Miralles Isabel, Ortega Raúl, Comeau André M
Department of Agronomy & Center for Intensive Mediterranean Agrosystems and Agri-food Biotechnology (CIAIMBITAL), University of Almeria, Almería, Spain.
Integrated Microbiome Resource (IMR), Dalhousie Universitygrid.55602.34, Halifax, Nova Scotia, Canada.
mSystems. 2021 Dec 21;6(6):e0075221. doi: 10.1128/mSystems.00752-21. Epub 2021 Nov 23.
The application of organic amendments to mining soils has been shown to be a successful method of restoration, improving key physicochemical soil properties. However, there is a lack of a clear understanding of the soil bacterial community taxonomic and functional changes that are brought about by these treatments. We present further metagenomic sequencing (MGS) profiling of the effects of different restoration treatments applied to degraded, arid quarry soils in southern Spain which had previously been profiled only with 16S rRNA gene (16S) and physicochemical analyses. Both taxonomic and functional MGS profiles showed clear separation of organic treatment amendments from control samples, and although taxonomic differences were quite clear, functional redundancy was higher than expected and the majority of the latter signal came from the aggregation of minor (<0.1%) community differences. Significant taxonomic differences were seen with the presumably less-biased MGS-for example, the phylum and the two genera () and () were determined to be major players by the MGS and this was consistent with their potential functional roles. The former phylum was much less present, and the latter two genera were either minor components or not detected in the 16S data. Mapping of reads to MetaCyc/BioCyc categories showed overall slightly higher biosynthesis and degradation capabilities in all treatments versus control soils, with sewage amendments showing highest values and vegetable-based amendments being at intermediate levels, matching higher nutrient levels, respiration rates, enzyme activities, and bacterial biomass previously observed in the treated soils. The restoration of soils impacted by human activities poses specific challenges regarding the reestablishment of functional microbial communities which will further support the reintroduction of plant species. Organic fertilizers, originating from either treated sewage or vegetable wastes, have shown promise in restoration experiments; however, we still do not have a clear understanding of the functional and taxonomic changes that occur during these treatments. We used metagenomics to profile restoration treatments applied to degraded, arid quarry soils in southern Spain. We found that the assortments of individual functions and taxa within each soil could clearly identify treatments, while at the same time they demonstrated high functional redundancy. Functions grouped into higher pathways tended to match physicochemical measurements made on the same soils. In contrast, significant taxonomic differences were seen when the treatments were previously studied with a single marker gene, highlighting the advantage of metagenomic analysis for complex soil communities.
向采矿土壤中添加有机改良剂已被证明是一种成功的修复方法，可改善土壤的关键物理化学性质。然而，对于这些处理所引起的土壤细菌群落分类和功能变化，我们仍缺乏清晰的认识。我们进一步展示了宏基因组测序（MGS）对西班牙南部退化干旱采石场土壤进行不同修复处理效果的分析，此前该土壤仅通过16S rRNA基因（16S）和物理化学分析进行过分析。分类学和功能MGS图谱均显示有机处理改良剂与对照样品明显分离，尽管分类学差异相当明显，但功能冗余高于预期，且后者的大部分信号来自微小（<0.1%）群落差异的聚集。在可能偏差较小的MGS分析中观察到了显著的分类学差异——例如，MGS确定门以及两个属（）和（）是主要参与者，这与其潜在的功能作用一致。前一个门的含量要少得多，而后两个属在16S数据中要么是次要成分，要么未被检测到。将读数映射到MetaCyc/BioCyc类别显示，与对照土壤相比，所有处理中的生物合成和降解能力总体略高，污水改良剂的值最高，蔬菜基改良剂处于中间水平，这与之前在处理过的土壤中观察到的较高养分水平、呼吸速率、酶活性和细菌生物量相匹配。受人类活动影响的土壤修复在功能性微生物群落重建方面带来了特殊挑战，而这将进一步支持植物物种的重新引入。源自处理过的污水或蔬菜废弃物的有机肥料在修复实验中已显示出前景；然而，我们仍不清楚这些处理过程中发生的功能和分类学变化。我们使用宏基因组学分析了西班牙南部退化干旱采石场土壤的修复处理。我们发现，每种土壤中个体功能和分类群的组合可以清晰地识别处理方式，同时它们也表现出较高的功能冗余。归为更高途径的功能往往与对同一土壤进行的物理化学测量结果相匹配。相比之下，当使用单一标记基因对处理进行先前研究时，观察到了显著的分类学差异，这突出了宏基因组分析对于复杂土壤群落的优势。
