# The connections of climate change with microbial ecology and their consequences for ecosystem, human, and plant health

Ludivine Guigard, Fanny Nazaret, Juliana Almario, Franck Bertolla, Hasna Boubakri, Amélie Cantarel, Benoit Cournoyer, Sabine Favre-Bonté, Alessandro Florio, Wessam Galia, et al.

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## To cite this version:

Ludivine Guigard, Fanny Nazaret, Juliana Almario, Franck Bertolla, Hasna Boubakri, et al. The connections of climate change with microbial ecology and their consequences for ecosystem, human, and plant health. Journal of Applied Microbiology, 2025, 136 (7), pp.lxfaf168. 10.1093/jbio/lxfaf168. hal-05258695

HAL Id: hal-05258695

https://hal.science/hal-05258695v1

Submitted on 15 Sep 2025

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Title: The connections of climate change with microbial ecology and their consequences for

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ecosystem, human, and plant health

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Authors

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Ludivine Guigard, Fanny Nazaret, Juliana Almario, Franck Bertolla, Hasna Boubakri, Amélie

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A.M. Cantarel, Benoit Cournoyer, Sabine Favre-Bonté, Alessandro Florio, Wessam Galia,

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Christina Hazard, Gwennaëlle Henry, Aude Herrera Belaroussi, Sandra Kim Tian Fook

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Chong, Céline Lavire, Clément Lobreau, Patricia Luis, Marion Maréchal, Thibault Meyer,

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Adrien CM Pozzi, Guillaume Minard, Sylvie Nazaret, Graeme W. Nicol, Claire Prigent-

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Combaret, Agnes Richaume, Veronica Rodriguez, Concepcion Sanchez-Cid, Claire Valiente

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Moro, Ludovic Vial, Aurélien Vigneron, Florence Wisniewski-Dye, Ashley Shade*

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Affiliation

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Universite Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, Laboratoire d'Ecologie

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Microbienne LEM, CNRS UMR5557, INRAE UMR1418, Villeurbanne, F-69100 France

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*corresponding; 16 Rue Raphaël Dubois, Bâtiment Mendel, 69622 Villeurbanne cedex,

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France; ashley.shade@cnrs.fr

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Running head: Microbiomes and climate change

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22 **Abstract**

The climate crisis presents an urgent challenge for Earth's living creatures and the habitats in which they have been adapted to thrive. Climate-related stress presents risks to microorganisms, the stability of the functions they provide, and their maintenance of beneficial interactions with their hosts and ecosystems. Microbes move across the continuum of anthropogenic influence on Earth's ecosystems, from pristine to human-managed to fully urbanized environments. Because microbial feedback within and across this continuum exists at multiple, connected scales from molecules to ecosystem-level processes, predicting microbial responses to climate stress and their potentially wide-ranging consequences remains difficult. Here, we discuss the broad implications of microbial and microbiome responses to climate change as they interface with human, plant, and ecosystem health. For each section on human, plant and ecosystem health, we briefly discuss the state of knowledge for each and follow with proposed future research, including some directions that are promising but require more work to evaluate. We end by considering overarching microbial ecology research needs across these systems and microbial solutions under investigation as possible climate-resilient interventions to maintain human, plant, and ecosystem health. This work draws on diverse expertise to identify broad research directions across typically separated disciplines and builds a holistic framework for considering their interrelationships.

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41 **Keywords**

One Health, agriculture, soil microbiota, biogeochemical cycles, greenhouse gas, plant microbiota, antibiotic resistance, phytopathogen, vector-borne pathogens, opportunistic pathogens, Sustainable Development Goals

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46 **Impact statement**

47 This work discusses critical interactions of microbial ecology with ecosystem, human, and
48 plant health given the changing climate.

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50 **Introduction**

51 The negative impacts of climate change are numerous, and their consequences vary.
52 Shifts in temperature and precipitation patterns increase the frequency and intensity of
53 extreme weather events, including storms, floods, heat waves, and droughts. Atmospheric
54 levels of greenhouse gases (GHG) are also increased, directly influencing Earth's
55 biogeochemical cycles. The abiotic stresses induced by climate change alter the dynamics,
56 dispersal, and metabolisms of animals, plants, and, of course, microorganisms (Ryan *et al.*,
57 2019, Jägermeyr *et al.*, 2021, Jin *et al.* 2022). Microorganisms are the fundamental functional
58 actors on Earth, mediating biogeochemical cycles and forming beneficial symbioses with
59 larger organisms, including animals and plants. Many of these microbes and their functions
60 are disrupted by climate change (Compant *et al.*, 2010, Tiedje *et al.*, 2022). The holistic
61 effects of the weakening, strengthening, gain, or loss of these microbial functions for human,
62 plant, and ecosystem health with the changing climate are unclear. Therefore, a critical
63 component in tackling the climate crisis is to understand, anticipate, and potentially manage
64 the impacts of climate change on the ecology of microorganisms, including their
65 communities, their patterns of dispersal, and their interactions with their ecosystems and
66 hosts. Understanding these multidirectional relationships is also prioritized within the One
67 Health framework, which considers the environment-human continuum as a connected
68 system (Cavicchioli *et al.*, 2019). To do so, interdisciplinary, systems-level microbiology
69 research is direly needed to build insights to direct microbiology-informed climate action.
The results of these microbial ecology research directions directly support several United Nations Sustainable Development Goals, including 2 (Zero Hunger), 3 (Good Health and Well-being), 6 (Clean Water and Sanitation), 11 (Sustainable Cities and Communities), 12 (Responsible Consumption and Production), 13 (Climate Action) and 15 (Life on Land). 70 71 72 73

The Microbial Ecology Research Unit (Laboratoire d'Ecologie Microbienne) in Lyon, France, has over seventy permanent scientists investigating broad and interconnected research themes that advance understanding of the reciprocal connections between microorganisms, microbial communities, and climate change. Initially established in the 1970s as a soil microbiology unit, the department has since broadened and now pursues interdisciplinary research at the interfaces of microbiology, ecology, and the environment. In this review, we leverage the expertise and breadth of the unit to discuss three principal research axes critical for comprehending and responding to microbial-mediated outcomes of climate change: Earth's biogeochemical cycles, human health, and plant health (Figure 1). 74 75 76 77 78 79 80 81 82

## Microbes, Climate Change, and Biogeochemical Feedback 83

Overview and state of knowledge. Climate change consequences for biogeochemical cycles are linked with disturbances in many supporting and regulating ecosystem services, including the maintenance of soil fertility (i.e. through the balance between mineral forms available for plants over time), climate regulation (i.e. through the emission of greenhouse gases (GHG) in the atmosphere), and water quality (i.e. through the release of mineral nitrogen (N) and phosphorus (P) along the soil profile reaching surface waters). Microbes produce and consume the three major GHG contributing to climate change: CO₂, nitrous oxide (N₂O), and methane (CH₄) (Tiedje *et al.*, 2022). On a global scale, microbes dominate the transformation of carbon (C) and N from complex organic matter, regulating the flux of GHG emissions (Ryan-Keogh *et al.*, 2023). Anthropogenic activities have both direct and indirect impacts on
94 microbial activity, accelerating natural processes that increase rates of GHG emissions. For
95 example, agroecosystems are the primary anthropogenic source of N₂O emissions because of
96 overfertilization, and the expansion of urban areas due to global population growth is leading
97 to significant changes in soil ecosystems and an increase in GHG emissions (Tian *et al.*,
98 2020, Zhan *et al.*, 2023). Furthermore, warming temperatures affect biogeochemical cycling
99 by disrupting the microbial community and metabolism (Tiedje *et al.*, 2022). This section
100 will focus on the N and C cycles, which produce N₂O and CH₄, the two more potent and
101 microbial-specialized GHG.

