Genome of a low-salinity ammonia-oxidizing archaeon determined by single-cell and metagenomic analysis.
Genome of a low-salinity ammonia-oxidizing archaeon determined by single-cell and metagenomic analysis.
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DOI：
10.1371/journal.pone.0016626
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发表时间：
2011-02-22
期刊：
影响因子：
3.7
通讯作者：
Quake SR
中科院分区：
文献类型：
--
作者：
Blainey PC;Mosier AC;Potanina A;Francis CA;Quake SR
氨氧化古菌（AOA）被认为是地球上最丰富的微生物之一，可能对全球氮和碳循环产生重大影响。我们利用单细胞和宏基因组基因组序列数据对旧金山湾低盐度沉积物中富集培养的AOA基因组进行了测序。用激光镊子在集成微流控装置内分离5个单细胞，用50 nL体积的多位移扩增（MDA）法扩增细胞基因组DNA，然后用高通量DNA焦磷酸测序法测序。这种基于显微镜的单细胞基因组学方法最大限度地减少了污染，并允许高分辨率细胞图像与基因组序列的相关性。覆盖五个单细胞的统计特性，结合宏基因组数据集的对比特性，允许组装高质量的草图基因组。该AOA（候选亚硝基古菌limnia SFB1）的基因组为~ 1.77 Mb，基因数为bb0 2100个，G+C含量为32%。在整个基因组中，与唯一纯培养的AOA - Nitrosopumilus maritimus的平均核苷酸同源性为~ 70%，表明该AOA代表了一个新的Crenarchaeota属。在系统发育上，该AOA的16S rRNA和氨单加氧酶亚单位A （amoA）基因与各种淡水生态系统中报道的序列最密切相关。与N. maritimus一样，低盐度AOA基因组似乎具有不同于氨氧化细菌（AOB）的氨氧化途径。与其他已描述的AOA相比，这些低盐度AOA似乎具有运动性，这是基于基因组中存在许多运动性和趋化性相关基因。这些基因组数据将用于对这一新型AOA群体进行有针对性的生理和代谢研究，这可能最终促进我们对AOA代谢及其对全球碳氮循环的影响的理解。
Ammonia-oxidizing archaea (AOA) are thought to be among the most abundant microorganisms on Earth and may significantly impact the global nitrogen and carbon cycles. We sequenced the genome of AOA in an enrichment culture from low-salinity sediments in San Francisco Bay using single-cell and metagenomic genome sequence data. Five single cells were isolated inside an integrated microfluidic device using laser tweezers, the cells' genomic DNA was amplified by multiple displacement amplification (MDA) in 50 nL volumes and then sequenced by high-throughput DNA pyrosequencing. This microscopy-based approach to single-cell genomics minimizes contamination and allows correlation of high-resolution cell images with genomic sequences. Statistical properties of coverage across the five single cells, in combination with the contrasting properties of the metagenomic dataset allowed the assembly of a high-quality draft genome. The genome of this AOA, which we designate Candidatus Nitrosoarchaeum limnia SFB1, is ∼1.77 Mb with >2100 genes and a G+C content of 32%. Across the entire genome, the average nucleotide identity to Nitrosopumilus maritimus, the only AOA in pure culture, is ∼70%, suggesting this AOA represents a new genus of Crenarchaeota. Phylogenetically, the 16S rRNA and ammonia monooxygenase subunit A (amoA) genes of this AOA are most closely related to sequences reported from a wide variety of freshwater ecosystems. Like N. maritimus, the low-salinity AOA genome appears to have an ammonia oxidation pathway distinct from ammonia oxidizing bacteria (AOB). In contrast to other described AOA, these low-salinity AOA appear to be motile, based on the presence of numerous motility- and chemotaxis-associated genes in the genome. This genome data will be used to inform targeted physiological and metabolic studies of this novel group of AOA, which may ultimately advance our understanding of AOA metabolism and their impacts on the global carbon and nitrogen cycles.
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影响因子：
14.9
作者：
Grissa, Ibtissem;Vergnaud, Gilles;Pourcel, Christine
通讯作者：
Pourcel, Christine
影响因子：
3.6
作者：
ASHKIN, A;DZIEDZIC, JM;CHU, S
通讯作者：
CHU, S
DOI：
10.1073/pnas.0506625102
发表时间：
2005-10-11
影响因子：
11.1
作者：
Francis, CA;Roberts, KJ;Oakley, BB
通讯作者：
Oakley, BB
影响因子：
11
作者：
Beman, J. Michael;Popp, Brian N.;Francis, Christopher A.
通讯作者：
Francis, Christopher A.
影响因子：
4.4
作者：
AMANN, RI;ZARDA, B;SCHLEIFER, KH
通讯作者：
SCHLEIFER, KH