Biology subjects

Hodges, M.

Publications and source records attributed to Hodges, M..

6 recordsLinked to original sources

bioRxiv2026

Leaf Damage Is Associated with Microbiome Dysbiosis in the Spartina alterniflora Phyllosphere

Spartina alterniflora, the dominant plant species in salt marshes along the Atlantic and Gulf of Mexico coastlines of the Americas, is affected by disease and sudden vegetation dieback. Despite the foundational role of S. alterniflora in low-elevation salt marshes, the response of the native leaf-associated microbiome (i.e., phyllosphere microbiome) to leaf damage resulting from disease and environmental stress has not been explored. We hypothesized that healthy and damaged plants would show differentiation in their phyllosphere microbiomes following primary infection or exposure to environmental stressors. Here, we analyzed changes in prokaryotic and fungal relative abundance, diversity, and community composition in the S. alterniflora phyllosphere microbiome. We compared natural marsh and greenhouse plants in Georgia and South Carolina, USA, and collected leaves from healthy and damaged natural plants across two contrasting Spartina phenotypes that differ in their exposure to environmental stress. Our results show that plant origin (i.e., greenhouse vs. natural marsh), plant health status (i.e., healthy vs. damaged), and plant phenotype (i.e., short vs. tall Spartina) affect microbial relative abundance, alpha diversity, and community composition in the S. alterniflora phyllosphere. Damaged leaves presented higher microbial abundance and alpha diversity than healthy leaves, suggesting microbial proliferation following leaf damage. Plants raised from seeds in the greenhouse presented the lowest microbial abundance and Shannon diversity for both prokaryotic and fungal communities, indicating that in natural ecosystems the phyllosphere microbiota is acquired predominantly through horizontal transmission from the environment. Overall, this study provides novel insights into the assembly of the S. alterniflora phyllosphere microbiome. ImportanceSalt marshes are tidally influenced coastal wetlands that provide a range of ecosystem services to global and local communities, including protection from storm surge, water purification, and carbon sequestration. Spartina alterniflora is the dominant plant species in Atlantic and Gulf of Mexico marshes in the Americas. Fungal disease and exposure to environmental stressors have previously been described in marsh ecosystems and linked to extensive and sudden vegetation dieback in the southeastern U.S. In this study, we propose that microbial proliferation follows plant damage caused by either fungal disease or environmental stress, leading to profound changes in native leaf-associated microbiota abundance, diversity, and composition. Using greenhouse plants as a control, we also demonstrate that microbes colonizing marsh leaves are acquired predominantly from the environment. Overall, this study advances the ecological understanding of the S. alterniflora leaf microbiome assembly, establishing a baseline to inform future work harnessing plant-associated microbes for ecosystem restoration.

microbiology↗

bioRxiv2025

Enhancement of Arabidopsis growth by Enterobacter sp. SA187 under elevated CO2 is dependent on ethylene signalling activation and primary metabolism reprogramming

As atmospheric CO2 levels continue to increase, optimizing the CO2 fertilization effect which often falls short of its potential due to the physiological and metabolic limitations of plants becomes crucial. This study investigates the role of Enterobacter sp. SA187 (SA187), a plant growth-promoting bacterium, in enhancing growth and development of Arabidopsis thaliana under elevated atmospheric CO2 (eCO2) conditions. While SA187 inoculation did not have major effects under ambient CO2, it was found to significantly enhance root and shoot biomass, and to increase N- and reduce C-contents under eCO2. Moreover, transcriptomics and metabolomics suggested that SA187 modulated phytohormonal homeostasis, with activation of the salicylic acid, jasmonic acid and ethylene signalling pathways, and increased primary metabolism including the TCA cycle, N and carbohydrate metabolisms. Finally, the growth-promoting effects of SA187 were shown to be mediated through ethylene-dependent pathways, as evidenced with the ethylene-insensitive mutant ein2-1 which did not show similar benefits in plant fresh weight and altered gene expression. This beneficial plant-microbe interaction under eCO2 in a non-leguminous plant highlights a novel aspect of microbial influence on plant physiology in the context of climate change. These insights underscore the potential of utilizing SA187 to enhance plant performance and adaptability in future high CO2 environments, providing a sustainable approach to agricultural productivity as global CO2 levels increase.

plant biology↗

bioRxiv2025

Enterobacter sp. SA187-induced coordinated regulation of high-affinity nitrate transporters and ethylene signaling enhances nitrogen content and plant growth under low nitrate

