The evolution of siderophore production as a competitive trait

Adaptations of the Genus Bradyrhizobium to Selected Elements, Heavy Metals and Pesticides Present in the Soil Environment

Rhizobial bacteria perform a number of extremely important functions in the soil environment. In addition to fixing molecular nitrogen and transforming it into a form available to plants, they participate in the circulation of elements and the decomposition of complex compounds present in the soil, sometimes toxic to other organisms. This review article describes the molecular mechanisms occurring in the most diverse group of rhizobia, the genus Bradyrhizobium, allowing these bacteria to adapt to selected substances found in the soil. Firstly, the adaptation of bradyrhizobia to low and high concentrations of elements such as iron, phosphorus, sulfur, calcium and manganese was shown. Secondly, the processes activated in their cells in the presence of heavy metals such as lead, mercury and arsenic, as well as radionuclides, were described. Additionally, due to the potential use of Bradyrhziobium as biofertilizers, their response to pesticides commonly used in agriculture, such as glyphosate, sulfentrazone, chlorophenoxy herbicides, flumioxazine, imidazolinone, atrazine, and insecticides and fungicides, was also discussed. The paper shows the great genetic diversity of bradyrhizobia in terms of adapting to variable environmental conditions present in the soil.

Stereospecific control of microbial growth by a combinatoric suite of chiral siderophores

Bacteria compete for iron by producing small-molecule chelators known as siderophores. The triscatechol siderophores trivanchrobactin and ruckerbactin, produced by Vibrio campbellii DS40M4 and Yersinia ruckeri YRB, respectively, are naturally occurring diastereomers that form chiral ferric complexes in opposing enantiomeric configurations. Chiral recognition is a hallmark of specificity in biological systems, yet the biological consequences of chiral coordination compounds are relatively unexplored. We demonstrate stereoselective discrimination of microbial growth and iron uptake by chiral Fe(III)-siderophores. The siderophore utilization pathway in V. campbellii DS40M4 is stereoselective for Λ-Fe(III)-trivanchrobactin, but not the mismatched Δ-Fe(III)-ruckerbactin diastereomer. Chiral recognition is likely conferred by the stereospecificity of both the outer membrane receptor (OMR) protein FvtA and the periplasmic binding protein (PBP) FvtB, both of which must interact preferentially with the Λ-configured Fe(III)-coordination complexes.

Multi-omic investigation identifies key antifungal biochemistry during fermentation of a Streptomyces biological control agent

The use of multi-omic approaches has significantly advanced the exploration of microbial traits, leading to the discovery of new bioactive compounds and their mechanisms of action. Streptomyces sp. MH71 is known for its antifungal properties with potential for use in crop protection. Using genomic, transcriptomic, and metabolomic analyses, the antifungal metabolic capacity of Streptomyces sp. MH71 was investigated. After 96 hours of liquid fermentation, cell-free spent media showed inhibitory activity against the fungal phytopathogen Verticillium dahliae, with the lowest IC50 value being 0.11 % (v/v) after 144 h. Through whole-genome sequencing, we obtained a near-complete genome of 11 Mb with a G+C content of 71 % for Streptomyces sp. MH71. Genome mining identified 50 putative biosynthetic gene clusters, six of which produced known antimicrobial compounds. To link antifungal activity with candidate biosynthetic pathways, a transcriptomic approach was applied to understand antifungal induction in MH71 cells during the observed increase in antifungal activity. This approach revealed 2774 genes that exhibited differential expression, with significant upregulation of genes involved in biosynthesis of secondary metabolites during the stationary growth phase. Metabolomic analyses using LC-MS and GC-MS of secreted compounds identified a cocktail of potent antifungal metabolites, including volatiles with antifungal activity. By combining genome mining, bioactivity data, transcriptomics, and metabolomics, we describe in detail the gene expression and metabolite products driving antifungal activity during microbial fermentation.

The Effects of Milk and Posterior Intestinal Microorganisms on the Lactation Performance of Dual-Purpose Cattle (Bos taurus) Revealed by 16S rRNA Sequencing

The aim of this research was to employ 16S rRNA high-throughput sequencing to thoroughly explore the interplay between milk and hindgut microbial communities and the effects of microorganisms in milk and the hindgut on the dairy quality of XJBC and CSC. In this study, 96 XJBC milk samples, 94 XJBC hindgut samples, 100 CSC milk samples, and 93 CSC hindgut samples were collected for microbial community analysis. The 16S rRNA sequencing data revealed that the microbial species richness in the milk of CSC exceeded that of XJBC, whereas the opposite was true for the hindgut microbial communities. A chi-square test was conducted using SPSS 19.0. The milk and posterior intestinal microbiota between individuals were analyzed with the Pearson chi-square test, maximum likelihood ratio, and Fisher's exact test. Nongenetic factors substantially influenced microbial community dynamics in both milk and the hindgut. In the milk of dairy cows, a significant negative correlation was observed between one genus and milk protein production. Nine genera were significantly negatively correlated with milk fat production, whereas one genus was positively correlated. Additionally, six genera were negatively correlated with lactose production, and two genera exhibited positive correlations. Notably, Phascolarctobacterium and Turicibacter were identified as genera originating from the hindgut, which led to reduced milk quality. In the hindgut microbial community of dairy cows, seven genera were significantly negatively associated with milk fat production, whereas one genus was positively associated with milk fat production. These findings indicate that certain mammary microorganisms may migrate from the hindgut, either endogenously or exogenously, disrupting the equilibrium of the mammary microbial community in dairy cows and potentially leading to inflammation. By enhancing feeding conditions and standardizing production practices, the invasion of harmful flora into mammary tissues can be minimized, reducing the risk of inflammation and thereby preserving the health of dairy cows and enhancing milk quality.

Streptomyces secretes a siderophore that sensitizes competitor bacteria to phage infection

To overtake competitors, microbes produce and secrete secondary metabolites that kill neighbouring cells and sequester nutrients. This metabolite-mediated competition probably evolved in complex microbial communities in the presence of viral pathogens. We therefore hypothesized that microbes secrete natural products that make competitors sensitive to phage infection. We used a binary-interaction screen and chemical characterization to identify a secondary metabolite (coelichelin) produced by Streptomyces sp. that sensitizes its soil competitor Bacillus subtilis to phage infection in vitro. The siderophore coelichelin sensitized B. subtilis to a panel of lytic phages (SPO1, SP10, SP50, Goe2) via iron sequestration, which prevented the activation of B. subtilis Spo0A, the master regulator of the stationary phase and sporulation. Metabolomics analysis revealed that other bacterial natural products may also provide phage-mediated competitive advantages to their producers. Overall, this work reveals that synergy between natural products and phages can shape the outcomes of competition between microbes.

Bioleaching of lanthanum from nickel metal hydride dry battery using siderophores produced by Pseudomonas sp

There is still much to be learned about the properties of siderophores and their applications. This study was designed to characterize and optimize the production of the siderophore produced by a marine bacterium Pseudomonas sp. strain ASA235 and then evaluate their use in bioleaching of rare earth elements (REEs) from spent Nickel-metal hydride (NiMH) batteries. The results of both Tetrazolium and Arnow's tests indicated that the test organism produces a mixed-type siderophore of pyoverdine family, a result that was confirmed by FT-IR and MALDI-TOFF analyses. Optimization of pH, temperature, incubation period, and iron concentration for siderophore production led to a noticeable shift from 44.5% up to 91% siderophore unit when the test bacterium was incubated at 28 °C and pH 7 after 72 h in the absence of iron. The purified siderophore showed the ability to bleach about 14.8% of lanthanum from the anode of the NiMH battery along with other elements, although in lower amounts. This data put siderophores in distinct focus for further prospective studies intending the bioleaching of such precious elements. The scaling up of this process and optimization would make a big difference in such a green bioleaching strategy, allowing us to recover such precious elements in an environmentally friendly way.

