Hetong Yang

Root-knot nematodes (RKNs; Meloidogyne incognita) pose a significant threat to tomato crops, necessitating sustainable control methods. This study investigated the inoculation efficacy of co-cultured Burkholderia vietnamiensis B418 and Trichoderma harzianum T11W compared with single-strain treatments for RKNs suppression and their influence on the structure and function of the rhizosphere microbiome. Co-inoculation with B418 + T11W achieved a 71.42% reduction in the disease index, significantly outperforming single inoculations of B418 (54.46%) and T11W (58.93%). Co-inoculation also increased plant height by 38.51% and fresh weight by 76.02% compared to the RKNs infested plants control, promoting robust tomato growth. Metagenomic analysis reveals that co-inoculation enhanced bacterial diversity, with 378 unique bacterial species and a high Shannon index, while fungal diversity decreased with Trichoderma dominance (83.31% abundance). Actinomycetota (46.42%) and Ascomycota (97.92%) were enriched in the co-inoculated rhizosphere, showing negative correlations with RKNs severity. Functional analysis indicates enriched metabolic pathways, including streptomycin and unsaturated fatty acid biosynthesis, enhancing microbial antagonism. Single inoculations altered pathways like steroid degradation (B418) and terpenoid biosynthesis (T11W), but co-inoculation uniquely optimized the rhizosphere microenvironment. These findings highlight co-inoculation with B418 + T11W effectively suppressing RKNs and fostering plant health by reshaping microbial communities and functions, offering a promising approach for sustainable agriculture.

Salt stress poses a major threat to plant growth, and breeding for salt-tolerant varieties is not always successful to ameliorate this threat. In the present experiment, the effect of T. asperellum 22043 inoculation on the growth of salt-stressed tomatoes and the mechanisms by which it improves salt tolerance were investigated. It was observed that tomato plants treated with T. asperellum 22043 spore suspension under salt tress (50 and 100 mM NaCl) consistently exhibited higher seeds germination, seedling survival rate, plant height, and chlorophyll content, but lower malondialdehyde and proline contents than the plants treated without the Trichoderma. T. asperellum 22043 effectively improved the stress resistance of tomato through regulating the transcriptional levels of reactive oxygen species (ROS) scavenging enzyme gene expression to modulate the activity of ROS scavenging enzymes and the expression of the genes related to transporter and aquaporin to maintain the balance of cell Na⁺. In conclusion, T. asperellum 22043 can enhance tomato seedlings’ salt tolerance by activating the antioxidant system and regulating the expression of stress-resistant genes.

This study aimed to investigate the efficiency of the secondary metabolites (SMs) produced by a co-culture of Trichoderma harzianum TW21990 and Burkholderia vietnamiensis B418 in the control of Colletotrichum siamense CM9. A fermentation filtrate of B418 + TW21990 co-culture (BT21) produced a notable increase in the inhibition rate of CM9 compared to those of TW21990 and B418 monocultures, which reached 91.40% and 80.46% on PDA plates and strawberry leaves, respectively. The BT21 fermentation broth exhibited high control efficiency on strawberry root rot of 68.95% in a pot experiment, which was higher than that in the monocultures and fluazinam treatment. In addition, BT21 treatment promoted strawberry root development, improved antioxidative enzyme activities in the leaves and roots, and enhanced the total chlorophyll content of the strawberry leaves. UHPLC-MS/MS analysis of fermentation filtrates was performed to elucidate SM variations, revealing 478 and 795 metabolites in BT21 co-culture in positive and negative ion modes, respectively. The metabolomic profiles suggested abundant SMs with antagonistic capabilities and growth-promoting effects: 3-(propan-2-yl)-octahydropyrrolo [1,2-a]pyrazine-1,4-dione (cyclo(L-Pro-L-Val)), 3-[(4-hydroxyphenyl)methyl]-octahydropyrrolo[1,2-a]pyrazine-1,4-dione (cyclo(L-Pro-L-Tyr)), 3-indoleacetic acid (IAA), 2-hydroxycinnamic acid, 4-aminobutyric acid (GABA), bafilomycin B1, and DL-indole-3-lactic acid (ILA) were significantly enhanced in the co-culture. Overall, this study demonstrates that a co-culture strategy is efficient for inducing bioactive SMs in T. harzianum and B. vietnamiensis, which could be exploited as a novel approach for developing biocontrol consortia.

