Biology subjects

Palanichamy, P.

Publications and source records attributed to Palanichamy, P..

5 recordsLinked to original sources

bioRxiv2025

Parallel Evolution of Bacteroidota as Long-Term Endosymbionts of Insects

Symbiotic relationships transform diverse aspects of both symbiont and host biology. The most visible changes include a massive reduction of the endosymbiont genome and the development of novel host organs, cells, and compartments specialized for harboring the symbionts. However, many insect symbiosis studies have previously focused either on Proteo-bacteria or only on a particular symbiosis stage, limiting our broad understanding of how and why symbiont diversity arises from specific microbial clades, how the symbiont genomes erode over evolutionary time, and what the consequences of symbiosis are for diverse host-symbiont pairs. Thanks to the repeated gains and losses of nutritional symbionts, scale insects provide an ideal evolutionary playground for tracking the parallel transitions of insect symbionts that originated as independent evolutionary replicates from the same bacterial phylum. Using extensive genome sampling across the scale insect phylogeny, we recapitulated the path of Bacteroidota transitioning from recently established host-associated bacteria to highly specialized insect endosymbionts with minimal gene sets. Their genomes exhibit strikingly parallel patterns of gene loss and pseudogenization across all gene categories, with some stochastic differences in essential genes for genetic processing and amino acid biosynthesis. In addition to the genetic transition, we show with imaging methods that the symbiotic cells and organs exhibit a trend from more dispersed bacteriocytes to highly compact (and likely more specialized) bacteriomes, which are closely localized to the hosts digestive system. Our results outline at both genomic and cellular levels a recurrent path by which insect symbioses independently arise, are temporarily maintained for up to several hundred million years, and then are replaced by new symbionts that repeat the process. The gradual nature of the process implies that the outcomes of symbiosis initially depend on how professional vs. naive the host and symbiont are. Over evolutionary time, compatible host-symbiont lineages emerge from these interactions and become preferred.

evolutionary biology↗

bioRxiv2025

Genomic diversity and functional potential of facultative bacterial symbionts across scale insects

Microbial symbionts play pivotal roles in the physiology, ecology, and evolution of insects. While obligate symbionts have been extensively characterized in insects feeding on nutritionally poor diets, the diversity and functional roles of facultative bacterial symbionts remain largely unexplored in many insect lineages, including scale insects (Hemiptera: Coccomorpha). Here, we present a genome-resolved metagenomic and comparative genomic analysis of facultative bacterial symbionts across 120 scale insect metagenomes from 20 different families. Our analyses reveal rich and taxonomically diverse facultative symbiont communities, dominated by the Pseudomonadota, such as Wolbachia, Rickettsia, Arsenophonus, and Sodalis. Genomic features reveal substantial variation in genome sizes, coding densities, metabolic potentials, and hostinteraction genes among symbiont clades, indicating lineage-specific lifestyles and host interactions. Interestingly, alphaproteobacterial and gammaproteobacterial symbionts mostly co-occur within their respective hosts. Gammaproteobacterial symbionts exhibit broader metabolic repertoires and potential defense capabilities via the APSE phage toxin cassettes, while alphaproteobacterial symbionts retain reduced metabolic capabilities, Type IV secretion systems, and reproductive manipulation genes (cifAB and wmk). We propose how the symbiont genes related to nutritional provisioning, defensive symbiosis, and reproductive manipulation may influence the biology and evolution of scale insects. Our results provide the first comprehensive genomic overview of facultative bacterial symbionts in scale insects, revealing their evolutionary dynamics and putative functions.

genomics↗

bioRxiv2025

A Midichloriaceae endosymbiont of terrestrial arthropods found as an endosymbiont in a marine nematode

