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Nitrogen (N) and phosphorus (P) have significant effects on soil microbial community diversity, composition, and function. Also, trees of different life stages have different fertilization requirements. In this study, we designed three N additions and three P levels (5 years of experimental treatment) at two Metasequoia glyptostroboides plantations of different ages (young, 6 years old; middle mature, 24 years old) to understand how different addition levels of N and P affect the soil microbiome. Here, the N fertilization of M. glyptostroboides plantation land (5 years of experimental treatment) significantly enriched microbes (e.g., Lysobacter, Luteimonas, and Rhodanobacter) involved in nitrification, denitrification, and P-starvation response regulation, which might further lead to the decreasing in alpha diversity (especially in 6YMP soil). The P addition could impact the genes involved in inorganic P-solubilization and organic P-mineralization by increasing soil AP and TP. Moreover, the functional differences in the soil microbiomes were identified between the 6YMP and 24YMP soil. This study provides valuable information that improves our understanding on the effects of N and P input on the belowground soil microbial community and functional characteristics in plantations of different stand ages.

Overaccumulation of allelochemicals in soil from trees has a negative effect on the growth of Panax notoginseng and cause root rot. Many plant secreted phenols are water-soluble substances that can be depleted by leaching. However, comprehensive understanding of the effect of leaching of phenols in Chinese fir soil on P. notoginseng root rot disease is still lacking. Soil with high level of phenols was leached with five intensities and their effect on the root rot of P. notoginseng was assessed. Then, the relationship of root rot with changes in soil chemical properties and phenol content as well as rhizospheric microorganisms was analyzed. With increasing leaching intensity, the levels of phenols in soils and the incidence of root rot decreased significantly. Decreased phenol content could alleviate root rot by modifying the soil microbial community. Network analysis showed that root rot incidence was positively correlated with the p-hydroxybenzoic acid-enriched pathogenic fungus Ilyonectria but negatively correlated with p-hydroxybenzoic acid (HA)-, ferulic acid (FA)- or vanillic acid (VA)-suppressed bacteria, including Sphingomonas, Lysobacter, Massilia and Burkholderia. Culture experiments confirmed that individual HA, FA and VA as well as a mixture of the five phenols with increasing concentrations could stimulate the growth and sporulation of I. destructans but suppress the growth and biofilm formation of bacteria (Burkholderia and Lysobacter). Moreover, Burkholderia isolates showed antagonistic activity against the growth of I. destructans. Leaching could relieve the stimulation of pathogenic fungi by phenols and reduce the pressure on phenolic-suppressed bacteria, thereby reducing the incidence of root rot disease.

Allyl isothiocyanate (AITC), as a fumigant, plays an important role in soil control of nematodes, soil-borne pathogens, and weeds, but its effects on soil microorganisms are unclear. In this study, the effects of AITC on microbial diversity and community composition of Capsicum annuum L. soil were investigated through Illumina high-throughput sequencing. The results showed that microbial diversity and community structure were significantly influenced by AITC. AITC reduced the diversity of soil bacteria, stimulated the diversity of the soil fungal community, and significantly changed the structure of fungal community. AITC decreased the relative abundance of dominant bacteria Planctomycetes, Acinetobacter, Pseudodeganella, and RB41, but increased that of Lysobacter, Sphingomonas, Pseudomonas, Luteimonas, Pseudoxanthomonas, and Bacillus at the genera level, while for fungi, Trichoderma, Neurospora, and Lasiodiplodia decreased significantly and Aspergillus, Cladosporium, Fusarium, Penicillium, and Saccharomyces were higher than the control. The correlation analysis suggested cellulase had a significant correlation with fungal operational taxonomic units (OTUs) and there was a significant correlation between cellulase and fungal diversity, while catalase, cellulose, sucrase, and urease were the major contributors in the shift of the community structure. Our results will provide useful information for the use of AITC in the assessment of environmental and ecological security.

Lysobacter are new biocontrol agents known for their prolific production of lytic enzymes and bioactive metabolites. L. enzymogenes is a predator of fungi and produces several structurally distinct antimicrobial compounds, such as the antifungal HSAF (heat stable antifungal factor) and analogs. The mechanism by which L. enzymogenes interacts with fungal prey is not well understood. Here, we found that the production of HSAF and analogs in L. enzymogenes OH11 was significantly induced in media supplemented with ground fungal mycelia or chitin. In the OH11 genome, we identified a gene (LeLPMO10A) that was annotated to encode a chitin-binding protein. The stimulation of HSAF and analogs by chitin was diminished when LeLPMO10A was deleted. We expressed the gene in E. coli and demonstrated that purified LeLPMO10A oxidatively cleaved chitin into oligomeric products, including 1,5 δ-lactones and aldonic acids. The results revealed that LeLPMO10A encodes a lytic polysaccharide monooxygenase, which has not been reported in Lysobacter. The metabolite analysis, antifungal assay, and proteomic analysis showed that the antifungal compounds and the chitin-cleaving LeLPMO10A are colocalized in outer membrane vesicles. The enzymatic products that resulted from in vitro LeLPMO10A-cleaved chitin also significantly induced HSAF and analogs in OH11. Scanning electron microscopic analysis indicated that spherical vesicles were formed outside of OH11 cells, and fewer OH11 cells were observed to attach to fungal hyphae when LeLPMO10A was deleted. Together, the study revealed a previously uncharacterized synergistic strategy utilized by the predatory Lysobacter during interaction with fungal prey.

In the soil gammaproteobacterium Lysobacter enzymogenes, a natural fungal predator, the response regulator PilR controls type IV pili (T4P)‐mediated twitching motility as well as synthesis of the heat‐stable antifungal factor (HSAF). Earlier we showed that PilR acts via the second messenger, c‐di‐GMP; however, the mechanism remained unknown. Here, we describe how PilR, c‐di‐GMP signalling, and HSAF synthesis are connected. We screened genes for putative diguanylate cyclases (c‐di‐GMP synthases) and found that PilR binds to the promoter region of lchD and down‐regulates its transcription. The DNA‐binding affinity of PilR, and therefore its repressor function, are enhanced by phosphorylation by its cognate histidine kinase, PilS. The lchD gene product is a diguanylate cyclase, and the decrease in LchD levels shifts the ratio of c‐di‐GMP‐bound and c‐di‐GMP‐free transcription factor Clp, a key activator of the HSAF biosynthesis operon expression. Furthermore, Clp directly interacts with LchD and enhances its diguanylate cyclase activity. Therefore, the PilS–PilR two‐component system activates T4P‐motility while simultaneously decreasing c‐di‐GMP levels and promoting HSAF production via the highly specific LchD–c‐di‐GMP–Clp pathway. Coordinated increase in motility and secretion of the “long‐distance” antifungal weapon HSAF is expected to ensure safer grazing of L. enzymogenes on soil or plant surfaces, unimpeded by fungal competitors, or to facilitate bacterial preying on killed fungal cells. This study uncovered the mechanism of coregulated pili‐based motility and production of an antifungal antibiotic in L. enzymogenes, showcased the expanded range of functions of the PilS–PilR system, and highlighted exquisite specificity in c‐di‐GMP‐mediated circuits., PilR phosphorylation mediated by PilS down‐regulates lchD expression via DNA binding to lower c‐di‐GMP synthesis and thus accumulate c‐di‐GMP‐free Clp, which activates heat‐stable antifungal factor production via DNA binding.

Graphical abstract Lysobacter enzymogenes, a robust bacterial warrior uses a “mobile-attack” antifungal strategy comprised of twitching motility powered by the type IV pilus and antifungal weapons. This strategy is controlled by a “busy” transcription factor Clp via multiple previously uncharacterized mechanisms, including binding with DNA in unique modes, interacting directly or responding to diverse small-molecule chemicals, as well as associating specifically with structurally-distinct proteins., Cyclic AMP receptor protein (CRP) is a well-characterized group of global transcription factors in bacteria. They are known to regulate numerous cellular processes by binding DNA and/or cAMP (a ligand called bacterial second messenger) to control target gene expression. Gram-negative Lysobacter enzymogenes is a soilborne, plant-beneficial bacterium without flagella that can fight against filamentous fungi and oomycete. Driven by the type IV pilus (T4P) system, this bacterium moves to nearby pathogens and uses a “mobile-attack” antifungal strategy to kill them via heat-stable antifungal factor (HSAF) and abundant lyases. This strategy is controlled by a unique “busy” transcription factor Clp, which is a CRP-like protein that is inactivated by binding of c-di-GMP, another ubiquitous second messenger of bacteria. In this review, we summarize the current progress in how Clp initiates a “mobile-attack” strategy through a series of previously uncharacterized mechanisms, including binding to DNA in a unique pattern, directly interacting with or responding to various small molecules, and interacting specifically with proteins adopting distinct structure. Together, these characteristics highlight the multifunctional roles of Clp in L. enzymogenes, a powerful bacterial warrior against fungal pathogens.

