Biology subjects

Kennedy, P.

Publications and source records attributed to Kennedy, P..

9 recordsLinked to original sources

bioRxiv2026

Chromosome-level genome and caste transcriptomes for Africa's most widespread social wasp (Belonogaster juncea) reveal unexpected genomic diversity

Belonogaster is an African genus of primitively eusocial wasps. They are widespread and conspicuous across sub-Saharan Africa and yet are among the least studied groups of social wasps. Here, we present the first high-quality, chromosome-level genome assembly for a representative of this genus, Belonogaster juncea, complemented by an RNA-seq analysis of brain transcription among individuals representing reproductive and non-reproductive castes. The assembled genome spans 315.8 Mb with a scaffold N50 of 7.91 Mb. The annotation contained 15,159 protein-coding genes and 20,046 isoforms, with Benchmarking Universal Single-Copy Orthologs (BUSCO) completeness of 98.0% for the genome and 97.8% for the annotation. Using this new assembly, we show that the B. juncea genome differs notably from other social wasp genomes: a single satellite repeat makes up a fifth of its chromosome-scale sequence, it has the highest putative chromosome number in a sequenced wasp genome to date, and it shows high levels of syntenic breaks. We find caste neuro-transcription differences between queens and workers, revealing 573 differentially expressed genes (341 worker biased, 232 queen biased), with significant overlap in caste-specific genes when compared to Polistes dominula and Liostenogaster flavolineata. This genomic resource provides a foundation for understanding the molecular mechanisms underlying primitive eusociality and social evolution in wasps, and opens up new research opportunities for a genus of little-studied insects from the Global South.

genomics↗

bioRxiv2026

Patterns of microbial load and community assembly in leaf microbiomes of summer and overwintering crops

Phyllosphere microbiomes are increasingly recognized as key regulators of plant health and stress responses, although they are also known to change considerably over both space and time. In the phyllosphere, members of the genus Methylobacterium are often abundant and ecologically important as plant growth promoting bacteria. However, knowledge about the temporal abundances and community dynamics of Methylobacterium in agricultural systems remains limited. To address this gap, we characterized seasonal shifts in Methylobacterium-specific and total phyllosphere bacterial loads and community structure on two common summer crops and one overwintering cover crop. Leaf samples of Zea mays (corn), Glycine max (soybean), and Thlaspi arvense L. (pennycress) plants were collected over one year in Minnesota, USA and analyzed with host-associated microbial PCR (hamPCR). Microbial loads and community composition varied strongly among hosts and across growing seasons. Corn supported the highest Methylobacterium and total bacterial loads, increasing towards senescence, while pennycress exhibited the lowest loads and the most distinct communities. While there were strong host-specific patterns, a group of most abundant genera were shared across all crops (Methylobacterium, Sphingomonas, Pseudomonas, and Massilia) and the most abundant Methylobacterium amplicon sequence variants were present on all three hosts. Our findings highlight how microbial loads and community composition change during phyllosphere assembly across diverse summer and overwintering crops, with a small core of versatile taxa dominating multiple agricultural hosts. Understanding these host and season-linked patterns provides a foundation of harnessing Methylobacterium strains to enhance crop productivity and resilience.

microbiology↗

bioRxiv2026

Methods for evaluating bacterial dispersal on hyphal networks

In heterogeneous environments, the hyphae of filamentous fungi and oomycetes can facilitate the dispersal of other microorganisms. The use of these "fungal highways" (FH) is regulated by both physical and biological factors with their interplay resulting in variable capabilities of different microbes to establish FH. Several devices have been developed to test the movement of bacteria across mycelium. However, these methods are usually time-consuming and cannot be applied either at a large scale or in a high throughput format. In this study, we developed 3D-printed experimental devices that physically separate two environments while allowing hyphal networks to act as bridges for bacterial movement. The final design allows for the simultaneous testing of up to 10 pairs and the inclusion of any culturing media. With these devices, we investigated how fungal-bacterial pairing, nutrient conditions, and inoculation strategies influence FH formation. Bacterial transport was limited in nutrient-rich media but increased under poorer nutrient conditions, consistent with enhanced exploratory growth of the mycelium. Both cis- and trans-inoculation supported FH formation, although bacterial arrival was delayed in the absence of co-inoculation. The devices were used to demonstrate that transport of bacteria by FH was relevant for the colonization of a natural substrate. Finally, we established a novel in planta assay to evaluate FH formation during host colonization. This assay demonstrated that Fusarium graminearum can transport bacteria during wheat spike colonization. Together, these results provide accessible, scalable tools to study hyphal-mediated bacterial dispersal and highlight the combined role of biological specificity and nutrient context in the establishment of FH. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=75 SRC="FIGDIR/small/719220v1_ufig1.gif" ALT="Figure 1"> View larger version (25K): org.highwire.dtl.DTLVardef@1cf39aforg.highwire.dtl.DTLVardef@1d41e6corg.highwire.dtl.DTLVardef@1196637org.highwire.dtl.DTLVardef@85cc6c_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2026

Global population structures and demographic history of Suillus luteus, a pine co-introduced ectomycorrhizal fungus associated with exotic forestry and invasion.

