Biology subjects

Kelly, J. B.

Publications and source records attributed to Kelly, J. B..

7 recordsLinked to original sources

bioRxiv2026

Convergent responses to light stress in oligohymenophorean ciliates bearing green algal symbionts

Photosymbiosis has evolved multiple times independently in ciliates. However, these associations can be antagonized by shifts in environmental parameters that impose stress on the host, necessitating the evolution of mechanisms to contend with this stress and to control the symbiont population. To investigate whether convergent strategies have evolved among algae-bearing ciliates in the class Oligohymenophorea, we imposed light stress on three host species that represent at least two independent evolutionary origins of photosymbiosis and measured their cellular responses. Under high light, all three species experienced an initial drop in host cell density which recovered to levels commensurate with those under low-light conditions as they decreased their symbiont loads. We then performed a comparative transcriptomic study to investigate whether a core set of genes exists that is involved in this response. Thirty-one gene families possess differentially expressed transcripts across all three species that included the upregulation C1 and S28 class peptidases, genes involved in ROS mitigation, and a gene with potential involvement in mitochondrial remodeling associated with changes in algal symbiont load. We additionally found downregulation in Dicer, which could mitigate the processing of algal transcripts by the hosts RNAi machinery that are freed upon algal digestion, and downregulation of motor proteins that may reflect changes in the hosts swimming behaviors and transport of intracellular vesicles in response to light. The 31 gene families are present and widespread in non-symbiotic oligohymenophoreans, illustrating that a pre-existing genetic toolkit exists in this clade that helps explain how it is predisposed to evolving photosymbioses.

genomics↗

bioRxiv2026

The β-lactam adjuvant guanosine potentiates anti-folate antibiotics and pyrimidine synthesis inhibitors by depleting thymidine in methicillin-resistant Staphylococcus aureus

Efforts to improve the effectiveness of existing interventions for antimicrobial-resistant (AMR) infections include identifying new ways to overcome resistance to licensed antibiotics using adjuvants or deploying antibiotics in novel combinations. Although antibiotics targeting the bacterial cell wall (e.g., {beta}-lactams) and folate metabolism (e.g., trimethoprim-sulfamethoxazole, TMP-SMX) remain cornerstones of modern healthcare, resistance to both classes poses an ongoing therapeutic challenge. We recently demonstrated that purine nucleosides can act as potent antibiotic adjuvants, restoring {beta}-lactam susceptibility in methicillin-resistant Staphylococcus aureus (MRSA). Here, we show that the {beta}-lactam adjuvant guanosine significantly reduces intracellular thymidine levels in MRSA and potentiates the activity of antifolate antibiotics (TMP-SMX) as well as the pyrimidine antimetabolites 5-fluorouracil (5-FU) and 5-fluorouridine (5-FUrd). Incorporation of oxacillin into guanosine-antifolate or guanosine-pyrimidine analogue combinations further enhanced killing of both planktonic and biofilm-associated MRSA. Thymidine depletion was accompanied by elevated intracellular reactive oxygen species (ROS) and dissipation of membrane potential, providing mechanistic insight into the bactericidal effects of these combinations. Together, these findings demonstrate that guanosine expands MRSA susceptibility beyond {beta}-lactams to include additional clinically relevant antimicrobial drug classes commonly used to treat bacterial infections. Author Summary.Finding new ways to help antibiotics to work against resistant bacteria is an important part of efforts to address the antimicrobial resistance crisis. Adjuvants, which are boosters that help antibiotics to work against resistant bacteria, are important in this regard. We recently discovered that, guanosine, which is involved in the synthesis of DNA, makes methicillin-resistant Staphylococcus aureus (MRSA) more sensitive to penicillin-type antibiotics. Here we report that guanosine also improves the effectiveness of two other types of antimicrobial drugs (anti-folate antibiotics and pyrimidine antimetabolites) that are also used in clinical practice, expanding the potential of this adjuvant to improve the management of difficult-to-treat MRSA infections.

microbiology↗

bioRxiv2024

Seasonal genotypic and phenotypic differentiation of a cosmopolitan freshwater diatom

Most ecosystems are characterized by seasonality, which, through biotic and abiotic changes, influences species biomass dynamics. Recent studies have shown that ecologically important traits can evolve rapidly in response to environmental changes, resulting in eco-evolutionary dynamics with consequences for population and community dynamics. Evidence for seasonal effects on intraspecific variation is still scarce and understanding eco-evolutionary dynamics in the presence of seasonal fluctuations remains a major challenge. Following the phytoplankton spring bloom in Lake Constance, we investigated how seasonal changes influence the intraspecific diversity of Asterionella formosa both at genotypic and phenotypic levels. We found a high degree of genetic and phenotypic differentiation characterizing Asterionella population, explained by a clustering of the isolates into early and late spring according to lake thermal stratification. Yet, most traits related to environmental parameters as well as fitness in different seasonal environments did not show a clear response to seasonality (i.e., temperature and nutrients), indicating that seasonal changes in biotic interactions (i.e., parasitic chytrids) were the major drivers of the observed seasonal shift in Asterionella genotypes. Our results highlight the importance of studying eco-evolutionary processes for understanding variations in population and community dynamics in response to seasonal environmental fluctuations.

ecology↗

bioRxiv2020

Microbiomes and host genetics provide evidence for ecological diversification among Caribbean members of the sponge genus Ircinia Nardo, 1833