Selection for toxin production in spatially structured environments increases with growth rate

Microbes adopt diverse strategies to successfully compete with coexisting strains for space and resources. One common strategy is the production of toxic compounds to inhibit competitors, but the strength and direction of selection for this strategy vary depending on the environment. Existing theoretical and experimental evidence suggests that growth in spatially structured environments makes toxin production more beneficial because competitive interactions are localized. Because higher growth rates reduce the length scale of interactions in structured environments, theory predicts that toxin production should be especially beneficial under these conditions. We tested this hypothesis by developing a genome-scale metabolic modeling approach and complementing it with comparative genomics to investigate the impact of growth rate on selection for costly toxin production. Our modeling approach expands the current abilities of the dynamic flux balance analysis platform Computation Of Microbial Ecosystems in Time and Space (COMETS) to incorporate signaling and toxin production. Using this capability, we find that our modeling framework predicts that the strength of selection for toxin production increases as growth rate increases. This finding is supported by comparative genomics analyses that include diverse microbial species. Our work emphasizes that toxin production is more likely to be maintained in rapidly growing, spatially structured communities, thus improving our ability to manage microbial communities and informing natural product discovery.

Lysis of Escherichia coli by colicin Ib contributes to bacterial cross-feeding by releasing active β-galactosidase

The diffusible toxin ColIb produced by Salmonella enterica serovar Typhimurium SL1344 is a potent inhibitor of Escherichia coli growth. To identify and parameterize metabolic cross-feeding in states of competition, we established defined communities in which E. coli was the only species able to access a sole carbon source, lactose. Although ColIb was predicted to undermine cross-feeding by killing the lactose-converting E. coli, S. enterica populations thrived in co-culture. We discovered that ColIb caused the release of active β-galactosidase from E. coli cells, which induced galactose uptake by S. enterica. Although iron limitation stimulates ColIb production and makes E. coli more sensitive to the toxin, ColIb killing in iron-limited conditions did not enhance iron acquisition or siderophore scavenging by S. enterica. Also unexpected was the rapid rate at which resistance to ColIb evolved in E. coli through spontaneous mutation of the ColIb receptor gene cirA or horizontal acquisition of the S. enterica colicin immunity gene imm. Mathematical modelling effectively predicted the growth kinetics of E. coli and S. enterica populations, revealing a tractable system in which ColIb can shrink a competitor population while simultaneously amplifying the metabolic contributions of the suppressed population.

Antimicrobial activity of iron-depriving pyoverdines against human opportunistic pathogens

The global rise of antibiotic resistance calls for new drugs against bacterial pathogens. A common approach is to search for natural compounds deployed by microbes to inhibit competitors. Here, we show that the iron-chelating pyoverdines, siderophores produced by environmental Pseudomonas spp., have strong antibacterial properties by inducing iron starvation and growth arrest in pathogens. A screen of 320 natural Pseudomonas isolates used against 12 human pathogens uncovered several pyoverdines with particularly high antibacterial properties and distinct chemical characteristics. The most potent pyoverdine effectively reduced growth of the pathogens Acinetobacter baumannii, Klebsiella pneumoniae, and Staphylococcus aureus in a concentration- and iron-dependent manner. Pyoverdine increased survival of infected Galleria mellonella host larvae and showed low toxicity for the host, mammalian cell lines, and erythrocytes. Furthermore, experimental evolution of pathogens combined with whole-genome sequencing revealed limited resistance evolution compared to an antibiotic. Thus, pyoverdines from environmental strains have the potential to become a new class of sustainable antibacterials against specific human pathogens.

Competition-driven phenotypic plasticity in Iron acquisition and aromatic utilization confers a fitness advantage to Pseudomonas putida in an Iron-limited rhizospheric environment

Iron scarcity poses a critical challenge for rhizospheric bacteria like Pseudomonas putida in the competitive rhizosphere. Despite its dependence on iron for essential functions such as root colonization, motility, and aromatic compound utilization, P. putida exhibits limited capability for heterologous siderophore utilization and primarily relies on the secretion of a single siderophore, pyoverdine. This study investigates the mechanisms by which P. putida acquires iron in an iron-limited, aromatic-rich, rhizosphere-like environment. Our findings demonstrate that P. putida exhibits significant phenotypic plasticity, dynamically modulating pyoverdine secretion in response to competitive pressures and substrate availability. This adaptive strategy optimizes energy expenditure and iron acquisition, providing a competitive advantage. Comparative gene expression analysis supports these observations, revealing the molecular underpinnings of this plasticity. Enhanced pyoverdine production driven by competition compensates for the bacterium's limited siderophore repertoire and facilitates rapid aromatic compound utilization, conferring a distinct fitness advantage in iron-deprived conditions. This study elucidates the complex interplay between competition, iron uptake, and aromatic compound utilization that underpins the rhizospheric success of P. putida.

Tradeoffs and constraints on the evolution of tailocins

Phage tail-like bacteriocins (tailocins) are protein complexes produced by bacteria with the potential to kill their neighbors. Widespread throughout Gram-negative bacteria, tailocins exhibit extreme specificity in their targets, largely killing closely related strains. Despite their presence in diverse bacteria, the impact of these competitive weapons on the surrounding microbiota is largely unknown. Recent studies revealed the rapid evolution and genetic diversity of tailocins in microbial communities and suggest that there are constraints on the evolution of specificity and resistance. Given the precision of their targeted killing and the ease of engineering new specificities, understanding the evolution and ecological impact of tailocins may enable the design of promising candidates for novel targeted antibiotics.

Experimental evolution of yeast shows that public-goods upregulation can evolve despite challenges from exploitative non-producers

Microbial secretions, such as metabolic enzymes, are often considered to be cooperative public goods as they are costly to produce but can be exploited by others. They create incentives for the evolution of non-producers, which can drive producer and population productivity declines. In response, producers can adjust production levels. Past studies suggest that while producers lower production to reduce costs and exploitation opportunities when under strong selection pressure from non-producers, they overproduce secretions when these pressures are weak. We challenge the universality of this trend with the production of a metabolic enzyme, invertase, by Saccharomyces cerevisiae, which catalyses sucrose hydrolysis into two hexose molecules. Contrary to past studies, overproducers evolve during evolutionary experiments even when under strong selection pressure from non-producers. Phenotypic and competition assays with a collection of synthetic strains - engineered to have modified metabolic attributes - identify two mechanisms for suppressing the benefits of invertase to those who exploit it. Invertase overproduction increases extracellular hexose concentrations that suppresses the metabolic efficiency of competitors, due to the rate-efficiency trade-off, and also enhances overproducers' hexose capture rate by inducing transporter expression. Thus, overproducers are maintained in the environment originally thought to not support public goods production.

Parallel ecological and evolutionary responses to selection in a natural bacterial community

Evolution can occur over ecological timescales, suggesting a potentially important role for rapid evolution in shaping community trait distributions. However, evidence of concordant eco-evolutionary dynamics often comes from in vitro studies of highly simplified communities, and measures of ecological and evolutionary dynamics are rarely directly comparable. Here, we quantified how ecological species sorting and rapid evolution simultaneously shape community trait distributions by tracking within- and between-species changes in a key trait in a complex bacterial community. We focused on the production of siderophores; bacteria use these costly secreted metabolites to scavenge poorly soluble iron and to detoxify environments polluted with toxic nonferrous metals. We found that responses to copper-imposed selection within and between species were ultimately the same-intermediate siderophore levels were favored-and occurred over similar timescales. Despite being a social trait, this level of siderophore production was selected regardless of whether species evolved in isolation or in a community context. Our study suggests that evolutionary selection can play a pivotal role in shaping community trait distributions within natural, highly complex, bacterial communities. Furthermore, trait evolution may not always be qualitatively affected by interactions with other community members.

Genomic insights and biocontrol potential of ten bacterial strains from the tomato core microbiome

Introduction

Despite their adverse environmental effects, modern agriculture relies heavily on agrochemicals to manage diseases and pests and enhance plant growth and productivity. Some of these functions could instead be fulfilled by endophytes from the plant microbiota, which have diverse activities beneficial for plant growth and health.

Methods

We therefore used a microbiome-guided top-down approach to select ten bacterial strains from different taxa in the core microbiome of tomato plants in the production chain for evaluation as potential bioinoculants. High-quality genomes for each strain were obtained using Oxford Nanopore long-read and Illumina short-read sequencing, enabling the dissection of their genetic makeup to identify phyto-beneficial traits.