102 Terrestrial N cycling is the most anthropogenically impacted biogeochemical process
103 (Rockström *et al.*, 2009). Industrially produced synthetic fertilizers are responsible for
104 feeding half of humanity. Application of fertilizer also increases the activity of
105 chemolithoautotrophic nitrifying microorganisms that decrease N fertilizer use efficiency by
106 removing N available to plants and contributing to N₂O emissions from agroecosystems
107 (Prosser *et al.*, 2019). GHG emissions are impacted by the general erosion of soil health as
108 well as by soil rehabilitation. For example, the covering of soil surfaces by impervious
109 materials (i.e. soil sealing) leads to a concentration of run-off water, which supports soil
110 anaerobiosis and promotes the activity of denitrifying and methanogenic communities,
111 increasing N₂O emissions and decreasing CH₄ uptake in urban greenspaces (Zhan *et al.*,
112 2023, Li *et al.*, 2024a). Climate change also substantially affects N cycling through changes
113 in microbial dynamics. In grassland ecosystems, combined warming, drought, and CO₂
114 enrichment affected microbial fluxes, activities, and community structure. In particular, these
115 combined stresses increased denitrifier activity, leading to an increase in N₂O fluxes
116 (Cantarel *et al.*, 2011 & 2012).
117 The biological production of CH₄ (methanogenesis) is responsible for over half of global
118 CH₄ emissions. Net fluxes from soils and sediments of CH₄ are regulated by the activity of
119 methane-cycling microbial guilds, specifically methanogenic archaea in anoxic environments
120 and methanotrophic soil bacteria, the latter consuming 5-7% of atmospheric CH₄ annually
121 (Saunois et al., 2020). CH₄ emissions are also influenced by land use change and climate-
122 driven alterations in hydrology and temperature that reduce the C storage capacity of
123 sedimentary and wetland ecosystems (Segarra et al., 2013). The warming of organic-rich
124 soils and wetland sediments enhances CH₄ emissions due to shifts in methanogen and
125 methanotroph communities (Turetsky et al., 2019, Conrad, 2020). Furthermore, climate-
126 sensitive ecosystems that typically store C are no longer stable (e.g. thawed Arctic tundra that
127 are now net sources of CO₂ and CH₄, Rantanen et al., 2022, Natali et al., 2024).

128 *Future research and opportunities.* Current strategies to reduce gaseous N losses and
129 pollution from cultivated soils include the use of enhanced-efficiency fertilizers and synthetic
130 nitrification inhibitors (Florio et al., 2016, Bachtsevani et al., 2021). However, there is an
131 urgent need for more efficient and sustainable alternatives. Developing solutions to decelerate
132 N cycling includes biological nitrification or denitrification inhibitors (BNI/BDI) derived
133 from plant root exudates or produced by litter decomposition. BNI/BDI compounds and
134 nitrifier/denitrifier groups targeted by these compounds have been identified only for a few
135 ecosystems, including perennial grasses and cultivated crops (Coskun et al., 2017, Bardon et
136 al., 2018). The efficacy of individual compounds against different taxonomic groups (e.g.
137 ammonia-oxidizing archaea or bacteria) varies due to differences in cell structures,
138 ecophysiology, and impacts of variation in soil physicochemistry (Bachtsevani et al., 2021).
139 Recently, BNI from crude extracts of litter and soil of two forest tree species was
140 demonstrated, suggesting the existence of yet-unknown specific BNI compounds released by
141 some tree species (Laffite et al., 2020). Procyanidins remain the only proven BDI (Bardon et
al., 2014), and they have been detected in the root system of young knotweed seedlings, which may favor plant establishment in its early stages of development (Cantarel et al., 2024). BDI induced by overproduction of root procyanidins also increases nitrate (NO3-) available in the soil and stimulates root growth (Bardon et al., 2017). Harnessing this complex network of soil microbial N transformations through the plants' natural BNI/BDI strategies could provide new methods to reduce N inputs by increasing N use efficiency, thereby mitigating N2O emissions and NO3-leaching into waterways from terrestrial ecosystems.

Understanding the functional diversity and ecophysiology of the soil microorganisms controlling biogeochemical cycling in various ecosystems is critical for predicting current and future GHG emissions (Prosser and Nicol, 2012). However, research should also consider virus-microbial host dynamics and their consequences for biogeochemical cycling (Hazard et al., 2025). Recently, nitrifier-specific soil viruses were shown to be active during nitrification and their predicted auxiliary metabolic genes encoded proteins involved in energy metabolism (Lee et al., 2024). Bacteriophages that are predicted to infect methanogens and methanotrophs are widely distributed in the environment (Zhong et al., 2024, Sun et al., 2024), and the demonstration of the transfer of CH4-derived C into viral biomass suggests an important role of viral predation in C cycling (Lee et al., 2021). Thus, an emerging potential mitigation to control microbial guilds responsible for GHG biogeochemistry is the use of host-specific viruses (i.e. environmental bacteriophage therapy).

163 Microbes, Climate Change, and Human Health

A. Non-vector bacterial pathogens
Overview and state of knowledge. Non-vector bacterial pathogens (NVBPs) can thrive in diverse outdoor environments, including urban and agricultural soils, watercourses of urban and rural watersheds, and drinking water and sanitation networks. They are considered opportunistic pathogens of humans and animals mainly because of their great metabolic versatility linked to acquiring mobile elements by horizontal gene transfer (HGT) (Aujoulat et al., 2012). Their remarkable plasticity allows them to thrive in extreme environments such as road surfaces and resist the effects of antimicrobial compounds. The ESKAPEE group, composed of *Enterococcus faecium*, *Staphylococcus aureus*, *Klebsiella pneumoniae*, *Acinetobacter baumannii*, *Pseudomonas aeruginosa*, *Enterobacter* species, and *Escherichia coli*, is an important concern in multi-drug resistant (MDR) infections (Oyenuga et al., 2024). This section discusses how climate change has altered NVBP human infections, including connections with anthropogenic systems.

Over the last decade, extreme weather events like cyclones have damaged health infrastructure, contaminating water and air and creating conditions that promote the spread of pathogenic bacteria and increase the risk of infectious outbreaks (Edelson et al., 2022).

Heavy rainfall has led to the overflow of sewer systems and spillovers of Legionella pneumophila, P. aeruginosa, Aeromonas caviae, Mycobacterium avium, and Vibrio spp. into drinking water and natural streams, exposing humans and other animals (LeChevallier et al., 2024, Acosta-España et al., 2024). Thus, vulnerable human populations and those with limited access to clean water face increasing risks of respiratory and skin infections such as bacterial cellulitis, tuberculosis, and gastroenteritis (Andrade et al., 2018, Acosta-España et al., 2024). Furthermore, declining groundwater levels due to irregular precipitation, shrinking glacier-fed inflows, and city overuse have prompted solutions like stormwater infiltration, rain gardens, and constructed wetlands to refill aquifers. However, these systems can support bacterial colonization by Aeromonas, Pseudomonas, and Stenotrophomonas species (Colin et
al., 2020). Heavy rainfall and flooding mobilize urban-surface bacteria into the receiving waterbodies, including intermittent streams and aquifers that receive stormwater (Bouchali et al., 2022 & 2024, Pozzi et al., 2024), ultimately putting water resources in jeopardy.

