Bacterial and fungal communities are differentially modified by melatonin in agricultural soils under abiotic stress

An extensive body of evidence from the last decade has indicated that melatonin enhances plant resistance to a range of biotic and abiotic stressors. This has led to an interest in the application of melatonin in agriculture to reduce negative physiological effects from environmental stresses that affect yield and crop quality. However, there are no reports regarding the effects of melatonin on soil microbial communities under abiotic stress, despite the importance of microbes for plant root health and function. Three agricultural soils associated with different land usage histories (pasture, canola or wheat) were placed under abiotic stress by cadmium (100 or 280 mg kg−1 soil) or salt (4 or 7 g kg−1 soil) and treated with melatonin (0.2 and 4 mg kg−1 soil). Automated Ribosomal Intergenic Spacer Analysis (ARISA) was used to generate Operational Taxonomic Units (OTU) for microbial community analysis in each soil. Significant differences in richness (α diversity) and community structures (β diversity) were observed between bacterial and fungal assemblages across all three soils, demonstrating the effect of melatonin on soil microbial communities under abiotic stress. The analysis also indicated that the microbial response to melatonin is governed by the type of soil and history. The effects of melatonin on soil microbes need to be regarded in potential future agricultural applications

Comparative analysis of structural variations due to genome shuffling of Bacillus subtilis VS15 for improved cellulase production

Cellulose is one of the most abundant and renewable biomass products used for the production of bioethanol. Cellulose can be efficiently hydrolyzed by Bacillus subtilis VS15, a strain isolate obtained from decomposing logs. A genome shuffling approach was implemented to improve the cellulase activity of Bacillus subtilis VS15. Mutant strains were created using ethyl methyl sulfonate (EMS), N-Methyl-N′ nitro-N-nitrosoguanidine (NTG), and ultraviolet light (UV) followed by recursive protoplast fusion. After two rounds of shuffling, the mutants Gb2, Gc8, and Gd7 were produced that had an increase in cellulase activity of 128%, 148%, and 167%, respectively, in comparison to the wild type VS15. The genetic diversity of the shuffled strain Gd7 and wild type VS15 was compared at whole genome level. Genomic-level comparisons identified a set of eight genes, consisting of cellulase and regulatory genes, of interest for further analyses. Various genes were identified with insertions and deletions that may be involved in improved celluase production in Gd7.. Strain Gd7 maintained the capability of hydrolyzing wheatbran to glucose and converting glucose to ethanol by fermentation with Saccharomyces cerevisiae of the wild type VS17. This ability was further confirmed by the acidified potassium dichromate (K2Cr2O7) method

New frontiers in agriculture productivity : optimised microbial inoculants and in situ microbiome engineering

Increasing agricultural productivity is critical to feed the ever-growing humanpopulation. Being linked intimately to plant health, growth and productivity, harnessing the plant microbiome is considered a potentially viable approach for the next green revolution, in an environmentally sustainable way. In recent years, our understanding of drivers, roles, mechanisms, along with knowledge to manipulate the plant microbiome, have significantly advanced. Yet, translating this knowledge to expand farm productivity and sustainability requires the development of solutions for a number of technological and logistic challenges. In this article, we propose new and emerging strategies to improve the survival and activity of microbial inoculants, including using selected indigenous microbes and optimising microbial delivery methods, as well as modern gene editing tools to engineer microbial inoculants. In addition, we identify multiple biochemical and molecular mechanisms and/approaches which can be exploited for microbiome engineering in situ to optimise plant-microbiome interactions for improved farm yields. These novel biotechnological approaches can provide effective tools to attract and maintain activities of crop beneficial microbiota that increase crop performance in terms of nutrient acquisition, and resistance to biotic and abiotic stresses, resulting in an increased agricultural productivity and sustainability

Plant microbiomes : do different preservation approaches and primer sets alter our capacity to assess microbial diversity and community composition?

The microbial communities associated with plants (the plant microbiome) play critical roles in regulating plant health and productivity. Because of this, in recent years, there have been significant increase in studies targeting the plant microbiome. Amplicon sequencing is widely used to investigate the plant microbiome and to develop sustainable microbial agricultural tools. However, performing large microbiome surveys at the regional and global scales pose several logistic challenges. One of these challenges is related with the preservation of plant materials for sequencing aiming to maintain the integrity of the original diversity and community composition of the plant microbiome. Another significant challenge involves the existence of multiple primer sets used in amplicon sequencing that, especially for bacterial communities, hampers the comparability of datasets across studies. Here, we aimed to examine the effect of different preservation approaches (snap freezing, fresh and kept on ice, and air drying) on the bacterial and fungal diversity and community composition on plant leaves, stems and roots from seven plant species from contrasting functional groups (e.g. C3, C4, N-Fixers, etc.). Another major challenge comes when comparing plant to soil microbiomes, as different primers sets are often used for plant vs. soil microbiomes. Thus, we also investigated if widely used 16S rRNA primer set (779F/1193R) for plant microbiome studies provides comparable data to those often used for soil microbiomes (341F/805R) using 86 soil samples. We found that the community composition and diversity of bacteria or fungi were robust to contrasting preservation methods. The primer sets often used for plants provided similar results to those often used for soil studies suggesting that simultaneous studies on plant and soil microbiomes are possible. Our findings provide novel evidence that preservation approaches do not significantly impact plant microbiome data interpretation and primer differences do not impact the treatment effect, which has significant implication for future large-scale and global surveys of plant microbiomes

Synthetic community improves crop performance and alters rhizosphere microbial communities

