Rhodococcus sp. 24CO, isolated from the olive phyllosphere, can accumulate significant amounts of neutral lipids, making it a promising candidate for biomass production from olive pruning waste. The strain efficiently converts this residue to neutral lipids, achieving a yield of over 20% of the cellular dry weight (CDW). This indicates that olive leaves, a by-product of the olive oil industry, could become a valuable resource for both the economy and the environment. Genome analysis revealed various metabolic pathways for converting carbon sources to neutral lipids, while phenotypic studies showed that the strain is selective about its carbon sources, thriving on specific monosaccharides and polyols found in olive leaves. Notably, fructose and mannitol were rapidly metabolized, leading to a content of stored triacylglycerides of up to 47% and 28% of the CDW, respectively. The strain also exhibited oleagenicity under high nitrogen availability when grown on mannitol. Finally, potential oleagenicity determinants were explored through an omics comparison.

The genome of Hydrogenophaga taeniospiralis 2K1T, the type and only strain of the species, was analysed. The genes encoding elements involved in autotrophic and chemolithotrophic growth that oxidize H2 in addition to other metabolic traits, such as potential nitrogen fixation capability, are described. A phylogenomic analysis of the taxonomy of members of the genus reveals a high number of species not yet described in the genus, especially if the numerous metagenomes obtained from environmental samples are included. The differences from the closest related genera, Malikia and Serpentinimonas, are highlighted and the delineation of the genus Hydrogenophaga is discussed based on phylogenomic analysis. Furthermore, a survey of metagenomes available in public databases demonstrates the wide environmental and geographic distribution of Hydrogenophaga strains. H. taeniospiralis 2K1T is the first free-living bacterium described for its ability to synthesize R- bodies, which are intracytoplasmic extendable protein ribbons associated mainly with toxic effects. The genetic determinants of R-body synthesis are analysed and compared with those found in other Hydrogenophaga genomes and strains from other genera.

Hospitals can carry high levels of bacterial diversity from all types of origins, such as human skin, outside environment and medical equipment. Sink drains in clinical settings are considered reservoirs for pathogenic bacteria and potential sources of hospital-acquired infections (HAI’s) and antibiotic resistance genes (ARGs). Therefore, infection control measures are crucial to minimizing the risks associated with these reservoirs. Recent research has focused primarily on intensive care units (ICUs) and known pathogens, often employing metagenomic approaches that do not include bacterial isolation. This study aims to evaluate bacterial diversity using culturomics, extending the investigation beyond the ICU to identify antibiotic-resistant bacteria. A total of four samplings were conducted over 1 year (March 2022 to March 2023) in five different hospital wards [ICU, General Medicine (GM), Hematology (H), Short stay unit (UCE), and Microbiology laboratory (MS)]. All samples were cultured on selective and non-selective culture media, resulting in 1,058 isolates identified using MALDI-TOF MS, with a subset confirmed through 16S rRNA gene sequencing. Isolates retrieved from antibiotic supplemented agar were subjected to antibiotic susceptibility testing. The highest bacterial diversity, as measured by the Shannon index, was observed in the ICU and GM wards, posing significant risks to patients in these areas. While bacterial genera were largely similar across wards and sampling times, with Pseudomonas and Stenotrophomonas being the most prevalent, different species were detected in each sampling, indicating no loss of diversity. This suggests that these environments undergo dynamic changes over time, influenced by their surroundings. The results also indicate a relationship between human activity and drain usage and the presence of Pseudomonas aeruginosa, the most commonly found species across most wards. Antibiotic susceptibility testing revealed that all tested isolates, except for one, were multi-resistant, including clinically relevant species, such as P. aeruginosa and K. pneumoniae. Hospital drains may serve as reservoirs for both known and emerging pathogens exhibiting high antibiotic resistance phenotypes. Their dynamic nature may provide insights into strategies for preventing the colonization of these environments by such species.

