Genome sequencing and assessment of plant growth-promoting properties of a Serratia marcescens strain isolated from vermicompost

Bioactive Metabolites of Serratia sp. NhPB1 Isolated from Pitcher of Nepenthes and its Application to Control Pythium aphanidermatum

Plant-associated bacteria have already been considered as the store house of bioactive compounds that confer the plant growth promotion and disease protection. Hence, the unique plant parts have already been expected to harbor diverse microbial communities with multi-beneficial properties. Based on this, the current study has been designed to identify the potential of Serratia sp. NhPB1 isolated from the pitcher of Nepenthes plant for its activity against the infamous pathogen Pythium aphanidermatum. The in vitro antifungal, plant growth promoting and enzymatic activities of the isolate indicated its promises for agricultural application. The isolate NhPB1 was also demonstrated to have positive effect on Solanum lycopersicum and Capsicum annuum, due to its plant beneficial metabolites. From the results of LC-MS/MS analysis, the isolate has also been revealed to have the ability to synthesize bioactive compounds including salicylic acid, cyclodipeptides, acyl homoserine lactone, indole-3-acetic acid, and serrawettin W1. These identified compounds and their known biological properties make the isolate characterized in the study to have significant promises as an eco-friendly solution for the improvement of agricultural productivity.

Pathogenicity of Serratia marcescens strains as biological control agent: Implications for sustainable pest management

The escalating demand for sustainable and eco-friendly pest management strategies has raised interest in harnessing the pathogenic potential of microorganisms. Serratia marcescens, a Gram-negative bacterium, has emerged as a potential biological control agent for sustainable pest management. This review critically examines the history, biology, identification, and pathogenicity of S. marcescens strain with their potential application in pest management. The diverse mechanisms employed by the strain to exert control over pests, including the production of metabolites and the induction of systemic resistance in plants, are examined. The review also summarizes the ecological significance and global distribution of S. marcescens associated with the use of S. marcescens in biological control strategies. Furthermore, the usage efficacy of S. marcescens over other conventional chemicals is discussed. A comprehensive understanding of the pathogenic potential of S. marcescens strains as biological control agents is crucial for developing effective and sustainable pest management strategies. This review consolidates current research advances on S. marcescens, and provides insights into the prospects and challenges of using S. marcescens for integrated pest management.

Performance Evaluation of Native Plant Growth-Promoting Bacteria Associated with Organic Tea Plantations for Development of Bioinoculants for Crop Plants

This study aimed at isolation of native plant growth-promoting bacteria (PGPB) associated with organic tea plantations. Most research on tea and associated microbes have been on Darjeeling and Assam, known for their world-class tea. However, emerging tea plantations in remote Northeast India are gaining prominence due to their unique geographical location, favorable climate, and organic practices. This study investigated PGBP associated with these organic tea plantations, aimed to assess their potential cross-infectivity on non-host plants. A total of 58 PGP bacterial isolates were isolated from four organic tea plantations. Six potential isolates were further evaluated individually and as consortium for their PGP on rice and maize. Bacillus, Pseudomonas, and Serratia spp. as individual and in consortium were found to have potent cross-infectivity with significant growth promotion in non-host plants indicated by plant height, root length, shoot, and root weight. The present findings suggest that PGPB native to organic tea plantations have potential cross-infectivity for use as a biofertilizers to improve the growth and productivity of non-host crops. This provides prospectives of using native bacteria on non-host plants paving the way for their potential application in sustainable agriculture practices for growth promotion of staple food crops.

Genome assembly, comparative genomics, and identification of genes/pathways underlying plant growth-promoting traits of an actinobacterial strain, Amycolatopsis sp. (BCA-696)

The draft genome sequence of an agriculturally important actinobacterial species Amycolatopsis sp. BCA-696 was developed and characterized in this study. Amycolatopsis BCA-696 is known for its biocontrol properties against charcoal rot and also for plant growth-promotion (PGP) in several crop species. The next-generation sequencing (NGS)-based draft genome of Amycolatopsis sp. BCA-696 comprised of ~ 9.05 Mb linear chromosome with 68.75% GC content. In total, 8716 protein-coding sequences and 61 RNA-coding sequences were predicted in the genome. This newly developed genome sequence has been also characterized for biosynthetic gene clusters (BGCs) and biosynthetic pathways. Furthermore, we have also reported that the Amycolatopsis sp. BCA-696 produces the glycopeptide antibiotic vancomycin that inhibits the growth of pathogenic gram-positive bacteria. A comparative analysis of the BCA-696 genome with publicly available closely related genomes of 14 strains of Amycolatopsis has also been conducted. The comparative analysis has identified a total of 4733 core and 466 unique orthologous genes present in the BCA-696 genome The unique genes present in BCA-696 was enriched with antibiotic biosynthesis and resistance functions. Genome assembly of the BCA-696 has also provided genes involved in key pathways related to PGP and biocontrol traits such as siderophores, chitinase, and cellulase production.

Plant communication with rhizosphere microbes can be revealed by understanding microbial functional gene composition

Understanding rhizosphere microbial ecology is necessary to reveal the interplay between plants and associated microbial communities. The significance of rhizosphere-microbial interactions in plant growth promotion, mediated by several key processes such as auxin synthesis, enhanced nutrient uptake, stress alleviation, disease resistance, etc., is unquestionable and well reported in numerous literature. Moreover, rhizosphere research has witnessed tremendous progress due to the integration of the metagenomics approach and further shift in our viewpoint from taxonomic to functional diversity over the past decades. The microbial functional genes corresponding to the beneficial functions provide a solid foundation for the successful establishment of positive plant-microbe interactions. The microbial functional gene composition in the rhizosphere can be regulated by several factors, e.g., the nutritional requirements of plants, soil chemistry, soil nutrient status, pathogen attack, abiotic stresses, etc. Knowing the pattern of functional gene composition in the rhizosphere can shed light on the dynamics of rhizosphere microbial ecology and the strength of cooperation between plants and associated microbes. This knowledge is crucial to realizing how microbial functions respond to unprecedented challenges which are obvious in the Anthropocene. Unraveling how microbes-mediated beneficial functions will change under the influence of several challenges, requires knowledge of the pattern and composition of functional genes corresponding to beneficial functions such as biogeochemical functions (nutrient cycle), plant growth promotion, stress mitigation, etc. Here, we focus on the molecular traits of plant growth-promoting functions delivered by a set of microbial functional genes that can be useful to the emerging field of rhizosphere functional ecology.