A Gram-stain-negative, aerobic, non-motile, non-spore-forming light-yellow-coloured rod-shaped bacterial strain, designated YJ15T, was isolated from soil at Bigeum island in Korea. Growth was observed at 10–37 °C (optimum, 28 °C), at pH 6.0–7.5 (optimum, pH 7.0) and in the absence of NaCl. Based on 16S rRNA gene sequence analysis, strain YJ15T was closely related to ‘Lysobacter tongrenensis’ YS037T (97.8%), Lysobacter pocheonensis Gsoil193T (96.5%) and Lysobacter daecheongensis Dae08T (95.8%) and phylogenetically grouped together with ‘Lysobacter tongrenensis’ YS037T, Lysobacter dokdonensis DS-58T and Lysobacter pocheonensis Gsoil 193T. The DNA–DNA relatedness between strain YJ15T and ‘Lysobacter tongrenensis’ KCTC 52206T was 12% and the phylogenomic analysis based on the whole genome sequence demonstrated that strain YJ20T formed a distinct phyletic line with Lysobacterlter dokdonensis DS-58T showing average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values of 76.3 and 21.3%, respectively. The predominant ubiquinone was identified as Q-8, and polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and two unidentified aminolipids. The major fatty acids were iso-C17:1 ω9c, iso-C15:0, iso-C16:0 and iso-C17:0. The genomic DNA G + C content was 68.2 mol %. On the basis of phenotypic, chemotaxonomic properties and phylogenetic analyses in this study, strain YJ15T is considered to represent a novel species of the genus Lysobacter, for which the name Lysobacter telluris sp. nov. is proposed. The type strain is YJ15T (= KACC 19552T = NBRC 113197T).

Strain HX-5-24T was isolated from the sludge collected from the outlet of the biochemical treatment facility of an agricultural chemical plant in Maanshan city, Anhui province, PR China (118° 28′ N, 31° 47′ E). Cells were observed to be Gram-reaction-negative, rod-shaped, non-motile and aerobic. Strain HX-5-24T shared 99.1% 16S rRNA gene sequence similarity with Lysobacter dokdonensis DS-58T and less than 97% similarities with other type strains. The phylogenetic analysis based on 16S rRNA indicated that strain HX-5-24T belonged to the genus Lysobacter and formed a subclade with L. dokdonensis DS-58T. The average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values between strain HX-5-24T and L. dokdonensis DS-58T were 87.5% and 35.3%, respectively. The genomic DNA G + C content of the strain was 66.4%. The major fatty acids (> 5%) were iso-C15:0, anteiso-C15:0, iso-C16:0, C16:0 and summed feature 9 (iso-C17:1 ω9c and/or C16:0 10-methyl). The predominant quinone was ubiquinone Q-8. The polar lipid profile consisted of diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE), phosphatidylglycerol (PG) and phospholipids (PL). On the basis of phenotypic and phylogenetic evidences, strain HX-5-24T is considered as a novel species in the genus Lysobacter, for which the name Lysobacter gilvus sp. nov. is proposed. The type strain is HX-5-24T (= KCTC 72470T = CCTCC AB 2019228T).

Aims Biological techniques can manage plant diseases safely and in environmentally friendly ways, but their efficacy needs improvement. It is of the utmost importance to search for powerful microbes for the effective control of plant diseases. Methods and results Unheated self-digestive solutions (SDS) that were heated at 100°C for 30 min(H-SDS) or stored for 12 months at room temperature (S-SDS) were prepared from Lysobacter enzymogenes LE16 broth culture to study their potential as biocontrol agents. This bacterium produced protease, phosphatase, lysozyme and siderophores in pure culture as well as 12 secondary metabolites including novel antibiotics lysobactin, WAP-8294A2 and mupirocin determined based on the antiSMASH 5.0.0 blast database. A poison plate assay revealed the antagonistic activities of SDS, H-SDS and S-SDS against an animal pathogenic bacterium Staphylococcus aureus, a phytopathogenic bacterium Pseudomonas syringae pv. tabaci, and numerous plant pathogenic fungi and oomycetes, including Colletotrichum gloeosporioides, Penicillium italicum, Alternaria alternate, Rhizoctonia solani, Didymella bryoniae, Sclerotinia sclerotiorum, Phytophthora nicotianae and Phytophthora capsici. The greenhouse experiment showed that SDS was highly effective in controlling pepper blight disease, which is caused by P. capsici. Compared with only pathogen inoculation, the application of SDS to the soil in preventive or curative treatments significantly reduced the disease incidence and index with relatively high control efficacy of 86·2-93·1%. Conclusions SDS enriched lytic enzymes, siderophores and antibiotics, has a wide antimicrobial spectrum, and shows potential as a new, safe and effective biocontrol agent against plant diseases. Significance and impact of the study Autolysates of the new biocontrol bacterium L. enzymogenes LE16 demonstrated the potential for industrial production and commercial use as a promising biocontrol agent in agriculture.

The Gram-negative gliding bacteria Lysobacter represent a new and rich source for bioactive natural products. In an effort to discover new antibiotics, we found a cryptic biosynthetic gene cluster (BGC) in Lysobacter sp. 3655 that shared a high similarity with the putative lysocin BGC identified in silico previously from Lysobacter sp. RH2180-5. Lysocins are cyclic lipodepsipeptides with potent activity against MRSA (methicillin-resistant Staphylococcus aureus) using a novel mode of action, but the lysocin BGC had not been experimentally verified so far. Using an activity-guided screening, we isolated the main antibiotic compound and confirmed it to be lysocin E. However, the putative lysocin BGC was barely transcribed in the wild type, in which lysocins were produced only in specific conditions and in a negligible amount. To activate the putative lysocin BGC, we screened for strongly transcribed housekeeping genes in strain 3655 and found several powerful promoters. Upon engineering the promoters into the BGC, the lysocin gene transcription was significantly enhanced and the lysocin yield was markedly increased. With readily detectable lysocins production in the engineered strains, we showed that lysocin production was abolished in the gene deletion mutant and then restored in the complementary strain, even when grown in conditions that did not support the wild type for lysocin production. Moreover, the engineered strain produced multiple new lysocin congeners. The determination of the lysocin BGC and the Lysobacter promoters will facilitate the ongoing efforts for yield improvement and new antibiotic biosynthesis using synthetic biology strategies.

A polyphasic taxonomic study was carried out on strains CHu50b-3-2T and CHu40b-3-1 isolated from a 67 cm-long sediment core collected from the Daechung Reservoir at a water depth of 17 m, Daejeon, Republic of Korea. The cells of the strains were Gram-stain-negative, non-spore-forming, non-motile and rod-shaped. Comparative 16S rRNA gene sequence studies showed a clear affiliation of two strains with γ-Proteobacteria, which showed the highest pairwise sequence similarities to Lysobacter hankyongensis KTce-2T (96.5 %), Lysobacter pocheonensis Gsoil193T (96.3 %), Lysobacter ginsengisoli Gsoil 357T (96.1 %), Lysobacter solanacearum T20R-70T (96.1 %), Lysobacter brunescens KCTC 12130T (95.4 %) and Lysobacter capsici YC5194T (95.3 %). The phylogenetic analysis based on 16S rRNA gene sequences showed that the strains formed a clear phylogenetic lineage with the genus Lysobacter . The major fatty acids were identified as summed feature 9 (iso-C17 : 1 ω9c and/or C18 : 1 10-methyl), iso-C15 : 0, iso-C16 : 0 and iso-C17 : 0. The respiratory quinone was identified as ubiquinone Q-8. The major polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and an unidentified phospholipid. The genomic DNA G+C content was determined to be 66.8 mol% (genome) for strain CHu50b-3-2T and 66.4 mol% (HPLC) for strain CHu40b-3-1. Based on the combined genotypic and phenotypic data, we propose that strains CHu50b-3-2T and CHu40b-3-1 represent a novel species of the genus Lysobacter , for which the name Lysobacter profundi sp. nov. is proposed. The type strain is CHu50b-3-2T (=KCTC 72973T=CCTCC AB 2019129T). Besides Lysobacter panaciterrae Gsoil 068T formed a phylogenetic group together with strain Luteimonas aquatica RIB1-20T (EF626688) that is clearly separated from all other known Lysobacter strains. Based on the phylogenetic relationships together with fatty acid compositions, Lysobacter panaciterrae Gsoil 068T should be reclassified as a member of the genus Luteimonas: Luteimonas aquatica comb. nov. (type strain Gsoil 068T=KCTC 12601T=DSM 17927T).

Marigold is reported to have antibacterial activity, and effectively protect crops against soil-borne diseases. However, it is not known whether and how tobacco bacterial wilt (TBW) could be mitigated via intercropping with marigold under field conditions. In this study, a field experiment was performed to measure and compare the occurrence of TBW, the soil chemical properties, and soil microbial composition and diversity between a tobacco-marigold intercropping system and a tobacco monocropping system. At 100 days (d) post-transplantation, the incidence (I) and disease index (DI) for the tobacco-marigold intercropping system were 30.12% and 58.25% lower than that for tobacco monocropping system, respectively. The results showed that Sobs, Shannon and Chao 1 index of soil bacterial communities in the tobacco-marigold intercropping system were 10.34%, 1.41% and 5.13% higher than that in the tobacco monocropping system at 100 d post-transplantation, respectively. It exhibited a higher richness and diversity of soil bacterial communities in the tobacco-marigold intercropping system. The relative abundance of some beneficial genera in tobacco-marigold intercropping system, such as Lysobacter, Burkholderia, Trichoderma, Mortierella, Chaetomium, Penicillium, was 1.50, 1.61, 3.35, 1.67, 4.40 and 4.50 fold higher than that in tobacco monocropping system. The presence of the intercropping system inhibited soil acidification and loss of soil calcium ions. The redundancy analysis (RDA) indicated that soil pH and exchange Ca2+ were the main environmental factors which seemed to influence the bacterial and fungal community. The results from this study provided valuable insight into the possible mechanisms enhancing soil health in the tobacco-marigold intercropping system.

