Beule Lukas, Arndt Markus, Karlovsky Petr
Molecular Phytopathology and Mycotoxin Research, University of Goettingen, 37077 Goettingen, Germany.
Microorganisms. 2021 Mar 13;9(3):589. doi: 10.3390/microorganisms9030589.
Plant production systems that are more sustainable than conventional monoculture croplands are the vision of future agriculture. With numerous environmental benefits, agroforestry is among the most promising alternatives. Although soil fungi are key drivers of plant productivity and ecosystem processes, investigations of these microorganisms in temperate agroforestry systems are scarce, leaving our understanding of agricultural systems under agroforestry practice incomplete. Here, we assessed the composition and diversity of the soil fungal community as well as the frequency (relative abundance) of fungal groups in three paired temperate poplar-based alley cropping (agroforestry) and monoculture cropland systems by amplicon sequencing. Analysis of microbiomes using relative abundances of species or sequence variants obtained from amplicon sequencing ignores microbial population size, which results in several problems. For example, species stimulated by environmental parameters may appear unaffected or suppressed in amplicon counts. Therefore, we determined absolute abundances of selected fungal groups as well as total fungal population size by real-time polymerase chain reaction (PCR). Tree rows strongly affected the community composition and increased the population size and species richness of soil fungi. Furthermore, ectomycorrhiza were strongly promoted by the tree rows. We speculate that mycorrhiza improved the nutrient acquisition in unfertilized tree rows, thereby contributing to the total productivity of the system. Comparison of relative and absolute abundances revealed dramatic discrepancies, highlighting that amplicon sequencing alone cannot adequately assess population size and dynamics. The results of our study highlight the necessity of combining frequency data based on amplicon sequencing with absolute quantification.
比传统单一栽培农田更具可持续性的植物生产系统是未来农业的愿景。由于具有众多环境效益，农林业是最有前景的替代方案之一。尽管土壤真菌是植物生产力和生态系统过程的关键驱动因素，但在温带农林业系统中对这些微生物的研究却很稀少，这使得我们对农林业实践下的农业系统的理解并不完整。在此，我们通过扩增子测序评估了三个配对的温带杨树间作（农林业）和单一栽培农田系统中土壤真菌群落的组成和多样性，以及真菌类群的频率（相对丰度）。使用从扩增子测序获得的物种或序列变体的相对丰度分析微生物群落会忽略微生物种群大小，这会导致一些问题。例如，受环境参数刺激的物种在扩增子计数中可能看起来未受影响或受到抑制。因此，我们通过实时聚合酶链反应（PCR）确定了选定真菌类群的绝对丰度以及真菌总种群大小。树木行强烈影响群落组成，并增加了土壤真菌的种群大小和物种丰富度。此外，树木行强烈促进了外生菌根的生长。我们推测菌根改善了未施肥树木行中的养分获取，从而对系统的总生产力做出了贡献。相对丰度和绝对丰度的比较揭示了巨大差异，突出表明仅扩增子测序无法充分评估种群大小和动态。我们的研究结果强调了将基于扩增子测序的频率数据与绝对定量相结合的必要性。
