Harkes Paula, van Steenbrugge Joris Johannes Matheus, van den Elsen Sven Johannes Josephus, Suleiman Afnan Khalil Ahmad, de Haan Johannes Jan, Holterman Martijn Hermanus Maria, Helder Johannes
Laboratory of Nematology, Department of Plant Sciences, Wageningen University & Research, Wageningen, Netherlands.
Department of Microbial Ecology, NIOO-KNAW, Wageningen, Netherlands.
Front Plant Sci. 2020 Jan 10;10:1697. doi: 10.3389/fpls.2019.01697. eCollection 2019.
Plants manipulate their rhizosphere community in a species and even a plant life stage-dependent manner. In essence plants select, promote and (de)activate directly the local bacterial and fungal community, and indirectly representatives of the next trophic level, protists and nematodes. By doing so, plants enlarge the pool of bioavailable nutrients and maximize local disease suppressiveness within the boundaries set by the nature of the local microbial community. MiSeq sequencing of specific variable regions of the 16S or 18S ribosomal DNA (rDNA) is widely used to map microbial shifts. As current RNA extraction procedures are time-consuming and expensive, the rRNA-based characterization of the active microbial community is taken along less frequently. Recently, we developed a relatively fast and affordable protocol for the simultaneous extraction of rDNA and rRNA from soil. Here, we investigated the long-term impact of three type of soil management, two conventional and an organic regime, on soil biota in fields naturally infested with the Columbian root-knot nematode with pea () as the main crop. For all soil samples, large differences were observed between resident (rDNA) and active (rRNA) microbial communities. Among the four organismal group under investigation, the bacterial community was most affected by the main crop, and unweighted and weighted UniFrac analyses (explaining respectively 16.4% and 51.3% of the observed variation) pointed at a quantitative rather than a qualitative shift. LEfSe analyses were employed for each of the four organismal groups to taxonomically pinpoint the effects of soil management. Concentrating on the bacterial community in the pea rhizosphere, organic soil management resulted in a remarkable activation of members of the Burkholderiaceae, Enterobacteriaceae, and Pseudomonadaceae. Prolonged organic soil management was also accompanied by significantly higher densities of bacterivorous nematodes, whereas levels of had dropped drastically. Though present and active in the fields under investigation Orbiliaceae, a family harboring numerous nematophagous fungi, was not associated with the decline. A closer look revealed that a local accumulation and activation of a genus that includes a number of nematode-suppressive species, paralleled the lower densities. This study underlines the relevance of taking along both resident and active fractions of multiple organismal groups while mapping the impact of crops and soil management regimes.
植物以物种甚至植物生命阶段依赖的方式操纵其根际群落。本质上，植物直接选择、促进和（去）激活当地的细菌和真菌群落，并间接影响下一个营养级的代表，即原生生物和线虫。通过这样做，植物在当地微生物群落性质所设定的范围内扩大了生物可利用养分的库，并使当地疾病抑制能力最大化。16S或18S核糖体DNA（rDNA）特定可变区域的MiSeq测序被广泛用于绘制微生物变化图谱。由于目前的RNA提取程序既耗时又昂贵，基于rRNA的活性微生物群落表征较少被采用。最近，我们开发了一种相对快速且经济实惠的方案，用于同时从土壤中提取rDNA和rRNA。在这里，我们研究了三种土壤管理类型（两种传统管理和一种有机管理方式）对自然感染哥伦比亚根结线虫且以豌豆（）为主作物的田间土壤生物群的长期影响。对于所有土壤样本，在常驻（rDNA）和活性（rRNA）微生物群落之间观察到了很大差异。在所研究的四个生物类群中，细菌群落受主要作物的影响最大，未加权和加权的UniFrac分析（分别解释了观察到的变异的16.4%和51.3%）表明是数量上的而非质量上的变化。对四个生物类群中的每一个都采用了LEfSe分析，以便从分类学上确定土壤管理的影响。聚焦于豌豆根际的细菌群落，有机土壤管理导致伯克霍尔德氏菌科、肠杆菌科和假单胞菌科成员的显著激活。长期的有机土壤管理还伴随着食细菌线虫密度的显著增加，而的水平则大幅下降。尽管在被调查的田间存在并活跃着含有许多捕食线虫真菌的 Orbiliaceae 科，但它与的下降无关。进一步观察发现，包括一些抑制线虫物种的一个属的局部积累和激活与较低的密度平行。这项研究强调了在绘制作物和土壤管理制度的影响时，同时考虑多个生物类群的常驻和活性部分的相关性。
