Beneficial microbes in coffee production and processing

Introduction

Coffee is a major plantation crop in southern India, cultivated over 292,000 hectares with an annual production of around 282,000 tonnes and export earnings of approximately $200 million. The two main commercially grown species are Coffea arabica and Coffea canephora (robusta), raised in proportions of 70 and 30 % respectively (Davis et al., 2006; Vieira et al., 2006) [15,83] . Despite being a monoculture, coffee is typically grown under the shade of diverse native trees, creating a forest-like environment that supports rich biodiversity (Venkatesha, 2010) [82] . The plant, a perennial from the Rubiaceae family, belongs to the Coffea genus, which includes about 100 species, though only C. arabica, C. canephora, and C. liberica are used for beverages. Arabica is native to Ethiopia's highlands (1,300-2,000 m), and Robusta is originating from tropical lowlands of Africa, together account for nearly all global coffee production. As the most traded tropical agricultural commodity and the second most consumed beverage after water. Coffee holds significant economic and ecological importance (Duongo et al., 2020) [23] . Coffee (Coffea spp.) is one of the most important global commodities and a major source of income for millions involved in its cultivation, particularly in countries like India where it is traditionally grown under a two-tier canopy of diverse shade trees. This agro-forestry based system contributes to the sustainability of coffee farming by adding substantial organic matter to the soil through leaf litter and biomass from routine pruning. However, the increasing reliance on chemical fertilizers to enhance yield poses significant threats to soil health and long term productivity. In this context, sustainable soil fertility management has become crucial. Among various strategies, biofertilizers and microbial inoculants have emerged as promising alternatives due to their ability to enhance nutrient availability, stimulate beneficial microbial activity in the rhizosphere, and improve soil structure while reducing dependence on synthetic inputs. Integrating such biologically based practices including biomass recycling, cover cropping, integrated nutrient management, and carbon-sequestering agroforestry systems not only supports soil health and crop yield but also aligns with the broader goals of eco-friendly and economically viable coffee production (Nadaf et al., 2024) [55] . The use of microbes in coffee farming and industry remains largely underutilized, despite their potential to reduce chemical inputs, enhance coffee quality, and improve farmer income through sustainable certifications (Mithöfer et al., 2017) [52] . Additionally, integrating the plant microbiome into modern breeding strategies offers promising avenues for sustaining productivity (Nogales et al., 2016; Orozco-Mosqueda et al., 2018) [57,58] . This review highlights (i) the role and potential of biofertilizers in sustainable coffee cultivation, particularly in enhancing soil fertility, plant health, and environmental resilience; (ii) summarizes current knowledge on the use of microorganisms for promoting plant growth and managing pests and diseases; and (iii) explores their possible applications in coffee processing.

Microorganisms associated with coffee

The microbiota associated with coffee is divided into two principal components. The first one is the indigenous microbiota composed of the microorganisms living in close association with the coffee plants in the soil at the vicinity of the roots (rhizosphere) at the surface (episphere), and inside the plant tissues (endosphere). The second component is related to the postharvest microbiota that encompasses all the microorganisms associated with the coffee cherries postharvest processing and its by-products including the fermentation, the drying steps, and the wastes.

The Indigenous Coffee Microbiota

The composition of plant-associated microbiota is influenced by a wide range of biotic and abiotic factors. These include the physical and chemical properties of the soil (Fierer, 2017; Tkacz et al., 2020) [28,74] , the specific plant compartment (such as the rhizosphere, episphere, or endosphere), and the particular plant organ being studied (Compant et al., 2019; Berg et al., 2020; Tkacz et al., 2020) [12,8,74] . Additionally, plant genotype has been shown to play a significant role in shaping the microbial community (Patel et al., 2015; Mina et al., 2020) [59,51] . It is important to highlight that the majority of microorganisms associated with coffee plants have been documented in Coffea arabica, with evidence from around 170 scientific publications. In contrast, comparatively fewer studies have focused on other species such as C. canephora, C. liberica, and C. congensis, or did not specify the Coffea species at all. Given the complex and multifactorial nature of microbiota composition, we categorized the indigenous microbial communities of coffee plants based on their association with three primary plant compartments; the rhizosphere, episphere, and endosphere.

