Microbial Diversity of Reconstituted, Degraded, and Agricultural Soils Assessed by 16S rDNA Multi-Amplicon Sequencing

The microbial diversity is, among soil key factors, responsible for soil fertility and nutrient biogeochemical cycles, and can be modified upon changes in main soil physicochemical properties and soil pollution. Over the years, many restoration techniques have been applied to restore degraded soils. However, the effect of these approaches on soil microbial diversity is less understood and thus requires more investigation. In this study, we analyzed the impact, on soil microbial diversity of a patented novel technology, used to restore degraded soils. Soil samples were collected from three nearby sites located in Borgotrebbia, Piacenza, Italy, and categorized as reconstituted, degraded, and agricultural soils. After total soil DNA extraction, 16S rDNA multi-amplicon sequencing was carried out using an Ion GeneStudio S5 System to compare soils’ bacterial community profiles. Sequenced reads were processed to assign taxonomy and then key microbial community differences were identified across the sampling sites. Species diversity featured significant abatement at all rank levels in the degraded soil when compared to the agricultural control. The 5 year restoration technique showed full recovery of this index at the genus level but not at the phylum level, displaying a rank-dependent gradient of restored richness. In parallel, the abundance of genes involved in the nitrogen (N) biogeochemical cycle was assessed using quantitative Real-Time PCR (qPCR). Total DNA content was significantly higher (p < 0.05) in degraded (μ = 12.69 ± 2.58 μg g−1) and reconstituted (μ = 11.73 ± 1.65 μg g−1) soil samples when compared to the agricultural soil samples (μ = 2.39 ± 0.50 μg g−1). The taxonomic diversity of each soil site was significantly different, with some instances unique of the agricultural soil even at the phylum level. The analysis of N functional genes showed that the relative abundance of bacterial amoA (p < 0.05) and nosZ (p < 0.01) genes were significantly lower in the agricultural than in the reconstituted and degraded soils. We concluded that the application of the soil reconstitution technique appears to enhance the active microbial community, with distinct diversity and functionality towards genes involved in N biogeochemical cycle, as compared to both the degraded and the agricultural soil.

Contrasting protist communities (Cercozoa: Rhizaria) in pristine and earthworm-invaded North American deciduous forests

Earthworms are considered ecosystem engineers due to their fundamental impact on soil structure, soil processes and on other soil biota. An invasion of non-native earthworm species has altered soils of North America since European settlement, a process currently expanding into still earthworm-free forest ecosystems due to continuous spread and increasing soil temperatures owing to climate change. Although earthworms are known to modify soil microbial diversity and activity, it is as yet unclear how eukaryote consumers in soil microbial food webs will be affected. Here, we investigated how earthworm invasion affects the diversity of Cercozoa, one of the most dominant protist taxa in soils. Although the composition of the native cercozoan community clearly shifted in response to earthworm invasion, the communities of the different forests showed distinct responses. We identified 39 operational taxonomic units (OTUs) exclusively indicating earthworm invasion, hinting at an earthworm-associated community of Cercozoa. In particular, Woronina pythii, a hyper-parasite of plant-parasitic Oomycota in American forests, increased strongly in the presence of invasive earthworms, indicating an influence of invasive earthworms on oomycete communities and potentially on forest health, which requires further research.

Soil Disinfestation: From Soil Treatment to Soil and Plant Health

This Feature Article tracks 100 years of soil disinfestation: from the goal of eradicating soilborne pathogens and pests to much milder approaches, aimed at establishing a healthier soil, by favoring or enhancing the beneficial soil microflora and introducing biological control agents. The restrictions on use of many chemical fumigants is favoring the adoption of nonchemical strategies, from soilless cultivation to the use of physical or biological control measures, with more focus on maintaining soil microbial diversity, thus enhancing soil and plant health. Such approached are described and discussed, with special focus on their integrated use.