- Email: [email protected]
Impact of farmland mulching practices on the soil bacterial community structure in the semiarid area of the loess plateau in China
European Journal of Soil Biology 92 (2019) 8–15
Contents lists available at ScienceDirect
European Journal of Soil Biology journal homepage: www.elsevier.com/locate/ejsobi
Impact of farmland mulching practices on the soil bacterial community structure in the semiarid area of the loess plateau in China
T
Fangyuan Huanga,b,c, Zihan Liua,b,c, Hongyan Moua,b, Jinglai Lia, Peng Zhanga,b,c,∗, Zhikuan Jiaa,b,c,∗∗ a
College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China The Chinese Institute of Water-saving Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi, China c Key Laboratory of Crop Physi-ecology and Tillage Science in Northwestern Loess Plateau, Ministry of Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi, China b
ARTICLE INFO
ABSTRACT
Handling Editor: C.C. Tebbe
Farmland mulching is widely used to preserve soil moisture and increase crop yield in the semiarid region of the Loess Plateau. However, the effect of different farmland mulching on soil bacterial communities is not clear. Therefore, the impact of a 5-year field management practice (surface mulching) on the soil bacterial communities was studied in dryland farmland of the Loess Plateau by using Illumina sequencing of the 16S rRNA gene. The following treatments were investigated: (1) ridge-furrow mulching pattern; (2) flat plastic film mulching; (3) flat biodegradable film mulching; (4) flat straw mulching; and (5) control (CK), conventional flat planting without mulch. All farmland mulching increased the diversity of soil bacteria and the diversity was greatest under the plastic film treatment. The dominant phyla across all soil samples were Proteobacteria, Acidobacteria, and Actinobacteria. Cluster analyses showed that bacterial communities under mulching treatments were different from that of CK. The bacterial community composition of plastic film and straw mulching treatments, biodegradable film and ridge-furrow mulching treatments were similar at the phylum level. Spearman correlation analysis indicated that the response of bacterial alpha-diversity was mainly negatively associated with the soil organic carbon and total nitrogen. The Mantel test showed that the beta-diversity depended primarily on the soil total nitrogen and soil temperature. The changes of the bacterial community distribution were significantly related to the soil moisture, which varied significantly with a range of 9.8–17.3 between treatments. These results indicated that soil properties changed after long-term farmland mulching, and these changes were related to soil bacterial diversity and community structure. According to this study, flat plastic firm mulching was found to being a good option for increasing soil bacterial diversity and richness and thereby potentially stabilize functional stability of soil biological processes.
Keywords: Bacterial community Mulching practices Semiarid area Soil moisture
1. Introduction Soil bacteria have vital effects on soil nutrient cycling, plant productivity, and the sustainability of soil productivity [1], and changes in their community structure may be important and sensitive indicators of short-term and long-term changes in soil health [2]. An increase in soil bacterial diversity could indicate an increase in functional diversity, thereby resulting in functional redundancy, which is an important biological strategy for buffering environmental stress, thus stabilizing soil biological functions [3]. The abundance and diversity of bacterial communities in farmland ecosystems could therefore be critical for maintaining soil quality, productivity, and ecological balance [4,5].
The Loess Plateau is a typical arid and semi-arid region and one of the most important regions for dryland farming in China. However, low air temperatures, limited water availability, and poor soil fertility limit agricultural productivity in this region [6]. Therefore, a lot of mulching measures, including straw mulching, degradable film mulching, plastic film mulching and ridge-furrow rainwater planting are widely used in this ecosystem. Relative to uncovered soil, mulching can reduce water evaporation and improve the soil temperature (ST) [7,8], and it can increase the yield and water use efficiency by crops under such environmental conditions [9,10]. However, mulching also has some potential drawbacks. For example, continuous plastic film mulching may consume excessive amounts of deep soil moisture [11]. In addition,
Corresponding author. The Chinese Institute of Water-saving Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi, China. Corresponding author. College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China. E-mail addresses: [email protected] (P. Zhang), [email protected] (Z. Jia).
∗∗ ∗
https://doi.org/10.1016/j.ejsobi.2019.04.001 Received 25 November 2018; Received in revised form 8 April 2019; Accepted 8 April 2019 Available online 24 April 2019 1164-5563/ © 2019 Elsevier Masson SAS. All rights reserved.
European Journal of Soil Biology 92 (2019) 8–15
F. Huang, et al.
changes in soil moisture and temperature due to mulching practices can change the biological characteristics of the soil, which may affect the soil quality and agroecosystem sustainability [12,13]. Thus, the longterm effects of farmland mulching practices need to be further studied. In addition to changing soil properties and crop growth, soil microbial communities are also sensitive to farmland mulching practices [14]. Modifications to soil microclimate under mulching practices affect soil bacterial communities [15]. Covering crops and plastic film significantly increased soil bacterial abundance and diversity in subtropical orchards and northeast rain-fed corn fields, respectively [16,17]. Continuous no-tillage coverage significantly increased the abundance of Gram-positive bacteria and Actinobacteria in cotton field soils [18]. In a brown soil, long-term manure fertilization coupled with film mulching increased relative abundances of Proteobacteria and Actinobacteria [19]. However, studies to date have focused on the effects of single mulching materials or planting methods on soil bacterial communities, comparisons between different mulching materials or planting methods have rarely been investigated. Moreover, most studies concentrated on the short-term effects of mulching practices, the longterm effect of farmland mulching measures on soil bacteria in the Loess Plateau is not well understood. Therefore, a 5-year field experiment of different farmland mulching practices, namely, ridge-furrow mulching pattern (R), flat plastic film mulching (P), flat biodegradable film mulching (B), flat straw mulching (S), and conventional flat planting without mulching as a control (CK) was set up. Soil samples were collected to analyze their physicochemical properties and bacterial diversity, the latter determined by Illumina sequencing of the PCR-amplified 16S rRNA gene. We hypothesized that: (1) mulching practices would change the soil physicochemical properties, thereby changing the soil bacterial community; (2) bacterial composition would respond differently to different mulching materials or planting methods. The objectives of this study were: (1) to study the effects of different farmland mulching practices on the soil physicochemical characteristics, bacterial diversity, and community composition; and (2) to detect the most important soil parameters affected by farmland mulching practices that cause changes in the bacterial community structure; and (3) to provide a scientific basis for evaluating the influence of common mulching practices on soil biological characteristics.
(width = 120 cm) was used to cover the flat surface completely. (4) Flat straw mulching (S) where complete maize straw was mulched evenly at an amount of 9000 kg ha−1 (5) Control (CK) comprising conventional flat planting without mulching. The plastic film was clear and impermeable polyethylene, with a thickness of 0.008 mm (produced by Guyuan Yuande Plastic Products Co. Ltd, Ningxia, China), and it was stable and did not decompose after harvesting the crop. After the crops were harvested in the previous season, the old mulch film was completely removed and the mulch film was covered again after the land preparation in the autumn. The white biodegradable film measured 1.2 m wide × 0.008 mm thick (produced by Bionolle Department, Showa Denko, Japan) and it eventually degraded to yield H2O and CO2. The complete degradation of the film required about 270 days depending on the temperature, humidity, fertility of the soil, and other factors. Different levels of damage to the biodegradable film were observed in June, and the film was completely degraded after harvesting the crop. The edges of the film were covered carefully and compacted with soil. Every 200 cm, a soil belt was set in the vertical direction to prevent the film from being removed by strong winds. In the S treatment, after the crops were harvested in the previous season, the non-decomposed straw was removed and the straw was covered again after land preparation in the autumn. All of the mulching treatments were conducted in autumn in the previous year. All of the trials started in 2012. Seeds of the spring maize cultivar “Dafeng 30” were sown in April each year and harvested in October (the accurate sowing and maturation dates between 2012 and 2016 are shown in Table S2). Maize was sown at a rate of 67,000 plants ha−1 (60 × 25 cm) using a hole-sowing/fertilization (3 cm in diameter) machine, with a sowing depth of 4–5 cm. A base fertilizer comprising 140 kg ha−1 N and 150 kg ha−1 P2O5 was applied using a hole-sowing/ fertilization machine. In addition, 140 kg ha−1 N was applied between the maize plants as a top dressing at 69–75 days after maize planting, with a fertilization depth of 4–5 cm. The sowing rate and fertilizer application rate were the same for all of the treatments. Irrigation was not applied throughout the entire year. No pests were found in all treatments during the experiment and manual weeding was performed as required according to the conditions.
2. Material and methods
Soil samples were obtained from depths of 0–20 cm at 85 days after sowing the maize on July 16, 2016. The sampling position of the R treatment was in the furrow planting area, and between the planting rows for all other treatments. Nine replicate samples (top 0–20 cm) were collected in an “S” shape by using a soil-drilling sampler (5 cm inner diameter), before mixing and homogenizing to obtain one composite sample per replicate site. The samples were then sieved through a 2-mm screen and any visible roots or other debris were removed. A portion of each soil sample was stored at 4 °C to analyze the soil dissolved organic carbon (DOC) and soil nitrate nitrogen (NO3-N). Part of each soil sample was also collected in a 100-mL centrifuge tube, transported from the field to the laboratory in an icebox, and then stored at −80 °C. The remaining soil sample was air dried before measuring the soil physicochemical properties (soil pH, soil organic carbon (SOC), and soil total nitrogen (TN)).
2.3. Soil sampling
2.1. Study area description The experiment was conducted in Changcheng Village, Pengyang County, Ningxia Province, China. This village is located in the hilly area of the Loess Plateau (35°51′N, 106°48′E) at an average elevation of 1658 m, which has a typical temperate semiarid continental monsoon climate with annual precipitation of 430 mm. The vast majority of the annual precipitation occurs between July and September. The average annual temperature was 8.1 °C, with a frost-free period of 140–160 days. The soil at the experimental site was Loessal soil (sandy clay loam). The annual precipitation during the test period (2012–2016) is shown in Table S1. 2.2. Experimental design
2.4. Soil physicochemical measurements
The experiment used a completely randomized block design with three replicates and each plot area was 58.8 m2 (14 × 4.2 m). The following five treatments were tested. (1) Ridge-furrow mulching pattern (R) with alternating ridges and furrows, where only the ridges were covered with plastic film (width = 70 cm) and maize was sown in the furrows. The ridges and furrows had equal widths of 60 cm and the ridge height was 15 cm. (2) Flat plastic film mulching (P) where plastic film (width = 120 cm) was used to cover the flat surface completely. (3) Flat biodegradable film mulching (B) where biodegradable film
Soil moisture and soil temperature (ST): The soil water content (SWC) (0–20 cm) was determined by oven drying to constant mass at 105 °C on the same day as sampling. ST measurements (at 5 cm, 10 cm, 15 cm, and 20 cm) were obtained using an angle stem earth thermometer for three consecutive days, and the average ST based on all four measurements was used as the ST for each plot. Soil pH: The soil pH was measured using a pH meter after shaking a soil:water (1:2.5 w/v) suspension comprising 10 g of air-dried soil and 9
European Journal of Soil Biology 92 (2019) 8–15
F. Huang, et al.
25 mL of water for 30 min. Soil carbon and soil nitrogen: The SOC content was assayed using the potassium dichromate oxidation method [20]. The soil TN content was determined using the Kjeldahl method [21]. The concentration of NO3-N was determined by adding 50 mL of 1.0 M KCl to 5 g of each fresh soil sample, shaking for 30 min, and then collecting the contents by filtration using a continuous flow analyzer (Autoanalyzer 3, Bran Luebbe, Germany). The soils were suspended in water (soil:water = 1:5), shaken for 5 h, centrifuged at 13,000 r/min for 10 min, and filtered through a 0.45-μm membrane to determine the soil DOC. Organic C in the extracts was determined using a total organic carbon analyzer (Elementar, Vario TOC, Germany).
Table 1Soil physicochemical properties and enzyme activities measured in the 0–20 cm soil layer. Treatments
pH
SWC %
ST °C
TN g/kg
SOC g/kg
NO3 -N mg/kg
DOC mg/kg
R P B S CK
7.25c 7.39b 7.45b 7.52a 7.59a
12.58c 13.92b 10.37d 17.29a 9.81e
23.37c 24.61b 22.25d 22.71d 25.82a
0.84b 0.82b 0.82b 0.88a 0.89a
9.54 ab 9.22b 9.22b 9.65a 9.47 ab
20.46c 27.03b 20.07d 31.79a 26.72b
23.21b 24.23b 25.44b 32.25a 26.05b
Different letters in the same column indicate significant differences at (P < 0.05) according to Duncan's test. pH: soil acidity; SWC: soil water content; ST: soil temperatures (the average values of 5, 10, 15, 20 cm soil layers were used in this table); TN: total nitrogen; SOC: soil organic carbon; NO3-N: nitrate nitrogen; DOC: dissolved organic carbon; R: Ridge-furrow mulching pattern; P: flat plastic film mulching; B: flat biodegradable film mulching; S: flat straw mulching; CK: conventional tillage without mulching.