Results

Bacterial strains included both taxa commonly used as biofertilizers and biocontrol agents (i.e. Pseudomonas and Bacillus) as well as the less studied genera Leclercia, Chryseobacterium, Glutamicibacter, and Paenarthorbacter. When inoculated in the tomato rhizosphere, these strains promoted plant growth and reduced the severity of Fusarium Crown and Root Rot and Bacterial Spot infections. Genome analysis yielded a comprehensive inventory of genes from each strain related to processes including colonization, biofertilization, phytohormones, and plant signaling. Traits directly relevant to fertilization including phosphate solubilization and acquisition of nitrogen and iron were also identified. Moreover, the strains carried several functional genes putatively involved in abiotic stress alleviation and biotic stress management, traits that indirectly foster plant health and growth.

Discussion

This study employs a top-down approach to identify new plant growth-promoting rhizobacteria (PGPRs), offering an alternative to the conventional bottom-up strategy. This method goes beyond the traditional screening of the strains and thus can expand the range of potential bioinoculants available for market application, paving the way to the use of new still underexplored genera.

RNA-Seq reveals that Pseudomonas aeruginosa mounts growth medium-dependent competitive responses when sensing diffusible cues from Burkholderia cenocepacia

Most habitats host diverse bacterial communities, offering opportunities for inter-species interactions. While competition might often dominate such interactions, little is known about whether bacteria can sense competitors and mount adequate responses. The competition sensing hypothesis proposes that bacteria can use cues such as nutrient stress and cell damage to prepare for battle. Here, we tested this hypothesis by measuring transcriptome changes in Pseudomonas aeruginosa exposed to the supernatant of its competitor Burkholderia cenocepacia. We found that P. aeruginosa exhibited significant growth-medium-dependent transcriptome changes in response to competition. In an iron-rich medium, P. aeruginosa upregulated genes encoding the type-VI secretion system and the siderophore pyoverdine, whereas genes encoding phenazine toxins and hydrogen cyanide were upregulated under iron-limited conditions. Moreover, general stress response and quorum sensing regulators were upregulated upon supernatant exposure. Altogether, our results reveal nuanced competitive responses of P. aeruginosa when confronted with B. cenocepacia supernatant, integrating both environmental and social cues.

Functional and Evolutionary Integration of a Fungal Gene With a Bacterial Operon

Siderophores are crucial for iron-scavenging in microorganisms. While many yeasts can uptake siderophores produced by other organisms, they are typically unable to synthesize siderophores themselves. In contrast, Wickerhamiella/Starmerella (W/S) clade yeasts gained the capacity to make the siderophore enterobactin following the remarkable horizontal acquisition of a bacterial operon enabling enterobactin synthesis. Yet, how these yeasts absorb the iron bound by enterobactin remains unresolved. Here, we demonstrate that Enb1 is the key enterobactin importer in the W/S-clade species Starmerella bombicola. Through phylogenomic analyses, we show that ENB1 is present in all W/S clade yeast species that retained the enterobactin biosynthetic genes. Conversely, it is absent in species that lost the ent genes, except for Starmerella stellata, making this species the only cheater in the W/S clade that can utilize enterobactin without producing it. Through phylogenetic analyses, we infer that ENB1 is a fungal gene that likely existed in the W/S clade prior to the acquisition of the ent genes and subsequently experienced multiple gene losses and duplications. Through phylogenetic topology tests, we show that ENB1 likely underwent horizontal gene transfer from an ancient W/S clade yeast to the order Saccharomycetales, which includes the model yeast Saccharomyces cerevisiae, followed by extensive secondary losses. Taken together, these results suggest that the fungal ENB1 and bacterial ent genes were cooperatively integrated into a functional unit within the W/S clade that enabled adaptation to iron-limited environments. This integrated fungal-bacterial circuit and its dynamic evolution determine the extant distribution of yeast enterobactin producers and cheaters.

The interplay between microbial communities and soil properties

In recent years, there has been considerable progress in determining the soil properties that influence the structure of the soil microbiome. By contrast, the effects of microorganisms on their soil habitat have received less attention with most previous studies focusing on microbial contributions to soil carbon and nitrogen dynamics. However, soil microorganisms are not only involved in nutrient cycling and organic matter transformations but also alter the soil habitat through various biochemical and biophysical mechanisms. Such microbially mediated modifications of soil properties can have local impacts on microbiome assembly with pronounced ecological ramifications. In this Review, we describe the processes by which microorganisms modify the soil environment, considering soil physics, hydrology and chemistry. We explore how microorganism-soil interactions can generate feedback loops and discuss how microbially mediated modifications of soil properties can serve as an alternative avenue for the management and manipulation of microbiomes to combat soil threats and global change.

Heme sequestration by hemophilin from Haemophilus haemolyticus reduces respiratory tract colonization and infection with non-typeable Haemophilus influenzae

Iron acquisition is a key feature dictating the success of pathogen colonization and infection. Pathogens scavenging iron from the host must contend with other members of the microbiome similarly competing for the limited pool of bioavailable iron, often in the form of heme. In this study, we identify a beneficial role for the heme-binding protein hemophilin (Hpl) produced by the non-pathogenic bacterium Haemophilus haemolyticus against its close relative, the opportunistic respiratory tract pathogen non-typeable Haemophilus influenzae (NTHi). Using a mouse model, we found that pre-exposure to H. haemolyticus significantly reduced NTHi colonization of the upper airway and impaired NTHi infection of the lungs in an Hpl-dependent manner. Further, treatment with recombinant Hpl was sufficient to decrease airway burdens of NTHi without exacerbating lung immunopathology or systemic inflammation. Instead, mucosal production of the neutrophil chemokine CXCL2, lung myeloperoxidase, and serum pro-inflammatory cytokines IL-6 and TNFα were lower in Hpl-treated mice. Mechanistically, H. haemolyticus suppressed NTHi growth and adherence to human respiratory tract epithelial cells through the expression of Hpl, and recombinant Hpl could recapitulate these effects. Together, these findings indicate that heme sequestration by non-pathogenic, Hpl-producing H. haemolyticus is protective against NTHi colonization and infection.

IMPORTANCE

The microbiome provides a critical layer of protection against infection with bacterial pathogens. This protection is accomplished through a variety of mechanisms, including interference with pathogen growth and adherence to host cells. In terms of immune defense, another way to prevent pathogens from establishing infections is by limiting the availability of nutrients, referred to as nutritional immunity. Restricting pathogen access to iron is a central component of this approach. Here, we uncovered an example where these two strategies intersect to impede infection with the respiratory tract bacterial pathogen Haemophilus influenzae. Specifically, we find that a non-pathogenic (commensal) bacterium closely related to H. influenzae called Haemophilus haemolyticus improves protection against H. influenzae by limiting the ability of this pathogen to access iron. These findings suggest that beneficial members of the microbiome improve protection against pathogen infection by effectively contributing to host nutritional immunity.

Prevalence and variability of siderophore production in the Achromobacter genus

Achromobacter spp. are opportunistic pathogens of environmental origin increasingly isolated in patients with underlying conditions like cystic fibrosis (CF). Despite recent advances, their virulence factors remain incompletely studied, and siderophore production has not yet been investigated in this genus. The aim of this study was to evaluate the production of siderophores in a large collection of Achromobacter spp. and evaluate the variability according to the origin of the strain and species. A total of 163 strains were studied, including 128 clinical strains (CF and non-CF patients) and 35 strains of environmental origin. Siderophores were quantified by the liquid chrome azurol-sulphonate assay. Species were identified by nrdA gene-based phylogeny. Strains were assigned to 20 species, with Achromobacter xylosoxidans being the most represented (51.5% of strains). Siderophore production was observed in 72.4% of the strains, with amounts ranging from 10.1% to 90% siderophore units. A significantly higher prevalence of siderophore-producing strains and greater production of siderophores were observed for clinical strains compared with strains of environmental origin. Highly variable observations were made according to species: A. xylosoxidans presented unique characteristics (one of the highest prevalence of producing strains and highest amounts produced, particularly by CF strains). Siderophores are important factors for bacterial growth commonly produced by members of the Achromobacter genus. The significance of the observations made during this study must be further investigated. Indeed, the differences observed according to species and the origin of strains suggest that siderophores may represent important determinants of the pathophysiology of Achromobacter spp. infections and also contribute to the particular epidemiological success of A. xylosoxidans in human infections.