Streptococcus pneumoniae (pneumococcus) is a prominent cause of bacterial pneumonia, meningitis, and septicemia, causing high morbidity and high mortality, particularly in children and the elderly. In this study, proteomics- and genomics-based approaches were used for the identification of pneumococcal protein and peptide biomarkers of S. pneumoniae for diagnostics and prospective targets for treatment. Through a pan-genome analysis, 11 S. pneumoniae strains, demonstrating genetic variation within the species, were selected for proteomic characterization. Mass spectrometry-based proteomics, in combination with bacterial surface-shaving, were used to study the cell-surface proteome of S. pneumoniae. The data obtained from three biological replicates per strain were analyzed to identify and rank the proteins and peptides according to their presence in the strains, as well as their presence in all available S. pneumoniae proteomes (8,892) archived in public databases. Several highly ranked proteins have been described as “species-specific” for S. pneumoniae and as surface-associated virulence factors or demonstrate highly antigenic properties. Proteins (34) previously not recognized as S. pneumoniae-specific were proposed to be novel biomarkers, demonstrating high degrees of prevalence in all analyzed proteomes, with little or no sequence similarities to closely related species but common among the genetically diverse strains included in this study.

In 2021, grapevines (Vitis vinifera L.) cv. Callet growing in a commercial vineyard located at Pollença (northeast of the island of Majorca, Spain) showed severe symptoms of shoot blight during spring and early summer, with an incidence of 70%. Symptoms consisted of elongated cankered-like lesions, surrounded by water-soaked darker tissues, that developed at the base or around the middle nodes of the shoot. For fungal isolation, shoot samples with lesions were collected, surface disinfected with 2% NaCl for 90s, rinsed twice with deionized water and placed in Petri plates containing potato dextrose agar (PDA). The plates were incubated at 25°C under 12 h light-darkness for 6 days. Isolations consistently yielded on kind of fungal colonies that produced white mycelium and black spherical to elongated sclerotia (2 to 10 mm in diameter). Morphological characterization was consistent with the description of Sclerotinia sclerotiorum (Lib.) de Bary (Bolton et al. 2006). Three isolates (UIB 118-1, UIB 118-26, and UIB 129-41) were preserved and deposited in the Culture Collection of Microbiology-Faculty of Sciences, University of Balearic Islands, Spain. Genomic DNA was extracted from isolates UIB 118-26 and UIB 129-41 using the EZNA Miniprep Kit (Omega Bio-Tek, Norcross, GA). The internal transcribed spacer (ITS) region of ribosomal DNA, β-tubulin (BTUB) and calmodulin (CAL) gene regions were amplified using ITS1F-ITS4 (Gardes and Bruns, 1996; White et al. 1990), Bt-2a/Bt-2b (Glass and Donaldson 1995) and CAL228F/CAL737R (Carbone and Kohn 1999) primer sets, respectively. Amplicons were sequenced and deposited in GenBank with accession numbers MZ604647 and MZ604648 for ITS, OK634402 and OK634403 for BTUB and OK634404 and OK634405 for CAL. BLASTn search showed that isolates were >99 % (ITS, BTUB and CAL) identical to S. sclerotiorum GenBank accession no. KF859933, CP017815 and KF871381, respectively. Pathogenicity tests were conducted using eight one-year old grapevines cv. Cabernet Sauvignon. Old and new green shoots were inoculated by inserting a 6-mm plug of mycelium taken from actively growing cultures on PDA into cuts made at the base and at the distal part of each shoot with a sterile scalpel with a total of eight inoculation points per plant. Inoculated wounds were sealed with Parafilm tape to avoid rapid dehydration. Inoculated plants and an equal number of wounded but non-inoculated plants (negative controls) were maintained at 25 ± 1°C for 48 h in plastic containers to ensure a high relative humidity (>90%). After 5 days, the infection girdled and rotted the green new shoots, whereas the older partially lignified shoots developed a localized long brown lesion that reached 16 cm in length. Due to the rotting of the basal part of the petiole, leaves turned gray, wilted, and died, easily detaching from the stem. In advanced stages of the disease, 7 days after infection, branches died and fell with the leaves remained attached (Fig 1 A, B). Reisolations from diseased shoots were successfully performed on PDA to fulfill Koch's postulates. S. slerotiorum was previously reported on grapevine causing shoot blight in Chile (Latorre and Guerrero, 2001), Korea (Jong-Han et al. 2009), California-USA (Boland and Hall, 1994) and Australia (Hall et al. 2002). AlsoS. sclerotiorum was reported among the endophytic mycobiota associated with Vitis vinifera in the Iberian Peninsula (Gonzalez and Tello, 2011) but not as a pathogen causing visible symptoms on that crop. So, this is the first report of the occurrence of S. slerotiorum as a pathogen of grapevines in Spain causing symptoms of canker and shoot blight. This finding highlights a potential risk of this fungal disease for the wine industry in the Mediterranean region and specially for Spain, the country with the largest acreage devoted to grapevines. Although chemical and biological are suitable control strategies, disease management is difficult as sclerotia of Sclerotinia can remain in the soil for up to eight years (Adams and Ayears, 1979), and preventive surveys are greatly recommended as an important epidemiological tool to monitor the epidemiology of disease and identify potential outbreaks of this new pathogen on grapevine in Spain.

