Biology subjects

Sanjenbam, P.

Publications and source records attributed to Sanjenbam, P..

6 recordsLinked to original sources

bioRxiv2026

Life on leaves left a lasting mark on the Methylobacterium core genome

The extent to which core genomes reflect strictly vertical inheritance remains debated, particularly in ecologically diverse bacterial lineages. Here, we investigate the evolution of the core genome of Methylobacterium, a major leaf-associated bacterial genus, to assess how evolutionary signals vary across genes and whether they relate to functions involved in adaptation to life at the surface of plant leaves (the phyllosphere). Identifying 1,099 protein-coding core genes across 293 genomes, we combined gene tree comparisons, phylogenetic network reconstruction, nucleotide polymorphism patterns, and functional enrichment analyses. We found that most core genes show some deviation from the consensus phylogenetic tree. However, this discordance is not randomly distributed. Across all analytical approaches, genes showing the strongest deviations are consistently associated with functions linked to life in the phyllosphere, including anoxygenic photosynthesis, protection against UV and osmotic stress. These genes are often grouped into conserved clusters in the genome. In particular, a large cluster involved in anoxygenic photosynthesis, including bacteriochlorophyll and carotenoid biosynthesis, shows strong variation in its evolutionary history and organization across lineages, despite maintaining a conserved core structure. Similar patterns of phylogenetic incongruence and gene organization are observed across related Hyphomicrobiales inhabiting the phyllosphere, suggesting that these functions extend beyond Methylobacterium. Together, these results indicate that evolutionary heterogeneity within the core genome is concentrated in genes involved in key ecological functions. While alternative explanations cannot be excluded, these patterns are consistent with horizontal gene transfer contributing to the diversification of traits important for survival and adaptation in phyllosphere bacterial communities.

evolutionary biology↗

bioRxiv2025

Ecological drift drives microbiome variation in the red flour beetle

Many eukaryotes harbor complex microbial communities that provide significant benefits to the host. However, recent work demonstrates substantial variation in microbiota across hosts and over time, though the causes and consequences of this instability are not always clear. We describe large temporal, among-individual and across-population variation in the microbiome of the red flour beetle Tribolium castaneum, a widespread pest of stored grain flour and a laboratory model organism. Across 5 years, the total load and composition of the bacterial community of laboratory beetle populations fluctuated dramatically, cycling between a few dominant taxa and hundreds of rare taxa. We show that this ecological drift is caused by a lack of maternal microbial transmission and large microbial load fluctuations in flour, which is the primary reservoir of microbial inocula. Newly hatched larvae (from eggs) and newly eclosed adults (from pupae) acquire microbes from ingested flour containing conspecific feces. The flour microbiome fluctuates with host population density and stage structure, with larval feces increasing microbial load and antimicrobial secretions from adults decreasing it. Periodic flour replacement during population maintenance also dramatically decreases flour bacterial load, contributing to stochasticity in microbial colonization. The resulting drift was associated with unstable fitness benefits for beetles, though we cannot disentangle cause vs. effect. Our work thus represents a case study of significant ecological drift even in a highly controlled laboratory environment. We suggest that such unstable microbial communities and variable host benefits may not be uncommon, and offer an opportunity to analyze early stages of the evolution and ecology of host-microbial interactions.

ecology↗

bioRxiv2024

Divergence and convergence in epiphytic and endophytic phyllosphere bacterial communities of rice landraces

Phyllosphere-associated microbes can significantly alter host plant fitness, with distinct functions provided by bacteria inhabiting the epiphytic (external surface) vs. endophytic niches (internal leaf tissue). Hence, it is important to understand the assembly and stability of these phyllosphere communities, especially in field conditions. Broadly, epiphytic communities should encounter more environmental changes and immigration, whereas endophytic microbiomes should face stronger host selection. We analysed the structure and stability of leaf phyllosphere microbiomes of four traditionally cultivated rice landraces and one commercial variety from northeast India grown in the field for three consecutive years, supplemented with opportunistic sampling of 8 other landraces. Epiphytic and endophytic bacterial communities shared dominant core genera such as Methylobacterium and Sphingomonas. Consistent with an overall strong environmental effect, both communities varied more across sampling years than across host landraces. Seeds sampled from a focal landrace did not support vertical transmission of phyllosphere bacteria, suggesting that both types of communities are assembled anew each generation. Despite these points of convergence, epiphytic communities had distinct composition and significantly higher microbial load, and were more rich, diverse, modular, and unstable than endophytic communities. Finally, focused sampling of one landrace across developmental stages showed that the divergence between the two types of communities arose primarily at the flowering stage. Thus, our results show both convergent and divergent patterns of community assembly and composition in distinct phyllosphere niches in rice, identifying key bacterial genera and host developmental stages that may aid agricultural interventions to increase rice yield.

