MBR1 is more distantly related to the other two strains. Proteomic analysis of actively growing cells of strain CSTR1 (growth rate ~ 0.33 d− 1) failed to detect the annotated cytochrome cd1-type nitrite reductase (NirS) although in total 1189 proteins were found in the proteome. Yet, this NirS was expressed when strain CSTR1 was under stress or starvation (growth rate < 0.06 d− 1). We also observed large sequence shifts in the strongly expressed S-layer protein compared to other “Ca. Kuenenia” strains, indicating the formation of hybrids of genes encoding the surface proteins. “Ca. Kuenenia” strains appear to be relatively stable in their basic physiological traits, but show high variability in overall genome structure and surface proteins.

中文翻译：

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在“比较基因组学暂定Kuenenia stuttgartiensis”揭示在整个基因组结构的基因组高可塑性，CRISPR基因座和表面蛋白

厌氧铵氧化细菌（厌氧细菌）对氮循环有重要贡献，已成功用于废水处理。由于数据库中缺少完整的基因组，人们对其基因组的稳定性和可变性以及基因组如何响应不断变化的环境而知之甚少。在这里，我们报告了厌氧细菌“ Candidatus Kuenenia stuttgartiensis”菌株CSTR1的完整基因组，该菌株在半连续搅拌釜反应器中浮游富集。菌株CSTR1的基因组与“ Ca. Ca.”的基因组的比较。Stuttgartiensis（Kuenenia stuttgartiensis）MBR1和KUST的基因组草图显示，所有基因组中的平均核苷酸同一性均> 99％。观察到大的基因组区域的重排，其中大多数与转座酶基因有关。系统发育分析表明，MBR1菌株与其他两个菌株的亲缘关系更远。尽管在蛋白质组中发现了总共1189种蛋白质，但对CSTR1菌株（生长速率〜0.33 d-1）的活跃生长细胞的蛋白质组学分析未能检测到带注释的细胞色素cd1型亚硝酸还原酶（NirS）。然而，当菌株CSTR1处于应激或饥饿状态（生长速率<0.06 d-1）时，表达了这种NirS。我们还观察到与其他“Ca。“ Kuenenia”菌株，表明形成了编码表面蛋白的基因的杂种。“ Ca. Kuenenia菌株在基本生理特征上似乎相对稳定，但在整体基因组结构和表面蛋白质方面表现出较高的变异性。