Microbial Communities in the Coffee Rhizosphere

Soil serves as a vast and underexplored reservoir of microbial diversity, much of which remains uncultivated and poorly understood (Mendes et al., 2013) [50] . Among these soil microorganisms, plants play an active role in shaping the microbial community of their rhizosphere the narrow zone of soil surrounding the roots. Through the release of root exudates, plants can selectively enrich beneficial microbes from the soil (Hartmann et al., 2008; Mendes et al., 2013) [50,36] .The growing interest in rhizosphere microbiology is evident from the increasing use of the term "plant growth-promoting rhizobacteria" (PGPR), first introduced by Kloepper and Schroth in 1978. These rhizosphere-associated microbes have gained recognition for their ability to support plant health by enhancing nutrient uptake and improving tolerance to both biotic and abiotic stresses (Avis et al., 2008; De Zelicourt et al., 2013; Meena et al., 2017) [5,22,48] . Studies conducted by Caldwell et al. (2015) [10] , Lamelas et al. (2020) [45] , and Rodríguez et al. (2020) [62] revealed that the bacterial diversity in the coffee rhizosphere is composed of eight phyla, 31 orders, 81 genera, and 42 species. The most frequently encountered and diversified phylum is Proteobacteria, with 45 genera and 22 species described. Within this phylum, Pseudomonas stands out as the most diversified and common genus. All studies that employed next-generation sequencing (NGS) to assess prokaryotic abundance and diversity in the coffee rhizosphere consistently reported the dominance of the Proteobacteria phylum and the Pseudomonas genus. The remaining bacterial diversity is distributed among the phyla Acidobacteria, Actinobacteria, Bacteroidetes, Firmicutes, and Verrucomicrobia. In terms of fungal diversity, three phyla, eight orders, 16 genera, and 16 species were reported, with the phylum Ascomycota being the most represented. In contrast, other fungal phyla such as Basidiomycota and Mucoromycota are significantly underrepresented, with only two isolates reported from these groups (Tkacz et al., 2020) [74] .

Epiphytic Microbiome of Coffee Plants

In general, the plant epiphytic microbiota consists of a highly diverse group of microorganisms that are capable of attaching to and surviving on the surfaces of both aboveground and belowground plant tissues. This microhabitat presents unique environmental challenges particularly on leaf surfaces requiring specific adaptations for microbial survival and persistence. Moreover, the episphere often acts as a transitional or boundary zone, limiting microbial entry into internal plant tissues and thereby influencing their potential to become endophytes (Vandenkoornhuyse et al., 2015; Duong et al., 2020) [79,23] . Two metabarcoding studies aimed to characterize the epiphytic communities on the surfaces of coffee leaves and cherries. However, both studies extracted DNA from crushed plant organs, making it impossible to distinguish epiphytic microorganisms from endophytes (James et al., 2016; Veloso et al., 2020) [37,81] . The known diversity of coffee epiphytic microbiota includes seven phyla, 25 orders, 52 genera, and 42 species. Among these, the fungal kingdom is the most extensively studied, comprising three phyla, 15 orders, 34 genera, and 25 species. The most frequently reported fungal phylum is Ascomycota, followed by Basidiomycota and Mucoromycota.

