an-improved-chemotaxis-assay-for-rapid-identification-rhizobacterial

An Improved Chemotaxis Assay for the Rapid Identification of Rhizobacterial Chemoattractants in Root Exudates

Chemotaxis identification is very important for the research and application of rhizosphere growth-promoting bacteria. We established a straightforward ...

Qiqihar University

Heilongjiang Provincial Technology Innovation Center of Agromicrobial Preparation Industrialization

The growth of watermelon is often threatened by Fusarium oxysporum f. sp. niveum (Fon) in successively monocultured soil, which results in economic loss. The objective of this study was to investigate the effect of D123 wheat as a companion crop on soil enzyme activities, microbial biomass and microbial communities in the rhizosphere of watermelon and to explore the relationship between the effect and the incidence of wilt caused by Fon. The results showed that the activities of soil polyphenol oxidase, urease and invertase were increased, the microbial biomass nitrogen (MBN) and microbial biomass phosphorus (MBP) were significantly increased, and the ratio of MBC/MBN was decreased (P < 0.05). Real-time PCR analysis showed that the Fon population declined significantly in the watermelon/wheat companion system compared with the monoculture system (P < 0.05). The analysis of microbial communities showed that the relative abundance of microbial communities was changed in the rhizosphere of watermelon. Compared with the monoculture system, the relative abundances of Alphaproteobacteria, Actinobacteria, Gemmatimonadetes and Sordariomycetes were increased, and the relative abundances of Gammaproteobacteria, Sphingobacteria, Cytophagia, Pezizomycetes, and Eurotiomycetes were decreased in the rhizosphere of watermelon in the watermelon/wheat companion system; importantly, the incidence of Fusarium wilt was also decreased in the watermelon/wheat companion system. In conclusion, this study indicated that D123 wheat as a companion crop increased soil enzyme activities and microbial biomass, decreased the Fon population, and changed the relative abundance of microbial communities in the rhizosphere of watermelon, which may be related to the reduction of Fusarium wilt in the watermelon/wheat companion system. 

The effect of D123 wheat as a companion crop on soil enzyme activities, microbial biomass and microbial communities in the rhizosphere of watermelon.

Dibutyl phthalate (DBP) is well known as a high-priority pollutant. This study explored the impacts of DBP on the metabolic pathways of microbes in black soils in the short term (20 days). The results showed that the microbial communities were changed in black soils with DBP. In nitrogen cycling, the abundances of the genes were elevated by DBP. DBP contamination facilitated 3'-phosphoadenosine-5'-phosphosulfate (PAPS) formation, and the gene flux of sulfate metabolism was increased. The total abundances of ABC transporters and the gene abundances of the monosaccharide-transporting ATPases MalK and MsmK were increased by DBP. The total abundance of two-component system (TCS) genes and the gene abundances of malate dehydrogenase, histidine kinase and citryl-CoA lyase were increased after DBP contamination. The total abundance of phosphotransferase system (PTS) genes and the gene abundances of phosphotransferase, Crr and BglF were raised by DBP. The increased gene abundances of ABC transporters, TCS and PTS could be the reasons for the acceleration of nitrogen, carbon and sulfate metabolism. The degrading-genes of DBP were increased markedly in soil exposed to DBP. In summary, DBP contamination altered the microbial community and enhanced the gene abundances of the carbon, nitrogen and sulfur metabolism in black soils in the short term.

Dibutyl phthalate alters the metabolic pathways of microbes in black soils.

Dimethyl phthalate (DMP) is a ubiquitous pollutant that is very harmful to organisms due to its mutagenicity, teratogenicity and carcinogenicity. Pseudomonas fluorescens (P. fluorescens) is one of the most important bacteria in the environment. In this study, the response of P. fluorescens to DMP was investigated. It was found that DMP greatly inhibited the growth and glucose utilization of P. fluorescens when the concentration of DMP was ranged from 20 to 40 mg/l. The surface hydrophobicity and membrane permeability of P. fluorescens were also increased by DMP. DMP could lead to the deformations of cell membrane and the mis-opening of membrane channels. RNA-Seq and RT-qPCR results showed that the expression of some genes in P. fluorescens were altered, including the genes involved in energy metabolism, ATP-binding cassette (ABC) transporting and two-component systems. Additionally, the productions of lactic acid and pyruvic acid were reduced and the activity of hexokinase was inhibited in P. fluorescens by DMP. Clearly, the results suggested that DMP contamination could alter the biological function of P. fluorescens in the environment.