Sponges live in symbioses with microbes that allow the hosts to exploit otherwise inaccessible resources. Given the potential of microbiomes to unlock new niche axes for the hosts, microbiomes may facilitate evolutionary innovation in the ecology of sponges. However, the hypothesis that ecological diversification evolves via the microbiome among multiple, closely related sponge species living in sympatry is yet untested. Here, we provide the first test of this hypothesis within Ircinia, a genus possessing diverse and abundant microbiomes that engage their hosts in nutritional symbioses. We used genome-wide SNP data (2bRAD) to delimit genetic species boundaries using BFD* among four Ircinia growth forms that putatively constitute distinct species and two nominal species, I. campana and I. strobilina. We also evaluated the performance of two single-locus genetic barcodes, CO1 and ITS, in resolving Ircinia species boundaries. We then used 16S rRNA metabarcoding to test whether the genetic species units uncovered by BFD* harbor microbiomes that are compositionally unique within each host lineage and distinct relative to seawater microbial communities. BFD* recovered genetic species boundaries that are generally reflected in the morphological differences of the growth forms and upheld the species designations of I. campana and I. strobilina, whereas CO1 and ITS provided comparatively little species-level phylogenetic resolution. The microbiomes were found to be compositionally distinct relative to seawater microbial communities, conserved within host lineages, and non-overlapping relative to the microbiomes of other host lineages. These results support a model by which microbiomes underly ecological divergence in resource use among closely related sponge species. This research provides insights into the roles of microbiomes in ecological speciation of sponges and sets the groundwork for further investigation of adaptive radiations in sponges.

evolutionary biology↗

bioRxiv2020

New shallow water species of Caribbean Ircinia Nardo, 1833 (Porifera: Irciniidae)

Seven Ircinia growth forms were collected from three sites in the Caribbean (Bocas del Toro, Panama; the Mesoamerican Barrier Reef, Belize; and the Florida Keys, United States of America). Previous research used an integrative taxonomic framework to delimit species boundaries among these growth forms. Here, we present descriptions for these species, six of which are new to science (Ircinia lowi sp. nov., Ircinia bocatorensis sp. nov., Ircinia radix sp. nov., Ircinia laeviconulosa sp. nov., Ircinia vansoesti sp. nov., Ircinia rutzleri sp. nov.) in addition to one species conferre (Ircinia cf. reteplana Topsent, 1923).

zoology↗

bioRxiv2020

The relationship between microbiomes and selective regimes in the sponge genus Ircinia.

Sponges are often densely populated by microbes that benefit their hosts through nutrition and bioactive secondary metabolites; however, sponges must simultaneously contend with the toxicity of microbes and thwart microbial overgrowth. Despite these fundamental tenets of sponge biology, the patterns of selection in the host sponges genomes that underlie tolerance and control of their microbiomes are still poorly understood. To elucidate these patterns of selection, we performed a population genetic analysis on multiple species of Ircinia from Belize, Florida, and Panama using an FST-outlier approach on transcriptome-annotated RADseq loci. As part of the analysis, we delimited species boundaries among seven growth forms of Ircinia. Our analyses identified balancing selection in immunity genes that have implications for the hosts tolerance of high densities of microbes. Additionally, our results support the hypothesis that each of the seven growth forms constitutes a distinct Ircinia species that is characterized by a unique microbiome. These results illuminate the evolutionary pathways that promote stable associations between host sponges and their microbiomes, and that potentially facilitate ecological divergence among Ircinia species.

evolutionary biology↗

bioRxiv2020

Comparative metagenomics evidence distinct evolutionary trends of genome evolution in sponge-dwelling bacteria and their pelagic counterparts

Prokaryotic associations with sponges are among the oldest host-microbiome relationships on Earth. In this study, we investigated how bacteria from several phyla have independently adapted to the sponge interior by comparing metagenome-assembled genomes of sponge-dwelling and pelagic bacteria sourced from broad phylogenetic and geographic samplings. We discovered that sponge-dwelling bacteria have more energetically expensive genomes and share patterns of depletion and enrichment for functional categories of genes that evidence evolution towards lower pathogenicity. We also identified a new defining genomic characteristic of sponge-dwelling bacteria that is virtually absent from pelagic bacteria, the presence of cassettes that contain eukaryotic steroid biosynthesis genes. Collectively, these results illuminate the trends in genome evolution that are associated with a sponge-dwelling life history strategy and have implications for furthering our understanding of how sponge-microbial symbioses have persisted through deep evolutionary time. ImportanceMuch attention has recently been devoted to investigating the evolution of microbes that live in symbiosis with sponge hosts using microbial metagenomic data. However, several biological questions regarding this symbiosis remain unanswered. Two questions that we address here are: 1) what are the long-term consequences of the symbiosis on the evolution of microbial symbiont genome size, protein content, and nucleotide content, and 2) how is the evolution of virulence in sponge-dwelling microbial symbionts, which generally undergo a mixed transmission modes (e.g. horizontal and vertical), related to long-term stability of the symbiosis? By employing the largest comparative metagenomic analysis to date in terms of host sponge species and geographic representation, we address these questions and provide further resolution into the evolutionary processes that are involved in mediating the crosstalk between sponge hosts and their microbial symbionts.

genomics↗