Endophytic Microbial Communities in Coffee Plants

Endophytic microorganisms are defined by their ability to colonize the internal tissues of plants without causing any visible disease symptoms to their host. This endophytic lifestyle can vary, with some microorganisms residing within plant tissues for part of their life cycle, while others may remain internal for its entirety (Hardoim et al., 2015) [35] . Notably, some endophytes can be transmitted vertically from parent to offspring, whereas others exhibit a range of colonization strategies (Frank et al., 2017) [29] . Their ability to inhabit internal plant tissues is thought to protect them from environmental fluctuations in the soil and reduce competition with other microbes (Santoyo et al., 2016) [63] . Furthermore, endophytes are known to offer a wide array of benefits to plants, including growth promotion and enhanced stress resistance. It is important to emphasize that over half of the studies on coffee endophytes have concentrated on arbuscular mycorrhizal fungi (AMF), a distinct group of endophytic symbiotic fungi classified within the Mucoromycotina phylum and the Glomeromycota subphylum (Spatafora et al., 2016) [67] . These fungi are considered mutualistic obligate symbionts that colonize plant roots, while their external mycelium extends into the soil to absorb water and inorganic nutrients such as phosphorus, nitrogen, and other essential elements which are then transferred to the host plant in exchange for carbon compounds (Genre et al., 2020) [30] . In addition to enhancing plant nutrition, AMF have been widely recognized for improving plant resilience to both biotic and abiotic stresses (Chen et al., 2018; Begum et al., 2019) [11,7] . Prates Júnior et al. (2019) [60] reported the presence of a wide range of arbuscular mycorrhizal fungi (AMF) species in soils associated with coffee plants in Brazil. The identified species included Glomus sp., Gl. spinuliferum, Gl. fuegianum, Gl. glomerulatum, Gl. aggregatum, Acaulospora sp., Ac. mellea, Ac. sieverdingii, Ac. tuberculata, Ac. scrobiculata, Ac. herrerae, Ac. foveata, Ac. nivalis, Ac. verna, Ac. morrowiae, Ac. denticulata, Scutellospora sp., Sc. pernambucana, Archaeospora trappei, Ambispora leptoticha, Am. leptoticha, Gigaspora sp. 1, Rhizophagus fasciculatus, Dentiscutata biornata, De. cerradensis, and Paraglomus occultum. The study compared plots under agro-ecological and conventional management, as well as forest fragments. Molecular analyses revealed a higher AMF diversity index in agro-ecological and agro-forestry systems compared to conventional systems, highlighting the significant influence of agricultural practices on AMF community structure. Similarly, Vallejo-Torres et al. (2019) [78] , working with the coffee variety Caturra in Peru, observed positive effects from applying an AMF consortium. These included increases in plant height, leaf area, root biomass, root colonization capacity, and extraradical mycelium density. The AMF species identified in this study included Acaulospora rugosa, Ac. foveata, Ac. mellea, Ac. tuberculata, Ac. rhemii, Acaulospora sp., Glomus sp. 1, Glomus sp. 2, Gl. geosporum, Gl. sinuosum, and Ambispora appendicula. Another Peruvian study reported Glomus brohultii, Gl. fuegianum, Funneliformis geosporum, Claroideoglomus claroideum, Glomus sp., Scutellospora sp., Sclerocystis sp., and Acaulospora mellea as the most common AMF species associated with coffee crops. In Saudi Arabia, Mahdi et al. (2010) investigated the diversity of AMF colonizing coffee roots. Molecular and phylogenetic analyses revealed Glomus as the predominant genus, followed by Claroideoglomus, Acaulospora, and Gigaspora. DNA sequence data showed similarities with species such as Claroideoglomus claroideum, Glomus microaggregatum, G. mosseae, Rhizophagus intraradices, Gigaspora rosea, and Acaulospora longula. These findings offer a valuable foundation for developing targeted AMF-based bioinoculants to enhance coffee crop health and productivity.