Climate change can also intensify air and water pollution (fine particles, nitrogen dioxide, ground-level ozone), impairing lung (asthma, alveolar bronchitis) and intestinal (epithelial cell desquamation) functions, making even healthy individuals more susceptible to infections (Lima de Albuquerque et al., 2021). Shifts in temperature, precipitation, humidity, and pollution can also alter soil dynamics and pathogen ecology, changing animal exposure pathways and increasing farmers' risks (Guzmán-Luna et al., 2022). Heat and moisture can promote bacterial spore formation, heightening respiratory infection risks from *Mycobacterium* spp. and *Nocardia cyriacigeorgica* (Vautrin et al., 2021, Baker et al., 2022).

In parallel, climate change has altered agricultural practices and transmission routes of animal-borne pathogens. As the global population's food demand increases, agriculture must balance higher productivity with energy efficiency and waste recycling. Climate change alters ecosystems, increasing human-livestock-wildlife interactions and intensifying resource competition for land and water (Duchenne et al., 2021, Pereira et al., 2024). This overlap facilitates the spread of zoonotic pathogens and antibiotic-resistant bacteria (ARB) (Jones et al., 2013, Peng et al., 2022). For instance, *Mycobacterium bovis* can spread through shared water sources, causing tuberculosis outbreaks in both wildlife and livestock (Cunha et al., 2012).

NVBP spread is affected by urban policies for infrastructure planning, including choice of the materials used in making physical structures. Cities can catalyze NVBP proliferation and exposure because of urban heat islands, impermeable surfaces, and dense populations. Poor urban planning, rapid land-use changes, and overstretched sanitation and
214 healthcare systems can contribute to the emergence of infection hotspots (Ahmed et al., 2019). High density can increase contact rates and transmission risks in inter-connected urban settings (Balbin et al., 2020). Additionally, urban encroachment into natural habitats can increase exposure to zoonotic pathogens such as *Leptospira spp.* from rodents, especially during floods (Garcia-Lopez et al., 2024). Rising temperatures can exacerbate urban water challenges by accelerating chlorine decay in distribution systems, fostering biofilms and pathogens like *P. aeruginosa* and *M. avium* (Calero Preciado et al., 2021). Warmer conditions can also increase the risks of bacterial waterborne and foodborne diseases (Anikeeva et al., 2024). The poor maintenance of drinking water, sanitation, and food storage systems will likely drive outbreaks in warming cities. Common heat mitigation measures may add to this burden, like ventilation and air conditioning that trap indoor air and misting systems that disperse water, which can be contaminated with potential pathogens.

226 *Future research and opportunities.* While the responses of many NVBPs to persistent but gradual climate stress, like warming, have been studied, a general understanding of how non-vector pathogen infections will be affected by extreme events (and extreme events compounded with persistent, gradual stress) remains unclear but critical to understand. There is a need for predictive modeling based on public long-term, large-scale datasets of high quality documenting the numerous field variables (temperature and precipitation patterns, solar radiance, pH, pollutants, soil/sediment contents, water depth, and flow) that can impact NVBP distribution patterns.

234 Additionally, bacterial survival and adaptation to extreme, harsh conditions remains poorly understood. NVBP must withstand temperature fluctuations, changes to their reservoirs, and resource scarcity, yet their persistence mechanisms remain unclear. Emerging evidence suggests that there are likely interactions between pathogens and other microbes, such as fungi or microeukaryotes like amoeba, which may support bacterial survival by
providing protection, environmental reservoirs, nutrients, or a means of dispersal (Deveau *et al.*, 2018). For example, temperature and protozoan predation could also act as co-selectors on antimicrobial resistance genes and antimicrobial resistant bacteria (Nguyen *et al.*, 2020).

Understanding these ecological relationships could help identify high-risk situations before outbreaks can occur.

Another major research need is understanding the complex relationships between human-driven factors and the distribution and dispersal of NVBPs. Climate research focuses on environmental variables, but human behaviors and policies can influence bacterial spread.

These elements should, again, be more integrated into climate health models or public health interventions (American Society for Microbiology, 2022).

## B. Climate change and vector-borne diseases

*Overview and state of knowledge.* Climate plays a crucial role in the spread, transmission dynamics, and emergence or re-emergence of vector-borne diseases by directly affecting pathogens, vectors of pathogens, their reservoirs, and human hosts. Beyond these direct effects, climate change reshapes ecosystems, including urban environments, creating conditions that may favor vector and host populations (de Souza and Weaver, 2024). As ectotherms, insects and other arthropods are highly sensitive to temperature shifts, which can influence many aspects of their biology, including population sizes, survival rates, and pathogen development within vectors. The ability of a vector population to transmit pathogens (i.e. capacity) is strongly temperature-dependent (Suh *et al.*, 2020, Lühken *et al.*, 2024). Key factors such as vector lifespan, transmission efficiency, feeding frequency, and the time required for a pathogen to develop within the vector are all shaped by temperature variations, highlighting the deep interplay between climate change and vector-borne disease
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dynamics. This section will discuss the consequences of climate change for vectors and pathogen transmission.

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Climate change is a major driver of arthropod vector distribution, with direct consequences for the spread of vector-borne diseases. Rising global temperatures, changes in precipitation patterns, and more frequent extreme weather events are transforming habitats and altering the population dynamics of vectors such as mosquitoes, ticks, and sandflies (Koch et al., 2017, Gilbert, 2021, Colón-González et al., 2021). Beyond human-driven spread through travel and trade, warming climates have facilitated the global spread of mosquito species like *Aedes aegypti* and *Aedes albopictus* mosquitoes into temperate regions, increasing the risk of diseases such as dengue, chikungunya, and Zika (Ryan et al., 2019, Rezza, 2024). Similarly, the increase in temperatures has favored the northward expansion of *Ixodes scapularis* and *Ixodes ricinus* ticks (Ostfeld and Brunner, 2015, Gilbert et al., 2021), amplifying the threat of Lyme disease and tick-borne encephalitis. Precipitation and humidity are also critical in influencing vector survival (with a lower limit at ~40% and a peak at ~90%, Brown et al., 2023) and determine the availability of mosquito breeding sites (Shaman and Day, 2007). Indeed, while increased rainfall can create new breeding habitats, drought conditions may force vectors to adapt or relocate (Brown and Murray, 2014, Roiz et al., 2015).

