Conversion of monoculture cropland and open grassland to agroforestry alters the abundance of soil bacteria, fungi and soil-N-cycling genes

Abstract

Integration of trees in agroforestry systems can increase the system sustainability compared to monocultures. The resulting increase in system complexity is likely to affect soil-N cycling by altering soil microbial community structure and functions. Our study aimed to assess the abundance of genes encoding enzymes involved in soil-N cycling in paired monoculture and agroforestry cropland in a Phaeozem soil, and paired open grassland and agroforestry grassland in Histosol and Anthrosol soils. The soil fungi-to-bacteria ratio was greater in the tree row than in the crop or grass rows of the monoculture cropland and open grassland in all soil types, possibly due to increased input of tree residues and the absence of tillage in the Phaeozem (cropland) soil. In the Phaeozem (cropland) soil, gene abundances of amoA indicated a niche differentiation between archaeal and bacterial ammonia oxidizers that distinctly separated the influence of the tree row from the crop row and monoculture system. Abundances of nitrate ( napA and narG ), nitrite ( nirK and nirS ) and nitrous oxide reductase genes ( nosZ clade I) were largely influenced by soil type rather than management system. The soil types’ effects were associated with their differences in soil organic C, total N and pH. Our findings show that in temperate regions, conversion of monoculture cropland and open grassland to agroforestry systems can alter the abundance of soil bacteria and fungi and soil-N-cycling genes, particularly genes involved in ammonium oxidation.

Poplar Rows in Temperate Agroforestry Croplands Promote Bacteria, Fungi, and Denitrification Genes in Soils

“…The decrease of AOB amoA gene copies in the tree row ( Figure 5B) was in line with our previous findings of suppression of AOB amoA gene abundance by poplar trees (Beule et al, 2019a). High abundance of AOB in cropland samples can likely be accounted for by fertilization, which is common in conventional agriculture as well as in crop rows of the agroforestry systems.…”

“…In an initial study, Udawatta et al (2008) found that total soil-extractable DNA, used as a proxy for soil microbial biomass, was higher in agroforestry than in cropland and grassland but recommended the use of taxon-specific PCR assays to assess differences in soil microbial communities between the tree and crop rows. Their suggestion has only recently been implemented in a study of temperate agroforestry cropland and grassland which showed increased fungi-to-bacteria ratio under trees, and alterations of ammonium-oxidizing populations (Beule et al, 2019a). The investigation of genes involved in soil-N cycling in agricultural systems is important as these genes reveal the genetic potential to control N fluxes such as nitrous oxide (N 2 O) emissions.…”

Agroforestry Benefits and Challenges for Adoption in Europe and Beyond

“…In addition, Bainard et al [66] found greater fungi richness in an agroforestry system than in a monocrop, and several taxa that were found in the AFS were not present in a monocrop system. However, AFS have been shown to increase in fungi-to-bacteria ratio [74,75], which suggests that AFS have varying effects on different groups of organisms.…”

The potential of ryegrass as cover crop to reduce soil N2O emissions and increase the population size of denitrifying bacteria

“…The freeze-dried material was finely ground using a swing mill (MM400, Retsch, Haan, Germany) for 60 s at 25 Hz. Total DNA was extract from 50 mg ground soil using a modified cetyltrimethylammonium bromide-based protocol (Brandfass & Karlovsky, 2008) as described previously (Beule et al, 2019). Following DNA extraction, the quality and quantity of DNA were examined on 0.8% (w/v) agarose gels stained with ethidium bromide.…”