Soil microbial diversity and metabolic gene expression respond to long-term fertilizations in simulated field experiments

Liu, Yanxia; Li, Xiang; Li, Han; Zhu, Jingwei; Wang, Xingguo; Shen, Biao

doi:10.1590/1678-992X-2024-0280

Soils and Plant Nutrition & Agricultural Microbiome • Sci. agric. (Piracicaba, Braz.) 83 • 2026 • https://doi.org/10.1590/1678-992X-2024-0280 linkcopy

Soil microbial diversity and metabolic gene expression respond to long-term fertilizations in simulated field experiments

Authorship SCIMAGO INSTITUTIONS RANKINGS

The extended and unscientific use of chemical fertilizers has significantly diminished soil microbial activity. A long-term field trial spanning for 12 years was conducted to assess soil fertility and microbial activity under different fertilization strategies. A soil column system was established, incorporating nine types of conventional chemical fertilizers across three concentration gradients to simulate the effects of consistent and intensive application commonly seen in agricultural practices. High-throughput sequencing and Biolog technology were employed to examine the soil structure, function, and metabolic gene profiles in microbes. Throughout the period of consistent fertilization, the annual yield of tobacco leaves showed a steady decline. However, the use of organic and bio-organic fertilizers has proven to be remarkably effective, reversing this drop in productivity by between 8.88 and 13.25 percentage points. In the soil column fertilization simulation system, the consistent use of nine different chemical fertilizers led to significant variations in the diversity of Actinobacteria and Proteobacteria. After an extended period of high-frequency application with a 50 % reduction in urea dosage, the Shannon index exhibited a significant (p < 0.05) increase of 1.77 % compared to its initial level. Notably, monoammonium phosphate and compound fertilizers markedly inhibited the abundance of Proteobacteria, whereas potassium nitrate displayed a promoting effect. Additionally, the expression of amino acid and nucleotide transport and metabolism genes in the calcium-magnesium phosphate fertilizer, when applied at the standard dosage, was found to upregulated. In conclusion, the prolonged application of various chemical fertilizers negatively impacts soil microbial activity, with a more pronounced effect observed from straight chemical fertilizers compared to compound fertilizers.

Keywords:
long-term localized trial; fertilization; column fertilization simulation system; soil microbial diversity; co-correlation networks

Treatments	Fertilizer Type	Base Fertilizer Dosage			Topdressing fertilizer		Other Fertilizer
Treatments	Fertilizer Type	N	P₂O₅	K₂O	N	K₂O	Other Fertilizer
		------------------------------------------------- kg hm⁻² -------------------------------------------------
N	Nitrogen	45	-	-	30	-	-
NP	Nitrogen+Phosphate	45	75	-	30	-	-
NK	Nitrogen+Potassium	45	-	90	30	60	-
NPK	Nitrogen+Phosphate+Potassium	45	75	90	30	60	-
NPK+M	NPK+Organic Fertilizer	13.95	46.65	74.55	30	60	1500
NPK+BIO	NPK+Bioorganic Fertilizer	13.50	58.05	81.90	30	60	750

Fertilizer type	Number	Fertilizer	Application Amount (g column⁻¹)
			T1	T2	T3
			Reduce 50 %	Conventional	Increase 50 %
Control/No fertilization	CK	-	-	-	-
Nitrogen fertilizer	A	Urea	5.36	10.72	16.08
Nitrogen fertilizer	B	Ammonium Nitrate	7.14	14.28	21.42
Phosphate fertilizer	D	Calcium Magnesium Phosphate	17.10	34.20	51.30
Phosphate fertilizer	E	Calcium Superphosphate	18.83	37.66	56.49
Potash fertilizer	H	Potassium Sulfate	9.28	18.56	27.84
Potash fertilizer	M	Potassium Chloride	7.93	15.86	23.79
Compound fertilizer	F	Monoammonium Phosphate	20.75	41.50	62.25
	N	Potassium Nitrate	18.03	36.07	54.11
	C	Compound Fertilizer	25.00	50.00	75.00

Treatments	Organic matter	pH	Available nitrogen	Available phosphorus	Available potassium	Microbial respiration
	g kg⁻¹		------------------------------------ mg kg⁻¹ ------------------------------------			µmol mol⁻¹
N	39.81 d	6.21 c	114.62 c	23.11 c	59.31 c	1207 e
NP	40.34 c	6.35 c	116.89 c	47.68 b	50.21 c	1461 d
NK	41.75 c	6.37 c	121.21 b	13.12 d	243.62 ab	1574 d
NPK	43.11 b	6.35 c	119.89 b	54.97 a	226.26 b	1846 c
NPK+M	50.16 a	6.68 b	132.12 a	56.86 a	256.33 a	2068 b
NPK+BIO	47.21 a	6.83 a	120.98 b	47.63 b	230.69 b	2450 a

Sampling Time	20 days			300 days
Treatments	T1 50 % Reduction	T2 Conventional	T3 50 % Increase	T1 50 % Reduction	T2 Conventional	T3 50 % Increase
Control	6.78 b	6.78 a	6.78 b	6.51 a	6.51 a	6.51 a
Urea	6.21 d	6.42 b	6.58 bc	6.32 ab	3.85 d	3.90 d
Ammonium Nitrate	6.52 bc	6.33 b	6.74 b	6.02 c	5.43 c	5.41 b
Calcium Magnesium Phosphate	6.38 c	6.41 b	6.26 c	5.81 c	6.03 b	5.69 b
Calcium Superphosphate	6.01 e	5.83 d	5.47 e	4.90 d	5.49 c	5.35 b
Potassium Sulfate	6.43 c	6.48 c	7.24 a	5.90 c	5.60 c	5.27 bc
Potassium Chloride	7.18 a	6.74 a	6.38 c	6.47 a	6.41 a	5.36 b
Monoammonium Phosphate	5.57 f	4.51 e	3.87 f	3.98 e	3.73 d	3.72 d
Potassium Nitrate	7.01 a	6.81 a	7.12 a	6.13 b	5.12 c	5.13 c
Compound Fertilizer	6.23 d	5.84 d	6.03 d	5.03 d	3.68 d	5.19 c

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[TFN1] T1 = treatment 1 – application of 50 % amount of conventional fertilizer; T2 = treatment 2 – application of normal dosage of conventional fertilizer; T3 = treatment 3 – application of 150 % amount of conventional fertilizer.