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Climate change also affects vector density by altering environmental conditions that regulate reproduction, development, and survival. Higher temperatures often accelerate arthropod life cycles, shortening development times and increasing reproduction rates up to an optimum, after which they tend to survive less and their population declines (Gilbert, 2021, Agyekum et al., 2022, Duval et al., 2023). Conversely, prolonged dry conditions can limit the occurrence of breeding and increase mortality, reducing vector populations. The outcomes of all these factors are region specific. For instance, in Europe, rising temperatures

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288 have led to higher densities of *Ixodes ricinus*, increasing Lyme disease risk (Voyiatzaki *et al*., 2022); in the United States, *Aedes albopictus* has expanded into new areas due to warmer 289 conditions (Rochlin *et al*., 2013). Meanwhile, in parts of Africa, extreme droughts have led to 290 temporary reductions in *Anopheles* populations, disrupting malaria transmission cycles 291 (Diouf *et al*., 2020). 292

293 Climate change also directly affects pathogen cycles and their maintenance within 294 various reservoirs, ultimately influencing disease transmission. The ecology of these 295 pathogens depends on the complex interplay between vectors, reservoir hosts, and 296 environmental conditions. For instance, rising temperatures, shifting precipitation patterns, 297 and habitat changes can expand or reduce the distribution of reservoir hosts, directly 298 influencing pathogen persistence (Liao *et al*., 2024). Moreover, temperature also impacts 299 pathogen development within vectors. Higher temperatures often accelerate viral replication, 300 as seen with the dengue virus in mosquitoes, leading to increased transmission rates (Samuel 301 *et al*., 2016). Vector competence, or the ability of an arthropod to acquire, maintain, and 302 transmit a pathogen, is also strongly affected by climate change. Warmer temperatures can 303 weaken the immune defenses of mosquitoes and ticks, making them more susceptible to 304 infection and increasing their likelihood of spreading diseases (Ostfeld and Brunner, 2015, 305 Liu *et al*., 2023). The replication rates of many vector-borne pathogens, such as *Plasmodium* 306 (malaria) or arboviruses, increase at higher temperatures, which shortens the time required for 307 the pathogen to become infectious within the vector (“extrinsic incubation,” Barr *et al*., 308 2024). Climate change also intensifies transmission dynamics. Increased temperatures and 309 humidity can drive higher feeding frequencies in vectors, leading to more frequent host- 310 vector contacts and a greater likelihood of disease spread (Suh *et al*., 2020). 311

312 *Future research and opportunities.* Climate change reshapes vector density and distribution, depending on the landscape and vector species, and requires vigilance and continuous
313 monitoring. Future climate scenarios obtained from predictive models suggest that the vector 314 ranges will continue to shift, necessitating improved surveillance and control strategies (Koch 315 et al., 2017, Caminade et al., 2019, Colón-González et al., 2021). As true for non-vector 316 pathogens, more research is needed to understand how extreme events, such as heatwaves 317 and floods, affect vector population dynamics and pathogen survival. Future research should 318 focus on improving predictive models that combine climate variables, vector ecology, and 319 human factors to anticipate and mitigate disease emergence. Among the various climate- 320 related factors, urban heat islands deserve particular attention. An urgent need is to 321 understand how the alteration of cities’ microclimates (e.g. heat islands) affects the biology 322 and ecology of arthropod vectors. Indeed, these localized microclimatic effects may interact 323 with broader climate change dynamics, creating unique ecological conditions in urban 324 settings. Finally, recent advances in understanding the interactions of the microbiota with 325 arthropod hosts offers promise, highlighting the potential of vector microbiota as a key 326 partner in arthropod adaptation to climate change.

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328 C. Climate change and consequences for antibiotic resistance

329 *Overview and state of knowledge.* Antibiotic resistance, including MDR, is increasing 330 worldwide and is a major current threat to global health (Youenou *et al.*, 2016, Naghavi *et 331 al.*, 2024). It is urgent to understand how climate change together with anthropogenic use 332 and misuse of antibiotics alters microbiome structure and dynamics, and how this 333 combination can select for MDR pathogens and generally increase the resistome of microbial 334 communities (Delgado-Baquerizo *et al.*, 2017 & 2020, Wang *et al.*, 2024). Antibiotic- 335 resistance genes (ARGs) selection and transmission are directly influenced by climate change 336 (Rodríguez-Verdugo et al. 2020, Kusi *et al.*, 2022), leading to the loss of effective treatments
337 for pathogen infections, especially among ESKAPEE pathogens. Here, we discuss the
338 impacts of rising temperatures on the maintenance and dissemination of ARGs and ARB.

339 There are at least two central ecological mechanisms through which ARGs can
340 propagate in response to temperature increases: the selection of ARB populations or the
341 induction of ARGs transfer mechanisms. Regarding the selection process, elevated
342 temperatures may favor the growth of ARB, leading to a higher abundance of ARB within
343 their communities (Kaba et al., 2020) and higher prevalence of ARGs due to vertical
344 transmission. Abundant populations are more prone to dispersal by chance (Woodcock et al.,
345 2007), thus increasing their probability of disseminating ARGs. One of the early studies to
346 examine the relationship between rising global temperatures and the development of
347 antibiotic resistance used extensive public databases of ARGs from U.S. hospitals,
348 laboratories, and surveillance units (MacFadden et al., 2018). The focus was on three priority
349 pathogenic bacteria: E. coli, K. pneumoniae, and S. aureus. It revealed that a 10°C rise in
350 temperature between 2013 and 2015 was correlated to an increase in antibiotic resistance in
351 different antibiotic classes ranging from 2.2 to 4.2% (MacFadden et al., 2018). A similar
352 temperature correlation was observed across Europe from 2010 to 2016, between E. coli and
353 K. pneumoniae (McGough et al., 2020). However, the same European study found a decrease
354 in the antibiotic-resistant S. aureus due to simultaneous efforts to reduce the burden of
355 methicillin-resistant S. aureus (McGough et al., 2020), suggesting that vigilance around
356 antibiotic stewardship and related health policies can be effective.

357 In natural aquatic environments, the abundance of ARB increased in biofilms
358 incubated at 30°C compared to 20°C and 25°C in river water (Bagra et al., 2024). Warmer
359 temperatures approaching the optimal growth temperatures of ARB could partially explain
360 the correlation between temperature and antibiotic resistance (Kaba et al., 2020). For
361 example, an underground fire that elevated the soil temperature for decades shifted the
362 microbial community structure and changed the antimicrobial resistance and production gene
363 profiles (Dunivin and Shade, 2018, Sorensen et al., 2019). Therefore, the observed
364 distributions and propagation of ARGs in the environment, especially those encoded on
365 chromosomes and less likely to be transmitted horizontally, can also be independent of the
366 selective pressures from antibiotic or other pollutant exposure.

367 Warmer temperatures may also increase the dissemination of ARGs across different
368 bacterial populations via HGT processes of transduction, transformation, and conjugation.
369 Several studies have shown that warmer environments often have higher HGT rates and
370 abundances of mobile genetic elements harboring ARGs (Yang et al., 2023, Li et al., 2024b,
371 Zhao et al., 2025). When multiple antibiotic or metal resistance genes are co-located on
372 plasmids and thus co-selected, these also can be transferred horizontally. Conducive co-
373 selective environments have been identified, including wastewater treatment streams that
374 receive input from various sources (e.g. hospital, agricultural, and industrial wastes), and
375 where climate change stress plus antibiotic residues and heavy metals can together drive
376 antimicrobial resistance (Kusi et al., 2022).

377 *Future research and opportunities.* Managing the spread of ARGs and ARB requires an
378 integrated approach that considers the interdependence of human, animal, and environmental
379 health. However, the environment remains the component for which the least knowledge is
380 available compared to human and animal systems (Arnold *et al.*, 2024). Indeed, improper
381 disposal of clinical or agronomic waste, linked with increased antibiotic concentrations in the
382 environment, could transform bacteria into MDR strains (Wang *et al.*, 2024, Kothari *et al.*,
383 2023) and select for antibiotic resistant populations (Sanchez-Cid *et al.*, 2022). For example,
384 *Stenotrophomonas maltophilia* strains isolated from soils amended with untreated urban
385 waste showed resistance to at least 10 antibiotics (Youenou *et al.*, 2016). In contrast, urban
386 stream environments in Brazil close to hospital effluent had lower standard water quality
indexes without having higher occurrences of ARGs (e.g. Stehling et al., 2024). This and
other research suggest that the dissemination and detection of ARGs from the clinic to the
environment is complicated by many yet-unknown factors.

