Groundwater Depth Overrides Tree-Species Effects on the Structure of Soil Microbial Communities Involved in Nitrogen Cycling in Plantation Forests

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.

Agricultural practice altering soil microbial diversity and nitrogen functional genes comparing to adjacent native forest soils

“…Quantitative PCR amplification of selected nitrification and denitrification genes (AOB amo A and nir K genes) with corresponding primers (Wu et al 2020) was performed using the QuantStudio 6 Flex Real-Time PCR System (Life Technologies, Carlsbad, CA, USA). The fluorescent dye SYBR-Green I which binds to double-stranded DNA was applied to quantify the relative abundance of nitrification AOB amo A and denitrification nir K genes.…”

“…Amplified gene products (AOB amo A and nir K) were run on 8% (w/v) acrylamide with a linear chemical gradient ranging from 40%-70% using a DGGEK-1001 Cipher DGGE Kit (C.B.S. Scientific, Del Mar, CA, USA) and obtained DGGE band patterns were exported for further nonparametric multivariate analyses of soil microbial and N functional gene communities as described previously (Wu et al 2020).…”

“…We used PRIMER-E including PERMANOVA+ statistical software (PRIMER-E, Plymouth, UK) to generate soil bacterial and N functional gene similarity matrices of each sample from three different locations and three different vegetation types with different disturbance intensity levels. Bio-Env function and Principal Coordinates Analysis (PCO) with Spearman's correlations of variables with the PCO axes of PRIMER-E were used to correlate the environmental factors with the similarity matrix (Wu et al 2015, Wu et al 2020).…”

Different responses of abundant and rare bacterial composition to groundwater depth and reduced nitrogen application in summer maize field

“…Nitrogen is one of the most important limiting factors for the growth of soil microbes ( Sun et al, 2015 ; Hou et al, 2018 ; Zhang et al, 2022 ). Nitrogen fertilizers can not only directly affect soil microbial communities but also indirectly affect soil microbial communities by regulating soil fertility, soil salt content and groundwater salt content ( She et al, 2018 ; Bai et al, 2020 ; Wu et al, 2020 ; Bai et al, 2023 ). However, over-application of nitrogen fertilizers may result in a series of severe environmental problems, including soil salinization, nitrate contamination and groundwater pollution ( Zhang et al, 2013 ; Lasagna et al, 2016 ).…”

“…In the past decades, its groundwater consumption increased sharply because of population growth, urbanization and development of industry and agriculture ( Changming et al, 2001 ; Chen et al, 2020 ; Jing et al, 2023 ; Xiao et al, 2023 ), causing various environmental geologic problems, including groundwater table fall, water quality worsening and surface subsidence ( Changming et al, 2001 ; Shi et al, 2020 ; Gan et al, 2022 ). Notably, groundwater table can regulate soil microbial species richness and composition ( Bai et al, 2020 ; Wu et al, 2020 ; Zhang et al, 2020 ). Besides, groundwater depth change can indirectly influence soil microbial communities by altering soil attributes such as salinity, pH and nutrients ( Bai et al, 2020 ; Zhang et al, 2020 ).…”