Biology subjects

Rice, D. W.

Publications and source records attributed to Rice, D. W..

8 recordsLinked to original sources

bioRxiv2026

Complex roles for a conserved two-component system in a honey bee symbiosis

Elucidating how microbes associate with their hosts and respond to different environments is fundamental to our understanding of symbiosis. Here, we investigate the molecular and genetic mechanisms enabling the honey bee symbiont Bombella apis to colonize and persist in harsh honey bee microenvironments, like royal jelly and the larval gut. By using evolved B. apis strains, we demonstrate that the broadly conserved two-component system (TCS) ChvGI is integral for the bacteriums ability to withstand royal jelly and the larval gut. Furthermore, we show that in B. apis ChvGI also regulates critical bacterial behaviors such as motility, flagellar production, and biofilm formation. In other Alphaproteobacteria, ChvGI is known as a master regulator that mediates the bacterial responses to stressors and is also found to be involved in symbiosis, often through the production of EPS and biofilm formation. Our work underscores the broader significance of ChvGI as an important TCS in Alphaproteobacteria that regulates bacterial behavior in response to different types of stressors and uncovers a genetic mechanism that allows an important honey bee symbiont to survive in diverse host environments.

microbiology↗

bioRxiv2026

Ancestral Hydrocarbon Metabolism Enables PET Degradation by a Natural Bacterial Consortium

Plastic biodegradation in natural environments is increasingly recognized as a multi-organism process, yet the mechanisms enabling coordinated depolymerization and metabolism of polyethylene terephthalate (PET) remain poorly understood. Previously, we demonstrated that a full consortium containing three Pseudomonas and two Bacillus strains isolated from hydrocarbon-rich coastal soils of Galveston Bay, Texas, can synergistically depolymerize PET plastic and utilize it as a sole carbon source, a capacity not observed in individual isolates. In this report, using integrated comparative genomics, proteomics, and chemical analyses, we show that PET degradation in this system reflects exaptation of hydrocarbon metabolism reinforced by metabolic division of labor. Within this naturally occurring consortium, Bacillus strains persist under environmental stress, establish biofilms, and perform essential secondary hydrolysis, while Pseudomonas strains catabolize aromatic monomers and buffer oxidative stress. Genes supporting these functions are enriched within the accessory genomes of the consortium strains, indicating consortium-enriched horizontal gene transfer (HGT). In addition to the canonical two-step hydrolytic pathway well documented in PET biodegradation, we identify a secondary methylation-and redox-associated process, mechanisms where the full consortium acts on the oligomer mono(2-hydroxyethyl) terephthalate (MHET), yielding nearly complete conversion to terephthalic acid (TPA) and methylated MHET (MMHET). Together, these findings demonstrate how cooperation and competition within consortia facilitate targeted gene exchange, enabling emergent plastic biodegradation in natural microbial communities. IMPORTANCEEnvironmental plastic degradation is rarely accomplished by a single organism, yet the microbial mechanisms enabling community-level PET plastic breakdown remain poorly understood. This study shows that a bacterial consortium isolated from crude petroleum-contaminated beaches biodegrades PET through exaptation of ancestral hydrocarbon pathways, metabolic division of labor, and targeted gene exchange rather than specialized PET-specific metabolic pathways. Pseudomonas strains initiate PET cleavage, while stress-tolerant Bacillus strains persist long enough to clear inhibitory intermediates and enable downstream aromatic and diol metabolism. PET degradation is observed to be an emergent property of ecological interactions and distant evolutionary history. These findings provide a community-level model for understanding how natural microbial communities may adapt to novel anthropogenic substrates such as synthetic polymers, sustaining prolonged biodegradation.

microbiology↗

bioRxiv2025

Nested Connections: Local Phage and Broad Plasmid Sharing in the Honey Bee Mobilome

Honey bees rely on bacterial symbionts for their nutritional needs and for protection against invading pathogens. Genetic diversity among strains within the colony has the potential to impact symbiont function and subsequently the benefits that honey bees receive from them. Mobilized genes vectored by mobile genetic elements (MGEs) like phages, transposons, conjugative elements and plasmids, are known to rapidly alter bacterial phenotypes. We identified phages and plasmids in genomes of the symbiont Bombella apis between two colonies, with the goal of understanding which MGEs contribute to strain diversification as well as MGE distribution across colonies and between microbial species. Interestingly, we found some B. apis strains carry plasmids while all harbor a diversity of integrated phages, with only one phage clusters conserved across all. Identified B. apis phages are not found outside of the Bombella and Saccaribacter species, suggesting some host specificity for these MGEs. Of the five plasmids discovered, two appear to be phage-plasmids with high similarity to phages found in previously sequenced B. apis genomes. Interestingly, three plasmids in B. apis shared significant average nucleotide identity with known plasmids from acetic acid bacteria isolated from flowers, plants, and fermented foods. This result suggests that B. apis has acquired MGEs, either vertically or horizontally, from plant- and fermented-food associated AABs. Overall, our findings suggest that MGE content varies between colonies and has the potential to shape genetic and phenotypic variation between strains.