2.5. DNA extraction, PCR amplification, and Illumina HiSeq sequencing Soil microbial DNA was extracted from 0.5 g of each sample using a FastDNA SPIN Kit for Soil (MP Biomedicals, USA) according to the manufacturer's instructions. The 16S rRNA gene V3–V4 region was amplified using the primers 341 F (CCTACGGGRSGCAGCAG) and 806 R (GGACTACVVGGGTATCTAATC) [22]. Amplicons were extracted from 2% agarose gels and purified with an AxyPrep DNA Gel Extraction Kit (Axygen Biosciences, Union City, CA, USA) according to the manufacturer's instructions, and quantified with a Qubit® dsDNA HS Assay Kit (Thermo Fisher, USA). Purified amplicons were pooled in equimolar concentrations and then subjected to paired-end sequencing (2 × 250) using the Illumina HiSeq PE250 platform according to the standard protocols. Illumina HiSeq sequencing was performed by Realbio Technology Co. Ltd (Shanghai, China). PANDAseq software was used to merge the paired-end sequence reads obtained from the original DNA fragments [23]. The sequences were further analyzed using USEARCH v5.2.32 to filter and denoise the data. The Quantitative Insights Into Microbial Ecology (QIIME) pipeline was used to define operational taxonomic units (OTUs) by combining reads of the clustered OTUs with ≥97% similarity [24]. Finally, the complete dataset was submitted to the Sequence Read Archive (SRA) database of the National Center for Biotechnology Information (NCBI) under accession number SRP136001.
rank correlation tests were performed using SPSS 18.0 (SPSS Inc., Chicago, IL, USA). ANOSIM, NMDS, RDA, and Mantel tests were performed using R v.3.3.3. 3. Results 3.1. Soil physicochemical properties The TN content was significantly higher (P < 0.05) in the straw mulching (S) and CK treatments than the other treatments (Table 1), and there were no significant differences in the TN contents under the ridge-furrow (R), plastic film (P), and biodegradable film (B) mulching treatments. DOC and SOC were highest in the S treatment, where they were 23.8% (P < 0.05) and 1.9% (P > 0.05) higher than those in CK, respectively, and no significant differences were observed among the other treatments. The NO3-N contents were significantly lower in the R and B treatments than CK, but not in the S and P treatments. SWC was highest in the S treatment, followed by the P, R, B, and CK treatments. ST was lowest in the S and B treatments, and there were significant differences between the R, P, and CK treatments. The soil pH values were significantly lower in the R, P, and B treatments than CK (P < 0.05), but not in the S treatment.
2.6. Statistical analyses Soil physicochemical and microbial abundance data were analyzed by one-way analysis of variance (ANOVA) to determine significant differences among the treatments. Significant differences were accepted at the 95% confidence level. If a significant difference was detected at P < 0.05, the post hoc Duncan's multiple range test was used for multiple comparisons. Alpha diversities were calculated using QIIME software [25]. The Chao1 estimation method and Shannon diversity index were used to calculate the richness and diversity of the bacterial community, respectively. To determine the beta diversity, the phylogenetic community composition and membership were compared using the weighted and unweighted UniFrac distance matrices [26]. Analysis of similarities (ANOSIM) was used to test for the significance of separations measured under different mulching treatments. Non-metric multidimensional scaling (NMDS) was conducted to visualize the clustering of different samples. Correlations between the soil bacterial community structure and soil characteristics were determined using Mantel tests based on 999 permutations. The characteristic microbial community features under each mulching treatment were determined using the linear discriminant analysis (LDA) effect size (LEfSe) method, which emphasizes statistical significance and biological relevance [27]. Redundancy analysis (RDA) was conducted to examine the relationships between the soil environmental variables and bacterial community abundance levels. Spearman's rank correlation test was used to investigate the associations between bacterial communities and soil physicochemical properties. All statistical analyses (ANOVA and Duncan's test) and Spearman's
3.2. Soil bacterial diversity After five consecutive years of mulching practices, the Chao1 indices were significantly higher in the plastic film (P) treatment (3,689) and straw mulching (S) treatment (3,789) than CK, i.e., 10.2% and 13.2% higher than CK (3,348), respectively (Fig. 1), but there were no significant differences in the Chao1 index among the ridge-furrow (R), biodegradable film (B) and CK treatments. Differences in the soil bacterial diversity under different mulching treatments were determined using the Shannon index, and the Shannon index of each mulching treatment was significantly higher than that for CK, with an average of 1.8%. The strongest effect was observed with P treatment, followed by B, R and S treatments, while there was no significant difference between P and B treatments, nor between R and S treatments. The Chao1 and Shannon indices showed that the soil bacterial abundance and diversity were both higher in the P treatment. The Spearman's rank correlation coefficients indicated significant correlations between the soil bacterial community richness and diversity and the soil physicochemical properties (Fig. 1). The Chao1 index was significantly positively correlated with SWC. The Shannon diversity index was significantly negatively correlated with TN and SOC (P < 0.05). 10
European Journal of Soil Biology 92 (2019) 8–15
F. Huang, et al.
the B and CK treatments. LEfSe analyses were performed to identify the statistical significance of differentially abundant taxa and the biological relevance of the species in each mulching treatment (Fig. 4), and the LDA values are shown in Supplementary Fig. S2. The LEfSe results showed that Proteobacteria, Nitrospirae, and Bacteroidetes mainly changed in the S treatment, P treatment mainly changed Proteobacteria, and the phylum Gemmatimonadetes changed in the B treatment. In Fig. 4, the orange color represents the significantly changed taxa in CK, which mainly comprised Actinobacteria. 3.4. OTU level bacterial beta-diversity analysis Two beta-diversity measures were used to compare the bacterial community structure in soils subjected to different mulching treatments. Phylogenetic analyses of the bacterial community composition and membership were performed using both the weighted and unweighted UniFrac distances. The NMDS plots indicated that the weighted and unweighted UniFrac distances were well separated in the different mulching treatments (Fig. 2). In addition, the soil bacterial community composition and memberships in the straw mulching, plastic film, and ridge-furrow mulching treatments differed significantly from those in CK. The weighted UniFrac distances showed that the soil bacteria composition in ridge-furrow was similar to that in biodegradable film (Fig. 2A). ANOSIM analysis indicated that the weighted and unweighted UniFrac distances both contributed significantly to the separation of the bacterial communities under different mulching treatments. (r = 0.599, P = 0.001; r = 0.938, P = 0.001).
Fig. 1. (A) The richness and diversity indices under the different mulching treatments. (B) Spearman's rank correlation coefficients between soil bacterial richness and diversity indices and the soil physicochemical properties. The values are the means of three replicates, and different letters within the same column indicate significant differences at P < 0.05. R: Ridgefurrow mulching pattern; P: flat plastic film mulching; B: flat biodegradable film mulching; S: flat straw mulching; CK: conventional tillage without mulching. pH: soil acidity; SWC: soil water content; ST: soil temperatures; TN: total nitrogen; SOC: soil organic carbon; NO3-N: nitrate nitrogen; DOC: dissolved organic carbon.
3.5. Relationship between bacterial community structure and soil properties The Mantel test results showed (Table 2) that TN, ST, and NO3-N had strong correlations with the bacterial phylogenetic community composition (weighted UniFrac metric; r = 0.358, 0.335, and 0.295; P = 0.005, 0.006, and 0.01) and membership (unweighted UniFrac metric; r = 0.302, 0.348, and 0.290; P = 0.011, 0.006, and 0.015) compared with other environmental factors. RDA showed that various bacterial taxa (phylum, class, and order) (Fig. 5, Fig. S3) responded in different ways to changes in the soil properties. The results indicated that the soil characteristics greatly affected the soil bacterial community (Table S3, Table S4). In particular, soil moisture had the main effect on changes in the bacterial community composition. Fig. 5 shows that SWC, DOC, and TN has significant correlations with the changes in Proteobacteria, Nitrospirae, Bacteroidetes, Acidobacteria, Actinobacteria, and Gemmatimonadetes. Among Proteobacteria, SWC was positively correlated with the abundances of Sphingomonadales, Rhodospirillales, and Rhizobiales (Fig. S3), which are branches of Alphaproteobacteria (Table 3). By contrast, SWC was negatively correlated with the abundances of Acidimicrobiales, Actinomycetales and Gaiellales, which are branches of Actinobacteria (Fig. S3).
3.3. Soil bacterial community composition In total, 542,500 sequences were obtained after analyzing all of the soil samples. The average number of sequences per sample was 36,167 (range = 33,156–38,546) and 97.7% of the sequences were classified at the phylum level. The dominant phyla in all treatments were Proteobacteria, Acidobacteria, and Actinobacteria, with relative abundances ranging from 33.5 to 45.0%, 20.6–24.1%, and 15.0–21.8%, respectively. In addition, Gemmatimonadetes and Bacteroidetes were subdominant groups. These five phyla represented more than 90% of the sequences in all of the samples. Cluster analyses were conducted to determine the relationships among all of the treatments. The bacterial communities differed in CK and the mulching treatments at the phylum and class level (Fig. 3, Fig. S1). At the order levels (Fig. S1), the bacterial communities were similar in the biodegradable film treatment and CK, but they differed from those in the other treatments. High relative abundances of Proteobacteria were found in the ridge-furrow (R), biodegradable film (B), plastic film (P), and straw (S) mulching treatments, whereas the abundance of Actinobacteria was higher in CK. At the class level (Fig. S1, Table 3), Actinobacteria, Alphaproteobacteria, and Betaproteobacteria were dominant. The relative abundances of Actinobacteria were high in the B treatment and CK. The relative abundances of Alphaproteobacteria and Betaproteobacteria did not differ significantly among the treatments (P > 0.05) except for in the S treatment and CK. The other two Proteobacteria branches comprising Gammaproteobacteria and Deltaproteobacteria were most abundant in the S and P treatments, respectively. At the order level (Table 3), the abundances of Sphingomonadales and Rhodospirillales, branches of Alphaproteobacteria, were significantly higher in the S treatment, whereas Gemmatimonadales, Actinomycetales, and Acidimicrobiales were relatively more abundant in
4. Discussion 4.1. Farmland mulching practices changed soil physicochemical properties After five years of continuous mulching, soil physicochemical properties were affected by different mulching practices to varying degrees. Previous studies have shown that mulching can improve soil moisture and ST, leading to improved crop growth and yield in this region [28]. Thus, the decrease of TN content under mulching treatments can be attributed to the absorption of nutrients by crops. Straw litter was incorporated into the soil as organic matter to supplement the soil nutrient sources [29]. Therefore, the TN content in the straw mulching treatment was not reduced, and the SOC and DOC contents are higher than other mulching treatments and CK, which is consistent 11
European Journal of Soil Biology 92 (2019) 8–15
F. Huang, et al.
Fig. 2. Bacterial community structure according to non-metric multidimensional scaling (NMDS) plots of the weighted (A) and unweighted UniFrac (B) distances. R: Ridge-furrow mulching pattern; P: flat plastic film mulching; B: flat biodegradable film mulching; S: flat straw mulching; CK: conventional tillage without mulching.
with the results in the orchard of the Loess Plateau [30]. It was suggested that different mulching materials and types used on the Loess Plateau can effectively inhibit the inefficient evaporation of soil moisture and preserve water [31]. Similar results were also found in this study, mulching practices significantly increased SWC, compared with CK. The variation in ST was attributed to the shading effect of the canopy and the characteristics of different mulching materials and types [32,33].
Table 2 Correlations among the overall bacterial community structure and soil proprieties according to the Mantel test. Distance
Soil variable
r
P value
unweighted UniFrac
TN ST NO3-N TN ST NO3-N
0.302 0.348 0.29 0.358 0.335 0.295
0.011∗∗ 0.006∗∗ 0.015∗∗ 0.005∗∗ 0.006∗∗ 0.01∗∗
weighted UniFrac
4.2. Farmland mulching practices increased soil bacterial diversity
ST: soil temperatures; TN: total nitrogen; NO3-N: nitrate nitrogen.
