Scientia Agricultura Sinica ›› 2023, Vol. 56 ›› Issue (18): 3615-3628.doi: 10.3864/j.issn.0578-1752.2023.18.010

• SOIL & FERTILIZER·WATER-SAVING IRRIGATION·AGROECOLOGY & ENVIRONMENT • Previous Articles     Next Articles

Effects of Long-Term Application of Organic Fertilizer on Rare and Abundant Bacterial Sub-Communities in Greenhouse Tomato Soil

LIU Lei(), SHI JianShuo(), ZHANG GuoYin, GAO Jing, LI Pin, REN Yanli, WANG LiYing()   

  1. Institute of Agricultural Resources and Environment, Hebei Academy of Agriculture and Forestry Sciences/Hebei Fertilizer Technology Innovation Center, Shijiazhuang 050051
  • Received:2022-10-09 Accepted:2023-03-20 Online:2023-09-16 Published:2023-09-21
  • Contact: WANG LiYing

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Abstract:

【Objective】The objective of the present study was to distinguish the rare and abundant bacteria from the whole community and to explore their responses to long-term application of organic fertilizer respectively, so as to provide new insights into the relationships between soil biodiversity and ecosystem functioning under major agricultural activities. 【Method】Based on the long-term fertilization experiment of greenhouse tomato, soils were collected under four different treatments, including no fertilizer (M0), low organic fertilizer 5.68 t·hm-2 (M1), medium organic fertilizer 8.52 t·hm-2 (M2), and high organic fertilizer 11.36 t·hm-2 (M3). Illumina MiSeq platform was used to analyze the diversity, community composition, co-occurrence network and potential functions differences of the rare and abundant bacterial sub-communities, and their various responses to long-term fertilization, to illustrate the key factors driving the distinct distribution patterns and responses for rare and abundant bacteria. 【Result】Compared with the abundant bacterial sub-community, the rare bacterial sub-community showed higher α- and β-diversity and distinct community composition, as well as potential functions. A functional prediction detected that abundant bacteria contributed primary functions in the greenhouse ecosystem, such as nutrient and energy metabolism, meanwhile rare bacteria contribute a substantial fraction of auxiliary functions (e.g., metabolism of cofactors), which indicated they played important roles in the functional redundancy of microbial communities. Contrasting responses of rare and abundant bacterial sub-communities to long-term fertilization were revealed in this study, in which the rare bacteria was more sensitive. Compared with no fertilizer, the long-term application of organic and chemical fertilizer significantly increased the OTU richness, Shannon diversity, and total relative abundance by 19.8%-53.8%, 5.8%-8.0%, and 1.1-1.2 times, respectively, and changed the community composition and structure of rare bacterial sub-communities. In addition, with the increased application rates of organic fertilizer, the OTU richness of rare bacteria also increased significantly, accompanied by obvious changing in community composition and structure. However, the abundant bacteria exhibited less sensitivity to long-term fertilization, with only the community composition altered. Besides, the co-occurrence network complexity increased with organic fertilizer rates, especially in rare sub-communities. Both the results of the NMDS and mantel test revealed that the controlling factors affecting rare and abundant bacterial sub-communities were different. A variety of soil factors associated with deterministic processes, i.e., SOC, soil nutrients of total N and P, Olsen-P and available K, and pH, as well as macro- and medium-aggregate, significantly influenced abundant bacteria. Structural equation model (SEM) further showed that soil organic matter and total phosphorus directly drove abundant bacterial diversity. On the other hand, less effects of environmental filtering and more scattered distribution patterns were found in rare bacteria, indicating different assemblies of rare and abundant sub-communities. 【Conclusion】Compared with the abundant bacteria and the whole community, the rare bacteria sub-community showed higher diversity and unique community composition, which improved the functional redundancy of the microbial community. Long-term fertilization altered the whole bacterial community mainly by affecting rare bacteria (i.e., increasing diversity, changing community composition, increasing co-occurrence network complexity) rather than the abundant bacteria. The controlling factors that mediated the assembly of the rare and abundant bacterial sub-communities were also different.

Key words: rare bacteria, abundant bacteria, organic fertilizer, greenhouse tomato, diversity, community assembly, ecosystem function

Table 1

Annual input of nutrient under different fertilizer treatments"

处理 Treatment 有机肥养分投入量
Organic nutrient input (kg·hm-2)		 化肥养分投入量
Inorganic nutrient input (kg·hm-2)		 总养分投入量
Total nutrient input (kg·hm-2)
氮 N 磷 P2O5 钾 K2O 氮 N 磷 P2O5 钾 K2O 氮 N 磷 P2O5 钾 K2O
M0 0 0 0 0 0 0 0 0 0
M1 157 88 118 192 88 327 349 177 445
M2 236 133 177 192 88 327 428 221 504
M3 315 177 236 192 88 327 506 265 563

Table 2

Soil properties under different application rates of manure"