Biocontrol efficiency and characterization of insecticidal protein from sugarcane endophytic Serratia marcescens (SM) against oriental armyworm Mythimna separata (Walker)

The plant endophytic bacteria are a great source of nature insecticides. However, no such endophytic bacteria have been found in sugarcane, to address this gap, we isolated and identified a strain of Serratia marcescens with moderate insecticidal activity from sugarcane. Taken armyworm Mythimna separata as example, the mortality rates of oral infection and injection infection were 47.06 % and 91 %, respectively. The SM has significant negative affect on the growth, development, and reproduction of M. separata. After determining that these insecticidal substances, 33 potential virulence proteins were screened through the identification and prediction of bacterial proteins. Later we confirmed serralysin was a vital toxic protein from SM that caused M. separata death by prokaryotic expression. In addition, we also found that the intestinal tissue cells infected with SM or serralysin were severely diseased, which may be a major factor in M. separata demise. Finally, through gene expression level, protein molecular docking, we found the aminopeptidase-N would be one of the potential receptors of serralysin. Taken together, our findings indicate that sugarcane endophyte S. marcescens may be beneficial for pest control in sugarcane and explain its insecticidal mechanism. This study provides new ideas and materials for the biological control of pests.

Serratia marcescens LYGN1 Reforms the Rhizosphere Microbial Community and Promotes Cucumber and Pepper Growth in Plug Seedling Cultivation

The vegetable plug seedling plays an important role in improving vegetable production. The process of plug seedling contributes to high-quality vegetable seedlings. The substrate composition and chemical fertilizer are widely studied to promote seedling growth. However, little is known about the effect of beneficial bacteria in the rhizosphere microbial community and vegetables' growth during plug seedling. The use of beneficial microbes to promote vegetable seedling growth is of great potential. In this study, we showed that the Serratia marcescens strain LYGN1 enhanced the growth of cucumber and pepper seedlings in plug seedling cultivation. The treatment with LYGN1 significantly increased the biomass and the growth-related index of cucumber and pepper, improving the seedling quality index. Specifically, LYGN1 also improved the cucumber and pepper root system architecture and increased the root diameter. We applied high-throughput sequencing to analyze the microbial community of the seedlings' rhizosphere, which showed LYGN1 to significantly change the composition and structure of the cucumber and pepper rhizosphere microbial communities. The correlation analysis showed that the Abditibacteriota and Bdellovibrionota had positive effects on seedling growth. The findings of this study provide evidence for the effects of Serratia marcescens LYGN1 on the cucumber and pepper rhizosphere microbial communities, which also promoted seedling quality in plug seedling cultivation.

A cyclic dipeptide for salinity stress alleviation and the trophic flexibility of endophyte provide insights into saltmarsh plant-microbe interactions

In response to climate change, the nature of endophytes and their applications in sustainable agriculture have attracted the attention of academics and agro-industries. This work focused on the endophytic halophiles of the endangered Taiwanese salt marsh plant, Bolboschoenus planiculmis, and evaluated the functions of these isolates through in planta salinity stress alleviation assay using Arabidopsis. The endophytic strain Priestia megaterium BP01R2, which can promote plant growth and salinity tolerance, was further characterized through multi-omics approaches. The transcriptomics results suggested that BP01R2 could function by tuning hormone signal transduction, energy-producing metabolism, multiple stress responses, etc. In addition, the cyclodipeptide cyclo(L-Ala-Gly), which was identified by metabolomics analysis, was confirmed to contribute to the alleviation of salinity stress in stressed plants via exogenous supplementation. In this study, we used multi-omics approaches to investigate the genomics, metabolomics, and tropisms of endophytes, as well as the transcriptomics of plants in response to the endophyte. The results revealed the potential molecular mechanisms underlying the occurrence of biostimulant-based plant-endophyte symbioses with possible application in sustainable agriculture.

Growth Kinetics of Prodigiosin (Food Color) Produced by Novel Serratia marcescens bhu prodig Under Submerged Fermentation (SMF)

Prodigiosin is a promising food color due to its antibacterial, antimalarial, antimycotic characteristics, immunomodulating, and antitumor activities. Novel prodigiosin producing strain isolated from sugarcane field soil of Banaras Hindu University, India, characterized as Serratia marcescens bhu prodig by 16 sRNA. The effect of carbon, nitrogen source, and physical parameters (pH and temperature) on pigment yield was studied. The highest amount of pigment produced, which was 800.95 ± 0.05 mg/L, was detected when sorbitol and peptone were used as nitrogen and carbon source with pH 7 at 30 °C. The optimized condition scale-up in a bioreactor with a working capacity of 3.0 L, gave maximum pigment yield of 825 ± 0.05 mg/L with µ (Maximum specific growth rate), Yp/x, which represents the product yield coefficient, and Yp/s, which signifies the specific product yield coefficient and productivity of 0.3/h, 0.62, 0.80, and 0.02 g/L/h, respectively, after 72 h of cultivation in submerged fermentation (SMF). The isolated pigment was characterized as prodigiosin by the analysis of spectral data and GC-MS. The mass spectrophotometry investigation characterized pigment as 4-methoxy-5(5 methyl-4-pentyl-2H-pyrrol-2-ylidene)- 2,2-bipyrrole ring structure. The GC-MS chromatogram showed m/z of 323, representing prodigiosin. The prodigiosin yield and productivity obtained in the current finding were higher than in previous reports.

The man, the plant, and the insect: shooting host specificity determinants in Serratia marcescens pangenome

Introduction

Serratia marcescens is most commonly known as an opportunistic pathogen causing nosocomial infections. It, however, was shown to infect a wide range of hosts apart from vertebrates such as insects or plants as well, being either pathogenic or growth-promoting for the latter. Despite being extensively studied in terms of virulence mechanisms during human infections, there has been little evidence of which factors determine S. marcescens host specificity. On that account, we analyzed S. marcescens pangenome to reveal possible specificity factors.

Methods

We selected 73 high-quality genome assemblies of complete level and reconstructed the respective pangenome and reference phylogeny based on core genes alignment. To find an optimal pipeline, we tested current pangenomic tools and obtained several phylogenetic inferences. The pangenome was rich in its accessory component and was considered open according to the Heaps' law. We then applied the pangenome-wide associating method (pan-GWAS) and predicted positively associated gene clusters attributed to three host groups, namely, humans, insects, and plants.

Results

According to the results, significant factors relating to human infections included transcriptional regulators, lipoproteins, ABC transporters, and membrane proteins. Host preference toward insects, in its turn, was associated with diverse enzymes, such as hydrolases, isochorismatase, and N-acetyltransferase with the latter possibly exerting a neurotoxic effect. Finally, plant infection may be conducted through type VI secretion systems and modulation of plant cell wall synthesis. Interestingly, factors associated with plants also included putative growth-promoting proteins like enzymes performing xenobiotic degradation and releasing ammonium irons. We also identified overrepresented functional annotations within the sets of specificity factors and found that their functional characteristics fell into separate clusters, thus, implying that host adaptation is represented by diverse functional pathways. Finally, we found that mobile genetic elements bore specificity determinants. In particular, prophages were mainly associated with factors related to humans, while genetic islands-with insects and plants, respectively.

Discussion

In summary, functional enrichments coupled with pangenomic inferences allowed us to hypothesize that the respective host preference is carried out through distinct molecular mechanisms of virulence. To the best of our knowledge, the presented research is the first to identify specific genomic features of S. marcescens assemblies isolated from different hosts at the pangenomic level.