In the present study, we found that compared with CK, the application of farmland mulching practices increased the soil bacterial diversity in a semiarid area, and the soil bacterial alpha diversity (indicated by the Shannon index) had significant negative correlations with TN and SOC (Fig. 1). Consistent with this, it was suggested that the ecological strategies of soil bacteria can be changed by the increased availability of C and N [34]. Therefore, the soil microbial diversity may be influenced by the availability of soil nutrients [35,36]. In addition, we found that after five consecutive years of mulching, the soil bacterial community diversity had negative correlations with TN and SOC, thereby indicating that increased bacterial diversity was associated with decreases in these soil nutrients, and vice versa. These findings may be explained by crops competing for the limited amounts of mineral nutrients with soil microorganisms [37], where the activity of soil
microorganisms will accelerate the decomposition of organic matter and increase its biomass. In addition, plants require more soil nutrients during the period of vigorous crop growth, so large amounts of soil nitrogen and carbon are transferred to the crop, which results in a decrease in the soil TN and SOC [38]. A higher correlation between the microbial diversity and soil nutrients indicates greater competition between the crops and soil microorganisms [39]. In the present study, the plastic film (P) and straw (S) mulching treatments significantly improved the Chao1 index for soil bacteria compared with CK, and SWC was the major contributor to the soil bacterial richness under mulching conditions. This finding is consistent with the results of bacterial community richness in dryland forest ecosystem [40]. Fig. 3. The relative abundance of the dominant bacterial phyla across all treatments, with the clustering tree on the left showing the similarities among treatments. R: Ridgefurrow mulching pattern; P: flat plastic film mulching; B: flat biodegradable film mulching; S: flat straw mulching; CK: conventional tillage without mulching.
12
European Journal of Soil Biology 92 (2019) 8–15
F. Huang, et al.
Table 3 Relative abundances (average values) of bacterial compositions across taxonomical classification (Phyla, Class, and Order) in each mulching treatment. Phylum Proteobacteria
Acidobacteria
Actinobacteria
Class Alphaproteobacteria Sphingomonadales Rhizobiales Rhodospirillales Betaproteobacteria Gammaproteobacteria Xanthomonadales Deltaproteobacteria Myxococcales Acidobacteria_Gp6 Acidobacteria_Gp4 Acidobacteria_Gp7
Actinobacteria Actinomycetales Acidimicrobiales Gaiellales Gemmatimonadetes Gemmatimonadetes Gemmatimonadales Bacteroidetes Sphingobacteriia Sphingobacteriales Verrucomicrobia Firmicutes Nitrospirae
Order
R
P
B
S
CK
p
40.44b 15.95b 17.63 ab 5.52a 2.75b 11.67a 8.45a 9.65a 6.42b 7.51a 21.58a 8.64a 6.29 ab 3.01 ab 17.40bc 17.80bc 10.86bc 8.48bc 4.50a 6.53bc 6.99bc 12.61 ab 5.64c 2.91b 5.24b 2.94a 0.49a 0.62b
41.42 ab 16.04b 16.46 ab 5.78a 4.04a 11.52a 8.38a 9.02a 7.41a 8.57a 22.71a 9.33a 6.17 ab 2.70b 14.73c 15.14c 9.55c 7.49c 4.20a 6.02c 6.45c 12.10b 6.80 ab 3.56a 6.67a 2.32 ab 0.53a 0.73b
37.77b 14.77b 14.79b 5.50a 3.03b 11.22a 7.17 ab 7.91 ab 6.37b 8.24a 20.58a 7.54a 5.63b 3.56a 20.02 ab 20.30 ab 12.52 ab 9.84 ab 4.67a 7.51a 8.03a 14.44a 6.21bc 3.03b 5.46b 3.10a 0.41a 0.61b
45.05a 20.65a 21.29a 6.01a 4.45a 11.42a 8.58a 9.19a 6.24b 7.08a 20.82a 8.54a 6.24 ab 2.99 ab 15.05c 15.36c 10.17c 6.92c 3.13b 6.14c 6.52c 11.21b 7.50a 3.55a 6.10 ab 1.37b 0.48a 0.92a
33.54c 13.97b 14.58b 5.68a 2.54b 9.45b 5.86b 6.52b 5.37c 7.26a 24.12a 9.58a 7.37a 3.29 ab 21.83a 22.13a 13.81a 11.31a 4.98a 7.40 ab 7.83 ab 14.40a 5.82c 3.11b 5.73b 2.99a 0.44a 0.39c
≤0.001 0.007 0.037 0.438 < 0.001 ≤0.001 0.025 0.03 0.004 0.16 0.268 0.256 0.164 0.069 ≤0.001 0.002 0.007 ≤0.001 0.018 0.01 0.007 0.013 0.007 0.007 0.023 0.026 0.836 ≤0.001
Different letters indicate significant differences (ANOVA, P < 0.05, Duncan's post-hoc analysis) among different mulching treatments. R: Ridge-furrow mulching pattern; P: flat plastic film mulching; B: flat biodegradable film mulching; S: flat straw mulching; CK: conventional tillage without mulching.
Fig. 4. A linear discriminant analysis effect size (LEfSe) method identifies the significantly different abundant taxa of bacteria in all of the treatments. The taxa with significantly different abundances among treatments are represented by colored dots, and from the center outward, they represent the kingdom, phylum, class, order, family, and genus levels. The colored shadows represent the significantly differed taxa which is indicated by “a:” “b:” “c:” etc. Gp12, Gp15, Gp16, and Gp3 are the genus of Acidobacteria. R: Ridge-furrow mulching pattern; P: flat plastic film mulching; B: flat biodegradable film mulching; S: flat straw mulching; CK: conventional tillage without mulching.
13
European Journal of Soil Biology 92 (2019) 8–15
F. Huang, et al.
increased the abundance of Acidobacteria in the CK treatment (Fig. 5, Fig. S2). Actinobacteria are distributed widely in terrestrial and aquatic ecosystems, especially in arid and acid soils, and they are considered important decomposers of soil organic matter [49]. In addition, members of this phylum have the capacity to produce spores, which increases the ability of this group to resist perturbation events [50]. The similar soil moisture and nutrient levels in the plastic film (P) and straw (S) mulching treatments may explain the lower abundance of Actinobacteria compared with the other treatments. 4.4. Relationship between bacterial community and soil properties The different effects of the mulching treatments and the associated bacterial communities can be explained by soil characteristics. The NMDS and ANOSIM results showed that there were significant differences in the beta-diversity under different mulching treatments, which indicated that different mulching patterns yielded different bacterial community structures. The differences were significantly associated with changes in the soil moisture, ST and soil nutrients (Table 2). We found that compared with other environmental factors, the soil TN had a greater influence on the phylogenetic components of the bacterial community structure, followed by ST, which is accordance with the results of the long-term fertilizations study [36]. Similarly, the microbial beta-diversity in forest soil was highly correlated with the ST [51]. In addition, we found that several highly abundant bacterial taxa were significantly associated with SWC. Furthermore, the bacterial compositions of the biodegradable film mulching and CK treatments were different from those of the plastic film and straw mulching treatments, which were attributed to the relatively high SWC (extended arrow in Fig. 5). These findings are consistent with the recent studies, who found that the bacterial communities were strongly correlated with SWC [40,52]. Under mulching conditions, increases in the soil moisture and temperature can change the growth of microorganisms, and thus the decomposition and utilization of soil nutrients [53], possibly due to changes in bacterial ecology strategies, which may ultimately contribute to differences in the bacterial communities [34]. In conclusion, the results of this study demonstrate that soil physical-chemical properties (TN, DOC, NO3-N, ST, and SWC), bacterial diversity and community structure were changed after five-year farmland mulching in a semiarid area. The change of bacterial community was mainly affected by SWC and ST, whereas SOC and TN were the primary factors that influenced the bacterial diversity. Overall, our results indicate that flat plastic film mulching should be recommended as it enhanced both soil bacterial diversity and richness in the Loess Plateau of China.
Fig. 5. Ordination plots of the results from the redundancy analysis (RDA) to identify the relationships among the bacterial taxa (phylum) and soil properties. pH: soil acidity; SWC: soil water content; ST: soil temperatures; TN: total nitrogen; SOC: soil organic carbon; NO3-N: nitrate nitrogen; DOC: dissolved organic carbon; R: Ridge-furrow mulching pattern; P: flat plastic film mulching; B: flat biodegradable film mulching; S: flat straw mulching; CK: conventional tillage without mulching.
4.3. Farmland mulching practices changed soil bacterial community The bacterial community showed a difference between CK and mulching treatments in the cluster analysis (Fig. 3). This conclusion is consistent with previous studies [14,41], which reported that mulching with organic matter strongly influences the composition of the soil bacterial community. According to the results of LEfSe analysis, Proteobacteria, Acidobacteria and Bacteroidetes changed significantly in plastic film (P) and straw (S) mulching treatments, the most significant taxa in the biodegradable film (B) mulching treatment was Gemmatimonadetes, while CK mainly changed Actinobacteria, indicating that mulching practices had a significant effect on bacterial communities. Proteobacteria have been described as fast-growing copiotrophs that are stimulated in carbon-rich environments [42]. However, we found that Proteobacteria were affected greatly by the soil moisture, but not by SOC (Fig. 5). This may be explained by the specific Proteobacteria compositions in the different mulching treatments (Fig. S2). At the class level, Betaproteobacteria are typically present at low abundances in dry soil [43] and we found that they were more sensitive to SWC (Fig. S2A). At the order level, Rhizobiales and Rhodospirillales, branches of alpha-Proteobacteria, were also significantly associated with soil moisture (SWC) (Fig. S2B), thereby indicating that the variations in the abundances of Proteobacteria were related to their responses to soil moisture under the different mulching treatments. Lower soil moisture contents limit the mineralization of soil nutrients [44] and the abundance of Proteobacteria was low in the CK treatment with high SOC and low soil moisture. Another obvious trend found in this study was the higher abundance of Bacteroidetes under the P and straw S treatments, particularly Sphlingobacteriales. It was suggested that Bacteriodetes were predominant in agricultural systems due to their ability to rapidly exploit bioavailable organic matter [4]. Studies have shown that the plastic film mulching has a higher root biomass due to the vigorous growth of plants [45], and the straw mulching has more plant litter [30]. Thus, the P and S treatments both provided highly suitable soil environments for Bacteroidetes by allowing them to utilize the readily degradable fraction of crop residues, thereby facilitating their rapid growth [34]. Actinobacteria and Acidobacteria are considered to be oligotrophs [46]. Acidobacteria are less abundant when the soil is moister and cooler [47,48]. The higher ST and lower soil moisture may have
Acknowledgements This study was supported by the Program of National Natural Science Foundation of China (No. 41671226 and No. 31801314) and China 111 Project (No. B12007), the Fundamental Research Fund for Universities and Colleges (2452017051), the Natural Science Basic Research Plan in Shaanxi Province of China (No. 2018JQ3024), the Young Talent fund of University Association for Science and Technology in Shaanxi, China (20180203), China National Science and Technology Support Program (2015BAD22B02) in the 12th 5-year plan period. We are also grateful to Nie Junfeng, Yang Baoping and Ding Ruixia for help during experimental period. Appendix A. Supplementary data Supplementary data to this article can be found online at https:// doi.org/10.1016/j.ejsobi.2019.04.001. 14
