Plant Microbiome Research Articles

Root rot destabilizes the Sanqi rhizosphere core fungal microbiome by reducing the negative connectivity of beneficial microbes.

The stability of microbial communities, especially among core taxa, is essential for supporting plant health. However, the impacts of disease infection on the stability of rhizosphere fungal core microbiome remain largely unexplored. In this study, we delved into the effects of root rot infestation on the community structure, function, network complexity, and stability of Sanqi fungal core microbiomes, employing amplicon sequencing combined with co-occurrence network and cohesion analyses. Our investigation revealed that root rot disease led to a decrease in the α-diversity but an increase in the β-diversity of the Sanqi fungal core microbiomes in the rhizosphere. Notably, Ilyonectria, Plectosphaerella, and Fusarium emerged as indicator species in the rhizosphere core microbiome of root rot-infected Sanqi plants, while Mortierella predominated as the dominant biomarker taxa in healthy soils. Additionally, root rot diminished the complexity and modularity of the rhizosphere networks by reducing the metrics associated with nodes, edges, degrees, and modularity. Furthermore, root rot resulted in a reduction in the proportion of negative connections in the network and the negative/positive cohesion of the entire core fungal microbiome. Particularly noteworthy was the observation that root rot infection destabilized the rhizosphere core fungal microbiome by weakening the negative connectivity associated with beneficial agents. Collectively, these results highlight the significance of the negative connectivity of beneficial agents in ensuring the stability of core microbial community.IMPORTANCERoot rot disease has been reported as the most devastating disease in the production process of artificial cultivated Sanqi ginseng, which seriously threatens the Sanqi industry. This study provides valuable insights into how root rot influences microbial relationships within the community. These findings open up opportunities for disease prevention and the promotion of plant health by regulating microbial interactions. In summary, the research sheds light on the ecological consequences of root rot on rhizosphere fungal microbiomes and offers potential strategies for managing soil-borne diseases and enhancing plant health.

Unveiling the microbiome of hydroponically cultivated lettuce: impact of Phytophthora cryptogea infection on plant-associated microorganisms.

Understanding the complex interactions between plants and their associated microorganisms is crucial for optimizing plant health and productivity. While microbiomes of soil-bound cultivated crops are extensively studied, microbiomes of hydroponically cultivated crops have received limited attention. To address this knowledge gap, we investigated the rhizosphere and root endosphere of hydroponically cultivated lettuce. Additionally, we sought to explore the potential impact of the oomycete pathogen Phytophthora cryptogea on these microbiomes. Root samples were collected from symptomatic and nonsymptomatic plants in three different greenhouses. Amplicon sequencing of the bacterial 16S rRNA gene revealed significant alterations in the bacterial community upon P. cryptogea infection, particularly in the rhizosphere. Permutational multivariate analysis of variance (perMANOVA) revealed significant differences in microbial communities between plants from the three greenhouses, and between symptomatic and nonsymptomatic plants. Further analysis uncovered differentially abundant zero-radius operational taxonomic units (zOTUs) between symptomatic and nonsymptomatic plants. Interestingly, members of Pseudomonas and Flavobacterium were positively associated with symptomatic plants. Overall, this study provides valuable insights into the microbiome of hydroponically cultivated plants and highlights the influence of pathogen invasion on plant-associated microbial communities. Further research is required to elucidate the potential role of Pseudomonas and Flavobacterium spp. in controlling P. cryptogea infections within hydroponically cultivated lettuce greenhouses.

Predictions of rhizosphere microbiome dynamics with a genome-informed and trait-based energy budget model

Soil microbiomes are highly diverse, and to improve their representation in biogeochemical models, microbial genome data can be leveraged to infer key functional traits. By integrating genome-inferred traits into a theory-based hierarchical framework, emergent behaviour arising from interactions of individual traits can be predicted. Here we combine theory-driven predictions of substrate uptake kinetics with a genome-informed trait-based dynamic energy budget model to predict emergent life-history traits and trade-offs in soil bacteria. When applied to a plant microbiome system, the model accurately predicted distinct substrate-acquisition strategies that aligned with observations, uncovering resource-dependent trade-offs between microbial growth rate and efficiency. For instance, inherently slower-growing microorganisms, favoured by organic acid exudation at later plant growth stages, exhibited enhanced carbon use efficiency (yield) without sacrificing growth rate (power). This insight has implications for retaining plant root-derived carbon in soils and highlights the power of data-driven, trait-based approaches for improving microbial representation in biogeochemical models.

