Degradation of the fungal cell wall by clostridial strains isolated from soil subjected to biological soil disinfestation and biocontrol of Fusarium wilt disease of spinach

Comparative genomic analysis and proposal of Clostridium yunnanense sp. nov., Clostridium rhizosphaerae sp. nov., and Clostridium paridis sp. nov., three novel Clostridium sensu stricto endophytes with diverse capabilities of acetic acid and ethanol production

OBJECTIVES

Genus Clostridium sensu stricto is generally regarded as the true Clostridium genus, which includes important human and animal pathogens and industrially relevant microorganisms. Besides, it is also a prominent member of plant-associated endophytes. However, our knowledge of endophytic Clostridium is limited.

METHODS

In this study, the endophytes were isolated under anaerobic condition from the roots of Paris polyphylla Smith var. yunnanensis. Subsequently, a polyphasic taxonomic approach was used to clarify their taxonomic positions. The fermentation products were measured in the isolates with HPLC analysis. Comparative genomics was performed on these new strains and other relatives.

RESULTS

In total, nine endophytic strains belonging to the genus Clostridium sensu stricto were isolated, and three of them were identified as new species. Seven of nine strains could produce acetate, propionate, and butyrate. Only two strains could produce ethanol, although genomics analysis suggested that only two of them were without genes for solventogenesis. Different from the endophytic strains, the phylogenetically closely related non-endophytic strains showed significant enrichment effects on some metabolic pathways involving environmental information processing, carbohydrate, and amino acid metabolisms, etc. It suggests that the genomes of these endophytic strains had undergone subtle changes associated with environmental adaptations.

CONCLUSION

Consequently, strains YIM B02505^T, YIM B02515^T, and YIM B02565^T are proposed to represent a new species of the genus Clostridium sensu stricto, for which the names Clostridium yunnanense sp. nov., Clostridium rhizosphaerae sp. nov., and Clostridium paridis sp. nov. are suggested.

Isolation and Characterization of Novel Biological Control Agent Clostridium beijerinckii against Meloidogyne incognita

One of the most severe soil-borne pathogens in the world is the root-knot nematode (Meloidogyne incognita). Biological control is gaining more importance as environmental awareness increases. Thus, keeping this in mind, a total of 712 bacterial strains were isolated from 117 rhizosphere soil samples and investigated for potential biological control activity against M. incognita. Strain Sneb518 (Clostridium beijerinckii) was identified as having solid biocontrol activity against M. incognita. Sneb518 demonstrated significant inhibition against M. incognita, with J2 mortality reaching 90.73% at 12 h and with eggs hatching at a rate of 6.00% at 24 h, compared to a hatchability level of 29.07% for the control. Additionally, Sneb518 was excellent for enhancing seed germination. The seeds coated with a fermentation broth containing Sneb518 efficiently boosted the germination rate to 88.49%. The effectiveness and stability of C. beijerinckii Sneb518 against M. incognita were then further evaluated in a greenhouse. According to the pot experiment data, Sneb518 considerably (p < 0.05) reduced the number of root galls and egg masses on roots and also significantly (p < 0.05) increased tomato plant growth. C. beijerinckii Sneb518-treated tomato seedlings exhibited 50.26% biocontrol effectiveness compared to the control group. Our results demonstrate that C. beijerinckii Sneb518 can be a potential biological control agent against root-knot nematode disease and a biomass enhancer. This research will give new options for the sustainable control of root-knot nematode disease in tomatoes and other host plants.

Isolation and Identification of Talaromyces sp. Strain Q2 and Its Biocontrol Mechanisms Involved in the Control of Fusarium Wilt

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.

Clostridium fungisolvens sp. nov., a new β-1,3-glucan-decomposing bacterium isolated from anoxic soil subjected to biological soil disinfestation

Biological soil disinfestation (BSD) or reductive soil disinfestation (RSD) is a bioremediation method used to suppress or eliminate soil-borne plant pathogens by stimulating activities of indigenous anaerobic bacteria of the soil. An anaerobic bacterial strain (TW1^T) was isolated from an anoxic soil sample subjected to the BSD treatment and comprehensively characterized. Cells of the strain were Gram-stain-positive, slightly curved and motile rods producing terminal spores. The strain was aerotolerant. Strain TW1^T was saccharolytic and produced acetate, butyrate, H₂ and CO₂ as fermentation end products. Strain TW1^T decomposed β-1,3-glucan (curdlan and laminarin) and degraded mycelial cells of an ascomycete Fusarium plant pathogen. Major cellular fatty acids of strain TW1^T were C_14 : 0, C_14 : 0 dimethylacetal (DMA), C_16 : 0 aldehyde and C_16 : 0 DMA. Strain TW1^T made a group on the phylogenetic tree constructed based on 16S rRNA gene sequences with species such as Clostridium fallax (96.3 %) and Clostridium polyendosporum (96.0 %). Whole genome analysis of strain TW1^T showed that the total length of the genome was 5.28 Mb with the DNA G+C content of 31.3 mol%. The average nucleotide identity (ANIb) between strain TW1^T and C. fallax was 71.2 %. Presence of the genes encoding laminarinase or GH16 β-glucosidase was confirmed from the genome analysis of strain TW1^T. Based on the genomic, phylogenetic and phenotypic properties obtained, we propose strain TW1^T should be assigned in the genus Clostridium in the family Clostridiaceae as Clostridium fungisolvens sp. nov. The type strain TW1^T (=NBRC 112097^T=DSM 110791^T).

