Rapid evolution of bacterial mutualism in the plant rhizosphere

Arbuscular mycorrhizal fungi build a bridge for soybeans to recruit Pseudomonas putida

The assembly of the rhizosphere microbiome determines its functionality for plant fitness. Although the interactions between arbuscular mycorrhizal fungi (AMF) and plant growth-promoting rhizobacteria (PGPR) play important roles in plant growth and disease resistance, research on the division of labor among the members of the symbionts formed among plants, AMF, and PGPR, as well as the flow of carbon sources, is still insufficient. To address the above questions, we used soybean (Glycine max), Funneliformis mosseae, and Pseudomonas putida KT2440 as research subjects to establish rhizobiont interactions and to elucidate the signal exchange and division of labor among these components. Funneliformis mosseae can attract P. putida KT2440 by secreting cysteine as a signaling molecule and can promote the colonization of P. putida KT2440 in the soybean rhizosphere. Colonized P. putida KT2440 can stimulate the l-tryptophan secretion of the host plant and can lead to the upregulation of genes involved in converting methyl-indole-3-acetic acid (Me-IAA) into IAA in response to l-tryptophan stimulation. Collectively, we decipher the tripartite mechanism of rhizosphere microbial community assembly via cross-kingdom interactions.

Sustainable remediation of butyl xanthate-contaminated mine wastewater by combining emergent macrophyte Cyperus alternifolius with a versatile bacterial isolate

Butyl xanthate (BuX) is an emerging pollutant due to wide use as flotation collector, posing a serious threat to ecosystem health in mining areas. Here we develop a combinational plant-microbe remediation strategy for restoration of BuX-contaminated mining areas. A novel bacterial strain that completely degraded up to 1000 mg/L of BuX within 12 h was isolated and identified as Pseudomonas monteilii W50. It was found to harbor good tolerance to extreme environmental conditions and multiple plant growth-promoting traits such as phosphate and potassium solubilization, indole-3-acetic acid and gibberellin production, and cellulose degradation. This strain can colonize in the rhizosphere of an emergent macrophyte Cyperus alternifolius, improving removal of BuX and chemical oxygen demand (COD) from simulated wastewater. Compared to the phytoremediation alone, the removal of BuX and COD increased from 70 % to 98 % and from 21 % to 46 % respectively in the combined remediation The strain W50 protected the macrophyte from the phytotoxicity of BuX and the macrophyte provided it with a suitable habitat for return, benefiting each other. Compared to the individual treatment using C. alternifolius or strain W50, the combinational treatment significantly improved the plant growth and the residence of inoculated bacteria. Overall, C. alternifolius and strain W50 are the perfect combination for efficient and sustainable remediation of BuX-contaminated mine wastewater, overcoming the constraints of individual phytoremediation or bioaugmentation methods.

Roles of the soil microbiome in sustaining grassland ecosystem health on the Qinghai-Tibet Plateau

Soil microbes, as intermediaries in plant-soil interactions, are closely linked to plant health in grassland ecosystems. In recent years, varying degrees of degradation have been observed in the alpine grasslands of the Qinghai-Tibet Plateau (QTP). Addressing grassland degradation, particularly under the influence of climate change, poses a global challenge. Understanding the factors driving grassland degradation on the QTP and developing appropriate mitigation measures is essential for the future sustainability of this fragile ecosystem. In this review, we discuss the environmental and anthropogenic factors affecting grassland degradation and the corresponding impacts on soil microbe community structure. We summarize the current research on the microbiome of the QTP, in particular the effect of vegetation, climate change, grazing, and land use, respectively on the alpine grassland microbiome. The results of these studies indicate that microbially mediated soil bioprocesses are important drivers of grassland ecosystem functional recovery. Therefore, a thorough understanding of the spatial distribution characteristics of the soil microbiome in alpine grasslands is required, and this necessitates an integrated approach in which the interactions among climatic factors, vegetation characteristics, and human activities are evaluated. Additionally, we assess and summarise current technological developments and prospects for applying soil microbiome technologies in sustainable agriculture, including: (i) single-strain inoculation, and (ii) inoculation of synthetic microbial communities, (iii) microbial community transplantation. Grassland restoration projects should be carried out with the understanding that each restoration measure has a unique effect on the soil microbial activity. We propose that the sustainable development of alpine grassland ecosystems can be achieved by adopting advanced microbiome technologies and integrating microbe-based sustainable agricultural practices to maximise grassland biomass, increase soil carbon, and optimise soil nutrient cycling.

Evidence for the role of soil C/N ratio in shaping plant responses to root-knot nematode infection

INTRODUCTION

Root-knot nematodes (RKNs) pose a major threat to global crop production. Soil properties influence plant responses to RKN infestation, but the specific soil factors that are most influential in determining these responses remain poorly understood.

OBJECTIVE

This study aims to identify the key soil factors that influence plant responses to Meloidogyne incognita, develop a dynamic model to quantify plant disease severity in response to variations in these soil factors, and further elucidate the underlying mechanisms driving this interaction.

METHODS

We collected 28 soils with diverse physicochemical and microbial properties at a national scale and conducted nematode infection experiments under controlled environmental conditions, using cucumber plants (a typical susceptible host for M. incognita) to assess disease severity. Based on the resulting dataset, a Mantel test was applied to identify the key soil factor influencing M. incognita infection. To further validate these findings, we performed organic carbon (C) addition experiments and M. incognita chemotaxis assays.

RESULTS

We found that 28 soils exhibit a broad range of plant performance indices (PPI) and disease indices (DI). The Mantel test revealed that soil carbon/nitrogen (C/N) ratio is the strongest correlate of both plant performance and disease symptoms. The DI follows an inverted hump-shaped response curve with increasing soil C/N ratio, indicating the existence of an optimal soil C/N ratio (about 8.0) for minimizing DI. This finding is further supported by the fact that organic C addition decreases DI in soils with low initial C/N ratio, but increases DI in soils with high initial C/N ratio. The shaping effects of soil C/N ratio are underpinned by its regulation of overall soil quality and plant resistance to M. incognita chemotaxis.

CONCLUSION

Optimizing C/N ratio reduces soil sensitivity and suppresses RKN infestation, offering valuable insights for sustainable agricultural management practices.

Turning antagonists into allies: Bacterial-fungal interactions enhance the efficacy of controlling Fusarium wilt disease

Intense microbial competition in soil has driven the evolution of resistance mechanisms, yet the implications of such evolution on plant health remain unclear. Our study explored the conversion from antagonism to coexistence between Bacillus velezensis (Bv) and Trichoderma guizhouense (Tg) and its effects on Fusarium wilt disease (FWD) control. We found a bacilysin transmembrane transporter (TgMFS4) in Tg, critical during cross-kingdom dialogue with Bv. Deleting Tgmfs4 (ΔTgmfs4) mitigated Bv-Tg antagonism, reduced bacilysin import into Tg, and elevated its level in the coculture environment. This increase acted as a feedback regulator, limiting overproduction and enhancing Bv biomass. ΔTgmfs4 coinoculation with Bv demonstrated enhanced FWD control relative to wild-type Tg (Tg-WT). In addition, the Tg-WT+ Bv consortium up-regulated antimycotic secretion pathways, whereas the ΔTgmfs4+ Bv consortium enriched the CAZyme (carbohydrate-active enzyme) family gene expression in the rhizosphere, potentiating plant immune responses. This study elucidates the intricacies of bacterial-fungal interactions and their ramifications for plant health.