Given this complexity, studying the influence of climate change on bacterial
populations expressing an MDR phenotype is crucial. One approach to predict future
pathogen epidemiology is modeling the emergence and dispersal of environmental
populations carrying ARGs, and, specifically, targeting genes encoding efflux pumps, which
have cellular functions beyond antibiotic resistance and thus face selective pressures not
necessarily linked to antibiotic exposure. For example, genes encoding efflux pumps were
shown to be involved in a MDR phenotype expressed in the clinic and also in the adaptation
of pathogenic bacteria to environmental niches (Blanco et al., 2016, Chauviat et al., 2023).
Finally, there is a clear need for the broad adoption of metadata and reporting standards,
common database infrastructure, and analysis tools (source tracking and risk assessment)
across clinical, agricultural, and environmental settings. This initiative is exemplified by
public efforts from the United States National Database of Antibiotic Resistant Organisms,
the European Antimicrobial Resistance Genes Surveillance Network (EURGen-Net), and
PROMISE, the network involved in the surveillance of antibiotic resistance in France.

404 Microbes, Climate Change, and Plants

A. Plant-rhizosphere microbiota interactions under climate change

*Overview and state of knowledge.* In the next 100 years, humanity will face the great
challenge of feeding a growing population under future climate conditions that are expected
to impact plant productivity severely. Plant nutrition and growth highly depend on the
activity of the root and rhizosphere microbiota. Plant photosynthates fuel these microbial
communities at the root-soil interface, which participate in the cycling and recycling of major
411 plant-essential nutrients like P and N via microbial processes like solubilization,
412 mineralization, and N-fixation. Current research suggests that higher temperatures, increased
413 drought, and elevated CO₂ will significantly reshape plant-microbe interactions in the
414 rhizosphere. It is, however, still unclear how exactly rhizosphere functioning will be
415 impacted, to what extent this will impact plant productivity, and most importantly, how
416 rhizosphere research can be used to find solutions or mitigation strategies.

417 There are several climate change-associated threats to beneficial plant-microbe
418 interactions. Under elevated CO₂ and warmer average temperatures, plant photosynthetic
419 rates are expected to change with estimated predicted effects on global mean crop
420 productivity, going from -24% for maize to +18% for wheat (Jägermeyr et al., 2021). These
421 changes in plant photosynthetic rates are linked to changes in plant exudation in the
422 rhizosphere, with as much as 31% more exudates released belowground under elevated CO₂
423 conditions (Dong et al., 2021). This is expected to boost microbial activity in the rhizosphere
424 in the short term, as shown in different experimental studies on bacterial and fungal
425 communities (Jin et al., 2022) and on plant-beneficial arbuscular mycorrhizal fungi (AMF)
426 (Almario et al., 2022). However, in the long run, as mineral N and P nutrients are depleted
427 from the rhizosphere by the plant's increasing demands, this could lead to a decrease in
428 microbial activity in the rhizosphere (Terrer et al., 2019 & 2021). This last point suggests that
429 CO₂'s positive effects will likely be limited by nutrient availability under climate change.

430 Despite these threats, there are also several potential microbial solutions. Over the
431 last 70 years, research on the plant root microbiota has revealed a diversity of
432 microorganisms capable of promoting plant growth (PGPR, for plant-growth-promoting
433 rhizobacteria) via a diversity of mechanisms, including (i) enhanced plant nutrition through,
434 among others, free-living N fixation by diazotrophs, P solubilisation, siderophores
435 production, (ii) increased rhizogenesis through phytohormones production, or (iii) indirect
effects involving the protection of plants against plant pathogens or parasites such as against abiotic stresses (e.g. drought, salinity) with the modulation of the plant ethylene pathway through the 1-aminocyclopropane-1-carboxylic acid deaminase (Vacheron et al. 2016, Besset-Manzoni et al. 2018). PGPR belong to a diverse range of genera within *Pseudomonadota*, *Actinomycetota*, and *Bacillota* and possess numerous beneficial traits that directly or indirectly promote plant growth. Notable PGPR models like *Azospirillum*, *Pseudomonas*, and *Bacillus* have been shown to improve plant growth under climate change-associated stresses like drought, high salinity, heat stress but also pest and pathogen pressures (Vacheron et al., 2015 & 2016, Rolfe et al., 2019, Besset-Manzoni et al., 2019, Valente et al., 2019, Delamare et al., 2025). The inoculation of plants with PGPR could be seen as an acclimatization lever. Recently, *Brassicaceae* plants such as rapeseed and camelina were shown to have contrasted responses to heat stress and to PGPR. Heat stress is known to be responsible for crop failures, particularly penalizing oleaginous crops during the reproductive stage, where it affects root exudation quantitatively and qualitatively, and thereby their interactions with PGPR (Delamare et al., 2023). The most domesticated *Brassicaceae*, rapeseed, was shown to allocate more C to exudates and to endure the stress, with PGPR acting as a C sink. At the same time, camelina prioritized the C for its development irrespective of the bacteria (Delamare et al., 2025). Some PGPR have shown promising effects on field trials and are even sold as commercial biostimulants/biofertilizers (Cassán et al., 2020, Sivasakthivelan et al., 2023). Since plant nutrition will be a key factor in helping crops adapt to climate change, exploiting PGPR as a biofertilizer is a promising strategy to support it. While there are several bacterial biofertilizers, research to develop fungal biofertilizers is rarer due to the unpredictable success of the inoculation or formulation of commercial or culture collection isolates (Berruti et al., 2016). New types of root endophytic fungi that do not belong to classical mycorrhizal groups but can transfer nutrients like P and
461

N to plants in a “mycorrhizal-like” manner have recently been described (Almario *et al.*,

462

2022, Bruyant *et al.*, 2024). However, the potential of these fungi as natural biofertilizers is

463

still untested.

464

*Future research and opportunities.* Given climate change, there are several complementary
directions to ensure that rhizosphere-associated microbes continue to benefit plants.

466

Research on the rhizosphere microbiota under climate change should focus first on better leveraging plant-microbiota interactions to sustain plant growth by improving the efficacy of available microbial inoculants under climate change conditions. Microbial diversity of the rhizosphere can be mined for novel plant growth-promoting microbes, focusing on potentially important but neglected lineages or by embracing the complexity of microbial communities and using complex solutions with highly tailored synthetic microbial communities as bioinoculants (Berruti *et al.*, 2016, Nunna and Balachandar, 2022).

467

468

469

470

471

472

473

A second research focus should be on improving plant nutrition under climate change.

474

Given that plant nutrition will be a key bottleneck for plant growth under future climate conditions (Terrer *et al.*, 2019), it is surprising that research investigating the combined effects of nutrient limitation and climate change conditions on plant growth and rhizosphere functioning is limited. More attention should be given to relationships between the root microbiota and nutrient cycling in the rhizosphere by, for example, identifying more precisely key microbial groups involved in N and P cycling in the rhizosphere that directly promote plant nutrition and then testing their short- and long-term responses to future climate conditions. Embracing natural variation in plant-microbiota association by studying wild plants adapted to low-nutrient environments could also be a way to identify key microbial players for plant nutrition and translate these solutions into crops.

