Comparative genomics of 16 Microbacterium spp. that tolerate multiple heavy metals and antibiotics

Effect of Mn-HA on ARGs and MRGs in nitrogen-culturing sludge

The simultaneous escalation in ARGs (antibiotic resistance genes) and MRGs (metal resistance genes) further complicates the intricate network of factors contributing to the proliferation of microbial resistance. Manganese, which has been reported to affect the resistance of bacteria to antibiotics and metals, plays a vital role in microbial nitrogen metabolism. Moreover, nitrifying and denitrifying populations are potential hosts for ARGs. In this study, manganese was introduced in its prevalent organic chelated form in the environment (Manganese humus chelates, Mn-HA) to a N metabolism sludge to explore the effect of manganese on MRGs and ARGs dissemination. Metagenomics results revealed that manganese availability enhances nitrogen metabolism, while a decrease in ARGs was noted which may be attributed to the inhibition of horizontal gene transfer (HGT), reflected in the reduced integrase -encoded gene int. Population analysis revealed that nitrifier and denitrifier genus harbor MRGs and ARGs, indicating that nitrifier and denitrifier are hosts of MRGs and ARGs. This raises the question of whether the prevalence of ARGs is always increased in metal-contained environments.

Stress mitigation mechanism of rice leaf microbiota amid atmospheric deposition of heavy metals

Leaf microbiota have been extensively applied in the biological control of plant diseases, but their crucial roles in mitigating atmospheric heavy metal (HM) deposition and promoting plant growth remain poorly understood. This study demonstrates that elevated atmospheric HM deposition on rice leaves significantly shapes distinct epiphytic and endophytic microbiota across all growth stages. HM stress consistently leads to the dominance of epiphytic Pantoea and endophytic Microbacterium in rice leaves, particularly during the booting and filling stages. Leaf-bound HMs stimulate the differentiation of specialized microbial communities in both endophytic and epiphytic compartments, thereby regulating leaf microbial interactions. Metagenomic binning retrieved high-quality genomes of keystone leaf microorganisms, indicating their potential for essential metabolic functions. Notably, Pantoea and Microbacterium show significant HM resistance, plant growth-promoting capabilities, and diverse element cycling functions. They possess genes associated with metal(loid) resistance, such as ars and czc, suggesting their ability to detoxify arsenic(As) and cadmium(Cd). They also support carbon, nitrogen, and sulfur cycling, with genes linked to carbon fixation, nitrogen fixation, and sulfur reduction. Additionally, these bacteria may enhance plant stress resistance and growth by producing antioxidants, phytohormones, and other beneficial compounds, potentially improving HM stress tolerance and nutrient availability in rice plants. This study shows that atmospheric HMs affect rice leaf microbial communities, prompting plants to seek microbial help to combat stress. The unique composition and metabolic potential of rice leaf microbiota offer a novel perspective for mitigating adverse stress induced by atmospheric HM deposition. This contributes to the utilization of leaf microbiota to alleviate the negative impact of heavy metal deposition on rice development and food security.

Chlamydomonas reinhardtii and Microbacterium forte sp. nov., a mutualistic association that favors sustainable hydrogen production

A naturally occurring multispecies bacterial community composed of Bacillus cereus and two novel bacteria (Microbacterium forte sp. nov. and Stenotrophomonas goyi sp. nov.) has been identified from a contaminated culture of the microalga Chlamydomonas reinhardtii. When incubated in mannitol- and yeast extract-containing medium, this bacterial community can promote and sustain algal hydrogen production up to 313 mL H2·L-1 for 17 days and 163.5 mL H2·L-1 for 25 days in high-cell (76.7 μg·mL-1 of initial chlorophyll) and low-cell density (10 μg·mL-1 of initial chlorophyll) algal cultures, respectively. In low-cell density algal cultures, hydrogen production was compatible with algal growth (reaching up to 60 μg·mL-1 of chlorophyll). Among the bacterial community, M. forte sp. nov. was the sole responsible for the improvement in hydrogen production. However, algal growth was not observed in the Chlamydomonas-M. forte sp. nov. consortium during hydrogen-producing conditions (hypoxia), suggesting that the presence of B. cereus and S. goyi sp. nov. could be crucial to support the algal growth during hypoxia. Still, under non‑hydrogen producing conditions (aerobiosis) the Chlamydomonas-M. forte sp. nov. consortium allowed algal growth (up to 40 μg·mL-1 of chlorophyll) and long-term algal viability (>45 days). The genome sequence and growth tests of M. forte sp. nov. have revealed that this bacterium is auxotroph for biotin and thiamine and unable to use sulfate as sulfur source; it requires S-reduced forms such as cysteine and methionine. Cocultures of Chlamydomonas reinhardtii and M. forte sp. nov. established a mutualistic association: the alga complemented the nutrient deficiencies of the bacterium, while the bacterium released ammonium (0.19 mM·day-1) and acetic acid (0.15 mM·day-1) for the alga. This work offers a promising avenue for photohydrogen production concomitant with algal biomass generation using nutrients not suitable for mixotrophic algal growth.

