Genome-Based Taxonomy of the Genus Stutzerimonas and Proposal of S. frequens sp. nov. and S. degradans sp. nov. and Emended Descriptions of S. perfectomarina and S. chloritidismutans

Biodegradation of triphenyl phosphate by a novel marine bacterial strain: Performance, mechanism, bioremediation and toxicity alleviation

Triphenyl phosphate (TPHP), a widely used organo-phosphorus flame retardant, poses environmental risks due to its persistence and bioaccumulation. In this study, Stutzerimonas frequens RL-XB02, a novel TPHP-degrading strain, was isolated from mangrove sediments. Strain RL-XB02 could completely degrade 50 mg/L of TPHP in 24 hours under various conditions (pH 6.0-9.0, 30-40°C and salinity 2.0-4.0 % (NaCl, w/v)) and the optimal conditions for biodegradation were characterized as pH 7.0, 30°C and salinity 3.0 %. TPHP degradation and growth of RL-XB02 aligned with first-order decay (R2=0.998) and S-Logistic (R2=0.997) model, respectively. Additionally, biofilm formation during TPHP degradation might explain its efficient degradation of hydrophobic compounds. Furthermore, strain RL-XB02 degraded TPHP via enzyme-mediated processes, with intracellular enzymes likely crucial. The metabolites identification and genomic analysis revealed that TPHP was transformed into phenol via stepwise de-esterification, which was assimilated by dual catechol branches of the β-ketoadipate pathway to cell growth. The molecular mechanisms of phenol catabolism were confirmed by RT-qPCR. Bioaugmentation of strain RL-XB02 could eliminate TPHP from marine samples and alleviate the toxicity of TPHP to plants. These findings advance our understanding of TPHP biodegradation pathways and propose a sustainable bioremediation strategy for TPHP contamination.

Facultative anaerobic bacteria enable syntrophic fatty acids degradation under micro-aerobic conditions

Trace amounts of oxygen stimulate facultative anaerobic bacteria (FAB) within anaerobic bioreactors, which was shown to correlate with enhanced methane production from long-chain fatty acids. The relationship between FAB and fatty acid-degrading syntrophic communities under micro-aerobic conditions is still unclear. In this work, two syntrophic co-cultures, Syntrophomonas wolfei + Methanospirillum hungatei and Syntrophomonas zehnderi + Methanobacterium formicicum, were assembled and incubated with short, medium and long-chain fatty acids, with 0-10 % O2, in the presence and absence of FAB, here represented by Pseudomonas spp. Without Pseudomonas, the syntrophic activity was inhibited by 79 % at 0.5 % O2, but with Pseudomonas, the syntrophic co-cultures successfully converted the fatty acids to methane with up to 2 % O2. These findings underscore the pivotal role of FAB in the protection of syntrophic fatty acid-degrading communities under micro-aerobic conditions and emphasizes its significance in real-scale anaerobic digesters where strictly anaerobic conditions may not consistently be maintained.

A Japanese man with community-onset carbapenem-resistant Stutzerimonas nitrititolerans bacteremia and a sacral pressure ulcer: a case report

BACKGROUND

Stutzerimonas is a recently proposed genus comprising strains formerly classified as Pseudomonas stutzeri. The genus includes at least 16 identified species. Stutzerimonas nitrititolerans, previously known as Pseudomonas nitrititolerans, was initially isolated from a bioreactor. Only one case of human infection has been reported to date, and its pathogenicity remains unknown.

CASE PRESENTATION

We present a case of community-acquired S. nitrititolerans bacteremia in a 77-year-old Japanese man with a sacral pressure ulcer. On admission for cerebral infarction, empirical ampicillin/sulbactam was administered because of an infected sacral pressure ulcer. Blood cultures revealed Gram-negative bacilli. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry was unable to identify the species, but 16 S ribosomal RNA gene sequencing identified the isolate NR5426 as S. nitrititolerans. Despite negative results for common carbapenem-resistance genes, the strain showed possible metallo-beta-lactamase production. The patient was treated with piperacillin/tazobactam and recovered.

CONCLUSIONS

This case confirms that S. nitrititolerans can cause infection in humans and highlights the antimicrobial susceptibility profile and the treatment strategy for infections caused by this rare bacterium. Further studies are required to determine its resistance mechanisms and the clinical implications.