An aerobic and Gram-stain-negative bacterial strain, designated UKS-15T, was isolated from lake water in the Republic of Korea. Results of 16S rRNA gene sequence and phylogenetic analyses indicated that the novel isolate belongs to the genus Lysobacter and was most closely related to Lysobacter xinjiangensis RCML-52T (98.0 %), Lysobacter mobilis 9 NM-14T (97.4 %) and Lysobacter humi FJY8T (97.2 %). The DNA G+C content was 69.1 mol%. Strain UKS-15T possessed ubiquinone-8 (Q-8) as the sole respiratory quinone and the fatty acid profile comprised iso-C15 : 0, iso-C17 : 0 and summed feature 9 (iso-C17 : 1 ω9c and/or C16 : 0 10-methyl) as its major components. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and one unidentified aminophospholipid. Moreover, the physiological and biochemical results and low level of DNA–DNA relatedness (T from other Lysobacter species. Therefore, on the basis of the data from this polyphasic taxonomic study, strain UKS-15T should represent a novel species of the genus Lysobacter , for which the name Lysobacter lacus sp. nov. is proposed. The type strain is UKS-15T (=JCM 30983T=KACC 18719T).

Biotreatment of triclosan is mainly performed in conventional activated sludge systems, which, however, are not capable of completely removing this antibacterial agent. As a consequence, triclosan ends up in surface and groundwater, constituting an environmental threat, due to its toxicity to aquatic life. However, little is known regarding the diversity and mechanism of action of microbiota capable of degrading triclosan. In this work, an immobilized cell bioreactor was setup to treat triclosan-rich wastewater. Bioreactor operation resulted in high triclosan removal efficiency, even greater than 99.5%. Nitrogen assimilation was mainly occurred in immobilized biomass, although nitrification was inhibited. Based on Illumina sequencing, Bradyrhizobiaceae, followed by Ferruginibacter, Thermomonas, Lysobacter and Gordonia, were the dominant genera in the bioreactor, representing 38.40 ± 0.62% of the total reads. However, a broad number of taxa (15 genera), mainly members of Xanthomonadaceae, Bradyrhizobiaceae and Chitinophagaceae, showed relative abundances between 1% and 3%. Liquid Chromatography coupled to Quadrupole Time-Of-Flight Mass Spectrometry (LC-QTOF-MS) resulted in the identification of catabolic routes of triclosan in the immobilized cell bioreactor. Seven intermediates of triclosan were detected, with 2,4-dichlorophenol, 4-chlorocatechol and 2-chlorohydroquinone being the key breakdown products of triclosan. Thus, the immobilized cell bioreactor accommodated a diverse bacterial community capable of degrading triclosan.

Fusarium wilt is an important disease of many food crops and often causes serious damages to yield and food quality. Consequently, numerous studies mainly focused on exploring the control strategy for Fusarium oxysporum as well as the mechanism of interaction between the F. oxysporum and other beneficial soil microorganisms. In this study, we have screened and identified an efficient biocontrol strain from the soil with infection of F. oxysporum f. sp. momordica (referred to as Fom), Talaromyces purpurogenus Q2 (referred to as TpQ2), which could be effective to reduce relative abundance of the rhizospheric Fom, leading to a significant decrease of Fusarium wilt disease incidence in bitter gourd during the greenhouse and field trails. TpQ2 can reduce the relative abundance of rhizospheric Fom through inhibition of growth and development of Fom. During the co-cultivation of TpQ2 and Fom, we confirmed that TpQ2 could significantly suppress the growth and development of Fom through disturbing the normal hyphae shape and function of the cell walls of Fom via secreting cell wall–degrading enzymes and suppression of the expression of cell wall biosynthesis genes, such as FomCFEM. In the meantime, TpQ2 showed a strong negative correlation with F. oxysporum in soil and positive correlation with beneficial indigenous microorganisms that had significant negative correlation with Fusarium populations, such as Streptomycetes, Lysobacter, and Sphingobium. To summarize, TpQ2 has a good biocontrol efficacy on Fusarium wilt of bitter gourd. The biocontrol mechanisms of TpQ2 on Fusarium wilt are complex and diverse.

Determining the mode of action of microbial biocontrol agents plays a key role in their development and registration as commercial biopesticides. The biocontrol rhizobacteriumLysobacter capsiciAZ78 (AZ78) is able to inhibit a vast array of plant pathogenic oomycetes and Gram-positive bacteria due to the release of antimicrobial secondary metabolites. A combination of MALDI-qTOF-MSI and UHPLC-HRMS/M was applied to finely dissect the AZ78 metabolome and identify the main secondary metabolites involved in the inhibition of plant pathogenic microorganisms. Under nutritionally limited conditions, MALDI-qTOF-MSI revealed that AZ78 is able to release a relevant number of antimicrobial secondary metabolites belonging to the families of 2,5-diketopiperazines, cyclic lipodepsipeptides, macrolactones and macrolides. In vitro tests confirmed the presence of secondary metabolites toxic againstPythium ultimumandRhodococcus fasciansin AZ78 cell-free extracts. Subsequently, UHPLC-HRMS/MS was used to confirm the results achieved with MALDI-qTOF-MSI and investigate for further putative antimicrobial secondary metabolites known to be produced byLysobacterspp. This technique confirmed the presence of several 2,5-diketopiperazines in AZ78 cell-free extracts and provided the first evidence of the production of the cyclic depsipeptide WAP-8294A2 in a member ofL. capsicispecies. Moreover, UHPLC-HRMS/MS confirmed the presence of dihydromaltophilin/Heat Stable Antifungal Factor (HSAF) in AZ78 cell-free extracts. Due to the production of HSAF by AZ78, cell-free supernatants were effective in controllingPlasmopara viticolaon grapevine leaf disks after exposure to high temperatures. Overall, our work determined the main secondary metabolites involved in the biocontrol activity of AZ78 against plant pathogenic oomycetes and Gram-positive bacteria. These results might be useful for the future development of this bacterial strain as the active ingredient of a microbial biopesticide that might contribute to a reduction in the chemical input in agriculture.

BACKGROUND Nitrous oxide (N2 O) is a potent greenhouse gas depleting the stratospheric ozone. Previous studies reported that the thiocyanate (TC) excretion in the urine of cattle fed rapeseed meals containing glucosinolates was positively correlated with the N2 O-nitrogen (N) emissions. The objectives of the experiment were to verify the effects and the mechanism of TC on the N2 O-N emissions from the soil applied with artificial urine using static incubation technique. Four levels of TC, that is 0.00, 0.26, 0.78 and 2.33 mmol L-1 were composited in artificial urine as experimental treatments. Soil inorganic N and bacterial community were analyzed to elucidate the effects of TC on the N2 O-N emissions of artificial urine. RESULTS Adding TC increased the N2 O-N fluxes, the N2 O-N to N application ratio, and the estimated N2 O-N emissions from the soil applied with artificial urine both linearly and quadratically. The estimated N2 O-N emission (Y, in μmol) was increased with the TC adding level (X, in μmol) in a quadratic manner: Y=52.57+4.47X-0.123X2 (R 2 = 0.70). Adding TC did not affect the soil bacterial diversity and richness, but increased the relative abundances of Nitrosomonas (both for nitrification and denitrification) and Hyphomicrobium, Lysobacter and Terrimonas (for denitrification), and tended to increase the relative abundances of denitrification and dissimilatory nitrate reduction to ammonium. CONCLUSION TC increased the N2 O-N emissions of the soil applied with artificial urine possibly through enhancing the denitrification of nitrifiers in the soil. Field experiments are necessary to verify the laboratory results. © 2021 Society of Chemical Industry.

The rhizosphere is a dynamic region governed by complex microbial interactions where diffusible communication signals produced by bacteria continuously shape the gene expression patterns of individual species and regulate fundamental traits for adaptation to the rhizosphere environment. Lysobacter spp. are common bacterial inhabitants of the rhizosphere and have been frequently associated with soil disease suppressiveness. However, little is known about their ecology and how diffusible communication signals might affect their behavior in the rhizosphere. To shed light on the aspects determining rhizosphere competence and functioning of Lysobacter spp., we carried out a functional and transcriptome analysis on the plant beneficial bacterium Lysobacter capsici AZ78 (AZ78) grown in the presence of the most common diffusible communication signals released by rhizosphere bacteria. Mining the genome of AZ78 and other Lysobacter spp. showed that Lysobacter spp. share genes involved in the production and perception of diffusible signal factors, indole, diffusible factors, and N-acyl-homoserine lactones. Most of the tested diffusible communication signals (i.e., indole and glyoxylic acid) influenced the ability of AZ78 to inhibit the growth of the phytopathogenic oomycete Pythium ultimum and the Gram-positive bacterium Rhodococcus fascians. Moreover, RNA-Seq analysis revealed that nearly 21% of all genes in AZ78 genome were modulated by diffusible communication signals. 13-Methyltetradecanoic acid, glyoxylic acid, and 2,3-butanedione positively influenced the expression of genes related to type IV pilus, which might enable AZ78 to rapidly colonize the rhizosphere. Moreover, glyoxylic acid and 2,3-butanedione downregulated tRNA genes, possibly as a result of the elicitation of biological stress responses. On its behalf, indole downregulated genes related to type IV pilus and the heat-stable antifungal factor, which might result in impairment of twitching motility and antibiotic production in AZ78. These results show that diffusible communication signals may affect the ecology of Lysobacter spp. in the rhizosphere and suggest that diffusible communication signals might be used to foster rhizosphere colonization and functioning of plant beneficial bacteria belonging to the genus Lysobacter.

