Advancements in Algal Microbiome Research: A Game-Changer for Climate Resilience and Invasion Success?

Abstract

While marine microbiomes have been getting more attention in recent years, they remain understudied compared to those of terrestrial systems. With the refinement of molecular methods, microbiome research has extended to other key marine organisms such as macroalgae. The microbiome plays a key role in macroalgal health, adaptation to environmental conditions, and resilience to climate stressors. The main factors affecting the algal microbiome are host specificity (genetics, functional profile, phylum and species identity), life stage, morphology, thallus region, and tissue age. Other significant drivers of microbiome community structure include spatiotemporal distribution and environmental conditions, especially as global stressors intensify with climate change. The mechanisms through which the microbiome of invasive seaweeds might enhance their competitiveness over native species are still unclear. However, there is evidence that, like climate resilience, invasive potential is linked to the functional flexibility of associated microbiota, allowing the host to adapt to the new environmental conditions. The main objective of this review was to synthesize the current understanding of the macroalgal microbiome and propose future directions in microbiome research based on identified shortcomings. Based on the knowledge gaps detected, there is an urgent need for multi-factorial experimental studies that link host and microbiome gene expression through chemical signals under future climate change scenarios, standardization of analytical methods, and a focus on underrepresented geographical regions and species. While algal microbiome research holds great promise for predicting and mitigating the effects of climate change and invasive species, embracing new tools and tackling ecologically relevant mechanistic and applied questions will be essential to advancing this field.

Introduction

A microbiome is a specific microbial community occupying a well-defined habitat or host, with distinct physicochemical properties and functions, and its interactions with the surrounding environment [1]. All the living microorganisms that are part of a microbiome (i.e., bacteria, archaea, algae, and fungi) are referred to as microbiota [2]. By these definitions, non-living microbial components (e.g., proteins, lipids, polysaccharides, and nucleic acids) and other structural elements (microbial metabolites and environmental conditions), together with the microbiota, form the microbiome. Microbiota are essential to the algal host as they play crucial growth-promoting and protective roles, forming a tight relationship that is analogous to the holobiont concept in coral ecology [3].

Although the components of the microbiome are constantly changing, it is useful to identify core microbiota (i.e., permanent members of the microbiome for a given host genotype or environment, often carrying out essential functions for the host) [4] and keystone taxa (i.e., members of the microbiota that have a major influence on microbiome composition and function regardless of their abundance) [5]. These key players contribute to nutrient cycling, disease suppression, and ecological interactions, and their functions are increasingly recognized as vital for the health and stability of ecosystems [3]. Interestingly, rare taxa also play an essential role across global microbiome communities through the production of antimicrobial toxins that regulate the growth of dominant taxa and enhance biodiversity [6]. Due to the high diversity of associated microbiota in some host organisms, defining their microbial components using molecular techniques can be very challenging [7].

The close link between hosts and their associated microbiota is likely the product of coevolution, and in order to have a comprehensive understanding of the processes affecting either one, they need to be studied conjointly [8]. Host and microbiome exert a mutual influence on one another, which makes discerning the direct versus indirect effects of external drivers extremely challenging [9]. On the one hand, a host may modulate its microbiome to dynamically adjust to changes in the environment [10], and biological and ecological traits of the host such as population density [11] and morphological complexity [12] directly affect microbiome diversity. On the other hand, microbiome genetic and functional composition influence the host’s health, ecological interactions, and resilience to external stressors [13]. In fact, disease development and worsening in host organisms, particularly in marine ecosystems, is often attributed to dysbiosis [14]. Dysbiosis refers to a disruption of the microbiome leading to imbalances in the microbiota and shifts in their functional composition and metabolic activity that can cause diseases in the host [15]. Interestingly, microbiome community composition is more variable among stressed hosts than healthy ones [16], possibly because stressors reduce the host’s ability to regulate microbiome composition.

The main objective of this review is to synthesize the current understanding of the macroalgal microbiome and propose future directions in microbiome research based on identified shortcomings. This study aims to answer the following questions: (i) What are the current knowledge gaps and limitations in the study of the algal microbiome? (ii) How does it contribute to its host’s health, and to its resilience in the face of environmental changes? (iii) What factors regulate the algal microbiome and mediate host-microbiome interactions? (iv) Does it mitigate or exacerbate the effects of climate change? and (v) How and to what extent does it influence the invasion success of non-native macroalgae? By establishing a clearer framework for understanding these complex relationships, this review intends to provide direction for future research and inform practical applications in marine ecosystem management.