Integrated biological-chemical system for phenol removal from petrochemicals wastewater

Phenol is a highly concerning pollutant in petrochemical industrial wastewater. It is extremely poisonous, carcinogenic, and persistent, therefore, it bioaccumulates in the food chain reaching humans, where it causes acute irritation to the skin, eyes, and respiratory tract, as well as chronic effects on the liver, kidneys, and nervous system. It spills or leaks easily into surface water or groundwater sources, leading to the creation of other harmful substituted compounds. Therefore, the present study aimed to design an integrated biological-chemical system (phenol degrader(s) and nanoparticle assemblage) for the efficient removal of phenolic compounds from wastewater of a poly-vinyl chloride production unit at a petrochemical company in Alexandria. Ten indigenous microbial isolates were obtained from phenol-contaminated wastewater and purified. Two fungal isolates were excluded, and eight bacterial isolates were screened for their efficiency in the degradation and removal of phenol. Three isolates (Stutzerimonas chloritidismutans strain AW-1 (A2), Stutzerimonas stutzeri ATCC 17588 = LMG 11199 (A4), and Arthrobacter ruber strain MDB1-42 (A9)) proved to be the most promising candidate(s) and were investigated as individual and mixed cultures. The mixed culture (A2, A4, and A9) proved to be the most efficient, and could achieve 98.85, 31.08, 45.83, and 45.83% removal of phenol, chemical oxygen demand (COD), biochemical oxygen demand (BOD), and total dissolved solids (TDS), respectively (all below their maximum permissible limits (MPLs)), for discharge or reuse. The bacterial consortium was decorated with the synthesized and characterized Fe3O4 Nanoparticles (NPs) at 1:3 (g/g), the optimum ratio for coating and immobilization (94.22%) of the bacterial consortium. Fe3O4 NP/bacteria assembly (trial 1) showed the highest RE of 20, 56.66, 47.06, 25.16, and 96.78% for TDS, total suspended solids (TSS), BOD, COD, and phenol, respectively, all after only 1 h except TSS (2 h), compared to the treatment with undecorated bacterial consortium (trial 2) or bacteria-free Fe3O4 NPs (trial 3). It is concluded that the proposed treatment system (Fe3O4 NP/bacterial assembly) is an extraordinarily effective, practical, quick, clean, renewable, long-lasting, ecologically friendly, and simply implemented technology for remediating phenol-contaminated wastewater compared to other conventional treatment methods. Concerning TSS, COD, and phenol residues that are still higher than their MPLs, it can be easily overcome by increasing the exposure (contact) time or the dose of the Fe3O4 NP/bacterial assembly, using multiple units of the proposed treatment in sequence, or fixing the decorated bacteria as a biofilm system and treating the effluent in a continuous mode.

Genomic Insights into Stutzerimonas kunmingensis TFRC-KFRI-1 Isolated from Manila Clam (Ruditapes philippinarum): Functional and Phylogenetic Analysis

Stutzerimonas kunmingensis TFRC-KFRI-1, isolated from the gut of Manila Clam in the sediment of the West Sea of Korea, was investigated for its potential as a probiotic bacterium. This strain, belonging to the family Pseudomonadaceae, was previously classified as Pseudomonas kunmingensis but later reclassified to the genus Stutzerimonas, known for species with bioremediation and probiotic properties. To evaluate its genomic features and potential applications, we performed draft-genome sequencing and analysis. The genome of S. kunmingensis TFRC-KFRI-1 was assembled into a 4,756,396 bp sequence with a 62.8% GC content. Genomic analysis suggested potential genes for carbohydrate degradation and lactic acid production. The strain exhibited high average nucleotide identity (ANI) and 16S rRNA similarity with S. kunmingensis HL22-2T, further supporting its potential as a probiotic. This genome sequence provides valuable insights into the functional capabilities of S. kunmingensis TFRC-KFRI-1 and its potential applications in various industries, including aquaculture and food biotechnology. The genome sequence is available under GenBank accession number JBGJJB000000000.1, with related project information under BioProject PRJNA1147901 and Bio-Sample SAMN43173893.