microbiology↗

bioRxiv2024

Physical confinement selectively favours bacterial growth based on cell shape

How are bacterial communities altered by changes in their microenvironment? Evidence from homogeneous liquid or flat plate cultures implicates biochemical cues -- such as variation in nutrient composition 1,2, response to chemoattractants and toxins 3,4, and inter-species signalling 5,6 -- as the primary modes of bacterial interaction with their microenvironment. However, these systems fail to capture the effect of physical confinement on bacteria in their natural habitats. Bacterial niches like the pores of soil, mucus, and infected tissues are disordered microenvironments with material properties defined by their internal pore sizes and shear moduli7-11. Here, using three-dimensional matrices that match the viscoelastic properties of gut mucus, we test how altering the physical properties of their microenvironment influences bacterial growth under confinement. We find that low aspect-ratio bacteria form compact, spherical colonies under confinement while high aspect-ratio bacteria push their progenies further outwards to create elongated colonies with a higher surface area, enabling increased access to nutrients. As a result, the population level growth of high aspect-ratio bacteria is more robust to increased physical confinement compared to that of low aspect-ratio bacteria. Thus, our results capture experimental evidence showing that physical constraints can play a selective role in bacterial growth based on cell shape.

biophysics↗

bioRxiv2022

IMPACT OF PHYLLOSPHERE METHYLOBACTERIUM ON HOST RICE LANDRACES

The genus Methylobacterium includes widespread plant-associated bacteria that dominate the plant phyllosphere (occupying leaf surfaces), consume plant-secreted methanol, and can produce plant growth promoting metabolites. However, despite the potential to increase agricultural productivity, their impact on host fitness in the natural environment is relatively poorly understood. Here, we conducted field experiments with three traditionally cultivated rice landraces from north eastern India. We inoculated seedlings with native vs. non-native phyllosphere Methylobacterium strains, finding significant impacts on plant growth and grain yield. However, these effects were variable: whereas some Methylobacterium isolates were beneficial for their host, others had no impact or were no more beneficial than the bacterial growth medium. Host plant benefits were not consistently associated with Methylobacterium colonization, altered phyllosphere microbiome composition, changes in early expression of plant stress response pathways, or bacterial auxin production. We provide the first clear demonstration of the benefits of phyllosphere Methylobacterium for rice yield under field conditions, and highlight the need for further analysis to understand the mechanisms underlying these benefits. Given that the host landrace-Methylobacterium relationship is not generalizable, future agricultural applications will require careful testing to identify coevolved host- bacterium pairs that may enhance the productivity of high-value rice varieties.

microbiology↗

bioRxiv2019

Phenotypic diversity of Methylobacterium associated with rice landraces in Northeast India

The ecology and distribution of many bacteria is strongly associated with specific eukaryotic hosts. However, the impact of such host association on bacterial ecology and evolution is not well understood. Bacteria from the genus Methylobacterium consume plant-derived methanol, and are some of the most abundant and widespread plant-associated bacteria. In addition, many of these species impact plant fitness. To determine the ecology and distribution of Methylobacterium in nature, we sampled bacteria from 36 distinct rice landraces, traditionally grown in geographically isolated locations in North-East (NE) India. These landraces have been selected for diverse phenotypic traits by local communities, and we expected that the divergent selection on hosts may have also generated divergence in associated Methylobacterium strains. We determined the ability of 91 distinct rice-associated Methylobacterium isolates to use a panel of carbon sources, finding substantial variability in carbon use profiles. Consistent with our expectation, across spatial scales this phenotypic variation was largely explained by host landrace identity rather than geographical factors or bacterial taxonomy. However, variation in carbon utilisation was not correlated with sugar exudates on leaf surfaces, suggesting that bacterial carbon use profiles do not directly determine bacterial colonization across landraces. Finally, experiments showed that at least some rice landraces gain an early growth advantage from their specific phyllosphere-colonizing Methylobacterium strains. Together, our results suggest that landrace-specific host-microbial relationships may contribute to spatial structure in rice-associated Methylobacterium in a natural ecosystem. In turn, association with specific bacteria may provide new ways to preserve and understand diversity in one of the most important food crops of the world.

ecology↗