IMPORTANCE

Achromobacter spp. are recognized as emerging opportunistic pathogens in humans with various underlying diseases, including cystic fibrosis (CF). Although their pathophysiological traits are increasingly studied, their virulence factors remain incompletely described. Particularly, siderophores that represent important factors of bacterial growth have not yet been studied in this genus. A population-based study was performed to explore the ability of members of the Achromobacter genus to produce siderophores, both overall and in relevant subgroups (Achromobacter species; strain origin, either clinical-from CF or non-CF patients-or environmental). This study provides original data showing that siderophore production is a common trait of Achromobacter strains, particularly observed among clinical strains. The major species, Achromobacter xylosoxidans, encompassed both one of the highest prevalence of siderophore-producing strains and strains producing the largest amounts of siderophores, particularly observed for CF strains. These observations may represent additional advantages accounting for the epidemiological success of this species.

Exploring the role and mechanism of potential probiotics in mitigating the shrimp pathogens

Shrimp aquaculture has rapidly developed into a significant industry worldwide, providing not only financial gain and high-quality food but also tens of thousands of trained and competent workers. Frequent diseases are now regarded as a significant risk factor for shrimp aquaculture, as they have the potential to significantly reduce shrimp production and result in economic losses. Over the years various traditional methods including the use of antibiotics have been followed to control diseases yet unsuccessful. Probiotic is considered potential supplements for shrimps during farming, they may also act beneficially as disease control and increased production. Probiotics are described as a live microbial supplement that benefits the host by modifying the microbial population associated with the host and its ambient. The present state of research about probiotics demonstrates notable impacts on the immune defences of the host's gastrointestinal system, which play a crucial role in safeguarding against diseases and managing inflammation inside the digestive tract. In the past ten years, many studies on probiotics have been published. However, there is a lack of information about the processes by which probiotics exert their effects in aquaculture systems, with only limited elucidations being offered. This study explores the variety of procedures behind the positive effects of probiotics in shrimp culture. These mechanisms include the augmentation of the immune system, control of growth, antagonistic action against pathogens, competitive exclusion, and modification of the gut microbiota. Mechanisms involved in the probiotic mode of action are mostly interlinked. This provides a greater understanding of the importance of probiotics in shrimp culture as an environmentally friendly practice.

Bacterium secretes chemical inhibitor that sensitizes competitor to bacteriophage infection

To overtake competitors, microbes produce and secrete secondary metabolites that kill neighboring cells and sequester nutrients. This natural product-mediated competition likely evolved in complex microbial communities that included viral pathogens. From this ecological context, we hypothesized that microbes secrete metabolites that "weaponize" natural pathogens (i.e., bacteriophages) to lyse their competitors. Indeed, we discovered a bacterial secondary metabolite that sensitizes other bacteria to phage infection. We found that this metabolite provides the producer (a Streptomyces sp.) with a fitness advantage over its competitor (Bacillus subtilis) by promoting phage infection. The phage-promoting metabolite, coelichelin, sensitized B. subtilis to a wide panel of lytic phages, and it did so by preventing the early stages of sporulation through iron sequestration. Beyond coelichelin, other natural products may provide phage-mediated competitive advantages to their producers-either by inhibiting sporulation or through yet-unknown mechanisms.

Siderophores and competition for iron govern myxobacterial predation dynamics

Bacterial predators are decisive organisms that shape microbial ecosystems. In this study, we investigated the role of iron and siderophores during the predatory interaction between two rhizosphere bacteria: Myxococcus xanthus, an epibiotic predator, and Sinorhizobium meliloti, a bacterium that establishes nitrogen-fixing symbiosis with legumes. The results show that iron enhances the motility of the predator and facilitates its predatory capability, and that intoxication by iron is not used by the predator to prey, although oxidative stress increases in both bacteria during predation. However, competition for iron plays an important role in the outcome of predatory interactions. Using combinations of predator and prey mutants (nonproducers and overproducers of siderophores), we have investigated the importance of competition for iron in predation. The results demonstrate that the competitor that, via the production of siderophores, obtains sufficient iron for growth and depletes metal availability for the opponent will prevail in the interaction. Consequently, iron fluctuations in soils may modify the composition of microbial communities by altering the activity of myxobacterial predators. In addition, siderophore overproduction during predation can alter soil properties, affecting the productivity and sustainability of agricultural operations.

The fitness benefit of pyoverdine cross-feeding by Pseudomonas protegens Pf-5

Under iron-limiting conditions, fluorescent pseudomonads acquire iron from the environment by secreting strain-specific, iron-chelating siderophores termed pyoverdines (PVD). The rhizosphere bacterium Pseudomonas protegens Pf-5 produces its own PVD but also can cross-feed on PVDs produced by other species. Previous work has found that Pf-5 continues to produce its own PVD when allowed to cross-feed, raising questions about the benefit of heterologous PVD utilisation. Here, we investigate this question using a defined, unidirectional P. protegens Pf-5/Pseudomonas aeruginosa PAO1 cross-feeding model. Quantifying the production of PVD in the presence of heterologous PVD produced by PAO1, we show that cross-feeding Pf-5 strains reduce the production of their own PVD, while non-cross-feeding Pf-5 strains increase the production of PVD. Measuring the fitness of cross-feeding and non-cross-feeding Pf-5 strains in triple coculture with PAO1, we find that cross-feeding provides a fitness benefit to Pf-5 when the availability of heterologous PVD is high. We conclude that cross-feeding can reduce the costs of self-PVD production and may thus aid in the colonisation of iron-limited environments that contain compatible siderophores produced by other resident microbes. Taken together, these results expand our understanding of the mechanisms of interspecific competition for iron in microbial communities.

Natural product biosynthetic potential reflects macroevolutionary diversification within a widely distributed bacterial taxon

IMPORTANCE

This is the most comprehensive study performed thus far on the biosynthetic potential within the Flavobacteriaceae family. Our findings reveal intertwined taxonomic and natural product biosynthesis diversification within the family. We posit that the carbohydrate, peptide, and secondary metabolism triad synergistically shaped the evolution of this keystone bacterial taxon, acting as major forces underpinning the broad host range and opportunistic-to-pathogenic behavior encompassed by species in the family. This study further breaks new ground for future research on select Flavobacteriaceae spp. as reservoirs of novel drug leads.

In Vitro Studies of Endophytic Bacteria Isolated from Ginger (Zingiber officinale) as Potential Plant-Growth-Promoting and Biocontrol Agents against Botrytis cinerea and Colletotrichum acutatum

Agriculture currently confronts a multitude of challenges arising from the excessive utilization of chemical pesticides and the proliferation of phytopathogenic fungi strains that exhibit resistance to commonly employed active compounds in the field. Botrytis cinerea and Colletotrichum acutatum are phytopathogenic fungi that inflict substantial economic losses within agriculture and food due to their high impacts on crops both pre- and post-harvest. Furthermore, the emergence of fungal strains that are resistant to commercial fungicides has exacerbated this problem. To explore more environmentally sustainable alternatives for the control of these pathogens, an investigation into the endophytic bacteria associated with ginger (Zingiber officinale Rosc.) was conducted. The primary focus of this study involved evaluating their inhibitory efficacy against the fungi and assessing their potential for promoting plant growth. The endophytic bacteria genera Lelliottia, Lysinibacillus, Kocuria, Agrococcus, Acinetobacter, Agrobacterium, Zymobacter, and Mycolicibacterium were identified. All isolates showed remarkable in vitro antagonistic ability against B. cinerea (>94%) and C. acutatum (>74%). Notably, the Lelliottia amnigena J29 strain exhibited a notable proficiency in producing extracellular enzymes and indole compounds (IAA), solubilizing phosphate and potassium, and forming biofilm. Furthermore, the Lysinibacillus capsici J26, Agrococcus citreus J28, and Mycolicibacterium sp. J5 strains displayed the capacity for atmospheric nitrogen fixation and siderophore production. These findings underscore the agricultural and biotechnological potential of endophytic bacteria derived from ginger plants and suggest the feasibility of developing alternative approaches to manage these two phytopathogenic fungi.

