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Article ; Online: Amino acid fertilizer strengthens its effect on crop yield and quality by recruiting beneficial rhizosphere microbes

Wang, Xiang / Zhang, Yu / Xu, Wanyu / Cheng, Jiarong / Liu, Jianjian / Pei, Wenxia / Wang, Jianfei / Chuang, Shaochuang

Journal of the Science of Food and Agriculture. 2023 Sept., v. 103, no. 12 p.5970-5980

2023

Abstract: BACKGROUND: There is currently an increase in the use of new types of fertilizers in modern agriculture. Studies have shown that amino acid fertilizers can improve crop yield and quality. However, their effects on crop rhizosphere ecology and their ... ...

Abstract	BACKGROUND: There is currently an increase in the use of new types of fertilizers in modern agriculture. Studies have shown that amino acid fertilizers can improve crop yield and quality. However, their effects on crop rhizosphere ecology and their ecological impacts on crop yield are largely unknown. This study evaluated the effects of a water‐soluble amino acid fertilizer (WAAF) on tomatoes and its ecological effects on rhizosphere bacterial communities using greenhouse pot experiments. RESULTS: The results showed that WAAF could promote the growth of tomatoes and improve the quality of fruits more effectively than water‐soluble chemical fertilizer controls. Interestingly, WAAF showed a different regulating pattern on root exudates and increased the secretion of 17 major water‐soluble root exudates, including hexadecanoic acid and 3‐hydroxy‐γ‐butyrolactone. Water‐soluble amino acid fertilizer also affected noticeably the composition, abundance, and beta‐diversity of rhizosphere bacterial communities, and strengthened the potential relationships between community members. Water‐soluble amino acid fertilizer showed a significant selective enrichment ability and recruited some members of the genera such as Cupriavidus, Ralstonia, Chitinophaga, Gemmatimonas, Mitsuaria, Mucilaginibacter, Paracoccus, Sphingopyxis, and Variovorax. Network analysis and functional prediction implied that, besides fertilizer effects, the recruiting of beneficial microbes involved in chemotaxis and biofilm formation was also a considerable factor in tomato yield and quality improvement. CONCLUSION: Our study revealed ecological and recruiting effects of WAAF on rhizosphere microbes and potentially beneficial microbiota, and provided a basis for the amino acid fertilizer regulation of rhizosphere ecology to improve soil health and further improve crop yield and quality. © 2023 Society of Chemical Industry.
Keywords	Chitinophaga ; Cupriavidus ; Gemmatimonas ; Mitsuaria ; Mucilaginibacter ; Ralstonia ; Sphingomonas ; Variovorax ; agriculture ; amino acids ; biofilm ; chemotaxis ; crop yield ; greenhouses ; microorganisms ; mineral fertilizers ; palmitic acid ; prediction ; rhizosphere ; secretion ; soil quality ; species diversity ; tomatoes ; water solubility
Language	English
Dates of publication	2023-09
Size	p. 5970-5980.
Publishing place	John Wiley & Sons, Ltd.
Document type	Article ; Online
Note	JOURNAL ARTICLE
ZDB-ID	184116-6
ISSN	1097-0010 ; 0022-5142
ISSN (online)	1097-0010
ISSN	0022-5142
DOI	10.1002/jsfa.12667
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Lysobacter lactosilyticus sp. nov., a Novel β-Galactosidase Producing Bacterial Strain Isolated from Farmland Soil Applied with Amino Acid Fertilizer

Wang, Xiang / Wang, Yu-Huan / Yang, Hong-Xing / Chuang, Shao-Chuang / Zhou, Chun-Fu / Yu, Xing / Zhang, Hao

Curr Microbiol. 2023 Jan., v. 80, no. 1 p.43-43

2023

Abstract: To isolate β-galactosidase producing bacterial resources, a novel Gram-stain-negative, strictly aerobic bacterial strain designated as A6ᵀ was obtained from a farmland soil sample. Cells of the strain were rod-shaped (0.4–0.7 μm × 1.8–2.2 μm) without ... ...

