Isolation of endophytic fungi from tropical forest in Indonesia

Penicillium citrinum, a Drought-Tolerant Endophytic Fungus Isolated from Wheat (Triticum aestivum L.) Leaves with Plant Growth-Promoting Abilities

Endophytic fungi have recently garnered significant attention as next-generation bioinoculants due to their plausible role in ameliorating abiotic and biotic stresses. This adaptation is achieved via various signalling molecules and mechanisms established by these symbionts with their hosts. The present study screened 61 endophytic isolates of culturable mycobiome associated with wheat variety PBW725 during their crop cycle. Three endophytic isolates exhibited a minimum reduction in their growth and maximum biomass production during the drought stress developed using polyethylene glycol 6000. Further, these isolates also exhibited plant growth promoting properties by virtue of the production of indole acetic acid, gibberellic acid and ammonia. These isolates also exhibited the propensity to solubilise phosphate and zinc, produce siderophores and further exhibit extracellular enzymatic activities, contributing to plants' adaptability to abiotic stresses. The best isolate amongst the three was #5TAKL-3a, identified as Penicillium citrinum based on multilocus phylogenetic analysis. The isolate as a bioinoculant enhances various biochemical and physiological properties in planta. Hence our studies indicate that Penicillium citrinum #5TAKL-3a is a potential candidate bioinoculant for field trials to improve the adaptability of the wheat plant under drought stress.

Nitrogen and phosphorus concentrations in growth media affect the relationship between root endophytic fungi and host plant

Endophytic fungi (EPF) colonize plant roots and enhance their growth. The relationship between host plant and EPF can be affected by several factors, such as growth media, host species, and fungal species. The objective of this study was to clarify the effect of nutrient concentration in growth media on the relationship between host plant and root EPF. Brassica campestris was grown in 1/100 Murashige and Skoog (MS), 1/10 MS, 1/100 MS and 1/10 nitrogen (high N), and 1/100 MS and 1/10 phosphorus (high P) media. B. campestris was inoculated with four root EPFs isolated from forest soils in Indonesia and harvested 28 days after transplant. Shoot dry weight (SDW) and colonization in roots were measured. All the isolates colonized roots of B. campestris. Two isolates increased the SDW of B. campestris grown on 1/100 MS media. The shoot growth response of B. campestris to EPF colonization on 1/100 MS was higher than that on 1/100 high N and 1/100 high P MS media. These results suggest that concentration of nitrogen and phosphorus in growth media determine the relationship between B. campestris and root EPF.

The Inhibitory Effect of Endophyte-Infected Tall Fescue on White Clover Can Be Alleviated by Glomus mosseae Instead of Rhizobia

In artificial ecosystems, mixed planting of gramineous and leguminous plants can have obvious advantages and is very common. Due to their improved growth performances and stress tolerance, endophyte-infected grasses are considered to be ideal plant species for grasslands. However, endophytic fungi can inhibit the growth of neighboring nonhost leguminous plants. In this study, we chose endophyte-infected and endophyte-free tall fescue (Lolium arundinaceum Darbyshire ex. Schreb.) and clover (Trifolium repens) as the experimental materials to explore whether arbuscular mycorrhizal fungi and rhizobium can alleviate the inhibitory effect of endophyte infection on clover. The results showed that endophytic fungi significantly reduced clover biomass. Arbuscular mycorrhizal fungi inoculation significantly increased the biomass of clover in both endophyte-infected tall fescue/clover and endophyte-free tall fescue/clover systems but the beneficial contribution of arbuscular mycorrhizal fungi was more obvious in the endophyte-infected tall fescue/clover system. Rhizobia inoculation could alleviate the detrimental effect of tall fescue on the growth of clover but did not alleviate the detrimental effect of endophyte infection on the growth of clover.

Isolation and screening of stress-resistant endophytic fungus strains from wild and cultivated soybeans in cold region of China

In this study, we firstly reported the large-scale screening and isolation of endophytic fungi from nine wild and six cultivated soybeans in the cold regions of China. We totally isolated 302 endophytic fungal strains, of which 215 strains are isolated from the wild soybeans and 87 are identified from cultivated soybeans. Among these endophytic fungal strains, in the roots, stems, and leaves, 24.17% were isolated from roots, 28.8% were isolated from stems, and 47.01% were isolated from leaves, respectively. Most endophytic fungal strains isolated from the wild soybean roots were the species of Fusarium genus, and the fungal strains in the stems were the species of ascomycetes and Fusarium fungi, whereas most strains in the leaves were Alternaria fungi. To analyze the taxonomy of the obtained samples, we sequenced and compared their rDNA internal transcribed spacer (ITS) sequences. The data showed that 6 strains are putatively novel strains exhibiting ≤ 97% homology with the known strains. We next measured the secondary metabolites produced by the different strains and we found 11 strains exhibited high-performance synthesis of triterpenoids, phenols, and polysaccharides. Furthermore, we characterized their tolerance to abiotic stresses. The results indicated that 4 strains exhibited high tolerance to cadmium, and some strains exhibited resistance to acid, and alkali. The results of the study could facilitate the further exploration of the diversity of plant endophytic fungi and the potential applications of the fungi to practical agriculture and medicine industries. KEY POINTS: • 302 endophytic fungal strains isolated from wild soybean and cultivated soybean • 11 strains had high contents of triterpenoids, phenols, and polysaccharides • 4 strains exhibited high Cd tolerance, and a few strains with strong tolerance to acid and alkali solution.