Introduction: Harnessing synthetic communities (SynCom) of plant growth‐promoting (PGP) microorganisms is considered a promising approach to improve crop fitness and productivity. However, biotic mechanisms that underpin improved plant performance and the effects of delivery mode of synthetic community are poorly understood. These are critical knowledge gaps that constrain field efficacy of SynCom and hence large‐ scale adoption by the farming community. Material & Methods: In this study, a SynCom of four PGP microbial species was constructed and applied to either as seed dressing (treatment T1, applied at the time of sowing) or to soil (treatment T2, applied in soil at true leaf stage) across five different cotton (Gossypium hirsutum) cultivars. The impact of SynCom on plant growth, rhizosphere microbiome and soil nutrient availability, and how this was modified by plant variety and mode of applications, was assessed. Results: Results showed that the seed application of SynCom had the strongest positive impact on overall plant fitness, resulting in higher germination (14.3%), increased plant height (7.4%) and shoot biomass (5.4%). A significant increase in the number of flowers (10.4%) and yield (8.5%) was also observed in T1. The soil nitrate availability was enhanced by 28% and 55% under T1 and T2, respectively. Results further suggested that SynCom applications triggered enrichment of members from bacterial phyla Actinobacteria, Firmicutes and Cyanobacteria in the rhizosphere. A shift in fungal communities was also observed, with a significant increase in the relative abundance of fungi from phyla Chytridiomycota and Basidiomycota in SynCom treatments. A structural equation model suggested that SynCom directly increased crop productivity but also indirectly via impacting the alpha diversity of bacteria. Conclusion: Overall, this study provides mechanistic evidence that SynCom applications can shift rhizosphere microbial communities and improve soil fertility, plant growth, and crop productivity, suggesting that their use could contribute toward sustainable increase in farm productivity

Incorporating fungal community ecology into invasion biology : challenges and opportunities

Recently, the role of the plant-associated mycobiome (i.e. the fungal community) in influencing the competitive success of invasive plant species has received increasing attention. Fungi act as primary drivers of the plant invasion process due to their ability to form both beneficial and detrimental relationships with terrestrial plant species. Here we review the role of the plant mycobiome in promoting or inhibiting plant species invasion into foreign ecosystems. Moreover, the potential to exploit these relationships for invasive plant control and restoration of native communities is discussed. Incorporating fungal community ecology into invasion and restoration biology will aid in the management and control of invasive plant species in Australia

Seeking the needle in the haystack : undetectability of mycorrhizal fungi outside of the plant rhizosphere associated with an endangered Australian orchid

Co-occurrence and abundance of suitable mycorrhizal fungi are expected to be important drivers for orchid seedling establishment and development, as well as mature plant distribution. However, limited information is available on the occurrence and spatial patterns of orchid mycorrhizal fungi in soil independent of the orchid host. In this study, we investigated the in situ distribution of Tulasnella spp. associated with the critically endangered Australian orchid Diuris fragrantissima. We tested and implemented a meta-barcoding approach (fungal ITS1 region) using three soil sources: orchid rhizosphere, orchid-associated bulk soil and bulk soil from the orchid native site. The quality-filtered data set revealed that the occurrence of Tulasnella spp. in situ is restricted to the orchid rhizosphere, suggesting that a limited number of potential recruitment micro-sites with suitable mycorrhizal taxa exists in the D. fragrantissima natural habitat. The meta-barcoding approach also revealed a distinctive fungal community associated with the orchid rhizosphere. Overall, Next Generation Sequencing technology has proven to be a suitable method for large-scale screening of mycorrhizal fungi in orchid-associated soil

Linking microbial diversity with ecosystem functioning through a trait framework

Trait-based microbial biogeography provides a path for the mechanistic understanding of relationships between microbial diversity and ecosystem functioning. In this mini-review, we identify the scenarios in which to use traits to characterize the microbial community and propose a simple trait-based conceptual framework to link microbial communities with ecosystem functions

Pentachlorophenol alters the acetate-assimilating microbial community and redox cycling in anoxic soils

Acetate is a common electron donor that can drive microbial reductive processes in anaerobic environments. Apart from acting as a terminal electron acceptor, chlorinated organic pollutant of pentachlorophenol (PCP) has antimicrobial properties but little is known about its effect on anaerobic microbial populations during bioremediation. To elucidate the effect of PCP on the anaerobic microbial community, DNA-based stable isotope probing was performed using 13 C-acetate as a substrate in two depths (0–20 cm and 80–100 cm) of mangrove soils. The addition of PCP had little influence on Fe(III) reduction, but dramatically inhibited the SO 4 2− reduction, resulting in a high emission of CH 4 under anoxic conditions. Correspondingly, PCP significantly affected the composition of prokaryotic 13 C-labeled OTUs (Operational Taxonomic Units) at both soil depths. Members of Clostridiales (Firmicutes) and Burkholderiales (Betaproteobacteria) were dominant 13 C-acetate utilizers and potential PCP degraders. The PCP addition decreased sulfate reduction process through inhibition of classical sulfate- and sulfur-reducing bacteria belonging to families of Desulfarculaceae, Desulfobulbaceae and Desulfobacteraceae. Our study showed that indigenous microbial communities associated with terminal electron-accepting pathways (e.g. Fe 3+ and SO 4 2− reduction) changed differently during PCP dechlorination. These findings suggest a great impact of chlorinated pollutants on the soil biogeochemical processes

New microbial tools to boost restoration and soil organic matters

Anthropogenic activities are causing unprecedented rates of soil and ecosystem degradation, and the current restoration practices take decades and are prone to high rates of failure. Here we propose, the development and application of emerging microbiome tools that can potentially improve the contents and diversity of soil organic matters, enhancing the efficacy and consistency of restoration outcomes