Abstract	To isolate β-galactosidase producing bacterial resources, a novel Gram-stain-negative, strictly aerobic bacterial strain designated as A6ᵀ was obtained from a farmland soil sample. Cells of the strain were rod-shaped (0.4–0.7 μm × 1.8–2.2 μm) without flagella and motility. Strain A6ᵀ grew optimally at 30 °C, pH 7.0 with 0% (w/v) NaCl. Based on phylogenetic analysis, strain A6ᵀ clustered within the genus Lysobacter clade and branched with Lysobacter dokdonensis KCTC 12822ᵀ (99.5%, 16S rRNA gene sequence similarity) and Lysobacter caseinilyticus KACC 19816ᵀ (98.5%). The average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values between strain A6ᵀ and Lysobacter dokdonensis KCTC 12822ᵀ were 82.7% and 26.2%, and the values for strain A6ᵀ and KACC 19816ᵀ were 81.4% and 23.8%, respectively. Iso-C₁₆:₀, iso-C₁₅:₀, summed feature 9 (C₁₇:₁ iso ω9c and/or C₁₆:₀ 10-methyl) and summed feature 3 (C₁₆:₁ω7c and/or C₁₆:₁ ω6c) were the major fatty acids, diphosphatidylglycerol, phosphatidylglycerol, and phosphatidylethanolamine were the major polar lipids, and ubiquinone 8 (Q-8) was the major ubiquinone. The genomic DNA G+C content was 67.2 mol%. Furthermore, under the condition of 30 °C, pH 7.0, 4% inoculation with 10.0 g L⁻¹ lactose, the β-galactosidase activity produced by strain A6ᵀ was highest, reaching 95.3 U mL⁻¹, indicating that this strain could be applied as a potential strain for β-galactosidase production. Strain A6ᵀ represents a novel species of the genus Lysobacter, and Lysobacter lactosilyticus sp. nov. is proposed on the basis of phenotypic, genotypic, and chemotaxonomic analysis. The type strain is A6ᵀ (=KCTC 82184ᵀ=CGMCC 1.18582ᵀ).
Keywords	DNA ; Lysobacter ; agricultural soils ; amino acids ; chemotaxonomy ; fertilizers ; flagellum ; lactose ; nucleic acid hybridization ; nucleotide sequences ; pH ; phenotype ; phosphatidylethanolamines ; phylogeny ; sequence homology ; ubiquinones
Language	English
Dates of publication	2023-01
Size	p. 43.
Publishing place	Springer US
Document type	Article ; Online
ZDB-ID	134238-1
ISSN	1432-0991 ; 0343-8651
ISSN (online)	1432-0991
ISSN	0343-8651
DOI	10.1007/s00284-022-03155-2
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Article ; Online: Amino acid fertilizer strengthens its effect on crop yield and quality by recruiting beneficial rhizosphere microbes.

Wang, Xiang / Zhang, Yu / Xu, Wanyu / Cheng, Jiarong / Liu, Jianjian / Pei, Wenxia / Wang, Jianfei / Chuang, Shaochuang

Journal of the science of food and agriculture

2023 Volume 103, Issue 12, Page(s) 5970–5980

Abstract: Background: There is currently an increase in the use of new types of fertilizers in modern agriculture. Studies have shown that amino acid fertilizers can improve crop yield and quality. However, their effects on crop rhizosphere ecology and their ... ...

Abstract	Background: There is currently an increase in the use of new types of fertilizers in modern agriculture. Studies have shown that amino acid fertilizers can improve crop yield and quality. However, their effects on crop rhizosphere ecology and their ecological impacts on crop yield are largely unknown. This study evaluated the effects of a water-soluble amino acid fertilizer (WAAF) on tomatoes and its ecological effects on rhizosphere bacterial communities using greenhouse pot experiments. Results: The results showed that WAAF could promote the growth of tomatoes and improve the quality of fruits more effectively than water-soluble chemical fertilizer controls. Interestingly, WAAF showed a different regulating pattern on root exudates and increased the secretion of 17 major water-soluble root exudates, including hexadecanoic acid and 3-hydroxy-γ-butyrolactone. Water-soluble amino acid fertilizer also affected noticeably the composition, abundance, and beta-diversity of rhizosphere bacterial communities, and strengthened the potential relationships between community members. Water-soluble amino acid fertilizer showed a significant selective enrichment ability and recruited some members of the genera such as Cupriavidus, Ralstonia, Chitinophaga, Gemmatimonas, Mitsuaria, Mucilaginibacter, Paracoccus, Sphingopyxis, and Variovorax. Network analysis and functional prediction implied that, besides fertilizer effects, the recruiting of beneficial microbes involved in chemotaxis and biofilm formation was also a considerable factor in tomato yield and quality improvement. Conclusion: Our study revealed ecological and recruiting effects of WAAF on rhizosphere microbes and potentially beneficial microbiota, and provided a basis for the amino acid fertilizer regulation of rhizosphere ecology to improve soil health and further improve crop yield and quality. © 2023 Society of Chemical Industry.
MeSH term(s)	Soil/chemistry ; Solanum lycopersicum/chemistry ; Fertilizers ; Rhizosphere ; Bacteroidetes ; Amino Acids/chemistry
Chemical Substances	Soil ; Fertilizers ; Amino Acids
Language	English
Publishing date	2023-05-11
Publishing country	England
Document type	Journal Article
ZDB-ID	184116-6
ISSN	1097-0010 ; 0022-5142
ISSN (online)	1097-0010
ISSN	0022-5142
DOI	10.1002/jsfa.12667
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Article: Bioaugmentation of acetamiprid-contaminated soil with Pigmentiphaga sp. strain D-2 and its effect on the soil microbial community