Heat-stable antifungal factor (HSAF) is a broad-spectrum antifungal antibiotic produced by the biological control agent, Lysobacter enzymogenes. In our earlier works, we have applied HSAF to effectively control wheat and pear fungal disease. However, a major bottleneck in its practical application is the low HSAF production level; therefore, boosting its production is essential for its wide application. In the past, we find that c-di-GMP, a universal bacterial second messenger, is inhibitory to HSAF production. In this work, we further identified eight active diguanylate cyclases (DGCs) responsible for c-di-GMP synthesis in Lysobacter enzymogenes via both bioinformatics and genetic analyses. We generated a strain lacking seven active DGC genes and found that this DGC-modified strain, OH11LC, produced a higher HSAF amount in a c-di-GMP concentration-dependent manner. Subsequently, by employing OH11LC as the host fermentation strain, we could even produce a much higher HSAF amount (> 200-fold). After improving the HSAF production, we further developed a technique of seed coating method with HSAF, which turned out to be effective in fighting against the maize seed-borne filamentous pathogen, Pythium gramineacola. Overall, via combining strain modification and fermentation optimization, we demonstrated a good example of translating fundamental knowledge of bacterial c-di-GMP signaling into biological control application in which we relieved the inhibitory effect of c-di-GMP on HSAF biosynthesis by deleting a bunch of potentially active L. enzymogenes DGC genes to improve HSAF yield and to expand its usage in antifungal seed coating.

A novel proteobacterial strain designated SYSU H10001T was isolated from a soil sample collected from plateau meadow in Hongyuan county, Sichuan province, south-western China. The taxonomic position of the strain was investigated using a polyphasic approach. On the basis of 16S rRNA gene sequence similarities and phylogenetic analysis, strain SYSU H10001T was most closely related to Lysobacter soli KCTC 22011T (98.6%, sequence similarity) and Lysobacter panacisoli JCM 19212T (98.2%). The prediction result of secondary metabolites based on genome shown that the strain SYSU H10001T contained 3 clusters of bacteriocins, 1 cluster of non-ribosomal peptide synthetase, 1 cluster of type 1 polyketide synthase and 1 cluster of arylpolyene. In addition, the major isoprenoid quinone was Q-8 and the major fatty acids were identified as iso-C15:0, iso-C17:0 and Summed feature 9. The polar lipids contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, and three unidentified phospholipids. The genomic DNA G + C content of strain SYSU H10001T was 66.5% (genome). On the basis of phenotypic, genotypic and phylogenetic data, strain SYSU H10001T represents a novel species of the genus Lysobacter, for which the name Lysobacter prati sp. nov. is proposed. The type strain is SYSU H10001T (= KCTC 72062T = CGMCC 1.16662T).

Colletotrichum capsici and Fusarium oxysporum are pathogenic fungi that cause anthracnose disease on chili plants (Capsicum annum L.) which can decrease the productivity of chili. The control of the fungus attack is carried out by biocontrol agent of the fungi utilizing chitinase-producing bacteria. Chitinase is an enzyme capable of destroying the fungal cell wall composed of chitin compounds. The aims of the research were to select and to characterize chitinase producing bacteria as biological control agent of Colletotrichum capsici and Fusarium oxysporum. Several methods were carried out in this research, among others: isolation of chitinase bacteria, characterization of chitinase bacteria, measurement of enzyme activity, bacterial antagonistic with pathogenic fungi, observation of fungal hypha damage, and identification of 16S rRNA. The BAE36 and BAD211 isolates are chitinase bacteria isolated from chili plant rhizosphere. The isolate belongs to the Gram-negative bacteria. The inhibitory properties of BAE36 and BAD211 against F. oxysporum and C. capsici are on a scale of 3 (51-75%). The percentage of inhibitory of BAE36 isolate was 66.1% capable of inhibiting the growth of C. capsici and 55% capable of inhibiting the growth of F. oxysporum. The hyphae of C. capsici fungus on the antagonistic test showed a thick and the surface of the hyphae was wavy while the F. oxysporum hyphae was thin and looks empty. Identification of isolate with 16S rRNA described that 99% of BAE36 and BAD211 isolates were similar to Lysobacter enzymogenes. Precipitation of chitinase enzyme of Lysobacter enzymogenes with 30% ammonium sulphate could increase the enzyme activity. The enzyme precipitation could inhibit the growth of mycelia fungi C. capsici and F. oxysporum. Keywords: chili, chitinolytic, Gram-negative, Lysobacter

Discovery of multidrug resistance (MDR) in environmental microorganisms provides unique resources for uncovering antibiotic resistomes, which could be vital to predict future emergence of MDR pathogens. Our previous studies indicated that Lysobacter sp. conferred intrinsic resistance to multiple antibiotics at high levels, especially ampicillin, the first broad-spectrum β-lactam antibiotics against both Gram-positive and Gram-negative bacteria. However, the underlying molecular mechanisms for resistance to ampicillin in Lysobacter enzymogenes strain C3 (LeC3) remain unknown. In this study, screening a Tn5 transposon mutant library of LeC3 recovered 12 mutants with decreased ampicillin resistance, and three mutants (i.e., tatC, lebla, and lpp) were selected for further characterization. Our results revealed that genes encoding β-lactamase (lebla) and twin-arginine translocation (tatC) system for β-lactamase transport played a pivotal role in conferring ampicillin resistance in L. enzymogenes. It was also demonstrated that the lpp gene was not only involved in resistance against β-lactams but also conferred resistance to multiple antibiotics in L. enzymogenes. Permeability assay results indicated that decreased MDR in the lpp mutant was in part due to its higher cellular permeability. Furthermore, our results showed that the difference of LeC3 and L. antibioticus strain LaATCC29479 in ampicillin susceptibility was partly due to their differences in cellular permeability, but not due to β-lactamase activities.

Plant communities growing in metal-contaminated areas can develop resistance mechanisms by establishing symbiotic associations with endophytic microorganisms. The functionality and diversity of endophytic communities depend on the amount and type of metal present in the soil. To characterise the response of endophytic bacterial communities to mercury-induced abiotic stress, we analysed the colonization frequency and number of bacterial isolates in the roots of Aeschynomene fluminensis (Joint Vetch) and Polygonum acuminatum (Smartweed), which represent the families Fabaceae and Polygonaceae, respectively. These two plant species are found in many mercury-contaminated areas. The isolates were characterised by morpho- and genotyping and identified by 16S rDNA gene sequencing. The bacteria belonged to the phyla Actinobacteria, Bacteriodetes, Firmicutes, and Proteobacteria. The Hill series and Venn diagram provided evidence that mercury affects the composition, diversity, and richness of the endophytic bacterial communities. Inoculation with Bacillus_sp_BacI34, Burkholderia_sp_BacI45, Enterobacter_sp_BacI14, Enterobacter_sp_BacI26, Enterobacter_sp_BacI18, Klebsiella_pneumoniae_BacI20, Lysobacter_soli_BacI39, Pantoea_sp_BacI16, and Pantoea_sp_BacI23 promoted the growth of corn (Zea mays) plants in mercury-supplemented substrata. It is noteworthy that Pantoea sp_BacI23 increased the host plant length (root and shoot) by 117.09 ± 0.28%. Endophytic bacterial strains may well provide important inoculants for plant growth promotion on metal-contaminated sites and in metal bioremediation programs.

Lysobacter are ubiquitous in the environment but remain largely underexplored, although the bacteria are considered "peptide specialists". Here, we identified a new cyclic lipodepsipeptide, WBP-29479A1 (1), through genome mining of L. antibioticus ATCC 29479. 1 is biosynthesized by a large NRPS gene cluster, and its structure, including the six nonproteinogenic residues and 3-hydroxy fatty acid, was determined by extensive spectroscopic analyses and chemical derivatization. 1 exhibits potent anti-MRSA activity in a menaquinone-dependent manner.

A novel bacterial strain, designated KVB24T, was isolated from sea-water of Busan Harbour in South Korea. Cells of strain KVB24T were Gram-stain negative, aerobic, rod shaped and non-motile. Strain KVB24T grew optimally at 25–28 °C and pH 6.5–7.0. Based on 16S rRNA gene sequence analysis, strain KVB24T was shown to belong to the genus Lysobacter within the class Gammaproteobacteria and to be closely related to Lysobacter dokdonensis DS-58T, Lysobacter hankyongensis KTce-2T and Lysobacter niastensis GH41-7T. DNA–DNA relatedness between strain KVB24T and its current closest relative was below 70%. The predominant fatty acids of strain KVB24T were iso-C11:0, iso-C11:0 3-OH, iso-C14:0, iso-C15:0, anteiso-C15:0, iso-C16:0 and summed feature 9 comprising (iso-C17:1 ω9c and/or 10 methyl C16:0); the prominent isoprenoid was Q-8 and the major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The G + C content of genomic DNA from strain KVB24T was determined to be 67.5 mol%. Based on the phenotypic, genotypic and chemotaxonomic analyses, strain KVB24T represents a novel species of the genus Lysobacter, for which the name Lysobacter caseinilyticus sp. nov. is proposed. The type strain is KVB24T (= KACC19816T = JCM32879T).

