Soil carbon and microbial diversity under conservation management practices

Agricultural systems are essential sources for provisioning services, such as production of food, forage, fibre and bioenergy, as well as regulation services, such as the control of climate and diseases. The intensity of management practices has potential negative environmental consequences and intensive plough-based systems along with inefficient use of chemical inputs are known to accelerate the oxidation of soil organic matter, disrupt soil physical structure, decrease soil moisture retention and modify biological diversity, with strong effects on biogeochemical cycles. In this study, the effect of long-term conservation management practices, such as reduced tillage systems and nitrogen (N) fertilization rates, was evaluated on soil organic carbon (SOC) and microbial diversity and functionality in a soybean-wheat rotation in the Mediterranean area. The long-term soybean and wheat production were determined, as well as the bio-/chemical and physical parameters and the soil biota diversity in bulk soil and in aggregates at different size-levels. The molecular characterization of prokaryotes, eukaryotes, fungi and arbuscular mycorrhizal fungi (AMF), as indicators of soil fertility, were also assessed. Averaged over the period 1993-2016, grain yield of wheat was significantly affected by tillage and N fertilization. Wheat grain yield was 21% higher in CT compared to MT and 92% higher in N200 compared to N0. Conversely, soybean grain yield was not affected either by tillage or N fertilization to wheat and, averaged over treatments, was 2.6 Mg ha-1. Tillage was the most discriminant factor explaining 72% and 60% of total variance of soil parameters at 0-15 cm and 15-30 cm soil depths, respectively, whereas N fertilization explained 22% and 29% of total variance at both soil depths. All enzyme activities were higher under minimum tillage (MT) than under conventional tillage (CT), whereas the majority of soil chemical parameters were higher under N200 than N0. Under MT a higher proportion of free microaggregates (+51%) was recorded compared to CT, suggesting a greater potential of conservation tillage to form macroaggregates. The proportion of small macroaggregates was not modified by tillage, but, when this fraction was fractionated, a higher proportion of occluded microaggregates was found under MT at 15-30 cm (+21%). In the occluded microaggregates, tillage x N fertilization explained 52% of total variance of soil parameters at 0-15 cm and the most discriminant parameters were the biochemical ones and SOC. All those parameters were higher in MT-N200. Specifically, SOC in occluded microaggregates was increased by N fertilization under MT (+16% at 0-15 cm; +84% at 15-30 cm), whereas was decreased under CT (-46% at 0-15 cm; -15% at 15-30 cm). In addition, the synthetic indexes for enzymatic activities and for those involved in C-cycle were reduced by N fertilization under MT up to 37% and increased up to 87% under CT. The differential response of CT and MT to N fertilization is attributable to the modification of soil biota community composition and structure. Overall, we did not found in bulk soil an increase of prokaryotic and fungal richness at different phylogenetic resolution (prokaryotes: class and phylum levels; fungi: family and phylum levels). An increase of the Shannon index (H’) of prokaryotes was found under the two tillage systems (MT and CT) due to N fertilization, while a general increase of the Simpson index (λ) was found under CT-N0 at both soil depths. The community structure of prokaryotes in bulk soil (0-15 cm) at phylum level was largely modified by N fertilization (24% of total variance), with increases in the relative abundance of Chloroflexi (green non-sulfur bacteria that are capable of C fixation), Actinobacteria (decomposers of chitinous material) and Planctomycetes (key-players in C- and N-cycles). Looking at a higher phylogenetic resolution level (class), N fertilization determined, at both soil depths, strong shifts in bulk soil under CT system. The shifts were due to the majority of bacteria and archaea classes, with the exception of α-, β- and δ-proteobacteria (agents in the C-N-P-S-cycling). Conversely, under MT systems only minor changes were detected. Concerning soil fungi, at 0-15 cm soil depth, CT systems had a similar community composition at family level (Glomeraceae; ascomycota: Phaffomycetaceae, Sporormiaceae, Togniniaceae, Herpotrichiellaceae, Bionectriaceae), although under the higher rate of N fertilization (N200 vs N0) the relative abundance of common taxa was higher in CT-N200 respect to CT-N0. By contrast, N fertilization determined a strong shift in the fungal community structure under MT system at both soil depths. At phylum level, it was highlighted that tillage played the strongest role in determining fungal community structure and composition, with Glomeromycota unexpectedly highly in CT systems and under N200. Moreover, in bulk soil, a higher determinant of prokaryotic and fungal community structure was soil depth. Variation partitioning highlighted that soil depth explained 37%, 10% and 21% of the total variance for prokaryotes at class and phylum level, and for fungi at family level, respectively. Finally, soil biota was firstly characterized in small macroaggregates (sM) and occluded microaggregates (mM), representing SOC accumulation in the short- and long-term. Tillage and N fertilization were shown to play, major roles in shaping the soil biota community composition and structure related to soil functionality and services. In particular, the community composition and structure of AMF were strongly affected by tillage and the interaction of tillage with N fertilization. Although the majority of taxa belonged to the genus Glomus, Claroideoglomus (virtual taxa VTX00056) was increased under N200 in both tillage systems and at both soil depths and Paraglomus (virtual taxa VTX00281) only occurred under CT-N0 at both soil depths. Variation partitioning highlighted that soil matrix (sM vs mM) explained 63%, 38% and 39% of the total variance for prokaryotes, eukaryotes and fungi at class level, respectively, and 45%, 38% and 58% at phylum level, respectively. In conclusions, these results gave new insights into the environmental perturbation caused by intensive agricultural practices in the Mediterranean area. Maintaining or even increasing SOC conservation may require both reduced tillage systems and N fertilization, to shift soil biota community towards a higher presence of functional taxa linked to nutrient cycling, with positive implication for agroecosystem functioning.