Metagenomics of the deep Mediterranean, a warm bathypelagic habitat.
Metagenomics of the deep Mediterranean, a warm bathypelagic habitat.
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深地中海的宏基因组学，一种温暖的男性气概栖息地。
DOI：
10.1371/journal.pone.0000914
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发表时间：
2007-09-19
期刊：
影响因子：
3.7
通讯作者：
Rodriguez-Valera, Francisco
中科院分区：
文献类型：
--
作者：
Martin-Cuadrado, Ana-Belen;Lopez-Garcia, Purificacion;Alba, Juan-Carlos;Moreira, David;Monticelli, Luis;Strittmatter, Axel;Gottschalk, Gerhard;Rodriguez-Valera, Francisco
元基因组学正在成为研究尚未探索的微生物生物圈的功能和生理的有力手段，并促使我们重新评估微生物生态学和进化的基本法则。大多数海洋元基因组分析几乎都是专门针对光亮水域的。我们用3,000米深的地中海浮游生物构建了一个超基因组骨架库，这比开阔海域类似深度的水域(∼14°C)要温暖得多(∼2°C)。我们通过从克隆库中扩增16S rRNA基因的系统发育筛选和对大约5,000个融合基因的两个插入末端测序的方法对文库进行分析。基因组招募策略显示，大多数高分对对应于来自根瘤菌的基因组，其中包括变形杆菌、共生根霉菌、植物真菌、酸杆菌、氯杆菌和变形伽马杆菌。我们发现了一种与太平洋远洋带相似的群落结构。然而，与太平洋中大洋(500-700米深)的相似性明显高于在该位置研究的4000米深的单一样本。代谢基因主要与复杂有机分子的分解、运输和降解有关，这与深海微生物普遍存在的异养生活方式相一致。然而，我们观察到编码脱氢酶的基因比例很高，其中包括COX基因，这表明有氧一氧化碳氧化作为一种额外的能源在深海中可能是重要的。对深海地中海和太平洋阿罗哈水柱的元基因组文库的比较表明，深海地中海群落更类似于太平洋的中上层群落，并表明，在缺乏光照的情况下，温度是海洋水柱中的一个主要分层因素，超过至少4000米深的压力。在这个最枯竭的栖息地，几条营养化学物质的代谢途径可以补充有机质的降解。
Metagenomics is emerging as a powerful method to study the function and physiology of the unexplored microbial biosphere, and is causing us to re-evaluate basic precepts of microbial ecology and evolution. Most marine metagenomic analyses have been nearly exclusively devoted to photic waters. We constructed a metagenomic fosmid library from 3,000 m-deep Mediterranean plankton, which is much warmer (∼14°C) than waters of similar depth in open oceans (∼2°C). We analyzed the library both by phylogenetic screening based on 16S rRNA gene amplification from clone pools and by sequencing both insert extremities of ca. 5,000 fosmids. Genome recruitment strategies showed that the majority of high scoring pairs corresponded to genomes from Rhizobiales within the Alphaproteobacteria, Cenarchaeum symbiosum, Planctomycetes, Acidobacteria, Chloroflexi and Gammaproteobacteria. We have found a community structure similar to that found in the aphotic zone of the Pacific. However, the similarities were significantly higher to the mesopelagic (500–700 m deep) in the Pacific than to the single 4000 m deep sample studied at this location. Metabolic genes were mostly related to catabolism, transport and degradation of complex organic molecules, in agreement with a prevalent heterotrophic lifestyle for deep-sea microbes. However, we observed a high percentage of genes encoding dehydrogenases and, among them, cox genes, suggesting that aerobic carbon monoxide oxidation may be important in the deep ocean as an additional energy source. The comparison of metagenomic libraries from the deep Mediterranean and the Pacific ALOHA water column showed that bathypelagic Mediterranean communities resemble more mesopelagic communities in the Pacific, and suggests that, in the absence of light, temperature is a major stratifying factor in the oceanic water column, overriding pressure at least over 4000 m deep. Several chemolithotrophic metabolic pathways could supplement organic matter degradation in this most depleted habitat.
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DOI：
10.1073/pnas.0510157103
发表时间：
2006-04-25
影响因子：
11.1
作者：
Ingalls, AE;Shah, SR;Pearson, A
通讯作者：
Pearson, A
影响因子：
56.9
作者：
DeLong, EF;Preston, CM;Karl, DM
通讯作者：
Karl, DM
DOI：
10.1098/rstb.2002.1105
发表时间：
2002-07-29
影响因子：
6.3
作者：
D'Amico, S;Claverie, P;Gerday, C
通讯作者：
Gerday, C
影响因子：
3
作者：
Falkowski, PG
通讯作者：
Falkowski, PG
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