Plant growth-promoting rhizobacteria (PGPR) substantially improve plant growth and health, but their effects on the succession of rhizosphere microbiota throughout the growth period triggered by pre-inoculation have not yet been considered. Pepper seedlings cultured from a bio-nursery substrate containing Bacillus velezensis NJAU-Z9 and ordinary nursery substrate were used in this study to evaluate the effects of pre-colonization of a PGPR strain at the seedling stage on yield enhancement. To elucidate the underlying mechanisms involved in the rhizosphere microbiota succession during the whole growth period and their association with yield enhancement, high-throughput sequencing combined with qPCR was conducted. The results showed that, compared to the control without inoculation, pre-inoculation led to a steady yield enhancement in two-season field trials, as well as higher rhizosphere bacterial richness (Chao1) and diversity (Shannon-Wiener). The plant growth stage as the first driving factor, followed by pre-colonization drove the variations of the rhizosphere microbial community composition according to multivariate regression tree analysis and principal coordinate analysis. Variance partitioning analysis (VPA) and Mantel test results showed that the previous plant growth period induced variations in the fungal and bacterial communities at the next stage. Compared to the seedling and flowering stages, the mature-stage microbial community showed a higher degree of explanation of yield enhancement. Additionally, pre-inoculation led to distinctive rhizosphere microbiota succession compared to the control, due to alteration of the initial community. The heat map analysis showed that the rhizosphere microbiota was related to crop yield. In addition to Bacillus velezensis NJAU-Z9, which showed stable abundance in the pepper rhizosphere, stable higher relative abundance of the bacterial genera Sphingomonas, Sphingopyxis, Bradyrhizobium, Chitinophaga, Dyadobacter, Streptomyces, Lysobacter, Pseudomonas and Rhizomicrobium, and the fungal genera Cladorrhinum, Cladosporium and Aspergillus throughout the growth period induced by pre-colonization was associated with yield enhancement. Overall, we conclude that pre-colonization with PGPR changed the initial rhizosphere microbiota and that the plant was triggered to further select distinctive microbes to form unique rhizosphere microbial consortia at the later growth stages, which resulted in plant growth promotion.

The aim of the present study was to prove the long-term efficiency of the amendments zerovalent iron grit, zeolite, and Divergan® for trace metal remediation in heavily contaminated soils and to attain a recovery of microbial functionality and diversity by remediation. For immobilization of the trace metals the amendments zerovalent iron grit, natural zeolite, and Divergan® were used. Trace metal total and mobile contents were determined and bacterial communities were assessed after a SIP experiment with 13C-labelled wheat root by Ion-Torrent Sequencing targeting the bacterial 16S rRNA gene and two trace metal resistant genes for copper and cadmium (copA and czcA gene). The results show that the remediation effect of the three amendments is still stable after five years. The mobile trace metal contents were significantly (≤0.001) reduced in all treatments, except the Cu content in the zeolite treatment. A higher diversity in active metabolizing and growing soil bacteria was observed in remediated soils as compared to the non-remediated control, especially for the Divergan® treatment. The bacterial genera Kribbella, Glycomyces, Inquilinus, Nocardioides, and Lysobacter are the most significantly enriched genera in the 13C fractions of the treated samples. The occurrence of bacterial families, which could be identified carrying efflux-mediated metal resistance genes for Cd/Zn and Cu, were reduced in the remediated soils as compared to the non-remediated control. The most abundant bacterial family for the copA and the czcA gene is Xanthomonadaceae. The pH-value and the trace metal concentration could be identified as key drivers of bacterial community composition, and functions in trace metal contaminated soils and remediated soils.

Two bacterial strains, designated D10T and U8T, were isolated from soil samples from the Dong-angyeong cave and Geommeolle wharf sea-coast, Udo-Island, Jeju, South Korea. Both novel bacterial strains are yellow-pigmented, Gram-stain negative, motile by means of monotrichous flagella, short rod shaped and strictly aerobic. A phylogenetic tree was reconstructed based on their 16S rRNA gene sequences, which indicated that these two strains belong to the genus Lysobacter within the family Xanthomonadaceae. Strain D10T showed high 16S rRNA gene sequence similarities with Lysobacter humi FJY8T (99.0%), Lysobacter xinjiangensis RCML-52T (98.9%) and Lysobacter mobilis 9NM-14T (97.2%), whereas strain U8T showed high sequence similarities to L. mobilis 9NM-14T (97.9%), L. xinjiangensis RCML-52T (97.8%), L. humi FJY8T (97.5%) and Lysobacter bugurensis ZLD-29T (97.1%). The 16S rRNA gene sequence similarity between D10T and U8T was 97.0%. Strain D10T showed low DNA–DNA relatedness to U8T (57.7 ± 3.4%), L. humi FJY8T (48.8 ± 4.3%), L. xinjiangensis RCML-52T (60.1 ± 2.4%) and L. mobilis 9NM-14T (55.9 ± 1.9%). The level of DNA–DNA relatedness for strain U8T with respect to D10T, L. mobilis 9NM-14T, L. xinjiangensis RCML-52T, L. humi FJY8T, and L. bugurensis ZLD-29T was 55.5 ± 0.5%, 54.5 ± 2.1%, 58.1 ± 0.8%, and 51.9 ± 3.4%, respectively. The major polar lipids for both strains were identified as diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol. The major cellular fatty acids for both strains were identified as iso-C15:0, iso-C16:0 and summed feature 9 (iso-C17:1 ω9c/C16:0 10-methyl), and ubiquinone (Q-8) as the only isoprenoid quinone for both strains. The DNA G + C contents of the strains D10T and U8T were determined to be 70.2 mol% and 70.6 mol%. On the basis of phenotypic, genotypic, chemotaxonomic, and phylogenetic analysis, both strains D10T and U8T represent a novel species in the genus Lysobacter, for which the names Lysobacter helvus sp. nov. and Lysobacter xanthus sp. nov. are proposed, respectively. The type strain of L. helvus is D10T (= KCTC 62111T = JCM 32364T) and the type strain of L. xanthus is U8T (= KCTC 62112T = JCM 32365T).

The impact of the heavy metal contamination and acidity on the bacterial community was studied in samples collected from the Akhtala copper mine tailing using molecular approaches. The bacterial community structure analysis by PCR-DGGE fingerprinting revealed an abundance of Firmicutes, Acidobacteria, and Proteobacteria in different layers of the Akhtala tailing. 454 pyrotag sequence analyses revealed that a significant part of the sequences originated from Proteobacteria (49%) and Bacteroidetes (43%). Bacterial taxa are distributed also in phyla Saccharibacteria (2%), Verrucomicrobia (1.5%), Gammatimonadetes (1%), and some minor additional bacterial groups. The main primary producers in the Akhtala tailing appear to be obligate autotrophic Thiobacillus and Sulfuritalea species. Representatives of Lutibacter and Lysobacter genera are the most abundant acid-tolerant heterotrophs in the studied tailing. The presence of a large number of yet-uncultivated species emphasizes the importance of the future exploration of the tailing as an important source of novel bacteria.

Colletotrichum fructicola, a fungal pathogen that causes bitter rot disease in pears, has recently emerged in Eastern Asia and caused enormous economic losses and crop penalties. For this reason, new strategies for the management of bitter rot disease are greatly needed and can have a great impact on the field. In this regard, our research group recently reported that p-aminobenzoic acid (pABA), which was found in the secretions of rhizobacterium Lysobacter antibioticus OH13, showed a broad spectrum of antifungal activities. Following this project, the antifungal mode of action of pABA has been elucidated in this work indicating that pABA affects the fungal cell cycle of C. fructicola by inhibiting septation during cell division. pABA stability and diffusion screening revealed that pABA degrades after 15 days and is able to cross the pear skin into the external parts of the mesocarp. In vivo studies demonstrated that pABA shows high curative ability against the infection of C. fructicola in pears. To show the efficacy of OH13 for the biocontrol of bitter rot disease, cultures of OH13 containing 379.4 mg/L pABA were sprayed on inoculated pears, significantly reducing the symptoms of the pathogen.

Lysobacter species produce lysobactin, a depsipeptide antibiotic that is effective against methicillin-resistant Staphylococcus aureus and vancomycin-resistant Staphylococcus aureus . Here, we report complete genome sequences of two Lysobacter strains, which were isolated from seawater ( Lysobacter caseinilyticus ) and soil ( Lysobacter helvus ) in South Korea.

