Members of the Candidate Phyla Radiation are functionally differentiated by carbon- and nitrogen-cycling capabilities.
Members of the Candidate Phyla Radiation are functionally differentiated by carbon- and nitrogen-cycling capabilities.
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DOI：
10.1186/s40168-017-0331-1
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发表时间：
2017-09-02
期刊：
影响因子：
15.5
通讯作者：
Wilkins MJ
中科院分区：
文献类型：
--
作者：
Danczak RE;Johnston MD;Kenah C;Slattery M;Wrighton KC;Wilkins MJ
候选门辐射 (CPR) 是最近描述的生命树的扩展，代表了所有细菌多样性的 15% 以上，可能包含 70 多个不同的门。尽管存在广泛的系统发育变异，但这些微生物似乎几乎没有功能多样性，其成员通常被描述为专性发酵罐。此外，描述 CPR 门的许多数据都是从有限数量的环境中生成的，限制了我们对其功能作用和生物地理分布的了解。为了扩大我们对地下 CPR 微生物的了解，我们在两年多的时间里对俄亥俄州三个县的四个独立地下水井进行了采样。使用 16S rRNA 基因扩增子和鸟枪法宏基因组测序对样品进行分析。扩增子结果表明，CPR 成员占微生物群落的 2% 至 20%，其相对丰度在雅典和格林样本中随时间推移保持稳定，但在舔地下水中则呈动态变化。鸟枪法宏基因组分析生成了 71 个假定的 CPR 基因组，代表大约 32 个已知门和 2 个假定的新门：Candidatus Brownbacteria 和 Candidatus Hugbacteria。虽然这些基因组在很大程度上反映了已知 CPR 成员的代谢特征，但一些特征以前未被表征。例如，在我们的四个 Parcubacteria 基因组和其他研究的多个 CPR 基因组中发现了由 nirK 编码的亚硝酸还原酶，这表明这些微生物在反硝化作用中可能具有未被描述的作用。此外，我们还分析了 71 个基因组和 2000 多个其他 CPR 基因组的糖苷水解酶 (GH) 家族谱，以表征其碳处理潜力。尽管整个辐射过程中存在共同的趋势，但差异凸显了可能允许微生物穿过 CPR 占据各种地下生态位的潜在机制。例如，与其他 CPR 门相比，Microgenomates 超门的成员似乎可以降解更广泛的碳底物。 CPR 成员存在于各种环境中，尤其是地下水系统中，它们通常占微生物种群的很大一部分。对此类环境的进一步采样将在更精细的分类水平上解析生命树的这一部分，这对于巩固生命树这一系统发育广泛区域的成员之间的功能差异至关重要。本文的在线版本 (10.1186/s40168-017-0331-1) 包含补充材料，可供授权用户使用。
The Candidate Phyla Radiation (CPR) is a recently described expansion of the tree of life that represents more than 15% of all bacterial diversity and potentially contains over 70 different phyla. Despite this broad phylogenetic variation, these microorganisms appear to feature little functional diversity, with members generally characterized as obligate fermenters. Additionally, much of the data describing CPR phyla has been generated from a limited number of environments, constraining our knowledge of their functional roles and biogeographical distribution. To expand our understanding of subsurface CPR microorganisms, we sampled four separate groundwater wells over 2 years across three Ohio counties. Samples were analyzed using 16S rRNA gene amplicon and shotgun metagenomic sequencing. Amplicon results indicated that CPR members comprised between 2 and 20% of the microbial communities with relative abundances stable through time in Athens and Greene samples but dynamic in Licking groundwater. Shotgun metagenomic analyses generated 71 putative CPR genomes, representing roughly 32 known phyla and 2 putative new phyla, Candidatus Brownbacteria and Candidatus Hugbacteria. While these genomes largely mirrored metabolic characteristics of known CPR members, some features were previously uncharacterized. For instance, nitrite reductase, encoded by nirK, was found in four of our Parcubacteria genomes and multiple CPR genomes from other studies, indicating a potentially undescribed role for these microorganisms in denitrification. Additionally, glycoside hydrolase (GH) family profiles for our 71 genomes and over 2000 other CPR genomes were analyzed to characterize their carbon-processing potential. Although common trends were present throughout the radiation, differences highlighted potential mechanisms that could allow microorganisms across the CPR to occupy various subsurface niches. For example, members of the Microgenomates superphylum appear to potentially degrade a wider range of carbon substrates than other CPR phyla. CPR members are present across a range of environments and often constitute a significant fraction of the microbial population in groundwater systems, particularly. Further sampling of such environments will resolve this portion of the tree of life at finer taxonomic levels, which is essential to solidify functional differences between members that populate this phylogenetically broad region of the tree of life. The online version of this article (10.1186/s40168-017-0331-1) contains supplementary material, which is available to authorized users.
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影响因子：
48
作者：
Langmead, Ben;Salzberg, Steven L.
通讯作者：
Salzberg, Steven L.
影响因子：
2.7
作者：
Kang DD;Froula J;Egan R;Wang Z
通讯作者：
Wang Z
影响因子：
3.7
作者：
Danczak, Robert E.;Sawyer, Audrey H.;Wilkins, Michael J.
通讯作者：
Wilkins, Michael J.
影响因子：
3.4
作者：
Gong, Jun;Qing, Yao;Warren, Alan
通讯作者：
Warren, Alan
DOI：
10.1093/bioinformatics/bts199
发表时间：
2012-06-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Kearse M;Moir R;Wilson A;Stones-Havas S;Cheung M;Sturrock S;Buxton S;Cooper A;Markowitz S;Duran C;Thierer T;Ashton B;Meintjes P;Drummond A
通讯作者：
Drummond A