Unravelling the effects of tropical land use conversion on the soil microbiome

BACKGROUND

The consequences of deforestation and agricultural treatments are complex and affect all trophic levels. Changes of microbial community structure and composition associated with rainforest conversion to managed systems such as rubber and oil palm plantations have been shown by 16S rRNA gene analysis previously, but functional profile shifts have been rarely addressed. In this study, we analysed the effects of rainforest conversion to different converted land use systems, including agroforestry ("jungle rubber") and monoculture plantations comprising rubber and oil palm, on soilborne microbial communities by metagenomic shotgun sequencing in Sumatra, Indonesia.

RESULTS

The diversity of bacteria and archaea decreased whereas diversity of fungi increased in the converted land use systems. The soil microbiome was dominated by bacteria followed by fungi. We detected negative effects of land use conversion on the abundance of Proteobacteria (especially on Rhizobiales and Burkholderiales) and positive effects on the abundance of Acidobacteria and Actinobacteria. These abundance changes were mainly driven by pH, C:N ratio, and Fe, C and N content. With increasing land use intensity, the functional diversity decreased for bacteria, archaea and fungi. Gene abundances of specific metabolisms such as nitrogen metabolism and carbon fixation were affected by land use management practices. The abundance of genes related to denitrification and nitrogen fixation increased in plantations while abundance of genes involved in nitrification and methane oxidation showed no significant difference. Linking taxonomic and functional assignment per read indicated that nitrogen metabolism-related genes were mostly assigned to members of the Rhizobiales and Burkholderiales. Abundances of carbon fixation genes increased also with increasing land use intensity. Motility- and interaction-related genes, especially genes involved in flagellar assembly and chemotaxis genes, decreased towards managed land use systems. This indicated a shift in mobility and interspecific interactions in bacterial communities within these soils.

CONCLUSIONS

Rainforest conversion to managed land use systems drastically affects structure and functional potential of soil microbial communities. The decrease in motility- and interaction-related functions from rainforest to converted land use systems indicated not only a shift in nutrient cycling but also in community dynamics. Fertilizer application and correspondingly higher availability of nutrients in intensively managed plantations lead to an environment in which interspecific interactions are not favoured compared to rainforest soils. We could directly link effects of land management, microbial community structure and functional potential for several metabolic processes. As our study is the first study of this size and detail on soil microbial communities in tropical systems, we provide a basis for further analyses.

Dark Septate Endophytes Improve the Growth and the Tolerance of Medicago sativa and Ammopiptanthus mongolicus Under Cadmium Stress

Although the ecological function of dark septate endophytes (DSEs) is well studied, little is known about the responses of the host plant to DSEs obtained from other plants, especially under conditions of heavy metal stress. This study aimed to investigate how DSEs from a heavy-metal habitat affect non-host plants in cadmium (Cd) stress soils, which then provides a basis for the application of DSEs in the cultivation of different plant and soil remediation strategies for polluted ecosystems. We isolated and identified two species of DSE (Acrocalymma vagum and Scytalidium lignicola) inhabiting the roots of Ilex chinensis (host plant) which are grown in metal-polluted habitats. Then, the Cd stress tolerance of the DSEs was tested using a pure culture of which the Cd concentration has been adjusted. Subsequently, we examined the performance of non-host plants (Medicago sativa and Ammopiptanthus mongolicus) which were inoculated with DSEs under Cd stress in a growth chamber. The results indicated that the two DSEs could grow under Cd stress in vitro, even when not exhibiting high levels of tolerance to Cd. The superoxide dismutase (SOD), malondialdehyde (MDA), glutathione (GSH), soluble protein, and melanin of the DSE fungi reached maximal levels at concentrations of 30-60 mg Cd/L, indicating the important preventive strategies adopted by the DSE fungi in environments contaminated by Cd. Despite a decreased biomass of DSE hyphae with enhanced Cd concentrations, the accumulation of Cd in the DSE hyphae tended to show an increasing trend. Both DSEs were effective colonizers of the non-host plants. A. vagum and S. lignicola inoculation significantly promoted the biomass and the root architecture of the two non-host plants under Cd stress. A. vagum inoculation increased the total nitrogen (TN) of A. mongolicus, whereas inoculation with S. lignicola significantly increased the organic carbon (OC) of M. sativa. In particular, the DSE inoculation significantly improved the accumulation of Cd in plant tissues under Cd stress, demonstrating a potential application in the bio-remediation of heavy-metal-pollution areas. Our findings suggest that the DSE inoculation improved the root growth and nutrient absorption of non-host plants, altered the soil Cd concentration, and facilitated plant growth and survival under Cd stress. These results contribute to a better understanding of DSE-plant interactions in habitats contaminated by heavy metals.