Table_1_Diversity of Rhizo-Bacteriome of Crocus sativus Grown at Various Geographical Locations and Cataloging of Putative PGPRs.XLSX

Earlier plant growth promoting rhizo-bacteria (PGPRs) were isolated from the plants, by cultivation based techniques and the interaction was mostly thought to be bilateral. The routine bilateral study, with no information on the associated microbiome, could be one of the reasons for the limited success of PGPRs in the field conditions. Keeping in view the role of PGPRs in rhizo-bacteriome on the growth and production of plant, the present study was aimed at studying the diversity of the rhizo-bacteriome of saffron grown across three geographical locations namely Kashmir, Kishtwar and Bengaluru. Variation in the rhizo-bacteriome of saffron growing across 10 different sites from 3 geographical locations was studied using 16S rDNA amplicon metagenomic sequencing. 16 bacterial phyla, 261 genera and 73 bacterial species were cataloged from all the rhizosphere samples. Proteobacteria was a dominant phylum in all the rhizosphere samples. Rhizo-bacteriome of saffron grown in Kishtwar was found to be significantly different from the rhizo-bacteriome of saffron grown in Kashmir and Bengaluru. Interestingly, the rhizo-bacteriome of saffron grown in Bengaluru was very similar to the saffron grown in Kashmir, thereby indicating that the rhizo-bacteriome in saffron is “plant driven” as the corm sown in Bengaluru were from Kashmir. Despite variation in rhizo-bacteriome, core rhizo-bacteriome in saffron was identified that was represented by 53 genera and eight bacterial species belonging to 11 phyla irrespective of their geographical distribution. In addition, 21 PGPRs were reported for the first time from the saffron rhizosphere. The high yielding saffron field Wuyan was found to have the highest number of PGPRs; this indicates that the presence of PGPR is important for yield enhancement than diversity. The two PGPR Rhizobium leguminosarum and Luteibacter rhizovicinus were reported from all the locations except Kishtwar that had escaped isolation in our previous attempts using cultivation based techniques. It is being proposed instead of going for random isolation and screening for PGPRs from plant rhizosphere, an alternate strategy using metagenomic cataloging of the rhizo-bacteriome community and cultivation of the dominant PGPR should be undertaken. This strategy will help in the selection of dominant PGPRs, specific to the plant in question.

此前，学界多通过传统培养分离技术从植物中分离得到植物促生根际细菌（plant growth promoting rhizo-bacteria, PGPR），且大多认为其互作模式为双边型。这类仅关注双边互作、未兼顾相关菌群信息的常规研究，或许是PGPR在田间应用效果有限的原因之一。鉴于PGPR在植物根际菌群调控植物生长与产量中的作用，本研究旨在探究生长于克什米尔（Kashmir）、基什特瓦尔（Kishtwar）以及班加罗尔（Bengaluru）三个地理区域的藏红花根际菌群多样性。本研究针对来自3个地理区域10个不同样地的藏红花根际样本，采用16S rDNA扩增子宏基因组测序技术解析其根际菌群的组成差异。所有根际样本中共鉴定得到16个细菌门、261个属以及73个细菌物种；变形菌门（Proteobacteria）为所有样本中的优势菌门。结果显示，生长于基什特瓦尔的藏红花根际菌群与克什米尔及班加罗尔地区的藏红花根际菌群存在显著差异。值得注意的是，班加罗尔地区藏红花的根际菌群与克什米尔地区样本高度相似——由于班加罗尔地区种植所用的藏红花球茎均引自克什米尔，该结果提示藏红花根际菌群受“植物驱动”。尽管不同样地的根际菌群存在区域差异，本研究仍鉴定得到藏红花核心根际菌群：该菌群包含隶属于11个门的53个属与8个细菌物种，不受地理分布影响。此外，本研究首次从藏红花根际中报道了21株PGPR。其中，高产藏红花种植地Wuyan的PGPR数量最多，这表明PGPR的存在对产量提升的作用甚于菌群多样性本身。除基什特瓦尔地区外，其余所有样地均分离得到了此前本研究通过传统培养分离技术未能获取的两种PGPR：豌豆根瘤菌（Rhizobium leguminosarum）与根际黄杆菌（Luteibacter rhizovicinus）。本研究提出，相较于从植物根际随机分离筛选PGPR的传统策略，应采用先通过宏基因组测序解析根际菌群组成，再针对性培养优势PGPR的替代方案。该策略将有助于筛选得到与目标植物特异性匹配的优势PGPR。