Efficient enriching high-performance denitrifiers using bio-cathode of microbial fuel cells

Recent advancements in microbial fuel cells (MFC) technology have significantly contributed to the development of bio-cathode denitrification as a promising method for eco-friendly wastewater treatment. This study utilized an efficient repeated replacement method to enrich a mixed bio-cathode denitrifying culture (MBD) within a bio-cathode MFC, achieving a stable maximum output voltage of 120 ± 5 mV and a NO3 --N removal efficiency of 69.99 ± 0.60%. The electrotrophic denitrification process appears to be facilitated by electron shuttles. Microbial community analysis revealed a predominance of Proteobacteria, with Paracoccus and Pseudomonas as functional genera. Additionally, the isolated strain Lyy (belonging to Stutzerimonas) from MBD demonstrated exceptional denitrification efficiencies exceeding 98% when treating wastewater with a broad range of C/N (2-12) ratios and KNO3 concentrations (500-3000 mg/L) within 60 h. These results demonstrated the effectiveness of the repeated replacement method in enriching bio-cathode denitrifiers and advancing MFC application in sustainable wastewater management.

Genomic characteristics of antimicrobial resistance and virulence factors of carbapenem-resistant Stutzerimonas nitrititolerans isolated from the clinical specimen

BACKGROUND

Stutzerimonas nitrititolerans (S. nitrititolerans) is a rare human pathogenic bacterium and has been inadequately explored at the genomic level. Here, we report the first case of carbapenem-resistant S. nitrititolerans isolated from the peritoneal dialysis fluid of a patient with chronic renal failure. This study analyzed the genomic features, antimicrobial resistance, and virulence factors of the isolated strain through whole genome sequencing (WGS).

METHODS

The bacterial isolate from the peritoneal dialysis fluid was named PDI170223, and preliminary identification was conducted through Matrix-assisted laser desorption ionization/time of flight mass spectrometry (MALDI-TOF MS). WGS of the strain PDI170223 was performed using the Illumina platform, and a phylogenetic tree was constructed based on the 16S rRNA gene sequences. Antimicrobial susceptibility test (AST) was conducted using the TDR-200B2 automatic bacteria identification/drug sensitivity tester.

RESULTS

S. nitrititolerans may emerge as a human pathogen due to its numerous virulence genes, including those encoding toxins, and those involved in flagellum and biofilm formation. The AST results revealed that the strain is multidrug- and carbapenem-resistant. The antimicrobial resistance genes of S. nitrititolerans are complex and diverse, including efflux pump genes and β⁃lactam resistance genes.

CONCLUSION

The analysis of virulence factors and antimicrobial resistance of S. nitrititolerans provides clinical insight into the pathogenicity and potential risks of this bacterium. It is crucial to explore the mechanisms through which S. nitrititolerans causes diseases and maintains its antimicrobial resistance, thereby contributing to development of effective treatment and prevention strategies.

Pangenomic landscapes shape performances of a synthetic genetic circuit across Stutzerimonas species

Engineering identical genetic circuits into different species typically results in large differences in performance due to the unique cellular environmental context of each host, a phenomenon known as the "chassis-effect" or "context-dependency". A better understanding of how genomic and physiological contexts underpin the chassis-effect will improve biodesign strategies across diverse microorganisms. Here, we combined a pangenomic-based gene expression analysis with quantitative measurements of performance from an engineered genetic inverter device to uncover how genome structure and function relate to the observed chassis-effect across six closely related Stutzerimonas hosts. Our results reveal that genome architecture underpins divergent responses between our chosen non-model bacterial hosts to the engineered device. Specifically, differential expression of the core genome, gene clusters shared between all hosts, was found to be the main source of significant concordance to the observed differential genetic device performance, whereas specialty genes from respective accessory genomes were not significant. A data-driven investigation revealed that genes involved in denitrification and components of trans-membrane transporter proteins were among the most differentially expressed gene clusters between hosts in response to the genetic device. Our results show that the chassis-effect can be traced along differences among the most conserved genome-encoded functions and that these differences create a unique biodesign space among closely related species.IMPORTANCEContemporary synthetic biology endeavors often default to a handful of model organisms to host their engineered systems. Model organisms such as Escherichia coli serve as attractive hosts due to their tractability but do not necessarily provide the ideal environment to optimize performance. As more novel microbes are domesticated for use as biotechnology platforms, synthetic biologists are urged to explore the chassis-design space to optimize their systems and deliver on the promises of synthetic biology. The consequences of the chassis-effect will therefore only become more relevant as the field of biodesign grows. In our work, we demonstrate that the performance of a genetic device is highly dependent on the host environment it operates within, promoting the notion that the chassis can be considered a design variable to tune circuit function. Importantly, our results unveil that the chassis-effect can be traced along similarities in genome architecture, specifically the shared core genome. Our study advocates for the exploration of the chassis-design space and is a step forward to empowering synthetic biologists with knowledge for more efficient exploration of the chassis-design space to enable the next generation of broad-host-range synthetic biology.