475

476

477

478

479

480

481

482

483
An emerging research direction is to remove the uncontrollability of “live” microbial solutions for plants by simplifying and managing the delivery of microbially-derived plant-beneficial molecules via biological nanoparticles. Extracellular vesicles (EVs) are lipid-based nanostructures secreted by bacteria (Briaud and Carroll, 2020) that can carry diverse molecular cargos, which makes them interesting in the context of biofertilizers (Ayala-Garcia et al., 2024). While bacterial EVs could possibly play a role in protecting plants from pathogens and supporting resilience to environmental stress (Meyer and Nodwel, 2024, Zannis-Peyrot et al., 2025), this potential plant-microbiome management strategy is in the early stages in investigation.

493

## B. Phytopathogen Interactions and Climate Change

*Overview and state of knowledge.* Plant pathogens, such as fungi, oomycetes, bacteria, and viruses, are the leading cause of crop loss worldwide, impacting food security and ecosystem stability (Singh et al., 2023, Lahlali et al., 2024). In recent years, the acceleration of climate change has disrupted the balance of plant-microorganism interactions, notably by modifying pathogen distribution, pathogen virulence, and the functioning of plant-pathogen interactions (Raza and Bebber, 2022). This, a critical goal for ensuring food security is to understand the impact of these climate-driven phytopathogen modifications so that the prevalence and severity of diseases that can impact agricultural yields can be anticipated.

Different bacterial phytopathogens respond differently to climate change-associated abiotic stresses, such as changes in temperature and humidity as well as elevated CO₂ levels. For example, drought has been shown to reduce *Ralstonia solanacearum* infection in tomatoes, probably because decreased soil moisture inhibits bacterial motility and thus host colonization (Islam and Toyota, 2004). Conversely, heat stress can enhance phytopathogen
508 virulence by altering key metabolic functions. For instance, the production of plant cell wall-
509 degrading enzymes is increased in *Erwinia carotovora* under high temperatures, potentially
510 accelerating tissue maceration and disease progression (Hasegawa *et al.*, 2005). In
511 contrast, *Pseudomonas syringae* shows reduced phytotoxin production under heat stress,
512 which may impact its ability to induce disease symptoms (Weingart *et al.*, 2004).

513 Fungal and oomycete pathogens are also highly responsive to climate change.
514 Drought stress enhances the aggressiveness of *Magnaporthe oryzae* in rice, mainly by
515 reducing plant defenses, resulting in the breakdown of major resistance genes (Bidzinski *et
516 al.*, 2016). In contrast, aridification of the Mediterranean climate modifies *Phytophthora
517 cinnamomi* abundances, although this is highly dependent on the predicted precipitation
518 (Serrano *et al.*, 2024). Moreover, elevated CO₂ levels differentially affect fungal diseases
519 depending on the host-pathogen system. For example, elevated CO₂ enhanced *Sphaerotheca
520 fuliginea* infections on cucurbits but reduced *Peronospora manshurica* susceptibility in
521 soybeans (Chaloner *et al.*, 2021). In cereals, elevated CO₂ levels promoted *Fusarium* head
522 blight and *Zymoseptoria tritici* blotch, with *Fusarium graminearum* isolates displaying
523 increased aggressiveness, leading to more severe wheat ear blight outbreaks (Hay *et al.*,
524 2021, Singh *et al.*, 2023). Additionally, rising temperatures promoted the emergence and
525 northward expansion of heat-adapted strains of *Puccinia striiformis f. sp. tritici*, the causative
526 agent of wheat stripe rust (Milus *et al.*, 2009). However, not all fungal pathogens benefit
527 from climate change; for example, the rust fungus *Triphragmium ulmarie* has declined in
528 some regions due to shifting climatic conditions (Zhan *et al.*, 2018), and there is a predicted
529 shift that will occur between potato and its pathogen *Ralstonia solanacearum* worldwide due
530 to climate change (Hubab *et al.*, 2025).

531 Compared to bacterial and fungal phytopathogens, there is less knowledge about how
532 climate change will impact plant viruses, but outcomes are also likely to be specific to the
plant pathosystem. Different virus species respond differently to elevated CO₂ levels. For example, the *potato virus X* infection of *Nicothiana benthamiana* was reduced under elevated CO₂. while the incidence of barley *yellow dwarf virus* was increased in wheat (Trebicki, 2020). The multiplication rate of the *tobacco mosaic virus* on tobacco leaves and *potato Y virus* in *Solanum tuberosum* increases with temperature until it reaches an inhibition threshold (32°C and 35°C, respectively) (Tsai *et al.*, 2022).

Beyond the direct effects on pathogens, climate change also alters plant-associated microbiomes and their plant hosts' physiology and immunity, often increasing host susceptibility to disease. Warming-induced changes in soil microbial communities have increased fungal pathogens while reducing populations of beneficial microbes capable of suppressing disease (Delgado-Baquerizo *et al.*, 2017 & 2020). Since elevated CO₂, increased temperature, and water availability changes affect plants physiology, they will indirectly impact viruses' populations distribution and incidence (Trebicki, 2020, Singh *et al.*, 2023).

Several studies have focused on climate change's impact on the plant immune system. The different models suggest that higher temperatures have distinct effects on plant resistance responses, with effector-triggered immunity preferentially activated at relatively low temperatures (10-23°C) and pattern-triggered immunity induced upon heat stress (Cheng *et al.*, 2013). Given the different effects of heat on plant defenses and pathogens, temperature variations could be involved in orchestrating the co-evolution dynamics of some plant immune pathways in response to pathogen physiological changes (Cheng *et al.*, 2013, Desaint *et al.*, 2020).

*Future research and opportunities.* Climate change will inevitably affect and increase the overall load of plant pathogens, in ways that needs to be anticipated to prevent significant crop losses (Delgado-Baquerizo *et al.*, 2020). Future studies will require developing new predictive tools and pathosystem-tailored strategies towards the challenges posed by the
558 impact of global warming on the dynamics of plant-pathogen interactions. On the one hand, 559 improved epidemiological models incorporating high-resolution climate projections are 560 already enabling us to improve disease emergence prevention and responsive biosafety 561 policies (Wang et al., 2021). A recent study has modeled how the distribution of potato and 562 tomato crops and their associated phytopathogens (Ralstonia solanacearum & Clavibacter 563 michiganensis respectively) will shift with climate change (Hubab et al., 2025). This study 564 showed that the areas suitable for tomato crop production overlap with its pathogen, whereas 565 potato will drift away from its pathogen (Hubab et al., 2025). The synergism of experimental 566 studies and models that consider compounded pressures of several environmental stressors 567 linked with climate change are necessary to accurately predict future plant-pathogen 568 interactions. Finally, exploring the emergence and evolution of phytopathogens with 569 historical, paleontological sources and geographically-informed surveys can also uncover the 570 impact of agriculture practices on the dispersal of pathogens between crops and wild plant 571 species (Bernardo et al., 2018, Malmstrom et al., 2022). This can help emerging pathogens 572 and future outbreaks that impact major food crops as the climate changes.

573

574 C. Nitrogen-fixing symbiosis under climate change

575 *Overview and state of knowledge.* Due to global change and intensification of land use, there 576 is a lower quantity of nitrogen available in terrestrial ecosystems, which can result in lower 577 levels of photosynthesis and subsequent removal of CO₂ from the atmosphere (Mason et al., 578 2022). In this context, high-yield cereal crops typically require substantial inputs of chemical 579 N fertilizers, 56% of which is estimated to be lost to land or water or reduced to N₂O (Guo et 580 al., 2023). However, both plants and microorganisms control N flows *in situ*. Soil 581 microorganisms release N from organic matter into soluble organic N (solubilization),
transform organic N into inorganic forms (mineralization), and oxidize ammonium ($NH_4^+$) to $NO_3^-$ (Mason *et al.*, 2022). They can also fix atmospheric nitrogen ($N_2$) as free-living microorganisms in soil or through nodulating symbioses with leguminous and actinorhizal plants (Smercina *et al.*, 2019). Thus, bioinoculation of plants with microorganisms known to impact N cycling can be used to reduce inputs of N fertilizers and thus GHG emissions. As there have been several reviews dedicated to climate change and its consequences for plant symbioses with rhizobia and AMF (Compant *et al.*, 2010, Liu *et al.*, 2024), we will focus on the outcomes of climate change for a specific plant-actinorhizal symbiosis, involving alders and a N-fixing actinobacteria from the *Frankia* genus.