Screening bacterial isolates for biocontrol of sheath blight in rice plants

Sheath blight (Rhizoctonia solani) causes significant yield losses in rice (Oryza sativa L.). Its sustainable management needs an efficient biocontrol agent. The objective was to screen bacterial isolates as an antagonist to R. solani and identify the most efficient ones as sheath blight suppressors under greenhouse conditions. Two assays (E1 and E2) were performed in a completely randomized design with three replications. E1 tested 21 bacterial isolates antagonists to R. solani in vitro. E2 was conducted under greenhouse conditions, with rice cultivar BRS Pampeira sown in plastic pots (7 kg) containing fertilized soil. Sixty old plants were inoculated with a segment of a toothpick containing fragments of R. solani, followed by spray inoculation of a bacterial suspension (108 CFU/mL). The severity of the disease was determined by calculating the relative lesion size formed on the colm. Isolates BRM32112 (Pseudomonas nitroreducens), BRM65929 (Priestia megaterium), and BRM65919 (Bacillus cereus) reduced R. solani colony radial growth by 92.8, 77.56, and 75.56%, respectively while BRM63523 (Serratia marcescens), BRM65923 and BRM65916 (P. megaterium) and BRM65919 (B. cereus) with 23.45, 23.37, 23.62, and 20.17 cm, respectively were effective at suppressing sheath blight in greenhouse, indicating their potential as a biofungicide for sheath blight suppression.

Molecular networking as a tool to annotate the metabolites of Bacillus sp. and Serratia marcescens isolates and evaluate their fungicidal effects against Magnapothe oryzae and Bipolaris oryzae

Rhizobacteria are valuable sources of compounds that can be used for the integrated management of diseases in rice. Here, we aimed to explore the metabolism and organize and annotate the metabolites of Bacillus sp. and Serratia marcescens isolates using molecular networking and evaluate their fungicidal effects against Magnaporthe oryzae and Bipolaris oryzae. We obtained bacterial extracts after 6 and 16-h incubation via liquid-liquid extraction using ethyl acetate as solvent. We performed UHPLC-MS analysis and data processing using molecular networking and conducted biological assays in rice plants. Using the Global Natural Product Social spectral libraries, we annotated the following compounds: austinoneol, Phe-Pro, N-acetyl-l-leucine, Leu-Gly, Ile-Leu, Phe-Pro, 2,5-piperazinedione, 3-(1H-indol-3-methyl)-6-methyl-cyclo(d-Trp-l-Pro), and cholic acid. Results of the biological assays showed that the bacterial extracts reduced the mycelial growth of both pathogens in all treatments compared to the control. In the greenhouse setup, 8 days after the challenge for leaf gray spot and leaf blast, all treatments affected up to 4.4% of the leaf area, with an area under disease progress curve of 13.24, showing significant difference compared to the control, which affected 23% of the leaf area, with an AUDPC of 44.65. Our study provides potential new sources of natural products to be applied in the integrated management of rice.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-023-03547-6.

Involvement of exogenous arsenic-reducing bacteria in root surface biofilm formation promoted phytoextraction of arsenic

Root surface biofilm (RSB) is the last window for pollutants entering plant roots and thus plays a critical role in the phytoextraction of pollutants. Exogenous arsenic-reducing bacteria (EARB) have been adopted to enhance the phytoextraction of arsenic (As). However, whether EARB would be involved in RSB formation together with indigenous bacteria and the role of EARB involvement in As phytoextraction are still unknown. Herein, two EARB strains and two phytoextractors (wheat and maize) were selected to investigate the involvement of EARB in RSB formation and its role in As phytoextraction. Results showed that EARB successfully participated in RSB formation together with indigenous bacteria, attributing to their strong chemotaxis and biofilm formation abilities induced by root exudates. The involvement of EARB in RSB formation significantly enhanced As accumulation in plant roots, since more arsenite (As(III)) caused by arsenate (As(V)) reduction in RSB was absorbed by roots. Its underlying mechanism was further elucidated. EARB involvement increased phylum Proteobacteria to produce more siderophores in RSB. Siderophores then improved photosynthesis by increasing catalase and peroxidase activities and decreasing the malondialdehyde of plants. These actions further raised the shoot fresh weight to enhance As accumulation in plant roots. Moreover, mesophyll cell in wheat has a stronger As(V) reduction ability than that in maize, resulting in opposite distribution patterns of As(III) and As(V) in wheat and maize shoots. This study provides a new understanding of phytoextraction enhanced by exogenous bacteria and fills the gap in the role of EARB in As phytoextraction from the perspective of the RSB microregion.

De novo Genome Assessment of Serratia marcescens SGT5.3, a Potential Plant Growth-Promoting Bacterium Isolated from the Surface of Capsicum annuum Fruit

Serratia marcescens SGT5.3, a potential plant growth-promoting strain with a wide range of functions, was isolated from the surface of Capsicum annuum fruit. Here, we report the whole-genome sequence of this bacterium. Gene prediction revealed various functional genes potentially involved in plant growth promotion and development.

Metaprofiling of the Bacterial Community in Colonized Compost Extracts by Agaricus subrufescens

It is well-known that bacteria and fungi play important roles in the relationships between mycelium growth and the formation of fruiting bodies. The sun mushroom, Agaricus subrufescens, was discovered in Brazil ca. 1960 and it has become known worldwide due to its medicinal and nutritional properties. This work evaluated the bacterial community present in mushroom-colonized compost extract (MCCE) prepared from cultivation of A. subrufescens, its dynamics with two different soaking times and the influence of the application of those extracts on the casing layer of a new compost block for A. subrufescens cultivation. MCCEs were prepared through initial submersion of the colonized compost for 1 h or 24 h in water followed by application on casing under semi-controlled conditions. Full-length 16S rRNA genes of 1 h and 24 h soaked MCCE were amplified and sequenced using nanopore technology. Proteobacteria, followed by Firmicutes and Planctomycetes, were found to be the most abundant phyla in both the 1 h and 24 h soaked MCCE. A total of 275 different bacterial species were classified from 1 h soaked MCCE samples and 166 species from 24 h soaked MCCE, indicating a decrease in the bacterial diversity with longer soaking time during the preparation of MCCE. The application of 24 h soaked MCCE provided increases of 25% in biological efficiency, 16% in precociousness, 53% in the number of mushrooms and 40% in mushroom weight compared to control. Further investigation is required to determine strategies to enhance the yield and quality of the agronomic traits in commercial mushroom cultivation.

