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Nonreductive biomineralization is a cost-effective method to remediate uranium (U) contaminated wastes. In this work, we explored the immobilization mechanism of U(VI) induced by Bacillus thuringiensis 016. Enzymes denaturation and functional groups shielding experiments revealed that the biosorption of uranium by B. thuringiensis 016 was a nonenzymatic process in which phosphate, amino, and carboxyl groups played a major role. Fe3+ and CO32− had a strong ability to inhibit uranium biosorption. The biomineralization of uranium by B. thuringiensis 016 was a synergistic effect of enzymes and cell metabolism. In addition, K+, Na+, and Mg2+ slightly promoted the ability of bacteria to mineralize U(VI). Besides, when the initial uranium concentration was 100 mg/L, the reaction of B. thuringiensis 016 with uranium was a rapid process consisting of extracellular biosorption and intracellular biomineralization. When the initial uranium concentration exceeded 200 mg/L, B. thuringiensis 016 can only adsorb uranium. Furthermore, by tracking the concentration of soluble U(VI) in the cells, it was confirmed that the amorphous compounds, formed on the cell surface, were an insoluble form when entering the cells. Our findings provide a further understanding of the mechanisms of uranium immobilization, which would be useful for the application of B. thuringiensis 016 in uranium pollution treatment.

The rhizospheric bacterial community associated with desert shrub is an important part of sandy land ecosystems. In this study, we isolated and characterized culturable bacteria associated with Caragana microphylla from a wide range of habitats in North China. We chose five habitats with different aridity index values and dune types. In both trials, soil physicochemical parameters and culturable bacterial populations showed the rhizosphere effects. The culturable bacterial communities of rhizosphere and bulk soil were determined using 16s rDNA sequencing. We identified that the proportions of beneficial bacterial strains with plant growth promoting (PGP) traits (nitrogen fixation, phosphate solubilization and indole acetic acid production) were significantly greater in rhizosphere soil than in bulk soil. Some of the strains screened in this study had significant effects on the growth of Arabidopsis seedlings. These effects included inhibiting the elongation of primary roots, promoting lateral root formation and increasing the shoot fresh weight. In conclusion, our study provides a comprehensive survey of the culturable bacterial populations of the rhizosphere in C. microphylla habitats and identifies potential PGPBs that may help develop an efficient revegetation strategy to manage desert land.

Background Minqin is suffering from a serious desertification, whereas the knowledge about its bacterial community is limited. Herein, based on Nitraria tangutorum and Haloxylon ammodendron from Minqin, the bacterial community diversities in fixed sandy land, semi-fixed sandy land and shifting sandy land were investigated by combining with culture-dependent and culture-independent methods. Results Minqin stressed with high salinity and poor nutrition is an oligotrophic environment. Bacterial community in Minqin was shaped primarily by the presence of host plants, whereas the type of plant and sandy land had no marked effect on those, which displayed a better survival in the rhizospheres of N. tangutorum and H. ammodendron. The dominant groups at phyla level were Actinobacteria, Firmicutes, Proteobacteria, Bacteroidetes, Planctomycetes, Chloroflexi, Acidobacteria and Candidate_division_TM7. The abundance of Firmicutes with ability of desiccation-tolerance was significantly higher in harsh environment, whereas Bacteroidetes were mainly distributed in areas with high nutrient content. The abundances of Proteobacteria and Bacteroidetes were relatively high in the rhizospheres of N. tangutorum and H. ammodendron, which had more plant-growth promoting rhizobacteria. A large number of Actinobacteria were detected, of which the most abundant genus was Streptomyces. The physicochemical factors related to the diversity and distribution of the bacterial community were comprehensively analyzed, such as pH, electrical conductivity, soil organic matter, C/N and sand, and the results indicated that Minqin was more suitable for the growth of N. tangutorum, which should be one of most important sand-fixing plants in Minqin. Conclusions The bacterial community diversities in different types of sandy lands of Minqin were comprehensively and systematically investigated by culture-dependent and culture-independent approaches, which has a great significance in maintaining/restoring biological diversity.