Identification of synthetic consortia from a set of plant-beneficial bacteria.

The use of microbial inoculants in agriculture as biofertilisers and/or biopesticides is an appealing alternative to replace or reduce the practice of agrochemicals. Plant microbiota studies are revealing the different bacterial groups which are populating plant microbiomes re-energising the plant probiotic bacteria (PPB) translational research sector. Some single-microbial strain bioinoculants have proven valid in agriculture (e.g., based on Trichoderma, mycorrhiza or rhizobia); however, it is now recommended to consider multistrain consortia since plant-beneficial effects are often a result of community-level interactions in plant microbiomes. A limiting step is the selection of a fitting combination of microbial strains in order to accomplish the best beneficial effect upon plant inoculation. In this study, we have used a subset of 23 previously identified and characterised rice-beneficial bacterial colonisers to design and test a series of associated experiments aimed to identify potential PPB consortia which are able to co-colonise and induce plant growth promotion. Bacterial strains were co-inoculated in vitro and in planta using several different methods and their co-colonisation and co-persistence monitored. Results include the identification of two 5-strain and one 2-strain consortia which displayed plant growth-promoting features. Future practical applications of microbiome research must include experiments aimed at identifying consortia of bacteria which can be most effective as crop amendments.

Impact of bacterial and fungal inoculants on the resident rhizosphere microbiome and the volatilome of tomato plants under leaf herbivory stress.

Various studies have addressed the impact of microbial inoculants on the composition of the resident microbiome. How microbial inoculants impact plant metabolism and interact with the resident rhizobiota under herbivory stress remains elusive. Here, we investigated the impact of two bacterial and two fungal inoculants, inoculated as single species and as a synthetic community, on the rhizosphere microbiome and volatilome of tomato plants (Solanum lycopersicum) comparing nonstress conditions to exposed to leaf herbivory by Spodoptera exigua. Based on amplicon sequencing analysis, rhizobacterial community composition was significantly affected by all four inoculants and the magnitude of this effect was dependent on herbivory stress. Fungal community composition was altered by the microbial inoculants but independent of herbivory stress. The rhizosphere volatilome was impacted by the microbial inoculation and differences between treatments were evened under herbivory stress. Each microbial inoculant caused unique changes in the volatilome of stressed plants but also shared similar responses, in particular the enhanced production of dimethyl disulfide and benzothiazole. In conclusion, the introduction of microbial inoculants in the tomato rhizosphere caused unique as well as common changes in the rhizosphere microbiome and volatilome, but these changes were minor compared to the microbiome changes induced by herbivory stress.

Rhizosphere microbiome of plants used in phytoremediation of mine tailing dams

Rhizospheric microbial communities improve the effectiveness of hyperaccumulators in the phytoremediation of heavy metals. However, limited access to tailing dams and inadequate assessment of plants’ phytoremediation potential limit the characterization of native accumulators, hindering the effectiveness of local remediation efforts. This study evaluates the heavy metal sequestration potentials of Pennisetum purpureum, Leucaena leucocephala, and Pteris vittata and their associated rhizospheric microbial communities at the Marlu and Pompora tailing dams in Ghana. The results indicate shoot hyperaccumulation of Cd (334.5 ± 6.3 mg/kg) and Fe (10,647.0 ± 12.6 mg/kg) in P. purpureum and L. leucocephala, respectively. Analysis of rhizospheric bacterial communities revealed the impact of heavy metal contamination on bacterial community composition, associating Fe and Cd hyperaccumulation with Bacillus, Arthrobacter, and Sphingomonas species. This study reports the hyperaccumulation potentials of L. leucocephala and P. purpureum enhanced by associated rhizosphere bacterial communities, suggesting their potential application as an environmentally friendly remediation process of heavy metals contaminated lands.

Influence of cultivation duration on microbial taxa aggregation in Panax ginseng soils across ecological niches.