Natural Substrates and Culture Conditions to Produce Pigments from Potential Microbes in Submerged Fermentation

Pigments from bacteria, fungi, yeast, cyanobacteria, and microalgae have been gaining more demand in the food, leather, and textile industries due to their natural origin and effective bioactive functions. Mass production of microbial pigments using inexpensive and ecofriendly agro-industrial residues is gaining more demand in the current research due to their low cost, natural origin, waste utilization, and high pigment stimulating characteristics. A wide range of natural substrates has been employed in submerged fermentation as carbon and nitrogen sources to enhance the pigment production from these microorganisms to obtain the required quantity of pigments. Submerged fermentation is proven to yield more pigment when added with agro-waste residues. Hence, in this review, aspects of potential pigmented microbes such as diversity, natural substrates that stimulate more pigment production from bacteria, fungi, yeast, and a few microalgae under submerged culture conditions, pigment identification, and ecological functions are detailed for the benefit of industrial personnel, researchers, and other entrepreneurs to explore pigmented microbes for multifaceted applications. In addition, some important aspects of microbial pigments are covered herein to disseminate the knowledge.

Identification of distinct capsule types associated with Serratia marcescens infection isolates

Serratia marcescens is a versatile opportunistic pathogen that can cause a variety of infections, including bacteremia. Our previous work established that the capsule polysaccharide (CPS) biosynthesis and translocation locus contributes to the survival of S. marcescens in a murine model of bacteremia and in human serum. In this study, we determined the degree of capsule genetic diversity among S. marcescens isolates. Capsule loci (KL) were extracted from >300 S. marcescens genome sequences and compared. A phylogenetic comparison of KL sequences demonstrated a substantial level of KL diversity within S. marcescens as a species and a strong delineation between KL sequences originating from infection isolates versus environmental isolates. Strains from five of the identified KL types were selected for further study and electrophoretic analysis of purified CPS indicated the production of distinct glycans. Polysaccharide composition analysis confirmed this observation and identified the constituent monosaccharides for each strain. Two predominant infection-associated clades, designated KL1 and KL2, emerged from the capsule phylogeny. Bacteremia strains from KL1 and KL2 were determined to produce ketodeoxynonulonic acid and N-acetylneuraminic acid, two sialic acids that were not found in strains from other clades. Further investigation of KL1 and KL2 sequences identified two genes, designated neuA and neuB, that were hypothesized to encode sialic acid biosynthesis functions. Disruption of neuB in a KL1 isolate resulted in the loss of sialic acid and CPS production. The absence of sialic acid and CPS production also led to increased susceptibility to internalization by a human monocytic cell line, demonstrating that S. marcescens phagocytosis resistance requires CPS. Together, these results establish the capsule genetic repertoire of S. marcescens and identify infection-associated clades with sialic acid CPS components.

Long-term spatiotemporal variation of antimicrobial resistance genes within the Serratia marcescens population and transmission of S. marcescens revealed by public whole-genome datasets

The development of antimicrobial resistance (AMR) is accelerated by the selective pressure exerted by the widespread use of antimicrobial drugs, posing an increasing danger to public health. However, long-term spatiotemporal variation in AMR genes in microorganisms, particularly in bacterial pathogens in response to antibiotic consumption, is not fully understood. Here, we used the NCBI RefSeq database to collect 478 whole-genome sequences for Serratia marcescens ranging from 1961 up to 2019, to document global long-term AMR trends in S. marcescens populations. In total, 100 AMR gene subtypes (16 AMR gene types) were detected in the genomes of S. marcescens populations. We identified 3 core resistance genes in S. marcescens genomes, and a high diversity of AMR genes was observed in S. marcescens genomes after corresponding antibiotics were discovered and introduced into clinical practice, suggesting the adaptation of S. marcescens populations to challenges with therapeutic antibiotics. Our findings indicate spatiotemporal variation of AMR genes in S. marcescens populations in relation to antibiotic consumption and suggest the potential transmission of S. marcescens isolates harboring AMR genes among countries and between the environment and the clinic, representing a public health threat that necessitates international solidarity to overcome.

Biodegradation of PAHs by Bacillus marsiflavi, genome analysis and its plant growth promoting potential

The biodegradation of hazardous petroleum hydrocarbons has recently received a lot of attention because of its many possible applications. Bacillus marsiflavi strain was isolated from oil contaminated soil of Rawalpindi, Pakistan. Initial sequencing was done by 16s rRNA sequencing technique. Bac 144 had shown 78% emulsification index and 72% hydrophobicity content. Further, the strain displayed production of 15.5 mg/L phosphate sloubilization and 30.25 μg/ml indole acetic acid (IAA) in vitro assay. The strain showed 65% biodegradation of crude oil within 5 days by using Gas Chromatography-Mass Spectrometry (GC-MS) analysis. Whole Genome analysis of Bac 144 was performed by PacBio sequencing and results indicated that Bacillus marsiflavi Bac144 strain consisted of size of 4,417,505bp with closest neighbor Bacillus cereus ATCC 14579. The number of the coding sequence was 4662 and number of RNAs was 141. The GC content comprised 48.1%. Various genes were detected in genome responsible for hydrocarbon degradation and plant defense mechanism. The toxic effect of petroleum hydrocarbons in soil and its mitigation with Bac 144 was tested by soil experiment with three levels of oil contamination (5%, 10% and 15%). Soil enzymatic activity such as dehydrogenase and fluorescein diacetate (FDA) increased up to 49% and 40% with inoculation of Bac 144, which was considered to be correlated with hydrocarbon degradation recorded as 46%. An increase of 20%, 14% and 9% in shoot length of plant at 5%, 10% and 15% level of oil was recorded treated with Bac 144 as compared to untreated plants. A percent increase of 14.89%, 16.85%, and 13.87% in chlorophyll, carotenoid, and proline content of plant was observed by inoculation with Bac 144 under oil stress. Significant reduction of 14% and 18%, 21% was recorded in the malondialdehyde content of plant due to inoculation of Bac 144. A considerable increase of 21.33%, 19.5%, and 24.5% in super oxide dismutase, catalase, and peroxidase dismutase activity was also observed in plants inoculated with strain Bac 144. These findings suggested that Bac-144 can be considered as efficient candidate for bioremediation of hydrocarbons.

The endophytic bacterial entomopathogen Serratia marcescens promotes plant growth and improves resistance against Nilaparvata lugens in rice

Entomopathogenic bacteria are commonly used as biological agents to control different insect pests. However, little is known about the role of bacterial entomopathogens as endophytes in regulating both plant growth and resistance against insect pests. Here, we applied the entomopathogenic bacterium Serratia marcescens S-JS1 via rice seed inoculation and evaluated its effects on host plant growth and resistance against the rice pest Nilaparvata lugens. Furthermore, the induction of defense-related secondary metabolites by the bacterium was assessed by GC-MS/MS. We showed that S-JS1 was able to endophytically colonize the roots and shoots of rice seedlings following seed inoculation. Colonized plants showed increased seed germination (9.4-13.3 %), root (8.2-36.4 %) and shoot lengths (4.1-22.3 %), and root (26.7-69.3 %) and shoot fresh weights (19.0-49.0 %) compared to plants without inoculation. We also identified the production of indole-3-acetic acid by S-JS1, which is likely involved in enhancing rice plant growth. In a two-choice test, N. lugens adults preferred to feed on untreated control plants than on plants treated with S-JS1. In the no-choice feeding tests, the survival of N. lugens nymphs that fed on S-JS1-treated plants was significantly lower than that of nymphs that fed on untreated plants. Additionally, seeds treated with 10⁹ cfu/mL S-JS1 resulted in elevated levels of secondary metabolites, which may be associated with N. lugens resistance in rice plants. Therefore, we suggest that the entomopathogenic bacterium S. marcescens be considered a potentially promising endophyte for use in an innovative strategy for the integrated management of insect pests.