F. Huang, et al.
European Journal of Soil Biology 92 (2019) 8–15
References
semiarid China, Front. Plant Sci. 8 (2017). [29] Q.G. Dong, Y.C. Yang, K. Yu, H. Feng, Effects of straw mulching and plastic film mulching on improving soil organic carbon and nitrogen fractions, crop yield and water use efficiency in the Loess Plateau, China, Agric. Water Manag. 201 (2018) 133–143. [30] Y. Chen, X. Wen, Y. Sun, J. Zhang, W. Wu, Y. Liao, Mulching practices altered soil bacterial community structure and improved orchard productivity and apple quality after five growing seasons, Sci. Hortic. 172 (2014) 248–257. [31] X. Zhang, M. Kamran, X. Xue, J. Zhao, T. Cai, Z. Jia, P. Zhang, Q. Han, Ridge-furrow mulching system drives the efficient utilization of key production resources and the improvement of maize productivity in the Loess Plateau of China, Soil Till. Res. 190 (2019) 10–21. [32] X. Zhang, J. Zhao, L. Yang, M. Kamran, X. Xue, Z. Dong, Z. Jia, Q. Han, Ridgefurrow mulching system regulates diurnal temperature amplitude and wettingdrying alternation behavior in soil to promote maize growth and water use in a semiarid region, Field Crop. Res. 233 (2019) 121–130. [33] X.L. Qin, Y.Z. Li, Y.L. Han, Y.C. Hu, Y.J. Li, X.X. Wen, Y.C. Liao, K.H.M. Siddique, Ridge-furrow mulching with black plastic film improves maize yield more than white plastic film in dry areas with adequate accumulated temperature, Agric. For. Meteorol. 262 (2018) 206–214. [34] N. Fierer, M.A. Bradford, R.B. Jackson, Toward an ecological classification of soil bacteria, Ecology 88 (2007) 1354–1364. [35] W.R. Cookson, D.A. Abaye, P. Marschner, D.V. Murphy, E.A. Stockdale, K.W.T. Goulding, The contribution of soil organic matter fractions to carbon and nitrogen mineralization and microbial community size and structure, Soil Biol. Biochem. 37 (2005) 1726–1737. [36] C.H. Li, K. Yan, L.S. Tang, Z.J. Jia, Y. Li, Change in deep soil microbial communities due to long-term fertilization, Soil Biol. Biochem. 75 (2014) 264–272. [37] R.C. Miatto, I.J. Wright, M.A. Batalha, Relationships between soil nutrient status and nutrient-related leaf traits in Brazilian cerrado and seasonal forest communities, Plant Soil 404 (2016) 13–33. [38] F.M. Li, J. Wang, J.Z. Xu, H.L. Xu, Productivity and soil response to plastic film mulching durations for spring wheat on entisols in the semiarid Loess Plateau of China, Soil Till. Res. 78 (2004) 9–20. [39] T. Miki, Microbe-mediated plant-soil feedback and its roles in a changing world, Ecol. Res. 27 (2012) 509–520. [40] F. Colombo, C.A. Macdonald, T.C. Jeffries, J.R. Powell, B.K. Singh, Impact of forest management practices on soil bacterial diversity and consequences for soil processes, Soil Biol. Biochem. 94 (2016) 200–210. [41] S. Sharma, A. Rangger, M. von Lutzow, H. Insam, Functional diversity of soil bacterial communities increases after maize litter amendment, Eur. J. Soil Biol. 34 (1998) 53–60. [42] S.N. Jenkins, S.P. Rushton, C.V. Lanyon, A.S. Whiteley, I.S. Waite, P.C. Brookes, S. Kemmitt, R.P. Evershed, A.G. O'Donnell, Taxon-specific responses of soil bacteria to the addition of low level C inputs, Soil Biol. Biochem. 42 (2010) 1624–1631. [43] D.A. Lipson, Relationships between temperature responses and bacterial community structure along seasonal and altitudinal gradients, FEMS Microbiol. Ecol. 59 (2007) 418–427. [44] S. Manzoni, J.P. Schimel, A. Porporato, Responses of soil microbial communities to water stress: results from a meta-analysis, Ecology 93 (2012) 930–938. [45] X. Zhang, L. Yang, X. Xue, M. Kamran, I. Ahmad, Z. Dong, T. Liu, Z. Jia, P. Zhang, Q. Han, Plastic film mulching stimulates soil wet-dry alternation and stomatal behavior to improve maize yield and resource use efficiency in a semi-arid region, Field Crop. Res. 233 (2019) 101–113. [46] N. Pascault, L. Ranjard, A. Kaisermann, D. Bachar, R. Christen, S. Terrat, O. Mathieu, J. Leveque, C. Mougel, C. Henault, P. Lemanceau, M. Pean, S. Boiry, S. Fontaine, P.A. Maron, Stimulation of different functional groups of bacteria by various plant residues as a driver of soil priming effect, Ecosystems 16 (2013) 810–822. [47] C.L. Lauber, K.S. Ramirez, Z. Aanderud, J. Lennon, N. Fierer, Temporal variability in soil microbial communities across land-use types, ISME J. 7 (2013) 1641–1650. [48] S.A. Placella, E.L. Brodie, M.K. Firestone, Rainfall-induced carbon dioxide pulses result from sequential resuscitation of phylogenetically clustered microbial groups, Proc. Natl. Acad. Sci. U.S.A. 109 (2012) 10931–10936. [49] P.H. Rampelotto, A.D. Ferreira, A.D.M. Barboza, L.F.W. Roesch, Changes in diversity, abundance, and structure of soil bacterial communities in Brazilian savanna under different land use systems, Microb. Ecol. 66 (2013) 593–607. [50] M. Ventura, C. Canchaya, A. Tauch, G. Chandra, G.F. Fitzgerald, K.F. Chater, D. van Sinderen, Genomics of Actinobacteria: tracing the evolutionary history of an ancient phylum, Microbiol. Mol. Biol. Rev. 71 (2007) 495–548. [51] C.J. Ren, W. Zhang, Z.K. Zhong, X.H. Han, G.H. Yang, Y.Z. Feng, G.X. Ren, Differential responses of soil microbial biomass, diversity, and compositions to altitudinal gradients depend on plant and soil characteristics, Sci. Total Environ. 610 (2018) 750–758. [52] R. Pastorelli, N. Vignozzi, S. Landi, R. Piccolo, R. Orsini, G. Seddaiu, P.P. Roggero, M. Pagliai, Consequences on macroporosity and bacterial diversity of adopting a notillage farming system in a clayish soil of Central Italy, Soil Biol. Biochem. 66 (2013) 78–93. [53] M.A. Kader, M. Senge, M.A. Mojid, K. Ito, Recent advances in mulching materials and methods for modifying soil environment, Soil Till. Res. 168 (2017) 155–166.
[1] A.C. Kennedy, Bacterial diversity in agroecosystems, Agric. Ecosyst. Environ. 74 (1999) 65–76. [2] G.T. Hill, N.A. Mitkowski, L. Aldrich-Wolfe, L.R. Emele, D.D. Jurkonie, A. Ficke, S. Maldonado-Ramirez, S.T. Lynch, E.B. Nelson, Methods for assessing the composition and diversity of soil microbial communities, Appl. Soil Ecol. 15 (2000) 25–36. [3] L.W. Mendes, M.J.D. Brossi, E.E. Kuramae, S.M. Tsai, Land-use system shapes soil bacterial communities in Southeastern Amazon region, Appl. Soil Ecol. 95 (2015) 151–160. [4] V. Acosta-Martinez, S. Dowd, Y. Sun, V. Allen, Tag-encoded pyrosequencing analysis of bacterial diversity in a single soil type as affected by management and land use, Soil Biol. Biochem. 40 (2008) 2762–2770. [5] L.W. Mendes, M.J.D. Brossi, E.E. Kuramae, S.M. Tsai, Land-use system shapes soil bacterial communities in Southeastern Amazon region, Appl. Soil Ecol. 95 (2015) 151–160. [6] X.L. Ren, T. Cai, X.L. Chen, P. Zhang, Z.K. Jia, Effect of rainfall concentration with different ridge widths on winter wheat production under semiarid climate, Eur. J. Agron. 77 (2016) 20–27. [7] Y.L. Chen, T. Liu, X.H. Tian, X.F. Wang, M. Li, S.X. Wang, Z.H. Wang, Effects of plastic film combined with straw mulch on grain yield and water use efficiency of winter wheat in Loess Plateau, Field Crop. Res. 172 (2015) 53–58. [8] Y.P. Wang, X.G. Li, T.T. Fu, L. Wang, N.C. Turner, K.H.M. Siddique, F.M. Li, Multisite assessment of the effects of plastic-film mulch on the soil organic carbon balance in semiarid areas of China, Agric. For. Meteorol. 228 (2016) 42–51. [9] M.M. Moreno, A. Moreno, Effect of different biodegradable and polyethylene mulches on soil properties and production in a tomato crop, Sci. Hortic. 116 (2008) 256–263. [10] A. Jordan, L.M. Zavala, J. Gil, Effects of mulching on soil physical properties and runoff under semi-arid conditions in southern Spain, Catena 81 (2010) 77–85. [11] Y. Wu, F.Y. Huang, C. Zhang, Z.K. Jia, Effects of different mulching patterns on soil moisture, temperature, and maize yield in a semi-arid region of the Loess Plateau, China, Arid Land Res. Manag. 30 (2016) 490–504. [12] Z. Steinmetz, C. Wollmann, M. Schaefer, C. Buchmann, J. David, J. Troeger, K. Munoz, O. Fror, G.E. Schaumann, Plastic mulching in agriculture. Trading shortterm agronomic benefits for long-term soil degradation? Sci. Total Environ. 550 (2016) 690–705. [13] M.M. Carreiro, R.E. Koske, Room-temperature isolations can bias against selection of low-temperature microfungi in temperate forest soils, Mycologia 84 (1992) 886–900. [14] C. Tu, J.B. Ristaino, S.J. Hu, Soil microbial biomass and activity in organic tomato farming systems: effects of organic inputs and straw mulching, Soil Biol. Biochem. 38 (2006) 247–255. [15] S. Bandopadhyay, L. Martin-Closas, A.M. Pelacho, J.M. DeBruyn, Biodegradable plastic mulch films: impacts on soil microbial communities and ecosystem functions, Front. Microbiol. 9 (2018). [16] W.Y. Dong, P.F. Si, E.K. Liu, C.R. Yan, Z. Zhang, Y.Q. Zhang, Influence of film mulching on soil microbial community in a rainfed region of northeastern China, Sci. Rep. UK 7 (2017). [17] H. Cui, Y. Zhou, Z.H. Gu, H.H. Zhu, S.L. Fu, Q. Yao, The combined effects of cover crops and symbiotic microbes on phosphatase gene and organic phosphorus hydrolysis in subtropical orchard soils, Soil Biol. Biochem. 82 (2015) 119–126. [18] L.W. Mbuthia, V. Acosta-Martinez, J. DeBruyn, S. Schaeffer, D. Tyler, E. Odoi, M. Mpheshea, F. Walker, N. Eash, Long term tillage, cover crop, and fertilization effects on microbial community structure, activity: implications for soil quality, Soil Biol. Biochem. 89 (2015) 24–34. [19] J. Farmer, B. Zhang, X.X. Jin, P. Zhang, J.K. Wang, Long-term effect of plastic film mulching and fertilization on bacterial communities in a brown soil revealed by high through-put sequencing, Arch. Agron Soil Sci. 63 (2017) 230–241. [20] D. Nelson, L. Sommers, A. Page, R. Miller, D. Keeney, Total carbon, organic carbon, and organic matter, Methods of Soil Analysis. Part 2. Chemical and Microbiological Properties, Soil Science Society of America, Madison, WI, USA, 1982, pp. 539–579. [21] J. Bremner, C. Mulvaney, Nitrogen-total, Methods of Soil Analysis. Part 2. Chemical and Microbiological Properties, 1982, pp. 595–624. [22] Y. Wang, P.Y. Qian, Conservative fragments in bacterial 16S rRNA genes and primer design for 16S ribosomal DNA amplicons in metagenomic studies, PLoS One 4 (2009). [23] A.P. Masella, A.K. Bartram, J.M. Truszkowski, D.G. Brown, J.D. Neufeld, PANDAseq: paired-end assembler for Illumina sequences, BMC Bioinf. 13 (2012). [24] R.C. Edgar, UPARSE: highly accurate OTU sequences from microbial amplicon reads, Nat. Methods 10 (2013) 996–998. [25] P.F. Kemp, J.Y. Aller, Bacterial diversity in aquatic and other environments: what 16S rDNA libraries can tell us, FEMS Microbiol. Ecol. 47 (2004) 161–177. [26] C. Lozupone, M.E. Lladser, D. Knights, J. Stombaugh, R. Knight, UniFrac: an effective distance metric for microbial community comparison, ISME J. 5 (2011) 169–172. [27] N. Segata, J. Izard, L. Waldron, D. Gevers, L. Miropolsky, W.S. Garrett, C. Huttenhower, Metagenomic biomarker discovery and explanation, Genome Biol. 12 (2011). [28] P. Zhang, T. Wei, T. Cai, S. Ali, Q.F. Han, X.L. Ren, Z.K. Jia, Plastic-film mulching for enhanced water-use efficiency and economic returns from maize fields in
15
Contents lists available at ScienceDirect
European Journal of Soil Biology journal homepage: www.elsevier.com/locate/ejsobi
Impact of farmland mulching practices on the soil bacterial community structure in the semiarid area of the loess plateau in China
T
Fangyuan Huanga,b,c, Zihan Liua,b,c, Hongyan Moua,b, Jinglai Lia, Peng Zhanga,b,c,∗, Zhikuan Jiaa,b,c,∗∗ a
College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China The Chinese Institute of Water-saving Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi, China c Key Laboratory of Crop Physi-ecology and Tillage Science in Northwestern Loess Plateau, Ministry of Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi, China b
ARTICLE INFO
ABSTRACT
Handling Editor: C.C. Tebbe
Farmland mulching is widely used to preserve soil moisture and increase crop yield in the semiarid region of the Loess Plateau. However, the effect of different farmland mulching on soil bacterial communities is not clear. Therefore, the impact of a 5-year field management practice (surface mulching) on the soil bacterial communities was studied in dryland farmland of the Loess Plateau by using Illumina sequencing of the 16S rRNA gene. The following treatments were investigated: (1) ridge-furrow mulching pattern; (2) flat plastic film mulching; (3) flat biodegradable film mulching; (4) flat straw mulching; and (5) control (CK), conventional flat planting without mulch. All farmland mulching increased the diversity of soil bacteria and the diversity was greatest under the plastic film treatment. The dominant phyla across all soil samples were Proteobacteria, Acidobacteria, and Actinobacteria. Cluster analyses showed that bacterial communities under mulching treatments were different from that of CK. The bacterial community composition of plastic film and straw mulching treatments, biodegradable film and ridge-furrow mulching treatments were similar at the phylum level. Spearman correlation analysis indicated that the response of bacterial alpha-diversity was mainly negatively associated with the soil organic carbon and total nitrogen. The Mantel test showed that the beta-diversity depended primarily on the soil total nitrogen and soil temperature. The changes of the bacterial community distribution were significantly related to the soil moisture, which varied significantly with a range of 9.8–17.3 between treatments. These results indicated that soil properties changed after long-term farmland mulching, and these changes were related to soil bacterial diversity and community structure. According to this study, flat plastic firm mulching was found to being a good option for increasing soil bacterial diversity and richness and thereby potentially stabilize functional stability of soil biological processes.