处理
Treatment		 pH 有机质
SOM
(g·kg-1)		 全氮
TN
(g·kg-1)		 全磷
TP
(g·kg-1)		 全钾
TK
(g·kg-1)		 硝态氮
NO3--N
(mg·kg-1)		 铵态氮
NH4+-N
(mg·kg-1)		 有效磷
Olsen-P
(mg·kg-1)
M0 8.39±0.05a 12.83±0.15d 0.75±0.01c 0.72±0.04c 1.94±0.02a 24.25±14.24a 4.03±0.85a 4.60±1.60c
M1 7.98±0.10b 26.23±0.38c 1.37±0.10b 1.09±0.02b 1.98±0.03a 12.76±5.73a 4.48±0.41a 55.27±2.90b
M2 7.82±0.10b 33.00±2.36b 1.63±0.15ab 1.21±0.04ab 1.99±0.02a 13.21±9.97a 5.67±1.08a 82.20±6.33a
M3 7.57±0.06c 37.11±0.43a 1.84±0.03a 1.29±0.06a 1.98±0.02a 11.69±1.71b 4.95±0.56a 90.63±5.08a
处理
Treatment		 速效钾
AK
(mg·kg-1)		 碳氮比
C/N		 电导率
EC
(μs·cm-1)		 质量含水量
W
(%)		 大团聚体
Maccoaggregate
(%)		 中团聚体
Mediumaggregate
(%)		 黏粒
Clay
(%)		 粉粒
Silt
(%)
M0 71.50±15.55c 8.53±3.44b 108.03±31.09a 14.89±0.71a 22.21±2.06b 15.27±4.27b 27.37±0.67a 49.33±3.71a
M1 189.00±30.05b 10.83±5.81ab 190.43±79.75a 14.52±1.83a 32.82±12.18a 36.35±6.40a 26.03±1.33a 50.00±1.15a
M2 233.00±36.51ab 21.26±0.10a 273.60±104.45a 15.16±1.01a 32.61±1.10a 46.13±4.61a 26.03±0.67a 48.67±2.40a
M3 283.50±6.87a 16.09±4.60a 518.33±198.95a 14.97±0.77a 39.85±4.85a 44.06±0.28a 24.70±1.15a 50.67±1.76a

Table 3

The α-diversities of bacterial sub-communities under different fertilizer treatment"

处理
Treatment		 OTU丰富度 OTU richness Shannon多样性指数 Shannon diversity index
稀有Rare 丰富Abundant 整体Whole 稀有Rare 丰富Abundant 整体Whole
M0 912.67±18.68d 26.33±2.73a 1947.00±91.11b 6.56±0.21b 2.95±0.20a 5.85±0.30b
M1 1093.00±31.32c 25.67±0.88a 2349.33±58.94a 6.94±0.03ab 3.16±0.05a 6.56±0.05a
M2 1153.33±16.59b 23.00±0.58a 2480.00±27.54a 6.99±0.01ab 3.07±0.03a 6.69±0.01a
M3 1403.67±92.65a 24.67±4.18a 2482.00±36.51a 7.079±0.06a 3.10±0.13a 6.74±0.06a

Fig. 1

Composition of bacterial sub-communities under different fertilizer treatment Rare: The rare bacterial sub-community; Abundant: The abundant bacterial sub-community; Whole: The whole bacterial community. The same as below"

Fig. 2

The bacterial β-diversities of different sub-communities according to the Bray-Curtis dissimilarity"

Fig. 3

Non-metric multidimensional scaling (NMDS) ordination of different sub-communities based on Bray-Curtis distances"

Fig. 4

Co-occurrence networks of different sub-communities"

Table 4

Mantel test on pearson correlations of different bacterial sub-communities with environmental factors"

土壤性质
Soil property		 稀有 Rare 丰富 Abundant 整体 Whole
r P r P r P
pH 0.328 0.005 0.545 0.001 0.610 0.002
SOM 0.215 0.044 0.690 0.001 0.761 0.001
TN 0.246 0.030 0.669 0.001 0.738 0.001
TP 0.229 0.043 0.707 0.001 0.767 0.001
TK 0.071 0.286 0.175 0.156 0.189 0.125
NO3--N 0.052 0.372 -0.204 0.853 -0.215 0.857
NH4+-N 0.156 0.156 0.008 0.416 0.036 0.394
Olsen-P 0.107 0.241 0.711 0.001 0.756 0.001
AK 0.136 0.149 0.619 0.005 0.660 0.003
C/N 0.248 0.024 0.394 0.020 0.445 0.009
EC 0.199 0.080 0.247 0.109 0.281 0.066
W -0.029 0.599 -0.141 0.702 -0.136 0.710
Macroaggregate 0.161 0.096 0.413 0.002 0.454 0.003
Mediumaggregate 0.177 0.096 0.601 0.013 0.667 0.005
Clay -0.558 0.646 -0.022 0.486 -0.020 0.460
Silt 0.063 0.332 0.058 0.247 0.111 0.266

Fig. 5

Structural euation model (SEM) illustrating the effects of fertilization and soil attributes on different bacterial sub-communities Solid and dotted lines indicate significant and non-significant paths, respectively. Numbers adjacent to the arrows indicatestandardized path coefficients. R2 value above each variable represents the proportion of the variance explained by the SEM model. R: The rare bacterial sub-community; A: The abundant bacterial sub-community; F: Fertilization rates"

Fig. 6

The differences in potential functions of abundant and rare taxa"

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