Response of Pseudomonas fluorescens to dimethyl phthalate.

Phthalic acid esters (PAEs), such as dimethyl phthalate (DMP) and dibutyl phthalate (DBP), are widely distributed as environmental pollutants. In this study, the effects of these chemicals were investigated in black soils using a metagenomics approach. The results clearly showed that DMP or DBP increased the abundance of genes involved in transcription, replication and repair in black soils. In addition, the abundances of genes associated with metabolic functions was improved following treatment with DMP or DBP, including those involved in lipid transport and metabolism, carbohydrate transport and metabolism, and energy production and conversion. There could be many reasons for these observed changes. First, the DMP or DBP treatments increased the abundances of genes associated with the LuxR family, the UvrABC repair system, DNA replication pathways, the RNA polymerase complex and base excision repair. Second, the abundances of genes associated with isocitrate lyase regulator (IclR) family transcriptional regulators, lipid metabolism and carbohydrate active enzymes (CAZys) were altered by the DMP or DBP treatments. Finally, the DMP or DBP treatments also increased the emission load of CO and altered the fluorescence intensity of humic acid. Therefore, the results of this study suggested that DMP and DBP contamination altered the abundances of genes associated with genetic information processing and improved the carbon metabolism in black soils.

Phthalic acid esters disturbed the genetic information processing and improved the carbon metabolism in black soils.

Ubiquitous dimethyl phthalate (DMP) has severely threatened environmental safety and the health of organisms. Therefore, it is necessary to degrade DMP, removing it from the environment. Microbiological degradation is an efficient and safe method for degrading DMP. In this study, the response of Arthrobacter QD 15-4 to DMP was investigated. The results showed that the growth of Arthrobacter QD 15-4 was not impacted by DMP and Arthrobacter QD 15-4 could degrade DMP. RNA-Seq and RT-qPCR results showed that DMP treatment caused some changes in the expression of key genes in Arthrobacter QD 15-4. The transcriptional expressions of pstSCAB and phoU were downregulated by DMP. The transcriptional expressions of potACD, gluBC, oppAB, pdhAB, aceAF, gltA were upregulated by DMP. The genes are mainly involved in regulating energy metabolism and ATP-binding cassette (ABC) transporters. The increasing of pyruvic acid and citrate in Arthrobacter QD 15-4 further supported the energy metabolism was improved by DMP. It was clearly shown that Arthrobacter QD 15-4 made response to dimethyl phthalate by regulating energy metabolism and ABC transporters.

Response of Arthrobacter QD 15-4 to dimethyl phthalate by regulating energy metabolism and ABC transporters.

Dimethyl phthalate (DMP), a phthalate ester (PAE), is a ubiquitous and organic pollutant. In this study, the toxicity of DMP to Escherichia coli K12 and its underlying mechanism were investigated. The results showed that DMP inhibited the growth of E. coli K12 and induced cell inactivation and/or death. DMP caused serious damage to the cell membrane of E. coli K12, and the damage increased with higher DMP concentrations. DMP exposure disrupted cell membranes, as evidenced by dose-dependent variations of cell structures, surface properties, and membrane compositions. Increases in the malondialdehyde (MDA) content indicated an increase in oxidative stress induced by DMP in E. coli K12. The activity of succinic dehydrogenase (SDH) was changed by DMP, which could affect energy metabolism in the membrane of E. coli K12. The expression levels of OmpA and OmpX were increased, and the expression levels of OmpF and OmpW were decreased, in E. coli K12 exposed to DMP. The toxicities of DMP to E. coli K12 could be ascribed to membrane disruption and oxidative stress-induced cell inactivation and/or death. The outcomes will shed new light on the assessment of the ecological effects of DMP.

Dimethyl phthalate damaged the cell membrane of Escherichia coli K12.

