Biology subjects

Dettman, J.

Publications and source records attributed to Dettman, J..

5 recordsLinked to original sources

bioRxiv2024

Analyses of transposable elements in arbuscular mycorrhizal fungi support evolutionary parallels with fungal plant pathogens

Transposable elements (TEs) are repetitive DNA sequences that excise or create copies that are inserted elsewhere in the genome. Their expansion shapes genome variability and evolution by impacting gene expression and rearrangement rates. Arbuscular mycorrhizal fungi (AMF) are beneficial plant symbionts with large, TE-rich genomes, and recent findings showed these elements vary significantly in abundance, evolution, and regulation among model AMF strains. Here, we aimed to obtain a more comprehensive understanding of TE function and evolution in AMF by investigating assembled genomes from representatives of all known families. We uncovered multiple, family-specific bursts of insertions in different species, indicating variable past and ongoing TE activity contributing to the diversification of AMF lineages. We also found that TEs are preferentially located within and around candidate effectors/secreted proteins, as well as in proximity to promoters. Altogether, these findings support the role of TEs in promoting the diversity in proteins involved in molecular dialogues with hosts and, more generally, in driving gene regulation. The mechanisms of TEs evolution we observed in these prominent plant symbionts bear striking similarities to those of many filamentous plant pathogens.

genomics↗

bioRxiv2024

Lipidomics and colistin resistance in non-human isolates of Acinetobacter seifertii

Acinetobacter baumannii is most well known for its role as a human pathogen and as a member of the Acinetobacter calcoaceticus-baumannii (ACB) complex. However, lesser characterised members of the ACB complex, have also been implicated in hospital-acquired infections. Once mainly considered opportunistic pathogens, many A. baumannii and non-baumannii strains are being isolated from agricultural, water and food sources. The surveillance and tracking of Acinetobacter spp. have been recently suggested to be part of the One Health consortium, to understand and prevent the spread of antimicrobial resistance. Here, we isolated four Acinetobacter strains from tank milk in Bogor, Indonesia and using ANI and dDDH techniques have identified them as Acinetobacter seifertii. MLST methods assigned these A. seifertii strains to a novel Sequence Types (ST), highlighting the diversity not only within the ACB complex but also in non-human Acinetobacter spp. These four A. seifertii strains are colistin-resistant and while they do not harbour any known mechanism of colistin resistance, they do share amino acid substitutions in regulatory proteins, AdeS, PmrAB, H-NS, and the membrane associated proteins, LpxACD, MlaD, PldA, LpsB and EptA that may contribute to this phenotype. Furthermore, down-regulation of the RND efflux pump AdeAB, may also be a key factor in colistin resistance in these non-human A. seifertii strains. Lipidomics revealed an acyl-homoserine lactone (AHL) molecule, and lyso-phosphatidylethanolamine (lyso-PE) in significant abundance compared to colistin-sensitive A. baumannii ATCC17978 revealing lipidomic differences between species. Finally, these four tank milk A. seifertii strains are avirulent in an insect model of virulence. It is possible that A. seifertii strains are intrinsically resistant to colistin and require further study. By investigating these less understood Acinetobacter spp. from non-human sources, our study supports the One Health approach to combatting antibiotic resistance.

microbiology↗

bioRxiv2023

Phylogenomic and phenotypic analyses highlight the diversity of antibiotic resistance and virulence in both human and non-human Acinetobacter baumannii

Acinetobacter baumannii is a Gram-negative opportunistic pathogen causing infections of the immunocompromised. With a high incidence of muti-drug resistance, carbapenem-resistant A. baumannii is as a priority 1 pathogen designated by the WHO. The current literature has expertly characterized clinical isolates of A. baumannii. As the challenge of these infections has recently been classified as a One Health issue, we set out to explore the diversity of isolates from human and non-clinical sources such as agricultural surface water, urban streams, various effluents from wastewater-treatment plants and tank milk; and, importantly, these isolates came from a wide geographic distribution. Phylogenomic analysis considering almost 200 isolates showed that our diverse set is well-differentiated from the main international clones of A. baumannii. We discovered novel sequence types in both hospital and non-clinical settings, and five strains that overexpress the RND efflux pump adeIJK without changes in susceptibility. Further, we detected a blaADC-79 in a non-human isolate despite its sensitivity to all antibiotics. There was no significant differentiation between the virulence profiles of clinical and non-clinical isolates in the Galleria mellonella insect model of virulence suggesting that virulence is neither dependent on geographic origin nor isolation source. Detection of antibiotic resistance and virulence genes in non-human strains suggests that these isolates may act as a genetic reservoir for clinical strains. This endorses the notion that in order to combat multi-drug resistant infection caused by A. baumannii, a One Health approach is required, and a deeper understanding of non-clinical strains must be achieved. ImportanceThe global crisis of antibiotic resistance is a silent one. More and more bacteria are becoming resistant to all antibiotics available for treatment, leaving no options remaining. This includes Acinetobacter baumannii. This Gram-negative opportunistic pathogen shows a high frequency of multi-drug resistance, and many strains are resistant to last-resort drugs carbapenem and colistin. Research has focused on strains of clinical origin, but there is a knowledge gap regarding virulence traits, particularly, how A. baumannii become the notorious pathogen of today. Antibiotic resistance and virulence genes have been detected in strains from animals, and environmental locations such as grass and soil. As such, A. baumannii is a One Health concern which includes the health of humans, animals and the environment. Thus, in order to truly combat the antibiotic resistance crisis, we need to understand antibiotic resistance and virulence gene reservoirs of this pathogen under the One Health continuum. RepositoriesNCBI GenBank Accession numbers: Bioproject PRJNA819071, Biosamples SAMN26898552 - SAMN26898587.