Research Trends and Knowledge Gaps in Microbiome Ecology

While marine microbiomes have been getting more attention in recent years, and particularly during the last decade, they remain understudied compared to those of terrestrial systems. Research on marine microbiomes has focused largely on animal hosts, particularly sponges [3] and corals [17], as these systems are highly impacted by climate change, disease, and other anthropogenic pressures [18]. With the refinement of methods for the study of microbiomes in the past few years, microbiome research has extended to other marine organisms such as macroalgae. In a recent study, 14 microbiome core genera were identified across the three macroalgal phyla, accounting on average for over half of the bacterial abundances, and with genomic potential to degrade algal polysaccharides and produce bioactive secondary metabolites [19]. Despite their ecological importance, kelp microbiomes remain relatively underexplored compared to their coral counterparts, with most studies focusing on the role of epiphytic bacteria [19, 20], while other key microbial groups such as fungi and microalgae receive less attention.

To identify knowledge gaps in marine microbiome research, systematic literature searches were conducted using the Scopus database on February 22nd, 2025. In addition to its comprehensive coverage of marine and environmental science research, Scopus was selected due to its higher number of indexed journals and lower provision of irrelevant searches compared to other commonly used databases [21, 22]. Boolean operators were applied to construct search queries that combined relevant scientific and common terms (e.g., “macroalgae” OR “seaweeds”) through sequential inclusion (e.g., “microbiome” AND “macroalgae”). The search was restricted to research articles published in English and containing the selected terms within the title, abstract, or keywords. Results were screened manually and further filtered and organized by country of publication and year to analyze temporal and geographic trends in the literature.

The results of these systematic searches bring attention to critical knowledge gaps in marine microbiome research, with articles focusing on marine microbiome representing less than 2% of the total microbiome research. Moreover, only 8% of these articles studied the macroalgal microbiome, and only 7% of these investigated the microbiome of macroalgae in the context of climate change. More importantly, the potential role of algal microbiomes in mediating the invasive capacity of non-native species, a rising global issue, has been largely overlooked (Fig. 1a). This analysis also highlights microbiome ecology as an emerging research area, as evidenced by the growing body of scientific literature in recent years. Specifically, 70% of research articles about microbiomes, and over 90% of the articles on marine microbiomes, were published within the last decade. This was also the case for over 90% of articles relating macroalgal microbiomes to climate change, and 100% of the articles linking macroalgal microbiomes to invasive success (Fig. 1b).

Fig. 1.

Results of systematic literature searches in Scopus including (a) the total number of published scientific articles focusing on microbiome research and containing each of the key terms (sequentially inclusive) in their title, abstract, or keywords, and (b) the percentage of articles published before or within the last decade including these key terms

The Macroalgal Microbiome: An Understudied Ecosystem

Compared to more extensively studied microbiomes, including those of corals, sponges, and terrestrial plants, the macroalgal microbiome remains significantly underrepresented in the literature. In coral holobionts, the microbial diversity and functional interactions have been well characterized, with studies highlighting the roles of bacteria, archaea, viruses, and eukaryotic microorganisms in coral health and resilience [23, 24]. Similarly, over 40 bacterial phyla, which contribute to nutrient cycling and chemical defense mechanisms, have been identified in the highly diverse microbiota of sponges [25, 26]. In terrestrial plants, microbiomes research has revealed consistent core microbiota that play crucial roles in nutrient uptake, stress tolerance, and disease resistance [27, 28]. In contrast, studies on macroalgal microbiomes are fewer and often limited in scope, highlighting a significant gap in our understanding of marine holobionts and emphasizing the need for more comprehensive and systematic research in this area [29].

The microbiome of macroalgae is highly dynamic, influenced by factors such as host species, environmental conditions, and interactions with other organisms [30]. Microbiome biodiversity of macroalgae is often underestimated, with most studies focusing exclusively on the bacterial community [31]. Other members of the microbiome that are also essential in shaping its overall structure and function, such as microalgae, fungi, archaea, and viruses, have received less attention [3]. Moreover, until recently, microbiome studies had primarily focused on taxonomic diversity, with only a few studies investigating the functional potential of microbiota [9, 32]. Consequently, there is still a need to build a comprehensive framework for assessing the functional roles of microbiota across different macroalgal species and ecosystems. Unfortunately, there is a clear under-representation of certain geographical areas in algal microbiome research, particularly from underdeveloped regions (Fig. 2). The bias towards marine ecosystems in the Northern Hemisphere is concerning, as it overlooks critical habitats in continents like Africa, with available data failing to represent the full microbiome diversity of global ecosystems.

Fig. 2.

