Short-Term Stable Isotope Probing of Proteins Reveals Taxa Incorporating Inorganic Carbon in a Hot Spring Microbial Mat
Short-Term Stable Isotope Probing of Proteins Reveals Taxa Incorporating Inorganic Carbon in a Hot Spring Microbial Mat
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蛋白质的短期稳定同位素探测揭示了温泉微生物垫中含有无机碳的类群
DOI：
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发表时间：
2020
影响因子：
4.4
通讯作者：
D. M. Ward
中科院分区：
文献类型：
--
作者：
L. Steinke;Gordon W. Slysz;M. Lipton;Christian G. Klatt;J. Moran;M. Romine;J. Wood;G. Anderson;D. Bryant;D. M. Ward
黄石温泉垫已被研究作为理解微生物群落生态学的自然模型，并作为地球上最早的群落化石--叠层石的现代类似物。稳定同位素探测的蛋白质（亲SIP）允许短期审讯的类群，参与光驱动的Ci固定在这个高度活跃的社会的重要过程，将是有用的，在连接其他代谢过程垫类群。在这里，有证据表明，Roseiflexus属，其使用3-羟基丙酸双环，在C1固定中是活性的。由于该途径赋予同位素重Ci的选择程度低于Calvin-Benson-Bassham循环，因此结果表明了一种机制，可以解释为什么如果仅涉及后一种途径，生物质中13 C的天然丰度大于预期。了解垫群落成员如何影响垫生物量的13 C/12 C比率将有助于地球化学家解释化石记录中有机碳的13 C/12 C比率。黄石国家公园碱性硅质温泉中的光合细菌垫的上层绿色由产氧蓝藻（聚球藻属）组成，无氧玫瑰弯藻属，和其他几种不产氧光合细菌。聚球藻属被认为是无机碳（Ci）的主要固定剂，但一些证据表明Roseiflexus spp.也有助于在低光、缺氧的早晨固定无机碳。其他光养类群的贡献尚未调查。为了遵循的途径，到不同的分类群，垫样品与[13 C]碳酸氢盐孵育3小时，在清晨，低光缺氧期间。用胰蛋白酶处理提取的蛋白质，并通过质谱法进行分析，得到肽鉴定和含有13 C标记掺入证据的肽同位素谱特征。通过与宏基因组组装序列的比较，从光谱特征中鉴定出总共25，483个肽，对应于7，221个蛋白质，并与mat分类群相关联。来自720种蛋白质的总共1，417种肽用13 C可检测地标记。大多数13 C标记的肽来源于聚球藻属的蛋白质。和Roseiflexus spp.分子伴侣和碳水化合物代谢的蛋白质是最丰富的标记。参与光合作用，C1固定和N2固定的蛋白质也被标记在聚球藻属中。重要的是，在Roseiflexus spp.中用于Ci固定的3-羟基丙酸双环的大多数蛋白质。被标记，建立该紫杉烯的成员有助于Ci固定。其他分类群显示出低得多的[13 C]碳酸氢根掺入。黄石温泉垫已被研究为理解微生物群落生态学的自然模型，并作为地球上最早的群落化石--叠层石的现代类似物。稳定同位素探测的蛋白质（亲SIP）允许短期审讯的类群，参与光驱动的Ci固定在这个高度活跃的社会的重要过程，将是有用的，在连接其他代谢过程垫类群。在这里，有证据表明，Roseiflexus属，其使用3-羟基丙酸双环，在C1固定中是活性的。由于该途径赋予同位素重Ci的选择程度低于Calvin-Benson-Bassham循环，因此结果表明了一种机制，可以解释为什么如果仅涉及后一种途径，生物质中13 C的天然丰度大于预期。了解垫群落成员如何影响垫生物量的13 C/12 C比率将有助于地球化学家解释化石记录中有机碳的13 C/12 C比率。
Yellowstone hot spring mats have been studied as natural models for understanding microbial community ecology and as modern analogs of stromatolites, the earliest community fossils on Earth. Stable-isotope probing of proteins (Pro-SIP) permitted short-term interrogation of the taxa that are involved in the important process of light-driven Ci fixation in this highly active community and will be useful in linking other metabolic processes to mat taxa. Here, evidence is presented that Roseiflexus spp., which use the 3-hydroxypropionate bi-cycle, are active in Ci fixation. Because this pathway imparts a lower degree of selection of isotopically heavy Ci than does the Calvin-Benson-Bassham cycle, the results suggest a mechanism to explain why the natural abundance of 13C in mat biomass is greater than expected if only the latter pathway were involved. Understanding how mat community members influence the 13C/12C ratios of mat biomass will help geochemists interpret the 13C/12C ratios of organic carbon in the fossil record. ABSTRACT The upper green layer of the chlorophototrophic microbial mats associated with the alkaline siliceous hot springs of Yellowstone National Park consists of oxygenic cyanobacteria (Synechococcus spp.), anoxygenic