The obligate endosymbiont Candidatus Lariskella (Alphaproteobacteria, Candidatus Midichloriaceae) has been found across a wide diversity of terrestrial arthropods, including ticks, true bugs, beetles, fleas, wasps and moths. However, to date, Ca. Lariskella had never been detected in nematodes or marine animals. Here we report the first known occurrence of Ca. Lariskella infecting a population of marine nematodes (Enoplida, Thoracostomopsideae). This nematode-infecting Ca. Lariskella is closely related to insect-infecting Ca. Lariskella, despite the drastic shift in both host phylum and habitat. TEM and FISH microscopy showed Ca. Lariskella is localized within both somatic cells and developing oocytes, strongly suggesting that Ca. Lariskella is a vertically transmitted endosymbiont within the nematode population. We found that Ca. Lariskella was present within approximately 20% of the nematode population, but notably failed to detect any Ca. Lariskella within adult males, potentially hinting at reproductive manipulation. Overall, our findings show that Ca. Lariskella is not limited to arthropods or terrestrial hosts, indicating a larger host range than previously described. Its presence within marine nematodes demonstrates the ability of Ca. Lariskella to infect nematode hosts, as well as hosts from marine environments, suggesting terrestrial nematodes, marine arthropods, and perhaps even other marine invertebrates could be potential hosts of Ca. Lariskella.

microbiology↗

bioRxiv2024

The diversification of mealybugs was triggered by new symbiont acquisitions and followed by adaptive radiations on host plants

Symbiotic microorganisms play a critical role in supplementing beneficial nutrients to herbivorous insects feeding on unbalanced diets. These microbial symbionts can both facilitate or constrain plant-feeding insects adaptations to certain host plants, depending on their gene content and metabolic potential. The diet breadth of herbivorous insects is considered an important evolutionary factor affecting genotypic and phenotypic changes associated with host shifts. Acquiring new symbionts can, therefore, drive changes in niche breadth and subsequent adaptive radiation(s). Mealybugs comprise one of the major groups of scale insects, most of which feed on diverse angiosperms. Different sub-lineages of mealybugs also house different lineages of bacteria and fungi as their obligate symbionts. Here, we use mealybugs as a model system to test the hypothesis that the evolution of herbivorous insects is driven by both obligate symbionts and host plants. Based on metagenome analyses of 28 host species as well as a literature survey, we identified Betaproteobacteria, Gammaproteobacteria, Flavobacteriia, and Ophiocordyceps fungi as obligate symbionts of the major clades of mealybugs. A time-calibrated phylogenetic tree of mealybugs allowed us to infer the ancestral obligate symbionts of the major mealybug clades. Our results indicate that the emergence of major mealybug lineages coincided with the acquisitions of new obligate endosymbionts. Subsequent radiations of mealybugs were inferred to have mostly resulted from the adaptive radiation through continuous host shifts on angiosperms. The contribution of microbial symbiosis to the diversification of herbivorous insects is thus likely limited by new symbiont origins or replacements, and insect adaptations play a larger role in further plant switches.

evolutionary biology↗

bioRxiv2024

Accelerated pseudogenization in ancient endosymbionts of giant scale insects

Symbiotic microorganisms are subject to a complex interplay of environmental and population-genetic pressures that drive their gene loss. Despite the widely held perception that ancient symbionts have stable genomes, even tiny genomes experience ongoing pseudogenization. Whether these tiny genomes also experience bursts of rapid gene loss is, however, less understood. Giant scale insects (Monophlebidae) feed on plant sap and rely on the symbiotic bacterium Walczuchella which provides them with essential nutrients. When compared to other ancient symbionts with similar genome sizes such as Karelsulcia, Walczuchellas genome was previously reported as unusually pseudogene-rich (10 % of coding sequences). However, this result was based on only one genome assembly raising questions about the assembly quality or a recent ecological shift such as co-symbiont acquisition driving the gene loss. Here, we generated six complete genomes of Walczuchella from three genera of giant scales, each with distinct co-symbiotic partners. We show that all the genomes are highly degraded and particularly genes related to the cellular envelope and energy metabolism seem to be ongoing pseudogenization. Apart from general mechanisms driving genome reduction such as the long-term intracellular lifestyle with transmission bottlenecks, we hypothesize that a more profound loss of DNA replication and repair genes together with recent co-obligate symbiont acquisitions likely contribute to the accelerated degradation of Walczuchella genomes. Our results highlight that even ancient symbionts with small genomes can experience significant bursts of gene loss when stochastic processes erase a gene that accelerates gene loss or when the selection pressure changes such as after cosymbiont acquisition.

genomics↗