Microbial communities are crucial for plant health and productivity. However, the influence of cultivation age on the ecological processes in assembling plant microbiomes at various ecological niches remains unclear. We selected 12 samples from ginseng farmlands with different cultivation years (N4: 4 years old, N6: 6 years old). We used soil physicochemical properties, enzyme activities, and high-throughput sequencing (16S rDNA and ITS) to examine the rhizoplane (RP), rhizosphere (RS), and bulk soil (BS). Our results indicated that cultivation years significantly affect the soil microbiome's diversity and community composition across different ecological niches. The BS microbiome experienced the largest effect, while the RS experienced the smallest. N6 showed a greater impact than N4. This effect was more pronounced on the fungal communities than the bacterial communities of various ecological niches and can be closely related to the soil's physicochemical properties. In N4 soils, we observed an upward trend in both the number of ASVs (amplicon sequence variations) and the diversity of soil microbial taxa across various ecological niches. In N4RP, the bacteria Sphingomonas, known for degrading toxic soil compounds, was present. All ecological niches in N4 showed significant enrichment of Tetracladium fungi, positively associated with crop yield (N4RP at 6.41%, N4RS at 11.31%, and N4BS at 3.45%). In N6 soils, we noted a stark decline in fungal diversity within the BS, with a 57.5% reduction in ASVs. Moreover, Sphingomonas was abundantly present in N6RS and N6BS soils. The relative abundance of the pathogen-inhibiting fungus Exophiala in N6RP and N6RS reached 34.18% and 13.71%, respectively, marking increases of 4.9-fold and 7.7-fold. Additionally, another pathogeninhibiting fungus, Humicola, showed significant enrichment in N6BS, with a 7.5-fold increase. The phenolic acid-producing fungus Pseudogymnoascus in N6RP, N6RS, and N6BS showed increases of 2.41-fold, 2.55-fold, and 4.32-fold, respectively. We hypothesize that functional genes related to the metabolism of terpenoids and polyketides, as well as signaling molecules and interactions, regulate soil microbial taxa in ginseng from different cultivation years. In conclusion, our study enhances understanding of plant-microbe interactions and aids the sustainable development of medicinal plants, particularly by addressing ginseng succession disorder.

Manipulation of the seagrass-associated microbiome reduces disease severity.

Host-associated microbes influence host health and function and can be a first line of defence against infections. While research increasingly shows that terrestrial plant microbiomes contribute to bacterial, fungal, and oomycete disease resistance, no comparable experimental work has investigated marine plant microbiomes or more diverse disease agents. We test the hypothesis that the eelgrass (Zostera marina) leaf microbiome increases resistance to seagrass wasting disease. From field eelgrass with paired diseased and asymptomatic tissue, 16S rRNA gene amplicon sequencing revealed that bacterial composition and richness varied markedly between diseased and asymptomatic tissue in one of the two years. This suggests that the influence of disease on eelgrass microbial communities may vary with environmental conditions. We next experimentally reduced the eelgrass microbiome with antibiotics and bleach, then inoculated plants with Labyrinthula zosterae, the causative agent of wasting disease. We detected significantly higher disease severity in eelgrass with a native microbiome than an experimentally reduced microbiome. Our results over multiple experiments do not support a protective role of the eelgrass microbiome against L. zosterae. Further studies of these marine host-microbe-pathogen relationships may continue to show new relationships between plant microbiomes and diseases.

Colonization compatibility with Bacillus altitudinis confers soybean seed rot resistance.