Effect of Arsenic on Fluoride Tolerance in Microbacterium paraoxydans Strain IR-1

Fluoride (F) and arsenic (As) are two major contaminants of water and soil systems around the globe, causing potential toxicity to humans, plants, animals, and microbes. These contaminated soil systems can be restored by microorganisms that can tolerate toxic stress and provide rapid mineralization of soil, organic matter, and contaminants, using various tolerance mechanisms. Thus, the present study was undertaken with the arsenic hyper-tolerant bacterium Microbacterium paraoxydans strain IR-1 to determine its tolerance and toxicity to increasing doses of fluoride, either individually or in combination with arsenic, in terms of growth inhibition using a toxicity unit model. The minimum inhibitory concentration (MIC)and half maximal inhibitory concentration (IC50) values for fluoride increased, from 9 g/L to 11 g/L and from 5.91 ± 0.1 g/L to 6.32 ± 0.028 g/L, respectively, in the combination (F + As) group. The statistical comparison of observed and expected additive toxicities, with respect to toxicity unit (TU difference), using Student's t-test, was found to be highly significant (p < 0.001). This suggests the antagonistic effect of arsenic on fluoride toxicity to the strain IR-1. The unique stress tolerance of IR-1 ensures its survival as well as preponderance in fluoride and arsenic co-contaminated sites, thus paving the way for its possible application in the natural or artificial remediation of toxicant-exposed degraded soil systems.

Acinetobacter radioresistens and Microbacterium paraoxydans endocarditis in patient with indwelling catheter and metastatic carcinoma

Acinetobacter radioresistens is a rare cause of nosocomial infection and is believed to confer antibiotic resistance to aggressive bacterial species. We present the first reported case of polymicrobial endocarditis caused by A. radioresistens and Microbacterium paraoxydans co-infection, a case of a woman in her late 60s with bacteraemia and ultimate finding of endometrial carcinoma. Bacteraemia with either agent in a previously healthy patient should prompt providers to search for underlying malignancy or immunological problem.We support the use of matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry for identifying these organisms in cultures, as well as the development of faster isolation techniques through PCR. Furthermore, we advocate for providers to order early antibiotic susceptibility testing, since our patient's Microbacterium sp was not susceptible to meropenem unlike most Microbacterium reported in literature.

Chromium Toxicity in Plants: Signaling, Mitigation, and Future Perspectives

Plants are very often confronted by different heavy metal (HM) stressors that adversely impair their growth and productivity. Among HMs, chromium (Cr) is one of the most prevalent toxic trace metals found in agricultural soils because of anthropogenic activities, lack of efficient treatment, and unregulated disposal. It has a huge detrimental impact on the physiological, biochemical, and molecular traits of crops, in addition to being carcinogenic to humans. In soil, Cr exists in different forms, including Cr (III) "trivalent" and Cr (VI) "hexavalent", but the most pervasive and severely hazardous form to the biota is Cr (VI). Despite extensive research on the effects of Cr stress, the exact molecular mechanisms of Cr sensing, uptake, translocation, phytotoxicity, transcript processing, translation, post-translational protein modifications, as well as plant defensive responses are still largely unknown. Even though plants lack a Cr transporter system, it is efficiently accumulated and transported by other essential ion transporters, hence posing a serious challenge to the development of Cr-tolerant cultivars. In this review, we discuss Cr toxicity in plants, signaling perception, and transduction. Further, we highlight various mitigation processes for Cr toxicity in plants, such as microbial, chemical, and nano-based priming. We also discuss the biotechnological advancements in mitigating Cr toxicity in plants using plant and microbiome engineering approaches. Additionally, we also highlight the role of molecular breeding in mitigating Cr toxicity in sustainable agriculture. Finally, some conclusions are drawn along with potential directions for future research in order to better comprehend Cr signaling pathways and its mitigation in sustainable agriculture.