Keywords: Bacterial community Mulching practices Semiarid area Soil moisture
1. Introduction Soil bacteria have vital effects on soil nutrient cycling, plant productivity, and the sustainability of soil productivity [1], and changes in their community structure may be important and sensitive indicators of short-term and long-term changes in soil health [2]. An increase in soil bacterial diversity could indicate an increase in functional diversity, thereby resulting in functional redundancy, which is an important biological strategy for buffering environmental stress, thus stabilizing soil biological functions [3]. The abundance and diversity of bacterial communities in farmland ecosystems could therefore be critical for maintaining soil quality, productivity, and ecological balance [4,5].
The Loess Plateau is a typical arid and semi-arid region and one of the most important regions for dryland farming in China. However, low air temperatures, limited water availability, and poor soil fertility limit agricultural productivity in this region [6]. Therefore, a lot of mulching measures, including straw mulching, degradable film mulching, plastic film mulching and ridge-furrow rainwater planting are widely used in this ecosystem. Relative to uncovered soil, mulching can reduce water evaporation and improve the soil temperature (ST) [7,8], and it can increase the yield and water use efficiency by crops under such environmental conditions [9,10]. However, mulching also has some potential drawbacks. For example, continuous plastic film mulching may consume excessive amounts of deep soil moisture [11]. In addition,
Corresponding author. The Chinese Institute of Water-saving Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi, China. Corresponding author. College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China. E-mail addresses: [email protected] (P. Zhang), [email protected] (Z. Jia).
∗∗ ∗
https://doi.org/10.1016/j.ejsobi.2019.04.001 Received 25 November 2018; Received in revised form 8 April 2019; Accepted 8 April 2019 Available online 24 April 2019 1164-5563/ © 2019 Elsevier Masson SAS. All rights reserved.
European Journal of Soil Biology 92 (2019) 8–15
F. Huang, et al.
changes in soil moisture and temperature due to mulching practices can change the biological characteristics of the soil, which may affect the soil quality and agroecosystem sustainability [12,13]. Thus, the longterm effects of farmland mulching practices need to be further studied. In addition to changing soil properties and crop growth, soil microbial communities are also sensitive to farmland mulching practices [14]. Modifications to soil microclimate under mulching practices affect soil bacterial communities [15]. Covering crops and plastic film significantly increased soil bacterial abundance and diversity in subtropical orchards and northeast rain-fed corn fields, respectively [16,17]. Continuous no-tillage coverage significantly increased the abundance of Gram-positive bacteria and Actinobacteria in cotton field soils [18]. In a brown soil, long-term manure fertilization coupled with film mulching increased relative abundances of Proteobacteria and Actinobacteria [19]. However, studies to date have focused on the effects of single mulching materials or planting methods on soil bacterial communities, comparisons between different mulching materials or planting methods have rarely been investigated. Moreover, most studies concentrated on the short-term effects of mulching practices, the longterm effect of farmland mulching measures on soil bacteria in the Loess Plateau is not well understood. Therefore, a 5-year field experiment of different farmland mulching practices, namely, ridge-furrow mulching pattern (R), flat plastic film mulching (P), flat biodegradable film mulching (B), flat straw mulching (S), and conventional flat planting without mulching as a control (CK) was set up. Soil samples were collected to analyze their physicochemical properties and bacterial diversity, the latter determined by Illumina sequencing of the PCR-amplified 16S rRNA gene. We hypothesized that: (1) mulching practices would change the soil physicochemical properties, thereby changing the soil bacterial community; (2) bacterial composition would respond differently to different mulching materials or planting methods. The objectives of this study were: (1) to study the effects of different farmland mulching practices on the soil physicochemical characteristics, bacterial diversity, and community composition; and (2) to detect the most important soil parameters affected by farmland mulching practices that cause changes in the bacterial community structure; and (3) to provide a scientific basis for evaluating the influence of common mulching practices on soil biological characteristics.
(width = 120 cm) was used to cover the flat surface completely. (4) Flat straw mulching (S) where complete maize straw was mulched evenly at an amount of 9000 kg ha−1 (5) Control (CK) comprising conventional flat planting without mulching. The plastic film was clear and impermeable polyethylene, with a thickness of 0.008 mm (produced by Guyuan Yuande Plastic Products Co. Ltd, Ningxia, China), and it was stable and did not decompose after harvesting the crop. After the crops were harvested in the previous season, the old mulch film was completely removed and the mulch film was covered again after the land preparation in the autumn. The white biodegradable film measured 1.2 m wide × 0.008 mm thick (produced by Bionolle Department, Showa Denko, Japan) and it eventually degraded to yield H2O and CO2. The complete degradation of the film required about 270 days depending on the temperature, humidity, fertility of the soil, and other factors. Different levels of damage to the biodegradable film were observed in June, and the film was completely degraded after harvesting the crop. The edges of the film were covered carefully and compacted with soil. Every 200 cm, a soil belt was set in the vertical direction to prevent the film from being removed by strong winds. In the S treatment, after the crops were harvested in the previous season, the non-decomposed straw was removed and the straw was covered again after land preparation in the autumn. All of the mulching treatments were conducted in autumn in the previous year. All of the trials started in 2012. Seeds of the spring maize cultivar “Dafeng 30” were sown in April each year and harvested in October (the accurate sowing and maturation dates between 2012 and 2016 are shown in Table S2). Maize was sown at a rate of 67,000 plants ha−1 (60 × 25 cm) using a hole-sowing/fertilization (3 cm in diameter) machine, with a sowing depth of 4–5 cm. A base fertilizer comprising 140 kg ha−1 N and 150 kg ha−1 P2O5 was applied using a hole-sowing/ fertilization machine. In addition, 140 kg ha−1 N was applied between the maize plants as a top dressing at 69–75 days after maize planting, with a fertilization depth of 4–5 cm. The sowing rate and fertilizer application rate were the same for all of the treatments. Irrigation was not applied throughout the entire year. No pests were found in all treatments during the experiment and manual weeding was performed as required according to the conditions.
2. Material and methods
Soil samples were obtained from depths of 0–20 cm at 85 days after sowing the maize on July 16, 2016. The sampling position of the R treatment was in the furrow planting area, and between the planting rows for all other treatments. Nine replicate samples (top 0–20 cm) were collected in an “S” shape by using a soil-drilling sampler (5 cm inner diameter), before mixing and homogenizing to obtain one composite sample per replicate site. The samples were then sieved through a 2-mm screen and any visible roots or other debris were removed. A portion of each soil sample was stored at 4 °C to analyze the soil dissolved organic carbon (DOC) and soil nitrate nitrogen (NO3-N). Part of each soil sample was also collected in a 100-mL centrifuge tube, transported from the field to the laboratory in an icebox, and then stored at −80 °C. The remaining soil sample was air dried before measuring the soil physicochemical properties (soil pH, soil organic carbon (SOC), and soil total nitrogen (TN)).
2.3. Soil sampling
2.1. Study area description The experiment was conducted in Changcheng Village, Pengyang County, Ningxia Province, China. This village is located in the hilly area of the Loess Plateau (35°51′N, 106°48′E) at an average elevation of 1658 m, which has a typical temperate semiarid continental monsoon climate with annual precipitation of 430 mm. The vast majority of the annual precipitation occurs between July and September. The average annual temperature was 8.1 °C, with a frost-free period of 140–160 days. The soil at the experimental site was Loessal soil (sandy clay loam). The annual precipitation during the test period (2012–2016) is shown in Table S1. 2.2. Experimental design
2.4. Soil physicochemical measurements
The experiment used a completely randomized block design with three replicates and each plot area was 58.8 m2 (14 × 4.2 m). The following five treatments were tested. (1) Ridge-furrow mulching pattern (R) with alternating ridges and furrows, where only the ridges were covered with plastic film (width = 70 cm) and maize was sown in the furrows. The ridges and furrows had equal widths of 60 cm and the ridge height was 15 cm. (2) Flat plastic film mulching (P) where plastic film (width = 120 cm) was used to cover the flat surface completely. (3) Flat biodegradable film mulching (B) where biodegradable film
Soil moisture and soil temperature (ST): The soil water content (SWC) (0–20 cm) was determined by oven drying to constant mass at 105 °C on the same day as sampling. ST measurements (at 5 cm, 10 cm, 15 cm, and 20 cm) were obtained using an angle stem earth thermometer for three consecutive days, and the average ST based on all four measurements was used as the ST for each plot. Soil pH: The soil pH was measured using a pH meter after shaking a soil:water (1:2.5 w/v) suspension comprising 10 g of air-dried soil and 9
European Journal of Soil Biology 92 (2019) 8–15
F. Huang, et al.
25 mL of water for 30 min. Soil carbon and soil nitrogen: The SOC content was assayed using the potassium dichromate oxidation method [20]. The soil TN content was determined using the Kjeldahl method [21]. The concentration of NO3-N was determined by adding 50 mL of 1.0 M KCl to 5 g of each fresh soil sample, shaking for 30 min, and then collecting the contents by filtration using a continuous flow analyzer (Autoanalyzer 3, Bran Luebbe, Germany). The soils were suspended in water (soil:water = 1:5), shaken for 5 h, centrifuged at 13,000 r/min for 10 min, and filtered through a 0.45-μm membrane to determine the soil DOC. Organic C in the extracts was determined using a total organic carbon analyzer (Elementar, Vario TOC, Germany).
Table 1Soil physicochemical properties and enzyme activities measured in the 0–20 cm soil layer. Treatments
pH
SWC %
ST °C
TN g/kg
SOC g/kg
NO3 -N mg/kg
DOC mg/kg
R P B S CK
7.25c 7.39b 7.45b 7.52a 7.59a
12.58c 13.92b 10.37d 17.29a 9.81e
23.37c 24.61b 22.25d 22.71d 25.82a
0.84b 0.82b 0.82b 0.88a 0.89a
9.54 ab 9.22b 9.22b 9.65a 9.47 ab
20.46c 27.03b 20.07d 31.79a 26.72b
23.21b 24.23b 25.44b 32.25a 26.05b
Different letters in the same column indicate significant differences at (P < 0.05) according to Duncan's test. pH: soil acidity; SWC: soil water content; ST: soil temperatures (the average values of 5, 10, 15, 20 cm soil layers were used in this table); TN: total nitrogen; SOC: soil organic carbon; NO3-N: nitrate nitrogen; DOC: dissolved organic carbon; R: Ridge-furrow mulching pattern; P: flat plastic film mulching; B: flat biodegradable film mulching; S: flat straw mulching; CK: conventional tillage without mulching.