Dibutyl phthalate (DBP) is widely used as plasticizer and has been detected in the environment, posing a threat to animal health. However, the effects of DBP on agricultural microbiomes are not known. In this study, DBP levels in black soil were evaluated, and the impact of DBP contamination on the uptake and metabolism of sugars in microbes was assessed by glucose absorption tests, metaproteomics, metabolomics, enzyme activity assays and computational simulation analysis. The results indicated that DBP contamination accelerated glucose consumption and upregulated the expression of porins and periplasmic monosaccharide ATP-binding cassette (ABC) transporter solute-binding proteins (SBPs). DBP and its metabolic intermediates (carboxymuconate and butanol) may form a stable complex with sugar transporters and enhance the rigidity and stability of these proteins. Sugar metabolism resulting in the generation of ATP and reducing agent (NADPH), as well as the expression of some key enzymes (dehydrogenases) were also upregulated by DBP treatment. Moreover, a diverse bacterial community appears to utilize sugar, suggesting that there are widespread effects of DBP contamination on soil microbial ecosystems. The results of this study provide a theoretical basis for investigating the toxicological effects of DBP on microbes in black soil.

Dibutyl phthalate contamination accelerates the uptake and metabolism of sugars by microbes in black soil.

Bacillus methylotrophicus has been demonstrated to promote growth of various plants, whereas the promoting effect of B. methylotrophicus on rice growth has been rarely reported. In this study, B. methylotrophicus DD-1, capable of efficiently promoting the growth of rice, was isolated from the root soil of rice plants. The isolate exhibited potassium-solubilizing (1.18 mg/L), Indole-3-acetic acid (IAA) (87.26 mg/L), Gibberellic acid (GA) (25.91 mg/L) and Siderophore production activity (52.32%). As indicated from the result, plant growth parameters (e.g., dry weight, tiller number, root and shoot length) of rice seedlings treated with the isolate DD-1 were more effective than those of the control group in pot and soilless culture experiments. Moreover, the adsorption capacity of rice roots which were soaked in the bacterial suspension of isolate increased with the increase in concentration and absorption time. In sterilized and unsterilized soil, conformation of root colonization activity by bacterial isolate established by its nearer existence to the rice root. Thus, the B. methylotrophicus DD-1 enhances plant growth promotion by multifarious growth promoting and root colonization traits, thereby augmenting potassium level in soil. Henceforth, the potential bacterium could be exploited for the development of biological fertilizer, leading towards sustainable agronomy.

Isolation and evaluation of the plant growth promoting rhizobacterium Bacillus methylotrophicus (DD-1) for growth enhancement of rice seedling.

Elucidation of the underlying mechanisms of plant growth promotion of rhizobacteria is very important. This study explored the mechanism by which  LZP02 promotes growth in rice roots through proteomic, transcriptomic, and metabolomic techniques. The results showed that  LZP02 promoted the absorption of phosphorous, calcium, and magnesium ions by colonization of rice roots and enhanced peroxidase, catalase, superoxide dismutase, and CaMg adenosine triphosphatase activities and chlorophyll contents in rice. The proteomic results showed that most of the differentially expressed proteins were involved in carbohydrate metabolism and that the biosynthesis of other secondary metabolites was also increased. According to RNA-seq and reverse transcription-quantitative PCR analyses, expression of some genes involved in carbohydrate metabolism and phenylpropanoid biosynthesis was upregulated in rice roots. Regarding metabolomics, phenylpropanoid biosynthesis, starch and sucrose metabolism, the pentose phosphate pathway, and glyoxylate and dicarboxylate metabolism were increased. The results indicated that  LZP02 promoted the growth of rice roots by enhancing carbohydrate metabolism and phenylpropanoid biosynthesis.

 LZP02 Promotes Rice Root Growth by Improving Carbohydrate Metabolism and Phenylpropanoid Biosynthesis.

Myriocin, which is produced by Bacillus amyloliquefaciens LZN01, can inhibit the growth of Fusarium oxysporum f. sp. niveum (Fon). In the present study, the antifungal mechanism of myriocin against Fon was investigated with a focus on the effects of myriocin on the cell membrane. Myriocin decreased the membrane fluidity and destroyed the membrane integrity of Fon. Significant microscopic morphological changes, including conidial shrinkage, the appearance of larger vacuoles and inhomogeneity of electron density, were observed in myriocin-treated cells. A membrane-targeted mechanism of action was also supported by transcriptomic and proteomic analyses; a total of 560 common differentially expressed genes (DEGs) and 285 common differentially expressed proteins (DEPs) were identified. The DEGs were further verified by using RT-qPCR. The combined analysis between the transcriptome and proteome revealed that the expression of some membrane-related genes and proteins, mainly those related to sphingolipid metabolism, glycerophospholipid metabolism, steroid biosynthesis, ABC transporters and protein processing in the endoplasmic reticulum, was disordered. Myriocin affected the serine palmitoyl transferase (SPT) activity as evidenced through molecular docking. Our results indicate that myriocin has significant antifungal activity owing to its ability to induce membrane damage in Fon.