*Frankia* through actinorhizal symbioses, is a key player in the N cycle because it biologically fixes 15 % to 25 % of $N_2$, and also enriches the soil with N-rich litter via decomposition (Dommergues, 1997). These Gram-positive bacteria present a complex morphology and development including: (i) hyphal growth of active cells, (ii) $N_2$ fixation in specialized cells (diazovesicles) and (iii) formation of multilocular sporangia containing numerous dormant offspring (spores). Two pathways for root infection have been described for compatible *Frankia* interactions: root hair infection or intercellular penetration depending on the host plant (Wall, 2000). Unlike the legume-rhizobium symbioses, the molecular mechanisms involved in *Frankia* interactions with the host plants are poorly understood.

However, studies suggest the participation of flavonoid substances in the nodulation process (Abdel-Lateif *et al.*, 2012).

Actinorhizal plants that can form symbioses with *Frankia* are distributed across 25 genera and 8 families. However, the most commonly used actinorhizal plants worldwide belong to the *Betulaceae* and *Casuarinaceae* families (Dommergues, 1997, Diagne *et al.*, 2013). From the *Betulaceae* family, *Alnus* is the most widely distributed genus of actinorhizal plants and is the dominant host of *Frankia* in the temperate Northern Hemisphere (Normand
et al., 2007, Põlme et al., 2014). Alder trees are early-successional species that can colonize open areas, forests, riparian habitats, glacial tills, mine spoils, riverbeds, wetlands, and gravel deposits (Normand et al., 1984, Alonso et al., 2022), and this colonization of difficult environments is enabled by their symbiosis with *Frankia*. The ecosystem services provided by alders result either directly from N₂ fixation by *Frankia* in their root nodules or indirectly through *Frankia*'s impact on tree fitness. Alder litter is rich in N and low in lignin, and has a low C/N ratio that makes it easily degradable by microorganisms (Yang and Zhu, 2014, Diao et al., 2020). This mineralization releases nitrogenous elements like NH₄⁺ and NO₃⁻ into the soil, enriching and fertilizing it (Špulák et al., 2019). By influencing N inputs into the soil, alders also affect microbial communities involved in the N cycle, which can, in turn, impact GHG fluxes, such as through N₂O production by alder rhizosphere microbial communities (Mander et al., 2014, Schindler et al., 2021). However, because the symbiosis between *Frankia* and *Alnus* leads to biological N fixation, their association could reduce the need for chemical fertilizers and thus GHG emissions, in a parallel manner to that of nodulating legumes in agroecosystems (Stagnari et al., 2017).

Climate change presents a severe risk for alders, their symbionts, and the stability of the ecosystem services they provide, with the possibility of local extinction if environmental conditions are no longer suitable and their symbiosis is compromised. For example, increased atmospheric CO₂, ozone pollution, and acid rain likely affect the physiological properties of *Frankia*-actinorhizal symbioses, impacting both the infection and nodulation processes and N fixation in actinorhizal plants (Tobita et al., 2013).

*Future research and opportunities.* A key strategy to sustain *Alnus*-related ecosystem services under climate change is to use tolerant *Frankia* strains to various environmental stresses (e.g. resistant to temperature increase, drought, heavy metals, salinity, desiccation) to
maintain or enhance alder fitness (Ngom et al., 2016). Some *Frankia* strains cope well with harsh conditions, while others may struggle to form effective symbioses under stress.

Understanding their different tolerances is essential for their ecological use under climatic changes. Among them, sporulating strains show great potential due to their ability to sporulate *in-planta* and exhibit a distinct ecological profile compared to non-sporulating strains (Schwintzer, 1990). They are preferentially associated with *A. viridis* in alpine environments (Pozzi et al., 2014, Schwob et al., 2018). Sporulating strain prevalence in extreme conditions suggests an adaptive advantage. By boosting the fitness of native alders under unfavorable conditions, these strains could be employed in inoculation protocols targeting enhanced adaptation potential. Their ability to sporulate *in planta* ensures soil persistence, providing infective propagules that can support alder growth and maintain N fixation, thus contributing to ecosystem stability under changing environmental conditions.

Another key strategy to sustain *Alnus*-related ecosystem services under climate change is to increase trees' genetic variability, which could enhance its tolerances to environmental extremes, particularly variations in temperature and humidity. For example, more flood-adapted species can be planted in riparian zones (Seavy et al., 2009), and more dry-tolerant species in zones more susceptible to drought (Hall and Burgess, 1990). This is also the case for other actinorhizal plants such as *Casuarina*, which are commonly used for land reclamation in arid ecosystems (Diagne et al., 2013). Alder could also be selected on their potential to mitigate N₂O emission by recruiting microbial communities that have low GHG emissions. Finally, more work is needed to understand the potential protection that *Frankia* symbiosis provides against pathogens that may become more of a threat with changing climate. We recently found that alder seedlings nodulated by *Frankia* have stronger defense responses against pathogen attacks than seedlings that are not nodulated, likely due to a priming effect of the symbiosis (Vincent et al., 2025).
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Microbial Ecology and Climate Change: Conclusions

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Some common themes for research opportunities emerged across the ecosystem, plant, and human perspectives, most notably needs for model development towards predictive modeling that can inform management. These effects of climate change on the microbial ecology that supports human, plant, and ecosystem health are intertwined across different abiotic and biotic interactors. This highlights the need for more holistic and systems-level approaches, where researchers accelerate the understanding of the complex and broad interactions within microbial populations and communities and across the levels of the ecosystems and hosts in and with which they thrive (Bittleston et al., 2025). We advocate interdisciplinarity initiatives for standardizing data and metadata surveillance, such as with the French Critical Zone Observatories (Gaillardet et al., 2018). These initiatives bring together scientists and experts from complementary fields to generate long-term environmental datasets, which lacks in the literature compared to other monitoring efforts (Arnold et al., 2024). These data types are indispensable to draw predictive scenarios on the impact of real-time extreme events on microbial communities. First reports have shown that future climate conditions will result in shifts in the ranges of vectors, crops, and pathogens (Koch et al., 2017, Caminade et al., 2019, Wang et al., 2021, Hubab et al., 2025). Including climate change in epidemiological models is expected to improve the prevention of disease emergence and inform responsive biosafety and biocontrol measures. Furthermore, inclusion of compounded climate-change stressors in experiments and modeling is necessary to understand their interactions for microbial ecology as it impacts human, plant, and ecosystem health. This may include, for example, scenarios of elevated atmospheric CO₂ or temperature combined with punctuated severe drought or heatwaves.
Another overarching challenge is translating research into policy and responding to real-time research information, such as needed during extreme weather events or infrastructure failures. While some climate-driven microbial outcomes are well-documented, these insights do not sufficiently inform, for example, urban planning, water quality management, or climate adaptation strategies. Closer collaboration between scientists, policymakers, and public health agencies is needed to ensure that research observations lead to actionable and reactive interventions (e.g. Pozzi et al., 2024). In addition, microbial genes or populations could serve as “sentinels” to impending functional shifts, because they have relatively fast generation times and are very sensitive to abiotic changes. Microbial tracking could serve as early warning signals to inform municipalities and their decision makers of responsive interventions. Thus, microbiologists and policy makers must engage more closely to proactively address these needs before the moment of a crisis.