Pseudomonas species constitute a significant group of pathogens in aquarium fish and frequently cause haemorrhagic septicaemia. This study conducted a taxonomic characterization of Pseudomonas isolates from aquarium fish exhibiting deep ulceration and general disease signs. A polyphasic approach was employed to ascertain the taxonomic affiliation of the strains. The overall genome relatedness indices of digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) between the strains and the other members of the genus Pseudomonas were found to be below the established thresholds of 70 and 95-96%, respectively. Whole-genome based phylogenetic analysis revealed that strains 119P(T) and 120P were closely related to P. arcuscaelestis. Strain 137P(T) was related to P. peradeniyensis, while strains 147P(T) and 148P were closely related to P. japonica. The morphological, physiological, and biochemical characteristics of the strains and the genome relatedness indices of dDDH and ANI below the established thresholds confirmed the classification of the strains as three novel species. Genome analyses of the strains were also conducted to determine their biosynthesis-related gene clusters, virulence features and ecological distribution patterns. Based on polyphasic characterization, the strains 119P(T), 120P, 137P(T), 147P(T), and 148P are novel species within the genus Pseudomonas, for which the following names are proposed: Pseudomonas auratipiscis sp. nov., with the strain 119P(T) as the type strain (=DSM 117162 (T), =LMG 33381(T)); Pseudomonas carassii sp. nov., with the strain 137P(T) as the type strain (=DSM 117060(T), =LMG 33378(T)); and Pseudomonas ulcerans sp. nov. 147P(T), as the type strain (=DSM 117163(T), =LMG 33377(T)).

Species in the phylogenetic group Pseudomonas syringae are considered the most relevant plant pathogenic bacteria, but their taxonomy is still controversial. Twenty named species are validated in the current taxonomy of this group and in recent years many strains have been genome-sequenced, putative new species have been proposed and an update in the taxonomy is needed. A taxonomic study based on the core-genome phylogeny, genomic indices (ANI and GGDC) and gene content (phyletic pattern and Jaccard index) have been applied to clarify the taxonomy of the group. A phylogenomic analysis demonstrates that at least 50 phylogenomic species can be delineated within the group and that many strains whose genomes have been deposited in the databases are not correctly classified at the species level. Other species names, like “Pseudomonas coronafaciens”, have been proposed but are not validated yet. One of the putative new species is taxonomically described, and the name Pseudomonas maioricensis sp. nov. is proposed. The taxonomies of Pseudomonas avellanae and Pseudomonas viridiflava are discussed in detail as case studies. Correct strain identification is a prerequisite for many studies, and therefore, criteria are given to facilitate identification.