Plant growth-promotion triggered by extracellular polymer is associated with facilitation of bacterial cross-feeding networks of the rhizosphere

Despite the critical role rhizosphere microbiomes play in plant growth, manipulating microbial communities for improved plant productivity remains challenging. One reason for this is the lack of knowledge on how complex substrates secreted in the microbiome ultimately shape the microbe-microbe and plant-microbe interaction in relation to plant growth. One such complex substrate is poly-γ-glutamic acid, which is a microbially derived extracellular polymer. While it has previously been linked with plant growth-promotion, the underlying mechanisms are not well understood. Here, we show that this compound benefits plants by fostering cross-feeding networks between rhizosphere bacteria. We first experimentally demonstrate that poly-γ-glutamic acid application increases potassium bioavailability for tomato plants by driving a shift in the rhizosphere bacterial community composition. Specifically, application of poly-γ-glutamic acid increased the relative abundance of Pseudomonas nitroreducens L16 and Pseudomonas monteilii L20 bacteria which both promoted tomato potassium assimilation by secreting potassium-solubilizing pyruvic acid and potassium-chelating siderophores, respectively. Although either Pseudomonas strain could not metabolize poly-γ-glutamic acid directly, the application of poly-γ-glutamic acid promoted the growth of Bacillus species, which in turn produced metabolites that could promote the growth of both P. nitroreducens L16 and P. monteilii L20. Moreover, the P. monteilii L20 produced 3-hydroxycapric acid, which could promote the growth of P. nitroreducens L16, resulting in commensal cross-feeding interaction between plant growth-promoting bacteria. Together, these results show that poly-γ-glutamic acid plays a crucial role in driving plant growth-promotion via bacterial cross-feeding networks, highlighting the opportunity for using microbially derived, complex substrates as catalysts to increase agricultural productivity.

Local microbial yield-associating signatures largely extend to global differences in plant growth

Rapid advancements in high-throughput DNA sequencing have opened new avenues for applying microbiome-based machine learning to predict and model determinants that enhance agricultural productivity and sustainability in agroecosystems. Although early attempts have been made to predict crop yield or measures of soil health through the soil microbiome, it is unclear if microbial patterns associated with plant growth or crop yield on a local scale can be generalized to predict differences in plant growth on a continental or global scale. Herein, we measured the soil bacterial microbiome on a single maize field in Germany with high spatial sampling resolution and correlated the community composition with corresponding volume flow-based high-resolution yield measurements. Applying machine learning techniques, a least absolute shrinkage and selection operator (LASSO) regression model could retrospectively predict ∼65 % of variation in maize yield through cross-validation. We validated this locally trained model, comprising 26 genera, using data from seven publicly available datasets. Predictions from this model correlated with various yield or plant growth metrics throughout the world and could predict up to 37 % of variation in global vegetation, as assessed by normalized difference vegetation index data. Further feature inspection showed that the genera Hyphomicrobium, Luedemannella, Reyranella, JGI.0001001.H03, Aeromicrobium, Flavitalea and Ellin6055 most consistently contributed to plant growth prediction. Finally, repeating LASSO regression, an optimized model could predict up to 50 % of variation in global vegetation. In summary, our data suggests a globally conserved set of soil bacterial taxa that correlates with vegetation and might be used to predict plant growth.

Diversity and Plant Growth-Promoting Properties of Rhodiola rosea Root Endophytic Bacteria

Plants inhabiting environments with suboptimal growth conditions often have a more pronounced capacity to attract and sustain microbial communities that improve nutrient absorption and expand abiotic stress tolerance. Rhodiola rosea L. is a succulent plant of the Crassulaceae family adapted to survive in sandy or rocky soils or dry tundra. The aim of the present study was to investigate the diversity and plant growth-stimulating potential of R. rosea endophytic microbiota. Metataxonomic analysis of the bacterial diversity in the rhizome of R. rosea revealed 108 families. Among these, three families were found exclusively in the core microbiome of 1-year-old plants, while nine families were unique to the core microbiome of mature plants grown in the field for more than 4 years. Seventy-three endophytic bacteria isolates were obtained from the rhizome of R. rosea plants and were assigned into 14 distinct bacterial genera of Firmicutes (26%) or Proteobacteria (74%) phyla. Screening for functional genes related to the nitrogen cycle, phosphorus mineralisation or dissolution, and traits associated with nitrogen fixation (56% of isolates), siderophore production (40%), inorganic phosphorus solubilisation (30%), and production of indole-related compounds (51%) led to the classification of the isolates into 16 distinct clusters. Co-cultivation of 45 selected isolates with germinating Arabidopsis seedlings revealed 18 and 5 isolates that resulted in more than a 20% increase in root or shoot growth, respectively. The study results established the complexity of the succulent R. rosea endophytic microbiome and identified isolates for potential plant growth-stimulating applications.

Effects of Deep Tillage on Rhizosphere Soil and Microorganisms During Wheat Cultivation

The production of wheat is fundamentally interconnected with worldwide food security. The practice of deep tillage (DT) cultivation has shown advantages in terms of soil enhancement and the mitigation of diseases and weed abundance. Nevertheless, the specific mechanisms behind these advantages are unclear. Accordingly, we aimed to clarify the influence of DT on rhizosphere soil (RS) microbial communities and its possible contribution to the improvement of soil quality. Soil fertility was evaluated by analyzing several soil characteristics. High-throughput sequencing techniques were utilized to explore the structure and function of rhizosphere microbial communities. Despite lowered fertility levels in the 0-20 cm DT soil layer, significant variations were noted in the microbial composition of the DT wheat rhizosphere, with Acidobacteria and Proteobacteria being the most prominent. Furthermore, the abundance of Bradyrhizobacteria, a nitrogen-fixing bacteria within the Proteobacteria phylum, was significantly increased. A significant increase in glycoside hydrolases within the DT group was observed, in addition to higher abundances of amino acid and carbohydrate metabolism genes in the COG and KEGG databases. Moreover, DT can enhance soil quality and boost crop productivity by modulating soil microorganisms' carbon and nitrogen fixation capacities.

Community standards and future opportunities for synthetic communities in plant-microbiota research

Harnessing beneficial microorganisms is seen as a promising approach to enhance sustainable agriculture production. Synthetic communities (SynComs) are increasingly being used to study relevant microbial activities and interactions with the plant host. Yet, the lack of community standards limits the efficiency and progress in this important area of research. To address this gap, we recommend three actions: (1) defining reference SynComs; (2) establishing community standards, protocols and benchmark data for constructing and using SynComs; and (3) creating an infrastructure for sharing strains and data. We also outline opportunities to develop SynCom research through technical advances, linking to field studies, and filling taxonomic blind spots to move towards fully representative SynComs.

Rhizobacterial diversity, community composition, and the influence of keystone taxa on O'Neal blueberry (Vaccinium corymbosum)

Rhizosphere microbiotas play vital roles in resisting environmental stress, transforming soil nutrients, and promoting plant health, growth, and productivity. The effects of rhizosphere microbial community shaping and the characteristics and functions of keystone taxa on blueberries were comprehensively studied by examining the rhizobacteria of healthy old trees (O), young seedlings (OG), and poorly growing seedlings (OB) of O'Neal blueberries. Our results showed that rhizobacterial diversity followed the order OB > > OG > O, and the microbial community of OG was similar to that of O, while that of OB was distinctly different. The predominant rhizobacteria identified included Actinobacteria, Proteobacteria, Firmicutes, Chloroflexi, and Acidobacteria. Firmicutes were highly enriched in healthy blueberries, with Bacillus identified as a key genus that significantly enhanced blueberry growth when inoculated. Bradyrhizobium and Gaiellales were common core bacteria in the blueberry rhizosphere. In contrast, Acidobacteria were the predominant phylum in poorly growing OB, with the specific Vicinamibacterales-related and Latescibacterota-related genera acting as keystone taxa that shaped the microbial community. In addition, bacterial species in Vicinamibacterales might act as a potential pathogen predicted by BugBase. Taken together, these findings provide fundamental insights into the development of the blueberry rhizosphere microbial community and highlight the role of beneficial rhizobacteria, such as Bacillus, in enhancing blueberry growth. This knowledge could contribute to the exploitation of beneficial rhizobacteria and the prevention of pathogens in modern agriculture.

Rooting for success: Evolutionary enhancement of Bacillus for superior plant colonization

Many strains from the Bacillus subtilis species complex exert strong plant growth-promoting activities. However, their efficacy in relevant conditions is variable, due in part to their inability to establish a strong interaction with roots in stressful environmental conditions. Adaptative laboratory evolution (ALE) is a powerful tool to generate novel strains with traits of interest. Many Bacillus evolved isolates, stemming from ALE performed with plants, possess a stronger root colonization capacity. An in-depth analysis of these isolates also allowed the identification of key features influencing the interaction with plant roots. However, many variables can influence the outcome of these assays, and thus, caution should be taken when designing ALE destined to generate better root colonizers.