2.5. DNA extraction, PCR amplification, and Illumina HiSeq sequencing Soil microbial DNA was extracted from 0.5 g of each sample using a FastDNA SPIN Kit for Soil (MP Biomedicals, USA) according to the manufacturer's instructions. The 16S rRNA gene V3–V4 region was amplified using the primers 341 F (CCTACGGGRSGCAGCAG) and 806 R (GGACTACVVGGGTATCTAATC) [22]. Amplicons were extracted from 2% agarose gels and purified with an AxyPrep DNA Gel Extraction Kit (Axygen Biosciences, Union City, CA, USA) according to the manufacturer's instructions, and quantified with a Qubit® dsDNA HS Assay Kit (Thermo Fisher, USA). Purified amplicons were pooled in equimolar concentrations and then subjected to paired-end sequencing (2 × 250) using the Illumina HiSeq PE250 platform according to the standard protocols. Illumina HiSeq sequencing was performed by Realbio Technology Co. Ltd (Shanghai, China). PANDAseq software was used to merge the paired-end sequence reads obtained from the original DNA fragments [23]. The sequences were further analyzed using USEARCH v5.2.32 to filter and denoise the data. The Quantitative Insights Into Microbial Ecology (QIIME) pipeline was used to define operational taxonomic units (OTUs) by combining reads of the clustered OTUs with ≥97% similarity [24]. Finally, the complete dataset was submitted to the Sequence Read Archive (SRA) database of the National Center for Biotechnology Information (NCBI) under accession number SRP136001.
rank correlation tests were performed using SPSS 18.0 (SPSS Inc., Chicago, IL, USA). ANOSIM, NMDS, RDA, and Mantel tests were performed using R v.3.3.3. 3. Results 3.1. Soil physicochemical properties The TN content was significantly higher (P < 0.05) in the straw mulching (S) and CK treatments than the other treatments (Table 1), and there were no significant differences in the TN contents under the ridge-furrow (R), plastic film (P), and biodegradable film (B) mulching treatments. DOC and SOC were highest in the S treatment, where they were 23.8% (P < 0.05) and 1.9% (P > 0.05) higher than those in CK, respectively, and no significant differences were observed among the other treatments. The NO3-N contents were significantly lower in the R and B treatments than CK, but not in the S and P treatments. SWC was highest in the S treatment, followed by the P, R, B, and CK treatments. ST was lowest in the S and B treatments, and there were significant differences between the R, P, and CK treatments. The soil pH values were significantly lower in the R, P, and B treatments than CK (P < 0.05), but not in the S treatment.
2.6. Statistical analyses Soil physicochemical and microbial abundance data were analyzed by one-way analysis of variance (ANOVA) to determine significant differences among the treatments. Significant differences were accepted at the 95% confidence level. If a significant difference was detected at P < 0.05, the post hoc Duncan's multiple range test was used for multiple comparisons. Alpha diversities were calculated using QIIME software [25]. The Chao1 estimation method and Shannon diversity index were used to calculate the richness and diversity of the bacterial community, respectively. To determine the beta diversity, the phylogenetic community composition and membership were compared using the weighted and unweighted UniFrac distance matrices [26]. Analysis of similarities (ANOSIM) was used to test for the significance of separations measured under different mulching treatments. Non-metric multidimensional scaling (NMDS) was conducted to visualize the clustering of different samples. Correlations between the soil bacterial community structure and soil characteristics were determined using Mantel tests based on 999 permutations. The characteristic microbial community features under each mulching treatment were determined using the linear discriminant analysis (LDA) effect size (LEfSe) method, which emphasizes statistical significance and biological relevance [27]. Redundancy analysis (RDA) was conducted to examine the relationships between the soil environmental variables and bacterial community abundance levels. Spearman's rank correlation test was used to investigate the associations between bacterial communities and soil physicochemical properties. All statistical analyses (ANOVA and Duncan's test) and Spearman's
3.2. Soil bacterial diversity After five consecutive years of mulching practices, the Chao1 indices were significantly higher in the plastic film (P) treatment (3,689) and straw mulching (S) treatment (3,789) than CK, i.e., 10.2% and 13.2% higher than CK (3,348), respectively (Fig. 1), but there were no significant differences in the Chao1 index among the ridge-furrow (R), biodegradable film (B) and CK treatments. Differences in the soil bacterial diversity under different mulching treatments were determined using the Shannon index, and the Shannon index of each mulching treatment was significantly higher than that for CK, with an average of 1.8%. The strongest effect was observed with P treatment, followed by B, R and S treatments, while there was no significant difference between P and B treatments, nor between R and S treatments. The Chao1 and Shannon indices showed that the soil bacterial abundance and diversity were both higher in the P treatment. The Spearman's rank correlation coefficients indicated significant correlations between the soil bacterial community richness and diversity and the soil physicochemical properties (Fig. 1). The Chao1 index was significantly positively correlated with SWC. The Shannon diversity index was significantly negatively correlated with TN and SOC (P < 0.05). 10
European Journal of Soil Biology 92 (2019) 8–15
F. Huang, et al.
the B and CK treatments. LEfSe analyses were performed to identify the statistical significance of differentially abundant taxa and the biological relevance of the species in each mulching treatment (Fig. 4), and the LDA values are shown in Supplementary Fig. S2. The LEfSe results showed that Proteobacteria, Nitrospirae, and Bacteroidetes mainly changed in the S treatment, P treatment mainly changed Proteobacteria, and the phylum Gemmatimonadetes changed in the B treatment. In Fig. 4, the orange color represents the significantly changed taxa in CK, which mainly comprised Actinobacteria. 3.4. OTU level bacterial beta-diversity analysis Two beta-diversity measures were used to compare the bacterial community structure in soils subjected to different mulching treatments. Phylogenetic analyses of the bacterial community composition and membership were performed using both the weighted and unweighted UniFrac distances. The NMDS plots indicated that the weighted and unweighted UniFrac distances were well separated in the different mulching treatments (Fig. 2). In addition, the soil bacterial community composition and memberships in the straw mulching, plastic film, and ridge-furrow mulching treatments differed significantly from those in CK. The weighted UniFrac distances showed that the soil bacteria composition in ridge-furrow was similar to that in biodegradable film (Fig. 2A). ANOSIM analysis indicated that the weighted and unweighted UniFrac distances both contributed significantly to the separation of the bacterial communities under different mulching treatments. (r = 0.599, P = 0.001; r = 0.938, P = 0.001).
Fig. 1. (A) The richness and diversity indices under the different mulching treatments. (B) Spearman's rank correlation coefficients between soil bacterial richness and diversity indices and the soil physicochemical properties. The values are the means of three replicates, and different letters within the same column indicate significant differences at P < 0.05. R: Ridgefurrow mulching pattern; P: flat plastic film mulching; B: flat biodegradable film mulching; S: flat straw mulching; CK: conventional tillage without mulching. pH: soil acidity; SWC: soil water content; ST: soil temperatures; TN: total nitrogen; SOC: soil organic carbon; NO3-N: nitrate nitrogen; DOC: dissolved organic carbon.
3.5. Relationship between bacterial community structure and soil properties The Mantel test results showed (Table 2) that TN, ST, and NO3-N had strong correlations with the bacterial phylogenetic community composition (weighted UniFrac metric; r = 0.358, 0.335, and 0.295; P = 0.005, 0.006, and 0.01) and membership (unweighted UniFrac metric; r = 0.302, 0.348, and 0.290; P = 0.011, 0.006, and 0.015) compared with other environmental factors. RDA showed that various bacterial taxa (phylum, class, and order) (Fig. 5, Fig. S3) responded in different ways to changes in the soil properties. The results indicated that the soil characteristics greatly affected the soil bacterial community (Table S3, Table S4). In particular, soil moisture had the main effect on changes in the bacterial community composition. Fig. 5 shows that SWC, DOC, and TN has significant correlations with the changes in Proteobacteria, Nitrospirae, Bacteroidetes, Acidobacteria, Actinobacteria, and Gemmatimonadetes. Among Proteobacteria, SWC was positively correlated with the abundances of Sphingomonadales, Rhodospirillales, and Rhizobiales (Fig. S3), which are branches of Alphaproteobacteria (Table 3). By contrast, SWC was negatively correlated with the abundances of Acidimicrobiales, Actinomycetales and Gaiellales, which are branches of Actinobacteria (Fig. S3).
3.3. Soil bacterial community composition In total, 542,500 sequences were obtained after analyzing all of the soil samples. The average number of sequences per sample was 36,167 (range = 33,156–38,546) and 97.7% of the sequences were classified at the phylum level. The dominant phyla in all treatments were Proteobacteria, Acidobacteria, and Actinobacteria, with relative abundances ranging from 33.5 to 45.0%, 20.6–24.1%, and 15.0–21.8%, respectively. In addition, Gemmatimonadetes and Bacteroidetes were subdominant groups. These five phyla represented more than 90% of the sequences in all of the samples. Cluster analyses were conducted to determine the relationships among all of the treatments. The bacterial communities differed in CK and the mulching treatments at the phylum and class level (Fig. 3, Fig. S1). At the order levels (Fig. S1), the bacterial communities were similar in the biodegradable film treatment and CK, but they differed from those in the other treatments. High relative abundances of Proteobacteria were found in the ridge-furrow (R), biodegradable film (B), plastic film (P), and straw (S) mulching treatments, whereas the abundance of Actinobacteria was higher in CK. At the class level (Fig. S1, Table 3), Actinobacteria, Alphaproteobacteria, and Betaproteobacteria were dominant. The relative abundances of Actinobacteria were high in the B treatment and CK. The relative abundances of Alphaproteobacteria and Betaproteobacteria did not differ significantly among the treatments (P > 0.05) except for in the S treatment and CK. The other two Proteobacteria branches comprising Gammaproteobacteria and Deltaproteobacteria were most abundant in the S and P treatments, respectively. At the order level (Table 3), the abundances of Sphingomonadales and Rhodospirillales, branches of Alphaproteobacteria, were significantly higher in the S treatment, whereas Gemmatimonadales, Actinomycetales, and Acidimicrobiales were relatively more abundant in
4. Discussion 4.1. Farmland mulching practices changed soil physicochemical properties After five years of continuous mulching, soil physicochemical properties were affected by different mulching practices to varying degrees. Previous studies have shown that mulching can improve soil moisture and ST, leading to improved crop growth and yield in this region [28]. Thus, the decrease of TN content under mulching treatments can be attributed to the absorption of nutrients by crops. Straw litter was incorporated into the soil as organic matter to supplement the soil nutrient sources [29]. Therefore, the TN content in the straw mulching treatment was not reduced, and the SOC and DOC contents are higher than other mulching treatments and CK, which is consistent 11
European Journal of Soil Biology 92 (2019) 8–15
F. Huang, et al.
Fig. 2. Bacterial community structure according to non-metric multidimensional scaling (NMDS) plots of the weighted (A) and unweighted UniFrac (B) distances. R: Ridge-furrow mulching pattern; P: flat plastic film mulching; B: flat biodegradable film mulching; S: flat straw mulching; CK: conventional tillage without mulching.
with the results in the orchard of the Loess Plateau [30]. It was suggested that different mulching materials and types used on the Loess Plateau can effectively inhibit the inefficient evaporation of soil moisture and preserve water [31]. Similar results were also found in this study, mulching practices significantly increased SWC, compared with CK. The variation in ST was attributed to the shading effect of the canopy and the characteristics of different mulching materials and types [32,33].
Table 2 Correlations among the overall bacterial community structure and soil proprieties according to the Mantel test. Distance
Soil variable
r
P value
unweighted UniFrac
TN ST NO3-N TN ST NO3-N
0.302 0.348 0.29 0.358 0.335 0.295
0.011∗∗ 0.006∗∗ 0.015∗∗ 0.005∗∗ 0.006∗∗ 0.01∗∗
weighted UniFrac
4.2. Farmland mulching practices increased soil bacterial diversity
ST: soil temperatures; TN: total nitrogen; NO3-N: nitrate nitrogen.