Yang, Hongxing / Zhang, Yanlin / Chuang, Shaochuang / Cao, Weimiao / Ruan, Zhepu / Xu, Xihui / Jiang, Jiandong

Ecotoxicology. 2021 Oct., v. 30, no. 8

2021

Abstract: Bioaugmentation, a strategy based on microbiome engineering, has been proposed for bioremediation of pollutant-contaminated environments. However, the complex microbiome engineering processes for soil bioaugmentation, involving interactions among the ... ...

Abstract	Bioaugmentation, a strategy based on microbiome engineering, has been proposed for bioremediation of pollutant-contaminated environments. However, the complex microbiome engineering processes for soil bioaugmentation, involving interactions among the exogenous inoculum, soil environment, and indigenous microbial microbiome, remain largely unknown. Acetamiprid is a widely used neonicotinoid insecticide which has caused environmental contaminations. Here, we used an acetamiprid-degrading strain, Pigmentiphaga sp. D-2, as inoculum to investigate the effects of bioaugmentation on the soil microbial community and the process of microbiome reassembly. The bioaugmentation treatment removed 94.8 and 92.5% of acetamiprid within 40 days from soils contaminated with 50 and 200 mg/kg acetamiprid, respectively. A decrease in bacterial richness and diversity was detected in bioaugmentation treatments, which later recovered with the removal of acetamiprid from soil. Moreover, the bioaugmentation treatment significantly influenced the bacterial community structure, whereas application of acetamiprid alone had little influence on the soil microbial community. Furthermore, the bioaugmentation treatment improved the growth of bacteria associated with acetamiprid degradation, and the inoculated and recruited taxa significantly influenced the keystone taxa of the indigenous microbiome, resulting in reassembly of the bacterial community yielding higher acetamiprid-degrading efficiency than that of the indigenous and acetamiprid-treated communities. Our results provide valuable insights into the mechanisms of microbiome engineering for bioaugmentation of acetamiprid-contaminated soils.
Keywords	Pigmentiphaga ; acetamiprid ; bacterial communities ; bioaugmentation ; community structure ; ecotoxicology ; edaphic factors ; inoculum ; microbiome ; soil microorganisms
Language	English
Dates of publication	2021-10
Size	p. 1559-1571.
Publishing place	Springer US
Document type	Article
ZDB-ID	34042-x
ISSN	1573-3017 ; 0963-9292
ISSN (online)	1573-3017
ISSN	0963-9292
DOI	10.1007/s10646-020-02336-8
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Article ; Online: Bioaugmentation of acetamiprid-contaminated soil with Pigmentiphaga sp. strain D-2 and its effect on the soil microbial community.

Yang, Hongxing / Zhang, Yanlin / Chuang, Shaochuang / Cao, Weimiao / Ruan, Zhepu / Xu, Xihui / Jiang, Jiandong

Ecotoxicology (London, England)