There is also the great potential to develop microbial solutions to face climate change challenges for human, plant, and ecosystem health. From environmental phage therapy to mitigate N₂O emissions or control plant pathogens, to leveraging genetic variation in plants associated with N-fixing microbes to build tighter symbioses, there are many possibilities to understand and exploit how microbial populations and communities work to find solutions (Table 1). Microbial rescue (Mueller et al., 2019) and microbiome rescue (Shade, 2023) have been proposed to recover essential beneficial symbionts and community-level functions that have been generally disrupted, respectively. In the context of climate change, the literature offers much evidence that while microbial communities are generally sensitive to abiotic disturbances (not resistant), they can be surprisingly resilient, even after disturbances that are severe or atypical to the local environment (e.g. Shade et al., 2012, Shade, 2023, Boyle et al., 2024). Understanding the ecological mechanisms that support functional stability for microbial populations, communities, their hosts, and their ecosystems is a grand scientific
706 pursuit that will the advance the development of microbial solutions for the myriad
707 challenges climate change imposes.

708 It is accepted that near-term continuation and even intensification of the effects of climate
709 change are inevitable, and that today's efforts to stop climate change will, at best, alleviate,
710 but likely not reverse its impact in the future. Both fundamental and applied research in
711 microbial ecology are needed to tackle this urgent challenge and harness microbial solutions
712 that can be leveraged to support healthy humans, plants, and ecosystems on our changing
713 planet. Interdisciplinary teams, such as in the Microbial Ecology Research Unit in Lyon, that
714 bring together diverse expertise and broad professional networks, including people from
715 research, public, and private sectors, have a key role to play in the generation of fundamental
716 knowledge, bridges to application, and connection of both to climate-responsive policies. We
717 call on microbiologists, especially microbial ecologists, to apply their expertise to address the
718 urgent climate crisis.

719

720 Acknowledgements

721 The Laboratoire Microbial Ecology Lyon thanks the institutions that co-support its research
722 mission: the Centre National de la Recherche Scientifique (CNRS), the Universite of Claude
723 Bernard Lyon 1 (UCBL), the Institut national de la recherche pour l'agriculture,
724 l'alimentation, et l'environnement (INRAE), and the Institut national d'enseignement
725 supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de
726 l'environnement (VetAgro Sup). AS and CP-C acknowledge the COST Action
727 MiCropBiomes, CA22158, supported by European Cooperation in Science and Technology.

728

729 Conflict of Interest
730 AS reports research funding from the European Research Council, United States Department of Agriculture; Unpaid advisory board memberships: Joint Genome Institute (US
731
732 Department of Energy), Bigelow Single Cell Genomics Center, German Science Foundation
733 Excellence Cluster Microverse, Swiss National Science Funding NCCR Microbiomes; and
734 editorship at the American Society for Microbiology journal mSystems.

735 A.A.M.C reports research funding from the Agence Nationale de la recherche.

736

737 **Funding**

738 This work was funded by the University of Claude Bernard Lyon 1 (UBCL) for AAP
739 ‘ETOILES’ 2023 to AS.

740

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1338
1339 **Authors contribution statement (CrediT).**
1340 LG and AS contributed to conceptualization and administration. LG and FN contributed to

1341 visualization. AS contributed to supervision. All authors contributed to writing- original draft

1342 and writing- review and editing.

1343

1344 **Data Availability**

1345 No new data were generated or analysed in support of this research
<table><thead><tr><td>Microbial solution or intervention</td><td>Purpose</td><td>Key reference</td></tr></thead><tbody><tr><td>Biofertilizers</td><td>Enhance soil fertility in agriculture</td><td>Berruti et al., 2016</td></tr><tr><td>Bioremediation</td><td>Enhance natural biodegradation processes</td><td>Kour et al., 2021</td></tr><tr><td>Synthetic communities</td><td>Support host or ecosystem health</td><td>Nunna & Balachandar, 2022</td></tr><tr><td>Priming</td><td>Providing favorable conditions (e.g. substrate) to initiate microbial growth and functions</td><td>Mermillod-Blondin et al., 2019</td></tr><tr><td>Microbiome rescue</td><td>Replace microbial community functions lost to disturbance</td><td>Shade, 2023</td></tr><tr><td>Microbial rescue</td><td>Targeted replacement or re-association of threatened host beneficial microbes</td><td>Mueller et al., 2019</td></tr><tr><td>Microbial source tracking</td><td>Tracking of genes or microorganisms across hosts and ecosystems to determine origins and directions of spread</td><td>Wybraniec et al., 2024</td></tr><tr><td>Microbial sentinels</td><td>Microbial early warning indicators of impending consequential shifts in health or function, including ARGs or ARBs</td><td>Pozzi et al., 2024</td></tr><tr><td>Microbiome stewardship</td><td>Managing microbiomes to maintain biodiversity and functions</td><td>Choudoir et al., 2025</td></tr><tr><td>Phage “therapy”</td><td>Selectively repress undesired microbial populations (e.g. pathogens, particular functions)</td><td>Blazanin et al., 2022</td></tr><tr><td>Extracellular vesicles</td><td>Delivery of chemical or biological interventions to hosts or ecosystems</td><td>Zannis-Peyrot et al., 2025</td></tr><tr><td>Host genetic engineering</td><td>Identifying host genetic loci that select for association with beneficial microbiome members as a trait for breeding</td><td>Henry and Bergelson, 2023</td></tr><tr><td>Host-mediated microbiome engineering</td><td>Enrich microbial community members that are selected by a host in a particular situation, typically used for plants to help them resist abiotic stress</td><td>Mueller et al., 2019</td></tr></tbody></table>
1351

1352 **Figures**

1353 **Figure 1:** An overview of the impact of climate change stressors, such as drought and warming, on microbial ecology with implications for ecosystem, human, and plant health.

1354 Climate change's impacts on plant and soil microbial communities encompass responses and interactions with both plant pathogens, mutualists, and symbionts, including with plant-growth-promoting rhizobacteria (PGPR) or fungi (PGPF). Biological nanoparticles, including bacteriophages and extracellular vesicles, can also influence these interactions. Carbon (C), nitrogen (N), phosphorus (P), and sulphur (S) biogeochemical cycles are predominantly facilitated by soil microbes; climate change affects these cycles and especially the greenhouse gases emissions (GHG) of microbially-derived carbon dioxide (CO₂), methane (CH₄) and nitrous oxide (N₂O). Non-vector and vector-borne microbiota that infect humans and animals also have alterations in their dispersal, diversity, and functions with climate change. The shift towards pathogenicity in non-vector-borne microbiota, triggered by elevated temperature and humidity enhancing their virulence, has consequences for both agriculture and clinical settings. Finally, increases in the dissemination of antibiotic resistance genes from climate change, including the emergence of multi-drug resistant (MDR) pathogens, also threaten human health.

1369
<figure><img src="image_3.png" /></figure>
1371 Table 1. Examples of microbial solutions and interventions under investigation that
1372 could support human, plants, and ecosystems facing climate change.

1373

1374

1375