The present study aimed to isolate and identify root endophytic bacteria with multifunctional plant growth promoting (PGP) traits from medicinal plant Rosmarinus officinalis grown in the North-Western Himalayas. A total of 42 strains were isolated, exhibiting variable degrees of PGP traits, including phosphate solubilization (10-375 µg/mL), indole-3-acetic acid (6-66 µg/mL), siderophore (32.37%-301.48% SU) production and antifungal activity in terms of percent growth inhibition (% GI) against Fusarium oxysporum (44.44%-77.77% GI), Fusarium graminearum (48.88%-71.42% GI) and Rhizoctonia solani (44.44%-77.7% GI). The 16S rDNA sequencing results showed lineage of these strains to 15 genera viz., Aneurinibacillus, Bacillus, Beijerinckia, Cedecea, Ensifer, Enterobacter, Kosakonia, Lactobacillus, Lysobacter, Oxynema, Pseudomonas, Pantoea, Paenibacillus, Pseudoxanthomonas and Serratia. Out of 42 strains, 11 potential strains were selected for in vivo growth studies of R. officinalis. The results showed that the inoculation of Bacillus subtilis KU21, Pseudomonas aeruginosa SI12, and Cedecea lapagei KU14 significantly increased the physical growth parameters of plant over uninoculated control viz., number of lateral of branches (43.95%-46.39%), stem height (29.04%-38.57%), root length (32.31%-37.14%), shoot (34.76%-40.91%) and root biomass (62.89%-70.70%). Physiological characteristics such as total chlorophyll (30.41%-30.96%), phenol (14.43%-24.55%) and carotenoids (34.26%-39.87%) content, also showed a relative increase as compared to uninoculated control; furthermore, the macronutrients (NPK) contents of the plant as well as soil also showed an increase. The developed module may be recommended for sustainable production of R. officinalis in the North-Western Himalayan region without hampering the soil health and fertility.

Bacteria interact with fungi in a variety of ways to inhibit fungal growth, while the underlying mechanisms remain only partially characterized. The plant-beneficial Bacillus and Pseudomonas species are well-known antifungal biocontrol agents, whereas Lysobacter are far less studied. Members of Lysobacter are easy to grow in fermenters and are safe to humans, animals and plants. These environmentally ubiquitous bacteria use a diverse arsenal of weapons to prey on other microorganisms, including fungi and oomycetes. The small molecular toxins secreted by Lysobacter represent long-range weapons effective against filamentous fungi. The secreted hydrolytic enzymes act as intermediate-range weapons against non-filamentous fungi. The contact-dependent killing devices are proposed to work as short-range weapons. We describe here the structure, biosynthetic pathway, action mode and applications of one of the best-characterized long-range weapons, the heat-stable antifungal factor (HSAF) produced by Lysobacter enzymogenes. We discuss how the flagellar type III secretion system has evolved into an enzyme secretion machine for the intermediate-range antifungal weapons. We highlight an intricate mechanism coordinating the production of the long-range weapon, HSAF and the proposed contact-dependent killing device, type VI secretion system. We also overview the regulatory mechanisms of HSAF production involving specific transcription factors and the bacterial second messenger c-di-GMP.

Background Angelica sinensis (Oliv.) Diels (A. sinensis) is a Chinese herb grown in different geographical locations. It contains numerous active components with therapeutic value. Rhizosphere microbiomes affect various aspects of plant performance, such as nutrient acquisition, growth and development and plant diseases resistance. So far, few studies have investigated how the microbiome effects level of active components of A. sinensis. This study investigated whether changes in rhizosphere microbial communities and metabolites of A. sinensis vary with the soil microenvironment. Soils from the two main A. sinensis-producing areas, Gansu and Yunnan Province, were used to conduct pot experiments. The soil samples were divided into two parts, one part was sterilized and the other was unsterilized planting with the seedling variety of Gansu danggui 90–01. All seedlings were allowed to grow for 180 days. At the end of the experiment, radix A. sinensis were collected and used to characterize growth targets and chemical compositions. Rhizosphere soils were subjected to microbial analyses. Results Changes in metabolic profiles and rhizosphere microbial communities of A. sinensis grown under different soil microenvironments were similar. The GN (Gansu non-sterilized), YN (Yunnan non-sterilized), GS (Gansu sterilized), and YS (Yunnan sterilized) groups were significantly separated. Notably, antagonistic bacteria such as Sphingomonas, Pseudomonas, Lysobacter, Pseudoxanthomonas, etc. were significantly (p Pseudomonas parafulva; organic acids (including chlorogenic acid, dicaffeoylquinic acid and 5-feruloylquinic acid) and their ester coniferyl ferulate which were enriched in YS Group were positively associated with Gemmatimonadetes bacterium WY71 and Mucilaginibater sp., respectively. Conclusions The soil microenvironment influences growth and level/type of active components in A. sinensis. Further studies should explore the functional features of quality-related bacteria, identify the key response genes and clarify the interactions between genes and soil environments. This will reveal the mechanisms that determine the quality formation of genuine A. sinensis.

A Ciboria sp. strain (Phylum Ascomycota) was isolated from hydrocarbon-polluted soil of an abandoned oil refinery in Italy. The strain was able to utilize diesel oil as a sole carbon source for growth. Laboratory-scale experiments were designed to evaluate the use of this fungal strain for treatment of the polluted soil. The concentration of total petroleum hydrocarbons (TPH) in the soil was 8,538 mg/kg. Mesocosms containing the contaminated soil were inoculated with the fungal strain at 1 or 7%, on a fresh weight base ratio. After 90 days of incubation, the depletion of TPH contamination was of 78% with the 1% inoculant, and 99% with the 7% inoculant. 16S rDNA and ITS metabarcoding of the bacterial and fungal communities was performed in order to evaluate the potential synergism between fungi and bacteria in the bioremediation process. The functional metagenomic prediction indicated Arthrobacter, Dietzia, Brachybacerium, Brevibacterium, Gordonia, Leucobacter, Lysobacter, and Agrobacterium spp. as generalist saprophytes, essential for the onset of hydrocarbonoclastic specialist bacterial species, identified as Streptomyces, Nocardoides, Pseudonocardia, Solirubrobacter, Parvibaculum, Rhodanobacter, Luteiomonas, Planomicrobium, and Bacillus spp., involved in the TPH depletion. The fungal metabolism accelerated the onset of specialist over generalist bacteria. The capacity of the Ciboria sp. to deplete TPH in the soil in treatment was also ascertained.

In animals with distinct life stages such as holometabolous insects, adult phenotypic variation is often shaped by the environment of immature stages, including their interactions with microbes colonizing larval habitats. Such carry-over effects were previously observed for several adult traits of the mosquito Aedes aegypti after larval exposure to different bacteria, but the mechanistic underpinnings are unknown. Here, we investigated the molecular changes triggered by gnotobiotic larval exposure to different bacteria in Ae. aegypti. We initially screened a panel of 16 bacterial isolates from natural mosquito breeding sites to determine their ability to influence adult life-history traits. We subsequently focused on four bacterial isolates (belonging to Flavobacterium, Lysobacter, Paenibacillus, and Enterobacteriaceae) with significant carry-over effects on adult survival and found that they were associated with distinct transcriptomic profiles throughout mosquito development. Moreover, we detected carry-over effects at the level of gene expression for the Flavobacterium and Paenibacillus isolates. The most prominent transcriptomic changes in gnotobiotic larvae reflected a profound remodeling of lipid metabolism, which translated into phenotypic differences in lipid storage and starvation resistance at the adult stage. Together, our findings indicate that larval exposure to environmental bacteria trigger substantial physiological changes that impact adult fitness, uncovering a mechanism underlying carry-over effects of mosquito-bacteria interactions during larval development.

In this study, a field-scale and pot experiment were performed to evaluate the remedial efficiency of Cd contaminated soil by tobacco and explore rhizosphere micro-characteristics under different cadmium levels, respectively. The results indicated that tobacco could remove 12.9 % of Cd from soil within a short growing period of 80 d. The pot experiment revealed that tobacco could tolerate soil Cd concentrations up to 5.8 mg kg−1 and bioaccumulate 68.1 and 40.8 mg kg−1 Cd in shoots and roots, respectively. The high Cd bioaccumulation in tobacco might be attributed to strong acidification in the rhizosphere soil and the increase in Cd bioavailability. Rhizobacteria did not appear to be involved in Cd mobilization. In contrast, tobacco tended to enrich sulfate-reducing bacteria (such as Desulfarculaceae) under high Cd treatment (5.8 mg kg−1) but enrich plant growth-promoting bacteria (such as Bacillus, Dyadobacter, Virgibacillus and Lysobacter) to improve growth under low Cd treatment (0.2 mg kg−1), suggesting that tobacco employed different microbes for responding to Cd stress. Our results demonstrate the advantages of using tobacco for bioremediating Cd contaminated soil and clarify the rhizosphere mechanisms underlying Cd mobilization and tolerance.

Soil ecosystem perturbation due to agronomic practices can negatively impact soil productivity by altering the diversity and function of soil health determinants. Currently, the influence of rice cultivation and off-season periods on the dynamics of soil health determinants is unclear. Therefore, soil enzyme activities (EAs) and bacterial community compositions in rice-cultivated fields at postharvest (PH) and after a 5-month off-season period (5mR), and fallow-fields (5-years-fallow, 5YF, 10-years-fallow, 10YF and/or one-year-fallow, 1YF) were assessed in two agroecological regions of Mozambique. EAs were mostly higher in fallow fields than in PH, with significant (p &lt, 0.05) differences detected for β-glucosidase and acid phosphatase activities. Only β-glucosidase activity was significantly (p &lt, 0.05) different between PH and 5mR, suggesting that β-glucosidase is responsive in the short-term. Bacterial diversity was highest in rice-cultivated soil and correlated with NO3−, NH4+ and electrical conductivity. Differentially abundant genera, such as Agromyces, Bacillus, Desulfuromonas, Gaiella, Lysobacter, Micromonospora, Norcadiodes, Rubrobacter, Solirubrobacter and Sphingomonas were mostly associated with fallow and 5mR fields, suggesting either negative effects of rice cultivation or the fallow period aided their recovery. Overall, rice cultivation and chemical parameters influenced certain EAs and shaped bacterial communities. Furthermore, the 5-month off-season period facilitates nutrient recovery and proliferation of plant-growth-promoting bacteria.

