'ARMAN' archaea depend on association with euryarchaeal host in culture and in situ.
'ARMAN' archaea depend on association with euryarchaeal host in culture and in situ.
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DOI：
10.1038/s41467-017-00104-7
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发表时间：
2017-07-05
影响因子：
16.6
通讯作者：
Golyshin PN
中科院分区：
文献类型：
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作者：
Golyshina OV;Toshchakov SV;Makarova KS;Gavrilov SN;Korzhenkov AA;La Cono V;Arcadi E;Nechitaylo TY;Ferrer M;Kublanov IV;Wolf YI;Yakimov MM;Golyshin PN
有趣的是，尚未培养的“ARMAN”样古菌在代谢上依赖于微生物群落的其他成员。然而，由于缺乏完整的基因组，目前尚不清楚它们依赖于哪些宿主，以及在多大程度上依赖于宿主。在此，我们报道了在Parys Mountain （Isle of Anglesey， UK）的酸性河流中分离arman -2相关生物Mia14与Cuniculiplasma泄密PM4的共培养过程。Mia14在二元培养中高度富集（约10%的基因组读数），其缺失的0.95 Mbp基因组指向中心代谢途径的严重空洞，表明对宿主C.泄密芽孢杆菌PM4的依赖性。从不同地点分离的密匙孢菌分离株和Parys山样本的霰弹枪序列数据分析表明Mia14与寄主之间存在广泛的遗传交换。在代表“DPANN”超门的具有高质量基因组组装的生物体子集中，Mia14谱系具有最大的基因通量，获得了数十个与宿主相互作用有关的基因。在没有完整基因组的情况下，未培养的arman样古菌的代谢能力一直是不确定的。在这里，Golyshina等人应用富集培养技术，发现arman样古菌Mia14缺失的基因组已经失去了关键的代谢途径，表明对宿主古菌Cuniculiplasma泄密菌的依赖。
Intriguing, yet uncultured ‘ARMAN’-like archaea are metabolically dependent on other members of the microbial community. It remains uncertain though which hosts they rely upon, and, because of the lack of complete genomes, to what extent. Here, we report the co-culturing of ARMAN-2-related organism, Mia14, with Cuniculiplasma divulgatum PM4 during the isolation of this strain from acidic streamer in Parys Mountain (Isle of Anglesey, UK). Mia14 is highly enriched in the binary culture (ca. 10% genomic reads) and its ungapped 0.95 Mbp genome points at severe voids in central metabolic pathways, indicating dependence on the host, C. divulgatum PM4. Analysis of C. divulgatum isolates from different sites and shotgun sequence data of Parys Mountain samples suggests an extensive genetic exchange between Mia14 and hosts in situ. Within the subset of organisms with high-quality genomic assemblies representing the ‘DPANN’ superphylum, the Mia14 lineage has had the largest gene flux, with dozens of genes gained that are implicated in the host interaction. In the absence of complete genomes, the metabolic capabilities of uncultured ARMAN-like archaea have been uncertain. Here, Golyshina et al. apply an enrichment culture technique and find that the ungapped genome of the ARMAN-like archaeon Mia14 has lost key metabolic pathways, suggesting dependence on the host archaeon Cuniculiplasma divulgatum.