Abstract
Microbial communities found in soil ecosystems play important roles in decomposing organic materials and recycling nutrients. A clear understanding on how biotic and abiotic factors influence the microbial community and its functional role in ecosystems is fundamental to terrestrial biogeochemistry and plant production. The purpose of this study was to investigate microbial communities and functional genes involved in nitrogen cycling as a function of groundwater depth (deep and shallow), tree species (pine and eucalypt), and season (spring and fall). Soil fungal, bacterial, and archaeal communities were determined by length heterogeneity polymerase chain reaction (LH-PCR). Soil ammonia oxidation archaeal (AOA) amoA gene, ammonia oxidation bacterial (AOB) amoA gene, nitrite oxidoreductase nrxA gene, and denitrifying bacterial narG, nirK, nirS, and nosZ genes were further studied using PCR and denaturing gradient gel electrophoresis (DGGE). Soil fungal and bacterial communities remained similar between tree species and groundwater depths, respectively, regardless of season. Soil archaeal communities remained similar between tree species but differed between groundwater depths in the spring only. Archaeal amoA for nitrification and bacterial nirK and nosZ genes for denitrification were detected in DGGE, whereas bacterial amoA and nrxA for nitrification and bacterial narG and nirS genes for denitrification were undetectable. The detected nitrification and denitrification communities varied significantly with groundwater depth. There was no significant difference of nitrifying archaeal amoA or denitrifying nirK communities between different tree species regardless of season. The seasonal difference in microbial communities and functional genes involved in nitrogen cycling suggests microorganisms exhibit seasonal dynamics that likely impact relative rates of nitrification and denitrification.
Highlights
Soil teems with diverse microorganisms, which regulate ecosystem functions such as decomposing organic materials and recycling nutrients [1]
No interactions (p > 0.05) among groundwater depth, tree species, and season were observed for all soil organic matter, nitrate, potassium, and soil CEC, but interaction between tree species and season was observed for soil phosphorus and magnesium contents (Table 2)
Soil fungal communities remained similar between tree species, whereas, soil bacterial communities are determined by groundwater depth regardless of season
Summary
Soil teems with diverse microorganisms, which regulate ecosystem functions such as decomposing organic materials and recycling nutrients [1]. Soil bacteria may regulate several key nutrient cycling processes including N, the essential nutrient for plant growth [3,8]. Forests 2020, 11, 275 thought to be restricted to extreme environments, have become a major contributor for N cycling processes in a wide variety of environments [9,10], including agricultural soils [11,12,13,14] and forest soils [15,16]. It is clear that soil microbes including fungi, bacteria, and previously undescribed archaea specialize in recycling nutrients and are the “backbone” to most biogeochemical cycles, especially nitrification and denitrification [14,17]
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