Human colonization since the 19th century has resulted in the global spread of pines across the Southern Hemisphere, well beyond their original northern boreal distribution. Such introductions moved not only the pines but also expanded the distribution of their symbiotic partners. Although the introduction of pines is documented through historical records, little is known about the introduction history of their ectomycorrhizal fungi, which are critical symbionts for the survival and invasion of pines. Using Suillus luteus as an example, population genomic analyses of 208 individuals across both native and introduced ranges showed that all introductions originated from Europe, likely mediated by human activities along with pine introductions. With the exception of North America, introduced populations were genetically differentiated from the Europe population, with varying magnitudes of population expansion in different introduced regions, often linked to forestry practices. Genetic variation within the native European population followed isolation by distance, but not in the introduced range, highlighting the disparity in the spatial genetic patterns of native versus exotic habitats. This study provides insight into the population genetics of a globally introduced ectomycorrhizal fungus whose introduction process is likely applicable to other pine-co-introduced ectomycorrhizal fungi.

evolutionary biology↗

bioRxiv2025

Expanded adaptive NKG2C+ NK cells exhibit potent ADCC and functional responses against HBV-infected hepatoma cell lines

BackgroundHepatitis B virus (HBV) infection remains a significant global health challenge, leading to chronic liver disease and hepatocellular carcinoma (HCC). Natural killer (NK) cells play an important role in the clearance of HBV-infected cells, but their efficacy is often compromised during chronic infection. Adaptive NK cells, characterised by NKG2C expression and enhanced functional responses, represent a promising therapeutic avenue for enhancing anti-HBV immunity and responses to HBV-driven cancers. MethodsWe applied an established protocol, involving K562-HLA-E expressing feeder cells and cytokines (IL-2), for the expansion of adaptive NK cells from cryopreserved T- and B cell depleted peripheral blood mononuclear cells (PBMCs) derived from donors with chronic HBV infection alone or with Human Immunodeficiency Virus (HIV) co-infection. We evaluated the adaptive profile of expanded NK cells, their antibody-dependent cellular cytotoxicity (ADCC) capacity and functional responses against hepatoma cell lines in the presence or absence of HBV infection. ResultsExpanded NK cells achieved >97% purity, with the NKG2C positive population exhibiting a mean 100-fold expansion. These cells demonstrated a predominantly adaptive phenotype with high surface expression of NKG2C and cytotoxic potential (Granzyme B). They maintained high levels of CD16 surface expression and upregulated CD2, essential for ADCC. Functionally, expanded adaptive NK cells showed enhanced ADCC capacity and functional responses to K562 targets, naive, HBV integrant-expressing, and de novo infected hepatoma cell lines. TGF-{beta} preconditioning induced tissue-resident features (CD103, CD49a) in expanded adaptive NK cells, while preserving their adaptive phenotype and functionality, enhancing their potential for liver targeted immunotherapy. Further, expanded adaptive NK cells demonstrated minimal reactivity against autologous activated T cells, suggesting limited off-target effects. ConclusionsOur study demonstrates the first successful expansion of adaptive NK cells with robust functional responses from donors with chronic viral infection. This approach creates opportunities for NK cell-based therapies alone or in combination with monoclonal antibodies contributing to HBV functional cure strategies and the treatment of HBV-driven cancers.

immunology↗

bioRxiv2025

Experimental suppression of a keystone protist triggers mesopredator release and biotic homogenization in complex soil microbial communities

The keystone species concept suggests that certain members of an ecological community, despite their low abundance, exert disproportionately large effects on species diversity and composition. In microbial ecology, experimental validation of this concept is limited due to significant technical challenges associated with selective species manipulation. Here, we tested this concept within a soil microbial food web by selectively suppressing a protist predator using phototoxicity induced by excessive excitation light during fluorescence microscopy within a microfluidic soil chip system. We targeted a Hypotrichia ciliate taxon--presumed primarily bacterivorous under our experimental conditions--and combined microscopy with metabarcoding of multiple microbial trophic levels to evaluate the effects of this suppression on microbial community abundance, diversity, and composition. Over the 20-day incubation, the chip system supported complex communities of bacteria, fungi, and protists. Following Hypotrichia suppression, two distinct ecological responses were observed: first, an increase in flagellate abundance that was consistent with mesopredator release and accompanied a significant rise in overall protist diversity; second, a convergence in protist community composition, indicative of biotic homogenization. Surprisingly, bacterial community abundance, richness, and composition remained unaffected, likely due to compensatory predation by increased numbers of bacterivorous flagellates. In contrast, fungal diversity decreased following Hypotrichia suppression, presumably resulting from the altered protist communities that favored facultative fungal consumers. Collectively, these findings provide direct experimental evidence that low-abundance microbial predators can function as keystone species, modulating predator community composition and diversity and having cascading effects on lower trophic levels within the brown microbial food web.