Genome sequencing of the vermicompost strain Stenotrophomonas maltophilia UENF-4GII and population structure analysis of the S. maltophilia Sm3 genogroup

The Stenotrophomonas maltophilia complex (Smc) is a cosmopolitan bacterial group that has been proposed an emergent multidrug-resistant pathogen. Taxonomic studies support the genomic heterogeneity of Smc, which comprises genogroups exhibiting a range of phenotypically distinct strains from different sources. Here, we report the genome sequencing and in-depth analysis of S. maltophilia UENF-4GII, isolated from vermicompost. This genome harbors a unique region encoding a penicillin-binding protein (pbpX) that was carried by a transposon, as well as horizontally-transferred genomic islands involved in anti-phage defense via DNA modification, and pili glycosylation. We also analyzed all available Smc genomes to investigate genes associated with resistance and virulence, niche occupation, and population structure. S. maltophilia UENF-4GII belongs to genogroup 3 (Sm3), which comprises three phylogenetic clusters (PC). Pan-GWAS analysis uncovered 471 environment-associated and 791 PC-associated genes, including antimicrobial resistance (e.g. blaL1 and blaR1) and virulence determinants (e.g. treS and katG) that provide insights on the resistance and virulence potential of Sm3 strains. Together, the results presented here provide the grounds for more detailed clinical and ecological investigations of S. maltophilia.

Down in the pond: Isolation and characterization of a new Serratia marcescens strain (LVF3) from the surface water near frog's lettuce (Groenlandia densa)

Serratia marcescens is a species that belongs to the family of Yersiniaceae. This family comprises taxa representing opportunistic human- and phytopathogens but also plant growth-promoting rhizobacteria (PGPR). This study describes a novel Gram-negative strain (LVF3R) of the species Serratia marcescens. The strain was characterized genomically, morphologically, and physiologically. In addition, the potential of the isolate to act as a host strain to assess the diversity of Serratia associated phages in environmental samples was explored. Average nucleotide identity analysis revealed that LVF3R belongs to the species Serratia marcescens. In silico analysis and ProphageSeq data resulted in the identification of one prophage, which is capable of viral particle formation. Electron microscopy showed cells of a rod-shaped, flagellated morphotype. The cells revealed a length and width of 1-1.6 μm and 0.8 μm, respectively. LVF3R showed optimal growth at 30 C and in the presence of up to 2% (w/v) NaCl. It exhibited resistances to ampicillin, erythromycin, oxacillin, oxytetracycline, rifampicin, tetracycline, and vancomycin. Genome data indicate that strain S. marcescens LVF3R is a potential PGPR strain. It harbors genes coding for indole acetic acid (IAA) biosynthesis, siderophore production, plant polymer degradation enzymes, acetoin synthesis, flagellar proteins, type IV secretion system, chemotaxis, phosphorous solubilization, and biofilm formation.

Mutualistic interaction of native Serratia marcescens UENF-22GI with Trichoderma longibrachiatum UENF-F476 boosting seedling growth of tomato and papaya

A plethora of bacteria-fungal interactions occur on the extended fungal hyphae network in soil. The mycosphere of saprophytic fungi can serve as a bacterial niche boosting their survival, dispersion, and activity. Such ecological concepts can be converted to bioproducts for sustainable agriculture. Accordingly, we tested the hypothesis that the well-characterised beneficial bacterium Serratia marcescens UENF-22GI can enhance plant growth-promoting properties when combined with Trichoderma longibrachiatum UENF-F476. The cultural and cell interactions demonstrated S. marcescens and T. longibrachiatum mutual compatibility. Bacteria cells were able to attach, forming aggregates to biofilms and migrating through the fungal hyphae network. Long-distance bacterial migration through growing hyphae was confirmed using a two-compartment Petri dishes assay. Fungal inoculation increased the bacteria survival rates into the vermicompost substrate over the experimental time. Also, in vitro indolic compound, phosphorus, and zinc solubilisation bacteria activities increased in the presence of the fungus. In line with the ecophysiological bacteria fitness, the bacterium-fungal combination boosted tomato and papaya plantlet growth when applied into the plant substrate under nursery conditions. Mutualistic interaction between mycosphere-colonizing bacterium S. marcescens UENF-22GI and the saprotrophic fungi T. longibrachiatum UENF-F467 increased the ecological fitness of the bacteria alongside with beneficial potential for plant growth. A proper combination and delivery of mutual compatible beneficial bacteria-fungal represent an open avenue for microbial-based products for the biological enrichment of plant substrates in agricultural systems.

Characterization of cellular, biochemical and genomic features of the diazotrophic plant growth-promoting bacterium Azospirillum sp. UENF-412522, a novel member of the Azospirillum genus

Given their remarkable beneficial effects on plant growth, several Azospirillum isolates currently integrate the formulations of various commercial inoculants. Our research group isolated a new strain, Azospirillum sp. UENF-412522, from passion fruit rhizoplane. This isolate uses carbon sources that are partially distinct from closely-related Azospirillum isolates. Scanning electron microscopy analysis and population counts demonstrate the ability of Azospirillum sp. UENF-412522 to colonize the surface of passion fruit roots. In vitro assays demonstrate the ability of Azospirillum sp. UENF-412522 to fix atmospheric nitrogen, to solubilize phosphate and to produce indole-acetic acid. Passion fruit plantlets inoculated with Azospirillum sp. UENF-41255 showed increased shoot and root fresh matter by 13,8% and 88,6% respectively, as well as root dry matter by 61,4%, further highlighting its biotechnological potential for agriculture. We sequenced the genome of Azospirillum sp. UENF-412522 to investigate the genetic basis of its plant-growth promotion properties. We identified the key nif genes for nitrogen fixation, the complete PQQ operon for phosphate solubilization, the acdS gene that alleviates ethylene effects on plant growth, and the napCAB operon, which produces nitrite under anoxic conditions. We also found several genes conferring resistance to common soil antibiotics, which are critical for Azospirillum sp. UENF-412522 survival in the rhizosphere. Finally, we also assessed the Azospirillum pangenome and highlighted key genes involved in plant growth promotion. A phylogenetic reconstruction of the genus was also conducted. Our results support Azospirillum sp. UENF-412522 as a good candidate for bioinoculant formulations focused on plant growth promotion in sustainable systems.