The plant microbiome and plant-associated bacteria are known to support plant health, but there are limited studies on seed and seedling microbiome to reveal how seed-associated bacteria may confer disease resistance. In this study, the application of antibiotics on soybean seedlings indicated that seed-associated bacteria were involved in the seed rot resistance against a soil-borne pathogen Calonectria ilicicola, but this resistance cannot be carried to withstand root rot. Using PacBio 16S rRNA gene full-length sequencing and microbiome analyses, 14 amplicon sequence variants (ASVs) including 2 ASVs matching to Bacillus altitudinis were found to be more abundant in the four most resistant varieties versus the four most susceptible varieties. Culture-dependent isolation obtained two B. altitudinis isolates that both exhibit antagonistic capability against six fungal pathogens. Application of B. altitudinis on the most resistant and susceptible soybean varieties revealed different colonization compatibility, and the seed rot resistance was restored in the five varieties showing higher bacterial colonization. Moreover, quantitative PCR confirmed the persistence of B. altitudinis on apical shoots till 21days post-inoculation (dpi), but 9 dpi on roots of the resistant variety TN5. As for the susceptible variety HC, the persistence of B. altitudinis was only detected before 6 dpi on both shoots and roots. The short-term colonization of B. altitudinis on roots may explain the absence of root rot resistance. Collectively, this study advances the insight of B. altitudinis conferring soybean seed rot resistance and highlights the importance of considering bacterial compatibility with plant varieties and colonization persistence on plant tissues.

Responses of plant immune system and rhizosphere soil microbiome to the elicitor BAR11 in Arabidopsis thaliana

Microbial elicitors have been shown to boost plant immunity by inducing defense responses to reduce plant disease. However, little is known about the changes in plant microbiome and metabolism in the process of enhancing plant immunity with elicitors. The protein elicitor BAR11, from Saccharothrix yanglingensis Hhs.015, induces defense responses in Arabidopsis thaliana that enhances resistance to pathogens. In this study, bar11 was inserted into Col-0 A. thaliana to obtain BAR11-Trans plant by Agrobacterium-mediated immersion transformation. BAR11-Trans exhibited an elevated defense level against Pseudomonas syringae pv. tomato DC3000 while experiencing a decline in biomass production of above-ground parts. In the process, BAR11-Trans increased the activity of phenylalanine ammonia lyase (PAL) and catalase (CAT), and up-regulated genes related to plant defense pathways. Furthermore, BAR11-Trans decreased root tip reactive oxygen species (ROS) levels while increasing ROS burst in the leaves. Soil transplantation experiments showed that soil planted with BAR11-Trans could enhance the resistance of Col-0 A. thaliana to DC3000. Analysis of A. thaliana rhizosphere soil through 16S rRNA amplified sequencing revealed that BAR11-Trans increased the relative abundance and diversity of the rhizosphere microbial community, leading to the recruitment of more plant probiotics. Additionally, the accumulation of kaempferitrin and robinin in BAR11-Trans influenced the physicochemical properties of rhizosphere soil and the composition of the bacterial community. In summary, BAR11-Trans exhibited heightened defense levels compared to Col-0, leading to increased secretion of secondary metabolites and the recruitment of a greater number of microorganisms to adapt to the environment. These findings offer novel insights for the potential application of elicitors in agricultural disease control.

Wild plant species with broader precipitation niches exhibit stronger host selection in rhizosphere microbiome assembly.

Plants actively recruit microbes from the soil, forming species-specific root microbiomes. However, their relationship with plant adaptations to temperature and precipitation remains unclear. Here we examined the host-selected and conserved microbiomes of 13 native plant species in the Xilingol steppe, Inner Mongolia, a semi-arid region in China. By calculating the global precipitation and temperature niches of these plants, considering plant phylogenetic distances, and analyzing functional traits, we found that these factors significantly influenced the rhizosphere microbiome assembly. We further quantified the strength of host selection and observed that plants with wider precipitation niches exhibited greater host selection strength in their rhizosphere microbiome assembly and higher rhizosphere bacterial diversity. In general, the rhizosphere microbiome showed a stronger link to plant precipitation niches than temperature niches. Haliangium exhibited consistent responsiveness to host characteristics. Our findings offer novel insights into host selection effects and the ecological determinants of wild plant rhizosphere microbiome assembly, with implications for steering root microbiomes of wild plants and understanding plant-microbiome evolution.

Potato Microbiome: Relationship with Environmental Factors and Approaches for Microbiome Modulation.