Globally distributed mining-impacted environments are underexplored hotspots of multidrug resistance genes

Mining is among the human activities with widest environmental impacts, and mining-impacted environments are characterized by high levels of metals that can co-select for antibiotic resistance genes (ARGs) in microorganisms. However, ARGs in mining-impacted environments are still poorly understood. Here, we conducted a comprehensive study of ARGs in such environments worldwide, taking advantage of 272 metagenomes generated from a global-scale data collection and two national sampling efforts in China. The average total abundance of the ARGs in globally distributed studied mine sites was 1572 times per gigabase, being rivaling that of urban sewage but much higher than that of freshwater sediments. Multidrug resistance genes accounted for 40% of the total ARG abundance, tended to co-occur with multimetal resistance genes, and were highly mobile (e.g. on average 16% occurring on plasmids). Among the 1848 high-quality metagenome-assembled genomes (MAGs), 85% carried at least one multidrug resistance gene plus one multimetal resistance gene. These high-quality ARG-carrying MAGs considerably expanded the phylogenetic diversity of ARG hosts, providing the first representatives of ARG-carrying MAGs for the Archaea domain and three bacterial phyla. Moreover, 54 high-quality ARG-carrying MAGs were identified as potential pathogens. Our findings suggest that mining-impacted environments worldwide are underexplored hotspots of multidrug resistance genes.

Plastisphere community assemblage of aquatic environment: plastic-microbe interaction, role in degradation and characterization technologies

It is undeniable that plastics are ubiquitous and a threat to global ecosystems. Plastic waste is transformed into microplastics (MPs) through physical and chemical disruption processes within the aquatic environment. MPs are detected in almost every environment due to their worldwide transportability through ocean currents or wind, which allows them to reach even the most remote regions of our planet. MPs colonized by biofilm-forming microbial communities are known as the ''plastisphere". The revelation that this unique substrate can aid microbial dispersal has piqued interest in the ground of microbial ecology. MPs have synergetic effects on the development, transportation, persistence, and ecology of microorganisms. This review summarizes the studies of plastisphere in recent years and the microbial community assemblage (viz. autotrophs, heterotrophs, predators, and pathogens). We also discussed plastic-microbe interactions and the potential sources of plastic degrading microorganisms. Finally, it also focuses on current technologies used to characterize those microbial inhabitants and recommendations for further research.

Development of an Autochthonous Microbial Consortium for Enhanced Bioremediation of PAH-Contaminated Soil

The main objectives of this study were to isolate bacteria from soil chronically contaminated with polycyclic aromatic hydrocarbons (PAHs), develop an autochthonous microbial consortium, and evaluate its ability to degrade PAHs in their native contaminated soil. Strains with the best bioremediation potential were selected during the multi-stage isolation process. Moreover, to choose bacteria with the highest bioremediation potential, the presence of PAH-degrading genes (pahE) was confirmed and the following tests were performed: tolerance to heavy metals, antagonistic behavior, phytotoxicity, and antimicrobial susceptibility. In vitro degradation of hydrocarbons led to the reduction of the total PAH content by 93.5% after the first day of incubation and by 99.22% after the eighth day. Bioremediation experiment conducted in situ in the contaminated area resulted in the average reduction of the total PAH concentration by 33.3% after 5 months and by over 72% after 13 months, compared to the concentration recorded before the intervention. Therefore, this study implicates that the development of an autochthonous microbial consortium isolated from long-term PAH-contaminated soil has the potential to enhance the bioremediation process.