Metapresence: a tool for accurate species detection in metagenomics based on the genome-wide distribution of mapping reads

Shotgun metagenomics allows comprehensive sampling of the genomic information of microbes in a given environment and is a tool of choice for studying complex microbial systems. Mapping sequencing reads against a set of reference or metagenome-assembled genomes is in principle a simple and powerful approach to define the species-level composition of the microbial community under investigation. However, despite the widespread use of this approach, there is no established way to properly interpret the alignment results, with arbitrary relative abundance thresholds being routinely used to discriminate between present and absent species. Such an approach can be affected by significant biases, especially in the identification of rare species. Therefore, it is important to develop new metrics to overcome these biases. Here, we present Metapresence, a new tool to perform reliable identification of the species in metagenomic samples based on the distribution of mapped reads on the reference genomes. The analysis is based on two metrics describing the breadth of coverage and the genomic distance between consecutive reads. We demonstrate the high precision and wide applicability of the tool using data from various synthetic communities, a real mock community, and the gut microbiome of healthy individuals and antibiotic-associated-diarrhea patients. Overall, our results suggest that the proposed approach has a robust performance in hard-to-analyze microbial communities containing contaminated or closely related genomes in low abundance.IMPORTANCEDespite the prevalent use of genome-centric alignment-based methods to characterize microbial community composition, there lacks a standardized approach for accurately identifying the species within a sample. Currently, arbitrary relative abundance thresholds are commonly employed for this purpose. However, due to the inherent complexity of genome structure and biases associated with genome-centric approaches, this practice tends to be imprecise. Notably, it introduces significant biases, particularly in the identification of rare species. The method presented here addresses these limitations and contributes significantly to overcoming inaccuracies in precisely defining community composition, especially when dealing with rare members.

Purines enrich root-associated Pseudomonas and improve wild soybean growth under salt stress

The root-associated microbiota plays an important role in the response to environmental stress. However, the underlying mechanisms controlling the interaction between salt-stressed plants and microbiota are poorly understood. Here, by focusing on a salt-tolerant plant wild soybean (Glycine soja), we demonstrate that highly conserved microbes dominated by Pseudomonas are enriched in the root and rhizosphere microbiota of salt-stressed plant. Two corresponding Pseudomonas isolates are confirmed to enhance the salt tolerance of wild soybean. Shotgun metagenomic and metatranscriptomic sequencing reveal that motility-associated genes, mainly chemotaxis and flagellar assembly, are significantly enriched and expressed in salt-treated samples. We further find that roots of salt stressed plants secreted purines, especially xanthine, which induce motility of the Pseudomonas isolates. Moreover, exogenous application for xanthine to non-stressed plants results in Pseudomonas enrichment, reproducing the microbiota shift in salt-stressed root. Finally, Pseudomonas mutant analysis shows that the motility related gene cheW is required for chemotaxis toward xanthine and for enhancing plant salt tolerance. Our study proposes that wild soybean recruits beneficial Pseudomonas species by exudating key metabolites (i.e., purine) against salt stress.