microbiology↗

bioRxiv2025

Evolutionary trends in Bombella apis CRISPR-Cas systems

Bacteria and archaea employ a rudimentary immune system, CRISPR-Cas, to protect against foreign genetic elements such as bacteriophage. CRISPR-Cas systems are found in Bombella apis, a microbe associated with honey bee queens, brood, and royal jelly. Unlike other honey bee microbiome members, B. apis does not colonize the worker bee midgut or hindgut and has therefore been understudied with regards to its importance in the honey bee colony. However, B. apis appears to play beneficial roles in the colony, by protecting developing brood from fungal pathogens and by bolstering their development under nutritional stress. Previously we identified CRISPR-Cas systems as being acquired by B. apis in its transition to bee association, as they are absent in a sister clade. Here we assess the variation and distribution of CRISPR-Cas types across B. apis strains. We found multiple CRISPR-Cas types, some of which have multiple arrays, within the same B. apis genomes and also in the honey bee queen gut metagenomes. We analyzed the spacers between strains to identify the history of mobile element interaction for each B. apis strain. Finally, we predict interactions between viral sequences and CRISPR systems from different honey bee microbiome members. Our analyses show that the B. apis CRISPR-Cas systems are dynamic, that microbes in the same niche have unique spacers which supports the functionality of these CRISPR-Cas systems, and that acquisition of new spacers may be occurring in multiple locations in the genome, allowing for a flexible antiviral arsenal for the microbe. IMPORTANCEHoney bee worker gut microbes have been implicated in everything from protection from pathogens to breakdown of complex polysaccharides in the diet. However, there are multiple niches within a honey bee colony that host a different group of microbes, including the acetic acid bacterium Bombella apis. B. apis is found in the colony food stores, in association with brood, in worker hypopharyngeal glands, and in the queen digestive tract. The roles that B. apis may serve in these environments are just beginning to be discovered and include production of a potent antifungal that protects developing bees and supplementation of dietary lysine to young larvae, bol-stering their nutrition. Niche specificity in B. apis may be affected by the pressures of bacteriophage and other mobile elements which may target different strains in each specific bee environment. Studying the interplay between B. apis and its mobile genetic elements (MGEs) may help us better understand microbial community dynamics within the colony and the potential ramifications for the honey bee host.

genomics↗

bioRxiv2023

Metagenomic analysis of the honey bee queen microbiome reveals low bacterial diversity and Caudoviricetes phages

In eusocial insects, the health of the queens - the colony founders and sole reproductive females - is a primary determinant for colony success. Queen failure in the honey bee Apis mellifera, for example, is a major concern of beekeepers that annually suffer with colony losses, necessitating a greater knowledge of queen health. Several studies on the microbiome of honey bees have characterized its diversity and shown its importance for the health of worker bees, the female non-reproductive caste. However, the microbiome of workers differs from that of queens, which in comparison is still poorly studied. Thus, direct investigations of the queen microbiome are required to understand colony-level microbiome assembly, functional roles, and evolution. Here we used metagenomics to comprehensively characterize the honey bee queen microbiome. Comparing samples from different geographic locations and breeder sources, we show that the microbiome of queens is mostly shaped by the environment experienced since early life, and is predicted to play roles in breakdown of the diet, and protection from pathogens and xenobiotics. We also reveal the microbiome of queens comprises only four core bacterial species, Apilactobacillus kunkeei, Lactobacillus apis, Bombella apis and Commensalibacter sp. Interestingly, in addition to bacteria, we show that bacteriophages infect the queen microbiome, for which Lactobacillaceae are predicted to be the main reservoirs. Together, our results provide the basis to understand the honey bee colony microbiome assemblage, can guide improvements in queen rearing processes, and highlight the importance of bacteriophages for queen microbiome health and microbiome homeostasis in eusocial insects. ImportanceThe queen caste plays a central role for colony success in eusocial insects, as queens lay eggs, and regulate colony behavior and development. Queen failure can cause colonies to collapse, which is one of the major concerns of beekeepers. Thus, understanding of the biology behind the queens health is a pressing issue. Previous studies have shown the bee microbiome plays an important role in worker bee health, but little is known about the queen microbiome and its function in vivo. Here, we characterized the queen microbiome identifying for the first time present species and their putative functions. We show that the queen microbiome have predicted nutritional and protective roles in queen association, and comprises only four consistently present bacterial species. Additionally, we bring to attention the spread of phages in the queen microbiome, which increased in abundance in failing queens and may impact the fate of the colony.