Isolation and characterization of a heavy metal- and antibiotic-tolerant novel bacterial strain from a contaminated culture plate of Chlamydomonas reinhardtii, a green micro-alga

Background:Chlamydomonas reinhardtii, a green micro-alga, is normally cultured in laboratories in Tris-Acetate Phosphate (TAP), a medium which contains acetate as the sole carbon source. Acetate in TAP can lead to occasional bacterial and fungal contamination. We isolated a yellow-pigmented bacterium from a Chlamydomonas TAP plate. It was named Clip185 based on the Chlamydomonas strain plate it was isolated from. In this article we present our work on the isolation, taxonomic identification and physiological and biochemical characterizations of Clip185. Methods: We measured sensitivities of Clip185 to five antibiotics and performed standard microbiological tests to characterize it. We partially sequenced the 16S rRNA gene of Clip185. We identified the yellow pigment of Clip185 by spectrophotometric analyses. We tested tolerance of Clip185 to six heavy metals by monitoring its growth on Lysogeny Broth (LB) media plates containing 0.5 mM -10 mM concentrations of six different heavy metals. Results: Clip185 is an aerobic, gram-positive rod, oxidase-negative, mesophilic, alpha-hemolytic bacterium. It can ferment glucose, sucrose and mannitol. It is starch hydrolysis-positive. It is very sensitive to vancomycin but resistant to penicillin and other bacterial cell membrane- and protein synthesis-disrupting antibiotics. Clip185 produces a C50 carotenoid, decaprenoxanthin, which is a powerful anti-oxidant with a commercial demand. Decaprenoxanthin production is induced in Clip185 under light. NCBI-BLAST analyses of the partial 16S rRNA gene sequence of Clip185 revealed a 99% sequence identity to that of Microbacterium binotii strain PK1-12M and Microbacterium sp. strain MDP6. Clip185 is able to tolerate toxic concentrations of six heavy metals. Conclusions: Our results show that Clip185 belongs to the genus Microbacterium. In the future, whole genome sequencing of Clip185 will clarify if Clip185 is a new Microbacterium species or a novel strain of Microbacterium binotii, and will reveal its genes involved in antibiotic-resistance, heavy-metal tolerance and regulation of decaprenoxanthin biosynthesis.

Isolation and characterization of a heavy metal- and antibiotic-tolerant novel bacterial strain from a contaminated culture plate of Chlamydomonas reinhardtii, a green micro-alga

Background:Chlamydomonas reinhardtii, a green micro-alga, is normally cultured in laboratories in Tris-Acetate Phosphate (TAP), a medium which contains acetate as the sole carbon source. Acetate in TAP can lead to occasional bacterial and fungal contamination. We isolated a yellow-pigmented bacterium from a Chlamydomonas TAP plate. It was named Clip185 based on the Chlamydomonas strain plate it was isolated from. In this article we present our work on the isolation, taxonomic identification and physiological and biochemical characterizations of Clip185. Methods: We measured sensitivities of Clip185 to five antibiotics and performed standard microbiological tests to characterize it. We partially sequenced the 16S rRNA gene of Clip185. We identified the yellow pigment of Clip185 by spectrophotometric analyses. We tested tolerance of Clip185 to six heavy metals by monitoring its growth on Lysogeny Broth (LB) media plates containing 0.5 mM -10 mM concentrations of six different heavy metals. Results: Clip185 is an aerobic, gram-positive rod, oxidase-negative, mesophilic, alpha-hemolytic bacterium. It can ferment glucose, sucrose and mannitol. It is starch hydrolysis-positive. It is very sensitive to vancomycin but resistant to penicillin and other bacterial cell membrane- and protein synthesis-disrupting antibiotics. Clip185 produces a C50 carotenoid, decaprenoxanthin, which is a powerful anti-oxidant with a commercial demand. Decaprenoxanthin production is induced in Clip185 under light. NCBI-BLAST analyses of the partial 16S rRNA gene sequence of Clip185 revealed a 99% sequence identity to that of Microbacterium binotii strain PK1-12M and Microbacterium sp. strain MDP6. Clip185 is able to tolerate toxic concentrations of six heavy metals. Conclusions: Our results show that Clip185 belongs to the genus Microbacterium. In the future, whole genome sequencing of Clip185 will clarify if Clip185 is a new Microbacterium species or a novel strain of Microbacterium binotii, and will reveal its genes involved in antibiotic-resistance, heavy-metal tolerance and regulation of decaprenoxanthin biosynthesis.