Phylogenetic analysis and population structure of Pseudomonas alloputida

The Pseudomonas putida group comprises strains with biotechnological and clinical relevance. P. alloputida was proposed as a new species and highlighted the misclassification of P. putida. Nevertheless, the population structure of P. alloputida remained unexplored. We retrieved 11,025 Pseudomonas genomes and used P. alloputida Kh7^T to delineate the species. The P. alloputida population structure comprises at least 7 clonal complexes (CCs). Clinical isolates are mainly found in CC4 and acquired resistance genes are present at low frequency in plasmids. Virulence profiles support the potential of CC7 members to outcompete other plant or human pathogens through a type VI secretion system. Finally, we found that horizontal gene transfer had an important role in shaping the ability of P. alloputida to bioremediate aromatic compounds such as toluene. Our results provide the grounds to understand P. alloputida genetic diversity and its potential for biotechnological applications.

The global population structure and beta-lactamase repertoire of the opportunistic pathogen Serratia marcescens

Serratia marcescens is a global spread nosocomial pathogen. This rod-shaped bacterium displays a broad host range and worldwide geographical distribution. Here we analyze an international collection of this multidrug-resistant, opportunistic pathogen from 35 countries to infer its population structure. We show that S. marcescens comprises 12 lineages; Sm1, Sm4, and Sm10 harbor 78.3% of the known environmental strains. Sm5, Sm6, and Sm7 comprise only human-associated strains which harbor smallest pangenomes, genomic fluidity and lowest levels of core recombination, indicating niche specialization. Sm7 and Sm9 lineages exhibit the most concerning resistome; bla_KPC-2 plasmid is widespread in Sm7, whereas Sm9, also an anthropogenic-exclusive lineage, presents highest plasmid/lineage size ratio and plasmid-diversity encoding metallo-beta-lactamases comprising bla_NDM-1. The heterogeneity of resistance patterns of S. marcescens lineages elucidated herein highlights the relevance of surveillance programs, using whole-genome sequencing, to provide insights into the molecular epidemiology of carbapenemase producing strains of this species.

Defining chaperone-usher fimbriae repertoire in Serratia marcescens

Chaperone-usher (CU) fimbriae are surface organelles particularly prevalent among the Enterobacteriaceae. Mainly associated to their adhesive properties, CU fimbriae play key roles in biofilm formation and host cell interactions. Little is known about the fimbriome composition of the opportunistic human pathogen Serratia marcescens. Here, by using a search based on consensus fimbrial usher protein (FUP) sequences, we identified 421 FUPs across 39 S. marcescens genomes. Further analysis of the FUP-containing loci allowed us to classify them into 20 conserved CU operons, 6 of which form the S. marcescens core CU fimbriome. A new systematic nomenclature is proposed according to FUP sequence phylogeny. We also established an in vivo transcriptional assay comparing CU promoter expression between an environmental and a clinical isolate of S. marcescens, which revealed that promoters from 3 core CU operons (referred as fgov, fpo, and fps) are predominantly expressed in the two strains and might represent key core adhesion appendages contributing to S. marcescens pathogenesis.

Physiological and genomic evidence supports the role of Serratia quinivorans PKL:12 as a biopriming agent for the biohardening of micropropagated Picrorhiza kurroa plantlets in cold regions

The medicinal herb, Picrorhiza kurroa Royle ex Benth has become endangered because of indiscriminate over-harvesting. Although micropropagation has been attempted for mass propagation of the plant, survival of in vitro plantlets under green house/open field poses a major challenge. Biopriming of micropropagated plantlets with plant growth-promoting rhizobacteria (PGPR) are among the successful methods to combat this problem. Serratia quinivorans PKL:12 was the best-characterized PGPR from rhizospheric soil of P. kurroa as it increased the vegetative growth and survival of the micropropagated plantlets most effectively. Complete genome (5.29 Mb) predicted genes encoding proteins for cold adaptation and plant growth-promoting traits in PKL:12. Antibiotic and biosynthetic gene cluster prediction supported PKL:12 as a potential biocontrol agent. Comparative genomics revealed 226 unique genes with few genes associated with plant growth-promoting potential. Physiological and genomic evidence supports S. quinivorans PKL:12 as a potential agent for bio-hardening of micropropagated P. kurroa plantlets in cold regions.

Proteomics insights into the Burkholderia cenocepacia phosphorus stress response

The Burkholderia cepacia complex is a group of Burkholderia species that are opportunistic pathogens causing high mortality rates in patients with cystic fibrosis. An environmental stress often encountered by these soil-dwelling and pathogenic bacteria is phosphorus limitation, an essential element for cellular processes. Here, we describe cellular and extracellular proteins differentially regulated between phosphate-deplete (0 mM, no added phosphate) and phosphate-replete (1 mM) growth conditions using a comparative proteomics (LC-MS/MS) approach. We observed a total of 128 and 65 unique proteins were downregulated and upregulated respectively, in the B. cenocepacia proteome. Of those downregulated proteins, many have functions in amino acid transport/metabolism. We have identified 24 upregulated proteins that are directly/indirectly involved in inorganic phosphate or organic phosphorus acquisition. Also, proteins involved in virulence and antimicrobial resistance were differentially regulated, suggesting B. cenocepacia experiences a dramatic shift in metabolism under these stress conditions. Overall, this study provides a baseline for further research into the biology of Burkholderia in response to phosphorus stress.

Whole genome sequence of Serratia marcescens 39_H1, a potential hydrolytic and acidogenic strain

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Serratia marcescens 39_H1 could enhance the hydrolysis of lignocellulosic biomass.

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Serratia marcescens 39_H1 is a plant growth promoting organism.

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Genome analysis showed diverse potential biotechnological application of organism.

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This is an original report on the hydrolytic and acidogenic attributes ofSerratia marcescens 39_H1 for biogas production.

Here, we report a high quality annotated draft genome of Serratia marcescens 39_H1, a Gram-negative facultative anaerobe that was isolated from an anaerobic digester. The strain exhibited hydrolytic/acidogenic properties by significantly improving methane production when used as a single isolate inoculum during anaerobic digestion of water hyacinth and cow dung. The total genome size of the isolate was 5,106,712 bp which corresponds to an N50 of 267,528 and G + C content of 59.7 %. Genome annotation with the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) predicted a total of 4,908 genes of which 4,755 were protein coding genes; there were no plasmids detected. A number of genes associated with hydrolytic/acidogenic activities as well as other metabolic activities were identified and discussed.

Study on the community structure and function of symbiotic bacteria from different growth and developmental stages of Hypsizygus marmoreus

BACKGROUND

The symbiotic bacteria associated with edible fungi are valuable microbial resources worthy of in-depth exploration. It is important to analyze the community structure and succession of symbiotic bacteria in mushrooms. This can assist in the isolation of growth-promoting strains that have an essential relationship with the cultivation cycle as well as the agronomic traits and yields of fruiting bodies.