Genomic Insights into Cyanide Biodegradation in the Pseudomonas Genus

Molecular studies about cyanide biodegradation have been mainly focused on the hydrolytic pathways catalyzed by the cyanide dihydratase CynD or the nitrilase NitC. In some Pseudomonas strains, the assimilation of cyanide has been linked to NitC, such as the cyanotrophic model strain Pseudomonas pseudoalcaligenes CECT 5344, which has been recently reclassified as Pseudomonas oleovorans CECT 5344. In this work, a phylogenomic approach established a more precise taxonomic position of the strain CECT 5344 within the species P. oleovorans. Furthermore, a pan-genomic analysis of P. oleovorans and other species with cyanotrophic strains, such as P. fluorescens and P. monteilii, allowed for the comparison and identification of the cioAB and mqoAB genes involved in cyanide resistance, and the nitC and cynS genes required for the assimilation of cyanide or cyanate, respectively. While cyanide resistance genes presented a high frequency among the analyzed genomes, genes responsible for cyanide or cyanate assimilation were identified in a considerably lower proportion. According to the results obtained in this work, an in silico approach based on a comparative genomic approach can be considered as an agile strategy for the bioprospection of putative cyanotrophic bacteria and for the identification of new genes putatively involved in cyanide biodegradation.

Application of response surface Methodology coupled with Artificial Neural network and genetic algorithm to model and optimize symbiotic interactions between Chlorella vulgaris and Stutzerimonas stutzeri strain J3BG for chlorophyll accumulation

Research on microalgae has surged due to its diverse biotechnological applications and capacity for accumulating bioactive compounds. Despite considerable advancements, microalgal cultivation remains costly, prompting efforts to reduce expenses while enhancing productivity. This study proposes a cost-effective approach through the coculture of microalgae and bacteria, exploiting mutualistic interactions. An engineered consortium of Chlorella vulgaris and Stutzerimonas stutzeri strain J3BG demonstrated biofilm-like arrangements, indicative of direct cell-to-cell interactions and metabolite exchange. Strain J3BG's enzymatic characterization revealed amylase, lipase, and protease production, sustaining mutual growth. Employing Response Surface Methodology (RSM), Artificial Neural Network (ANN), and Genetic Algorithm (GA) in a hybrid modeling approach resulted in a 2.1-fold increase in chlorophyll production. Optimized conditions included a NaNO3 concentration of 128.52 mg/l, a 1:2 (Algae:Bacteria) ratio, a 6-day cultivation period, and a pH of 5.4, yielding 10.92 ± 0.88 mg/l chlorophyll concentration.

Identification of the aldolase responsible for the production of 22-hydroxy-23,24-bisnorchol-4-ene-3-one from natural sterols in Mycolicibacterium smegmatis

Mycobacterial mutants blocked in ring degradation constructed to achieve C19 synthons production, also accumulate by-products such as C22 intermediates throughout an alternative pathway reducing the production yields and complicating the downstream purification processing of final products. In this work, we have identified the MSMEG_6561 gene, encoding an aldolase responsible for the transformation of 22-hydroxy-3-oxo-cholest-4-ene-24-carboxyl-CoA (22-OH-BCN-CoA) into the 22-hydroxy-23,24-bisnorchol-4-ene-3-one (4-HBC) precursor (20S)-3-oxopregn-4-ene-20-carboxaldehyde (3-OPA). The deletion of this gene increases the production yield of the C-19 steroidal synthon 4-androstene-3,17-dione (AD) from natural sterols, avoiding the production of 4-HBC as by-product and the drawbacks in the AD purification. The molar yield of AD production using the MS6039-5941-6561 triple mutant strain was checked in flasks and bioreactor improving very significantly compared with the previously described MS6039-5941 strain.

Microbiological insight into various underground gas storages in Vienna Basin focusing on methanogenic Archaea

