IMPACT OF PHYLLOSPHERE <i>METHYLOBACTERIUM</i> ON HOST RICE LANDRACES

AbstractThe 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.</jats:p

Phenotypic diversity of Methylobacterium associated with rice landraces in North-East 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

Phenotypic diversity of <i>Methylobacterium</i> associated with rice landraces in Northeast India

ABSTRACTThe 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.</jats:p

Phenotypic variation in the <i>Methylobacterium</i> isolates from phyllosphere and seed.

(A) Piecharts showing Methylobacterium clade composition from phyllosphere vs. seed surface. (B) A summary of the ability of 43 Methylobacterium isolates (from sources described in panel A) to utilize a panel of 11 carbon sources. Each row represents one isolate; each column represents a carbon source; and cells are colored based on qualitative growth of each isolate in each carbon source. Isolates are clustered (see dendrogram on the left) based on Euclidian distances and Ward clustering, given their carbon use phenotype. Columns to the right represent potential explanatory variables for the carbon use profile of each isolate, and are colored by state, source, Methylobacterium clade, and landrace. (C-F) Canonical variance analysis biplots of carbon use profiles, showing the clustering of all 43 Methylobacterium isolates by (C) state, (D) Methylobacterium clade, (E) source, and (F) landrace. Each point represents an isolate, and numbers in parentheses indicate the number of isolates in each group. Convex hulls represent 95% confidence intervals.</p

The effect of <i>Methylobacterium</i> on early growth of host rice landraces.

Change in plant height (mean±SD) over time, measured for (A) two different landraces inoculated either with their associated Methylobacterium strain or with bacterial growth medium (control) (B) plants from the landrace Ammo inoculated either with Methylobacterium isolated from various (other) landraces, or with bacterial growth medium (control). In both experiments, n = 3 plants / treatment. Arrows indicate the day on which plants were inoculated with the respective Methylobacterium strain (or growth media, for controls). Pictures show plant height on the last day of the experiment (day 40).</p