Proteomic Stable Isotope Probing Reveals Taxonomically Distinct Patterns in Amino Acid Assimilation by Coastal Marine Bacterioplankton.
Proteomic Stable Isotope Probing Reveals Taxonomically Distinct Patterns in Amino Acid Assimilation by Coastal Marine Bacterioplankton.
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DOI：
10.1128/msystems.00027-15
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发表时间：
2016-03
期刊：
影响因子：
6.4
通讯作者：
Mueller RS
中科院分区：
文献类型：
--
作者：
Bryson S;Li Z;Pett-Ridge J;Hettich RL;Mayali X;Pan C;Mueller RS
据估计，每年有50亿吨碳固定在海洋系统中，其中近一半由异养微生物种群处理。这些社区的组成和活动在不同的空间和时间尺度上各不相同，因此，要了解这些变化如何影响全球进程，就需要划定各个成员的职能作用。在确定这些角色的一个步骤中，我们应用蛋白质组学稳定同位素探测来量化从DFAAs到微生物蛋白质生物量的有机碳同化，因为DFAAs的营业额占海洋微生物碳代谢的很大一部分，直接进入生物质生产。我们在北太平洋两个沿海地区进行了实验，发现分类学上不同的反应。这种方法使我们能够比较特定的浮游细菌种群的氨基酸同化，并表征其分配这种基板之间的细胞功能。异养海洋浮游细菌是碳循环的重要组成部分，处理近四分之一的年度初级生产，但如何确定基板利用偏好和资源分配结构微生物群落仍然是一个挑战。在这项研究中，蛋白质组学稳定同位素探测（蛋白质组学SIP）被用来表征人口特异性同化的溶解游离氨基酸（DFAAs），溶解有机碳的主要来源，在水生环境中的细菌次级生产。将从俄勒冈州的纽波特和加州的蒙特雷湾采集的海水缩影与1 µM 13 C标记的氨基酸孵育15和32 h。微宇宙元蛋白质组的分类组成与采样的自然群落高度相似，以红细菌目、SAR 11和黄细菌目为优势类群。13 C掺入蛋白质生物量的分析允许定量的同位素富集的确定的蛋白质和随后的测定特定的浮游细菌种群之间的差异氨基酸同化模式。与Rhodocalales相关的蛋白质倾向于具有显着高频率的13 C-富集肽，与Flavobacteriales和SAR 11蛋白的趋势相反。与氨基酸运输和代谢相关的Rhodocalales蛋白在时间点2具有增加的13 C富集光谱的频率。交替单胞菌目蛋白质也具有显著高频率的13 C-富集肽，特别是在核糖体蛋白内，证明它们在孵育期间快速生长。总的来说，蛋白质组SIP促进定量比较DFAA同化的特定类群，同域种群之间和离散种群内的蛋白质功能组之间，允许前所未有的人口水平的代谢反应，在复杂的微生物群落的资源收购。海洋系统中每年固定的碳估计为50亿吨，其中近一半由异养微生物群处理。这些社区的组成和活动在不同的空间和时间尺度上各不相同，因此，要了解这些变化如何影响全球进程，就需要划定各个成员的职能作用。在确定这些角色的一个步骤中，我们应用蛋白质组学稳定同位素探测来量化从DFAAs到微生物蛋白质生物量的有机碳同化，因为DFAAs的营业额占海洋微生物碳代谢的很大一部分，直接进入生物质生产。我们在北太平洋两个沿海地区进行了实验，发现分类学上不同的反应。这种方法使我们能够比较特定的浮游细菌种群的氨基酸同化，并表征其分配这种基板之间的细胞功能。
An estimated 50 gigatons of carbon is annually fixed within marine systems, of which heterotrophic microbial populations process nearly half. These communities vary in composition and activity across spatial and temporal scales, so understanding how these changes affect global processes requires the delineation of functional roles for individual members. In a step toward ascertaining these roles, we applied proteomic stable isotope probing to quantify the assimilation of organic carbon from DFAAs into microbial protein biomass, since the turnover of DFAAs accounts for a substantial fraction of marine microbial carbon metabolism that is directed into biomass production. We conducted experiments at two coastal North Pacific locations and found taxonomically distinct responses. This approach allowed us to compare amino acid assimilation by specific bacterioplankton populations and characterize their allocation of this substrate among cellular functions. Heterotrophic marine bacterioplankton are a critical component of the carbon cycle, processing nearly a quarter of annual primary production, yet defining how substrate utilization preferences and resource partitioning structure microbial communities remains a challenge. In this study, proteomic stable isotope probing (proteomic SIP) was used to characterize population-specific assimilation of dissolved free amino acids (DFAAs), a major source of dissolved organic carbon for bacterial secondary production in aquatic environments. Microcosms of seawater collected from Newport, Oregon, and Monterey Bay, California, were incubated with 1 µM 13C-labeled amino acids for 15 and 32 h. The taxonomic compositions of microcosm metaproteomes were highly similar to those of the sampled natural communities, with Rhodobacteriales, SAR11, and Flavobacteriales representing the dominant taxa. Analysis of 13C incorporation into protein biomass allowed for quantification of the isotopic enrichment of identified proteins and subsequent determination of differential amino acid assimilation patterns between specific bacterioplankton populations. Proteins associated with Rhodobacterales tended to have a significantly high frequency of 13C-enriched peptides, opposite the trend for Flavobacteriales and SAR11 proteins. Rhodobacterales proteins associated with amino acid transport and metabolism had an increased frequency of 13C-enriched spectra at time point 2. Alteromonadales proteins also had a significantly high frequency of 13C-enriched peptides, particularly within ribosomal proteins, demonstrating their rapid growth during incubations. Overall, proteomic SIP facilitated quantitative comparisons of DFAA assimilation by specific taxa, both between sympatric populations and between protein functional groups within discrete populations, allowing an unprecedented examination of population level metabolic responses to resource acquisition in complex microbial communities. IMPORTANCE An estimated 50 gigatons of carbon is annually fixed within marine systems, of which heterotrophic microbial populations process nearly half. These communities vary in composition and activity across spatial and temporal scales, so understanding how these changes affect global processes requires the delineation of functional roles for individual members. In a step toward ascertaining these roles, we applied proteomic stable isotope probing to quantify the assimilation of organic carbon from DFAAs into microbial protein biomass, since the turnover of DFAAs accounts for a substantial fraction of marine microbial carbon metabolism that is directed into biomass production. We conducted experiments at two coastal North Pacific locations and found taxonomically distinct responses. This approach allowed us to compare amino acid assimilation by specific bacterioplankton populations and characterize their allocation of this substrate among cellular functions.