In the present study, we found that compared with CK, the application of farmland mulching practices increased the soil bacterial diversity in a semiarid area, and the soil bacterial alpha diversity (indicated by the Shannon index) had significant negative correlations with TN and SOC (Fig. 1). Consistent with this, it was suggested that the ecological strategies of soil bacteria can be changed by the increased availability of C and N [34]. Therefore, the soil microbial diversity may be influenced by the availability of soil nutrients [35,36]. In addition, we found that after five consecutive years of mulching, the soil bacterial community diversity had negative correlations with TN and SOC, thereby indicating that increased bacterial diversity was associated with decreases in these soil nutrients, and vice versa. These findings may be explained by crops competing for the limited amounts of mineral nutrients with soil microorganisms [37], where the activity of soil
microorganisms will accelerate the decomposition of organic matter and increase its biomass. In addition, plants require more soil nutrients during the period of vigorous crop growth, so large amounts of soil nitrogen and carbon are transferred to the crop, which results in a decrease in the soil TN and SOC [38]. A higher correlation between the microbial diversity and soil nutrients indicates greater competition between the crops and soil microorganisms [39]. In the present study, the plastic film (P) and straw (S) mulching treatments significantly improved the Chao1 index for soil bacteria compared with CK, and SWC was the major contributor to the soil bacterial richness under mulching conditions. This finding is consistent with the results of bacterial community richness in dryland forest ecosystem [40]. Fig. 3. The relative abundance of the dominant bacterial phyla across all treatments, with the clustering tree on the left showing the similarities among treatments. R: Ridgefurrow mulching pattern; P: flat plastic film mulching; B: flat biodegradable film mulching; S: flat straw mulching; CK: conventional tillage without mulching.
12
European Journal of Soil Biology 92 (2019) 8–15
F. Huang, et al.
Table 3 Relative abundances (average values) of bacterial compositions across taxonomical classification (Phyla, Class, and Order) in each mulching treatment. Phylum Proteobacteria
Acidobacteria
Actinobacteria
Class Alphaproteobacteria Sphingomonadales Rhizobiales Rhodospirillales Betaproteobacteria Gammaproteobacteria Xanthomonadales Deltaproteobacteria Myxococcales Acidobacteria_Gp6 Acidobacteria_Gp4 Acidobacteria_Gp7
Actinobacteria Actinomycetales Acidimicrobiales Gaiellales Gemmatimonadetes Gemmatimonadetes Gemmatimonadales Bacteroidetes Sphingobacteriia Sphingobacteriales Verrucomicrobia Firmicutes Nitrospirae
Order
R
P
B
S
CK
p
40.44b 15.95b 17.63 ab 5.52a 2.75b 11.67a 8.45a 9.65a 6.42b 7.51a 21.58a 8.64a 6.29 ab 3.01 ab 17.40bc 17.80bc 10.86bc 8.48bc 4.50a 6.53bc 6.99bc 12.61 ab 5.64c 2.91b 5.24b 2.94a 0.49a 0.62b
41.42 ab 16.04b 16.46 ab 5.78a 4.04a 11.52a 8.38a 9.02a 7.41a 8.57a 22.71a 9.33a 6.17 ab 2.70b 14.73c 15.14c 9.55c 7.49c 4.20a 6.02c 6.45c 12.10b 6.80 ab 3.56a 6.67a 2.32 ab 0.53a 0.73b
37.77b 14.77b 14.79b 5.50a 3.03b 11.22a 7.17 ab 7.91 ab 6.37b 8.24a 20.58a 7.54a 5.63b 3.56a 20.02 ab 20.30 ab 12.52 ab 9.84 ab 4.67a 7.51a 8.03a 14.44a 6.21bc 3.03b 5.46b 3.10a 0.41a 0.61b
45.05a 20.65a 21.29a 6.01a 4.45a 11.42a 8.58a 9.19a 6.24b 7.08a 20.82a 8.54a 6.24 ab 2.99 ab 15.05c 15.36c 10.17c 6.92c 3.13b 6.14c 6.52c 11.21b 7.50a 3.55a 6.10 ab 1.37b 0.48a 0.92a
33.54c 13.97b 14.58b 5.68a 2.54b 9.45b 5.86b 6.52b 5.37c 7.26a 24.12a 9.58a 7.37a 3.29 ab 21.83a 22.13a 13.81a 11.31a 4.98a 7.40 ab 7.83 ab 14.40a 5.82c 3.11b 5.73b 2.99a 0.44a 0.39c
≤0.001 0.007 0.037 0.438 < 0.001 ≤0.001 0.025 0.03 0.004 0.16 0.268 0.256 0.164 0.069 ≤0.001 0.002 0.007 ≤0.001 0.018 0.01 0.007 0.013 0.007 0.007 0.023 0.026 0.836 ≤0.001
Different letters indicate significant differences (ANOVA, P < 0.05, Duncan's post-hoc analysis) among different mulching treatments. R: Ridge-furrow mulching pattern; P: flat plastic film mulching; B: flat biodegradable film mulching; S: flat straw mulching; CK: conventional tillage without mulching.
Fig. 4. A linear discriminant analysis effect size (LEfSe) method identifies the significantly different abundant taxa of bacteria in all of the treatments. The taxa with significantly different abundances among treatments are represented by colored dots, and from the center outward, they represent the kingdom, phylum, class, order, family, and genus levels. The colored shadows represent the significantly differed taxa which is indicated by “a:” “b:” “c:” etc. Gp12, Gp15, Gp16, and Gp3 are the genus of Acidobacteria. R: Ridge-furrow mulching pattern; P: flat plastic film mulching; B: flat biodegradable film mulching; S: flat straw mulching; CK: conventional tillage without mulching.
13
European Journal of Soil Biology 92 (2019) 8–15
F. Huang, et al.
increased the abundance of Acidobacteria in the CK treatment (Fig. 5, Fig. S2). Actinobacteria are distributed widely in terrestrial and aquatic ecosystems, especially in arid and acid soils, and they are considered important decomposers of soil organic matter [49]. In addition, members of this phylum have the capacity to produce spores, which increases the ability of this group to resist perturbation events [50]. The similar soil moisture and nutrient levels in the plastic film (P) and straw (S) mulching treatments may explain the lower abundance of Actinobacteria compared with the other treatments. 4.4. Relationship between bacterial community and soil properties The different effects of the mulching treatments and the associated bacterial communities can be explained by soil characteristics. The NMDS and ANOSIM results showed that there were significant differences in the beta-diversity under different mulching treatments, which indicated that different mulching patterns yielded different bacterial community structures. The differences were significantly associated with changes in the soil moisture, ST and soil nutrients (Table 2). We found that compared with other environmental factors, the soil TN had a greater influence on the phylogenetic components of the bacterial community structure, followed by ST, which is accordance with the results of the long-term fertilizations study [36]. Similarly, the microbial beta-diversity in forest soil was highly correlated with the ST [51]. In addition, we found that several highly abundant bacterial taxa were significantly associated with SWC. Furthermore, the bacterial compositions of the biodegradable film mulching and CK treatments were different from those of the plastic film and straw mulching treatments, which were attributed to the relatively high SWC (extended arrow in Fig. 5). These findings are consistent with the recent studies, who found that the bacterial communities were strongly correlated with SWC [40,52]. Under mulching conditions, increases in the soil moisture and temperature can change the growth of microorganisms, and thus the decomposition and utilization of soil nutrients [53], possibly due to changes in bacterial ecology strategies, which may ultimately contribute to differences in the bacterial communities [34]. In conclusion, the results of this study demonstrate that soil physical-chemical properties (TN, DOC, NO3-N, ST, and SWC), bacterial diversity and community structure were changed after five-year farmland mulching in a semiarid area. The change of bacterial community was mainly affected by SWC and ST, whereas SOC and TN were the primary factors that influenced the bacterial diversity. Overall, our results indicate that flat plastic film mulching should be recommended as it enhanced both soil bacterial diversity and richness in the Loess Plateau of China.
Fig. 5. Ordination plots of the results from the redundancy analysis (RDA) to identify the relationships among the bacterial taxa (phylum) and soil properties. pH: soil acidity; SWC: soil water content; ST: soil temperatures; TN: total nitrogen; SOC: soil organic carbon; NO3-N: nitrate nitrogen; DOC: dissolved organic carbon; R: Ridge-furrow mulching pattern; P: flat plastic film mulching; B: flat biodegradable film mulching; S: flat straw mulching; CK: conventional tillage without mulching.
4.3. Farmland mulching practices changed soil bacterial community The bacterial community showed a difference between CK and mulching treatments in the cluster analysis (Fig. 3). This conclusion is consistent with previous studies [14,41], which reported that mulching with organic matter strongly influences the composition of the soil bacterial community. According to the results of LEfSe analysis, Proteobacteria, Acidobacteria and Bacteroidetes changed significantly in plastic film (P) and straw (S) mulching treatments, the most significant taxa in the biodegradable film (B) mulching treatment was Gemmatimonadetes, while CK mainly changed Actinobacteria, indicating that mulching practices had a significant effect on bacterial communities. Proteobacteria have been described as fast-growing copiotrophs that are stimulated in carbon-rich environments [42]. However, we found that Proteobacteria were affected greatly by the soil moisture, but not by SOC (Fig. 5). This may be explained by the specific Proteobacteria compositions in the different mulching treatments (Fig. S2). At the class level, Betaproteobacteria are typically present at low abundances in dry soil [43] and we found that they were more sensitive to SWC (Fig. S2A). At the order level, Rhizobiales and Rhodospirillales, branches of alpha-Proteobacteria, were also significantly associated with soil moisture (SWC) (Fig. S2B), thereby indicating that the variations in the abundances of Proteobacteria were related to their responses to soil moisture under the different mulching treatments. Lower soil moisture contents limit the mineralization of soil nutrients [44] and the abundance of Proteobacteria was low in the CK treatment with high SOC and low soil moisture. Another obvious trend found in this study was the higher abundance of Bacteroidetes under the P and straw S treatments, particularly Sphlingobacteriales. It was suggested that Bacteriodetes were predominant in agricultural systems due to their ability to rapidly exploit bioavailable organic matter [4]. Studies have shown that the plastic film mulching has a higher root biomass due to the vigorous growth of plants [45], and the straw mulching has more plant litter [30]. Thus, the P and S treatments both provided highly suitable soil environments for Bacteroidetes by allowing them to utilize the readily degradable fraction of crop residues, thereby facilitating their rapid growth [34]. Actinobacteria and Acidobacteria are considered to be oligotrophs [46]. Acidobacteria are less abundant when the soil is moister and cooler [47,48]. The higher ST and lower soil moisture may have
Acknowledgements This study was supported by the Program of National Natural Science Foundation of China (No. 41671226 and No. 31801314) and China 111 Project (No. B12007), the Fundamental Research Fund for Universities and Colleges (2452017051), the Natural Science Basic Research Plan in Shaanxi Province of China (No. 2018JQ3024), the Young Talent fund of University Association for Science and Technology in Shaanxi, China (20180203), China National Science and Technology Support Program (2015BAD22B02) in the 12th 5-year plan period. We are also grateful to Nie Junfeng, Yang Baoping and Ding Ruixia for help during experimental period. Appendix A. Supplementary data Supplementary data to this article can be found online at https:// doi.org/10.1016/j.ejsobi.2019.04.001. 14