Map representing the scientific production (total number of articles published) on algal microbiomes by country. Data are extracted from systematic literature searches in Scopus

Although host specificity is one of the main factors influencing microbiota [33], the great majority of studies are limited to the study of “model” kelp species such as Macrocystis pyrifera (giant kelp) and Nereocystis leutkeana (bull kelp), and other commercially valuable species [31, 34, 35]. Chlorophytes are the most unrepresented phylum in algal microbiome research, followed by rhodophytes [29]. With increasing environmental stress on macroalgae, there is an urgent need for studying the microbial taxa across all life history stages of host organisms, as this remains a critical research gap [36]. Another key limitation in current research is the lack of longitudinal studies that track stressor-induced microbiome changes over time. The majority of studies provide a snapshot of microbiome diversity at a single point in time, which limits our understanding of microbiome’s short- and long-term responses to environmental change [37]. Furthermore, the lack of standardization in sampling methods, especially in underrepresented areas like the Southern Hemisphere, skews our understanding of global marine microbiomes [38].

Recent technological and methodological advances have allowed for more precise characterization of macroalgal microbiomes, though there is still no standardized protocol in microbiome research. A widely used approach to quantify microbiota in macroalgae is 16S rDNA amplicon sequencing [39]. Despite advancements including multi-omics, improved extraction methods, and development of specialized primers [40, 41], quantifying the core microbiome taxa remains challenging due to inconsistencies in analytical protocols [42], which introduce variability in the data [7]. This lack of standardization is further complicated by the high variability in macroalgal host species, including differences in tissue structure, surface chemistry, and production of antimicrobial compounds, all of which influence microbial colonization and persistence. For instance, macroalgae produce a variety of antimicrobial compounds that can affect the composition of their associated microbiota [43].

Additionally, taxonomic classifications of microbial molecular data heavily rely on the availability of comprehensive and high-quality reference databases. However, there remains a significant gap in genomic representation of marine microbes, especially compared to those from terrestrial and freshwater environments. This limitation reduces the accuracy of taxonomic assignments and constrains functional interpretation of microbial community data [44]. While technological improvements continue to advance the field, challenges related to contamination, database completeness, and host-specific variability remain critical barriers to studying macroalgal microbiomes effectively.

Friend or Foe? How the Microbiome Influences the Health of Its Algal Host

The macroalgal microbiome plays a critical role in host health, encompassing a spectrum of interactions, from beneficial symbioses that enhance growth and defense to pathogenic associations that can lead to disease and tissue degradation [3]. Understanding these dynamics is crucial, as environmental stressors can shift the balance of microbiota, influencing the overall health and resilience of macroalgal hosts (Fig. 3).

Fig. 3.

Impact of environmental stressors (climatic, natural, and anthropogenic) on the macroalgal microbiome, including composition and functional changes linked to dysbiosis. Under environmental stress, benign microbiota may become pathogenic, putative pathogens increase, and key functions are lost, often leading to disease. Microbiome diversity is overall higher in stressed than healthy holobionts, as new microbial taxa and functions emerge to adapt to the new environmental conditions

Beneficial Interactions

The macroalgal microbiome can have a symbiotic relationship with its host, promoting its growth [3, 45], morphogenesis [46], and defense [47, 48] under non-stressful environmental conditions across different taxa. In fact, bacteria isolated from algal microbiomes only express inhibiting properties against alien microorganisms in the presence of the algal host [49], indicating adaptation to an epiphytic lifestyle [50]. Microbiome community abundance directly affects propagule success in M. pyrifera, modulating its recruitment success and the health of kelp forest ecosystems [51]. Kelp-specific microbiome taxa often include bacteria that prevent the colonization of eukaryotic larvae and exhibit antibacterial activity [52]. Similarly, Ghaderiardakani et al. [53] found that morphogenesis and resilience of Antarctic Ulva spp. depend on algal growth and morphogenesis-promoting factors released by cold-adapted bacteria. The presence of certain bacterial groups with specific ecological strategies within the microbiome is linked to harmful macroalgal blooms such as the green tides caused by Ulva prolifera [54]. Among the most common growth-promoting bacteria are Maribacter sp. and Sulfitobacter sp., both found in the microbiome of red and green algae [55]. In many brown algae, the predominant family are Proteobacteria, which produce organic compounds called siderophores that can enhance algal growth under iron-deficient conditions [50].

