Poplar phyllosphere harbors disparate isoprene-degrading bacteria.
Poplar phyllosphere harbors disparate isoprene-degrading bacteria.
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DOI：
10.1073/pnas.1812668115
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发表时间：
2018-12-18
影响因子：
11.1
通讯作者：
Murrell JC
中科院分区：
文献类型：
--
作者：
Crombie AT;Larke-Mejia NL;Emery H;Dawson R;Pratscher J;Murphy GP;McGenity TJ;Murrell JC
异戊二烯是一种气候活跃的气体，由树木大量产生，但我们对其生物地球化学循环知之甚少。能够在异戊二烯上生长的细菌已经从土壤和沉积物中分离出来，但异戊二烯的主要来源叶圈仍未被探索。使用与栽培无关的定向技术，我们证明了异戊二烯排放树的叶圈包含一个多样化和活跃的异戊二烯降解种群。我们重建了一株降解异戊二烯的Variovorax菌株的基因组，并证明它含有一个功能性的异戊二烯单加氧酶。这项详细的研究以叶圈中的异戊二烯降解者为目标，将代谢组学应用于异戊二烯的降解，并分离和测序了变形杆菌中异戊二烯降解的成员。气候活跃的气体异戊二烯(2-甲基-1，3-丁二烯)被大量释放到大气中，几乎相当于甲烷的排放量，但我们对异戊二烯在环境中的生物循环知之甚少。尽管以前从土壤和沉积物中分离出能够以异戊二烯为唯一碳和能源来源的细菌，但还没有针对异戊二烯的主要来源的微生物学研究，并检查异戊二烯排放树的叶圈中是否存在这种丰富碳源的降解物。在这里，我们通过DNA稳定同位素探针法在杨树衍生的微宇宙中鉴定了异戊二烯降解菌。构建了异戊二烯降解菌的基因组，鉴定了可能的异戊二烯代谢基因，并用鸟枪式元基因组学和元转录组学方法分析了异戊二烯相关基因的转录。正如以前在土壤中发现的那样，红球菌属的革兰氏阳性细菌被证明是异戊二烯的主要降解者。然而，异戊二烯利用者的多样性也被揭示出来，特别是Variovorax，一个以前没有这种特征的属。Variovorax的异戊二烯单加氧酶在异源宿主中的表达证实了这一发现。分离到一株能以异戊二烯为唯一碳源和能源生长的变色曲霉菌株。对其基因组的分析证实，它含有异戊二烯代谢基因，与DNA稳定同位素探测和超基因组学鉴定的基因具有相同的布局和高度的相似性。这项研究为异戊二烯排放树叶圈中异戊二烯降解菌的广泛多样性提供了证据，并极大地加深了我们对这种重要代谢物和气候活性气体的生物降解的了解。
Isoprene is a climate-active gas, produced in huge amounts by trees, yet we know little about its biogeochemical cycle. Bacteria able to grow on isoprene have been isolated from soils and sediments, but the phyllosphere, the principal isoprene source, has remained unexplored. Using targeted cultivation-independent techniques, we show that the phyllosphere of an isoprene-emitting tree contains a diverse and active isoprene-degrading population. We reconstruct the genome of an isoprene-degrading Variovorax strain and show that it contains a functional isoprene monooxygenase. This detailed study targets isoprene degraders from the phyllosphere, applies metaomics to isoprene degradation, and isolates and sequences an isoprene-degrading member of the Proteobacteria. The climate-active gas isoprene (2-methyl-1,3-butadiene) is released to the atmosphere in huge quantities, almost equaling that of methane, yet we know little about the biological cycling of isoprene in the environment. Although bacteria capable of growth on isoprene as the sole source of carbon and energy have previously been isolated from soils and sediments, no microbiological studies have targeted the major source of isoprene and examined the phyllosphere of isoprene-emitting trees for the presence of degraders of this abundant carbon source. Here, we identified isoprene-degrading bacteria in poplar tree-derived microcosms by DNA stable isotope probing. The genomes of isoprene-degrading taxa were reconstructed, putative isoprene metabolic genes were identified, and isoprene-related gene transcription was analyzed by shotgun metagenomics and metatranscriptomics. Gram-positive bacteria of the genus Rhodococcus proved to be the dominant isoprene degraders, as previously found in soil. However, a wider diversity of isoprene utilizers was also revealed, notably Variovorax, a genus not previously associated with this trait. This finding was confirmed by expression of the isoprene monooxygenase from Variovorax in a heterologous host. A Variovorax strain that could grow on isoprene as the sole carbon and energy source was isolated. Analysis of its genome confirmed that it contained isoprene metabolic genes with an identical layout and high similarity to those identified by DNA-stable isotope probing and metagenomics. This study provides evidence of a wide diversity of isoprene-degrading bacteria in the isoprene-emitting tree phyllosphere and greatly enhances our understanding of the biodegradation of this important metabolite and climate-active gas.
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影响因子：
6.9
作者：
Abanda-Nkpwatt, Daniel;Muesch, Martina;Schwab, Wilfried
通讯作者：
Schwab, Wilfried
影响因子：
5.1
作者：
El Khawand, Myriam;Crombie, Andrew T.;Murrell, J. Colin
通讯作者：
Murrell, J. Colin
影响因子：
4.4
作者：
Heine, Thomas;Zimmerling, Juliane;Tischler, Dirk
通讯作者：
Tischler, Dirk
DOI：
10.1128/genomea.01256-17
发表时间：
2017-11-09
期刊：
Genome announcements
影响因子：
--
作者：
Crombie AT;Emery H;McGenity TJ;Murrell JC
通讯作者：
Murrell JC
影响因子：
5.2
作者：
Bringel F;Couée I
通讯作者：
Couée I