Community-integrated omics links dominance of a microbial generalist to fine-tuned resource usage

被引：61

作者：

Muller, Emilie E. L. ^{[1
]}

Pinel, Nicolas ^{[1
,2
]}

Laczny, Cedric C. ^{[1
]}

Hoopmann, Michael R. ^{[2
]}

Narayanasamy, Shaman ^{[1
]}

Lebrun, Laura A. ^{[1
]}

Roume, Hugo ^{[1
]}

Lin, Jake ^{[1
]}

May, Patrick ^{[1
]}

Hicks, Nathan D. ^{[3
]}

Heintz-Buschart, Anna ^{[1
]}

Wampach, Linda ^{[1
]}

Liu, Cindy M. ^{[3
]}

Price, Lance B. ^{[3
]}

Gillece, John D. ^{[3
]}

Guignard, Cedric ^{[4
]}

Schupp, James M. ^{[3
]}

Vlassis, Nikos ^{[1
]}

Baliga, Nitin S. ^{[2
]}

Moritz, Robert L. ^{[2
]}

Keim, Paul S. ^{[3
]}

Wilmes, Paul ^{[1
]}

机构：

[1] Univ Luxembourg, Luxembourg Ctr Syst Biomed, L-4362 Esch Sur Alzette, Luxembourg

[2] Inst Syst Biol, Seattle, WA 98109 USA

[3] TGen North, Flagstaff, AZ 86001 USA

[4] Ctr Rech Publ Gabriel Lippmann, L-4422 Belvaux, Luxembourg

来源：

NATURE COMMUNICATIONS | 2014年 / 5卷

基金：

美国国家科学基金会; 美国国家卫生研究院;

关键词：

MICROTHRIX-PARVICELLA; MAXIMUM-LIKELIHOOD; STATISTICAL-MODEL; READ ALIGNMENT; RAST SERVER; RNA; BACTERIAL; SEQUENCE; QUANTIFICATION; EVOLUTION;

D O I：

10.1038/ncomms6603

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

Microbial communities are complex and dynamic systems that are primarily structured according to their members' ecological niches. To investigate how niche breadth (generalist versus specialist lifestyle strategies) relates to ecological success, we develop and apply an integrative workflow for the multi-omic analysis of oleaginous mixed microbial communities from a biological wastewater treatment plant. Time- and space-resolved coupled metabolomic and taxonomic analyses demonstrate that the community-wide lipid accumulation phenotype is associated with the dominance of the generalist bacterium Candidatus Microthrix spp. By integrating population-level genomic reconstructions (reflecting fundamental niches) with transcriptomic and proteomic data (realised niches), we identify finely tuned gene expression governing resource usage by Candidatus Microthrix parvicella over time. Moreover, our results indicate that the fluctuating environmental conditions constrain the accumulation of genetic variation in Candidatus Microthrix parvicella likely due to fitness trade-offs. Based on our observations, niche breadth has to be considered as an important factor for understanding the evolutionary processes governing (microbial) population sizes and structures in situ.

引用

页数：10

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