Epiphytic microorganisms can increase nutrient availability to their macroalgal hosts by converting nutrients into bioavailable forms, as observed in Nereocystis leutkeana [56]. Beyond inorganic nutrients, microbial symbionts may also contribute essential organic compounds. For instance, several macroalgal-associated bacteria possess genes for synthesizing vitamins such as B₁₂, which are crucial for algal metabolism but cannot be synthesized by the hosts themselves [39, 57]. This aligns with broader findings across algal systems demonstrating widespread auxotrophy (i.e., the inability to synthesize a particular organic compound needed specifically for growth) for B₁₂ and other vitamins, as shown in the model green alga Chlamydomonas reinhardtii [58]. Metabolic exchange has been directly shown in co-culture experiments, which found reciprocal metabolite transfer between Lobomonas rostrata and vitamin B₁₂-producing bacteria [59]. Similarly, in Saccharina japonica, folate biosynthesis genes expressed by associated bacteria have been linked to microbial community stability and host health [60]. Together, these studies emphasize that nutrient and vitamin exchange is not only genetically possible but functionally important for host-microbe interactions in macroalgae.

Pathogenic Interactions

Pathogens are common in marine microbiomes, and increases in relative abundance of putative pathogens due to dysbiosis can cause diseases in the host [61, 62]. Many pathogens have a similar detrimental impact on macroalgae, such as bleaching disease in the rhodophyte Delisea pulchra [62], malformation disease in kelp S. japonica [63], and fungal diseases in the fucoid Phyllospora comosa [64], and the commercially valued Saccharina japonica [65]. Thus, monitoring variations in the epibacterial communities and functional groups across the different life stages of a macroalga can be useful to anticipate disease outbreaks.

Several bacterial taxa commonly found in macroalgal microbiomes can shift from benign or mutualistic roles to pathogenic under environmental stress, particularly elevated temperatures. In brown algae such as Fucus vesiculosus and Saccharina latissima, warming has been associated with increased abundance of Vibrio spp., including V. alginolyticus and V. splendidus, which can cause tissue damage and biofilm formation [66]. Similarly, Pseudoalteromonas and Alteromonas, typically considered part of the core microbiota, have been observed to contribute to tissue degradation when host-microbiome interactions are destabilized [3, 67]. In red algae, the bleaching of D. pulchra under heat stress has been linked to opportunistic pathogens such as Nautella italica R11, which disrupts the host’s chemical defenses, as well as to members of Ruegeria and Thalassobius [68, 69]. While fewer specific pathogens have been identified in green algae, similar dysbiotic shifts involving Vibrio, Alteromonadaceae, and Flavobacteriaceae have been reported in Caulerpa spp. under eutrophic and warming conditions [70]. These findings highlight how environmental stress can tip the balance of algal microbiomes, enabling opportunistic bacteria to proliferate and contribute to host decline.

What Factors Regulate the Algal Microbiome?

The water column microbiome differs significantly from the algal microbiome across the three main groups (i.e., Chlorophyta, Rhodophyta, and Phaeophyceae), and regardless of geographical location [71, 72]. Pfister et al. [73] reported higher taxonomic and phylogenetic diversity within the kelp microbiome compared to microbiota in the seawater outside of the kelp bed, likely because in addition to environmental conditions, community structure and diversity of algal microbiomes highly depend on host specificity [30, 33, 49]. In fact, macroalgal microbiomes induce significant shifts in water column microbiota but only minor changes in the microbiomes of co-occurring algae [74], further supporting the idea that the macroalgal hosts have a strong influence on the microbiota that associate with them.

Host Specificity

Core microbiome composition is determined by factors including host genetic relatedness [75], functional traits [76], and taxonomic level, from species identity [35] to phylum-level classifications [77]. However, the structure of bacterial communities within algal microbiomes appears to be more strongly influenced by microbial functional traits than by taxonomy, as taxonomical grouping does not always correlate with microbiome composition [20]. Differences in the microbiomes of genetically similar hosts can be due to life stage [78], morphological complexity [77, 79], tissue or thallus region [80, 81], and tissue age [12, 35, 82]. The core microbiome might be absent during early life stages of macroalgae and associate with the host organism at the adult stages [83]. Microbiome variability across different thallus regions might be due to physiological processes like oxygen metabolism [84] and chemical production [41], with epimicrobial communities generally regulated by the host’s surface metabolites [40]. Interestingly, older tissues usually have higher species abundance [79] and a more diverse microbiota [82], possibly as a result of transitory microorganisms accumulating over time [85] or increased maximum quantum yield of photosystem II [86]. Higher photosynthetic efficiency may enhance the release of organic exudates, creating a richer chemical environment that supports greater microbial diversity [87].

Environmental Conditions

Environmental conditions can deeply affect the algal microbiome [88], often explaining spatial variability across oceans, intertidal regions [89], or between nursery and natural ecosystems [90]. The majority of studies on the impact of environmental stressors on microbiome community structure and host-microbiome interactions consider either the effects of temperature alone or the combined effects of temperature and light, carbon dioxide, or nutrient concentrations [91, 92].