Protease-producing bacteria play vital roles in degrading organic matter of aquaculture system, while the knowledge of diversity and bacterial community structure of protease-producing bacteria is limited in this system, especially in the tropical region. Herein, 1,179 cultivable protease-producing bacterial strains that belonged to Actinobacteria, Firmicutes, and Proteobacteria were isolated from tropical aquaculture systems, of which the most abundant genus was Bacillus, followed by Vibrio. The diversity and relative abundance of protease-producing bacteria in sediment were generally higher than those in water. Twenty-one genera from sediment and 16 genera from water were identified, of which Bacillus dominated by Bacillus hwajinpoensis in both and Vibrio dominated by Vibrio owensii in water were the dominant genera. The unique genera in sediment or water accounted for tiny percentage may play important roles in the stability of community structure. Eighty V. owensii isolates were clustered into four clusters (ET-1–ET-4) at 58% of similarity by ERIC-PCR (enterobacterial repetitive intergenic consensus-polymerase chain reaction), which was identified as a novel branch of V. owensii. Additionally, V. owensii strains belonged to ET-3 and ET-4 were detected in most aquaculture ponds without outbreak of epidemics, indicating that these protease-producing bacteria may be used as potential beneficial bacteria for wastewater purification. Environmental variables played important roles in shaping protease-producing bacterial diversity and community structure in aquaculture systems. In sediment, dissolved oxygen (DO), chemical oxygen demand (COD), and salinity as the main factors positively affected the distributions of dominant genus (Vibrio) and unique genera (Planococcus and Psychrobacter), whereas temperature negatively affected that of Bacillus (except B. hwajinpoensis). In water, Alteromonas as unique genus and Photobacterium were negatively affected by NO3−-N and NO2−-N, respectively, whereas pH as the main factor positively affected the distribution of Photobacterium. These findings will lay a foundation for the development of protease-producing bacterial agents for wastewater purification and the construction of an environment-friendly tropical aquaculture model.

SummaryPlant immunity is tightly controlled by a complex and dynamic regulatory network, which ensures optimal activation upon detection of potential pathogens. Accordingly, each component of this network is a potential target for manipulation by pathogens. Here, we report that RipAC, a type III-secreted effector from the bacterial pathogenRalstonia solanacearum, targets the plant E3 ubiquitin ligase PUB4 to inhibit pattern-triggered immunity (PTI). PUB4 plays a positive role in PTI by regulating the homeostasis of the central immune kinase BIK1. Before PAMP perception, PUB4 promotes the degradation of non-activated BIK1, while, after PAMP perception, PUB4 contributes to the accumulation of activated BIK1. RipAC leads to BIK1 degradation, which correlates with its PTI-inhibitory activity. RipAC causes a reduction in pathogen-associated molecular pattern (PAMP)-induced PUB4 accumulation and phosphorylation. Our results shed light on the role played by PUB4 in immune regulation, and illustrate an indirect targeting of the immune signalling hub BIK1 by a bacterial effector.

In both animals and plants, the perception of bacterial flagella by immune receptors elicits the activation of defence responses. Most plants are able to perceive the highly conserved epitope flg22 from flagellin, the main flagellar protein, from most bacterial species. However, flagellin from Ralstonia solanacearum, the causal agent of the bacterial wilt disease, presents a polymorphic flg22 sequence (flg22Rso) that avoids perception by all plants studied to date. In this work, we show that soybean has developed polymorphic versions of the flg22 receptors that are able to perceive flg22Rso. Furthermore, we identify key residues responsible for both the evasion of perception by flg22Rso in Arabidopsis and the gain of perception by the soybean receptors. Heterologous expression of the soybean flg22 receptors in susceptible plant species, such as tomato, enhances resistance to bacterial wilt disease, demonstrating the potential of these receptors to enhance disease resistance in crop plants., Ralstonia solanacearum evades plant immunity by producing an atypical flagellin protein, thus causing bacterial wilt disease. Here, Wei et al. show that soybean has evolved a divergent flagellin receptor that recognises R. solanacearum flagellin and enhances wilt resistance when transferred to other plants.