RESULTS

In all of the samples from cultivation bags of Hypsizygus marmoreus, 34 bacterial phyla were detected. Firmicutes was the most abundant bacterial phylum (78.85%). The genus Serratia showed an exponential increase in abundance in samples collected from the cultivation bags in the mature period, reaching a peak abundance of 55.74% and the dominant symbiotic flora. The most predominant strain was Serratia odorifera HZSO-1, and its abundance increased with the amount of hyphae of H. marmoreus. Serratia odorifera HZSO-1 could reside in the hyphae of H. marmoreus, promote growth and development, shorten the fruiting cycle by 3-4 days, and further increase the fruiting body yield by 12%.

CONCLUSIONS

This study is a pioneering demonstration of the community structure of the symbiotic microbiota and bacteria-mushroom interaction in the growth and development of edible fungi. This work lays a theoretical foundation to improve the industrial production of mushrooms with symbiotic bacteria as assisting agents.

Is Long-Term Heavy Metal Exposure Driving Carriage of Antibiotic Resistance in Environmental Opportunistic Pathogens: A Comprehensive Phenomic and Genomic Assessment Using Serratia sp. SRS-8-S-2018

The carriage of both, heavy metal and antibiotic resistance appears to be a common trait in bacterial communities native to long-term contaminated habitats, including the Savannah River Site (SRS). There is widespread soil contamination at the SRS; a United States Department of Energy (DOE) facility with long-term contamination from past industrial and nuclear weapons production activities. To further evaluate the genomic and metabolic traits that underpin metal and antibiotic resistance, a robust mercury (Hg) and uranium (U)-resistant strain- SRS-8-S-2018, was isolated. Minimum inhibitory concentration of this strain revealed resistance to Hg (10 μg/ml) and U (5 mM), the two main heavy metal contaminants at the SRS. Metabolic assessment of strain SRS-8-S-2018 using Biolog metabolic fingerprinting analysis revealed preference for carbohydrate utilization followed by polymers, amino acids, carboxy acids, and esters; this physiological activity diminished when Hg stress was provided at 1 and 3 μg/ml and completely ceased at 5 μg/ml Hg, indicating that continued release of Hg will have negative metabolic impacts to even those microorganisms that possess high resistance ability. Development of antibiotic resistance in strain SRS-8-S-2018 was evaluated at a functional level using phenomics, which confirmed broad resistance against 70.8% of the 48 antibiotics tested. Evolutionary and adaptive traits of strain SRS-8-S-2018 were further assessed using genomics, which revealed the strain to taxonomically affiliate with Serratia marcescens species, possessing a genome size of 5,323,630 bp, 5,261 proteins (CDS), 55 genes for transfer RNA (tRNA), and an average G + C content of 59.48. Comparative genomics with closest taxonomic relatives revealed 360 distinct genes in SRS-8-S-2018, with multiple functions related to both, antibiotic and heavy metal resistance, which likely facilitates the strain’s survival in a metalliferous soil habitat. Comparisons drawn between the environmentally isolated Serratia SRS-8-S-2018 with 31 other strains revealed a closer functional association with medically relevant isolates suggesting that propensity of environmental Serratia isolates in acquiring virulence traits, as a function of long-term exposure to heavy metals, which is facilitating development, recruitment and proliferation of not only metal resistant genes (MRGs) but antibiotic resistant genes (ARGs), which can potentially trigger future bacterial pathogen outbreaks emanating from contaminated environmental habitats.

Plant growth promoting rhizobacteria isolated from halophytes and drought-tolerant plants: genomic characterisation and exploration of phyto-beneficial traits

Plant growth promoting rhizobacteria (PGPR) are able to provide cross-protection against multiple stress factors and facilitate growth of their plant symbionts in many ways. The aim of this study was to isolate and characterize rhizobacterial strains under natural conditions, associated with naturally occurring representatives of wild plant species and a local tomato cultivar, growing in differently stressed Mediterranean ecosystems. A total of 85 morphologically different rhizospheric strains were isolated; twenty-five exhibited multiple in vitro PGP-associated traits, including phosphate solubilization, indole-3-acetic acid production, and 1-aminocyclopropane-1-carboxylate deaminase activity. Whole genome analysis was applied to eight selected strains for their PGP potential and assigned seven strains to Gammaproteobacteria, and one to Bacteroidetes. The genomes harboured numerous genes involved in plant growth promotion and stress regulation. They also support the notion that the presence of gene clusters with potential PGP functions is affirmative but not necessary for a strain to promote plant growth under abiotic stress conditions. The selected strains were further tested for their ability to stimulate growth under stress. This initial screening led to the identification of some strains as potential PGPR for increasing crop production in a sustainable manner.

Coal-Degrading Bacteria Display Characteristics Typical of Plant Growth Promoting Rhizobacteria

Coal mining produces large quantities of discard that is stockpiled in large dumps. This stockpiled material, termed coal discard, poses an environmental threat emphasising the need for appropriate bioremediation. Here, metagenomic analysis of the 16S rRNA from ten coal-degrading strains previously isolated from coal slurry from discard dumps and from the rhizosphere of diesel-contaminated sites was used to establish genetic relatedness to known plant growth-promoting (PGP) bacteria in the NCBI database. Measurement of indole and ammonium production and solubilisation of P and K were used to screen bacteria for PGP characteristics. BLAST analysis revealed ≥ 99% homology of six isolates with reference PGP strains of Bacillus, Escherichia, Citrobacter, Serratia, Exiguobacterium and Microbacterium, while two strains showed 94% and 91% homology with Proteus. The most competent PGP strains were Proteus strain ECCN 20b, Proteus strain ECCN 23b and Serratia strain ECCN 24b isolated from diesel-contaminated soil. In response to L-trp supplementation, the concentration of indolic compounds (measured as indole-3-acetic acid) increased. Production of ammonium and solubilisation of insoluble P by these strains was also apparent. Only Serratia strain ECCN 24b was capable of solubilising insoluble K. Production of indoles increased following exposure to increasing aliquots of coal discard, suggesting no negative effect of this material on indole production by these coal-degrading bacterial isolates and that these bacteria may indeed possess PGP characteristics.

Whole-Genome Sequence of a Plant Growth-Promoting Strain, Serratia marcescens BTL07, Isolated from the Rhizoplane of Capsicum annuum L

Serratia marcescens strain BTL07, which has the ability to promote growth and suppress plant diseases, was isolated from the rhizoplane of a chili plant. The draft genome sequence data of the strain will contribute to advancing our understanding of the molecular mechanisms underlying plant growth promotion and tolerance to different stresses.

Serratia marcescens strain BTL07, which has the ability to promote growth and suppress plant diseases, was isolated from the rhizoplane of a chili plant. The draft genome sequence data of the strain will contribute to advancing our understanding of the molecular mechanisms underlying plant growth promotion and tolerance to different stresses.

