Long-term effects of two organic amendments on bacterial communities of calcareous mediterranean soils degraded by mining

Abstract

The application of organic amendments to improve the chemical and biological properties of degraded soils from calcareous quarries is necessary to accelerate restoration processes. The aim of this study is to assess the success of different restoration treatments in the long-term using two organic amendments (sewage sludge from urban waste water (SS) and compost from domestic solid waste (CW)). The chemical properties and bacterial communities of restored soils were compared with unamended soils (NA) and surrounding natural soils (NS) from a limestone quarry in a semi-arid ecosystem. After 10 years of the addition of organic amendments, the abundance of soil bacteria, diversity, and taxonomic composition at the phylum and genus level in each soil type was analysed by rRNA 16 S amplification (PCR), sequencing using Illumina, and comparison with the SILVA database using QIIME2 software. The relationships between soil bacterial taxa and chemical soil properties (pH, electrical conductivity (EC), total organic carbon (TOC), and total nitrogen content (TN)) were also studied, as well as the interrelations between soil bacterial taxa at the genus level or the next upper taxonomic level identified. The organic amendments changed the chemical properties of the restored soils, influencing the microbial communities of the restored soils. CW treatment was the organic amendment that most resembled NS, favouring in the long-term a greater diversity and proliferation of bacteria. Several bacterial communities, more abundant in NA and CW soils, were strongly correlated with each other (Craurococcus, Phaselicystis, Crossiella, etc.), forming a bacterial co-occurrence pattern (Co-occurrence pattern 1). Those bacteria showed high significant positive correlations with TOC, TN, and EC and negative correlations with the soil pH. In contrast, NA soils presented other groups of bacterial communities (Co-occurrence pattern 2) represented by Sphingomonas, Rubellimicrobium, Noviherbaspirillum, Psychroglaciecola and Caenimonas, which showed high significant positive correlations with soil pH and negative correlations with TOC, TN, and EC. The distance-based redundancy analysis indicated that SS soils remained in an intermediate stage of chemical and biological quality between NS and NA soils. Our results demonstrate that soil chemical properties and soil bacterial communities significantly changed with organic amendments in calcareous Mediterranean soils degraded by mining.

Keywords: Bacterial diversity; Metagenomics; Semi-arid ecosystems; Soil bacterial co-occurrence patterns; Soil degradation; Soil restoration.