The Pseudomonas chlororaphis phylogenetic subgroup of species, within the Pseudomonas fluorescens group, currently includes seven bacterial species, all of which have environmental relevance. Phylogenomic analyses help clarify the taxonomy of strains in the group and allow for precise identification. Thirteen antibiotic-resistant strains isolated in a previous study from nine different sampling sites in the Danube River were suspected to represent a novel species and are investigated taxonomically in the present study, together with four other strains isolated from the Woluwe River (Belgium) that were phylogenetically closely related in their rpoD gene sequences. The strains were characterized phenotypically, chemotaxonomically (fatty acid composition and main protein profiles), and phylogenetically. They could not be assigned to any known Pseudomonas species. Three genomes of representative strains were sequenced and analyzed in the context of the genome sequences of closely related strains available in public databases. The phylogenomic analysis demonstrates the need to differentiate new genomic species within the P. chlororaphis subgroup and that Pseudomonas piscis and Pseudomonas aestus are synonyms. This taxonomic study demonstrates that 14 of the characterized isolates are members of the Pseudomonas_E protegens_A species in the GTDB taxonomy and that they represent a novel species in the genus Pseudomonas, for which we propose the name Pseudomonas danubii sp. nov. with strain JDS02PS016T (=CECT 30214T = CCUG 74756T) as the type strain. The other three strains (JDS08PS003, rDWA16, and rDWA64) are members of the species Pseudomonas_E protegens_B in the GTDB taxonomy and need further investigation for proposal as a new bacterial species.

Strains 19SMN4T 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 19SMN4T and ST27MN3 were extensively characterized with phenotypic, chemotaxonomic, genomic and phylogenomic data. Strain 19SMN4T 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 19SMN4T 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 19SMN4T 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 19SMN4T and ST27MN3 represent a novel species of Stutzerimonas, for which the name Stutzerimonas decontaminans is proposed; the type strain is 19SMN4T (=CCUG44593T = DSM6084T = LMG18521T).

The Klebsiella pneumoniae complex is comprised of ubiquitous bacteria that can be found in soils, plants or water, and as humans’ opportunistic pathogens. This study aimed at inferring common and distinctive features in clinical and environmental K. pneumoniae. Whole genome sequences of members of the K. pneumoniae complex (including K. variicola, n = 6; and K. quasipneumoniae, n = 7), of clinical (n = 78) and environmental (n = 61) origin from 21 countries were accessed from the GenBank. These genomes were compared based on phylogeny, pangenome and selected clinically relevant traits. Phylogenetic analysis based on 2704 genes of the core genome showed close relatedness between clinical and environmental strains, in agreement with the multi-locus sequence typing. Eight out of the 62 sequence types (STs) identified, included both clinical and environmental genomes (ST11, ST14, ST15, ST37, ST45, ST147, ST348, ST437). Pangenome-wide association studies did not evidence significant differences between clinical and environmental genomes. However, the genomes of clinical isolates presented significantly more exclusive genes related to antibiotic resistance/plasmids, while the environmental isolates yielded significantly higher allelic diversity of genes related with functions such as efflux or oxidative stress. The study suggests that K. pneumoniae can circulate among the natural environment and clinical settings, probably under distinct adaptation pressures.

Background Klebsiella pneumoniae are ubiquitous bacteria and recognized multidrug-resistant opportunistic pathogens that can be released into the environment, mainly through sewage, where they can survive even after wastewater treatment. A major question is if once released into wastewater, the selection of lineages missing clinically-relevant traits may occur. Wastewater ( n = 25) and clinical ( n = 34) 3 rd generation cephalosporin-resistant K. pneumoniae isolates were compared based on phenotypic, genotypic and genomic analyses. Results Clinical and wastewater isolates were indistinguishable based on phenotypic and genotypic characterization. The analysis of whole genome sequences of 22 isolates showed that antibiotic and metal resistance or virulence genes, were associated with mobile genetic elements, mostly transposons, insertion sequences or integrative and conjugative elements. These features were variable among isolates, according to the respective genetic lineage rather than the origin. Conclusions It is suggested that once acquired, clinically relevant features of K. pneumoniae may be preserved in wastewater, even after treatment. This evidence highlights the high capacity of K. pneumoniae for spreading through wastewater, enhancing the risks of transmission back to humans.

