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Short-term stable isotope probing of proteins reveals taxa incorporating inorganic carbon in a hot spring microbial mat
Applied and Environmental Microbiology ( IF 4.4 ) Pub Date : 2020-01-17
Steinke, L., Slysz, G. W., Lipton, M. S., Klatt, C., Moran, J. J., Romine, M. F., Wood, J. .M., Anderson, G., Bryant, D. A., Ward, D. M.

The upper green layer of the chlorophototrophic microbial mats associated with the alkaline siliceous hot springs of Yellowstone National Park consist 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. 25,483 peptides, corresponding to 7,221 proteins, were identified from spectral features and associated with mat taxa by comparison to metagenomic assembly sequences. 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. Protein-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 for 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.



中文翻译:

蛋白质的短期稳定同位素探测揭示了在温泉微生物垫中结合了无机碳的分类单元

与黄石国家公园的碱性硅质温泉相关联的chlorophototrophic微生物席的上生坯层由含氧蓝藻(聚球藻属物种),不产氧Roseiflexus属,和其他一些不产氧chlorophototrophs。聚球藻属。被认为是无机碳(C i)的主要固定剂,但一些证据表明Roseiflexus spp。在弱光,缺氧的早晨,也有助于固定无机碳。尚未研究其他光养类群的贡献。为了遵循C i纳入不同类群的途径,将席子样品与13早间,弱光缺氧期间,碳酸氢盐持续3 h。提取的蛋白质用胰蛋白酶处理,并通过质谱分析,从而得到包含13 C-标记掺入证据的肽鉴定和肽同位素特征。通过与宏基因组组装序列比较,从光谱特征中鉴定出25,483个肽,对应于7,221个蛋白,并与垫分类群相关。从720种蛋白质衍生的1,417个肽段被13 C可检测地标记。大多数13 C标记的肽衍生自Synechococcus spp的蛋白质。和Roseiflexusspp。伴侣和碳水化合物代谢的蛋白质标记最丰富。在Synchococcus spp中也标记了参与光合作用,C i固定和N 2固定的蛋白质。重要的是,3-羟基丙酸酯的双循环对C的大多数蛋白质固定在Roseiflexus属。进行标记,在建立这taxocene成员有助于Ç固定。其他类群的13 C-碳酸氢盐掺入量要低得多。

重要性黄石温泉地垫已被研究为理解微生物群落生态的自然模型,并被作为叠层石的现代类似物,即地球上最早的群落化石。蛋白-SIP允许的参与的光驱动C中的重要过程中的类群的短期询问固定在这个高度活跃的社区,将在连接其他代谢过程到垫类群是有用的。在这里,证据表明使用3-羟基丙酸酯双环的Roseiflexus spp。在C i固定中具有活性。因为此途径赋予同位素重C i较低的选择度与Calvin-Benson-Bassham循环相比,该结果提出了一种机制,说明了如果仅涉及后者的途径,为什么垫层生物量中13 C的自然丰度大于预期。了解垫群落成员如何影响垫生物量的13 C / 12 C比值将有助于地球化学家解释化石记录中有机碳的13 C / 12 C比值。

更新日期:2020-01-21
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