Polyethylene film is the most widely used plastic film in agricultural production activities, and its depolymerization products are mainly polyethylene-particles (PE-particles) of different molecular weights. However, the impact of the molecular weights of the PE-particles on soil-crop microenvironment has not been elucidated. In this study, a potted microcosmic simulation system was used to evaluate the impact of low, medium and high molecular weight PE-particles on soil metabolism, microbial community structure, and crop growth. There were obvious differences in the shape and surface microstructure of PE-particles with different molecular weights. Soil sucrase and peroxidase had significant responses to PE-particles of different molecular weights. In the rhizosphere, the number of microorganisms and the microbial alpha diversity index increased with increasing PE-particles molecular weight. Rhizobacter, Nitrospira, and Sphingomonas were the dominant microorganisms induced by PE-particles to regulate the metabolism of elements. Carbohydrate and amino acid contents in rhizosphere soils were the key factors affecting the species abundance of Lysobacter, Polyclovorans, Rhizobacter, and Sphingomonas. In plants, PE-particles treatment reduced the plant biomass and photosynthetic rate and disrupted normal mineral nutrient metabolism. Different molecular weight PE-particles may therefore have adverse effects on the soil-plant system.

Microbes can establish a pathogenetic or symbiotic relationship with plants in soil and aquatic ecosystems. Although change in bacterial and fungal community in soil and their interaction with plants have been widely studied, little is known about their community structure in hydroponic systems across plant growth stages under different nutrient treatments. This study used next-generation sequencing analysis to assess the temporal changes in melon rhizosphere bacterial and fungal community structure across six different nutrient treatments. We found significant changes in the microbial community composition (especially for bacteria) between growth stages (R = 0.25–0.63, p &lt, 0.01) than nutrient treatments. Proteobacteria dominated the bacterial community at the phylum level across melon growth stages (59.8% ± 16.1%). The genera Chryseobacterium, Pseudomonas, and Massilia dominated the rhizosphere in the flowering and pollination stage, while Brevibacillius showed the highest relative abundance in the harvesting stage. However, the rhizosphere was dominated by uncultured fungal taxa, likely due to the application of fungicides (Ridomil MZ). Further, linear regression analysis revealed a weak influence of bacterial community structure on melon yield and quality, while fruit weight and quality moderately responded to Mg and K deficiency. Nevertheless, the relative abundance of bacterial genus Chryseobacterium in the vegetative stage showed a strong correlation with fruit weight (R2 = 0.75, p &lt, 0.05), while genera Brevibacillus, Lysobacter, and Bosea in late growth stages strongly correlated with fruit sweetness. Overall, temporal variability in the microbial (especially bacterial) community structure exceeds the variability between nutrient treatments for the given range of nutrient gradient while having little influence on melon yield.

Background Continuous cropping obstacles from sweet potatoes are widespread, which seriously reduce the yield and quality, causing certain economic losses. Bacteria of rhizospheric soil are the richest and are associated with obstacles to continuous cropping. However, few studies have examined how continuous sweet potato cropping affects the rhizospheric soil bacterial community structure. Results In the study, the Illumina MiSeq method was used to explore the variations in rhizospheric soil bacterial community structure of different sweet potato varieties after continuous cropping, as well as the correlation between soil characteristics and the bacterial community. The results showed that (1) the dominant bacterial phyla in rhizospheric soils from both Xushu 18 and Yizi 138 were Proteobacteria, Acidobacteria, and Actinobacteria. The most dominant genus was Subgroup 6_norank. The relative abundance of rhizospheric soil bacteria varied significantly between the two sweet potato varieties. (2) The richness and diversity indexes of bacteria were higher in Xushu 18 rhizospheric soil than in Yizi 138 soil after continuous cropping. Moreover, beneficial Lysobacter and Bacillus were more prevalent in Xushu 18, while Yizi 138 contained more harmful Gemmatimonadetes. (3) Soil pH decreased after continuous cropping, and redundancy analysis indicated that soil pH was significantly correlated with the bacterial community. Spearman’s rank correlation coefficient analysis demonstrated that pH was positively associated with Planctomycetes and Acidobacteria, but negatively associated with Actinobacteria and Firmicutes. Conclusions After continuous cropping, the bacterial community structure and physicochemical properties of sweet potato rhizospheric soil were changed, and the changes from different sweet potato varieties were different. The contents of Lysobacter and Bacillus were higher in the sweet potato variety resistant to continuous cropping. It provides a basis for developing new microbial fertilizers for sweet potatoes to alleviate the continuous cropping obstacle.

The discovery of novel therapeutic antimicrobials has become an urgent issue in response to the global crisis of the spread of multi-drug-resistant bacteria. In this report, we propose an efficient screening method for antimicrobial agents with therapeutic potential from soil bacteria. With this method, colonies of the soil bacteria were formed first on agar plates containing only an extract of soil, followed by an overlay of soft agar containing the pathogens, an antibiotic target. Then, we selected the colonies that formed the inhibitory zones on soft agar and evaluated the therapeutic efficacy of their culture supernatants using a silkworm bacterial infection model. Using Staphylococcus aureus as an indicator strain to obtain bacteria that produce therapeutically effective antimicrobials, we succeeded in reducing the screening size by 20-fold compared to the conventional method. An analysis of 86 antibiotics producers identified in this study indicated that the majority belonged to Streptomyces sp. and Lysobacter sp., well-known producers of secondary metabolites. Besides, the presence of eight genera and 37 species among the identified species indicated the diversity of antibiotic producers. Based on the finding of our study, we propose this method as an efficient way to discover novel antimicrobial agents that are therapeutically effective.

In this study, two bacterial strains, IRP7 and IRP8, were selected to induce resistance against pine wilt disease (PWD). Foliar application with these strains to nematode-inoculated pine seedlings significantly reduced PWD severity. The effect of nematode inoculation and bacterial treatment on the rhizosphere bacterial community was investigated. The results indicated that the rhizosphere of nematode-inoculated seedlings contained a lower relative abundance of beneficial microbes such as Paraburkholderia, Bradyrhizobium, Rhizobacter, Lysobacter, and Caballeronia. Bacterial treatment resulted in significant changes in the microbes that were represented in relatively low relative abundance. Treatment with IRP7 resulted in an increase in the relative abundance of Nitrospirillum, Bacillus, and Luteibacter, which might be useful for protection against infection. Treatment with IRP8 resulted in an increase in the relative abundance of obligate bacterial predators of the Bdellovibrio genus that were previously shown to control several bacterial phytopathogens and may have a role in the management of nematode-carried bacteria. The selected bacteria were identified as Pseudomonas koreensis IRP7 and Lysobacter enzymogenes IRP8 and are suggested as a potential treatment for induced resistance against PWD. To our knowledge, this is the first report on the effect of foliar treatment with resistance-inducing bacteria on the rhizosphere microbiota.

Soil microbiome comprises numerous microbial species that continuously interact with each other. Among the modes of diverse interactions, cell-cell killing may play a key role in shaping the microbiome composition. Bacteria deploy various secretion systems to fend off other microorganisms and Type IV Secretion System (T4SS) in pathogenic bacteria was shown to function as a contact-dependent, inter-bacterial killing system only recently. The present study investigated the role played by T4SS in the killing behaviour of the soilborne biocontrol bacterium Lysobacter enzymogenes OH11. Results showed that L. enzymogenes OH11 genome encompasses genes encoding all the components of T4SS and effectors potentially involved in inter-bacterial killing system. Generation of knock-out mutants revealed that L. enzymogenes OH11 uses T4SS as the main contact-dependent weapon against other soilborne bacteria. The T4SS-mediated killing behaviour of L. enzymogenes OH11 decreased the antibacterial and antifungal activity of two Pseudomonas spp. but at the same time, protected carrot from infection by Pectobacterium carotovorum. Overall, this study showed for the first time the involvement of T4SS in the killing behaviour of L. enzymogenes and its impact on the multiple interactions occurring in the soil microbiome. This article is protected by copyright. All rights reserved.

Soil pollution generally causes huge losses in the world’s agricultural output, and therefore, soil pollution control is essential in agriculture crop production system. For soil pollution management, we usually reduce the use of chemical fertilizers, manures, and pesticide, reuse the domestic waste product materials such as glass containers, plastic bags, paper, and cloth, and recycle the materials such as some kinds of plastics and glass cane, but their indiscriminate use causes environmental problems and human health hazards. Moreover, the continuous use of those products without safe disposal leads to soil pollution. Thus, bioremediation of soil pollution is an alternate eco-friendly method for soil pollution management, in which plant growth–promoting rhizobacteria are used in alleviating the contaminated soil. Many rhizosphere microorganisms including Azotobacter spp., Pseudomonas aeruginosa, Glomus spp., Acaulospora spp., Scutellospora spp., Streptomyces spp., Klebsiella spp., Lysobacter spp., Rhizobium leguminosarum, Burkholderia spp., Diaphorobacter nitroreducens, Planomicrobium chinense, Promicromonospora spp., Mesorhizobium spp., Psychrobacillus psychrodurans, Pantoea spp., Arthrobacter spp., and Variovorax spp. have been found as plant growth–promoting rhizobacteria. These PGPR have been found to bioremediate the polluted soil by using various types of mechanisms such as through siderophore production, phosphate solubilization, biological nitrogen fixation, production of 1-aminocyclopropane-1-carboxylate deaminase (ACC), quorum sensing, signal interference and phytohormone production, exhibiting antifungal activity, production of volatile organic compounds, and induction of systemic resistance, promoting beneficial plant-–microbe symbioses. Thus, there are immense possibilities for identifying other growth-promoting rhizobacteria that could help in bioremediation of polluted soil as well as promote sustainable agriculture.

