Effects of increasing lime application rates on microbial diversity and community structure in paddy soils

Highlights

• Prokaryotes were more responsive to liming than fungi.

• Liming effects on prokaryotes vanished when application rates exceeded 900 kg ha⁻¹.

• AOA lineages showed distinct responses to increasing lime inputs.

• pH was the key factor shaping the prokaryotic community.

• Fungal community diversity and composition were linked to both pH and SOM.

Abstract

Liming is widely used to ameliorate acidic soils. However, few studies have addressed the effects of different lime application rates on soil microbial communities. Specifically, the effects of liming on fungal communities remain largely unknown. Here, we set up a gradient of increasing lime application rates, 0, 450, 900, 1350, 1800, 2250, 3000, and 3750 kg ha⁻¹, to investigate the effects of lime inputs on soil properties and community diversity and composition of prokaryotes and fungi in paddy soils. Our results showed that the effect of liming on soil pH improvement become insignificant when the application rate exceeded 1800 kg ha⁻¹. Prokaryotic diversity and community composition were both significantly influenced by liming, whereas fungal communities were less responsive. Nonetheless, the promotive effects of liming on soil prokaryotic diversity declined when lime application rates exceeded 900 kg ha⁻¹ (or pH > 6.5). Soil pH was the key factor shaping the prokaryotic community, while pH and SOM were both important in explaining the observed variation in fungal communities. Distinct responses of ammonia oxidizing archaea (AOA) lineages were also observed as pH increased. Our results provide insights into the complex responses of both prokaryotic and fungal communities to lime application in paddy soils, and suggest that the amount of lime applied is also important for maintaining a healthy and sustainable soil environment.

Introduction

Intensive agriculture has developed rapidly in recent years to feed the large and growing population in China. The use of excessive chemical fertilizers and pesticides has resulted in serious environmental problems and soil acidification has become one of the most serious problems threatening agricultural production (Guo et al., 2010). Nearly 40% of arable soils in the world are acidic and this proportion is still increasing (Bian et al., 2013). Soil acidification can lead to nutrient deficiency, reduce water uptake, and heavy metal toxicity (Probst et al., 1999; Zhao et al., 2015), rendering soil unsuitable for production. Consequently, sustainable agricultural practices that ensure high production but also maintain healthy soil environment are needed.

Liming is widely used to ameliorate acidic soils. It can not only neutralize soil pH, but also promote soil nutrient cycling, immobilize toxic heavy metals, and even decrease greenhouse gas emissions (Holland et al., 2018; Jiang et al., 2018; Shi et al., 2019). Soil microorganisms, including prokaryotes (archaea and bacteria) and fungi, are key players in these soil functional processes (Mau et al., 2015; Zhang et al., 2018). Any changes in soil microbial communities can affect the soil ecosystem. Consequently, soil microbial diversity and community composition are some of the most important indicators of soil quality (Bending et al., 2004; Lee et al., 2011).

A range of studies have addressed the effects of liming on soil microbial communities. For example, continuous lime amendment can significantly increase soil bacterial diversity and richness (Shi et al., 2019). Microbial biomass and respiration have also been shown to increase under liming treatment (Guo et al., 2019). The effects of lime application on specific microbial functional groups have also been reported. Particularly, soil nitrifying and nitrogen-fixing communities have received great attention because of their key roles in global nitrogen (N) cycling. The nitrification, which converts ammonia to nitrate via nitrite, can not only lead to lower N-fertilizer efficiency, but also groundwater and atmospheric pollution through nitrate leaching and emission of reactive N species (Corre et al., 2003; Farmaha, 2014; Zhang et al., 2017). Ammonia oxidizing archaea (AOA) and ammonia oxidizing bacteria (AOB) are the main contributors to soil nitrification (Gruber and Galloway, 2008; Li et al., 2018). It has been reported that activities, abundances, and community structures of both AOA and AOB are sensitive to liming (Zhang et al., 2017). The abundance of AOB increases significantly under liming treatments, whereas that of AOA shows lower variation (Egan et al., 2018). Long-term application of lime has also been found to suppress the abundance and diversity of diazotrophs and shift their community structure in an acidic Ultisol (Lin et al., 2018). Soil pH is an important factor in shaping bacterial communities in limed and un-limed soils (Guo et al., 2019; Lin et al., 2018; Shi et al., 2019). However, most previous studies examined either the bacterial community or a specific functional microbial guild.

Besides, the influence of liming on fungal communities remains largely unknown. Fungi are pivotal microbial components and mediate a variety of microbial functions and processes, including parasitism, pathogenesis, and organic matter decomposition (Buée et al., 2009; Chaer et al., 2009; Zeilinger et al., 2015). Although a correlation between soil pH and fungal diversity has been found, the relationship was much weaker compared to that of pH and bacteria (Rousk et al., 2010; Wang et al., 2015). Plant diversity and soil organic carbon are crucial factors driving fungal communities (T. Yang et al., 2017; Y. Yang et al., 2017). Thus, we hypothesized that lime application can significantly affect prokaryotic diversity and community composition, but has limited effects on fungal diversity and community composition.

The amount of lime applied is also important for maintaining healthy soils. Insufficient lime application is not effective, whereas over-application can harm crops, decrease soil permeability, and accelerate soil compaction (Guo et al., 2019; Osinubi Kolawole, 1998). Furthermore, few studies have scrutinized how different lime application rates affect soil microbial communities. Currently, an application rate of approximately 750–1500 kg ha⁻¹ CaO is recommended and commonly used in paddy soils in southern China (Guo et al., 2019; Shi et al., 2019). Based on this content, we set up a gradient of lime application rates between 0 and 3750 kg ha⁻¹ to investigate microbial responses to increased lime application rates in paddy soils. Variations in prokaryotic and fungal communities were examined using high-throughput sequencing. The main aims of the study were to (1) investigate how different lime application rates affect paddy soil properties and microbial communities; (2) study how the nitrifying communities responded to increasing lime inputs; (3) verify whether fungal communities are less sensitive to lime application than prokaryotic communities; (4) identify the key factors influencing prokaryotic and fungal community diversity and composition.