O_LISustainable crop production demands solutions to reduce the overuse of synthetic nitrogen fertilizers, and plant-growth-promoting bacteria offer a promising strategy by enhancing nutrients acquisition. This study investigated ability of a non-diazotrophic bacterium, Enterobacter sp. SA187 (SA187), in enhancing Arabidopsis growth under low nitrate conditions and the underlying mechanisms. C_LIO_LIArabidopsis seedlings were grown under different nitrate concentrations with or without SA187 inoculation. Growth traits were quantified alongside shoot and root nitrate and total nitrogen contents, and C:N ratios. Transcriptomic profiling (RNA-seq) and qRT-PCR were used to assess modified gene expression. Functional validation was conducted using ethylene-insensitive (ein2-1) and high-affinity nitrate transporter (HATS) mutants (nrt2.5, nrt2.6). C_LIO_LISA187 significantly enhanced fresh weight, primary root length, and lateral root density under low nitrate, with benefits increasing as nitrate availability decreased. SA187 improved nitrate accumulation and shoot nitrogen allocation, reducing shoot C:N ratios. SA187 regulated expression of HATS and hormone-responsive genes. The growth-promoting effects were abolished in ein2-1, nrt2.5, and nrt2.6 mutants, and SA187-induced regulation of NRT2.5 occurred downstream of ethylene signaling, while NRT2.6 was partly ethylene-independent. C_LIO_LISA187 promotes growth under low nitrate possibly through ethylene-mediated and HATS-dependent reprogramming of nitrate accumulation and nitrogen allocation, supporting its use as a microbial solution for low-input agriculture. C_LI

plant biology↗

bioRxiv2022

Severe drought events trigger long-term salt marsh dieback in the Southeastern and Gulf of Mexico USA

The frequency of salt marsh dieback events has increased over the last 25 years with unknown consequences to the resilience of the ecosystem to accelerated sea level rise (SLR). Salt marsh ecosystems impacted by sudden vegetation dieback events were previously thought to recover naturally within a few months to years. In this study, we provide evidence that approximately 14% of total marsh area has not revegetated 10-years after a dieback event in Charleston, SC. Dieback onset coincided with a severe drought in 2012, and a second dieback event occurred in 2016 after a historic flood influenced by Hurricane Joaquin in October of 2015, with unvegetated zones reaching nearly 30% of total marsh area in 2017. Most affected areas were associated with lower elevation zones in the interior of the marsh (midmarsh). During the 2013 dieback event, we estimate that unvegetated midmarsh area expanded by 300%. Grass planting was shown to be an effective restoration practice, with restored plants having greater aboveground biomass than relict sites after two years of transplanting. A positive restoration outcome indicated that the stressors that caused the initial dieback are no longer present. Despite that, many dieback areas have not recovered naturally even as they are located within the typical elevation range of a healthy vegetated marsh. A mechanistic modelling approach was used to assess the effects of vegetation dieback on salt marsh resilience to SLR. Predictions indicate that a highly productive restored marsh (2000 g m-2 y-1) would persist at a moderate SLR rate of 60 cm 100 y-1, whereas a non- restored mudflat would lose all of its elevation capital after 100 years. Thus, rapid restoration of marsh dieback is critical to avoid further degradation. Also, failure to incorporate the increasing frequency and intensity of extreme climatic events which trigger irreversible marsh diebacks underestimates salt marsh vulnerability to climate change. At an elevated SLR rate of 122 cm 100 y-1, most likely an extreme climate change scenario, even highly productive ecosystems augmented by sediment placement would not keep pace with SLR. Thus, climate change mitigation actions are also urgently needed to preserve present-day marsh ecosystems.

ecology↗

bioRxiv2019

An edge-based formulation of elastic network models

We present an edge-based framework for the study of geometric elastic network models to model mechanical interactions in physical systems. We use a formulation in the edge space, instead of the usual node-centric approach, to characterise edge fluctuations of geometric networks defined in d-dimensional space and define the edge mechanical embeddedness, an edge mechanical susceptibility measuring the force felt on each edge given a force applied on the whole system. We further show that this formulation can be directly related to the infinitesimal rigidity of the network, which additionally permits three- and four-centre forces to be included in the network description. We exemplify the approach in protein systems, at both the residue and atomistic levels of description.

biophysics↗

bioRxiv2018

Allostery and cooperativity in multimeric proteins: bond-to-bond propensities in ATCase

Aspartate carbamoyltransferase (ATCase) is a large dodecameric enzyme with six active sites that exhibits allostery: its catalytic rate is modulated by the binding of various substrates at distal points from the active sites. A recently developed method, bond-to-bond propensity analysis, has proven capable of predicting allosteric sites in a wide range of proteins using an energy-weighted atomistic graph obtained from the protein structure and given knowledge only of the location of the active site. Bond-to-bond propensity establishes if energy fluctuations at given bonds have significant effects on any other bond in the protein, by considering their propagation through the protein graph. In this work, we use bond-to-bond propensity analysis to study different aspects of ATCase activity using three different protein structures and sources of fluctuations. First, we predict key residues and bonds involved in the transition between inactive (T) and active (R) states of ATCase by analysing allosteric substrate binding as a source of energy perturbations in the protein graph. Our computational results also indicate that the effect of multiple allosteric binding is non linear: a switching effect is observed after a particular number and arrangement of substrates is bound suggesting a form of long range communication between the distantly arranged allosteric sites. Second, cooperativity is explored by considering a bisubstrate analogue as the source of energy fluctuations at the active site, also leading to the identification of highly significant residues to the T{leftrightarrow}R transition that enhance cooperativity across active sites. Finally, the inactive (T) structure is shown to exhibit a strong, non linear communication between the allosteric sites and the interface between catalytic subunits, rather than the active site. Bond-to-bond propensity thus offers an alternative route to explain allosteric and cooperative effects in terms of detailed atomistic changes to individual bonds within the protein, rather than through phenomenological, global thermodynamic arguments.

biophysics↗