Plant-microbe Interactions for Sustainable Agriculture in the Post-genomic Era

Plant-microbe interactions are both symbiotic and antagonistic, and the knowledge of both these interactions is equally important for the progress of agricultural practice and produce. This review gives an insight into the recent advances that have been made in the plant-microbe interaction study in the post-genomic era and the application of those for enhancing agricultural production. Adoption of next-generation sequencing (NGS) and marker assisted selection of resistant genes in plants, equipped with cloning and recombination techniques, has progressed the techniques for the development of resistant plant varieties by leaps and bounds. Genome-wide association studies (GWAS) of both plants and microbes have made the selection of desirable traits in plants and manipulation of the genomes of both plants and microbes effortless and less time-consuming. Stress tolerance in plants has been shown to be accentuated by association of certain microorganisms with the plant, the study and application of the same have helped develop stress-resistant varieties of crops. Beneficial microbes associated with plants are being extensively used for the development of microbial consortia that can be applied directly to the plants or the soil. Next-generation sequencing approaches have made it possible to identify the function of microbes associated in the plant microbiome that are both culturable and non-culturable, thus opening up new doors and possibilities for the use of these huge resources of microbes that can have a potential impact on agriculture.

Pseudomonas PS01 Isolated from Maize Rhizosphere Alters Root System Architecture and Promotes Plant Growth

The objectives of this study were to evaluate the plant growth promoting effects on Arabidopsis by Pseudomonas sp. strains associated with rhizosphere of crop plants grown in Mekong Delta, Vietnam. Out of all the screened isolates, Pseudomonas PS01 isolated from maize rhizosphere showed the most prominent plant growth promoting effects on Arabidopsis and maize (Zea mays). We also found that PS01 altered root system architecture (RSA). The full genome of PS01 was resolved using high-throughput sequencing. Phylogenetic analysis identified PS01 as a member of the Pseudomonas putida subclade, which is closely related to Pseudomonas taiwanensis.. PS01 genome size is 5.3 Mb, assembled in 71 scaffolds comprising of 4820 putative coding sequence. PS01 encodes genes for the indole-3-acetic acid (IAA), acetoin and 2,3-butanediol biosynthesis pathways. PS01 promoted the growth of Arabidopsis and altered the root system architecture by inhibiting primary root elongation and promoting lateral root and root hair formation. By employing gene expression analysis, genetic screening and pharmacological approaches, we suggested that the plant-growth promoting effects of PS01 and the alteration of RSA might be independent of bacterial auxin and could be caused by a combination of different diffusible compounds and volatile organic compounds (VOCs). Taken together, our results suggest that PS01 is a potential candidate to be used as bio-fertilizer agent for enhancing plant growth.

Rhizosphere assisted biodegradation of benzo(a)pyrene by cadmium resistant plant-probiotic Serratia marcescens S2I7, and its genomic traits

Melia azedarach-rhizosphere mediated degradation of benzo(a)pyrene (BaP), in the presence of cadmium (Cd) was studied, using efficient rhizobacterial isolate. Serratia marcescens S2I7, isolated from the petroleum-contaminated site, was able to tolerate up to 3.25 mM Cd. In the presence of Cd, the isolate S2I7 exhibited an increase in the activity of stress-responsive enzyme, glutathione-S-transferase. Gas Chromatography-Mass spectroscopy analysis revealed up to 59% in -vitro degradation of BaP after 21 days, while in the presence of Cd, the degradation was decreased by 14%. The bacterial isolate showed excellent plant growth-promoting attributes and could enhance the growth of host plant in Cd contaminated soil. The 52,41,555 bp genome of isolate S. marcescens S2I7 was sequenced, assembled and annotated into 4694 genes. Among these, 89 genes were identified for the metabolism of aromatic compounds and 172 genes for metal resistance, including the efflux pump system. A 2 MB segment of the genome was identified to contain operons for protocatechuate degradation, catechol degradation, benzoate degradation, and an IclR type regulatory protein pcaR, reported to be involved in the regulation of protocatechuate degradation. A pot trial was performed to validate the ability of S2I7 for rhizodegradation of BaP when applied through Melia azedarach rhizosphere. The rhizodegradation of BaP was significantly higher when augmented with S2I7 (85%) than degradation in bulk soil (68%), but decreased in the presence of Cd (71%).

Draft Genome Sequence of a Serratia marcescens Strain Isolated from the Pitcher Fluids of a Sarracenia Pitcher Plant

The genome of a Serratia marcescens strain (C7) that was found in the pitcher fluids of a Sarracenia rosea pitcher plant was sequenced using the Illumina platform. A 5,543,750-bp genome assembly was obtained. A total of 6,278 coding sequences are predicted from this assembly.

The genome of a Serratia marcescens strain (C7) that was found in the pitcher fluids of a Sarracenia rosea pitcher plant was sequenced using the Illumina platform. A 5,543,750-bp genome assembly was obtained. A total of 6,278 coding sequences are predicted from this assembly.

Population structure and pangenome analysis of Enterobacter bugandensis uncover the presence of blaCTX-M-55, blaNDM-5 and blaIMI-1, along with sophisticated iron acquisition strategies

Enterobacter bugandensis is a recently described species that has been largely associated with nosocomial infections. We report the genome of a non-clinical E. bugandensis strain, which was integrated with publicly available genomes to study the pangenome and general population structure of E. bugandensis. Core- and whole-genome multilocus sequence typing allowed the detection of five E. bugandensis phylogroups (PG-A to E), which contain important antimicrobial resistance and virulence determinants. We uncovered several extended-spectrum β-lactamases, including bla_CTX-M-55 and bla_NDM-5, present in an IncX replicon type plasmid, described here for the first time in E. bugandensis. Genetic context analysis of bla_NDM-5 revealed the resemblance of this plasmid with other IncX plasmids from other bacteria from the same country. Three distinctive siderophore producing operons were found in E. bugandensis: enterobactin (ent), aerobactin (iuc/iut), and salmochelin (iro). Our findings provide novel insights on the lifestyle, physiology, antimicrobial, and virulence profiles of E. bugandensis.

Pangenome of Serratia marcescens strains from nosocomial and environmental origins reveals different populations and the links between them

Serratia marcescens is a Gram-negative bacterial species that can be found in a wide range of environments like soil, water and plant surfaces, while it is also known as an opportunistic human pathogen in hospitals and as a plant growth promoting bacteria (PGPR) in crops. We have used a pangenome-based approach, based on publicly available genomes, to apply whole genome multilocus sequence type schemes to assess whether there is an association between source and genotype, aiming at differentiating between isolates from nosocomial sources and the environment, and between strains reported as PGPR from other environmental strains. Most genomes from a nosocomial setting and environmental origin could be assigned to the proposed nosocomial or environmental MLSTs, which is indicative of an association between source and genotype. The fact that a few genomes from a nosocomial source showed an environmental MLST suggests that a minority of nosocomial strains have recently derived from the environment. PGPR strains were assigned to different environmental types and clades but only one clade comprised strains accumulating a low number of known virulence and antibiotic resistance determinants and was exclusively from environmental sources. This clade is envisaged as a group of promissory MLSTs for selecting prospective PGPR strains.