Every land plant exists in a close relationship with microbial communities of several niches: rhizosphere, endosphere, phyllosphere, etc. The growth and yield of potato-a critical food crop worldwide-highly depend on the diversity and structure of the bacterial and fungal communities with which the potato plant coexists. The potato plant has a specific part, tubers, and the soil near the tubers as a sub-compartment is usually called the "geocaulosphere", which is associated with the storage process and tare soil microbiome. Specific microbes can help the plant to adapt to particular environmental conditions and resist pathogens. There are a number of approaches to modulate the microbiome that provide organisms with desired features during inoculation. The mechanisms of plant-bacterial communication remain understudied, and for further engineering of microbiomes with particular features, the knowledge on the potato microbiome should be summarized. The most recent approaches to microbiome engineering include the construction of a synthetic microbial community or management of the plant microbiome using genome engineering. In this review, the various factors that determine the microbiome of potato and approaches that allow us to mitigate the negative impact of drought and pathogens are surveyed.

Selective regulation of endophytic bacteria and gene expression in soybean by water-soluble humic materials

BackgroundAs part of the plant microbiome, endophytic bacteria play an essential role in plant growth and resistance to stress. Water-soluble humic materials (WSHM) is widely used in sustainable agriculture as a natural and non-polluting plant growth regulator to promote the growth of plants and beneficial bacteria. However, the mechanisms of WSHM to promote plant growth and the evidence for commensal endophytic bacteria interaction with their host remain largely unknown. Here, 16S rRNA gene sequencing, transcriptomic analysis, and culture-based methods were used to reveal the underlying mechanisms.ResultsWSHM reduced the alpha diversity of soybean endophytic bacteria, but increased the bacterial interactions and further selectively enriched the potentially beneficial bacteria. Meanwhile, WSHM regulated the expression of various genes related to the MAPK signaling pathway, plant-pathogen interaction, hormone signal transduction, and synthetic pathways in soybean root. Omics integration analysis showed that Sphingobium was the genus closest to the significantly changed genes in WSHM treatment. The inoculation of endophytic Sphingobium sp. TBBS4 isolated from soybean significantly improved soybean nodulation and growth by increasing della gene expression and reducing ethylene release.ConclusionAll the results revealed that WSHM promotes soybean nodulation and growth by selectively regulating soybean gene expression and regulating the endophytic bacterial community, Sphingobium was the key bacterium involved in plant-microbe interaction. These findings refined our understanding of the mechanism of WSHM promoting soybean nodulation and growth and provided novel evidence for plant-endophyte interaction.

Structural modelling and functional analysis of Pseudomonas ACC deaminase: An in silico study

The activity of 1-aminocyclopropane-1-carboxylate (ACC) deaminase enzyme and its impact on regulating ethylene concentrations and plant ACC are fundamental characteristic found in plant-associated rhizobacteria. ACC deaminase-producing bacteria, such as Pseudomonas mitigate the detrimental effects of high levels of ethylene and ACC in plant-microbe interactions, resulting in improved plant growth and development. Different species within the Pseudomonas genus are commonly found in plant microbiome worldwide. Their adaptation to the plant-associated environment makes several Pseudomonas strains highly promising for advancing novel sustainable biotechnological and agricultural solutions, particularly those exhibiting ACC deaminase activity. Thus, the present study conducted a comprehensive in silico analysis focusing on the structural and functional characteristics of ACC deaminase protein of Pseudomonas spp. The study explored correlations based on phylogenetic relatedness using both ACC deaminase enzymes and their respective genes across different Pseudomonas species and strains. This study also investigated physiochemical properties, CATH classification and STRING analysis using various bioinformatics tools. Pseudomonas brassicacearum was selected as the representative species from the Pseudomonas genus for the 3D modeling of ACC deaminase protein. The acidic ACC deaminase protein has an average molecular weight of around 25.30 kDa, with a high percentage of alpha helices in its secondary structure, demonstrating its thermal stability. This theoretical assessment of the structure and function of ACC deaminase-producing Pseudomonas could assist researchers in understanding the ACC deaminase protein, potentially facilitating a better understanding of plant-microbe interactions, and aiding in the selection of highly efficient strains for various agricultural applications.

Understanding the bacterial community structure associated with the Eichhornia crassipes rootzone.