Overview on the role of heavy metals tolerance on developing antibiotic resistance in both Gram-negative and Gram-positive bacteria

Environmental health is a critical concern, continuously contaminated by physical and biological components (viz., anthropogenic activity), which adversely affect on biodiversity, ecosystems and human health. Nonetheless, environmental pollution has great impact on microbial communities, especially bacteria, which try to evolve in changing environment. For instance, during the course of adaptation, bacteria easily become resistance to antibiotics and heavy metals. Antibiotic resistance genes are now one of the most vital pollutants, provided as a source of frequent horizontal gene transfer. In this review, the environmental cause of multidrug resistance (MDR) that was supposed to be driven by either heavy metals or combination of environmental factors was essentially reviewed, especially focussed on the correlation between accumulation of heavy metals and development of MDR by bacteria. This kind of correlation was seemed to be non-significant, i.e. paradoxical. Gram-positive bacteria accumulating much of toxic heavy metal (i.e. highly stress tolerance) were unlikely to become MDR, whereas Gram-negative bacteria that often avoid accumulation of toxic heavy metal by efflux pump systems were come out to be more prone to MDR. So far, other than antibiotic contaminant, no such available data strongly support the direct influence of heavy metals in bacterial evolution of MDR; combinations of factors may drive the evolution of antibiotic resistance. Therefore, Gram-positive bacteria are most likely to be an efficient member in treatment of industrial waste water, especially in the removal of heavy metals, perhaps inducing the less chance of antibiotic resistance pollution in the environment.

Techniques Used for Analyzing Microplastics, Antimicrobial Resistance and Microbial Community Composition: A Mini-Review

Antimicrobial resistance (AMR) is a global health threat. Antibiotics, heavy metals, and microplastics are environmental pollutants that together potentially have a positive synergetic effect on the development, persistence, transport, and ecology of antibiotic resistant bacteria in the environment. To evaluate this, a wide array of experimental methods would be needed to quantify the occurrence of antibiotics, heavy metals, and microplastics as well as associated microbial communities in the natural environment. In this mini-review, we outline the current technologies used to characterize microplastics based ecosystems termed "plastisphere" and their AMR promoting elements (antibiotics, heavy metals, and microbial inhabitants) and highlight emerging technologies that could be useful for systems-level investigations of AMR in the plastisphere.

Comparative Genomics of Microbacterium Species to Reveal Diversity, Potential for Secondary Metabolites and Heavy Metal Resistance

Microbacterium species have been isolated from a wide range of hosts and environments, including heavy metal-contaminated sites. Here, we present a comprehensive analysis on the phylogenetic distribution and the genetic potential of 70 Microbacterium belonging to 20 different species isolated from heavy metal-contaminated and non-contaminated sites with particular attention to secondary metabolites gene clusters. The analyzed Microbacterium species are divided in three main functional clades. They share a small core genome (331 gene families covering basic functions) pointing to high genetic diversity. The most common secondary metabolite gene clusters encode pathways for the production of terpenoids, type III polyketide synthases and non-ribosomal peptide synthetases, potentially responsible of the synthesis of siderophore-like compounds. In vitro tests showed that many Microbacterium strains produce siderophores, ACC deaminase, auxins (IAA) and are able to solubilize phosphate. Microbacterium isolates from heavy metal contaminated sites are on average more resistant to heavy metals and harbor more genes related to metal homeostasis (e.g., metalloregulators). On the other hand, the ability to increase the metal mobility in a contaminated soil through the secretion of specific molecules seems to be widespread among all. Despite the widespread capacity of strains to mobilize several metals, plants inoculated with selected Microbacterium isolates showed only slightly increased iron concentrations, whereas concentrations of zinc, cadmium and lead were decreased.