Stutzerimonas is a recently proposed genus within the Pseudomonadaceae comprising strains in the formerly phylogenetic group of Pseudomonas stutzeri. At least sixteen named species have to be included in the genus, together with 22 genomovars of Stutzerimonas stutzeri. To clarify the taxonomy of Stutzerimonas, a core-genome phylogeny of 200 strains in the genus was inferred and monophyletic strains with average nucleotide identities (ANIb) with values equal to or higher than 95 were grouped in the same phylogenomic species. A total of 45 phylogenomic species within the genus Stutzerimonas were detected in the present study. Sixteen phylogenomic species correspond to already named species, although three of them are not yet validated and two are proposed in the present study. A synonymy was detected between P. kunmingensis and S. chloritidismutans, both members of phylogenomic species 3, with a prevalence of the S. chloritidismutans name. The correspondence of the phylogenomic species to the genome taxonomy database classification (GTDB taxonomy) is discussed. Combining phylogenomic and phenotypic data, two novel species are described (Stutzerimonas frequens and Stutzerimonas degradans) and two species descriptions are emended (Stutzerimonas perfectomarina and Stutzerimonas chloritidismutans).

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The isolation of Pseudomonas haemolytica from different habitats as well as its distribution over a wide geographical area, possible reservoir role for antibiotic resistance and zoonotic potential, all require the detailed characterization of P. haemolytica strains. In the present study, we describe 18 phenotypically similar strains isolated from the rainbow trout, Oncorhynchus mykiss (Walbaum, 1792). The strains were collected from seemingly healthy, symptomatic or moribund rainbow trout of all sizes, from fry to broodstock. The strains were morphologically, phenotypically (API20 NE and VITEK 2) and chemotaxonomically characterized by their methyl-fatty acid content (FAME), and mass spectrometry (MALDI-TOF) by their protein profiles. The 16S rRNA sequence similarity values grouped them into the Pseudomonas fluorescens phylogenetic group of species. The 18 strains were compared to 6 other previously described P. haemolytica strains, 2 of which were isolated from milk products and 4 from chicken products. A multilocus sequence analysis was performed for all strains. Strain P45 was selected to represent the 18 new isolates for genomic comparisons by ANIb, and GGDC was used to confirm the identification at species level. The presence of genes related to antimicrobial resistance, secretion systems and virulence was also assessed using comparative genomic analyses. This is the first comprehensive report on P. haemolytica strains isolated from fish.

Cells of strains P66T, V1 and W15Feb18 are Gram-stain-negative short rods and motile by one polar flagellum. Strain P66T was isolated from rainbow trout (Oncorhynchus mykiss) cultivated at a fish farm in Turkey. Strain V1 was isolated from sand of an intertidal shore on the Galicia coast in Spain and strain W15Feb18 was isolated from water collected at the Woluwe River in Belgium. Based on 16S rRNA sequence similarity values, the strains were grouped under the genus Pseudomonas and the Pseudomonas putida phylogenetic group of species. The DNA G+C content ranged from 58.5 to 58.9 mol%. The strains were characterized phenotypically by the API 20NE and Biolog GEN III tests, and chemotaxonomically by their whole-cell MALDI-TOF MS protein profiles and fatty acid contents. The absence of the hydrolysis of gelatin and the assimilation of arabinose, mannose and mannitol differentiated these strains from the closest species, Pseudomonas alkylphenolica. The major fatty acid components were C16:0 (29.91-31.68 %) and summed feature 3 (36.44-37.55 %). Multilocus sequence analysis with four and 83 housekeeping gene sequences and a core proteome analysis showed that these strains formed a phylogenetic cluster in the P. putida group of species. Genome comparisons by the average nucleotide identity based on blast and the Genome-to-Genome Distance Calculator demonstrated that the three strains belonged to the same genomic species and were distant from any known species, with similarity values lower than the thresholds established for species in the genus Pseudomonas. These data permitted us to conclude that strains P66T, V1 and W15Feb18 belong to a novel species in the genus Pseudomonas, for which the name Pseudomonas arcuscaelestis sp. nov. is proposed. The type strain is P66T (=CECT 30176T=CCUG 74872T). The other strains have been deposited in the CECT with the corresponding collection numbers: V1 (=CECT 30356) and W15Feb18 (=CECT 30355).

