Abstract
Application of chemical fertilizer or manure can affect soil microorganisms directly by supplying nutrients and indirectly by altering soil pH. However, it remains uncertain which effect mostly shapes microbial community structure. We determined soil bacterial diversity and community structure by 454 pyrosequencing the V1-V3 regions of 16S rRNA genes after 7-years (2007–2014) of applying chemical nitrogen, phosphorus and potassium (NPK) fertilizers, composted manure or their combination to acidic (pH 5.8), near-neutral (pH 6.8) or alkaline (pH 8.4) Eutric Regosol soil in a maize-vegetable rotation in southwest China. In alkaline soil, nutrient sources did not affect bacterial Operational Taxonomic Unit (OTU) richness or Shannon diversity index, despite higher available N, P, K, and soil organic carbon in fertilized than in unfertilized soil. In contrast, bacterial OTU richness and Shannon diversity index were significantly lower in acidic and near-neutral soils under NPK than under manure or their combination, which corresponded with changes in soil pH. Permutational multivariate analysis of variance showed that bacterial community structure was significantly affected across these three soils, but the PCoA ordination patterns indicated the effect was less distinct among nutrient sources in alkaline than in acidic and near-neural soils. Distance-based redundancy analysis showed that bacterial community structures were significantly altered by soil pH in acidic and near-neutral soils, but not by any soil chemical properties in alkaline soil. The relative abundance (%) of most bacterial phyla was higher in near-neutral than in acidic or alkaline soils. The most dominant phyla were Proteobacteria (24.6%), Actinobacteria (19.7%), Chloroflexi (15.3%) and Acidobacteria (12.6%); the medium dominant phyla were Bacterioidetes (5.3%), Planctomycetes (4.8%), Gemmatimonadetes (4.5%), Firmicutes (3.4%), Cyanobacteria (2.1%), Nitrospirae (1.8%), and candidate division TM7 (1.0%); the least abundant phyla were Verrucomicrobia (0.7%), Armatimonadetes (0.6%), candidate division WS3 (0.4%) and Fibrobacteres (0.3%). In addition, Cyanobacteria and candidate division TM7 were more abundant in acidic soil, whereas Gemmatimonadetes, Nitrospirae and candidate division WS3 were more abundant in alkaline soil. We conclude that after 7-years of fertilization, soil bacterial diversity and community structure were shaped more by changes in soil pH rather than the direct effect of nutrient addition.
Highlights
In agroecosystems, it is well established that soil microbial communities respond to N, P and/or K fertilizer (Allison and Martiny, 2008; Beauregard et al, 2010), manure, compost (Hartmann et al, 2015; Francioli et al, 2016) and their combinations (Sun et al, 2015; Chen et al, 2016)
The AP accumulated most in the manure-amended alkaline soil compared with the other nutrient sources, while AK accumulated most in the manure-amended near-neutral and acidic soil compared with the chemical NPK fertilizers (CF) treatments
Fertilization with M increased soil pH by 0.5 and 0.2 units compared with CF and CT treatments, while in both the acidic and near-neutral soil, fertilization with M increased soil pH by 2.2 and 2.4 units compared with CF treatments and 0.6 and 1.1 units compared with CT treatments, respectively
Summary
It is well established that soil microbial communities respond to N, P and/or K fertilizer (Allison and Martiny, 2008; Beauregard et al, 2010), manure, compost (Hartmann et al, 2015; Francioli et al, 2016) and their combinations (Sun et al, 2015; Chen et al, 2016). Researchers have linked changes in soil bacterial community structure and composition to nutrient availability. While fertilizers affect soil bacterial biomass and community composition by increasing nutrient availability, they exert indirect effects on the microbial community by altering soil pH. Under simulated single N deposition or fertilization, soil bacterial richness, and diversity were negatively affected by increased N availability, while the bacterial community composition was indirectly altered due to soil acidification (Zeng et al, 2016). Research from the Hoosfield and Park Grass Experiment at Rothamsted, UK showed that soil pH was the main edaphic property controlling microbial activity (Pietri and Brookes, 2008; Rousk et al, 2009, 2010; Zhalnina et al, 2015), and that bacterial richness and 16S rRNA copy numbers increased linearly within a soil pH range of 4.0 to 8.3 (Rousk et al, 2010). In a diverse set of ecosystems across South and North America, soil bacterial community structure was strongly shaped by soil pH at the continental scale, while differences in site-specific characteristics were poor predictors of bacterial community structure (Fierer and Jackson, 2006; Lauber et al, 2009)
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