ecology↗

bioRxiv2022

Common and lifestyle-specific traits of mycorrhiza-associated metabolite alterations in plant roots reflects strategies of root-mycorrhizal interactions

Convergent patterns in morphological and genetic traits of mycorrhizas have been well-documented and reflect common selection forces that define mycorrhizas. However, generalizable patterns of mycorrhiza-associated chemical alterations, which are immediately linked to plant and fungal strategies for successful symbiosis, have yet to be emerged. Comparing root metabolomes of phylogenetically-diverse plants inoculated by mycorrhizal fungi across two major lifestyles (arbuscular- vs. ecto-mycorrhizas), our study uncovers metabolite changes unique to each mycorrhizal lifestyle and those common across plant-mycorrhizal combinations irrespective of lifestyles. Arbuscular and ecto- mycorrhizal colonized roots accumulated different sets of carbohydrates, indicating unique carbon partitioning strategies: particularly, arbuscular mycorrhizal roots accumulated cyclic polyols inaccessible for symbionts, suggesting tighter regulation of plants in carbon partitioning. Mycorrhizas also altered specialized metabolism, featuring frequent increases of flavan-3-ols and decreases of flavanols irrespective of mycorrhizal lifestyles, suggesting tactical reconfiguration of specialized metabolites to facilitate/contain symbiosis. Our data show for the first time, to our knowledge, that part of the root metabolite alterations by mycorrhizas were relatively common across plant-mycorrhizal systems, highlighting their potentially critical regulatory and evolutionary role for successful symbiosis. This commonality appears robust to phylogenetic diversity of host plants and thus may be widespread in land plants. Our findings offer future research venues to elucidate the finer roles of these common traits of mycorrhiza-associated metabolite alterations and thus help to eventually develop a comprehensive understanding of this omnipresent plant-fungus partnership.

ecology↗

bioRxiv2020

Oxylipin metabolism is controlled by mitochondrial b-oxidation during bacterial inflammation.

Oxylipins are potent biological mediators requiring strict control, but how they are removed en masse during infection and inflammation is unknown. Here we show that lipopolysaccharide (LPS) dynamically enhances oxylipin removal via mitochondrial {beta}-oxidation. Specifically, genetic or pharmacological targeting of carnitine palmitoyl transferase 1 (CPT1), a mitochondrial importer of fatty acids, reveal that many oxylipins are removed by this protein during inflammation in vitro and in vivo. Using stable isotope-tracing lipidomics, we find secretion-reuptake recycling for 12-HETE and its intermediate metabolites. Meanwhile, oxylipin {beta}-oxidation is uncoupled from oxidative phosphorylation, thus not contributing to energy generation. Testing for genetic control checkpoints, transcriptional interrogation of human neonatal sepsis finds upregulation of many genes involved in mitochondrial removal of long-chain fatty acyls, such as ACSL1,3,4, ACADVL, CPT1B, CPT2 and HADHB. Also, ACSL1/Acsl1 upregulation is consistently observed following the treatment of human/murine macrophages with LPS and IFN-{gamma}. Last, dampening oxylipin levels by {beta}-oxidation is suggested to impact on their regulation of leukocyte functions. In summary, we propose mitochondrial {beta}-oxidation as a regulatory metabolic checkpoint for oxylipins during inflammation.

biochemistry↗

bioRxiv2020

Does fungal competitive ability explain host specificity or rarity in ectomycorrhizal symbioses?

Two common ecological assumptions are that host generalist and rare species are poorer competitors relative to host specialist and more abundant counterparts. While these assumptions have received considerable study in both plant and animals, how they apply to ectomycorrhizal fungi remains largely unknown. To investigate how interspecific competition may influence the anomalous host associations of the rare ectomycorrhizal generalist fungus, Suillus subaureus, we conducted a seedling bioassay. Pinus strobus seedlings were inoculated in single- or two-species treatments of three Suillus species: S. subaureus, S. americanus, and S. spraguei. After 4 and 8 months of growth, seedlings were harvested and scored for mycorrhizal colonization as well as dry biomass. At both time points, we found a clear competitive hierarchy among these species: S. americanus > S. subaureus > S. spraguei, with the competitive inferior, S. spraguei, having significantly delayed colonization relative to S. americanus and S. subaureus. In the single-species treatments, we found no significant differences in the dry biomasses of seedlings colonized by each Suillus species, suggesting none of these species was a more effective plant symbiont relative to each other. Taken together, these results indicate that the rarity and anomalous host associations exhibited by S. subaureus in natural settings are not driven by inherently poor competitive ability or host growth promotion, but that the timing of colonization is a key factor determining the outcome of ectomycorrhizal fungal competitive interactions.

ecology↗