Ammonia-oxidising archaea living at low pH: Insights from comparative genomics.
Ammonia-oxidising archaea living at low pH: Insights from comparative genomics.
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DOI：
10.1111/1462-2920.13971
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发表时间：
2017-12
影响因子：
5.1
通讯作者：
Gubry-Rangin C
中科院分区：
文献类型：
--
作者：
Herbold CW;Lehtovirta-Morley LE;Jung MY;Jehmlich N;Hausmann B;Han P;Loy A;Pester M;Sayavedra-Soto LA;Rhee SK;Prosser JI;Nicol GW;Wagner M;Gubry-Rangin C
专性嗜酸性成员的thaumarchaeotal属Nitrosotalea在酸性土壤中的硝化作用中起着重要作用，但他们的进化和生理适应酸性环境仍然知之甚少，只有一个单一的成员（Ca. N. devanaterra）进行基因组测序。在这项研究中，我们对另外两个培养的Ca。亚硝化菌菌株，提取了一个几乎完整的Ca。亚硝化菌宏基因组组装基因组从酸性沼泽，并进行比较基因组学的四个Ca。亚硝化菌基因组与其他19个古菌氨氧化剂基因组。平均核苷酸和氨基酸的身份表明，四个Ca。亚硝化菌属菌株代表该属内的单独物种。四个Ca。亚硝化菌基因组包含103个在所有其他氨氧化古菌中不存在的正向基因家族的核心集合，并且对于这些基因家族中的大多数，可以分别通过蛋白质组学或元转录组学分析在实验室培养物或环境中证明表达。系统发育分析表明，这些核心基因家族中的四个获得的Ca。亚硝化菌共同祖先通过水平基因转移从嗜酸代表的广古菌。我们推测，基因交换与这些嗜酸菌的竞争成功的Ca。酸性环境中的亚硝化菌属谱系。
Obligate acidophilic members of the thaumarchaeotal genus Candidatus Nitrosotalea play an important role in nitrification in acidic soils, but their evolutionary and physiological adaptations to acidic environments are still poorly understood, with only a single member of this genus (Ca. N. devanaterra) having its genome sequenced. In this study, we sequenced the genomes of two additional cultured Ca. Nitrosotalea strains, extracted an almost complete Ca. Nitrosotalea metagenome‐assembled genome from an acidic fen, and performed comparative genomics of the four Ca. Nitrosotalea genomes with 19 other archaeal ammonia oxidiser genomes. Average nucleotide and amino acid identities revealed that the four Ca. Nitrosotalea strains represent separate species within the genus. The four Ca. Nitrosotalea genomes contained a core set of 103 orthologous gene families absent from all other ammonia‐oxidizing archaea and, for most of these gene families, expression could be demonstrated in laboratory culture or the environment via proteomic or metatranscriptomic analyses respectively. Phylogenetic analyses indicated that four of these core gene families were acquired by the Ca. Nitrosotalea common ancestor via horizontal gene transfer from acidophilic representatives of Euryarchaeota. We hypothesize that gene exchange with these acidophiles contributed to the competitive success of the Ca. Nitrosotalea lineage in acidic environments.
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DOI：
10.1073/pnas.1109000108
发表时间：
2011-12-27
影响因子：
11.1
作者：
Gubry-Rangin, Cecile;Hai, Brigitte;Nicol, Graeme W.
通讯作者：
Nicol, Graeme W.
影响因子：
4.2
作者：
Hwang, Sungmin;Cordova, Bryan;Maupin-Furlow, Julie A.
通讯作者：
Maupin-Furlow, Julie A.
影响因子：
1.7
作者：
Bankevich, Anton;Nurk, Sergey;Pevzner, Pavel A.
通讯作者：
Pevzner, Pavel A.
DOI：
10.1074/jbc.m113.542993
发表时间：
2014-05-09
期刊：
The Journal of biological chemistry
影响因子：
--
作者：
Călinescu O;Paulino C;Kühlbrandt W;Fendler K
通讯作者：
Fendler K
影响因子：
3.7
作者：
Alkoby D;Rimon A;Budak M;Patino-Ruiz M;Călinescu O;Fendler K;Padan E
通讯作者：
Padan E