Soil microbial communities and their relationships to soil properties at different depths in an alpine meadow and desert grassland in the Qilian mountain range of China

Highlights

• Alpine meadow and desert grasslands harbor distinct bacterial and fungal communities.

• The bacterial phyla Actinobacteria dominated both grasslands, with significantly more so in the desert.

• The fungal phyla Ascomycota and Basidiomycota dominated both grasslands, but were unaffected by grassland type and soil depth.

• Carbon, nitrogen and water changes along the soil depth shaped microbial diversity.

Abstract

This study examined whether soil microbial composition would respond differently between alpine meadow and desert grasslands located in the Qilian mountain range in the semi-arid region of northwestern China. The measurements were carried out along a soil profile up to 40 cm. The total nitrogen (TN), total carbon (TC), soil organic carbon (SOC) and soil water content (SWC) were significantly higher (P-value < 0.05) in alpine meadow than in desert. In alpine meadows, all these properties decreased with increasing soil depth, and in desert grassland these properties – except SWC and TN - remained the same at all soil depths. The bacterial phyla Actinobacteria dominated both grasslands, significantly more so in desert grassland (P-value< 0.05). In alpine meadows Proteobacteria, Acidobacteria, Gemmatimonadetes, Planctomycetes and Rokubacteria abundance was significantly higher (P-value < 0.05). The distribution pattern of bacterial phyla along soil depth was different between the two grasslands. The abundance of Ascomycota and Basidiomycota was unaffected by grassland type or soil depth. Alpha and beta diversity analysis revealed two grasslands harbored distinct bacterial and fungal communities. We identified soil carbon, nitrogen and water as important factors that shaped the bacterial and fungal community in these semi-arid grasslands.

Introduction

Biodiversity loss has become a global concern as evidence accumulates that these losses will negatively affect ecosystem services on which society depends (Wagg et al., 2014). The below-ground biodiversity is as equally important as above-ground biodiversity because healthy and diverse below-ground communities directly enhance the quantity and quality of food production, the ability of soils to hold water (and thus reduce both flooding and runoff of pollutants like phosphorus), and even human health (Vries and Wallenstein, 2017). It has been well recognized that declining soil biodiversity can impede many ecosystem properties, such as aboveground plant diversity, nutrient retention, and nutrient cycling (Wagg et al., 2014). Soil microbes are distributed throughout soil profiles, from the surface organic matter containing horizon to deeper horizons populated by special microbes (Buckley and Schmidt, 2003). Soil microbial communities in deeper soils have been found to be fundamentally different from surface microbial communities, playing an important role in soil formation, ecosystem biogeochemistry and pollutant degradation, etc. (Deyn and Putten, 2005). Several studies have reported the soil microbial communities are vulnerable to losses due to human activities and climate change (Zhang et al., 2016; Wang et al., 2017). Bacteria and fungi are the key organisms contributing to soil microbial community and are particularly responsible for energy flow and nutrient cycling within an ecosystem (Schulz et al., 2013). The gradients in resource availability in different ecosystems are likely to be primary factors controlling the nature and properties of the microbial communities residing in the soil profile (Fierer et al., 2003).

Microbial community structure is influenced by both biotic and abiotic factors. Soil carbon, nitrogen, organic matter, pH, soil moisture, phosphorus and soil texture appear to be important predictors of the structure of soil microbial communities. Soil pH has been widely reported as a key factor affecting the distribution of soil bacteria, but to a lesser extent for spatial distribution of soil fungi (Lauber et al., 2008), possibly due to wider range of pH adaptability by fungi than bacteria (Rousk et al., 2010). Several studies have reported C availability for microbes as a major factor that determine microbial community composition in soil (Ko et al., 2017). Other studies have found that soil moisture had a greater impact on bacterial communities than C or N did, while fungal communities were greatly impacted by soil C and N but not by soil moisture (Singh et al., 2009; Kamble and Bååth, 2018). Soil bulk density affects the soil environment by configuring the space for air, water and plant roots and their movements, consequently influencing microbial populations. Microbial population abundance has been shown to be at their greatest in the low-density soils, presumably due to the favorable soil physical conditions and greater substrate availability provided by plant roots (Uroz et al., 2016; Li et al., 2002).

Grasslands are the largest area and most important land use type in the Qilian mountain region in north west of China (Wang et al., 2016). Among the different grassland types, alpine meadow and desert grassland are widely distributed and have typical regional representation (Liu et al., 2002; Xu et al., 2005). In the Qilian mountain region, alpine meadows and desert grasslands provide an important means of production and livelihood, where they have vital and valuable ecological functions such as protecting biodiversity and maintaining water, soil, and ecological balance (Kang et al., 2015; Zhang et al., 2015; Zhao et al., 2015). The unreasonable use of land resources on the Qilian Mountains in China have caused environmental degradation of grassland areas (Ji and Yang, 2013), potentially impacting the biological functions. A soil microbial community's nature and relative abundance are important indicators to define and evaluate ecosystem functions (Jason et al., 2005) and soil resilience (Bond-Lamberty et al., 2016). While the above ground diversity and productivity in the Qilian Mountain region has been examined previously (Zhang et al., 2015, 2019; Yang et al., 2016), little attention has been paid to soil microbiome studies. In order to contribute to the efforts that fill this research gap, we examined soil bacteria and fungi composition at different soil depths (0–10, 10–20, 20–30, 30–40 cm) in an alpine meadow grassland northeast of the Qilian mountains in the Qinghai province, and a desert grassland in the Hexi corridor of the Ganzhou District. We analyzed the physicochemical properties of soil and microbial (bacteria and fungi) diversity, where the latter was determined by Illumina sequencing of PCR-amplified 16S rRNA and the ITS gene, respectively, and then correlated to the former. We addressed the following two hypotheses in this study: 1) Microbial composition would respond differently to different grassland types, and 2) Soil depths would change the soil physicochemical properties, thereby changing the soil microbial community. In this study we specifically addressed the following scientific questions: 1) What is the composition of soil bacteria and fungi in a soil profile up to 40 cm below the surface in alpine meadow and desert grassland found in the Qilian mountain range? 2) What are the links between soil physicochemical properties and microbial groups? 3) Would the soil physicochemical properties change with soil depth, thereby altering the soil microbial community?