Temperature

The impact of warming on macroalgae is highly species-specific. Elevated temperatures have been shown to impair growth, reproduction, and tissue integrity in some brown algae [93, 94]. However, some species can benefit from moderate warming, depending on local adaptation and baseline thermal tolerance [95]. However, across multiple algal lineages, warming is consistently associated with microbiome dysbiosis [96, 97]. These shifts often involve an increase in opportunistic or pathogenic bacteria, weakening beneficial host-microbiome interactions and compromising algal health [30, 66].

In addition to compositional changes, elevated temperatures can disrupt key microbial functions, such as the production of antifouling or protective compounds by epiphytic bacteria. This disruption has been linked to increased susceptibility to infection and disease in both brown and red algae [69, 70]. Moreover, temperature-induced shifts in the microbiome can cascade beyond the algal host, altering trophic interactions and herbivore responses in kelp-dominated systems [14, 97]. These findings emphasize the central role of temperature in modulating not only algal physiology but also the ecological stability of host-microbe relationships.

Light Availability

Light availability is another factor that shapes the macroalgal microbiome, with a direct impact on the host’s production of surface metabolites associated with photosynthesis, and leading to changes in epiphytic community structure [92]. Prolonged exposure to ultraviolet (UV) radiation causes a reduction in diversity and evenness of the associated bacterial community in red macroalgae [71]. Conversely, shading, often as a result of habitat transformation due to coastal urbanization, can make algal hosts, and particularly kelp species, more susceptible to colonization by fouling organisms [34]. However, the effects of light on brown algae are species-specific, since studies have shown that antifouling defense mechanisms against epibacteria are minimally altered by shading in fucoids [98]. Within the Fucus genus, varying levels of abiotic stressors (i.e., desiccation, temperature, and light) across the intertidal zone explain differences in the relative abundance of specific bacterial groups, suggesting that the drivers of a host’s distribution also affect its microbiome [89].

CO₂ Levels

Although increased CO₂ levels do not affect the algal microbiome as much as temperature [91], they can affect the host organism’s physiology and significantly disrupt the water microbiome [14]. Ocean acidification may affect the photosynthetic efficiency of kelp, leading to bleaching and degrading tissues, potentially having indirect effects on the microbiome [61]. In giant kelp, high CO₂ concentrations prompt the release of stress-response molecules that affect microbiome community structure, particularly targeting potentially pathogenic bacteria, to adapt to the new conditions [99]. Similarly, coralline algae rely on a tightly regulated host-microbiome interaction that guarantees the stability of the algal microbiome when exposed to high CO₂ levels, conferring on their hosts some resilience against ocean acidification [100].

Salinity

Salinity also impacts taxonomic composition of the microbiome while minimally altering functional profiles, likely due to the presence of high salinity-adapted bacteria that contribute to stress mitigation when exposed to a wide salinity gradient [101]. This functional stability, despite shifts in community structure, reflects a degree of redundancy that enables host acclimation across a wide salinity gradient [102].

Nutrients

Nutrients can affect microbiome community composition directly or indirectly by driving physiological changes in the host macroalgae. Nutrient enrichment affects the taxonomic and functional structure of kelp-associated bacteria, which have shown a low community resistance index throughout the thallus [103]. Rot diseases that disrupt the bacterial community of brown algae in favor of degraders that alter community functions, and in turn exacerbate the disease, have been attributed to seawater nutrient levels [65]. Both phosphorus and nitrogen concentrations are strongly correlated with the relative abundance of Bacteroidetes and Vibrio species in green [104] and brown [105] algae, respectively. These microbiome responses are potentially linked to higher algal dissolved organic carbon (DOC) and dissolved organic matter (DOM) release rates under high nutrient availability and the subsequent consumption by these bacteria [67]. Nitrogen availability modulates the role of bacteria-kelp interactions in enhancing kelp growth, although its regulatory effect depends on the genetic background of the host [106]. Apart from changes in the water’s physicochemical properties, the presence of epiphytic bryozoans also alters the kelp microbiome, potentially causing dysbiosis and the proliferation of opportunistic pathogens that can have a detrimental effect on the host’s health and productivity [107].

Biogeography

At the interface between host and environmental factors that influence microbiome composition are spatial distribution and seasonal variation. The relative influence of geographic location on algal microbiome structure depends on phylum and species, with a generally greater influence in red than green or brown algae [104]. While kelp microbiomes exhibit intraspecific differences among largely disconnected geographical areas, some remain relatively stable within regions [37]. In fact, several studies have found a very high correspondence in bacterial communities among sympatric species’ microbiomes regardless of geographical location [97, 108]. Notably, microbiome community structure, and particularly bacterial composition, can greatly vary at small spatial scales (< 100 m) [72, 109]. Roth-Schulze et al. [110] described core functional genes in the microbiome of Ulva spp. spanning a large geographical area and suggesting functional biogeography might be more strongly linked to microbiome composition than geographical distance. Another study reported similar structure and alpha diversity in the microbiome of F. vesiculosus across a latitudinal gradient [111]. These data suggest that spatial distribution is secondary to host identity in regulating algal microbiomes.