2021 Volume 30, Issue 8, Page(s) 1559–1571

Abstract	Bioaugmentation, a strategy based on microbiome engineering, has been proposed for bioremediation of pollutant-contaminated environments. However, the complex microbiome engineering processes for soil bioaugmentation, involving interactions among the exogenous inoculum, soil environment, and indigenous microbial microbiome, remain largely unknown. Acetamiprid is a widely used neonicotinoid insecticide which has caused environmental contaminations. Here, we used an acetamiprid-degrading strain, Pigmentiphaga sp. D-2, as inoculum to investigate the effects of bioaugmentation on the soil microbial community and the process of microbiome reassembly. The bioaugmentation treatment removed 94.8 and 92.5% of acetamiprid within 40 days from soils contaminated with 50 and 200 mg/kg acetamiprid, respectively. A decrease in bacterial richness and diversity was detected in bioaugmentation treatments, which later recovered with the removal of acetamiprid from soil. Moreover, the bioaugmentation treatment significantly influenced the bacterial community structure, whereas application of acetamiprid alone had little influence on the soil microbial community. Furthermore, the bioaugmentation treatment improved the growth of bacteria associated with acetamiprid degradation, and the inoculated and recruited taxa significantly influenced the keystone taxa of the indigenous microbiome, resulting in reassembly of the bacterial community yielding higher acetamiprid-degrading efficiency than that of the indigenous and acetamiprid-treated communities. Our results provide valuable insights into the mechanisms of microbiome engineering for bioaugmentation of acetamiprid-contaminated soils.
MeSH term(s)	Biodegradation, Environmental ; Microbiota ; Neonicotinoids ; Soil ; Soil Microbiology ; Soil Pollutants/analysis
Chemical Substances	Neonicotinoids ; Soil ; Soil Pollutants ; acetamiprid (5HL5N372P0)
Language	English
Publishing date	2021-01-14
Publishing country	United States
Document type	Journal Article
ZDB-ID	34042-x
ISSN	1573-3017 ; 0963-9292
ISSN (online)	1573-3017
ISSN	0963-9292
DOI	10.1007/s10646-020-02336-8
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Article ; Online: Potential effects of Rhodococcus qingshengii strain djl-6 on the bioremediation of carbendazim-contaminated soil and the assembly of its microbiome.

Chuang, Shaochuang / Yang, Hongxing / Wang, Xiang / Xue, Chao / Jiang, Jiandong / Hong, Qing

Journal of hazardous materials

2021 Volume 414, Page(s) 125496

Abstract: As a widely used fungicide, the environmental fate of carbendazim and its residues in agricultural products have caused great concern. However, its effects on soil microbial communities are largely unknown. Herein, we used high-throughput sequencing to ... ...

Abstract	As a widely used fungicide, the environmental fate of carbendazim and its residues in agricultural products have caused great concern. However, its effects on soil microbial communities are largely unknown. Herein, we used high-throughput sequencing to reveal the effects of high and low dose of carbendazim and its degrading strain, Rhodococcus qingshengii strain djl-6, on the composition, diversity, and interrelationship of soil bacterial and fungal communities in short- and medium-term under laboratory conditions. The results showed that carbendazim exhibited an increased negative impact on bacterial communities and reduced the proportion of dominant fungal phylum Ascomycota during a 14-day incubation period. Only the impacts of low-dose carbendazim (2 mg·kg
MeSH term(s)	Benzimidazoles ; Biodegradation, Environmental ; Carbamates ; Microbiota ; Rhodococcus ; Soil ; Soil Microbiology ; Soil Pollutants/analysis ; Soil Pollutants/toxicity
Chemical Substances	Benzimidazoles ; Carbamates ; Soil ; Soil Pollutants ; carbendazim (H75J14AA89)
Language	English
Publishing date	2021-02-24
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1491302-1
ISSN	1873-3336 ; 0304-3894
ISSN (online)	1873-3336
ISSN	0304-3894
DOI	10.1016/j.jhazmat.2021.125496
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Article: Shift in Bacterial Community Structure Drives Different Atrazine-Degrading Efficiencies.

Liu, Xiaowei / Chen, Kai / Chuang, Shaochuang / Xu, Xihui / Jiang, Jiandong

Frontiers in microbiology

2019 Volume 10, Page(s) 88

Abstract: Compositions of pollutant-catabolic consortia and interactions between community members greatly affect the efficiency of pollutant catabolism. However, the relationships between community structure and efficiency of catabolic function in pollutant- ... ...

Abstract	Compositions of pollutant-catabolic consortia and interactions between community members greatly affect the efficiency of pollutant catabolism. However, the relationships between community structure and efficiency of catabolic function in pollutant-catabolic consortia remain largely unknown. In this study, an original enrichment (AT) capable of degrading atrazine was obtained. And two enrichments - with a better/worse atrazine-degrading efficiency (ATB/ATW) - were derived from the original enrichment AT by continuous sub-enrichment with or without atrazine. Subsequently, an
Language	English
Publishing date	2019-01-30
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2587354-4
ISSN	1664-302X
ISSN	1664-302X
DOI	10.3389/fmicb.2019.00088
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Article ; Online: Pigmentiphaga

Yang, Hongxing / Hu, Shunli / Wang, Xiang / Chuang, Shaochuang / Jia, Weibin / Jiang, Jiandong

Applied and environmental microbiology

2020 Volume 86, Issue 6

Abstract: Acetamiprid, a chloronicotinyl neonicotinoid insecticide, is among the most commonly used insecticides worldwide, and its environmental fate has caused considerable concern. The compound 1-(6-chloropyridin-3-yl)- ...

