Organic manure managements increases soil microbial community structure and diversity in double-cropping paddy field of Southern China

The soil physicochemical properties were affected by different fertilizer managements, and the soil microbial communities were changed. Fertilizer regimes were closely relative to the soil texture and nutrient status in a double-cropping paddy field of southern China. However, there was limited information about the influence of different long-term fertilizer management practices on the soil microbial communities in a double-cropping rice (Oryza sativa L.) fields. Therefore, the 39-year long-term fertilizer regimes on soil bacterial and fungal diversity in a double-cropping paddy field of southern China were studied by using Illumina sequencing and quantitative PCR technology in the present paper. The filed experiment were including chemical fertilizer alone (MF), rice straw residue and chemical fertilizer (RF), 30% organic manure and 70% chemical fertilizer (OM), and without fertilizer input as a control (CK). The results showed that diversity indices of soil microbial communities with application of organic manure and rice straw residue treatments were higher than that without fertilizer input treatment. Application of organic manure and rice straw residue managements increase soil bacterial abundance of the phylum Proteobacteria, Actinobacteria, and Gammaproteobacteria, and soil fungi abundance of the phylum Basidiomycota, Zygomycota and Tremellales were also increased. Compared with CK treatment, the value of Richness, Shannon and McIntosh indices, and taxonomic diversity were increased with RF and OM treatments. This finding demonstrated that RF and OM treatments modify soil bacterial and fungal diversity. Therefore, the combined application of organic manure or rice straw residue with chemical fertilizer managements could significantly increase the abundance of profitable functional bacteria and fungi species in double-cropping rice fields of southern China.

Soil microbial plays an important role in soil nutrient cycle, which were affected by different 29 fertilizer regimes and was closely relative with crop growth, soil fertility, and sustainability of soil return of organic manure and crop residues to soils. In contrast, some study indicated that 23 application of chemical fertilizer management practices increased soil microbial community and 24 activity [11]. However, there is still limited information about the change of soil microbial 25 community structure and diversity under different long-term fertilizer management practices 26 conditions.

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Rice (Oryza sativa L.) is the major crop in the tropical and subtropical monsoon climate 28 regions of Asia [12]. The early rice and late rice (double-cropping) production system is the 29 mainly crop system in southern of China, and the fertilizer regime (organic manure, crop residues, 30 inorganic fertilizer, and so on) is an important influence factors that maintain the quality and 4 1 fertility of paddy soils [13]. And the soil properties including the soil pH, soil organic carbon 2 (SOC) content were affected by different long-term fertilizer management practices, which in turn 3 influence the soil bacteria and fungi community structure and function [14][15]. However, there is 4 little information about the influences of 39-year long-term fertilizer regimes on soil microbial 5 activities and communities structure in double-cropping paddy field of southern China. We 6 hypothesized that the function and structure of soil bacteria and fungi communities were changed 7 under taken different fertilization management's conditions. Therefore, the abundance and 8 community structure of soil bacteria and fungi were investigated by using Illumina sequencing and 9 quantitative quantitative real-time polymerase chain reaction (PCR) technology, respectively. The results of every measured item were presented in mean values and standard error. The 5 data of each treatment means were compared by using one-way analysis of variance (Anova) 6 following standard procedures at the 5% probability level. All statistical analyses of correlations 7 between soil properties and abundant phyla were calculated by using the SAS 9.3 software 10 Results

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Soil properties

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The effects of different long-term fertilizer management practices on soil pH, soil organic 13 carbon (SOC) content, porosity, total N, soil microbial biomass carbon (SMBC), and soil 14 microbial biomass nitrogen (SMBN) contents in a double-cropping rice field were shown in Table   15 1

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The results revealed there was a significant correlation between soil bacterial abundant phyla 10 and soil chemical properties (Fig. 3 a). The soil properties can explain the variation (85.78% and

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The results indicated that the soil properties can explain the variation (87.82% and 13.68%) 20 in soil fungal abundant phyla between the MF, RF, OM and CK treatments (Fig. 3 b). Under In the present study, the results showed that soil microbial community were mainly affected 5 and changed by different long-term fertilizer management practices, including soil structure, soil 6 pH, SOC, total nitrogen, SMBC, and SMBN contents (Table 1), the soils total nitrogen, SOC, 7 SMBC, and SMBN contents were increased with application of organic manure and crop residues 8 incorporation treatments compared with the chemical fertilizer alone and without fertilizer input 9 treatment soils, consistent with the results of a previous study [1,4]. Application of organic 10 manure and crop residues practices significantly increased the SOC content, the reason maybe that of organic manure and crop residues management practices ( Fig. 1, Fig. 2), which may be the 22 disturb of microbiota were moderated, the soil texture and moisture content were increased, 23 therefore, the competitive niche and selection mechanisms among different populations were 24 excluded. As a result, the Richness, Shannon and McIntosh indices were increased in agree with 25 the previous study [1,4,6]. This result maybe explained from the soil texture and moisture 26 conditions using organic matter (organic manure and crop residues) management practices. The 27 soil pore connectivity were mainly affected by soil texture and moisture, which was the important 28 influence factor of changes in soil bacterial and fungal diversity, and was closely related to the 29 Simpson and Shannon indices [7]. There were more nutrient and C source with organic manure 30 and crop residues management practices than that with chemical fertilizer and without fertilizer 1 input treatments, which was provide an appropriate soil environment and nutrient for soil bacteria 2 and fungal multiplying. Therefore, this study was supports the idea that soil bacteria and fungal 3 alpha diversity and abundance were changed with application of organic manure and crop residues 4 management practices, which the soil texture, soil moisture content, and soil properties were 5 obvious altered.
6 Some studies showed that the structure and diversity of soil bacterial community were 7 changed under different fertilizer conditions [4, 10, 11]. In the present study, the relative 8 abundance of Proteobacteria and Actinobacteria with RF and OM treatments were higher than 9 that with MF and CK treatments (Fig. 1), which were provide an appropriate soil environment and 10 nutrient for Proteobacteria and Actinobacteria multiplying under application of organic manure 11 and crop residues conditions. The relative abundance of Fimicutes with CK treatment were higher 12 than that with MF, RF and OM treatments, which were mainly benefit for produce endospores There were significantly differences in response patterns of soil fungal community structure 5 and diversity to different long-term fertilizer regimes. In this study, the results showed that phyla 6 Ascomycota, Sordariales, Basidiomycota and Zygomycota were the most abundant in the soil 7 samples, consistent with the results of previous study [30]. And the phyla Ascomycota with 8 organic manure and crop residues treatments were significantly lower than that of with CK 9 treatment (Fig. 2), which were considered as the growth of Ascomycota was not good with 10 application of organic manure and crop residues management practices. The main reason maybe 11 that it was not benefit for the growth and reproduction of Ascomycota under application of organic 12 manure and crop residues conditions. on the other hand, the application of organic manure and 13 crop residues contains a lot of nitrogen, phosphorus and potassium nutrients, and the excessive 14 application of organic manure and crop residues in the soils will promote the pathogenic

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In the present study, the redundancy analysis results indicated that soil bacterial community 25 structure was closely related to soil porosity, SOC, total nitrogen, SMBC, and SMBN contents, 26 and soil fungal community structure was closely related to soil porosity, total nitrogen, SMBN and 27 SOC contents. Meanwhile, there were also obvious effects of soil pH on the soil bacteria and fungi 28 community structure (Fig. 3). Many studies have shown that soil microbial growth was affected by