BackgroundSoil microbiomes play an important role in the services and functioning of terrestrial ecosystems. However, little is known of their vertical responses to restoration process and their contributions to soil nutrient cycling in the subsurface profiles. Here, we investigated the community assembly of soil bacteria, archaea, and fungi along vertical (i.e., soil depths of 0–300 cm) and horizontal (i.e., distance from trees of 30–90 cm) profiles in a chronosequence of reforestation sites that represent over 30 years of restoration.ResultsIn the superficial layers (0–80 cm), bacterial and fungal diversity decreased, whereas archaeal diversity increased with increasing soil depth. As reforestation proceeded over time, the vertical spatial variation in bacterial communities decreased, while that in archaeal and fungal communities increased. Vertical distributions of the soil microbiomes were more related to the variation in soil properties, while their horizontal distributions may be driven by a gradient effect of roots extending from the tree. Bacterial and archaeal beta-diversity were strongly related to multi-nutrient cycling in the soil, respectively, playing major roles in deep and superficial layers.ConclusionsTaken together, these results reveal a new perspective on the vertical and horizontal spatial variation in soil microbiomes at the fine scale of single trees. Distinct response patterns underpinned the contributions of soil bacteria, archaea, and fungi as a function of subsurface nutrient cycling during the reforestation of ex-arable land.Electronic supplementary materialThe online version of this article (10.1186/s40168-018-0526-0) contains supplementary material, which is available to authorized users.

To improve the knowledge about the biogeographic patterns of bacteria in soils contaminated with crude oil, we studied the effects of local geochemical properties and geographic distance on bacterial community structure in oil contaminated soil in five oil refineries (46 to 360 km apart). The microbial structure was significantly affected by soil environmental factors such as pH, total petroleum hydrocarbons (TPH), total nitrogen, and cadmium level. Microbial alpha-diversity was positively correlated with pH but negatively correlated with TPH. Among sampling sites, the community dissimilarities increased with spatial distance. Variation of bacterial community was mostly attributed to simultaneous effects of spatial distance and environmental factors, and purely spatial distance contributed more to the variation. Microbial generalist OTUs were broadly distributed and dominant in contaminated soils. Their populations were in low proportion (15.75%), but they had high relative abundance (65.05%), and some were associated with TPH-degradation. Network analysis indicated that microbial communities had non-random co-occurrence patterns. Keystone taxa were Rubrivivax, Nitrospira, Methylotenera, Methyloversatilis and Acidaminobacter. Microbial taxa from the same module had strong ecological linkages and were involved in biological electron-transfer, C and N-cycles, and organic contaminant degradation. Our results indicate that the same microbial groups with TPH-degradation ability can be assembled from indigenous microorganisms in separate regions through long term exposure to contamination.

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The microbiomes of rhizocompartments (nodule endophytes, root endophytes, rhizosphere and root zone) in soya bean and alfalfa were analysed using high-throughput sequencing to investigate the interactions among legume species, microorganisms and soil types. A clear hierarchical filtration of microbiota by plants was observed in the four rhizocompartments - the nodule endosphere, root endosphere, rhizosphere and root zone - as demonstrated by significant variations in the composition of the microbial community in the different compartments. The rhizosphere and root zone microbial communities were largely influenced by soil type, and the nodule and root endophytes were primarily determined by plant species. Diverse microbes inhabited the root nodule endosphere, and the corresponding dominant symbiotic rhizobia belonged to Ensifer for alfalfa and Ensifer-Bradyrhizobium for soya bean. The nonsymbiotic nodule endophytes were mainly Proteobacteria, Actinobacteria, Firmicutes and Bacteroidetes. The variation in root microbial communities was also affected by the plant growth stage. In summary, this study demonstrated that the enrichment process of nodule endophytes follows a hierarchical filtration and that the bacterial communities in nodule endophytes vary according to the plant species.

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