Roseiflexus spp., and several other anoxygenic chlorophototrophs. Synechococcus spp. are believed to be the main fixers of inorganic carbon (Ci), but some evidence suggests that Roseiflexus spp. also contribute to inorganic carbon fixation during low-light, anoxic morning periods. Contributions of other phototrophic taxa have not been investigated. In order to follow the pathway of Ci incorporation into different taxa, mat samples were incubated with [13C]bicarbonate for 3 h during the early-morning, low-light anoxic period. Extracted proteins were treated with trypsin and analyzed by mass spectrometry, leading to peptide identifications and peptide isotopic profile signatures containing evidence of 13C label incorporation. A total of 25,483 peptides, corresponding to 7,221 proteins, were identified from spectral features and associated with mat taxa by comparison to metagenomic assembly sequences. A total of 1,417 peptides, derived from 720 proteins, were detectably labeled with 13C. Most 13C-labeled peptides were derived from proteins of Synechococcus spp. and Roseiflexus spp. Chaperones and proteins of carbohydrate metabolism were most abundantly labeled. Proteins involved in photosynthesis, Ci fixation, and N2 fixation were also labeled in Synechococcus spp. Importantly, most proteins of the 3-hydroxypropionate bi-cycle for Ci fixation in Roseiflexus spp. were labeled, establishing that members of this taxocene contribute to Ci fixation. Other taxa showed much lower [13C]bicarbonate incorporation. IMPORTANCE Yellowstone hot spring mats have been studied as natural models for understanding microbial community ecology and as modern analogs of stromatolites, the earliest community fossils on Earth. Stable-isotope probing of proteins (Pro-SIP) permitted short-term interrogation of the taxa that are involved in the important process of light-driven Ci fixation in this highly active community and will be useful in linking other metabolic processes to mat taxa. Here, evidence is presented that Roseiflexus spp., which use the 3-hydroxypropionate bi-cycle, are active in Ci fixation. Because this pathway imparts a lower degree of selection of isotopically heavy Ci than does the Calvin-Benson-Bassham cycle, the results suggest a mechanism to explain why the natural abundance of 13C in mat biomass is greater than expected if only the latter pathway were involved. Understanding how mat community members influence the 13C/12C ratios of mat biomass will help geochemists interpret the 13C/12C ratios of organic carbon in the fossil record.
DOI：
10.1007/978-94-007-1533-2_3
发表时间：
2012-01-01
期刊：
FUNCTIONAL GENOMICS AND EVOLUTION OF PHOTOSYNTHETIC SYSTEMS
影响因子：
--
作者：
Bryant, Donald A.;Liu, Zhenfeng;Overmann, Joerg
通讯作者：
Overmann, Joerg
一种用于评估精确质量和时间标签蛋白质组学中肽鉴定置信度的统计方法。
影响因子：
7.4
作者：
Stanley,JeffreyR;Adkins,JoshuaN;Slysz,GordonW;Monroe,MatthewE;Purvine,SamuelO;Karpievitch,YuliyaV;Anderson,GordonA;Smith,RichardD;Dabney,AlanR
通讯作者：
Dabney,AlanR