Amino acid fertilizer strengthens its effect on crop yield and quality by recruiting beneficial rhizosphere microbes.

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.

Lysobacter lactosilyticus sp. nov., a Novel ß-Galactosidase Producing Bacterial Strain Isolated from Farmland Soil Applied with Amino Acid Fertilizer.

To isolate ß-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 ß-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 ß-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).

Bioaugmentation of acetamiprid-contaminated soil with Pigmentiphaga sp. strain D-2 and its effect on the soil microbial community.

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.

Pigmentiphaga sp. Strain D-2 Uses a Novel Amidase To Initiate the Catabolism of the Neonicotinoid Insecticide Acetamiprid.

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)-N-methylmethanamine (IM 1-4) has been reported to be the main intermediate during acetamiprid catabolism in microorganisms, honeybees, and spinach. However, the molecular mechanism underlying the hydrolysis of acetamiprid to IM 1-4 has not yet been elucidated. In this study, a novel amidase (AceAB) that initially hydrolyzes the C-N bond of acetamiprid to generate IM 1-4 was purified and characterized from the acetamiprid-degrading strain Pigmentiphaga sp. strain D-2. Based on peptide profiling of the purified AceAB and the draft genome sequence of strain D-2, aceA (372 bp) and aceB (2,295 bp), encoding the α and ß subunits of AceAB, respectively, were cloned and found to be necessary for acetamiprid hydrolysis in strain D-2. The characteristics of AceAB were also systematically investigated. Though AceA and AceB showed 35% to 56% identity to the α and ß subunits of the N,N-dimethylformamidase from Paracoccus aminophilus, AceAB was specific for the hydrolysis of acetamiprid and showed no activities to N,N-dimethylformamide or its structural analogs.IMPORTANCE Acetamiprid, among the top neonicotinoid insecticides used worldwide, is one of the most important commercial insecticides. Due to its extensive use, the environmental fate of acetamiprid, especially its microbial degradation, has caused considerable concern. Although the catabolic pathways of acetamiprid in microorganisms have been extensively studied, the molecular mechanisms underlying acetamiprid biodegradation (except for a nitrile hydratase) remain largely unknown, and the enzyme responsible for the biotransformation of acetamiprid into its main intermediate, IM 1-4, have not yet been elucidated. The amidase AceAB and its encoding genes, aceA and aceB, characterized in this study, were found to be necessary and specific for the initial hydrolysis of the C-N bond of acetamiprid to generate IM 1-4 in Pigmentiphaga sp. strain D-2. The finding of the novel amidase AceAB will greatly enhance our understanding of the microbial catabolism of the widely used insecticide acetamiprid at the molecular level.

Microbial catabolism of chemical herbicides: Microbial resources, metabolic pathways and catabolic genes.

Chemical herbicides are widely used to control weeds and are frequently detected as contaminants in the environment. Due to their toxicity, the environmental fate of herbicides is of great concern. Microbial catabolism is considered the major pathway for the dissipation of herbicides in the environment. In recent decades, there have been an increasing number of reports on the catabolism of various herbicides by microorganisms. This review presents an overview of the recent advances in the microbial catabolism of various herbicides, including phenoxyacetic acid, chlorinated benzoic acid, diphenyl ether, tetra-substituted benzene, sulfonamide, imidazolinone, aryloxyphenoxypropionate, phenylurea, dinitroaniline, s-triazine, chloroacetanilide, organophosphorus, thiocarbamate, trazinone, triketone, pyrimidinylthiobenzoate, benzonitrile, isoxazole and bipyridinium herbicides. This review highlights the microbial resources that are capable of catabolizing these herbicides and the mechanisms involved in the catabolism. Furthermore, the application of herbicide-degrading strains to clean up herbicide-contaminated sites and the construction of genetically modified herbicide-resistant crops are discussed.

Potential effects of Rhodococcus qingshengii strain djl-6 on the bioremediation of carbendazim-contaminated soil and the assembly of its microbiome.

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-1 dry soil) on fungal community were weakened. Network analysis showed that carbendazim increased the connectivity and modularity of microbial co-occurrence networks. Strain djl-6 exhibited good potential for bioremediation of carbendazim-contaminated soils. Moreover, it driven the assembly of potential carbendazim-degrading consortia from indigenous microbial communities; and members of the genera Arthrobacter, Bacillus, Brevundimonas, Lysinibacillus, Massilia, Mycobacterium, Paenibacillus, and Pseudarthrobacter might be participated in the degradation of carbendazim. Taken together, our study provides a relatively comprehensive understanding of the effects of carbendazim and its degrading strain djl-6 on soil microbial communities.

Microbial catabolism of lindane in distinct layers of acidic paddy soils combinedly affected by different water managements and bioremediation strategies.

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.

Shift in Bacterial Community Structure Drives Different Atrazine-Degrading Efficiencies.

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 Arthrobacter sp. strain, AT5, that was capable of degrading atrazine was isolated from enrichment AT. The bacterial community structures of these three enrichments were investigated using high-throughput sequencing analysis of the 16S rRNA gene. The atrazine-degrading efficiency improved as the abundance of Arthrobacter species increased in enrichment ATB. The relative abundance of Arthrobacter was positively correlated with those of Hyphomicrobium and Methylophilus, which enhanced atrazine degradation via promoting the growth of Arthrobacter. Furthermore, six genera/families such as Azospirillum and Halomonas showed a significantly negative correlation with atrazine-degrading efficiency, as they suppressed atrazine degradation directly. These results suggested that atrazine-degrading efficiency was affected by not only the degrader but also some non-degraders in the community. The promotion and suppression of atrazine degradation by Methylophilus and Azospirillum/Halomonas, respectively, were experimentally validated in vitro, showing that shifts in both the composition and abundance in consortia can drive the change in the efficiency of catabolic function. This study provides valuable information for designing enhanced bioremediation strategies.