Genomic Insights into Pseudomonas protegens E1BL2 from Giant Jala Maize: A Novel Bioresource for Sustainable Agriculture and Efficient Management of Fungal Phytopathogens

The relationships between plants and bacteria are essential in agroecosystems and bioinoculant development. The leaf endophytic Pseudomonas protegens E1BL2 was previously isolated from giant Jala maize, which is a native Zea mays landrace of Nayarit, Mexico. Using different Mexican maize landraces, this work evaluated the strain's plant growth promotion and biocontrol against eight phytopathogenic fungi in vitro and greenhouse conditions. Also, a plant field trial was conducted on irrigated fields using the hybrid maize Supremo. The grain productivity in this assay increased compared with the control treatment. The genome analysis of P. protegens E1BL2 showed putative genes involved in metabolite synthesis that facilitated its beneficial roles in plant health and environmental adaptation (bdhA, acoR, trpE, speE, potA); siderophores (ptaA, pchC); and extracellular enzymes relevant for PGPB mechanisms (cel3, chi14), protection against oxidative stress (hscA, htpG), nitrogen metabolism (nirD, nit1, hmpA), inductors of plant-induced systemic resistance (ISR) (flaA, flaG, rffA, rfaP), fungal biocontrol (phlD, prtD, prnD, hcnA-1), pest control (vgrG-1, higB-2, aprE, pslA, ppkA), and the establishment of plant-bacteria symbiosis (pgaA, pgaB, pgaC, exbD). Our findings suggest that P. protegens E1BL2 significantly promotes maize growth and offers biocontrol benefits, which highlights its potential as a bioinoculant.

Effects of Deep Tillage on Wheat Regarding Soil Fertility and Rhizosphere Microbial Community

Wheat production is intrinsically linked to global food security. However, wheat cultivation is constrained by the progressive degradation of soil conditions resulting from the continuous application of fertilizers. This study aimed to examine the effects of deep tillage on rhizosphere soil microbial communities and their potential role in improving soil quality, given that the specific mechanisms driving these observed benefits remain unclear. Soil fertility in this research was evaluated through the analysis of various soil parameters, including total nitrogen, total phosphorus, total potassium, available phosphorus, and available potassium, among others. The high-throughput sequencing technique was utilized to examine the rhizosphere microbial community associated with deep tillage wheat. The findings indicated that deep tillage cultivation of wheat led to reduced fertility levels in the 0-20 cm soil layer in comparison with non-deep tillage cultivation. A sequencing analysis indicated that Acidobacteria and Proteobacteria are the dominant bacterial phyla, with Proteobacteria being significantly more abundant in the deep tillage group. The dominant fungal phyla identified were Ascomycota, Mortierellomycota, and Basidiomycota. Among bacterial genera, Arthrobacter, Bacillus, and Nocardioides were predominant, with Arthrobacter showing a significantly higher presence in the deep tillage group. The predominant fungal genera included Mortierella, Alternaria, Schizothecium, and Cladosporium. Deep tillage cultivation has the potential to enhance soil quality and boost crop productivity through the modulation of soil microbial community structure.

Protective role of native root-associated bacterial consortium against root-knot nematode infection in susceptible plants

Root-knot nematodes (RKNs) are a global menace to agricultural crop production. The role of root-associated microbes (RAMs) in plant protection against RKN infection remains unclear. Here we observe that cucumber (highly susceptible to Meloidogyne incognita) exhibits a consistently lower susceptibility to M. incognita in the presence of native RAMs in three distinct soils. Nematode infection alters the assembly of bacterial RAMs along the life cycle of M. incognita. Particularly, the loss of bacterial diversity of RAMs exacerbates plant susceptibility to M. incognita. A diverse range of native bacterial strains isolated from M. incognita-infected roots has nematode-antagonistic activity. Increasing the number of native bacterial strains causes decreasing nematode infection, which is lowest when six or more bacterial strains are present. Multiple simplified synthetic communities consisting of six bacterial strains show pronounced inhibitory effects on M. incognita infection in plants. These inhibitory effects are underpinned via multiple mechanisms including direct inhibition of infection, secretion of anti-nematode substances, and regulation of plant defense responses. This study highlights the role of native bacterial RAMs in plant resistance against RKNs and provides a useful insight into the development of a sustainable way to protect susceptible plants.

Auxin-mediated regulation of susceptibility to toxic metabolites, c-di-GMP levels, and phage infection in the rhizobacterium Serratia plymuthica

The communication between plants and their microbiota is highly dynamic and involves a complex network of signal molecules. Among them, the auxin indole-3-acetic acid (IAA) is a critical phytohormone that not only regulates plant growth and development, but is emerging as an important inter- and intra-kingdom signal that modulates many bacterial processes that are important during interaction with their plant hosts. However, the corresponding signaling cascades remain largely unknown. Here, we advance our understanding of the largely unknown mechanisms by which IAA carries out its regulatory functions in plant-associated bacteria. We showed that IAA caused important changes in the global transcriptome of the rhizobacterium Serratia plymuthica and multidisciplinary approaches revealed that IAA sensing interferes with the signaling mediated by other pivotal plant-derived signals such as amino acids and 4-hydroxybenzoic acid. Exposure to IAA caused large alterations in the transcript levels of genes involved in amino acid metabolism, resulting in significant metabolic alterations. IAA treatment also increased resistance to toxic aromatic compounds through the induction of the AaeXAB pump, which also confers resistance to IAA. Furthermore, IAA promoted motility and severely inhibited biofilm formation; phenotypes that were associated with decreased c-di-GMP levels and capsule production. IAA increased capsule gene expression and enhanced bacterial sensitivity to a capsule-dependent phage. Additionally, IAA induced the expression of several genes involved in antibiotic resistance and led to changes in the susceptibility and responses to antibiotics with different mechanisms of action. Collectively, our study illustrates the complexity of IAA-mediated signaling in plant-associated bacteria.

IMPORTANCE

Signal sensing plays an important role in bacterial adaptation to ecological niches and hosts. This communication appears to be particularly important in plant-associated bacteria since they possess a large number of signal transduction systems that respond to a wide diversity of chemical, physical, and biological stimuli. IAA is emerging as a key inter- and intra-kingdom signal molecule that regulates a variety of bacterial processes. However, despite the extensive knowledge of the IAA-mediated regulatory mechanisms in plants, IAA signaling in bacteria remains largely unknown. Here, we provide insight into the diversity of mechanisms by which IAA regulates primary and secondary metabolism, biofilm formation, motility, antibiotic susceptibility, and phage sensitivity in a biocontrol rhizobacterium. This work has important implications for our understanding of bacterial ecology in plant environments and for the biotechnological and clinical applications of IAA, as well as related molecules.

Deciphering Microbial Adaptation in the Rhizosphere: Insights into Niche Preference, Functional Profiles, and Cross-Kingdom Co-occurrences

Rhizosphere microbial communities are to be as critical factors for plant growth and vitality, and their adaptive differentiation strategies have received increasing amounts of attention but are poorly understood. In this study, we obtained bacterial and fungal amplicon sequences from the rhizosphere and bulk soils of various ecosystems to investigate the potential mechanisms of microbial adaptation to the rhizosphere environment. Our focus encompasses three aspects: niche preference, functional profiles, and cross-kingdom co-occurrence patterns. Our findings revealed a correlation between niche similarity and nucleotide distance, suggesting that niche adaptation explains nucleotide variation among some closely related amplicon sequence variants (ASVs). Furthermore, biological macromolecule metabolism and communication among abundant bacteria increase in the rhizosphere conditions, suggesting that bacterial function is trait-mediated in terms of fitness in new habitats. Additionally, our analysis of cross-kingdom networks revealed that fungi act as intermediaries that facilitate connections between bacteria, indicating that microbes can modify their cooperative relationships to adapt. Overall, the evidence for rhizosphere microbial community adaptation, via differences in gene and functional and co-occurrence patterns, elucidates the adaptive benefits of genetic and functional flexibility of the rhizosphere microbiota through niche shifts.