Membrane disruption of Fusarium oxysporum f. sp. niveum induced by myriocin from Bacillus amyloliquefaciens LZN01.

Myriocin is a natural product with antifungal activity and is derived from Bacillus amyloliquefaciens LZN01. Our previous work demonstrated that myriocin can inhibit the growth of Fusarium oxysporum f. sp. niveum (Fon) by inducing membrane damage. In this study, the antifungal actions of myriocin against Fon were investigated with a focus on the effects of myriocin on intracellular molecules.

Comprehensive transcriptomic and proteomic analyses identify intracellular targets for myriocin to induce Fusarium oxysporum f. sp. niveum cell death.

The Bacillus velezensis YYC strain was isolated from the tomato rhizosphere. In a previous experiment, it increased tomato growth and induced systemic resistance against Ralstonia solanacearum. However, information on its genomic content is lacking. The complete genome sequence of the bacterium was described in this study. The genome size was 3,973,236 bp and consisted of 4034 genes in total, with a mean G + C content of 46.52%. In addition, 86 tRNAs and 27 ribosomal RNAs were identified. Fourteen clusters of secondary metabolites were identified. The KEGG database analysis showed that 69 genes were related to quorum sensing, which were important for microbe-plant interaction. In addition, genes involved in promoting plant growth and triggering plant immunity were identified from the genome. Based on digital DNA-DNA hybridizations (dDDH), B. velezensis YYC was most closely related with B. velezensis FZB42. The complete genome data of B. velezensis YYC will provide a basis for explanation of its growth-promoting mechanism and biocontrol mechanism.

Article	Year
The effect of D123 wheat as a companion crop on soil enzyme activities, microbial biomass and microbial communities in the rhizosphere of watermelon. Frontiers in microbiology\| PubMed ID: 26388851	2015
Dibutyl phthalate alters the metabolic pathways of microbes in black soils. Scientific reports\| PubMed ID: 29422490	2018
Response of Pseudomonas fluorescens to dimethyl phthalate. Ecotoxicology and environmental safety\| PubMed ID: 30292974	2019
Phthalic acid esters disturbed the genetic information processing and improved the carbon metabolism in black soils. The Science of the total environment\| PubMed ID: 30408669	2019
Response of Arthrobacter QD 15-4 to dimethyl phthalate by regulating energy metabolism and ABC transporters. Ecotoxicology and environmental safety\| PubMed ID: 30825737	2019
Dimethyl phthalate damaged the cell membrane of Escherichia coli K12. Ecotoxicology and environmental safety\| PubMed ID: 31096126	2019
Dibutyl phthalate contamination accelerates the uptake and metabolism of sugars by microbes in black soil. Environmental pollution (Barking, Essex : 1987)\| PubMed ID: 32182534	2020
Isolation and evaluation of the plant growth promoting rhizobacterium Bacillus methylotrophicus (DD-1) for growth enhancement of rice seedling. Archives of microbiology\| PubMed ID: 32519022	2020
LZP02 Promotes Rice Root Growth by Improving Carbohydrate Metabolism and Phenylpropanoid Biosynthesis. Molecular plant-microbe interactions : MPMI\| PubMed ID: 32597697
Membrane disruption of Fusarium oxysporum f. sp. niveum induced by myriocin from Bacillus amyloliquefaciens LZN01. Microbial biotechnology\| PubMed ID: 32954686	2021
Comprehensive transcriptomic and proteomic analyses identify intracellular targets for myriocin to induce Fusarium oxysporum f. sp. niveum cell death. Microbial cell factories\| PubMed ID: 33731109	2021
Complete genome sequence of Bacillus velezensis YYC, a bacterium isolated from the tomato rhizosphere. Archives of microbiology\| PubMed ID: 34932137	2021

Weihui Xu

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