Plant microbiome acts as an interface between plants and their environment, aiding in the functioning of the ecosystem, such as protection against abiotic and biotic stress along with improving nutrient uptake. The rhizosphere is an essential interface for the interaction between plants and microbes and plays a substantial part in the removal as well as uptake of heavy metals and antibiotics from contaminated locations. Eichhornia crassipes is a promising plant that contains a rich community of microbes in its rhizosphere. Microorganism's association with plants embodies a crucial pathway via which humans can also be exposed to antibiotic-resistant genes and bacteria. In our earlier study enhanced removal of ciprofloxacin was observed by plant growth-promoting Microbacterium sp. WHC1 in the presence of E. crassipes root exudates. Therefore, the V3-V4, hypervariable region of the 16S rRNA gene was studied to assess the bacterial diversity and functional profiles of the microbiota associated with plant roots. Using the QIIME software program, 16S rRNA data from the Next Generation Sequencing (NGS) platform was examined. Alpha diversity including Chao1, Observed Shannon, and Simpson index denote significantly higher bacterial diversity. Proteobacteria (79%) was the most abundant phylum which was present in the root samples followed by Firmicutes (8%) and Cyanobacteria (8%). Sulfuricurvum (36%) is the most abundant genus belonging to the family Helicobacteraceae and the species kujiense in the genus Sulfuricurvum is the most abundant species present in the root sample. Also, the bacterial communities in the rhizoplane of Eichhornia crassipes harbor the genes conferring resistance to beta-lactams, tetracycline, fluoroquinolones, and penams. Metagenomic studies on the E. crassipes microbiome showed that the bacterial communities constituting the root exudates of the Eichhornia aid them to survive in a polluted environment.

Insights into Endophytic and Rhizospheric Bacteria of Five Sugar Beet Hybrids in Terms of Their Diversity, Plant-Growth Promoting, and Biocontrol Properties

Sugar beet is the most important crop for sugar production in temperate zones. The plant microbiome is considered an important factor in crop productivity and health. Here, we investigated the bacterial diversity of seeds, roots, and rhizosphere of five sugar beet hybrids named Eduarda (ED), Koala (KO), Tibor (T), Tajfun (TF), and Cercospora-resistant (C). A culture-independent next-generation sequencing approach was used for the further investigation of seed-borne endophytes. Hybrid-associated bacteria were evaluated for their plant growth–promoting (PGP) characteristics, antagonistic activity towards Cercospora beticola and several Fusarium strains in dual culture assays, and drought and salinity tolerance. High-throughput sequencing revealed that the Proteobacteria phylum was most dominant in the seeds of all hybrids, followed by Cyanobacteria and Actinobacteriota. The predominant genus in all hybrids was Pantoea, followed by Pseudomonas, Acinetobacter, Chalicogloea, Corynebacterium, Enterobacter, Enterococcus, Glutamicibacter, Kosakonia, and Marinilactibacillus. Unique genera in the hybrids were Pleurocapsa and Arthrobacter (T), Klebsiella (TF), Apibacter (ED), and Alloscardovia (KO). The genera that were most represented in one hybrid were Weissella and Staphylococcus (TF); Streptococcus (T); Gardnerella, Prevotella, and Rothia (KO); and Gilliamella, Lactobacillus, and Snodgrassella (ED). Thirty-two bacteria out of 156 isolates from the rhizosphere, roots, and seeds were selected with respect to various plant growth–promoting activities in vitro, i.e., nitrogen fixation, phosphate solubilization, siderophore production, indole-3-acetic acid production, 1-aminocyclopropane-1-carboxylic acid deaminase activity, hydrogen cyanide production, exoenzymatic activity (amylase, protease, lipase, cellulase, xylanase, mannanases, gelatinase, and pectinase), mitigation of environmental stresses, and antifungal activity. Mixta theicola KO3-44, Providencia vermicola ED3-10, Curtobacterium pusillum ED2-6, and Bacillus subtilis KO3-18 had the highest potential to promote plant growth due to their multiple abilities (nitrogen fixation, phosphate solubilization, production of siderophores, and IAA). The best antagonistic activity towards phytopathogenic fungi was found for Bacillus velezensis C3-19, Paenibacillus polymyxa C3-36 and Bacillus halotolerans C3-16/2.1. Only four isolates B. velezensis T2-23, B. subtilis T3-4, B. velezensis ED2-2, and Bacillus halotolerans C3-16/2.1 all showed enzymatic activity, with the exception of xylanase production. B. halotolerans C3-16/2.1 exhibited the greatest tolerance to salinity, while two B. subtilis strains (C3-62 and TF2-1) grew successfully at the maximum concentration of PEG. The current study demonstrates that sugar beet–associated bacteria have a wide range of beneficial traits and are therefore highly promising for the formulation of biological control and PGP agents.