In recent years, there has been a growing interest in extending the potential of underground gas storage (UGS) facilities to hydrogen and carbon dioxide storage. However, this transition to hydrogen storage raises concerns regarding potential microbial reactions, which could convert hydrogen into methane. It is crucial to gain a comprehensive understanding of the microbial communities within any UGS facilities designated for hydrogen storage. In this study, underground water samples and water samples from surface technologies from 7 different UGS objects located in the Vienna Basin were studied using both molecular biology methods and cultivation methods. Results from 16S rRNA sequencing revealed that the proportion of archaea in the groundwater samples ranged from 20 to 58%, with methanogens being the predominant. Some water samples collected from surface technologies contained up to 87% of methanogens. Various species of methanogens were isolated from individual wells, including Methanobacterium sp., Methanocalculus sp., Methanolobus sp. or Methanosarcina sp. We also examined water samples for the presence of sulfate-reducing bacteria known to be involved in microbially induced corrosion and identified species of the genus Desulfovibrio in the samples. In the second part of our study, we contextualized our data by comparing it to available sequencing data from terrestrial subsurface environments worldwide. This allowed us to discern patterns and correlations between different types of underground samples based on environmental conditions. Our findings reveal presence of methanogens in all analyzed groups of underground samples, which suggests the possibility of unintended microbial hydrogen-to-methane conversion and the associated financial losses. Nevertheless, the prevalence of methanogens in our results also highlights the potential of the UGS environment, which can be effectively leveraged as a bioreactor for the conversion of hydrogen into methane, particularly in the context of Power-to-Methane technology.

Valid and accepted novel bacterial taxa derived from human clinical specimens and taxonomic revisions published in 2022

Although some nomenclature changes have caused consternation among clinical microbiologists, the discovery of novel taxa and improving classification of existing groups of organisms is exciting and adds to our understanding of microbial pathogenesis. In this mini-review, we present an in-depth summary of novel taxonomic designations and revisions to prokaryotic taxonomy that were published in 2022. Henceforth, these bacteriology taxonomic summaries will appear annually. Several of the novel Gram-positive organisms have been associated with disease, namely, the Corynebacterium kroppenstedtii-like organisms Corynebacterium parakroppenstedtii sp. nov. and Corynebacterium pseudokroppenstedtii sp. nov. A newly described Streptococcus species, Streptococcus toyakuensis sp. nov., is noteworthy for exhibiting multi-drug resistance. Among the novel Gram-negative pathogens, Vibrio paracholerae sp. nov. stands out as an organism associated with diarrhea and sepsis and has probably been co-circulating with pandemic Vibrio cholerae for decades. Many new anaerobic organisms have been described in this past year largely from genetic assessments of gastrointestinal microbiome collections. With respect to revised taxa, as discussed in previous reviews, the genus Bacillus continues to undergo further division into additional genera and reassignment of existing species into them. Reassignment of two subspecies of Fusobacterium nucleatum to species designations (Fusobacterium animalis sp. nov. and Fusobacterium vincentii sp. nov.) is also noteworthy. As was typical of previous reviews, literature updates for selected clinically relevant organisms discovered between 2017 and 2021 have been included.

Characterization and genomic analysis of Stutzerimonas stutzeri phage vB_PstS_ZQG1, representing a novel viral genus

Stutzerimonas stutzeri is an opportunistic pathogenic bacterium belonging to the Gammaproteobacteria, exhibiting wide distribution in the environment and playing significant ecological roles such as nitrogen fixation or pollutant degradation. Despite its ecological importance, only two S. stutzeri phages have been isolated to date. Here, a novel S. stutzeri phage, vB_PstS_ZQG1, was isolated from the surface seawater of Qingdao, China. Transmission electron microscopy analysis indicates that vB_PstS_ZQG1 has a morphology characterized by a long non-contractile tail. The genomic sequence of vB_PstS_ZQG1 contains a linear, double-strand 61,790-bp with the G+C content of 53.24% and encodes 90 putative open reading frames. Two auxiliary metabolic genes encoding TolA protein and nucleotide pyrophosphohydrolase were identified, which are likely involved in host adaptation and phage reproduction. Phylogenetic and comparative genomic analyses demonstrated that vB_PstS_ZQG1 exhibits low similarity with previously isolated phages or uncultured viruses (average nucleotide identity values range from 21.7 to 29.4), suggesting that it represents a novel viral genus by itself, here named as Fuevirus. Biogeographic analysis showed that vB_PstS_ZQG1 was only detected in epipelagic and mesopelagic zone with low abundance. In summary, our findings of the phage vB_PstS_ZQG1 will provide helpful insights for further research on the interactions between S. stutzeri phages and their hosts, and contribute to discovering unknown viral sequences in the metagenomic database.