Abstract	Acetamiprid, a chloronicotinyl neonicotinoid insecticide, is among the most commonly used insecticides worldwide, and its environmental fate has caused considerable concern. The compound 1-(6-chloropyridin-3-yl)-
MeSH term(s)	Alcaligenaceae/metabolism ; Amidohydrolases/metabolism ; Bacterial Proteins/metabolism ; Hydrolysis ; Insecticides/metabolism ; Neonicotinoids/metabolism
Chemical Substances	Bacterial Proteins ; Insecticides ; Neonicotinoids ; acetamiprid (5HL5N372P0) ; Amidohydrolases (EC 3.5.-) ; amidase (EC 3.5.1.4)
Language	English
Publishing date	2020-03-02
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	223011-2
ISSN	1098-5336 ; 0099-2240
ISSN (online)	1098-5336
ISSN	0099-2240
DOI	10.1128/AEM.02425-19
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Article ; Online: Erratum for Yang et al., "

Yang, Hongxing / Hu, Shunli / Wang, Xiang / Chuang, Shaochuang / Jia, Weibin / Jiang, Jiandong

Applied and environmental microbiology

2020 Volume 86, Issue 12

Language	English
Publishing date	2020-06-02
Publishing country	United States
Document type	Journal Article ; Published Erratum
ZDB-ID	223011-2
ISSN	1098-5336 ; 0099-2240
ISSN (online)	1098-5336
ISSN	0099-2240
DOI	10.1128/AEM.00957-20
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Article ; Online: Microbial catabolism of lindane in distinct layers of acidic paddy soils combinedly affected by different water managements and bioremediation strategies.

Chuang, Shaochuang / Wang, Baozhan / Chen, Kai / Jia, Weibin / Qiao, Wenjing / Ling, Wanting / Tang, Xiangyu / Jiang, Jiandong

The Science of the total environment

2020 Volume 746, Page(s) 140992

Abstract: The environmental fate of the recalcitrant organic chlorine insecticide lindane and its removal from contaminated soils are still of great concern. However, the key factors influencing microbial removal of lindane from paddy soils with intermittent ... ...

Abstract	The environmental fate of the recalcitrant organic chlorine insecticide lindane and its removal from contaminated soils are still of great concern. However, the key factors influencing microbial removal of lindane from paddy soils with intermittent flooding and draining remain largely unknown. Here, we conducted laboratory experiments to investigated lindane biodegradation in different layers of typical acidic paddy soils under different water managements and bioremediation strategies, together with the changes of functional bacterial consortium, key genes and metabolic pathways. It was found that under flooded conditions, lindane spiking significantly stimulated the growth of some bacterial genera with potential anaerobic catabolic functions in both top- (0-20 cm depth) and subsoil (20-40 cm depth), leading to the shortest half-life of lindane with 7.6-9.0 d in the topsoil. In contrary, lindane spiking dramatically stimulated the growth of bacterial members with aerobic catabolic functions under drained conditions, exhibiting half-lives of lindane with 85-131 d and 18-23 d in the top- and subsoil, respectively. Overall, biostimulation coupled with flooding management would be the better combination for increased lindane bioremediation. Functional genes involved in lindane degradation and retrieved from metagenomic data further supported the anaerobic and aerobic biodegradation of lindane under flooded and drained conditions, respectively. Moreover, the integrated network analysis suggested water management and organic matter were the primary factors shaped the assembly of functional bacteria in lindane degradation, among which Clostridium and Rhodanobacter were the key anaerobic and aerobic functional genera, respectively. Taken together, our study provides a comprehensive understanding of lindane biodegradation in distinct layers of acidic paddy soils that were combinedly affected by different water managements and bioremediation strategies.
MeSH term(s)	Biodegradation, Environmental ; Hexachlorocyclohexane ; Soil ; Soil Microbiology ; Soil Pollutants/analysis ; Water ; Water Supply
Chemical Substances	Soil ; Soil Pollutants ; Water (059QF0KO0R) ; Hexachlorocyclohexane (59NEE7PCAB)
Language	English
Publishing date	2020-07-18
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	121506-1
ISSN	1879-1026 ; 0048-9697
ISSN (online)	1879-1026
ISSN	0048-9697
DOI	10.1016/j.scitotenv.2020.140992
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