Pseudomonas is one the best studied bacterial genera, and it is the genus with the highest number of species among the gram-negative bacteria. Pseudomonas spp. are widely distributed and play relevant ecological roles; several species are commensal or pathogenic to humans, animals and plants. The main aim of the present minireview is the discussion of how the Pseudomonas taxonomy has evolved with the development of bacterial taxonomy since the first description of the genus in 1894. We discuss how the successive implementation of novel methodologies has influenced the taxonomy of the genus and, vice versa, how the taxonomic studies developed in Pseudomonas have introduced novel tools and concepts to bacterial taxonomy. Current phylogenomic analyses of the family Pseudomonadaceae demonstrate that a considerable number of named Pseudomonas spp. are not monophyletic with P. aeruginosa, the type species of the genus, and that a reorganization of several genera can be foreseen. Phylogenomics of Pseudomonas, Azomonas and Azotobacter within the Pseudomonadaceae is presented as a case study. Five new genus names are delineated to accommodate five well-defined phylogenetic branches that are supported by the shared genes in each group, and two of them can be differentiated by physiological and ecological properties: the recently described genus Halopseudomonas and the genus Stutzerimonas proposed in the present study. Five former Pseudomonas species are transferred to Halopseudomonas and 10 species to Stutzerimonas.

In a study carried out between 2013 and 2018 in fish farms in Turkey, several putative novel species were isolated. The 16S rRNA nucleotide sequences of fourteen strains of Gram-negative rods, which were isolated from asymptomatic and symptomatic rainbow trouts (Onchorhynchus mykiss), placed them under the genus Pseudomonas. The similarity values of the concatenated nucleotide sequences of the rpoD, rpoB, gyrB and 16S rRNA genes clustered these isolates into the P. fluorescens phylogenetic group of species and into the Pseudomonas koreensis subgroup, close to Pseudomonas helmanticensis and Pseudomonas baetica. An isolate of a totally different origin, strain CCUG 67011, clustered with these isolates. Phenotypic characterization, together with the chemotaxonomic data, whole-cell MALDI-TOF MS and fatty acids methyl esters analyses were performed. The DNA G + C content was 58.7 mol% for isolate P9T and 58.8 mol% for isolate P42T. The phylogenomic analysis and whole genome nucleotide sequences of four of these isolates confirmed that the isolates P9T, P25 and P141, represent a novel species for which the name Pseudomonas anatoliensis sp. nov. is proposed, with P9T as the type strain (=CCUG 74755T = CECT 3172T). The isolates P1, P2, P10, P27, P30, P24a, P42T, P117, P139, P152 and CCUG 67011 represent another novel sècies, for which the name Pseudomonas iridis sp. nov. is proposed, with P42T as the type strain (=CCUG 74870T = CECT 3174T).