The genome of Symbiodiniaceae-associated Stutzerimonas frequens CAM01 reveals a broad spectrum of antibiotic resistance genes indicating anthropogenic drift in the Palk Bay coral reef of south-eastern India

An increase in antibiotic pollution in reef areas will lead to the emergence of antibiotic-resistant bacteria, leading to ecological disturbances in the sensitive coral holobiont. This study provides insights into the genome of antibiotics-resistant Stutzerimonas frequens CAM01, isolated from Favites-associated Symbiodiniaceae of a near-shore polluted reef of Palk Bay, India. The draft genome contains 4.67 Mbp in size with 52 contigs. Further genome analysis revealed the presence of four antibiotic-resistant genes, namely, adeF, rsmA, APH (3")-Ib, and APH (6)-Id that provide resistance by encoding resistance-nodulation-cell division (RND) antibiotic efflux pump and aminoglycoside phosphotransferase. The isolate showed resistance against 73% of the antibiotics tested, concurrent with the predicted AMR genes. Four secondary metabolites, namely Aryl polyene, NRPS-independent-siderophore, terpenes, and ectoine were detected in the isolate, which may play a role in virulence and pathogenicity adaptation in microbes. This study provides key insights into the genome of Stutzerimonas frequens CAM01 and highlights the emergence of antibiotic-resistant bacteria in coral reef ecosystems.

Update of the list of qualified presumption of safety (QPS) recommended microbiological agents intentionally added to food or feed as notified to EFSA 18: Suitability of taxonomic units notified to EFSA until March 2023

The qualified presumption of safety (QPS) approach was developed to provide a regularly updated generic pre-evaluation of the safety of microorganisms, intended for use in the food or feed chains, to support the work of EFSA's Scientific Panels. The QPS approach is based on an assessment of published data for each agent, with respect to its taxonomic identity, the body of relevant knowledge and safety concerns. Safety concerns identified for a taxonomic unit (TU) are, where possible, confirmed at the species/strain or product level and reflected by 'qualifications'. In the period covered by this Statement, no new information was found that would change the status of previously recommended QPS TUs. Of 38 microorganisms notified to EFSA between October 2022 and March 2023 (inclusive) (28 as feed additives, 5 as food enzymes, food additives and flavourings, 5 as novel foods), 34 were not evaluated because: 8 were filamentous fungi, 4 were Enterococcus faecium and 2 were Escherichia coli (taxonomic units that are excluded from the QPS evaluation) and 20 were taxonomic units (TUs) that already have a QPS status. Three of the other four TUs notified within this period were evaluated for the first time for a possible QPS status: Anaerobutyricum soehngenii, Stutzerimonas stutzeri (former Pseudomonas stutzeri) and Nannochloropsis oculata. Microorganism strain DSM 11798 has also been notified in 2015 and as its taxonomic unit is notified as a strain not a species, it is not suitable for the QPS approach. A. soehngenii and N. oculata are not recommended for the QPS status due to a limited body of knowledge of its use in the food and feed chains. S. stutzeri is not recommended for inclusion in the QPS list based on safety concerns and limited information about the exposure of animals and humans through the food and feed chains.

Comparative genomics of Stutzerimonas balearica (Pseudomonas balearica): diversity, habitats, and biodegradation of aromatic compounds

Stutzerimonas balearica (Pseudomonas balearica) has been found principally in oil-polluted environments. The capability of S. balearica to thrive from the degradation of pollutant compounds makes it a species of interest for potential bioremediation applications. However, little has been reported about the diversity of S. balearica. In this study, genome sequences of S. balearica strains from different origins were analyzed, revealing that it is a diverse species with an open pan-genome that will continue revealing new genes and functionalities as the genomes of more strains are sequenced. The nucleotide signatures and intra- and inter-species variation of the 16S rRNA genes of S. balearica were reevaluated. A strategy of screening 16S rRNA gene sequences in public databases enabled the detection of 158 additional strains, of which only 23% were described as S. balearica. The species was detected from a wide range of environments, although mostly from aquatic and polluted environments, predominantly related to petroleum oil. Genomic and phenotypic analyses confirmed that S. balearica possesses varied inherent capabilities for aromatic compounds degradation. This study increases the knowledge of the biology and diversity of S. balearica and will serve as a basis for future work with the species.