Microbiome analysis reveals Microcystis blooms endogenously seeded from benthos within wastewater maturation ponds.

Toxigenic Microcystis blooms periodically disrupt the stabilization ponds of wastewater treatment plants (WWTPs). Dense proliferations of Microcystis cells within the surface waters (SWs) impede the water treatment process by reducing the treatment efficacy of the latent WWTP microbiome. Further, water quality is reduced when conventional treatment leads to Microcystis cell lysis and the release of intracellular microcystins into the water column. Recurrent seasonal Microcystis blooms cause significant financial burdens for the water industry and predicting their source is vital for bloom management strategies. We investigated the source of recurrent toxigenic Microcystis blooms at Australia's largest lagoon-based municipal WWTP in both sediment core (SC) and SW samples between 2018 and 2020. Bacterial community composition of the SC and SW samples according to 16S rRNA gene amplicon sequencing showed that Microcystis sp. was dominant within SW samples throughout the period and reached peak relative abundances (32%) during the summer. The same Microcystis Amplicon sequence variants were present within the SC and SW samples indicating a potential migratory population that transitions between the sediment water and SWs during bloom formation events. To investigate the potential of the sediment to act as a repository of viable Microcystis cells for recurrent bloom formation, a novel in-vitro bloom model was established featuring sediments and sterilized SW collected from the WWTP. Microcystin-producing Microcystis blooms were established through passive resuspension after 12 weeks of incubation. These results demonstrate the capacity of Microcystis to transition between the sediments and SWs in WWTPs, acting as a perennial inoculum for recurrent blooms.IMPORTANCECyanobacterial blooms are prevalent to wastewater treatment facilities owing to the stable, eutrophic conditions. Cyanobacterial proliferations can disrupt operational procedures through the blocking of filtration apparatus or altering the wastewater treatment plant (WWTP) microbiome, reducing treatment efficiency. Conventional wastewater treatment often results in the lysis of cyanobacterial cells and the release of intracellular toxins which pose a health risk to end users. This research identifies a potential seeding source of recurrent toxigenic cyanobacterial blooms within wastewater treatment facilities. Our results demonstrate the capacity of Microcystis to transition between the sediments and surface waters (SWs) of wastewater treatment ponds enabling water utilities to develop adequate monitoring and management strategies. Further, we developed a novel model to demonstrate benthic recruitment of toxigenic Microcystis under laboratory conditions facilitating future research into the genetic mechanisms behind bloom development.

Cultivation modes impacting root microbiomes and metabolites in medicinal orchid Dendrobium denneanum

IntroductionThe plant microbiome is the second genome of plants and is important for plant growth and health. Dendrobium is an epiphytic herbal plant of the family Orchidaceae that is often found attached to tree trunks or rocks and exhibits different cultivation modes. Microbiological and metabolite studies of Dendrobium denneanum Kerr (D. denneanum) in different cultivation modes can reveal important relationships between Dendrobium spp., their microbiomes, and their pharmacological substances, which is important for sustainable agricultural development and human health, particularly in the study of medicinal plants.MethodsIn this study, three cultivation modes, living tree epiphytic (LT), stone epiphytic (SE), and pot cultivation (PO) of D. denneanum in the same environment were selected, and the metabolites were using ultra-high performance liquid chromatography-quadrupole time-of-flight mass spectrometry (UPLC-Q-TOF-MS). Subsequently, differential metabolites were screened, the rhizosphere and root endosphere microorganisms were sequenced via high-throughput sequencing, and the 16S rRNA gene/ITS sequences were obtained.ResultsThe main microbial taxa in the rhizosphere and root endosphere of D. denneanum included bacteria belonging to Proteobacteria, Actinobacteria, and Actinobacteria, and the fungi Basidiomycota and Ascomycota, whose abundances varied in different cultivation modes. Soil properties affect the composition of D. denneanum metabolites and root microbiome, among which, soil total phosphorus (TP) and pH in particular are important factors for soil microorganisms. Studies of root microbial communities have shown that root endosphere fungi are similar to rhizosphere fungi with microbial enrichment occurring from the external environment to the internal structures. Root microbial communities and metabolites correlation analyses revealed significant correlations between rhizosphere microbes, as well as endophytes and metabolites. For example, the rhizosphere bacterium genus Occallatibacter and root endosphere fungus Clonostachys showed a significant negative correlation with the pharmacodynamic substance gigantol in D. denneanum (P<0.05).ConclusionThis study elucidates the effects of different cultivation modes on D. denneanum from the perspective of microorganisms and metabolites, and investigates the effects of root microorganisms on metabolites. The findings enhance the current understanding of root microorganisms in orchid plants and provide a theoretical basis for the cultivation of Dendrobium spp., represented here by D. denneanum.