The role of rhizosphere phages in soil health

While the One Health framework has emphasized the importance of soil microbiomes for plant and human health, one of the most diverse and abundant groups-bacterial viruses, i.e. phages-has been mostly neglected. This perspective reviews the significance of phages for plant health in rhizosphere and explores their ecological and evolutionary impacts on soil ecosystems. We first summarize our current understanding of the diversity and ecological roles of phages in soil microbiomes in terms of nutrient cycling, top-down density regulation, and pathogen suppression. We then consider how phages drive bacterial evolution in soils by promoting horizontal gene transfer, encoding auxiliary metabolic genes that increase host bacterial fitness, and selecting for phage-resistant mutants with altered ecology due to trade-offs with pathogen competitiveness and virulence. Finally, we consider challenges and avenues for phage research in soil ecosystems and how to elucidate the significance of phages for microbial ecology and evolution and soil ecosystem functioning in the future. We conclude that similar to bacteria, phages likely play important roles in connecting different One Health compartments, affecting microbiome diversity and functions in soils. From the applied perspective, phages could offer novel approaches to modulate and optimize microbial and microbe-plant interactions to enhance soil health.

Speciation Features of Ferdinandcohnia quinoae sp. nov to Adapt to the Plant Host

The bacterial strain SECRCQ15T was isolated from seeds of Chenopodium quinoa in Spain. Phylogenetic, chemotaxonomic, and phenotypic analyses, as well as genome similarity indices, support the classification of the strain into a novel species of the genus Ferdinandcohnia, for which we propose the name Ferdinandcohnia quinoae sp. nov. To dig deep into the speciation features of the strain SECRCQ15T, we performed a comparative genomic analysis of the genome of this strain and those of the type strains of species from the genus Ferdinandcohnia. We found several genes related with plant growth-promoting mechanisms within the SECRCQ15T genome. We also found that singletons of F. quinoae SECRCQ15T are mainly related to the use of carbohydrates, which is a common trait of plant-associated bacteria. To further reveal speciation events in this strain, we revealed genes undergoing diversifying selection (e.g., genes encoding ribosomal proteins) and functions likely lost due to pseudogenization. Also, we found that this novel species contains 138 plant-associated gene-cluster functions that are unique within the genus Ferdinandcohnia. These features may explain both the ecological and taxonomical differentiation of this new taxon.

Evaluating the role of rhizosphere microbial home-field advantage in Betula luminifera adaptation to antimony mining areas

It has been established that the coevolution of plants and the rhizosphere microbiome in response to abiotic stress can result in the recruitment of specific functional microbiomes. However, the potential of inoculated rhizosphere microbiomes to enhance plant fitness and the inheritance of adaptive traits in subsequent generations remains unclear. In this study, cross-inoculation trials were conducted using seeds, rhizosphere microbiome, and in situ soil collected from areas of Betula luminifera grown in both antimony mining and control sites. Compared to the control site, plants originating from mining areas exhibited stronger adaptive traits, specifically manifested as significant increases in hundred-seed weight, specific surface area, and germination rate, as well as markedly enhanced seedling survival rate and biomass. Inoculation with mining microbiomes could enhance the fitness of plants in mining sites through a "home-field advantage" while also improving the fitness of plants originating from control sites. During the initial phase of seedling development, bacteria play a crucial role in promoting growth, primarily due to their mechanisms of metal resistance and nutrient cycling. This study provided evidence that the outcomes of long-term coevolution between plants and the rhizosphere microbiome in mining areas can be passed on to future generations. Moreover, it has been demonstrated that transgenerational inheritance and rhizosphere microbiome inoculation are important factors in improving the adaptability of plants in mining areas. The findings have important implications for vegetation restoration and ecological environment improvement in mining areas.

Plant pathogenic bacterium Ralstonia solanacearum can rapidly evolve tolerance to antimicrobials produced by Pseudomonas biocontrol bacteria

Soil-borne plant pathogens significantly threaten crop production due to lack of effective control methods. One alternative to traditional agrochemicals is microbial biocontrol, where pathogen growth is suppressed by naturally occurring bacteria that produce antimicrobial chemicals. However, it is still unclear if pathogenic bacteria can evolve tolerance to biocontrol antimicrobials and if this could constrain the long-term efficacy of biocontrol strategies. Here we used an in vitro experimental evolution approach to investigate if the phytopathogenic Ralstonia solanacearum bacterium, which causes bacterial wilt disease, can evolve tolerance to antimicrobials produced by Pseudomonas bacteria. We further asked if tolerance was specific to pairs of R. solanacearum and Pseudomonas strains and certain antimicrobial compounds produced by Pseudomonas. We found that while all R. solanacearum strains could initially be inhibited by Pseudomonas strains, this inhibition decreased following successive subculturing with or without Pseudomonas supernatants. Using separate tolerance assays, we show that the majority of R. solanacearum strains evolved increased tolerance to multiple Pseudomonas strains. Mechanistically, evolved tolerance was most likely linked to reduced susceptibility to orfamide lipopeptide antimicrobials secreted by Pseudomonas strains in our experimental conditions. Some levels of tolerance also evolved in the control treatments, which was likely correlated response due to adaptations to the culture media. Together, these results suggest that plant-pathogenic bacteria can rapidly evolve increased tolerance to bacterial antimicrobial compounds, which could reduce the long-term efficacy of microbial biocontrol.

Root colonization by beneficial rhizobacteria

Rhizosphere microbes play critical roles for plant's growth and health. Among them, the beneficial rhizobacteria have the potential to be developed as the biofertilizer or bioinoculants for sustaining the agricultural development. The efficient rhizosphere colonization of these rhizobacteria is a prerequisite for exerting their plant beneficial functions, but the colonizing process and underlying mechanisms have not been thoroughly reviewed, especially for the nonsymbiotic beneficial rhizobacteria. This review systematically analyzed the root colonizing process of the nonsymbiotic rhizobacteria and compared it with that of the symbiotic and pathogenic bacteria. This review also highlighted the approaches to improve the root colonization efficiency and proposed to study the rhizobacterial colonization from a holistic perspective of the rhizosphere microbiome under more natural conditions.

Differential Nitrous oxide emission and microbiota succession in constructed wetlands induced by nitrogen forms

Nitrous oxide (N2O) emission during the sewage treatment process is a serious environmental issue that requires attention. However, the N2O emission in constructed wetlands (CWs) as affected by different nitrogen forms in influents remain largely unknown. This study investigated the N2O emission profiles driven by microorganisms in CWs when exposed to two typical nitrogen sources (NH4+-N or NO3--N) along with different carbon source supply (COD/N ratios: 3, 6, and 9). The results showed that CWs receiving NO3--N caused a slight increase in total nitrogen removal (by up to 11.8 %). This increase was accomplished by an enrichment of key bacteria groups, including denitrifiers, dissimilatory nitrate reducers, and assimilatory nitrate reducers, which enhanced the stability of microbial interaction. Additionally, it led to a greater abundance of denitrification genes (e.g., nirK, norB, norC, and nosZ) as inferred from the database. Consequently, this led to a gradual increase in N2O emission from 66.51 to 486.77 ug-N/(m2·h) as the COD/N ratio increased in CWs. Conversely, in CWs receiving NH4+-N, an increasing influent COD/N ratio had a negative impact on nitrogen biotransformation. This resulted in fluctuating trend of N2O emissions, which decreased initially, followed by an increase at later stage (with values of 122.87, 44.00, and 148.59 ug-N/(m2·h)). Furthermore, NH4+-N in the aquatic improved the nitrogen uptake by plants and promoted the production of more root exudates. As a result, it adjusted the nitrogen-transforming function, ultimately reducing N2O emissions in CWs. This study highlights the divergence in microbiota succession and nitrogen transformation in CWs induced by nitrogen form and COD/N ratio, contributing to a better understanding of the microbial mechanisms of N2O emission in CWs with NH4+-N or NO3--N at different COD/N ratios.