β-1,3-Glucanase production as an anti-fungal enzyme by phylogenetically different strains of the genus Clostridium isolated from anoxic soil that underwent biological disinfestation

Biological (or reductive) soil disinfestation (BSD or RSD) is a bioremediation process to control soil-borne plant pathogens using activities of indigenous bacteria in the soil. Three obligate anaerobic bacterial strains (TW1, TW10, and TB10), which were isolated from anoxic soil subjected to BSD treatments, were examined for their abilities to produce anti-fungal enzymes. All strains were affiliated with the different lineages of the genus Clostridium. The three strains decomposed β-1,3-glucans (curdlan and laminarin), and β-1,3-glucanase activities were detected from their culture supernatants with these glucans. The three strains also produced the enzyme with wheat bran as a growth substrate and killed the Fusarium pathogen (Fusarium oxysporum f. sp. spinaciae) in the anaerobic co-incubation conditions. Observation by fluorescence microscopy of the pathogen cells showed that the three strains had degraded the fungal cells in different manners upon co-incubation with wheat bran. When the three strains were cultivated with the dead cells or the cell wall samples prepared from the Fusarium pathogen, strain TW1 utilized these materials as easily decomposable substrates by releasing β-1,3-glucanase. When observed by fluorescence microscopy, it appeared that strain TW1 degraded the mycelial cell wall nearly thoroughly, with the septa remaining as undecomposed luminous rings. In contrast, the other two strains decomposed neither the dead cells nor the cell wall samples directly. The results indicate that the various anaerobic bacteria proliferated in the soil under the BSD treatments should play key roles as an organized bacterial community to eliminate fungal pathogens, namely by release of anti-fungal enzymes with different properties.

Key points •Three clostridial strains isolated from BSD-treated soils produced β-1,3-glucanase. •All strains killed the Fusarium pathogen in the anaerobic co-incubation conditions. •One of the strains produced β-1,3-glucanase with the fungal cell wall as a substrate. •The strain degraded the cell wall almost completely, except for the mycelial septa.

Anaerobic Soil Disinfestation Reduces Viability of Sclerotinia sclerotiorum and S. minor Sclerotia and Root-Knot Nematodes in Muck Soils

Experiments were conducted to evaluate potential functional and mechanistic differences in the suppression of Sclerotinia sclerotiorum and S. minor and root-knot nematodes in muck soils by anaerobic soil disinfestation (ASD) using different carbon source amendments. Volatile compounds produced during ASD in muck soil amended with molasses, wheat bran, or mustard greens at 20.2 Mg/ha or a 2% ethanol solution significantly reduced the mycelial growth and number of sclerotia produced by both Sclerotinia spp. compared with the anaerobic control. In amended soils, acetic and butyric acids were detected in concentrations that reduced the viability of sclerotia of both pathogens. Higher concentrations of carbon dioxide were observed in ASD-treated soils, regardless of the amendment, than in the nonamended anaerobic control. Only amendment with wheat bran did not increase the production of methane gas during ASD compared with the controls. Meloidogyne hapla survival was completely suppressed in soils treated with ASD regardless of carbon source. Field trials were conducted in Ohio muck soil to assess survival of sclerotia of both Sclerotinia spp. The viability of sclerotia of both Sclerotinia spp. was significantly reduced in soil subjected to ASD amended with wheat bran (20.2 Mg/ha), molasses (10.1 Mg/ha), or wheat bran (20.2 Mg/ha) plus molasses (10.1 Mg/ha) compared with the controls. A consistent negative correlation between soil reduction and viability of sclerotia of both pathogens was observed. Wheat bran and molasses are both widely available amendments that can be used as ASD carbon sources for the management of soilborne pathogens in muck soils.

Production of β-1,3-glucanase and chitosanase from clostridial strains isolated from the soil subjected to biological disinfestation

Biological soil disinfestation (BSD) or anaerobic (reductive) soil disinfestation (ASD/RSD) is a bioremediation method used to eliminate soil-borne plant pathogens by exploiting the activities of anaerobic bacteria in soil. In this study, two obligate anaerobic bacterial strains isolated from BSD-treated soil and identified as Clostridium beijerinckii were examined for their abilities to suppress the spinach wilt disease pathogen (Fusarium oxysporum f. sp. spinaciae) as a representative soil-borne fungal plant pathogen. Both strains degraded β-1,3-glucan and chitosan, two major polysaccharide components of ascomycetes fungal cell wall, supplemented in the medium. β-1,3-Glucanase was detected in the supernatants of cultures supplemented with different types of glucan. Similarly, chitosanase was detected in cultures supplemented with chitosan. Both the enzyme activities were also detected in cultures containing glucose as a substrate. Live cells of F. oxysporum f. sp. spinaciae that were co-incubated with each anaerobic strain under anaerobic conditions using glucose as a substrate died during incubation. Freeze-dried dead fungal biomass of the pathogen, when added to the culture, supported good growth of both anaerobes and production of both enzymes. Severe and nearly complete degradation of both live and dead fungal cells during incubation with anaerobic bacteria was observed by fluorescence microscopy. When individual anaerobic bacterial strain was co-incubated with live pathogenic fungal cells in wheat bran, a popular material for BSD-treatment, both the strains grew well and killed the fungal pathogen promptly by producing both enzymes. These results indicate that both the bacterial strains attack the fungal cells by releasing extracellular fungal cell wall-degrading enzymes, thereby eliminating the pathogen.