Functional and evolutionary integration of a fungal gene with a bacterial operon

Siderophores are crucial for iron-scavenging in microorganisms. While many yeasts can uptake siderophores produced by other organisms, they are typically unable to synthesize siderophores themselves. In contrast, Wickerhamiella/Starmerella (W/S) clade yeasts gained the capacity to make the siderophore enterobactin following the remarkable horizontal acquisition of a bacterial operon enabling enterobactin synthesis. Yet, how these yeasts absorb the iron bound by enterobactin remains unresolved. Here, we demonstrate that Enb1 is the key enterobactin importer in the W/S-clade species Starmerella bombicola. Through phylogenomic analyses, we show that ENB1 is present in all W/S clade yeast species that retained the enterobactin biosynthetic genes. Conversely, it is absent in species that lost the ent genes, except for Starmerella stellata, making this species the only cheater in the W/S clade that can utilize enterobactin without producing it. Through phylogenetic analyses, we infer that ENB1 is a fungal gene that likely existed in the W/S clade prior to the acquisition of the ent genes and subsequently experienced multiple gene losses and duplications. Through phylogenetic topology tests, we show that ENB1 likely underwent horizontal gene transfer from an ancient W/S clade yeast to the order Saccharomycetales, which includes the model yeast Saccharomyces cerevisiae, followed by extensive secondary losses. Taken together, these results suggest that the fungal ENB1 and bacterial ent genes were cooperatively integrated into a functional unit within the W/S clade that enabled adaptation to iron-limited environments. This integrated fungal-bacterial circuit and its dynamic evolution determines the extant distribution of yeast enterobactin producers and cheaters.

Siderophore-mediated iron partition promotes dynamical coexistence between cooperators and cheaters

Microbes shape their habitats by consuming resources and producing a diverse array of chemicals that can serve as public goods. Despite the risk of exploitation by cheaters, genes encoding sharable molecules like siderophores are widely found in nature, prompting investigations into the mechanisms that allow producers to resist invasion by cheaters. In this work, we presented the chemostat-typed "resource partition model" to demonstrate that dividing the iron resource between private and public siderophores can promote stable or dynamic coexistence between producers and cheaters in a well-mixed environment. Moreover, our analysis shows that when microbes not only consume but also produce resources, chemical innovation leads to stability criteria that differ from those of classical consumer resource models, resulting in more complex dynamics. Our work sheds light on the role of chemical innovations in microbial communities and the potential for resource partition to facilitate dynamical coexistence between cooperative and cheating organisms.

Screening microbial inoculants and their interventions for cross-kingdom management of wilt disease of solanaceous crops- a step toward sustainable agriculture

Microbial inoculants may be called magical bullets because they are small in size but have a huge impact on plant life and humans. The screening of these beneficial microbes will give us an evergreen technology to manage harmful diseases of cross-kingdom crops. The production of these crops is reducing as a result of multiple biotic factors and among them the bacterial wilt disease triggered by Ralstonia solanacearum is the most important in solanaceous crops. The examination of the diversity of bioinoculants has shown that more microbial species have biocontrol activity against soil-borne pathogens. Reduced crop output, lower yields, and greater cost of cultivation are among the major issues caused by diseases in agriculture around the world. It is universally true that soil-borne disease epidemics pose a greater threat to crops. These necessitate the use of eco-friendly microbial bioinoculants. This review article provides an overview of plant growth-promoting microorganisms bioinoculants, their various characteristics, biochemical and molecular screening insights, and modes of action and interaction. The discussion is concluded with a brief overview of potential future possibilities for the sustainable development of agriculture. This review will be useful for students and researchers to obtain existing knowledge of microbial inoculants, their activities, and their mechanisms, which will facilitate the development of environmentally friendly management strategies for cross-kingdom plant diseases.

DSF inactivator RpfB homologous FadD upregulated in Bradyrhizobium japonicum under iron limiting conditions

Phytopathogenic bacteria Xanthomonas campestris pv. campestris (Xcc) causes black rot and other plant diseases. Xcc senses diffusible signal factor (DSF) as a quorum-sensing (QS) signal that mediates mainly iron uptake and virulence. RpfB deactivates DSF in this DSF-QS circuit. We examined differential gene expression profiles of Bradyrhizobium japonicum under low versus high iron conditions and found that fadD and irr were upregulated under low iron (log2 fold change 0.825 and 1.716, respectively). In addition to having similar protein folding patterns and functional domain similarities, FadD shared 58% sequence similarity with RpfB of Xcc. The RpfB-DSF and FadD-DSF complexes had SWISSDock molecular docking scores of - 8.88 kcal/mol and - 9.85 kcal/mol, respectively, and the 100 ns molecular dynamics simulation results were in accord with the docking results. However, significant differences were found between the binding energies of FadD-DSF and RpfB-DSF, indicating possible FadD-dependent DSF turnover. The protein-protein interaction network showed that FadD connected indirectly with ABC transporter permease (ABCtp), which was also upregulated (log2 fold change 5.485). We speculate that the low iron condition may be a mimetic environmental stimulus for fadD upregulation in B. japonicum to deactivate DSF, inhibit iron uptake and virulence of DSF-producing neighbors. This finding provides a new option of using B. japonicum or a genetically improved B. japonicum as a potential biocontrol agent against Xcc, with the added benefit of plant growth-promoting properties.

The role of the ecological scaffold in the origin and maintenance of whole-group trait altruism in microbial populations

BACKGROUND

Kin and multilevel selection provide explanations for the existence of altruism based on traits or processes that enhance the inclusive fitness of an altruist individual. Kin selection is often based on individual-level traits, such as the ability to recognize other altruists, whereas multilevel selection requires a metapopulation structure and dispersal process. These theories are unified by the general principle that altruism can be fixed by positive selection provided the benefit of altruism is preferentially conferred to other altruists. Here we take a different explanatory approach based on the recently proposed concept of an "ecological scaffold". We demonstrate that ecological conditions consisting of a patchy nutrient supply that generates a metapopulation structure, episodic mixing of groups, and severe nutrient limitation, can support or "scaffold" the evolution of altruism in a population of microbes by amplifying drift. This contrasts with recent papers in which the ecological scaffold was shown to support selective processes and demonstrates the power of scaffolding even in the absence of selection.

RESULTS

Using computer simulations motivated by a simple theoretical model, we show that, although an altruistic mutant can be fixed within a single population of non-altruists by drift when nutrients are severely limited, the resulting altruistic population remains vulnerable to non-altruistic mutants. We then show how the imposition of the "ecological scaffold" onto a population of non-altruists alters the balance between selection and drift in a way that supports the fixation and subsequent persistence of altruism despite the possibility of invasion by non-altruists.

CONCLUSIONS

The fixation of an altruistic mutant by drift is possible when supported by ecological conditions that impose a metapopulation structure, episodic mixing of groups, and severe nutrient limitation. This is significant because it offers an alternative explanation for the evolution of altruism based on drift rather than selection. Given the ubiquity of low-nutrient "oligotrophic" environments in which microbes exist (e.g., the open ocean, deep subsurface soils, or under the polar ice caps) our results suggest that altruistic and cooperative behaviors may be highly prevalent among microbial populations.

Cross-protection and cross-feeding between Klebsiella pneumoniae and Acinetobacter baumannii promotes their co-existence

Acinetobacter baumannii and Klebsiella pneumoniae are opportunistic pathogens frequently co-isolated from polymicrobial infections. The infections where these pathogens co-exist can be more severe and recalcitrant to therapy than infections caused by either species alone, however there is a lack of knowledge on their potential synergistic interactions. In this study we characterise the genomes of A. baumannii and K. pneumoniae strains co-isolated from a single human lung infection. We examine various aspects of their interactions through transcriptomic, phenomic and phenotypic assays that form a basis for understanding their effects on antimicrobial resistance and virulence during co-infection. Using co-culturing and analyses of secreted metabolites, we discover the ability of K. pneumoniae to cross-feed A. baumannii by-products of sugar fermentation. Minimum inhibitory concentration testing of mono- and co-cultures reveals the ability for A. baumannii to cross-protect K. pneumoniae against the cephalosporin, cefotaxime. Our study demonstrates distinct syntrophic interactions occur between A. baumannii and K. pneumoniae, helping to elucidate the basis for their co-existence in polymicrobial infections.