From microbiome composition to functional engineering, one step at a time

SUMMARYCommunities of microorganisms (microbiota) are present in all habitats on Earth and are relevant for agriculture, health, and climate. Deciphering the mechanisms that determine microbiota dynamics and functioning within the context of their respective environments or hosts (the microbiomes) is crucially important. However, the sheer taxonomic, metabolic, functional, and spatial complexity of most microbiomes poses substantial challenges to advancing our knowledge of these mechanisms. While nucleic acid sequencing technologies can chart microbiota composition with high precision, we mostly lack information about the functional roles and interactions of each strain present in a given microbiome. This limits our ability to predict microbiome function in natural habitats and, in the case of dysfunction or dysbiosis, to redirect microbiomes onto stable paths. Here, we will discuss a systematic approach (dubbed the N+1/N-1 concept) to enable step-by-step dissection of microbiome assembly and functioning, as well as intervention procedures to introduce or eliminate one particular microbial strain at a time. The N+1/N-1 concept is informed by natural invasion events and selects culturable, genetically accessible microbes with well-annotated genomes to chart their proliferation or decline within defined synthetic and/or complex natural microbiota. This approach enables harnessing classical microbiological and diversity approaches, as well as omics tools and mathematical modeling to decipher the mechanisms underlying N+1/N-1 microbiota outcomes. Application of this concept further provides stepping stones and benchmarks for microbiome structure and function analyses and more complex microbiome intervention strategies.

Diversification during cross-kingdom microbial experimental evolution

Experimental evolution in a laboratory helps researchers to understand the genetic and phenotypic background of adaptation under a particular condition. Simultaneously, the simplified environment that represents certain aspects of a complex natural niche permits the dissection of relevant parameters behind the selection, including temperature, oxygen availability, nutrients, and biotic factors. The presence of other microorganisms or a host has a major influence on microbial evolution that often differs from the adaptation paths observed in response to abiotic conditions. In the current issue of the ISME Journal, Cosetta and colleagues reveal how cross-kingdom interaction representing the cheese microbiome succession promotes distinct evolution of the food- and animal-associated bacterium, Staphylococcus xylosus. The authors also identified a global regulator-dependent adaption that leads to evolved derivatives exhibiting reduced pigment production and colony morphologies in addition to altered differentiation phenotypes that potentially contribute to increased fitness.

Crotalaria juncea L. enhances the bioremediation of sulfentrazone-contaminated soil and promotes changes in the soil bacterial community

Sulfentrazone (STZ) is an efficient tool for the pre- and post-emergence control of monocotyledonous and dicotyledonous weeds in fields of crops such as pineapple, coffee, sugarcane, citrus, eucalyptus, tobacco, and soybean. However, this herbicide persists in the soil, causing phytotoxicity in the subsequent crop. Therefore, it is important to use efficient strategies for the remediation of STZ-contaminated areas. The aim of this study was to evaluate the effects of Crotalaria juncea L. on the remediation of STZ-contaminated soil and on the microbial activity and bacterial community structure therein. The study was conducted in three stages: (i) cultivation of C. juncea in soil contaminated with 200, 400, and 800 g ha-1 STZ; (ii) determination of the soil microbial activity (basal respiration, microbial biomass carbon, and bacterial community structure); and (iii) cultivation of a bioindicator species and determination of the residual fraction of STZ. The soil microbial activity was impacted by the soil type and STZ dose. Soil previously cultivated with C. juncea (rhizospheric soil) displayed higher CO2 and lower qCO2 values than non-rhizospheric soil (no previous C. juncea cultivation). Increasing doses of STZ reduced the activity and lowered the diversity indices of the soil microorganisms. The bacterial community structure was segregated between the rhizospheric and non-rhizospheric soils. Regardless of soil type, the bioindicator of remediation (Pennisetum glaucum R.Br.) grew only at the STZ dose of 200 g ha-1, and the plant intoxication level was also lower in rhizospheric soil treated with this herbicide dose. All P. glaucum plants died in the soils treated with 400 and 800 g ha-1 STZ. Previous cultivation of C. juncea in soils contaminated with 200, 400, and 800 g ha-1 STZ reduced the residual fraction of the herbicide by 4.8%, 12.5%, and 17.4%, respectively, compared with that in the non-rhizospheric soils. In conclusion, previous cultivation with C. juncea promoted increases in the soil bacterial activity and diversity indices, mitigated the deleterious effects of STZ on the bioindicator crop, and reduced the residual fraction of the herbicide in the soil.

Growth rate is a dominant factor predicting the rhizosphere effect

The root microbiome is shaped by plant root activity, which selects specific microbial taxa from the surrounding soil. This influence on the microorganisms and soil chemistry in the immediate vicinity of the roots has been referred to as the rhizosphere effect. Understanding the traits that make bacteria successful in the rhizosphere is critical for developing sustainable agriculture solutions. In this study, we compared the growth rate potential, a complex trait that can be predicted from bacterial genome sequences, to functional traits encoded by proteins. We analyzed 84 paired rhizosphere- and soil-derived 16S rRNA gene amplicon datasets from 18 different plants and soil types, performed differential abundance analysis, and estimated growth rates for each bacterial genus. We found that bacteria with higher growth rate potential consistently dominated the rhizosphere, and this trend was confirmed in different bacterial phyla using genome sequences of 3270 bacterial isolates and 6707 metagenome-assembled genomes (MAGs) from 1121 plant- and soil-associated metagenomes. We then identified which functional traits were enriched in MAGs according to their niche or growth rate status. We found that predicted growth rate potential was the main feature for differentiating rhizosphere and soil bacteria in machine learning models, and we then analyzed the features that were important for achieving faster growth rates, which makes bacteria more competitive in the rhizosphere. As growth rate potential can be predicted from genomic data, this work has implications for understanding bacterial community assembly in the rhizosphere, where many uncultivated bacteria reside.

Soil moisture incidentally selects for microbes that facilitate locally adaptive plant response

While a plant's microbiome can facilitate adaptive phenotypes, the plant's role in selecting for these microbes is unclear. Do plants actively recruit microbes beneficial to their current environment, or are beneficial microbes only an incidental by-product of microbial adaptation? We addressed these questions through a multigeneration greenhouse experiment, selecting for either dry- or wet-adapted soil microbial communities, either with or without plants. After three plant generations, we conducted a full reciprocal transplant of each soil community onto wet- and dry-treated plants. We found that plants generally benefited from soil microbes, and this benefit was greater whenever their current watering conditions matched the microbes' historical watering conditions. Principally, the plant's presence was not necessary in the historical treatments for this environmental matching benefit to emerge. Moreover, we found microbes from droughted soils could better tolerate drought stress. Taken together, these results suggest that the moisture environment selects for microbes that benefit plants under those specific moisture conditions, and that these beneficial properties arise as a by-product of microbial adaptation to the watering environment and not as a co-adapting plant-microbe system. This work highlights that understanding the selective agents on these plant-associated microbes will lead to a better understanding of plant adaptation.

Biotic stress-induced changes in root exudation confer plant stress tolerance by altering rhizospheric microbial community

Every organism on the earth maintains some kind of interaction with its neighbours. As plants are sessile, they sense the varied above-ground and below-ground environmental stimuli and decipher these dialogues to the below-ground microbes and neighbouring plants via root exudates as chemical signals resulting in the modulation of the rhizospheric microbial community. The composition of root exudates depends upon the host genotype, environmental cues, and interaction of plants with other biotic factors. Crosstalk of plants with biotic agents such as herbivores, microbes, and neighbouring plants can change host plant root exudate composition, which may permit either positive or negative interactions to generate a battlefield in the rhizosphere. Compatible microbes utilize the plant carbon sources as their organic nutrients and show robust co-evolutionary changes in changing circumstances. In this review, we have mainly focused on the different biotic factors responsible for the synthesis of alternative root exudate composition leading to the modulation of rhizosphere microbiota. Understanding the stress-induced root exudate composition and resulting change in microbial community can help us to devise strategies in engineering plant microbiomes to enhance plant adaptive capabilities in a stressful environment.

The temporal and spatial dimensions of plant-soil feedbacks

Feedbacks between plants and soil microbes form a keystone to terrestrial community and ecosystem dynamics. Recent advances in dissecting the spatial and temporal dynamics of plant-soil feedbacks (PSFs) have challenged longstanding assumptions of spatially well-mixed microbial communities and exceedingly fast microbial assembly dynamics relative to plant lifespans. Instead, PSFs emerge from interactions that are inherently mismatched in spatial and temporal scales, and explicitly considering these spatial and temporal dynamics is crucial to understanding the contribution of PSFs to foundational ecological patterns. I propose a synthetic spatiotemporal framework for future research that pairs experimental and modeling approaches grounded in mechanism to improve predictability and generalizability of PSFs.