Outbreaks of fish bacterial diseases have become quite frequent with the intensification of practices in aquaculture. Vaccination has become an increasingly important prevention strategy against infectious agents in farmed fishes. However, only a few licensed fish bacterial vaccines are commercially available worldwide, and the majority of them are conventional inactivated vaccines. The use of bacterial ghosts (BGs) as novel candidate vaccines has attracted increasing attention from researchers. BGs are nonliving empty cell envelopes mainly derived from gram-negative bacteria. Pores in gram-negative bacteria are formed most commonly through the strictly controlled expression of bacteriophage PhiX174 lysis gene E, whereas pores in gram-positive bacteria can be formed through minimally inhibitory gentle chemical protocols. In biological protocols, the temperature-sensitive λ system has been widely used for quick and efficient lysis without the need for any addition of chemical inducers. To produce BGs with enhanced safety, the incorporation of the staphylococcal nuclease A gene, holin-endolysin system, or antimicrobial peptide genes into gene E-mediated lysis cassettes has been applied to improve lysis efficiency. The ghosts of a few fish pathogenic bacteria, such as Edwardsiella spp., Aeromonas spp., Vibrio spp., and Streptococcus spp., have been successfully developed by gene E-mediated lysis, which maintain the original cell morphology but eliminate genetic contents. Although the lysis efficiency of these BGs does not reach 100%, the lyophilized BGs were free of any living cells. These lyophilized BGs not only have high biological safety for fish, but also can induce stronger humoral, cellular and mucosal immune responses compared to conventional inactivated vaccines. Moreover, BGs are easy to produce in large quantities by fermentation without laborious purification procedures and easy to administer through oral or immersion immunization. Therefore, BGs are good fish vaccine candidates and can be engineered to display heterologous antigens or deliver DNA for use as multivalent vaccines against fish pathogen infection. Yet, completely inactivation was not achieved by the gene E-mediated lysis procedure, how to improve the lysis efficiency of BGs is an important problem for BG production. It is believed that the BG system will play an increasingly important role in the prevention and control of fish diseases with further research and continuous biotechnological development.

The Tianshan Mountains hold important and complex ecosystems. They host some unique biological resources, especially some microbes that have very crucial application values. In this study, the composition and distribution of bacterial communities from soil at different elevations of the Tianshan Mountains, China, were investigated using culture-based and molecular-based methods. The relationship between the abundance of culturable bacteria and environmental factors was also analysed. A total of 121 isolates showing different phenotypic characteristics were obtained from soil and identified by 16S rRNA gene sequencing analysis. All strains were assigned to four phyla: Proteobacteria, Actinobacteria, Bacteroidetes and Firmicutes. Actinobacteria and Proteobacteria were the dominating bacterial phyla; Arthrobacter, Pseudomonas and Sphingomonas were the most prevalent genera. The community structures of culturable bacteria were significantly different at different elevations, there being some common bacterial communities and some unique groups at each altitude. The principal component analysis (PCA) showed that the abundance of culturable bacterial communities has a significant positive correlation with the NO3− content in the soil. It indicated that NO3− was a better predictor of soil culturable bacterial abundance in this region. The strains isolated from alpine soil in this study are not only an invaluable part of microbial diversity, but also good candidates for further elucidating the interaction relationship between plants and microorganisms.

Summary Many bacterial plant pathogens employ a type III secretion system to inject effector proteins within plant cells to suppress plant immunity. Whether and how effector proteins also co-opt plant metabolism to support extensive bacterial replication remains an open question. Here, we show that Ralstonia solanacearum, the causal agent of bacterial wilt disease, secretes the effector protein RipI, which interacts with plant glutamate decarboxylases (GADs) to alter plant metabolism and support bacterial growth. GADs are activated by calmodulin and catalyze the biosynthesis of gamma-aminobutyric acid (GABA), an important signaling molecule in plants and animals. RipI promotes the interaction of GADs with calmodulin, enhancing the production of GABA. R. solanacearum is able to replicate efficiently using GABA as a nutrient, and both RipI and plant GABA contribute to a successful infection. This work reveals a pathogenic strategy to hijack plant metabolism for the biosynthesis of nutrients that support microbial growth during plant colonization.