Plant-associated Bacillus mobilizes its secondary metabolites upon perception of the siderophore pyochelin produced by a Pseudomonas competitor

Bacillus velezensis is considered as model species for plant-associated bacilli providing benefits to its host such as protection against phytopathogens. This is mainly due to the potential to secrete a wide range of secondary metabolites with specific and complementary bioactivities. This metabolite arsenal has been quite well defined genetically and chemically but much remains to be explored regarding how it is expressed under natural conditions and notably how it can be modulated upon interspecies interactions in the competitive rhizosphere niche. Here, we show that B. velezensis can mobilize a substantial part of its metabolome upon the perception of Pseudomonas, as a soil-dwelling competitor. This metabolite response reflects a multimodal defensive strategy as it includes polyketides and the bacteriocin amylocyclicin, with broad antibiotic activity, as well as surfactin lipopeptides, contributing to biofilm formation and enhanced motility. Furthermore, we identified the secondary Pseudomonas siderophore pyochelin as an info-chemical, which triggers this response via a mechanism independent of iron stress. We hypothesize that B. velezensis relies on such chelator sensing to accurately identify competitors, illustrating a new facet of siderophore-mediated interactions beyond the concept of competition for iron and siderophore piracy. This phenomenon may thus represent a new component of the microbial conversations driving the behavior of members of the rhizosphere community.

Phytoremediation of industrial effluents assisted by plant growth promoting bacteria

Industrialization plays a crucial role in the economic development of a country; however, the effluents produced as a byproduct generally contain toxic substances which are detrimental to living organisms. In this regard, it is essential to treat these toxic effluents before exposing them to the natural environment by selecting the most appropriate method accordingly. Several techniques are used to remediate industrial effluents including physical, chemical, and biological. Although some physical and chemical remediation technologies are of substantially important in remediation of industrial effluents, however, these technologies are either expensive to be applied by developing countries or not suitable for remediation of all kinds of effluents. In contrast, biological remediation is cost effective, nature friendly, and easy to use for almost all kinds of effluents. Among biological remediation strategies, phytoremediation is considered to be the most suitable method for remediation of industrial effluents; however, the phytoremediation process is slow, takes time in application and some effluents even affect plants growth and development. Alternately, plant microbe interactions could be a winning partner to remediate industrial effluents more efficiently. Among the microbes, plant growth promoting bacteria (PGPB) not only improve plant growth but also help in degradation, sequestration, volatilization, solubilization, mobilization, and bioleaching of industrial effluents which subsequently improve the phytoremediation process. The current study discusses the role of PGPB in enhancing the phytoremediation processes of industrial effluents.

A comprehensive genomic analysis provides insights on the high environmental adaptability of Acinetobacter strains

Acinetobacter is ubiquitous, and it has a high species diversity and a complex evolutionary pattern. To elucidate the mechanism of its high ability to adapt to various environment, 312 genomes of Acinetobacter strains were analyzed using the phylogenomic and comparative genomics methods. It was revealed that the Acinetobacter genus has an open pan-genome and strong genome plasticity. The pan-genome consists of 47,500 genes, with 818 shared by all the genomes of Acinetobacter, while 22,291 are unique genes. Although Acinetobacter strains do not have a complete glycolytic pathway to directly utilize glucose as carbon source, most of them harbored the n-alkane-degrading genes alkB/alkM (97.1% of tested strains) and almA (96.7% of tested strains), which were responsible for medium-and long-chain n-alkane terminal oxidation reaction, respectively. Most Acinetobacter strains also have catA (93.3% of tested strains) and benAB (92.0% of tested strains) genes that can degrade the aromatic compounds catechol and benzoic acid, respectively. These abilities enable the Acinetobacter strains to easily obtain carbon and energy sources from their environment for survival. The Acinetobacter strains can manage osmotic pressure by accumulating potassium and compatible solutes, including betaine, mannitol, trehalose, glutamic acid, and proline. They respond to oxidative stress by synthesizing superoxide dismutase, catalase, disulfide isomerase, and methionine sulfoxide reductase that repair the damage caused by reactive oxygen species. In addition, most Acinetobacter strains contain many efflux pump genes and resistance genes to manage antibiotic stress and can synthesize a variety of secondary metabolites, including arylpolyene, β-lactone and siderophores among others, to adapt to their environment. These genes enable Acinetobacter strains to survive extreme stresses. The genome of each Acinetobacter strain contained different numbers of prophages (0-12) and genomic islands (GIs) (6-70), and genes related to antibiotic resistance were found in the GIs. The phylogenetic analysis revealed that the alkM and almA genes have a similar evolutionary position with the core genome, indicating that they may have been acquired by vertical gene transfer from their ancestor, while catA, benA, benB and the antibiotic resistance genes could have been acquired by horizontal gene transfer from the other organisms.

Iron acquisition strategies in pseudomonads: mechanisms, ecology, and evolution

Iron is important for bacterial growth and survival, as it is a common co-factor in essential enzymes. Although iron is very abundant in the earth crust, its bioavailability is low in most habitats because ferric iron is largely insoluble under aerobic conditions and at neutral pH. Consequently, bacteria have evolved a plethora of mechanisms to solubilize and acquire iron from environmental and host stocks. In this review, I focus on Pseudomonas spp. and first present the main iron uptake mechanisms of this taxa, which involve the direct uptake of ferrous iron via importers, the production of iron-chelating siderophores, the exploitation of siderophores produced by other microbial species, and the use of iron-chelating compounds produced by plants and animals. In the second part of this review, I elaborate on how these mechanisms affect interactions between bacteria in microbial communities, and between bacteria and their hosts. This is important because Pseudomonas spp. live in diverse communities and certain iron-uptake strategies might have evolved not only to acquire this essential nutrient, but also to gain relative advantages over competitors in the race for iron. Thus, an integrative understanding of the mechanisms of iron acquisition and the eco-evolutionary dynamics they drive at the community level might prove most useful to understand why Pseudomonas spp., in particular, and many other bacterial species, in general, have evolved such diverse iron uptake repertoires.

A Disturbed Siderophore Transport Inhibits Myxobacterial Predation

BACKGROUND

Understanding the intrinsic mechanisms of bacterial competition is a fundamental question. Iron is an essential trace nutrient that bacteria compete for. The most prevalent manner for iron scavenging is through the secretion of siderophores. Although tremendous efforts have focused on elucidating the molecular mechanisms of siderophores biosynthesis, export, uptake, and regulation of siderophores, the ecological aspects of siderophore-mediated competition are not well understood.

METHODS

We performed predation and bacterial competition assays to investigate the function of siderophore transport on myxobacterial predation.

RESULTS

Deletion of msuB, which encodes an iron chelate uptake ABC transporter family permease subunit, led to a reduction in myxobacterial predation and intracellular iron, but iron deficiency was not the predominant reason for the decrease in the predation ability of the ∆msuB mutant. We further confirmed that obstruction of siderophore transport decreased myxobacterial predation by investigating the function of a non-ribosomal peptide synthetase for siderophore biosynthesis, a TonB-dependent receptor, and a siderophore binding protein in M. xanthus. Our results showed that the obstruction of siderophores transport decreased myxobacterial predation ability through the downregulation of lytic enzyme genes, especially outer membrane vesicle (OMV)-specific proteins.

CONCLUSIONS

This work provides insight into the mechanism of siderophore-mediated competition in myxobacteria.

The potential of novel bacterial isolates from healthy ginseng for the control of ginseng root rot disease (Fusarium oxysporum)

Ginseng root rot caused by Fusarium oxysporum is serious disease that impacts ginseng production. In the present study, 145 strains of bacteria were isolated from the rhizosphere soil of healthy ginseng plants. Three strains with inhibitory activity against Fusarium oxysporum (accession number AF077393) were identified using the dual culture tests and designated as YN-42(L), YN-43(L), and YN-59(L). Morphological, physiological, biochemical, 16S rRNA gene sequencing and phylogenetic analyses were used to identify the strains as Bacillus subtilis [YN-42(L)] (accession number ON545980), Delftia acidovorans [YN-43(L)] (accession number ON545981), and Bacillus polymyxae [YN-59(L)] (accession number ON545982). All three isolates effectively inhibited the growth of Fusarium oxysporum in vitro and the antagonistic mechanism used by the three strains involved the secretion of multiple bioactive metabolites responsible for the hydrolysis of the fungal cell wall. All three biocontrol bacteria produce indoleacetic acid, which has a beneficial effect on plant growth. From our findings, all three antagonistic strains can be excellent candidates for ginseng root rot caused by the pathogenic fungus Fusarium oxysporum. These bacteria have laid the foundation for the biological control of ginseng root rot and for further research on the field control of ginseng pathogens.