Rhizosphere phage communities drive soil suppressiveness to bacterial wilt disease

BACKGROUND

Bacterial viruses, phages, play a key role in nutrient turnover and lysis of bacteria in terrestrial ecosystems. While phages are abundant in soils, their effects on plant pathogens and rhizosphere bacterial communities are poorly understood. Here, we used metagenomics and direct experiments to causally test if differences in rhizosphere phage communities could explain variation in soil suppressiveness and bacterial wilt plant disease outcomes by plant-pathogenic Ralstonia solanacearum bacterium. Specifically, we tested two hypotheses: (1) that healthy plants are associated with stronger top-down pathogen control by R. solanacearum-specific phages (i.e. 'primary phages') and (2) that 'secondary phages' that target pathogen-inhibiting bacteria play a stronger role in diseased plant rhizosphere microbiomes by indirectly 'helping' the pathogen.

RESULTS

Using a repeated sampling of tomato rhizosphere soil in the field, we show that healthy plants are associated with distinct phage communities that contain relatively higher abundances of R. solanacearum-specific phages that exert strong top-down pathogen density control. Moreover, 'secondary phages' that targeted pathogen-inhibiting bacteria were more abundant in the diseased plant microbiomes. The roles of R. solanacearum-specific and 'secondary phages' were directly validated in separate greenhouse experiments where we causally show that phages can reduce soil suppressiveness, both directly and indirectly, via top-down control of pathogen densities and by alleviating interference competition between pathogen-inhibiting bacteria and the pathogen.

CONCLUSIONS

Together, our findings demonstrate that soil suppressiveness, which is most often attributed to bacteria, could be driven by rhizosphere phage communities that regulate R. solanacearum densities and strength of interference competition with pathogen-suppressing bacteria. Rhizosphere phage communities are hence likely to be important in determining bacterial wilt disease outcomes and soil suppressiveness in agricultural fields. Video Abstract.

Characterization of the endophytic bacterial community of Bituminaria bituminosa plant grown in vitro and its interaction with the plant extract

INTRODUCTION

Bituminaria bituminosa is a medicinal plant recognized for its phytochemicals, such as furanocoumarins, pterocarpans, and flavonoids. Since the secondary metabolism is influenced by the plant-endophyte interactions, the endophytic bacterial community of B. bituminosa was explored and the possible interactions with the plant were described.

MATERIALS AND METHODS

Different bacterial strains were isolated from different organs of in vitro plants as shoots, roots, and seeds. The bacterial strains were identified and phenotypically characterized for different traits; strains were also exposed to different concentrations of B. bituminosa plant extract showing different susceptibility, probably determined by different secondary metabolites produced by the plant in the different organs (i.e. aerial parts and roots).

RESULTS AND DISCUSSION

Bacterial strains showed different phenotypic characteristics; the 6 detected haplotypes were dominated by a single species related to Stenotrophomonas rhizophila. Endophytes isolated from the aerial parts produced a higher indole-3-acetic acid (IAA) amount than those of the roots, while all strains were unable to produce biosurfactants and antagonistic activity toward the other strains. The research opens new perspectives for future analysis addressed to test the susceptibility of the endophytic bacterial community of B. bituminosa toward the pure compounds extracted from the plants, and to investigate the role of these compounds on the distribution of endophytes within the different plant tissues.

Coumarin biosynthesis genes are required after foliar pathogen infection for the creation of a microbial soil-borne legacy that primes plants for SA-dependent defenses

Plants deposit photosynthetically-fixed carbon in the rhizosphere, the thin soil layer directly around the root, thereby creating a hospitable environment for microbes. To manage the inhabitants of this nutrient-rich environment, plant roots exude and dynamically adjust microbe-attracting and -repelling compounds to stimulate specific members of the microbiome. Previously, we demonstrated that foliar infection of Arabidopsis thaliana by the biotrophic downy mildew pathogen Hyaloperonospora arabidopsidis (Hpa) leads to a disease-induced modification of the rhizosphere microbiome. Soil conditioned with Hpa-infected plants provided enhanced protection against foliar downy mildew infection in a subsequent population of plants, a phenomenon dubbed the soil-borne legacy (SBL). Here, we show that for the creation of the SBL, plant-produced coumarins play a prominent role as coumarin-deficient myb72 and f6'h1 mutants were defective in creating a Hpa-induced SBL. Root exudation profiles changed significantly in Col-0 upon foliar Hpa infection, and this was accompanied by a compositional shift in the root microbiome that was significantly different from microbial shifts occurring on roots of Hpa-infected coumarin-deficient mutants. Our data further show that the Hpa-induced SBL primes Col-0 plants growing in SBL-conditioned soil for salicylic acid (SA)-dependent defenses. The SA-signaling mutants sid2 and npr1 were unresponsive to the Hpa-induced SBL, suggesting that the protective effect of the Hpa-induced shift in the root microbiome results from an induced systemic resistance that requires SA-signaling in the plant.

Rhizosphere microorganisms of Crocus sativus as antagonists against pathogenic Fusarium oxysporum

Introduction

Several microorganisms in the plant root system, especially in the rhizosphere, have their own compositions and functions. Corm rot is the most severe disease of Crocus sativus, leading to more than 50% mortality in field production.

Methods

In this study, metagenomic sequencing was used to analyze microbial composition and function in the rhizosphere of C. sativus for possible microbial antagonists against pathogenic Fusarium oxysporum.

Results

The microbial diversity and composition were different in the C. sativus rhizosphere from different habitats. The diversity index (Simpson index) was significantly lower in the C. sativus rhizospheric soil from Chongming (Rs_CM) and degenerative C. sativus rhizospheric soil from Chongming (RsD_CM) than in others. Linear discriminant analysis effect size results showed that differences among habitats were mainly at the order (Burkholderiales, Micrococcales, and Hypocreales) and genus (Oidiodendron and Marssonina) levels. Correlation analysis of the relative lesion area of corm rot showed that Asanoa was the most negatively correlated bacterial genus (ρ = -0.7934, p< 0.001), whereas Moniliophthora was the most negatively correlated fungal genus (ρ = -0.7047, p< 0.001). The relative lesion area result showed that C. sativus from Qiaocheng had the highest resistance, followed by Xiuzhou and Jiande. C. sativus groups with high disease resistance had abundant pathogen resistance genes, such as chitinase and β-1,3-glucanase genes, from rhizosphere microorganisms. Further, 13 bacteria and 19 fungi were isolated from C. sativus rhizosphere soils, and antagonistic activity against pathogenic F. oxysporum was observed on potato dextrose agar medium. In vivo corm experiments confirmed that Trichoderma yunnanense SR38, Talaromyces sp. SR55, Burkholderia gladioli SR379, and Enterobacter sp. SR343 displayed biocontrol activity against corm rot disease, with biocontrol efficiency of 20.26%, 31.37%, 39.22%, and 14.38%, respectively.

Discussion

This study uncovers the differences in the microbial community of rhizosphere soil of C. sativus with different corm rot disease resistance and reveals the role of four rhizospheric microorganisms in providing the host C. sativus with resistance against corm rot. The obtained biocontrol microorganisms can also be used for application research and field management.

Unique Insights into How Plants and Soil Microbiomes Interact Are at Our Fingertips

Global warming endangers our world, with probably a drastic drop in food production as one of the first vital consequences for humanity. To maintain or improve quality and sustainable yields, the burning imperative for agriculture is to rapidly integrate the essential component for plant development and soil regeneration, namely, the soil microbiome. Although enormous progress has been made in identifying the components of this microbiome, the way in which they interact with each other and with plants remains poorly understood. Lidbury I, Raguideau S, Borsetto C, Murphy A, et al. (mSystems 7:e00025-22, 2022, https://doi.org/10.1128/mSystems.00025-22) illustrate how metaproteomics helps define key interactions between plants and microorganisms at the rhizospheric interface. The many extracellular proteins identified and quantified by this methodology uniquely explain the observed phenotype. This study shows that the adoption of metaproteomics is no longer an option that microbiologists should consider but a must!

