Rüger Lioba, Feng Kai, Dumack Kenneth, Freudenthal Jule, Chen Yan, Sun Ruibo, Wilson Monica, Yu Peng, Sun Bo, Deng Ye, Hochholdinger Frank, Vetterlein Doris, Bonkowski Michael
Terrestrial Ecology, Institute of Zoology, University of Cologne, Cologne, Germany.
CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.
Front Microbiol. 2021 Feb 12;12:614501. doi: 10.3389/fmicb.2021.614501. eCollection 2021.
It is by now well proven that different plant species within their specific root systems select for distinct subsets of microbiota from bulk soil - their individual rhizosphere microbiomes. In maize, root growth advances several centimeters each day, with the locations, quality and quantity of rhizodeposition changing. We investigated the assembly of communities of prokaryotes (archaea and bacteria) and their protistan predators (Cercozoa, Rhizaria) along the longitudinal root axis of maize ( L.). We grew maize plants in an agricultural loamy soil and sampled rhizosphere soil at distinct locations along maize roots. We applied high-throughput sequencing, followed by diversity and network analyses in order to track changes in relative abundances, diversity and co-occurrence of rhizosphere microbiota along the root axis. Apart from a reduction of operational taxonomic unit (OTU) richness and a strong shift in community composition between bulk soil and root tips, patterns of microbial community assembly along maize-roots were more complex than expected. High variation in beta diversity at root tips and the root hair zone indicated substantial randomness of community assembly. Root hair zone communities were characterized by massive co-occurrence of microbial taxa, likely fueled by abundant resource supply from rhizodeposition. Further up the root where lateral roots emerged processes of community assembly appeared to be more deterministic (e.g., through competition and predation). This shift toward significance of deterministic processes was revealed by low variability of beta diversity, changes in network topology, and the appearance of regular phylogenetic co-occurrence patterns in bipartite networks between prokaryotes and their potential protistan predators. Such patterns were strongest in regions with fully developed laterals, suggesting that a consistent rhizosphere microbiome finally assembled. For the targeted improvement of microbiome function, such knowledge on the processes of microbiome assembly on roots and its temporal and spatial variability is crucially important.
现已充分证明，不同植物物种在其特定根系中会从大量土壤中选择不同的微生物亚群——它们各自的根际微生物群落。在玉米中，根系每天生长数厘米，根际沉积的位置、质量和数量都在变化。我们研究了原核生物（古菌和细菌）群落及其原生生物捕食者（Cercozoa、Rhizaria）沿玉米（L.）根系纵向轴的组装情况。我们在农业壤土中种植玉米植株，并在玉米根的不同位置采集根际土壤。我们应用高通量测序，随后进行多样性和网络分析，以追踪根际微生物群沿根轴的相对丰度、多样性和共现性的变化。除了操作分类单元（OTU）丰富度的降低以及大量土壤和根尖之间群落组成的强烈变化外，沿玉米根的微生物群落组装模式比预期的更为复杂。根尖和根毛区的β多样性高度变化表明群落组装存在大量随机性。根毛区群落的特征是微生物类群大量共现，这可能是由根际沉积提供的丰富资源供应所推动的。在根上侧根出现的更高位置，群落组装过程似乎更具确定性（例如，通过竞争和捕食）。β多样性的低变异性、网络拓扑结构的变化以及原核生物与其潜在原生生物捕食者之间二分网络中规则的系统发育共现模式的出现揭示了这种向确定性过程显著性的转变。这种模式在侧根完全发育的区域最为明显，表明最终组装成了一致的根际微生物群落。对于有针对性地改善微生物群落功能而言，关于根上微生物群落组装过程及其时空变异性的此类知识至关重要。