F. Huang, et al.
European Journal of Soil Biology 92 (2019) 8–15
References
semiarid China, Front. Plant Sci. 8 (2017). [29] Q.G. Dong, Y.C. Yang, K. Yu, H. Feng, Effects of straw mulching and plastic film mulching on improving soil organic carbon and nitrogen fractions, crop yield and water use efficiency in the Loess Plateau, China, Agric. Water Manag. 201 (2018) 133–143. [30] Y. Chen, X. Wen, Y. Sun, J. Zhang, W. Wu, Y. Liao, Mulching practices altered soil bacterial community structure and improved orchard productivity and apple quality after five growing seasons, Sci. Hortic. 172 (2014) 248–257. [31] X. Zhang, M. Kamran, X. Xue, J. Zhao, T. Cai, Z. Jia, P. Zhang, Q. Han, Ridge-furrow mulching system drives the efficient utilization of key production resources and the improvement of maize productivity in the Loess Plateau of China, Soil Till. Res. 190 (2019) 10–21. [32] X. Zhang, J. Zhao, L. Yang, M. Kamran, X. Xue, Z. Dong, Z. Jia, Q. Han, Ridgefurrow mulching system regulates diurnal temperature amplitude and wettingdrying alternation behavior in soil to promote maize growth and water use in a semiarid region, Field Crop. Res. 233 (2019) 121–130. [33] X.L. Qin, Y.Z. Li, Y.L. Han, Y.C. Hu, Y.J. Li, X.X. Wen, Y.C. Liao, K.H.M. Siddique, Ridge-furrow mulching with black plastic film improves maize yield more than white plastic film in dry areas with adequate accumulated temperature, Agric. For. Meteorol. 262 (2018) 206–214. [34] N. Fierer, M.A. Bradford, R.B. Jackson, Toward an ecological classification of soil bacteria, Ecology 88 (2007) 1354–1364. [35] W.R. Cookson, D.A. Abaye, P. Marschner, D.V. Murphy, E.A. Stockdale, K.W.T. Goulding, The contribution of soil organic matter fractions to carbon and nitrogen mineralization and microbial community size and structure, Soil Biol. Biochem. 37 (2005) 1726–1737. [36] C.H. Li, K. Yan, L.S. Tang, Z.J. Jia, Y. Li, Change in deep soil microbial communities due to long-term fertilization, Soil Biol. Biochem. 75 (2014) 264–272. [37] R.C. Miatto, I.J. Wright, M.A. Batalha, Relationships between soil nutrient status and nutrient-related leaf traits in Brazilian cerrado and seasonal forest communities, Plant Soil 404 (2016) 13–33. [38] F.M. Li, J. Wang, J.Z. Xu, H.L. Xu, Productivity and soil response to plastic film mulching durations for spring wheat on entisols in the semiarid Loess Plateau of China, Soil Till. Res. 78 (2004) 9–20. [39] T. Miki, Microbe-mediated plant-soil feedback and its roles in a changing world, Ecol. Res. 27 (2012) 509–520. [40] F. Colombo, C.A. Macdonald, T.C. Jeffries, J.R. Powell, B.K. Singh, Impact of forest management practices on soil bacterial diversity and consequences for soil processes, Soil Biol. Biochem. 94 (2016) 200–210. [41] S. Sharma, A. Rangger, M. von Lutzow, H. Insam, Functional diversity of soil bacterial communities increases after maize litter amendment, Eur. J. Soil Biol. 34 (1998) 53–60. [42] S.N. Jenkins, S.P. Rushton, C.V. Lanyon, A.S. Whiteley, I.S. Waite, P.C. Brookes, S. Kemmitt, R.P. Evershed, A.G. O'Donnell, Taxon-specific responses of soil bacteria to the addition of low level C inputs, Soil Biol. Biochem. 42 (2010) 1624–1631. [43] D.A. Lipson, Relationships between temperature responses and bacterial community structure along seasonal and altitudinal gradients, FEMS Microbiol. Ecol. 59 (2007) 418–427. [44] S. Manzoni, J.P. Schimel, A. Porporato, Responses of soil microbial communities to water stress: results from a meta-analysis, Ecology 93 (2012) 930–938. [45] X. Zhang, L. Yang, X. Xue, M. Kamran, I. Ahmad, Z. Dong, T. Liu, Z. Jia, P. Zhang, Q. Han, Plastic film mulching stimulates soil wet-dry alternation and stomatal behavior to improve maize yield and resource use efficiency in a semi-arid region, Field Crop. Res. 233 (2019) 101–113. [46] N. Pascault, L. Ranjard, A. Kaisermann, D. Bachar, R. Christen, S. Terrat, O. Mathieu, J. Leveque, C. Mougel, C. Henault, P. Lemanceau, M. Pean, S. Boiry, S. Fontaine, P.A. Maron, Stimulation of different functional groups of bacteria by various plant residues as a driver of soil priming effect, Ecosystems 16 (2013) 810–822. [47] C.L. Lauber, K.S. Ramirez, Z. Aanderud, J. Lennon, N. Fierer, Temporal variability in soil microbial communities across land-use types, ISME J. 7 (2013) 1641–1650. [48] S.A. Placella, E.L. Brodie, M.K. Firestone, Rainfall-induced carbon dioxide pulses result from sequential resuscitation of phylogenetically clustered microbial groups, Proc. Natl. Acad. Sci. U.S.A. 109 (2012) 10931–10936. [49] P.H. Rampelotto, A.D. Ferreira, A.D.M. Barboza, L.F.W. Roesch, Changes in diversity, abundance, and structure of soil bacterial communities in Brazilian savanna under different land use systems, Microb. Ecol. 66 (2013) 593–607. [50] M. Ventura, C. Canchaya, A. Tauch, G. Chandra, G.F. Fitzgerald, K.F. Chater, D. van Sinderen, Genomics of Actinobacteria: tracing the evolutionary history of an ancient phylum, Microbiol. Mol. Biol. Rev. 71 (2007) 495–548. [51] C.J. Ren, W. Zhang, Z.K. Zhong, X.H. Han, G.H. Yang, Y.Z. Feng, G.X. Ren, Differential responses of soil microbial biomass, diversity, and compositions to altitudinal gradients depend on plant and soil characteristics, Sci. Total Environ. 610 (2018) 750–758. [52] R. Pastorelli, N. Vignozzi, S. Landi, R. Piccolo, R. Orsini, G. Seddaiu, P.P. Roggero, M. Pagliai, Consequences on macroporosity and bacterial diversity of adopting a notillage farming system in a clayish soil of Central Italy, Soil Biol. Biochem. 66 (2013) 78–93. [53] M.A. Kader, M. Senge, M.A. Mojid, K. Ito, Recent advances in mulching materials and methods for modifying soil environment, Soil Till. Res. 168 (2017) 155–166.
[1] A.C. Kennedy, Bacterial diversity in agroecosystems, Agric. Ecosyst. Environ. 74 (1999) 65–76. [2] G.T. Hill, N.A. Mitkowski, L. Aldrich-Wolfe, L.R. Emele, D.D. Jurkonie, A. Ficke, S. Maldonado-Ramirez, S.T. Lynch, E.B. Nelson, Methods for assessing the composition and diversity of soil microbial communities, Appl. Soil Ecol. 15 (2000) 25–36. [3] L.W. Mendes, M.J.D. Brossi, E.E. Kuramae, S.M. Tsai, Land-use system shapes soil bacterial communities in Southeastern Amazon region, Appl. Soil Ecol. 95 (2015) 151–160. [4] V. Acosta-Martinez, S. Dowd, Y. Sun, V. Allen, Tag-encoded pyrosequencing analysis of bacterial diversity in a single soil type as affected by management and land use, Soil Biol. Biochem. 40 (2008) 2762–2770. [5] L.W. Mendes, M.J.D. Brossi, E.E. Kuramae, S.M. Tsai, Land-use system shapes soil bacterial communities in Southeastern Amazon region, Appl. Soil Ecol. 95 (2015) 151–160. [6] X.L. Ren, T. Cai, X.L. Chen, P. Zhang, Z.K. Jia, Effect of rainfall concentration with different ridge widths on winter wheat production under semiarid climate, Eur. J. Agron. 77 (2016) 20–27. [7] Y.L. Chen, T. Liu, X.H. Tian, X.F. Wang, M. Li, S.X. Wang, Z.H. Wang, Effects of plastic film combined with straw mulch on grain yield and water use efficiency of winter wheat in Loess Plateau, Field Crop. Res. 172 (2015) 53–58. [8] Y.P. Wang, X.G. Li, T.T. Fu, L. Wang, N.C. Turner, K.H.M. Siddique, F.M. Li, Multisite assessment of the effects of plastic-film mulch on the soil organic carbon balance in semiarid areas of China, Agric. For. Meteorol. 228 (2016) 42–51. [9] M.M. Moreno, A. Moreno, Effect of different biodegradable and polyethylene mulches on soil properties and production in a tomato crop, Sci. Hortic. 116 (2008) 256–263. [10] A. Jordan, L.M. Zavala, J. Gil, Effects of mulching on soil physical properties and runoff under semi-arid conditions in southern Spain, Catena 81 (2010) 77–85. [11] Y. Wu, F.Y. Huang, C. Zhang, Z.K. Jia, Effects of different mulching patterns on soil moisture, temperature, and maize yield in a semi-arid region of the Loess Plateau, China, Arid Land Res. Manag. 30 (2016) 490–504. [12] Z. Steinmetz, C. Wollmann, M. Schaefer, C. Buchmann, J. David, J. Troeger, K. Munoz, O. Fror, G.E. Schaumann, Plastic mulching in agriculture. Trading shortterm agronomic benefits for long-term soil degradation? Sci. Total Environ. 550 (2016) 690–705. [13] M.M. Carreiro, R.E. Koske, Room-temperature isolations can bias against selection of low-temperature microfungi in temperate forest soils, Mycologia 84 (1992) 886–900. [14] C. Tu, J.B. Ristaino, S.J. Hu, Soil microbial biomass and activity in organic tomato farming systems: effects of organic inputs and straw mulching, Soil Biol. Biochem. 38 (2006) 247–255. [15] S. Bandopadhyay, L. Martin-Closas, A.M. Pelacho, J.M. DeBruyn, Biodegradable plastic mulch films: impacts on soil microbial communities and ecosystem functions, Front. Microbiol. 9 (2018). [16] W.Y. Dong, P.F. Si, E.K. Liu, C.R. Yan, Z. Zhang, Y.Q. Zhang, Influence of film mulching on soil microbial community in a rainfed region of northeastern China, Sci. Rep. UK 7 (2017). [17] H. Cui, Y. Zhou, Z.H. Gu, H.H. Zhu, S.L. Fu, Q. Yao, The combined effects of cover crops and symbiotic microbes on phosphatase gene and organic phosphorus hydrolysis in subtropical orchard soils, Soil Biol. Biochem. 82 (2015) 119–126. [18] L.W. Mbuthia, V. Acosta-Martinez, J. DeBruyn, S. Schaeffer, D. Tyler, E. Odoi, M. Mpheshea, F. Walker, N. Eash, Long term tillage, cover crop, and fertilization effects on microbial community structure, activity: implications for soil quality, Soil Biol. Biochem. 89 (2015) 24–34. [19] J. Farmer, B. Zhang, X.X. Jin, P. Zhang, J.K. Wang, Long-term effect of plastic film mulching and fertilization on bacterial communities in a brown soil revealed by high through-put sequencing, Arch. Agron Soil Sci. 63 (2017) 230–241. [20] D. Nelson, L. Sommers, A. Page, R. Miller, D. Keeney, Total carbon, organic carbon, and organic matter, Methods of Soil Analysis. Part 2. Chemical and Microbiological Properties, Soil Science Society of America, Madison, WI, USA, 1982, pp. 539–579. [21] J. Bremner, C. Mulvaney, Nitrogen-total, Methods of Soil Analysis. Part 2. Chemical and Microbiological Properties, 1982, pp. 595–624. [22] Y. Wang, P.Y. Qian, Conservative fragments in bacterial 16S rRNA genes and primer design for 16S ribosomal DNA amplicons in metagenomic studies, PLoS One 4 (2009). [23] A.P. Masella, A.K. Bartram, J.M. Truszkowski, D.G. Brown, J.D. Neufeld, PANDAseq: paired-end assembler for Illumina sequences, BMC Bioinf. 13 (2012). [24] R.C. Edgar, UPARSE: highly accurate OTU sequences from microbial amplicon reads, Nat. Methods 10 (2013) 996–998. [25] P.F. Kemp, J.Y. Aller, Bacterial diversity in aquatic and other environments: what 16S rDNA libraries can tell us, FEMS Microbiol. Ecol. 47 (2004) 161–177. [26] C. Lozupone, M.E. Lladser, D. Knights, J. Stombaugh, R. Knight, UniFrac: an effective distance metric for microbial community comparison, ISME J. 5 (2011) 169–172. [27] N. Segata, J. Izard, L. Waldron, D. Gevers, L. Miropolsky, W.S. Garrett, C. Huttenhower, Metagenomic biomarker discovery and explanation, Genome Biol. 12 (2011). [28] P. Zhang, T. Wei, T. Cai, S. Ali, Q.F. Han, X.L. Ren, Z.K. Jia, Plastic-film mulching for enhanced water-use efficiency and economic returns from maize fields in
15