Biochar-mediated changes in the microbial communities of rhizosphere soil alter the architecture of maize roots

Aeolian sandy soil is a key resource for supporting food production on a global scale; however, the growth of crops in Aeolian sandy soil is often impaired due to its poor physical properties and lack of nutrients and organic matter. Biochar can be used to enhance the properties of Aeolian sandy soil and create an environment more suitable for crop growth, but the long-term effects of biochar on Aeolian sandy soil and microbial communities need to be clarified. Here, a field experiment was conducted in which biochar was applied to a maize (Zea mays L.) field in a single application at different rates: CK, 0 Mg ha-1; C1, 15.75 Mg ha-1; C2, 31.50 Mg ha-1; C3, 63.00 Mg ha-1; and C4, 126.00 Mg ha-1. After 7 years of continuous maize cropping, verify the relationship between root architecture and soil microbial communities under biochar application using a root scanner and 16S/ITS rRNA gene sequencing. The application of biochar promoted the growth of maize. Specifically, total root length, total root surface area, total root volume, and root biomass were 13.99-17.85, 2.52-4.69, 23.61-44.41, and 50.61-77.80% higher in treatments in which biochar was applied (C2, C3, and C4 treatments) compared with the control treatment, respectively. Biochar application increased the diversity of bacterial communities, the ACE index, and Chao 1 index of C1, C2, C3, and C4 treatments increased by 5.83-8.96 and 5.52-8.53%, respectively, compared with the control treatment, and significantly changed the structure of the of bacterial communities in rhizosphere soil. However, there was no significant change in the fungal community. The growth of maize roots was more influenced by rhizosphere bacteria and less by fungal community. A microbial co-occurrence network revealed strong associations among rhizosphere microorganisms. The core taxa (Module hubs taxa) of the bulk soil microbial co-occurrence network were closely related to the total length and total surface area of maize roots, and the core taxa (Connectors taxa) of the rhizosphere soil were closely related to total root length. Overall, our findings indicate that the application of biochar promotes the growth of maize roots in aeolian sandy soil through its effects on bacterial communities in rhizosphere soil.

Evolution of manipulative microbial behaviors in the rhizosphere

The rhizosphere has been called "one of the most complex ecosystems on earth" because it is a hotspot for interactions among millions of microbial cells. Many of these are microbes are also participating in a dynamic interplay with host plant tissues, signaling pathways, and metabolites. Historically, breeders have employed a plant-centric perspective when trying to harness the potential of microbiome-derived benefits to improve productivity and resilience of economically important plants. This is potentially problematic because: (i) the evolution of the microbes themselves is often ignored, and (ii) it assumes that the fitness of interacting plants and microbes is strictly aligned. In contrast, a microbe-centric perspective recognizes that putatively beneficial microbes are still under selection to increase their own fitness, even if there are costs to the host. This can lead to the evolution of sophisticated, potentially subtle, ways for microbes to manipulate the phenotype of their hosts, as well as other microbes in the rhizosphere. We illustrate this idea with a review of cases where rhizosphere microbes have been demonstrated to directly manipulate host root growth, architecture and exudation, host nutrient uptake systems, and host immunity and defense. We also discuss indirect effects, whereby fitness outcomes for the plant are a consequence of ecological interactions between rhizosphere microbes. If these consequences are positive for the plant, they can potentially be misconstrued as traits that have evolved to promote host growth, even if they are a result of selection for unrelated functions. The ubiquity of both direct microbial manipulation of hosts and context-dependent, variable indirect effects leads us to argue that an evolutionary perspective on rhizosphere microbial ecology will become increasingly important as we continue to engineer microbial communities for crop production.

Management of Rhizosphere Microbiota and Plant Production under Drought Stress: A Comprehensive Review

Drought generates a complex scenario worldwide in which agriculture should urgently be reframed from an integrative point of view. It includes the search for new water resources and the use of tolerant crops and genotypes, improved irrigation systems, and other less explored alternatives that are very important, such as biotechnological tools that may increase the water use efficiency. Currently, a large body of evidence highlights the role of specific strains in the main microbial rhizosphere groups (arbuscular mycorrhizal fungi, yeasts, and bacteria) on increasing the drought tolerance of their host plants through diverse plant growth-promoting (PGP) characteristics. With this background, it is possible to suggest that the joint use of distinct PGP microbes could produce positive interactions or additive beneficial effects on their host plants if their co-inoculation does not generate antagonistic responses. To date, such effects have only been partially analyzed by using single omics tools, such as genomics, metabolomics, or proteomics. However, there is a gap of information in the use of multi-omics approaches to detect interactions between PGP and host plants. This approach must be the next scale-jump in the study of the interaction of soil–plant–microorganism. In this review, we analyzed the constraints posed by drought in the framework of an increasing global demand for plant production, integrating the important role played by the rhizosphere biota as a PGP agent. Using multi-omics approaches to understand in depth the processes that occur in plants in the presence of microorganisms can allow us to modulate their combined use and drive it to increase crop yields, improving production processes to attend the growing global demand for food.

Genetic Circuit Design in Rhizobacteria

Genetically engineered plants hold enormous promise for tackling global food security and agricultural sustainability challenges. However, construction of plant-based genetic circuitry is constrained by a lack of well-characterized genetic parts and circuit design rules. In contrast, advances in bacterial synthetic biology have yielded a wealth of sensors, actuators, and other tools that can be used to build bacterial circuitry. As root-colonizing bacteria (rhizobacteria) exert substantial influence over plant health and growth, genetic circuit design in these microorganisms can be used to indirectly engineer plants and accelerate the design-build-test-learn cycle. Here, we outline genetic parts and best practices for designing rhizobacterial circuits, with an emphasis on sensors, actuators, and chassis species that can be used to monitor/control rhizosphere and plant processes.

Characterization of the Cultivable Endophytic Bacterial Community of Seeds and Sprouts of Cannabis sativa L. and Perspectives for the Application as Biostimulants

Endophytes are beneficial microorganisms exerting growth-promoting activities in plants; they are most often located within the plant intercellular spaces and can be found in all plant tissues, including roots, leaves, stems, flowers, and seeds. In this work, we investigated the cultivable bacterial community of the seeds and the two-week sprouts of the Cannabis sativa L. cultivar “Futura 75”. Endophytes were genotypically and phenotypically characterized and were exposed to different concentrations of seed extracts to verify their susceptibility. A bacterial strain among all the isolates was selected for germination tests of C. sativa in different experimental conditions. The results revealed the dominance of Firmicutes (Staphylococcus sp.) among the isolated strains. Two strains were different from the others for indole-3-acetic acid (IAA) production and for their resistance patterns towards abiotic and biotic stresses. The Sphingomonas sp. strain Can_S11 (Alphaproteobacteria) showed a potential ability to increase the nutraceutical features of its sprouts, particularly an increase in the polyphenol content and antioxidant activity. None of the isolated strains were susceptible to the seed extracts, which were previously tested as antimicrobial and antibiofilm agents against human pathogenic bacteria. The results open new perspectives for the study of the endophytes of C. sativa as possible biostimulants.

The secret life of plant-beneficial rhizosphere bacteria: insects as alternative hosts

Root-colonizing bacteria have been intensively investigated for their intimate relationship with plants and their manifold plant-beneficial activities. They can inhibit growth and activity of pathogens or induce defence responses. In recent years, evidence has emerged that several plant-beneficial rhizosphere bacteria do not only associate with plants but also with insects. Their relationships with insects range from pathogenic to mutualistic and some rhizobacteria can use insects as vectors for dispersal to new host plants. Thus, the interactions of these bacteria with their environment are even more complex than previously thought and can extend far beyond the rhizosphere. The discovery of this secret life of rhizobacteria represents an exciting new field of research that should link the fields of plant-microbe and insect-microbe interactions. In this review, we provide examples of plant-beneficial rhizosphere bacteria that use insects as alternative hosts, and of potentially rhizosphere-competent insect symbionts. We discuss the bacterial traits that may enable a host-switch between plants and insects and further set the multi-host lifestyle of rhizobacteria into an evolutionary and ecological context. Finally, we identify important open research questions and discuss perspectives on the use of these rhizobacteria in agriculture.