EFSA Supporting PublicationsVolume 18, Issue 10 6925E External scientific reportOpen Access Collection of data and information in Balearic Islands on biology of vectors and potential vectors of Xylella fastidiosa (GP/EFSA/ALPHA/017/01) J. López-Mercadal, Corresponding Author J. López-Mercadal ALPHA@efsa.europa.eu Applied Zoology and Animal Conservation Research Group. University of the Balearic Islands, Spain Correspondence:ALPHA@efsa.europa.euSearch for more papers by this authorS. Delgado, S. Delgado Applied Zoology and Animal Conservation Research Group. University of the Balearic Islands, SpainSearch for more papers by this authorP. Mercadal, P. Mercadal Applied Zoology and Animal Conservation Research Group. University of the Balearic Islands, SpainSearch for more papers by this authorG. Seguí, G. Seguí Microbiology (Biology Department). University of the Balearic Islands, SpainSearch for more papers by this authorJ. Lalucat, J. Lalucat Microbiology (Biology Department). University of the Balearic Islands, SpainSearch for more papers by this authorA. Busquets, A. Busquets Microbiology (Biology Department). University of the Balearic Islands, SpainSearch for more papers by this authorM. Gomila, M. Gomila Microbiology (Biology Department). University of the Balearic Islands, SpainSearch for more papers by this authorK. Lester, K. Lester Diagnostics, Wildlife & Molecular Biology. Science and Advice for Scottish Agriculture, ScotlandSearch for more papers by this authorD.M. Kenyon, D.M. Kenyon Diagnostics, Wildlife & Molecular Biology. Science and Advice for Scottish Agriculture, ScotlandSearch for more papers by this authorM. Ruiz-Pérez, M. Ruiz-Pérez GIS & Remote Sensing Service. University of the Balearic IslandsSearch for more papers by this authorC. Paredes-Esquivel, C. Paredes-Esquivel Applied Zoology and Animal Conservation Research Group. University of the Balearic Islands, SpainSearch for more papers by this authorM. A. Miranda, M. A. Miranda Applied Zoology and Animal Conservation Research Group. University of the Balearic Islands, SpainSearch for more papers by this author J. López-Mercadal, Corresponding Author J. López-Mercadal ALPHA@efsa.europa.eu Applied Zoology and Animal Conservation Research Group. University of the Balearic Islands, Spain Correspondence:ALPHA@efsa.europa.euSearch for more papers by this authorS. Delgado, S. Delgado Applied Zoology and Animal Conservation Research Group. University of the Balearic Islands, SpainSearch for more papers by this authorP. Mercadal, P. Mercadal Applied Zoology and Animal Conservation Research Group. University of the Balearic Islands, SpainSearch for more papers by this authorG. Seguí, G. Seguí Microbiology (Biology Department). University of the Balearic Islands, SpainSearch for more papers by this authorJ. Lalucat, J. Lalucat Microbiology (Biology Department). University of the Balearic Islands, SpainSearch for more papers by this authorA. Busquets, A. Busquets Microbiology (Biology Department). University of the Balearic Islands, SpainSearch for more papers by this authorM. Gomila, M. Gomila Microbiology (Biology Department). University of the Balearic Islands, SpainSearch for more papers by this authorK. Lester, K. Lester Diagnostics, Wildlife & Molecular Biology. Science and Advice for Scottish Agriculture, ScotlandSearch for more papers by this authorD.M. Kenyon, D.M. Kenyon Diagnostics, Wildlife & Molecular Biology. Science and Advice for Scottish Agriculture, ScotlandSearch for more papers by this authorM. Ruiz-Pérez, M. Ruiz-Pérez GIS & Remote Sensing Service. University of the Balearic IslandsSearch for more papers by this authorC. Paredes-Esquivel, C. Paredes-Esquivel Applied Zoology and Animal Conservation Research Group. University of the Balearic Islands, SpainSearch for more papers by this authorM. A. Miranda, M. A. Miranda Applied Zoology and Animal Conservation Research Group. University of the Balearic Islands, SpainSearch for more papers by this author First published: 25 October 2021 https://doi.org/10.2903/sp.efsa.2021.EN-6925 Question number: EFSA-Q-2021-00581 Disclaimer: The present document has been produced and adopted by the bodies identified above as author(s). In accordance with Article 36 of Regulation (EC) No 178/2002 this task has been carried out exclusively by the author(s) in the context of a grant agreement between the European Food Safety Authority and the author(s). The present document is published complying with the transparency principle to which the Authority is subject. It cannot be considered as an output adopted by the Authority. The European Food Safety Authority reserves its rights view and position as regards the issues addressed and the conclusions reached in the present document without prejudice to the rights of the authors. AboutPDF ToolsExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onFacebookTwitterLinked InRedditWechat Abstract The pathogenic bacteria Xylella fastidiosa (Proteobacteria: Xanthomonadaceae) was detected in the Balearic Islands in October 2016. In November 2017 EFSA granted the data collection on the biology of vectors in the Balearic Islands. The grant included the following objectives: i) Data collection in the Balearic Islands by macrocosm and microcosm observations of the vectors in the major agroecosystems; ii) Proposal on field sampling protocols of vectors; iii) Identification of the major vectors of X. fastidiosa in the Balearic Islands. For the study of macrocosm, samplings were conducted in Majorca, Ibiza, Formentera and Minorca. For the microcosm study, cages containing one male and one female of P. spumarius and one plant per cage were placed at semi-field conditions. For the development of the guidelines, literature research was conducted. For the vector competence experiments, field collected insects were caged with X. fastidiosa free plants of Medicago sativa. From the macrocosm results, two Aphrophoridae (Hemiptera; Cicadomorpha) species of vectors have been detected in the Balearic Islands, Philaenus spumarius and Neophilaenus campestris. Nymphs of Aphrophoridae were more abundant from early March to the end of May in the cover vegetation of olive crops, followed by vineyard and almond ones. Adults of Aphrophoridae were more abundant in the cover vegetation from May to June and from October to November, in the tree canopy from June to August and in the border vegetation from August to October. The microcosm trials showed that P. spumarius and N. campestris were able to develop in Lavandula dentata, Rosmarinus officinalis, Menta x piperita, Pistacia lentiscus and Ocinum basilicum. The average prevalence of X. fastidiosa from vectors collected from 2017 to 2020 was 23 %. Adults of P. spumarius and N. campestris collected from infected areas of Majorca successfully transmitted X. fastidiosa to uninfected plants of M. sativa. Supporting Information Filename Description efs36925e-sup-0001-SupInfo.xlsxapplication/excel, 3.2 MB Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article. Volume18, Issue10October 20216925E This article also appears in:Xylella fastidiosa ReferencesRelatedInformation