New Plant Growth-Promoting, Chromium-Detoxifying Microbacterium Species Isolated From a Tannery Wastewater: Performance and Genomic Insights

Hexavalent chromium [Cr(VI)], widely generated by tannery activities, is considered among the most toxic substances and causes a serious damage for the environment and for human health. Interestingly, some microorganisms have a potential of bioremediation of chromium-contaminated wastewaters and soils through the reduction of Cr(VI) (soluble and harmful form) into Cr(III) (stable and non-toxic form). Here, we present the full genome sequence of a novel heavy-metal-resistant, plant growth-promoting bacterium (PGPB), Microbacterium metallidurans TL13, which was isolated from a Tunisian leather industry. The strain TL13 was resistant to many heavy metals, such as chromium, copper, nickel, cobalt, and arsenic. The 50% TL13 growth inhibitory concentration (IC₅₀) values of HgCl₂, CoCl₂, K₂Cr₂O₇, CuSO₄, NiCl₂, FeSO₄, and Na₂HAsO₄ are 368, 445, 676, 1,590, 1,680, 4,403, and 7,007 mg/L, respectively, with the following toxicity order: HgCl₂ > CoCl₂ > K₂Cr₂O₇ > CuSO₄ > NiCl₂ > FeSO₄ > Na₂HAsO₄. This new strain was also able to promote the growth of the hybrid tomato (Elika F1) under chromium metal stress. Its whole genome sequence length was estimated to be 3,587,460 bp (3,393 coding sequences) with a G + C content of 70.7%. Functional annotation of the genome of TL13 revealed the presence of open reading frames (ORFs) involved in adaptation to metal stress, such as the chromate transport protein, cobalt–zinc–cadmium resistance protein, copper resistance protein, copper responsive transcriptional regulator, multidrug resistance transporters, arsenical resistance operon repressor, arsenate reductase, arsenic resistance protein, mercuric resistance operon regulatory protein, mercuric ion reductase, and organomercurial lyase. Moreover, genes for the production of glutathione peroxidase, catalase, superoxide dismutase, and thioredoxin reductase, which confer a higher tolerance to oxidative/metal stresses, were identified in TL13 genome. In addition, genes for heat shock tolerance, cold shock tolerance, glycine-betaine production, mineral phosphate solubilization, ammonia assimilation, siderophores, exopolysaccharides, polyketides, and lytic enzymes (cellulase, chitinase, and proteases) production that enable bacteria to survive biotic/abiotic stress and to promote plant growth and health were also revealed. Based on genome analysis and experimental approaches, strain TL13 appears to have evolved from various metabolic strategies and could play a role in ensuring sustainable environmental and agricultural systems.

Mercury alters the rhizobacterial community in Brazilian wetlands and it can be bioremediated by the plant-bacteria association

This study examined how soil mercury contamination affected the structure and functionality of rhizobacteria communities from Aeschynomene fluminensis and Polygonum acuminatum and how rhizobacteria mediate metal bioremediation. The strains were isolated using culture-dependent methods, identified through 16S rDNA gene sequencing, and characterized with respect to their functional traits related to plant growth promotion and resistance to metals and antibiotics. The bioremediation capacity of the rhizobacteria was determined in greenhouse using corn plants. The isolated bacteria belonged to the phyla Actinobacteria, Deinococcus-Thermus, Firmicutes, and Proteobacteria, with great abundance of the species Microbacterium trichothecenolyticum. The rhizobacteria abundance, richness, and diversity were greater in mercury-contaminated soils. Bacteria isolated from contaminated environments had higher minimum inhibitory concentration values, presented plasmids and the merA gene, and were multi-resistant to metals and antibiotics. Enterobacter sp._C35 and M. trichothecenolyticum_C34 significantly improved (Dunnett's test, p < 0.05) corn plant growth in mercury-contaminated soil. These bacteria helped to reduce up to 87% of the mercury content in the soil, and increased the mercury bioaccumulation factor by up to 94%. Mercury bioremediation mitigated toxicity of the contaminated substrate. Enterobacter sp._C35, Bacillus megaterium_C28, and Bacillus mycoides_C1 stimulated corn plant growth and could be added to biofertilizers produced in research and related industries.