Does the Microbiome Exacerbate or Mitigate the Impact of Climate Change on Its Algal Host?

Climate change poses a complex and growing threat to marine macroalgae, not only by directly affecting their physiology, but also through indirect effects on their microbiomes. Key stressors such as ocean warming, acidification, nutrient enrichment, and increased irradiance can impair macroalgal metabolism and growth, ultimately influencing population health and ecosystem function [51]. For instance, elevated temperatures may reduce photosynthetic efficiency, damage cellular structures, and affect reproductive timing in various macroalgal groups [91]. Acidification may inhibit calcification processes and alter nutrient uptake, while eutrophication can cause nutrient imbalances that further affect macroalgal hosts [96, 112]. These stressors, when combined, can severely disrupt the functional equilibrium of the holobiont.

Beyond the direct effects on algal physiology, climate change can destabilize the intricate relationships between macroalgae and their associated microbiota, leading to a state of microbial imbalance often associated with negative health outcomes known as dysbiosis. As seen in corals, warming can lead to shifts in microbial community composition that favor opportunistic or pathogenic taxa, triggering bleaching or disease outbreaks [113]. A similar pattern has been observed in red algae such as D. pulchra, where thermal stress resulted in microbiota restructuring and increased pathogenicity, ultimately causing bleaching and tissue loss [114]. In addition to the increase in opportunistic pathogens, there is a risk of losing beneficial or essential symbionts that contribute to host resilience through nutrient cycling, stress protection, and immune regulation [115, 116]. An example of this is the inhibition of key microbiome functions in rhodoliths and subsequent resilience loss due to ocean acidification [100]. Thus, climate-driven microbiome disruption can simultaneously amplify harmful microbial interactions and compromise essential mutualistic functions.

Despite the growing concern over the destabilizing effects of climate stress, the joint effects of multiple environmental stressors on algal microbiomes remain understudied compared to free-living aquatic microbiota. Multiple-stressor effects on the microbiome have mostly been evaluated in descriptive studies rather than controlled mesocosms or laboratory conditions. The few studies that assessed the joint effects of temperature and other drivers on macroalgae found both additive [91] and synergistic [14] effects with CO₂, synergistic effects with light [92], and additive effects with nutrient stress [96, 103]. Minich et al. [14] observed stimulated kelp growth and an increase in microbiome diversity under the combined impacts of high temperature and CO₂ levels, consistent with a broader trend observed in other marine hosts where environmental stress leads to a diversification of the microbiome [16, 112, 117]. These shifts may reflect both adaptive microbial responses and increased holobiont instability, with more targeted research needed to disentangle the two.

In this context, an important emerging question is whether the microbiome can also mitigate or buffer the negative impacts of climate change on macroalgae. Some microbial taxa provide functions that help the host tolerate abiotic stress, such as enhancing nitrogen uptake, producing antioxidants, or modulating hormone signaling pathways [115, 116]. For example, specific bacterial taxa have been shown to improve thermal tolerance or support recovery after bleaching events [118], akin to “beneficial probiotics” in corals and terrestrial plants. Bonthond et al. [117] found that non-native populations of Gracilaria vermiculophylla exhibited more stable microbiota under thermal stress than native ones, suggesting that invasion processes may select for microbiome configurations that are more resilient or protective. Similarly, Molnar et al. [112] showed that shifts in microbial functional traits under combined stress conditions could help maintain host performance through metabolic compensation. However, these protective capacities appear to be context-dependent, highlighting the need for a mechanistic understanding of host-microbe interactions under variable environmental conditions.

The responses of algal microbiomes under future climate scenarios are uncertain, and identifying their regulatory factors (i.e., the molecular, physiological, and ecological mechanisms that shape microbial community dynamics in changing environments) remains a challenge [119]. Studying climate impacts on algal microbiomes is not only crucial for predicting ecosystem responses, but also provides broader insights into holobiont dynamics, particularly under new environmental scenarios [120]. Many of the traits that facilitate macroalgal resilience to climate change, such as microbiome flexibility, compositional stability, and functional redundancy, are also central to the success of biological invasions [117]. Just as invasive macroalgal species must rapidly adapt to unfamiliar environments, climate change imposes sudden and shifting conditions that challenge the stability of host-microbiome systems. Exploring this overlap may help identify general principles of holobiont adaptability and guide strategies for ecosystem restoration, biocontrol, or assisted adaptation.