Siderophore Synthesis Ability of the Nitrogen-Fixing Bacterium (NFB) GXGL-4A is Regulated at the Transcriptional Level by a Transcriptional Factor (trX) and an Aminomethyltransferase-Encoding Gene (amt)

Kosakonia radicincitans GXGL-4A, a gram-negative nitrogen-fixing (NF) bacterial strain is coated with a thick capsulatus on the surface of cell wall, which becomes a physical barrier for exogenous DNA to enter the cell, so the operation of genetic transformation is difficult. In this study, an optimized Tn5 transposon mutagenesis system was established by using a high osmotic HO-1 medium combined with the electroporation transformation. Eventually, a mutant library containing a total of 1633 Tn5 insertional mutants were established. Of these mutants, the mutants M81 and M107 were found to have an enhanced capability to synthesize siderophore through the CAS agar plate assay and the spectrophotometric determination. The bacterial cells of two mutants were applied in cucumber growth-promoting experiment. Cucumber seedlings treated with M81 and M107 cells had a significant increase in biomass including seedling height, seedling fresh weight, root fresh weight, and root length. The whole genome sequencing of the mutants M81 and M107 showed that the integration sites of Tn5 transposon element were located in MmyB-like helix-turn-helix transcription regulator (locus tag: A3780_19720, trX) and aminomethyltransferase-encoding genes (locus tag: A3780_01680, amt) in the genome of GXGL-4A, respectively. The ability of siderophore synthesis of the target mutants was improved by Tn5 insertion mutagenesis, and the mutants obtained showed a good plant growth-promoting effect when applied to the cucumber seedlings. The results suggest that the identified functional genes regulates the biosynthesis of siderophore in azotobacter GXGL-4A, and the specific mechanism needs to be further investigated.

Overexpression of Nicotianamine Synthase (AtNAS1) Increases Iron Accumulation in the Tuber of Potato

Iron (Fe) deficiency is a global health problem, especially in underdeveloped countries. Biofortification with genetic engineering methods has been used to improve Fe nutrition in a number of crops. Various steps, e.g., uptake, distribution, and storage, involved in Fe homeostasis have been manipulated to increase the Fe concentration in the edible portions of plants. Nicotianamine (NA) is an important metal ion chelator in plants. It promotes the mobility of Fe and decreases cellular Fe toxicity. Increasing the Fe content in crops by promoting NA synthesis could help decrease human diseases associated with Fe deficiency. In the present study, Arabidopsis thaliana nicotianamine synthase 1 (AtNAS1) was overexpressed in potato (Solanum tuberosum, St) under the control of the cauliflower mosaic virus 35S promoter. Transgenic plants had a significantly increased amount of Fe in tubers (52.7 µg/g dry weight, 2.4-fold the amount in wild-type tubers), while no differences in plant phenotype or yield were detected between transgenic and wild-type plants. The expression of genes involved in root mineral uptake and homeostasis, such as StYSL1, StIRT1, StFRO1, and StNAS, was also altered in the roots and leaves of the transgenic plants. Our results demonstrate that the manipulation of Fe chelation is a useful strategy for Fe nutrition improvement, and the increased Fe accumulation in tubers of transgenic potato plants is most likely caused by the increased movement of Fe from the leaf to the tuber.

The evolution of spectrum in antibiotics and bacteriocins

A key property of many antibiotics is that they will kill or inhibit a diverse range of microbial species. This broad-spectrum of activity has its evolutionary roots in ecological competition, whereby bacteria and other microbes use antibiotics to suppress other strains and species. However, many bacteria also use narrow-spectrum toxins, such as bacteriocins, that principally target conspecifics. Why has such a diversity in spectrum evolved? Here, we develop an evolutionary model to understand antimicrobial spectrum. Our first model recapitulates the intuition that broad-spectrum is best, because it enables a microbe to kill a wider diversity of competitors. However, this model neglects an important property of antimicrobials: They are commonly bound, sequestered, or degraded by the cells they target. Incorporating this toxin loss reveals a major advantage to narrow-spectrum toxins: They target the strongest ecological competitor and avoid being used up on less important species. Why then would broad-spectrum toxins ever evolve? Our model predicts that broad-spectrum toxins will be favored by natural selection if a strain is highly abundant and can overpower both its key competitor and other species. We test this prediction by compiling and analyzing a database of the regulation and spectrum of toxins used in inter-bacterial competition. This analysis reveals a strong association between broad-spectrum toxins and density-dependent regulation, indicating that they are indeed used when strains are abundant. Our work provides a rationale for why bacteria commonly evolve narrow-spectrum toxins such as bacteriocins and suggests that the evolution of antibiotics proper is a signature of ecological dominance.

RNA-Seq Provides Insights into the Mechanisms Underlying Ilyonectria robusta Responding to Secondary Metabolites of Bacillus methylotrophicus NJ13

(1) Background: Ilyonectria robusta can cause ginseng to suffer from rusty root rot. Secondary metabolites (SMs) produced by Bacillus methylotrophicus NJ13 can inhibit the mycelial growth of I. robusta. However, the molecular mechanism of the inhibition and response remains unclear. (2) Methods: Through an in vitro trial, the effect of B. methylotrophicus NJ13’s SMs on the hyphae and conidia of I. robusta was determined. The change in the physiological function of I. robusta was evaluated in response to NJ13’s SMs by measuring the electrical conductivity, malondialdehyde (MDA) content, and glucose content. The molecular interaction mechanism of I. robusta’s response to NJ13’s SMs was analyzed by using transcriptome sequencing. (3) Results: NJ13’s SMs exhibited antifungal activity against I. robusta: namely, the hyphae swelled and branched abnormally, and their inclusions leaked out due to changes in the cell membrane permeability and the peroxidation level; the EC50 value was 1.21% (v/v). In transcripts at 4 dpi and 7 dpi, the number of differentially expressed genes (DEGs) (|log2(fold change)| > 1, p adj ≤ 0.05) was 1960 and 354, respectively. NJ13’s SMs affected the glucose metabolism pathway, and the sugar-transporter-related genes were downregulated, which are utilized by I. robusta for energy production. The cell wall structure of I. robusta was disrupted, and chitin-synthase-related genes were downregulated. (4) Conclusions: A new dataset of functional responses of the ginseng pathogenic fungus I. robusta was obtained. The results will benefit the development of targeted biological fungicides for I. robusta and the study of the molecular mechanisms of interaction between biocontrol bacteria and phytopathogenic fungi.

Understanding the Potential and Risk of Bacterial Siderophores in Cancer

Siderophores are iron chelating molecules produced by nearly all organisms, most notably by bacteria, to efficiently sequester the limited iron that is available in the environment. Siderophores are an essential component of mammalian iron homeostasis and the ongoing interspecies competition for iron. Bacteria produce a broad repertoire of siderophores with a canonical role in iron chelation and the capacity to perform versatile functions such as interacting with other microbes and the host immune system. Siderophores are a vast area of untapped potential in the field of cancer research because cancer cells demand increased iron concentrations to sustain rapid proliferation. Studies investigating siderophores as therapeutics in cancer generally focused on the role of a few siderophores as iron chelators; however, these studies are limited and some show conflicting results. Moreover, siderophores are biologically conserved, structurally diverse molecules that perform additional functions related to iron chelation. Siderophores also have a role in inflammation due to their iron acquisition and chelation properties. These diverse functions may contribute to both risks and benefits as therapeutic agents in cancer. The potential of siderophore-mediated iron and bacterial modulation to be used in the treatment of cancer warrants further investigation. This review discusses the wide range of bacterial siderophore functions and their utilization in cancer treatment to further expand their functional relevance in cancer detection and treatment.

Potential probiotic approaches to control Legionella in engineered aquatic ecosystems

Opportunistic pathogens belonging to the genus Legionella are among the most reported waterborne-associated pathogens in industrialized countries. Legionella colonize a variety of engineered aquatic ecosystems and persist in biofilms where they interact with a multitude of other resident microorganisms. In this review, we assess how some of these interactions could be used to develop a biological-driven “probiotic” control approach against Legionella. We focus on: (i) mechanisms limiting the ability of Legionella to establish and replicate within some of their natural protozoan hosts; (ii) exploitative and interference competitive interactions between Legionella and other microorganisms; and (iii) the potential of predatory bacteria and phages against Legionella. This field is still emergent, and we therefore specifically highlight research for future investigations, and propose perspectives on the feasibility and public acceptance of a potential probiotic approach.