Burkholderia vietnamiensis B418 is a multifunctional plant growth-promoting rhizobacteria (PGPR) strain with nitrogen-fixing and phosphate-solubilizing capability which can be employed for root-knot nematode (RKN) management on various crops and vegetables. Here we investigated the control efficacy of B. vietnamiensis B418 inoculation against RKN on watermelon, applied either alone or combined with nematicides fosthiazate or avermectin, and their effects on bacterial and fungal microbiomes in rhizosphere soil. The results of field experiments showed individual application of B418 displayed the highest control efficacy against RKN by 71.15%. The combinations with fosthiazate and avermectin exhibited slight incompatibility with lower inhibitory effects of 62.71% and 67.87%, respectively, which were still notably higher than these nematicides applied separately. Analysis of microbiome assemblages revealed B418 inoculation resulted in a slight reduction for bacterial community and a significant increment for fungal community, suggesting that B418 could compete with other bacteria and stimulate fungal diversity in rhizosphere. The relative abundance of Xanthomonadales, Gemmatimonadales and Sphingomonadales increased while that of Actinomycetales reduced with B418 inoculation. The predominate Sordariomycetes of fungal community decreased dramatically in control treatment with B418 inoculation whereas there were increments in fosthiazate and avermectin treatments. Additionally, nitrogen (N) cycling by soil microbes was estimated by quantifying the abundance of microbial functional genes involved in N-transformation processes as B418 has the capability of N-fixation. The copy number of N-fixing gene nifH increased with B418 inoculation, and the highest increment reached 35.66% in control treatment. Our results demonstrate that B. vietnamiensis B418 is an effective biological nematicide for nematode management, which acts through the modulation of rhizosphere microbial community.

Soil nitrification (microbial oxidation of ammonium to nitrate) can lead to nitrogen leaching and environmental pollution. A number of plant species are able to suppress soil nitrifiers by exuding inhibitors from roots, a process called biological nitrification inhibition (BNI). However, the BNI activity of perennial grasses in the nutrient-poor soils of Australia and the effects of BNI activity on nitrifying microbes in the rhizosphere microbiome have not been well studied. Here we evaluated the BNI capacity of bermudagrass (Cynodon dactylon L.), St. Augustinegrass (Stenotaphrum secundatum (Walt.) Kuntze), saltwater couch (Sporobolus virginicus), seashore paspalum (Paspalum vaginatum Swartz.), and kikuyu grass (Pennisetum clandestinum) compared with the known positive control, koronivia grass (Brachiaria humidicola). The microbial communities were analysed by sequencing 16S rRNA genes. St. Augustinegrass and bermudagrass showed high BNI activity, about 80 to 90% of koronivia grass. All the three grasses with stronger BNI capacities suppressed the populations of Nitrospira in the rhizosphere, a bacteria genus with a nitrite-oxidizing function, but not all of the potential ammonia-oxidizing archaea. The rhizosphere of saltwater couch and seashore paspalum exerted a weak recruitment effect on the soil microbiome. Our results demonstrate that BNI activity of perennial grasses played a vital role in modulating nitrification-associated microbial populations.

Trichoderma species are widely used to control fungal and nematode diseases of crops. To date, only one complete Trichoderma genome has been sequenced, T. reesei QM6a, a model fungus for industrial enzyme production, while the species or strains used for biological control of plant diseases are only available as draft genomes. Previously, we demonstrated that two Trichoderma strains (T. afroharzianum and T. cyanodichotomus) provide effective control of nematode and fungal plant pathogens. Based on deep sequencing using Illumina and Pacbio platforms, we have assembled high-quality genomes of the above two strains, with contig N₅₀ reaching 4.2 and 1.7 Mbp, respectively, which is greater than those of published draft genomes. The genome data will provide a resource to assist research on the biological control mechanisms of Trichoderma spp.