microbiology↗

bioRxiv2020

Molecular phylogeny and historical biogeography of andrenine bees (Hymenoptera: Andrenidae)

The mining bee subfamily Andreninae (Hymenoptera: Andrenidae) is a widely distributed and diverse group of ground-nesting solitary bees, including numerous species known as important pollinators. Most of the species diversity of Andreninae is concentrated in the mainly Holarctic genus Andrena, comprising ca. 1500 described species. The subfamily and especially the genus have remained relatively neglected by recent molecular phylogenetic studies, with current classifications relying largely on morphological characters. We sampled ultraconserved element (UCE) sequences from 235 taxa, including all andrenine genera and 98 out of 104 currently recognized Andrena subgenera. Using 419,858 aligned nucleotide sites from 1009 UCE loci, we present a comprehensive molecular phylogenetic analysis of the subfamily. Our analysis supports the recognition of seven distinct genera in the Andreninae: Alocandrena, Ancylandrena, Andrena, Cubiandrena, Euherbstia, Megandrena, and Orphana. Within the genus Andrena, present-day subgeneric concepts revealed high degrees of paraphyly and polyphyly, due to heavy morphological character homoplasy, necessitating a thorough, extensive revision of the higher classification of the genus. Our results also show that the MRCA of Andrena+Cubiandrena dispersed from the New World to the Palaearctic probably during the Eocene- early Oligocene, followed by 10-14 Neogene dispersal events from the Palaearctic to the Nearctic and 1-6 Neogene dispersals back into the Palaearctic, all within the genus Andrena. HighlightsO_LIA phylogeny is presented for the bee subfamily Andreninae based on UCE sequences C_LIO_LIThe Eastern Mediterranean subgenus Cubiandrena is sister to all remaining Andrena C_LIO_LIMany Andrena subgenera exhibit paraphyly or polyphyly, requiring recircumscription C_LIO_LIAt least 11 Old World-New World exchange events have occurred within Andrena C_LI

evolutionary biology↗

bioRxiv2020

Genus-wide comparison reveals divergence and evolution of the four sections within the genus Claviceps are the result of varying mechanisms driving genome evolution and host range

The genus Claviceps has been known for centuries as an economically important fungal genera for pharmacology and agricultural research. Only recently have researchers begun to unravel the evolutionary history of the genus, with origins in South America and classification of four distinct sections through ecological, morphological, and metabolic features (Claviceps sects. Citrinae, Paspalorum, Pusillae, and Claviceps). The first three sections are additionally characterized by narrow host range, while sect. Claviceps is considered evolutionarily more successful and adaptable as it has the largest host range and biogeographical distribution. However, the reasons for this success and adaptability remain unclear. Our study elucidates factors influencing adaptability by sequencing and annotating 50 Claviceps genomes, representing 21 species, for a comprehensive comparison of genome architecture and plasticity in relation to host range potential. Our results show the trajectory from specialized one-speed genomes (sects. Citrinae and Paspalorum) towards adaptive two-speed genomes (sects. Pusillae and Claviceps) through co-localization of transposable elements around predicted effectors and a putative loss of repeat-induced point mutation resulting in unconstrained tandem gene duplication coinciding with increased host range potential and speciation. Alterations of genomic architecture and plasticity can substantially influence and shape the evolutionary trajectory of fungal pathogens and their adaptability. Furthermore, our study provides a large increase in available genomic resources to propel future studies of Claviceps in pharmacology and agricultural research, as well as, research into deeper understanding of the evolution of adaptable plant pathogens.

evolutionary biology↗