Interplay between Amaryllidaceae alkaloids, the bacteriome and phytopathogens in Lycoris radiata.

Alkaloids are a large group of plant secondary metabolites with various structures and activities. It is important to understand their functions in the interplay between plants and the beneficial and pathogenic microbiota. Amaryllidaceae alkaloids (AAs) are unique secondary metabolites in Amaryllidaceae plants. Here, we studied the interplay between AAs and the bacteriome in Lycoris radiata, a traditional Chinese medicinal plant containing high amounts of AAs. The relationship between AAs and bacterial composition in different tissues of L. radiata was studied. In vitro experiments revealed that AAs have varying levels of antimicrobial activity against endophytic bacteria and pathogenic fungi, indicating the importance of AA synthesis in maintaining a balance between plants and beneficial/pathogenic microbiota. Using bacterial synthetic communities with different compositions, we observed a positive feedback loop between bacteria insensitive to AAs and their ability to increase accumulation of AAs in L. radiata, especially in leaves. This may allow insensitive bacteria to outcompete sensitive ones for plant resources. Moreover, the accumulation of AAs enhanced by insensitive bacteria could benefit plants when challenged with fungal pathogens. This study highlights the functions of alkaloids in plant-microbe interactions, opening new avenues for designing plant microbiomes that could contribute to sustainable agriculture.

Nano-Iron Oxide (Fe3O4) Mitigates the Effects of Microplastics on a Ryegrass Soil-Microbe-Plant System.

To understand microplastic-nanomaterial interactions in agricultural systems, a randomized block 90-day pot experiment was set up to cultivate ryegrass seedings in a typical red sandy soil amended with compost (1:9 ratio). Polyvinyl chloride (PVC) and polyethylene (PE) microplastic (MP) contaminants were added into pot soils at 0.1 and 10%, whereas nano-Fe3O4 (as nanoenabled agrochemicals) was added at 0.1% and 0.5% in comparison with chemical-free controls. The combination of nano-Fe3O4 and MPs significantly increased the soil pH (+3% to + 17%) but decreased the total nitrogen content (-9% to - 30%; P < 0.05). The treatment group with both nano-Fe3O4 and PE had the highest total soil C (29 g kg-1 vs 20 g kg-1 in control) and C/N ratio (13 vs 8 in control). Increased rhizosphere nano-Fe3O4 concentrations promoted ryegrass growth (+42% dry weight) by enhancing the chlorophyll (+20%) and carotenoid (+15%) activities. Plant leaf and root peroxidase enzyme activity was more significantly affected by nano-Fe3O4 with PVC (+15%) than with PE (+6%). Nano-Fe3O4 significantly changed the ryegrass bacterial community structure from belowground (the rhizoplane and root endosphere) to aboveground (the phylloplane). Under MP contamination, the addition of nano-Fe3O4 increased bacterial diversity (+0.35%) and abundance (+30%) in the phylloplane and further intensified the connectivity of ryegrass aboveground bacterial networks (positive association increased 17%). The structural equation model showed that the change in the plant microbiome was associated with the rhizosphere microbiome. Overall, these findings imply the positive influences of nano-Fe3O4 on the soil-microbe-plant system and establish a method to alleviate the harmful effects of MP accumulation in soils.