Field experiments was conducted to evaluate the effectiveness of sepiolite (S), sepiolite + fungi residues (SFR) and sepiolite + vermicompost (SVC) on in situ immobilization remediation of Cd contaminated soils. The results showed that treatments of S, SFR and SVC decreased soil Cd availability by 15.2–47.8%, 17.5–44.9% and 13.2–44.9%, respectively, when compared with the control groups. Moreover, the content of Cd in edible parts of Lactuca sativa L., Cichorium endivia L. and Brassica campestris L. was experienced a decrease of 15.9–41.9%, 1.6–38.0% and 29.0–37.4% reduction, respectively, under the amended soil. The improvement of soil fertility was obtained under addition of SVC and SFR, while the amounts of available P, K, organic matter, microbial carbon, microbial nitrogen and dehydrogenase activity were increased by 9.6–68.2%, 1.2–28.3%, 37.5–70.5%, 4.1–121.0%, 220–640% and 6.8–56.8%, respectively, in contrast to CK. Moreover, high-throughput sequencing analysis showed that the combined treated soils got higher values of alpha diversity indices, Chao1, ACE and Shannon. The number of dominant phyla (Proteobacteria, Acidobacteria, Gemmatimonadetes, Crenarchaeota) and genera (Aquicella, Lysobacter, Candidatus Nitrososphaera, Sphingopyxis, Mesorhizobium) were enhanced. Therefore, the use of sepiolite and organic amendments could be an adequate strategy to immobilization remediation of Cd–contaminated soils.

The toxicity, volatility and persistence of the obsolete organochlorine pesticide hexachlorocyclohexane (HCH), makes reclamation of contaminated areas a priority for the health and welfare of neighboring human communities. Microbial diversity and functions and their relation to spontaneous vegetation in post-excavation situations, are essential indicators to consider in bioaugmentation or microbe-assisted phytoremediation strategies at field scale. Our study aimed to evaluate the effects of long-term HCH contamination on soil and plant-associated microbial communities, and whether contaminated soil has the potential to act as a bacterial inoculum in post-excavation bioremediation strategies. To scrutinize the role of vegetation, the potential nitrogen fixation of free-living and symbiotic diazotrophs of the legume Lotus tenuis was assessed as a measure of nutrient cycling functions in soil under HCH contamination. Potential nitrogen fixation was generally not affected by HCH, with the exception of lower nifH gene counts in excavated contaminated rhizospheres, most probably a short-term HCH effect on early bacterial succession in this compartment. HCH shaped microbial communities in long-term contaminated bulk soil, where we identified possible HCH tolerants such as Sphingomonas and Altererythrobacter. In L. tenuis rhizosphere, microbial community composition was additionally influenced by plant growth stage. Sphingobium and Massilia were the bacterial genera characteristic for HCH contaminated rhizospheres. Long-term HCH contamination negatively affected L. tenuis growth and development. However, root-associated bacterial community composition was driven solely by plant age, with negligible HCH effect. Results showed that L. tenuis acquired possible HCH tolerant bacteria such as the Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium clade, Sphingomonas, Massilia or Pantoea which could simultaneously offer plant growth promoting (PGP) benefits for the host. Finally, we identified an inoculum with possibly HCH tolerant, PGP bacteria transferred from the contaminated bulk soil to L. tenuis roots through the rhizosphere compartment, consisting of Mesorhizobium loti, Neorhizobium galegae, Novosphingobium lindaniclasticum, Pantoea agglomerans and Lysobacter bugurensis.

Disease suppressive soils are instrumental in combating phytopathogens, which cause severe diseases in plants. They provide an eco-friendly way to mitigate biotic stresses in agricultural systems worldwide. Efforts have been made to understand the mechanisms of disease suppressiveness in soil using culture-dependent and culture-independent methods. Omics approaches have provided useful insights into the key markers responsible for imparting antagonism against soil-borne plant pathogens. Specific genera such as Pseudomonas, Bacillus, Streptomyces, Lysobacter, and Trichoderma, along with antibiotics and siderophores, are the key constituents in disease suppressive soils. Disease suppressive potential of a soil is dependent on several factors such as soil pH and soil type, with one of the critical factors being the type of nutrient amendment applied to the soil. While the underlying mechanisms of growth inhibition of specific fungal pathogens such as Fusarium and Rhizoctonia solani in soil ecosystem have been well elucidated, there is restricted knowledge regarding “general-disease suppression”. The mechanisms responsible for imparting broad range suppressiveness can help us develop economically favourable agricultural management practices. In this chapter, we have critically reviewed significant investigations related to specific- and general-disease suppression where omics-based approaches have been adopted to study the microbial community dynamics of disease suppressive soils. Based on the reported studies, we have identified the potential role of diverse markers, compost amendments, and different microbial strains (producing key metabolites) in disease suppressiveness of soil. Thus, we propose that using different molecular and microbial markers, mapping of disease suppressive soils can efficiently be done across the globe. In addition, the effectiveness of synthetic microbial communities, and possibilities of transforming conducive soil by microbiome transfer from suppressive soil may be explored in the context of disease suppressiveness in the future.

The soil microbiome consists of a vast variety of microorganisms which contribute to essential ecosystem services including nutrient recycling, protecting soil structure, and pathogen suppression. Recalcitrant organic compounds present in soils contaminated with fuel oil can lead to a decrease in functional redundancy within soil microbiomes. Ecopiling is a passive bioremediation technique involving biostimulation of indigenous hydrocarbon degraders, bioaugmentation through inoculation with known petroleum-degrading consortia, and phytoremediation. The current study investigates the assemblage of soil microbial communities and pollutant-degrading potential in soil undergoing the Ecopiling process, through the amplicon marker gene and metagenomics analysis of the contaminated soil. The analysis of key community members including bacteria, fungi, and nematodes revealed a surprisingly diverse microbial community composition within the contaminated soil. The soil bacterial community was found to be dominated by Alphaproteobacteria (60–70%) with the most abundant genera such as Lysobacter, Dietzia, Pseudomonas, and Extensimonas. The fungal community consisted mainly of Ascomycota (50–70% relative abundance). Soil sequencing data allowed the identification of key enzymes involved in the biodegradation of hydrocarbons, providing a novel window into the function of individual bacterial groups in the Ecopile. Although the genus Lysobacter was identified as the most abundant bacterial genus (11–46%) in all of the contaminated soil samples, the metagenomic data were unable to confirm a role for this group in petrochemical degradation. Conversely, genera with relatively low abundance such as Dietzia (0.4–9.0%), Pusillimonas (0.7–2.3%), and Bradyrhizobium (0.8–1.8%) did possess genes involved in aliphatic or aromatic compound degradation.

The rhizosphere microbiome is critical for plant growth and protection against plant pathogens. However, rhizosphere microbial communities are likely to be restructured upon plant infection by fungal pathogens. Our objective was to determine the shifts in rhizosphere bacterial communities of avocado trees (Persea americana Mill.) after Fusarium dieback (FD), a disease triggered by the symbiotic fungi of invasive ambrosia beetles (Euwallacea kuroshio and Euwallacea sp. nr. fornicatus), using 16S rDNA gene amplicon sequencing and a culture-dependent approach. Rhizosphere soil samples were collected from five asymptomatic and five FD-symptomatic avocado trees in a Californian orchard. Sequence analysis showed that diversity metrics of the rhizosphere bacterial communities associated with asymptomatic avocado trees were larger than those of communities from FD-symptomatic trees. Moreover, FD produced significant shifts in rhizobacterial community structure, which were mainly caused by rare OTUs. Bacterial taxa such as Armatimonadetes, Sporocytophaga or Cellvibrio were exclusively associated with the rhizosphere of asymptomatic trees and may act as an insurance mechanism against fungal invasions. Conversely, genera such as Myxococcus or Lysobacter, which have been described as effective biocontrol agents against Fusarium oxysporum, Colletotrichum gloeosporioides or Rhizoctonia spp., among other phytopathogens, were only found in the rhizosphere of FD-symptomatic trees. The culturable bacterial communities in the rhizosphere of both FD-symptomatic and asymptomatic trees were dominated by isolates from the Bacillus and Pseudomonas genera, indicating that potential biocontrol agents against FD may be isolated from healthy and diseased avocado trees. Altogether, our results showed that FD elicited shifts in the avocado rhizosphere microbiome, which could potentially affect soil microbial processes, and provide a basis for the selection of biocontrol agents that could be used for FD prevention., This research was funded by a 2015 UC MEXUS −CONACYT collaborative research grant and by a CONACYT postgraduate fellowship awarded to the first author.