Soil populations of bacteria rapidly degrading atrazine are critical to the environmental fate of the herbicide. An enrichment bias from the routine isolation procedure prevents studying the diversity of atrazine degraders. In the present work, we analyzed the occurrence, diversity and community structure of soil atrazine-degrading bacteria based on their direct isolation. Atrazine-degrading bacteria were isolated by direct plating on a specially developed SM agar. The atrazine degradation genes trzN and atzABC were detected by multiplex PCR. The diversity of atrazine degraders was characterized by enterobacterial repetitive intergenic consensus-PCR (ERIC-PCR) genotyping followed by 16S rRNA gene phylogenetic analysis. The occurrence of atrazine-degrading bacteria was also assessed by conventional PCR targeting trzN and atzABC in soil DNA. A total of 116 atrazine-degrading isolates were recovered from bulk and rhizosphere soils sampled near an atrazine factory and from geographically distant maize fields. Fifteen genotypes were distinguished among 56 industrial isolates, with 13 of them representing eight phylogenetic groups of the genus Arthrobacter. The remaining two were closely related to Pseudomonas alcaliphila and Gulosibacter molinativorax and constituted major components of the atrazine-degrading community in the most heavily contaminated industrial plantless soil. All isolates from the adjacent sites inhabited by cogon grass or common reed were various Arthrobacter spp. with a strong prevalence of A. aurescens group. Only three genotypes were distinguished among 60 agricultural strains. Genetically similar Arthrobacter ureafaciens bacteria which occurred as minor inhabitants of cogon grass roots in the industrial soil were ubiquitous and predominant atrazine degraders in the maize rhizosphere. The other two genotypes represented two distant Nocardioides spp. that were specific to their geographic origins. Direct plating on SM agar enabled rapid isolation of atrazine-degrading bacteria and analysis of their natural diversity in soil. The results obtained provided evidence that contaminated soils harbored communities of genetically distinct bacteria capable of individually degrading and utilizing atrazine. The community structures of culturable atrazine degraders were habitat-specific. Bacteria belonging to the genus Arthrobacter were the predominant degraders of atrazine in the plant rhizosphere.

Mushrooms have been valued as a traditional source of natural bioactive compounds for centuries and have recently been exploited for potential components in the cosmetics industry. Numerous mushrooms and their ingredients have been known to be beneficial to the skin and hair. The representative ingredients are as follows: phenolics, polyphenolics, terpenoids, selenium, polysaccharides, vitamins, and volatile organic compounds. These compounds show excellent antioxidant, anti-aging, anti-wrinkle, skin whitening, and moisturizing effects, which make them ideal candidates for cosmetics products. This review provides some perspectives of mushrooms (and/or extracts) and their ingredients presently used, or patented to be used, in both cosmeceuticals for topical administration and nutricosmetics for oral administration. With the small percentage of mushrooms presently identified and utilized, more mushroom species will be discovered, verified, and cultivated in the future, boosting the development of relevant industry. Combining with progress in genomics, proteomics, metabolomics, and systems pharmacology, mushrooms can find their way into cosmetics with multiple approaches.

Trichoderma afroharzianum is one of the best characterized Trichoderma species, and strains have been utilized as plant disease suppressive inoculants. In contrast, Trichoderma gamsii has only recently been described, and there is limited knowledge of its disease suppressive efficacies. Comparative studies of changes in gene expression during interactions of these species with their target plant pathogens will provide fundamental information on pathogen antibiosis functions. In the present study, we used complementary DNA amplified fragment length polymorphism (cDNA-AFLP) analysis to investigate changes in transcript profiling of T. afroharzianum strain LTR-2 and T. gamsii strain Tk7a during in vitro interactions with plant pathogenic Rhizoctonia solani and Pythium irregulare. Considerable differences were resolved in the overall expression profiles of strains LTR-2 and Tk7a when challenged with either plant pathogen. In strain LTR-2, previously reported mycoparasitism-related genes such as chitinase, polyketide synthase, and non-ribosomal peptide synthetase were found to be differentially expressed. This was not so for strain Tk7a, with the only previously reported antibiosis-associated genes being small secreted cysteine-rich proteins. Although only one differentially expressed gene was common to both strains LTR-2 and Tk7a, numerous genes reportedly associated with pathogen antibiosis processes were differentially expressed in both strains, including degradative enzymes and membrane transport proteins. A number of novel potential antibiosis-related transcripts were found from strains LTR-2 and Tk7a and remain to be identified. The expression kinetics of 20 Trichoderma (10 from strain LTR-2, 10 from strain Tk7a) transcript-derived fragments (TDFs) were quantified by quantitative reverse transcription PCR (RT-qPCR) at pre- and post-mycelia contact stages of Trichoderma-prey interactions, thereby confirming differential gene expression. Collectively, this research is providing information to elucidate the antibiosis mechanisms and disease suppressive activities of T. afroharzianum and T. gamsii against soilborne fungal and oomycete plant pathogens.

Stenotrophomonas maltophilia strain B418 was isolated from a barley rhizosphere in China. This bacterium exhibits broad-spectrum inhibitory activities against plant pathogens and root-knot nematode along with growth-promoting effects. Here, we present the draft genome sequence of S. maltophilia B418.