Taken together, these findings underscore the importance of integrating microbiome research into marine climate resilience frameworks. Future studies should aim for multi-factorial experimental designs, broader taxonomic and geographic coverage, and a deeper focus on microbial functionality rather than taxonomy alone. These approaches will help clarify the dual role of the microbiome, conferring resilience or exacerbating stress, in shaping the future of macroalgal ecosystems.

The Role of the Microbiome in the Invasive Potential of Macroalgae

Despite the growing evidence that the microbiome strongly influences invasive potential (i.e., the development, spread, and potential impact on native ecosystems) of non-native macroalgae, very little is known about the underlying dynamics and processes. The exact mechanisms through which the microbiomes of invasive seaweeds confer on them a competitive advantage over native species differ among species. However, there are some similarities across phyla, and even with invasive corals [17]. Generally speaking, the successful introduction of invasive brown algae to new environments is attributed to the high diversity and successional rate of their associated microbiota. For example, the microbiome of Sargassum muticum shows high spatiotemporal and tissue-specific variability, supporting the idea that microbiota associated with invasive species are very dynamic and adaptable, which can potentially enhance their ecological success and competitive advantage [85]. Moreover, studies on the invasive Sargassum horneri suggest that the host organism may alter its surrounding microbial environment, exacerbating the impact of other external disturbances and delaying the recovery of native kelp populations [51].

The flexibility of host-microbiome associations in non-native seaweeds has also been reported in red and green algae. For instance, microbial interactions are crucial for understanding the spread of Asparagopsis spp., whose microbiome is influenced by both the host and environmental factors, possibly contributing to its success in new ecosystems [49]. Similarly, studies on the microbiomes of Asparagopsis spp. [121] and Gracilaria spp. [122] show that host promiscuity (i.e., its ability to form relationships with a diverse number of species within the microbiome) can facilitate invasion processes by enhancing ecological adaptability and allowing these species to better adjust to new environments. Moreover, a recent experimental study found that microbiome beta diversity increased more in native than non-native G. vermiculophylla populations under thermal stress, suggesting that invasion processes may select for traits that make non-native hosts more stable and resilient to microbial disruptions under stress [117].

Research on the microbiome of non-native green algae has mostly focused on invasive Caulerpa taxifolia, and particularly its spread in the Mediterranean. Studies have found a strong alignment between the algal host’s genomic and endophytic microbial diversities, reinforcing the holobiont concept as the core unit of invasion and spread [70]. In fact, C. taxifolia’s recent regression in the Mediterranean might be linked to the holobiont’s low genetic diversity, highlighting the potential adaptive advantages provided by metabolically active bacterial communities. In addition to microbiome flexibility, some environmental stressors can strengthen the resistance and resilience of invasive green algae. For example, nutrient enrichment contributes to the proliferation of Caulerpa spp. through alterations in its associated bacterial communities [76, 123]. These findings highlight the adaptive potential of invasive seaweeds, with microbiota that may provide them with ecological advantages, including stress tolerance and enhanced growth.

Characterizing bacterial communities that support the proliferation of invasive macroalgae can be used to trace the origin of invasion and implement more informed management strategies [49]. Comparing the microbiomes of co-occurring native and non-native macroalgae can help assess invasion risk, as microbiome transfer may indicate increased potential for invasive success [124]. Similarly, understanding the microbiome of native macroalgae could help identify microbial factors that enhance resilience to both environmental stressors and invasions [9]. By focusing on the functional roles within the microbiome and understanding host-microbiome interactions, future research could help develop strategies to anticipate and mitigate the impacts of invasive species.

Applications of the Algal Microbiome in Sustainable Industrial Development

The potential of the algal microbiome for industrial applications is immense. Specifically, it can be used to improve the sustainability and efficiency of seaweed farming, either for consumption or for the development of bio-stimulants that offer an environmentally friendly alternative to the chemicals traditionally used in agricultural practices [54]. Identification of ecological and functional core microbiome taxa, particularly polysaccharide depolymerizing and growth-promoting groups, can be useful to develop new aquaculture strategies for commercially valuable seaweeds. Several studies have shown that specific bacterial strains can significantly increase the biomass of Ulva spp. [53, 125], highlighting the potential of microbiome manipulation to enhance seaweed productivity.

