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

Lukas Beule; Ena Lehtsaar; Marife D Corre; Marcus Schmidt; Edzo Veldkamp; Petr Karlovsky

doi:10.3389/fmicb.2019.03108

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

Front Microbiol. 2020 Jan 22:10:3108. doi: 10.3389/fmicb.2019.03108. eCollection 2019.

Authors

Lukas Beule¹, Ena Lehtsaar¹, Marife D Corre², Marcus Schmidt², Edzo Veldkamp², Petr Karlovsky¹

Affiliations

¹ Molecular Phytopathology and Mycotoxin Research, Faculty of Agricultural Sciences, University of Goettingen, Göttingen, Germany.
² Soil Science of Tropical and Subtropical Ecosystems, Faculty of Forest Sciences and Forest Ecology, University of Goettingen, Göttingen, Germany.

Abstract

Agroforestry, which is the integration of trees into monoculture cropland, can alter soil properties and nutrient cycling. Temperate agroforestry practices have been shown to affect soil microbial communities as indicated by changes in enzyme activities, substrate-induced respiration, and microbial biomass. Research exploring soil microbial communities in temperate agroforestry with the help of molecular tools which allow for the quantification of microbial taxa and selected genes is scarce. Here, we quantified 13 taxonomic groups of microorganisms and nine genes involved in N cycling (N₂ fixation, nitrification, and denitrification) in soils of three paired temperate agroforestry and conventional monoculture croplands using real-time PCR. The agroforestry croplands were poplar-based alley-cropping systems in which samples were collected in the tree rows as well as within the crop rows at three distances from the tree rows. The abundance of Acidobacteria, Actinobacteria, Alpha- and Gammaproteobacteria, Firmicutes, and Verrucomicrobia increased in the vicinity of poplar trees, which may be accounted for by the presence of persistent poplar roots as well as by the input of tree litter. The strongest population increase was observed for Basidiomycota, which was likely related to high soil moisture, the accumulation of tree litter, and the absence of tillage in the tree rows. Soil microorganisms carrying denitrification genes were more abundant in the tree rows than in the crop rows and monoculture systems, suggesting a greater potential for nitrate removal through denitrification, which may reduce nitrate leaching. Since microbial communities are involved in critical soil processes, we expect that the combination of real-time PCR with soil process measurements will greatly enhance insights into the microbial control of important soil functions in agroforestry systems.

Keywords: N-cycling genes; alley-cropping; soil bacteria; soil fungi; temperate agroforestry cropland.