High quality 3C de novo assembly and annotation of a multidrug resistant ST-111 Pseudomonas aeruginosa genome: Benchmark of hybrid and non-hybrid assemblers

Genotyping methods and genome sequencing are indispensable to reveal genomic structure of bacterial species displaying high level of genome plasticity. However, reconstruction of genome or assembly is not straightforward due to data complexity, including repeats, mobile and accessory genetic elements of bacterial genomes. Moreover, since the solution to this problem is strongly influenced by sequencing technology, bioinformatics pipelines, and selection criteria to assess assemblers, there is no systematic way to select a priori the optimal assembler and parameter settings. To assembly the genome of Pseudomonas aeruginosa strain AG1 (PaeAG1), short reads (Illumina) and long reads (Oxford Nanopore) sequencing data were used in 13 different non-hybrid and hybrid approaches. PaeAG1 is a multiresistant high-risk sequence type 111 (ST-111) clone that was isolated from a Costa Rican hospital and it was the first report of an isolate of P. aeruginosa carrying both blaVIM-2 and blaIMP-18 genes encoding for metallo-β-lactamases (MBL) enzymes. To assess the assemblies, multiple metrics regard to contiguity, correctness and completeness (3C criterion, as we define here) were used for benchmarking the 13 approaches and select a definitive assembly. In addition, annotation was done to identify genes (coding and RNA regions) and to describe the genomic content of PaeAG1. Whereas long reads and hybrid approaches showed better performances in terms of contiguity, higher correctness and completeness metrics were obtained for short read only and hybrid approaches. A manually curated and polished hybrid assembly gave rise to a single circular sequence with 100% of core genes and known regions identified, >98% of reads mapped back, no gaps, and uniform coverage. The strategy followed to obtain this high-quality 3C assembly is detailed in the manuscript and we provide readers with an all-in-one script to replicate our results or to apply it to other troublesome cases. The final 3C assembly revealed that the PaeAG1 genome has 7,190,208 bp, a 65.7% GC content and 6,709 genes (6,620 coding sequences), many of which are included in multiple mobile genomic elements, such as 57 genomic islands, six prophages, and two complete integrons with blaVIM-2 and blaIMP-18 MBL genes. Up to 250 and 60 of the predicted genes are anticipated to play a role in virulence (adherence, quorum sensing and secretion) or antibiotic resistance (β-lactamases, efflux pumps, etc). Altogether, the assembly and annotation of the PaeAG1 genome provide new perspectives to continue studying the genomic diversity and gene content of this important human pathogen.

The Landscape of Genetic Content in the Gut and Oral Human Microbiome

Despite substantial interest in the species diversity of the human microbiome and its role in disease, the scale of its genetic diversity, which is fundamental to deciphering human-microbe interactions, has not been quantified. Here, we conducted a cross-study meta-analysis of metagenomes from two human body niches, the mouth and gut, covering 3,655 samples from 13 studies. We found staggering genetic heterogeneity in the dataset, identifying a total of 45,666,334 non-redundant genes (23,961,508 oral and 22,254,436 gut) at the 95% identity level. Fifty percent of all genes were "singletons," or unique to a single metagenomic sample. Singletons were enriched for different functions (compared with non-singletons) and arose from sub-population-specific microbial strains. Overall, these results provide potential bases for the unexplained heterogeneity observed in microbiome-derived human phenotypes. One the basis of these data, we built a resource, which can be accessed at https://microbial-genes.bio.

Metal tolerant bacteria enhanced phytoextraction of lead by two accumulator ornamental species

Microbially enhanced availability and phytoextraction is a promising technique for phytoremediation of lead (Pb). In this study, Pb resistant strains were isolated and investigated for potential effects on plant growth and Pb phytoextraction. Incubation experiments were carried for inoculated and un-inoculated soil containing different levels of Pb. Results revealed that 20% of the isolated bacteria could tolerate Pb up to 800 mg L^-1. Five Pb resistant strains with plant growth promoting (PGP) abilities were evaluated for possible influence on water soluble Pb through soil incubation experiments and significant increase i.e. 1.85- and 1.49-folds in water soluble Pb was observed for NCCP-1848 and NCCP-1862 strains, respectively. Pot experiments indicated significantly higher uptake by Pelargonium hortorum than that by Mesembryanthemum criniflorrum at all levels of soil Pb concentrations with the highest increase (1.9-folds) in plants inoculated with NCCP-1848 followed by NCCP-1862 (1.8-folds increase) compared to the control (Pb and without bacterial strain). The strains NCCP-1848 and NCCP-1862 were identified by 16S rRNA gene sequencing as Microbacterium sp. and Klebsiella sp. The results of present study suggest that Pb resistant plant growth promoting bacteria can serve as an effective bio-inoculant through wide action spectrum for maximizing efficiency of phytoremediation system.