The use of beneficial microbes to reduce pathogens can ensure healthier and more robust seaweed crops for both environmental and industrial use. The “microbial gardening” approach has been shown to attract beneficial bacteria that provide protection against pathogens in Agarophyton vermiculophyllum, thereby enhancing seaweed health [126]. A combination of reductionist and systems biology (i.e., breaking down the components of the system and then putting them together for a comprehensive network analysis) might be an effective approach in microbiome engineering, with potential to increase the adaptability of macroalgae to stress [120]. Manipulating algal microbiomes across multiple species could make seaweed aquaculture more efficient, contributing to carbon capture efforts and sustainable resource production [127].

Understanding and manipulating microbial interactions within the microbiome can be used to enhance algal lipid production, lowering operational costs and improving the feasibility of biofuels derived from algae [128]. For instance, microorganisms capable of breaking down complex carbohydrates like agarase and carrageenase hold promise for converting seaweed biomass into bioethanol [129]. Moreover, host-bacteria associations could be harnessed for industrial benefits, as they regulate the microbiome’s functional roles of supporting the health and growth of seaweeds [67]. The enzymatic potential of seaweed-associated microbes opens avenues for applications in multiple sectors, and with reduced environmental impacts relative to conventional biofuel production.

Future Directions in Microbiome Research

Future microbiome research should prioritize determining whether the host or the microbiota respond first to global stressors, and studying the shifts in host-microbiome dynamics and their underlying infochemical mechanisms in response to climate change [130]. Despite being secondary to host specificity in shaping microbiota, seasonal fluctuations in environmental factors shape the presence of infochemicals in macroalgae and therefore must be carefully considered in microbiome studies [41]. In addition to descriptive studies across natural gradients of environmental drivers, experimental manipulations are needed to shed light on how holobionts will interact with their environment under future climate change scenarios [115]. Rather than focusing on the regulating effect of a single factor, studies should include multiple-stressor and multi-factorial experimental designs that consider host genetics, morphology, geography, and water quality parameters, all of which are essential in structuring the microbiome of foundational seaweeds [131].

Besides direct species restoration, maintaining a functional microbiota may be the key to the success of microbiome-assisted restoration of marine habitats [132]. To achieve this, there is an urgent need to catalog microbiome genes and their functions using meta-omic approaches to link host and microbiome gene expression [115]. Furthermore, the possibility of forecasting abrupt microbiome events by applying classic ecological concepts to diverse microbial systems [133] could be extremely useful to anticipate macroalgal responses to climate change, including harmful algal blooms. Expanding microbiome research to kelp species in the Southern Hemisphere will also provide a more comprehensive understanding of how microbiota vary across different ecological contexts and environmental gradients, helping to inform conservation and management strategies.

Future research should also explore the role of microbiomes in developing sustainable macroalgae farming strategies. Countries such as China, Indonesia, Norway, and Chile are major producers of farmed macroalgae species like Saccharina, Gracilaria, and Macrocystis [134, 135], facing challenges including disease, environmental stress, and reduced productivity [136]. Microbiome manipulation, using techniques such as microbial inoculation or the selection of microbiome-compatible host genotypes, can be an extremely effective approach to support host health, increase resilience, and enhance yield [67, 127]. These practices could help overcome issues in large-scale seaweed farming and promote environmentally sustainable aquaculture practices.

Moving forward, microbiome research should be centered around comprehensive experimental studies integrating chemical ecology and drawing lessons from coral microbiome manipulation research [137] to enhance long-term resilience against global stressors, particularly in foundational seaweeds like kelp forests. The detection of early warning indicators in microbiomes anticipating the potential ecological impact of non-native macroalgae can provide valuable insights into how to manage and control invasions. Finally, the application of new technologies, such as high-throughput sequencing and metabolomic profiling, offers unprecedented opportunities to explore the full complexity of kelp microbiomes.

Conclusion

Macroalgal microbiomes are central to the health and resilience of marine ecosystems, yet significant knowledge gaps remain regarding their roles in host adaptation, ecological dynamics, and responses to global change. While research has highlighted their potential in informing conservation and restoration, there is an urgent need for a more critical understanding of microbial function, biogeographic variability, and long-term ecosystem impacts. Integrating microbiome studies with climate science, invasion biology, and ecosystem management, especially in underrepresented regions and taxa, will be essential for developing predictive and actionable strategies. While algal microbiome research holds great promise for predicting and mitigating the effects of climate change and invasive species, embracing new tools and tackling ecologically relevant mechanistic and applied questions will be essential to advancing this field.

Author Contribution

M.V.D. is the sole author of this review article. She conceptualized the study, conducted the literature review, analyzed the relevant research, and wrote the manuscript.

Funding

Funding for open access publishing: Universidad de Granada/CBUA.

Data Availability

No datasets were generated or analysed during the current study.

Declarations

Competing interests

The authors declare no competing interests.