Harnessing rhizobacteria to fulfil inter-linked nutrient dependency on soil and alleviate stresses in plants

Plant rhizo-microbiome comprises of complex microbial communities that colonizes at the interphase of plant roots and soil. Plant-growth-promoting rhizobacteria (PGPR) in the rhizosphere provides important ecosystem services ranging from release of essential nutrients for enhancing soil quality and improving plant health to imparting protection to plants against rising biotic and abiotic stresses. Hence, PGPR serve as restoring agents to rejuvenate soil health and mediate plant fitness in the facet of changing climate. Though, it is evident that nutrients availability in soil are managed through inter-linked mechanisms, how PGPR expediate these processes remain less recognized. Promising results of PGPR inoculation on plant growth are continually reported in controlled environmental conditions, however, their field application often fails due to competition with native microbiota and low colonization efficiency in roots. The development of highly efficient and smart bacterial synthetic communities by integrating bacterial ecological and genetic features provides better opportunities for successful inoculant formulations. This review provides an overview of the inter-play between nutrient availability and disease suppression governed by rhizobacteria in soil followed by the role of synthetic bacterial communities in developing efficient microbial inoculants. Moreover, an outlook on the beneficial activities of rhizobacteria in modifying soil characteristics to sustainably boost agroecosystem functioning is also provided.

Commensal Pseudomonas protect Arabidopsis thaliana from a coexisting pathogen via multiple lineage-dependent mechanisms

Plants are protected from pathogens not only by their own immunity but often also by colonizing commensal microbes. In Arabidopsis thaliana, a group of cryptically pathogenic Pseudomonas strains often dominates local populations. This group coexists in nature with commensal Pseudomonas strains that can blunt the deleterious effects of the pathogens in the laboratory. We have investigated the interaction between one of the Pseudomonas pathogens and 99 naturally co-occurring commensals, finding plant protection to be common among non-pathogenic Pseudomonas. While protective ability is enriched in one specific lineage, there is also a substantial variation for this trait among isolates of this lineage. These functional differences do not align with core-genome phylogenies, suggesting repeated gene inactivation or loss as causal. Using genome-wide association, we discovered that different bacterial genes are linked to plant protection in each lineage. We validated a protective role of several lineage-specific genes by gene inactivation, highlighting iron acquisition and biofilm formation as prominent mechanisms of plant protection in this Pseudomonas lineage. Collectively, our work illustrates the importance of functional redundancy in plant protective traits across an important group of commensal bacteria.

Soybean-Nodulating Rhizobia: Ecology, Characterization, Diversity, and Growth Promoting Functions

The worldwide increase in population continues to threaten the sustainability of agricultural systems since agricultural output must be optimized to meet the global rise in food demand. Sub-Saharan Africa (SSA) is among the regions with a fast-growing population but decreasing crop productivity. Pests and diseases, as well as inadequate nitrogen (N) levels in soils, are some of the biggest restrictions to agricultural production in SSA. N is one of the most important plant-limiting elements in agricultural soils, and its deficit is usually remedied by using nitrogenous fertilizers. However, indiscriminate use of these artificial N fertilizers has been linked to environmental pollution calling for alternative N fertilization mechanisms. Soybean (Glycine max) is one of the most important legumes in the world. Several species of rhizobia from the four genera, Bardyrhizobium, Rhizobium, Mesorhizobium, and Ensifer (formerly Sinorhizobium), are observed to effectively fix N with soybean as well as perform various plant-growth promoting (PGP) functions. The efficiency of the symbiosis differs with the type of rhizobia species, soybean cultivar, and biotic factors. Therefore, a complete understanding of the ecology of indigenous soybean-nodulating rhizobia concerning their genetic diversity and the environmental factors associated with their localization and dominance in the soil is important. This review aimed to understand the potential of indigenous soybean-nodulating rhizobia through a synthesis of the literature regarding their characterization using different approaches, genetic diversity, symbiotic effectiveness, as well as their functions in biological N fixation (BNF) and biocontrol of soybean soil-borne pathogens.

Alterins, a new family of marine antibacterial cyclolipopeptides

Five strains of Pseudoalteromonas, isolated from oyster hemolymph, exhibited antibacterial activity against several Gram-negative bacteria. Bioactive compounds were identified in their cell-free supernatant and characterized as alterins, which are cyclolipopeptides composed of an heptapeptidic ring connected to a fatty acid chain. Using UPLC-HRMS, we describe here 37 structural analogs differing from each other by one or more amino acid residue, the length of the fatty acid chain, its hydroxylation and the presence of unsaturation.

Successful microbial colonization of space in a more dispersed manner

Many organisms live in habitats with limited nutrients or space, competition for these resources is ubiquitous. Although spatial factors related to the population's manner of colonizing space influences its success in spatial competition, what these factors are and to what extent they influence the outcome remains underexplored. Here, we applied a simulated competitive model to explore the spatial factors affecting outcomes of competition for space. By quantifying spatial factors, we show that colonizing space in a more dispersed manner contributes to microbial competitive success. We also find that the competitive edge deriving from a more dispersed manner in colonization can compensate for the disadvantage arising from either a lower growth rate or lower initial abundance. These findings shed light on the role of space colonization manners on maintaining biodiversity within ecosystems and provide novel insights critical for understanding how competition for space drives evolutionary innovation.

Siderophores drive invasion dynamics in bacterial communities through their dual role as public good versus public bad

Microbial invasions can compromise ecosystem services and spur dysbiosis and disease in hosts. Nevertheless, the mechanisms determining invasion outcomes often remain unclear. Here, we examine the role of iron‐scavenging siderophores in driving invasions of Pseudomonas aeruginosa into resident communities of environmental pseudomonads. Siderophores can be ‘public goods’ by delivering iron to individuals possessing matching receptors; but they can also be ‘public bads’ by withholding iron from competitors lacking these receptors. Accordingly, siderophores should either promote or impede invasion, depending on their effects on invader and resident growth. Using supernatant feeding and invasion assays, we show that invasion success indeed increased when the invader could use its siderophores to inhibit (public bad) rather than stimulate (public good) resident growth. Conversely, invasion success decreased the more the invader was inhibited by the residents’ siderophores. Our findings identify siderophores as a major driver of invasion dynamics in bacterial communities under iron‐limited conditions.

Evolutionary genomics and biosynthetic potential of novel environmental Actinobacteria

Actinobacteria embroil Gram-positive microbes with high guanine and cytosine contents in their DNA. They are the source of most antimicrobials of bacterial origin utilized in medicine today. Their genomes are among the richest in novel secondary metabolites with high biotechnological potential. Actinobacteria reveal complex patterns of evolution, responses, and adaptations to their environment, which are not yet well understood. We analyzed three novel plant isolates and explored their habitat adaptation, evolutionary patterns, and potential secondary metabolite production. The phylogenomically characterized isolates belonged to Actinoplanes sp. TFC3, Streptomyces sp. L06, and Embleya sp. NF3. Positively selected genes, relevant in strain evolution, encoded enzymes for stress resistance in all strains, including porphyrin, chlorophyll, and ubiquinone biosynthesis in Embleya sp. NF3. Streptomyces sp. L06 encoded for pantothenate and proteins for CoA biosynthesis with evidence of positive selection; furthermore, Actinoplanes sp. TFC3 encoded for a c-di-GMP synthetase, with adaptive mutations. Notably, the genomes harbored many genes involved in the biosynthesis of at least ten novel secondary metabolites, with many avenues for future new bioactive compound characterization-specifically, Streptomyces sp. L06 could make new ribosomally synthesized and post-translationally modified peptides, while Embleya sp. NF3 could produce new non-ribosomal peptide synthetases and ribosomally synthesized and post-translationally modified peptides. At the same time, TFC3 has particularly enriched in terpene and polyketide synthases. All the strains harbored conserved genes in response to diverse environmental stresses, plant growth promotion factors, and degradation of various carbohydrates, which supported their endophytic lifestyle and showed their capacity to colonize other niches. This study aims to provide a comprehensive estimation of the genomic features of novel Actinobacteria. It sets the groundwork for future research into experimental tests with new bioactive metabolites with potential application in medicine, biofertilizers, and plant biomass residue utilization, with potential application in medicine, as biofertilizers and in plant biomass residues utilization. KEY POINTS: • Potential of novel environmental bacteria for secondary metabolites production • Exploring the genomes of three novel endophytes isolated from a medicinal tree • Pan-genome analysis of Actinobacteria genera.