Plant receptor-like kinases (RLKs) exert an essential function in the transduction of signals from the cell exterior to the cell interior, acting as important regulators of plant development and responses to environmental conditions. A growing body of evidence suggests that RLKs may play relevant roles in plant-virus interactions, although the details and diversity of effects and underlying mechanisms remain elusive. The C4 protein from different geminiviruses has been found to interact with RLKs in the CLAVATA 1 (CLV1) clade. However, whether C4 can interact with RLKs in other subfamilies and, if so, what the biological impact of such interactions might be, is currently unknown. In this work, we explore the interaction landscape of C4 from the geminivirus Tomato yellow leaf curl virus within the Arabidopsis RLK family. Our results show that C4 can interact with RLKs from different subfamilies including, but not restricted to, members of the CLV1 clade. Functional analyses of the interaction of C4 with two well-characterized RLKs, FLAGELLIN SENSING 2 (FLS2) and BRASSINOSTEROID INSENSITIVE 1 (BRI1), indicate that C4 might affect some, but not all, RLK-derived outputs. The results presented here offer novel insight on the interface between RLK signaling and the infection by geminiviruses, and point at C4 as a potential broad manipulator of RLK-mediated signaling.

Bacterial diseases are a threat to food security. Most bacterial pathogens inject effector proteins inside plant cells, using a type-III secretion system, to suppress plant immunity. However, whether and how effector proteins co-opt plant metabolism to produce nutrients that support extensive bacterial replication is not understood. In this work, we found that Ralstonia solanacearum, the causal agent of bacterial wilt disease, secretes an effector protein, named RipI, which interacts with host glutamate decarboxylases (GADs) inside plant cells. GADs catalyse the biosynthesis of GABA, and are activated by calmodulin. RipI promotes the interaction of GADs with calmodulin, enhancing the production of GABA. Unlike other pathogens, Ralstonia is able to replicate efficiently using GABA as a nutrient, and requires both RipI and plant GABA to achieve a successful infection. This reveals a pathogenic strategy to hijack plant metabolism for the biosynthesis of nutrients to support microbial growth during plant colonization.

Understanding the response of soil properties and bacterial communities in rhizosphere soil to aridity and dune types is fundamental to desertification control. This study investigated soil properties and bacterial communities of both rhizosphere and bulk soils of Caragana microphylla from four sites with different aridity indices, and one site with three different types of dunes. All sites were located in the desert regions of northern China. The results indicated that compared with the bulk soil, the soil nutrient content of rhizosphere, especially the content of total phosphorus, was generally significantly improved in different desertification environments. The bacterial richness and diversity were also higher than those of bulk soil, especially in arid regions and fixed dunes. Firmicutes, Actinobacteria, Proteobacteria, and Acidobacteria were the most dominant phyla in all samples. The regression analyses showed that at different sites, soil total organic C, total N, Na+, and total P played key roles in determining the bacterial community structure while total organic carbon, electronic conductivity, pH and total phosphorus were the dominant factors at the different dunes. The results further revealed that the dominant phyla strongly affected by environmental factors at different sites were Acidobacteria, Gemmatimonadetes, and Actinobacteria among which, Acidobacteria and Gemmatimonadetes were negatively correlated with Na+ content. At different types of dunes, Actinobacteria, Planctomycetes, and Gemmatimonadetes were particularly affected by environmental factors. The increased abundance of Actinobacteria in the rhizosphere soil was mainly caused by the decreased soil pH.

Effector proteins delivered inside plant cells are powerful weapons for bacterial pathogens, but this exposes the pathogen to potential recognition by the plant immune system. Therefore, the effector repertoire of a given pathogen must be balanced for a successful infection. Ralstonia solanacearum is an aggressive pathogen with a large repertoire of secreted effectors. One of these effectors, RipE1, is conserved in most R. solanacearum strains sequenced to date. In this work, we found that RipE1 triggers immunity in N. benthamiana, which requires the immune regulator SGT1, but not EDS1 or NRCs. Interestingly, RipE1-triggered immunity induces the accumulation of salicylic acid (SA) and the overexpression of several genes encoding phenylalanine-ammonia lyases (PALs), suggesting that the unconventional PAL-mediated pathway is responsible for the observed SA biosynthesis. Surprisingly, RipE1 recognition also induces the expression of jasmonic acid (JA)-responsive genes and JA biosynthesis, suggesting that both SA and JA may act cooperatively in response to RipE1. Finally, we found that RipE1 expression leads to the accumulation of glutathione in plant cells, which precedes the activation of immune responses. R. solanacearum encodes another effector, RipAY, which is known to inhibit immune responses by degrading cellular glutathione. Accordingly, we show that RipAY inhibits RipE1-triggered immune responses. This work shows a strategy employed by R. solanacearum to counteract the perception of its effector proteins by the plant immune system.