Soil pH Determines the Spatial Distribution, Assembly Processes, and Co-existence Networks of Microeukaryotic Community in Wheat Fields of the North China Plain

Soil microeukaryotes play a pivotal role in soil nutrient cycling and crop growth in agroecosystems. However, knowledge of microeukaryotic community distribution patterns, assembly processes, and co-existence networks is greatly limited. Here, microbial eukaryotes in bulk and rhizosphere soils of the North China Plain were investigated. The results showed that soil pH was the driving factor for the microeukaryotic community composition in the bulk and rhizosphere soils. The soil microeukaryotic community could significantly differ between alkaline and acidic soils. The results indicated that the soil pH had a stronger effect than niche differences on community composition. Partial Mantel tests showed that soil pH and spatial distance had similar effects on the microeukaryotic community composition in the bulk soil. However, in the rhizosphere soil, spatial distance had a stronger effect than soil pH. Infer Community Assembly Mechanisms by Phylogenetic bin-based null model (iCAMP) analysis revealed that drift was the most important process driving microeukaryotic community assembly, with an average relative importance of 37.4-71.1%. Dispersal limitation displayed slightly greater importance in alkaline rhizosphere than in alkaline bulk soils. Meanwhile, the opposite trend was observed in acidic soils. In addition, the contribution of each assembly process to each iCAMP lineage "bin" varied according to the acidic or alkaline conditions of the soil and the niche environment. High proportions of positive links were found within the four ecological networks. Alkaline soil networks, especially the alkaline bulk soil network, showed greater complexity than the acidic soil networks. Natural connectivity analysis revealed that the rhizosphere community had a greater stability than the bulk soil community in alkaline soil. This study provides a foundation for understanding the potential roles of microbial eukaryotes in agricultural soil ecosystem functioning.

Micro(nano)plastic size and concentration co-differentiate nitrogen transformation, microbiota dynamics, and assembly patterns in constructed wetlands

Micro/nano-sized plastics (MPs/NPs) existing in wastewater system are the potential threats to nitrogen (N) biotransformation. Constructed wetlands (CWs) as wastewater treatment systems are considered the important barriers preventing MPs/NPs from entering the open water. However, little is known about how the accumulation of MPs/NPs affects microbial N transformation, dynamics, assembly, and metabolism of wetland microbiota. Herein, we constructed 12 wetland systems to address the above knowledge gaps over 300-day exposure to different sizes (3 mm - 60 nm) and concentrations (10 - 1000 μg/L) of MPs/NPs. The results showed that MPs/NPs accumulation caused decrease in NH₄⁺-N removal (by 7.6% - 71.2%) and microbial diversity and intriguingly altered microbiota composition (especially in the high-concentration groups) without damage on the high removal efficiency of NO₃^--N and NO₂^--N (66.2% - 99.8%) in all except for the nano-sized plastic-exposed wetlands. Moreover, MPs/NPs exposure induced shift in the strengths of non-random species aggregation and segregation patterns co-differentiated by the size and concentration of MPs/NPs, and MPs/NPs accumulation created size-differentiated alternative niches for nitrogen-transforming bacteria, e.g., canonical nitrifiers (Nitrospira and Nitrosomonas) and denitrifiers (Thauera, Comamonas, and Aquabacterium), which were enriched in MPs groups where denitrifying enzyme-coding genes were also enriched, suggesting potential positive impact of larger plastics on denitrification. Our study highlights MPs/NPs-induced divergence in microbiota dynamics and nitrogen transformation in CWs, and provides important insights into how microbiota structurally and functionally respond to long-term MPs/NPs disturbance.

Phenotypic and genomic signatures of interspecies cooperation and conflict in naturally occurring isolates of a model plant symbiont

Given the need to predict the outcomes of (co)evolution in host-associated microbiomes, whether microbial and host fitnesses tend to trade-off, generating conflict, remains a pressing question. Examining the relationships between host and microbe fitness proxies at both the phenotypic and genomic levels can illuminate the mechanisms underlying interspecies cooperation and conflict. We examined naturally occurring genetic variation in 191 strains of the model microbial symbiont Sinorhizobium meliloti, paired with each of two host Medicago truncatula genotypes in single- or multi-strain experiments to determine how multiple proxies of microbial and host fitness were related to one another and test key predictions about mutualism evolution at the genomic scale, while also addressing the challenge of measuring microbial fitness. We found little evidence for interspecies fitness conflict; loci tended to have concordant effects on both microbe and host fitnesses, even in environments with multiple co-occurring strains. Our results emphasize the importance of quantifying microbial relative fitness for understanding microbiome evolution and thus harnessing microbiomes to improve host fitness. Additionally, we find that mutualistic coevolution between hosts and microbes acts to maintain, rather than erode, genetic diversity, potentially explaining why variation in mutualism traits persists in nature.

Experimental evolution of Bacillus subtilis on Arabidopsis thaliana roots reveals fast adaptation and improved root colonization

Bacillus subtilis is known to promote plant growth and protect plants against disease. B. subtilis rapidly adapts to Arabidopsis thaliana root colonization, as evidenced by improved root colonizers already after 12 consecutive transfers between seedlings in a hydroponic setup. Re-sequencing of single evolved isolates and endpoint populations revealed mutations in genes related to different bacterial traits, in accordance with evolved isolates displaying increased root colonization associated with robust biofilm formation in response to the plant polysaccharide xylan and impaired motility. Interestingly, evolved isolates suffered a fitness disadvantage in a non-selective environment, demonstrating an evolutionary cost of adaptation to the plant root. Finally, increased root colonization by an evolved isolate was also demonstrated in the presence of resident soil microbes. Our findings highlight how a plant growth-promoting rhizobacterium rapidly adapts to an ecologically relevant environment and reveal evolutionary consequences that are fundamental to consider when evolving strains for biocontrol purposes.

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Bacillus subtilis shows fast adaptation to Arabidopsis thaliana roots in a hydroponic setup

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Evolved isolates exhibit robust biofilms in response to xylan and impaired motility

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Adaptation to A. thaliana roots is accompanied by an evolutionary cost

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An evolved isolate shows higher root colonization in the presence of soil bacteria

Plant-microbe eco-evolutionary dynamics in a changing world

Both plants and their associated microbiomes can respond strongly to anthropogenic environmental changes. These responses can be both ecological (e.g. a global change affecting plant demography or microbial community composition) and evolutionary (e.g. a global change altering natural selection on plant or microbial populations). As a result, global changes can catalyse eco-evolutionary feedbacks. Here, we take a plant-focused perspective to discuss how microbes mediate plant ecological responses to global change and how these ecological effects can influence plant evolutionary response to global change. We argue that the strong and functionally important relationships between plants and their associated microbes are particularly likely to result in eco-evolutionary feedbacks when perturbed by global changes and discuss how improved understanding of plant-microbe eco-evolutionary dynamics could inform conservation or even agriculture.

Effect ofBacillus velezensis JC-K3 on Endophytic Bacterial and Fungal Diversity in Wheat Under Salt Stress

Plant growth-promoting bacteria (PGPB) can effectively reduce salt damage in plants. Currently, there are many studies on the effects of PGPB on the microbial community structure of rhizosphere soil under salt stress, but fewer studies on the community structure of endophytic bacteria and fungi. We propose that inoculation of endophytic bacteria into the rhizosphere of plants can significantly affect the microbial community structure of the plant's above-ground and underground parts, which may be the cause of the plant's "Induced Systemic Tolerance." The isolated endophytes were re-inoculated into the rhizosphere under salinity stress. We found that, compared with the control group, inoculation with endophytic Bacillus velezensis JC-K3 not only increased the accumulation of wheat biomass, but also increased the content of soluble sugar and chlorophyll in wheat, and reduced the absorption of Na in wheat shoots and leaves. The abundance of bacterial communities in shoots and leaves increased and the abundance of fungal communities decreased after inoculation with JC-K3. The fungal community richness of wheat rhizosphere soil was significantly increased. The diversity of bacterial communities in shoots and leaves increased, and the richness of fungal communities decreased. JC-K3 strain improved wheat's biomass accumulation ability, osmotic adjustment ability, and ion selective absorption ability. In addition, JC-K3 significantly altered the diversity and abundance of endophytic and rhizosphere microorganisms in wheat. PGPB can effectively reduce plant salt damage. At present, there are many studies on the effect of PGPB on the microbial community structure in rhizosphere soil under salt stress, but there are few studies on the community structure changes of endophytic bacteria and fungi in plants.