genomics↗

bioRxiv2022

A honey bee symbiont buffers larvae against nutritional stress through lysine supplementation

Honey bees, the worlds most significant agricultural pollinator, have suffered dramatic losses in the last few decades (1,2). These losses are largely due to the synergistic effects of multiple stressors, the most pervasive of which is limited nutrition (3-5). The effects of poor nutrition are most damaging in the developing larvae of honey bees, who mature into workers unable to meet the needs of their colony (6-8). It is therefore essential that we better understand the nutritional landscape experienced by honey bee larvae. In this study, we characterize the metabolic capabilities of a honey bee larvae-associated bacterium, Bombella apis (formerly Parasaccharibacter apium), and its effects on the nutritional resilience of larvae. We found that B. apis is the only bacterium associated with larvae that can withstand the antimicrobial larval diet. Further, we found that B. apis can synthesize all essential amino acids and significantly alters the amino acid content of synthetic larval diet, largely by increasing the essential amino acid lysine. Analyses of gene gain/loss across the phylogeny suggest that two distinct cationic amino acid transporters were gained by B. apis ancestors, and the transporter LysE is conserved across all sequenced strains of B. apis. This result suggests that amino acid export is a key feature conserved within the Bombella clade. Finally, we tested the impact of B. apis on developing honey bee larvae subjected to nutritional stress and found that larvae supplemented with B. apis are bolstered against mass reduction despite limited nutrition. Together, these data suggest an important role of B. apis as a nutritional mutualist of honey bee larvae.

microbiology↗

bioRxiv2020

Adaptive evolution in DNMT2 supports its role in the dipteran immune response

Eukaryotic nucleic acid methyltransferase (MTase) proteins are essential mediators of epigenetic and epitranscriptomic regulation. DNMT2 belongs to a large, conserved family of DNA MTases found in many organisms, including holometabolous insects like fruit flies and mosquitoes, where it is the lone MTase. Interestingly, despite its nomenclature, DNMT2 is not a DNA MTase, but instead targets and methylates RNA species. A growing body of literature suggest DNMT2 mediates the host immune response against a wide range of pathogens, including RNA viruses. Evidence of adaptive evolution, in the form of positive selection, can often be found in genes that are engaged in conflict with pathogens like viruses. Here we identify and describe evidence of positive selection that has occurred at different times over the course of DNMT2 evolution within dipteran insects. We identify specific codons within each ortholog that are under positive selection, and find they are restricted to four distinct domains of the protein and likely influence substrate binding, target recognition, and adaptation of unique intermolecular interactions. Additionally, we describe the role of the Drosophila-specific host protein IPOD, in regulating the expression and/or function of fruit fly DNMT2. Finally, heterologous expression of these orthologs suggest that DNMT2s role as an antiviral is host dependent, indicating a requirement for additional host-specific factors. Collectively, our findings highlight the adaptive evolution of DNMT2 in Dipteran insects, underscoring its role as an important, albeit non-canonical, regulator of host-pathogen interactions in mosquitoes and fruit flies.

microbiology↗

bioRxiv2017

Evolutionary genetics of cytoplasmic incompatibility genes cifA and cifB in prophage WO of Wolbachia

The bacterial endosymbiont Wolbachia manipulates arthropod reproduction to facilitate its maternal spread through populations. The most common manipulation is cytoplasmic incompatibility (CI): Wolbachia-infected males produce modified sperm that cause embryonic mortality, unless rescued by eggs harboring the same Wolbachia. The genes underlying CI, cifA and cifB, were recently identified in the eukaryotic association module of Wolbachias prophage WO. Here, we use transcriptomic and genomic approaches to address three important evolutionary facets of these genes. First, we assess whether or not cifA and cifB comprise a classic toxin-antitoxin operon, and show they do not form an operon in strain wMel. They coevolve but exhibit strikingly distinct expression across host development. Second, we provide new domain and functional predictions across homologs within Wolbachia, and we show amino acid sequences vary substantially across the genus. Lastly, we investigate conservation of cifA and cifB and find degradation and loss of the genes is common in strains that no longer induce CI. Taken together, we find no evidence for the operon hypothesis in wMel, provide functional annotations that broaden the potential mechanisms of CI induction, illuminate recurrent erosion of cifA and cifB in non-CI strains, and advance an understanding of the most widespread form of reproductive parasitism.

evolutionary biology↗