Current studies reveal that the biomineralization of U(VI) by anaerobes normally produces nano-sized U(IV) minerals that can easily re-migrate/re-oxidize, while the biomineralization of U(VI) by aerobes has been constrained because the general mechanism has not yet been fully characterized. The biomineralization of U(VI) by Bacillus cereus 12-2 was investigated in this work. The maximum biosorption capability of intact cells was 448.68 mg U/g biomass (dry weight) at pH 5, while a decrease over 60% was induced when phosphate, amino, and especially carboxyl groups were shielded. X-ray diffraction, electron microscopy, and tracing the concentration of soluble intracellular U(VI) demonstrated that extracellular amorphous uranium particles can directly enter cells as solid, and about 10 nm-sized (NH4)(UO2)PO4·3H2O was formed subsequently. It was also revealed that the biosorption capability was not affected by a high uranium concentration, while biomineralization was inhibited, suggesting that a high concentration of heavy metals may inhibit the enzyme activity involved in biomineralization. Besides, U(VI) could trigger the overexpression of proteins with a molecular weight of 22 kD, including various phosphatases, kinases, and other enzymes that are related to metabolism and stimulus response, which may contribute to the intracellular transformation of U(VI) compounds from amorphous to crystalline phase. Taken together, the immobilization of U(VI) by B. cereus 12-2 contains two major steps: (1) fast immobilization of U(VI) on the cell surface as amorphous compounds, in which the carboxyl groups served as the predominant coordination functional groups and (2) transport of amorphous particles to cells directly and enzyme-related formation of uramphite.

Most bacterial pathogens subvert plant cellular functions using effector proteins delivered inside plant cells. In the plant pathogen Ralstonia solanacearum, several of these effectors contain domains with predicted enzymatic activities, including acetyltransferases, phosphatases, and proteases, among others. How these enzymatic activities get activated inside plant cells, but not in the bacterial cell, remains unknown in most cases. In this work, we found that the R. solanacearum effector RipAY is phosphorylated in plant cells. One phosphorylated serine residue, S131, is required for the reported gamma-glutamyl cyclotransferase activity of RipAY, responsible for the degradation of gamma-glutamyl compounds (such as glutathione) inside host cells. Accordingly, non-phosphorylable mutants in S131 abolish RipAY-mediated degradation of glutathione in plant cells and the subsequent suppression of plant immune responses. In this article, we examine our results in relation to the recent reports on the biochemical activities of RipAY, and discuss the potential implications of phosphorylation in plant cells as a mechanism to modulate the enzymatic activity of RipAY.

Summary Ralstonia solanacearum, the causal agent of bacterial wilt disease, is considered one of the most destructive bacterial pathogens due to its lethality, unusually wide host range, persistence and broad geographical distribution. In spite of the extensive research on plant immunity over the last years, the perception of molecular patterns from R. solanacearum that activate immunity in plants is still poorly understood, which hinders the development of strategies to generate resistance against bacterial wilt disease. The perception of a conserved peptide of bacterial flagellin, flg22, is regarded as paradigm of plant perception of invading bacteria; however, no elicitor activity has been detected for R. solanacearum flg22. Recent reports have shown that other epitopes from flagellin are able to elicit immune responses in specific species from the Solanaceae family, yet our results show that these plants do not perceive any epitope from R. solanacearum flagellin. Searching for elicitor peptides from R. solanacearum, we found several protein sequences similar to the consensus of the elicitor peptide csp22, reported to elicit immunity in specific Solanaceae plants. A R. solanacearum csp22 peptide (csp22Rsol) was indeed able to trigger immune responses in Nicotiana benthamiana and tomato, but not in Arabidopsis thaliana. Additionally, csp22Rsol treatment conferred increased resistance to R. solanacearum in tomato. Transgenic A. thaliana plants expressing the tomato csp22 receptor (SlCORE) gained the ability to respond to csp22Rsol and became more resistant to R. solanacearum infection. Our results shed light on the mechanisms for perception of R. solanacearum by plants, paving the way for improving current approaches to generate resistance against R. solanacearum.