Caves are extreme underground environments colonized by oligotrophic bacterial communities that influence mineral transformations. The identification at the species level is important and this study aims to the taxonomic characterisation of four bacterial strains previously isolated from rock surfaces and water samples from a karstic cave located on Mallorca (Spain) that were assigned to the genus Pseudomonas according to 16S rRNA nucleotide sequence analysis. Sequence analysis of the RNA polymerase sigma factor gene (rpoD) allocated these strains to the P. fluorescens lineage within the P. anguilliseptica phylogenetic group, close to the P. benzenivorans type strain. A polyphasic taxonomic approach included phenotypic characterization, fatty acid composition analysis, and whole-cell protein profiling, together with phylogenomic data. The results supported the proposal of a new species in the Pseudomonas genus. Characteristic fatty acid methyl esters of members of the Pseudomonas genus were present (C16:0, C10:0 3-OH, C12:0 2-OH and C12:0 3-OH) and the C12:1 3OH content differentiated these strains from P. benzenivorans. The genomic G + C mol% content of the four sequenced genomes was 66.9%. The average nucleotide indices based on BLAST analysis and the calculation of genome-to-genome distance with respect to their closest relative were lower than 88% and 30%, respectively. These data confirm that the four isolates, R1b-4, R1b-52A, A2bC-1 and R1b-54T, represent a new species, for which the name Pseudomonas lalucatii is proposed, with strain R1b-54T as the type strain (=CCUG 74754T = CECT 30179T). This is the first species in the P. anguilliseptica group isolated from this extreme habitat.

Six Gram negative, motile bacteria were isolated from rainbow trout (Oncorhynchus mykiss). The 16S rRNA sequence similarity values grouped them in the Pseudomonas mandelii (strains P49, P50T, 154aT and P154b), Pseudomonas fluorescens (strain P115T) and Pseudomonas koreensis (strain P155T) phylogenetic subgroups in the genus Pseudomonas. The DNA G+C content ranged from 58.5 to 60 mol%. The strains were characterized phenotypically using API 20NE and Biolog GENIII tests, and chemotaxonomically by their whole-cell MALDI-TOF MS protein profiles and fatty acid contents. Multi-locus sequence analysis with four housekeeping gene sequences (rpoD, rpoB, gyrB and 16S rRNA) together with genome comparisons by average nucleotide identity and genome-to-genome distance calculations were performed. Results showed that the similarity values of these strains to known species type strains were lower than the thresholds established for species in the genus Pseudomonas. Based on these data, we concluded that strains P49, P50T, P115T, P154aT, P154b and P155T belonged to four novel species. The names proposed are: Pseudomonas piscium sp. nov. for strains P49 and P50T with P50T (=CECT 30175T=CCUG 74871T) as the type strain; Pseudomonas pisciculturae sp. nov. for strain P115T (CECT 30173T=CCUG 74873T); Pseudomonas mucoides sp. nov. for strains P154aT and P154b with P154aT (=CECT 30177T=CCUG 74874T) as the type strain; and Pseudomonas neuropathica sp. nov. for strain P155T (=CECT 30178T=CCUG 74875T).