Complete Genome Sequence of Stutzerimonas stutzeri Strain SOCE 002, a Marine Bacterium Isolated from the Surface Seawater of Dapeng Bay

We report the complete genome sequence of Stutzerimonas stutzeri strain SOCE 002, obtained from Illumina and Oxford Nanopore sequencing. The genome is 4.68 Mb long, with a GC content of 63.5%, and contains 4,334 protein-coding genes, 60 tRNAs, and 12 rRNAs. We expect that this complete genome sequence will provide a reference for both genomic and metabolic analyses of S. stutzeri.

Stutzerimonas decontaminans sp. nov. isolated from marine polluted sediments

Strains 19SMN4^T and ST27MN3 were isolated from marine sediments after enrichment with 2-methylnaphthalene and were classified as Pseudomonas stutzeri genomovar 4. Four other strains, BG 2, HT20, HT24, and A7, were isolated from sulphide-oxidizing bioreactors or activated sludge affiliated with the same clade in the 16S rRNA phylogenetic tree. P. stutzeri has been recently reclassified as a new genus, Stutzerimonas, and a preliminary analysis indicated that the strains in this study were distinct from any classified Stutzerimonas and are considered representatives of phylogenomic species 4 (pgs4). Strains 19SMN4^T and ST27MN3 were extensively characterized with phenotypic, chemotaxonomic, genomic and phylogenomic data. Strain 19SMN4^T had a well-characterized naphthalene degradative plasmid that has been compared with other plasmids, while in strain ST27MN3, the naphthalene degradative genes were detected in the chromosome sequence. Phylogenomic analysis of the core gene sequences showed that strains 19SMN4^T and ST27MN3 shared 3,995 genes and were closely related to members of the species "Stutzerimonas songnenensis" and Stutzerimonas perfectomarina, as well as to the Stutzerimonas phylogenomic species, pgs9, pgs16 and pgs24. The aggregate average nucleotide identity (ANI) indicated that strains 19SMN4^T and ST27MN3 belonged to the same genomic species, whereas the genomic indices with their closest-related type strains were below the accepted species threshold (95 %). We therefore conclude that strains 19SMN4^T and ST27MN3 represent a novel species of Stutzerimonas, for which the name Stutzerimonas decontaminans is proposed; the type strain is 19SMN4^T (=CCUG44593^T = DSM6084^T = LMG18521^T).

Isolation of Novel Bacterial Strains Pseudomonas extremaustralis CSW01 and Stutzerimonas stutzeri CSW02 from Sewage Sludge for Paracetamol Biodegradation

Paracetamol is one of the most used pharmaceuticals worldwide, but due to its widespread use it is detected in various environmental matrices, such as surface and ground waters, sediments, soils or even plants, where it is introduced mainly from the discharge of wastewater and the use of sewage sludge as fertilizer in agriculture. Its accumulation in certain organisms can induce reproductive, neurotoxic or endocrine disorders, being therefore considered an emerging pollutant. This study reports on the isolation, from sewage sludge produced in wastewater treatment plants (WWTPs), of bacterial strains capable of degrading paracetamol. Up to 17 bacterial strains were isolated, but only two of them, identified as Pseudomonas stutzeri CSW02 and Pseudomonas extremaustralis CSW01, were able to degrade very high concentrations of paracetamol in solution as a sole carbon and energy source, and none of them had been previously described as paracetamol degraders. These bacteria showed the ability to degrade up to 500 mg L^-1 of paracetamol in only 6 and 4 h, respectively, much quicker than any other paracetamol-degrader strain described in the literature. The two main paracetamol metabolites, 4-aminophenol and hydroquinone, which present high toxicity, were detected during the degradation process, although they disappeared very quickly for paracetamol concentrations up to 500 mg L^-1. The IC₅₀ of paracetamol for the growth of these two isolates was also calculated, indicating that P. extremaustralis CSW01 was more tolerant than S. stutzeri CSW02 to high concentrations of paracetamol and/or its metabolites in solution, and this is the reason for the much lower paracetamol degradation by S. stutzeri CSW02 at 2000-3000 mg L^-1. These findings indicate that both bacteria are very promising candidates for their use in paracetamol bioremediation in water and sewage sludge.