Microbial Communities in Coffee Post harvest Stages

Microorganisms are known to play crucial roles during coffee postharvest processes, particularly in the degradation of the mucilage layer during fermentation (Agate and Bhat, 1966). Beyond this, they can significantly influence the organoleptic quality of the final product either positively (Elhalis et al., 2020a) [25] or negatively (Ndayambaje et al., 2019) [56] as well as its safety, particularly in relation to the presence of mycotoxins (Urbano et al., 2001) [75] . A review of existing studies reveals that the coffee postharvest microbiota comprises 18 phyla, 93 orders, 346 genera, and 446 species from both the bacterial and fungal kingdoms. Fungi, including yeasts, are the most extensively studied microorganisms in this context. Among yeasts, the most frequently cited genera include Pichia (28 citations), Candida (26), Saccharomyces (21), Hanseniaspora (16), Torulaspora (15), Wickerhamomyces (13), Meyerozyma (12), and Debaryomyces (10). Notably, metabarcoding studies have consistently reported Pichia and Candida as the dominant genera in terms of relative abundance during coffee fermentation (De Bruyn et al., [16,19,86,25,26] . The bacterial component of the postharvest microbiota spans 14 phyla, 59 orders, 227 genera, and 176 species documented across 51 publications. The most commonly reported phyla include Firmicutes (38 citations), Proteobacteria (33), Actinobacteria (14), and Bacteroidetes (7). At the genus level, frequently cited bacteria include Bacillus (21), Leuconostoc (20), Lactobacillus (18), Enterobacter (18), Pseudomonas (17), Klebsiella (16), Pantoea (12), Erwinia (11), Serratia (11), Lactococcus (10), and Acinetobacter (10). These findings align with results from metabarcoding and metagenomic studies, which consistently identify lactic acid bacteria (LAB), particularly from the genus Leuconostoc, and acetic acid bacteria (AAB) as dominant during fermentation. Additional dominant bacterial genera, such as Bacillus, Erwinia, and Pseudomonas, are primarily associated with the [16,17,19,86,87,25,26] . In total, 22 species of AAB have been identified during coffee postharvest stages, belonging to the genera Acetobacter, Gluconacetobacter, Gluconobacter, and Kozakia. Additionally, 23 LAB species have been reported, including members of Bifidobacterium, Bacillus, Clostridium, Enterococcus, Lactobacillus, Lactococcus, Leuconostoc, Pediococcus, Streptococcus, and Weissella. These microorganisms collectively contribute to the biochemical transformations that occur during postharvest handling, affecting both the quality and safety of coffee.

Native microbes as biofertilizers in coffee cultivation

The term 'rhizosphere' was first introduced by the German agronomist and plant physiologist Lorenz Hiltner to describe the interface between plant roots and soil a zone characterized by intense microbial activity. The word is partly derived from the Greek term "rhiza," meaning root (Hartmann et al., 2008) [36] . The microbial population in the rhizosphere differs significantly from that of the surrounding bulk soil, primarily due to the presence of root exudates that serve as a nutrient source for microbes (Burdman et al., 2000) [9] . Research has demonstrated that many plant-associated microbes can positively influence plant growth, nutrient uptake, seed germination, and disease control (Gevers et al., 2012) [31] . Therefore, the plant-microbe interaction plays a crucial role in enriching microbial communities and shaping their structure and activity. The rhizosphere is frequently targeted as a preferred niche for isolating plant growth-promoting (PGP) microorganisms with potential use as biofertilizers. Plant growth-promoting microbes are broadly categorized into two types; plant growth-promoting rhizobacteria (PGPR) and plant growth-promoting fungi. PGPR were initially recognized as bacteria capable of enhancing plant growth while simultaneously suppressing plant pathogens. Among the most extensively studied genera are Alcaligenes, Pseudomonas, Azospirillum, Bacillus, Klebsiella, Azotobacter, Enterobacter, Gluconacetobacter, Burkholderia, Arthrobacter, Rhizobium, Bradyrhizobium, and Serratia. Numerous studies have shown that, when appropriately inoculated into soil or applied to seeds with suitable strains, formulations, and agronomic practices PGPR not only offer biocontrol against pathogens but also enhance nutrient uptake, stimulate root and shoot development, improve seed germination, and increase plant resilience to environmental stresses. Additionally, they play a crucial role in biological nitrogen fixation and phosphate solubilization. PGPR also influence the production of key phytohormones such as indole acetic acid (IAA) [76] , gibberellins, cytokinins, and ethylene. Among, Plant growth promoting fungi like Arbuscular mycorrhizal fungi, and other beneficial fungi act as Biocontrol agent. Inoculation of bacteria of the genus Azospirillum spp on coffee seeds helps their growth, thereby reducing the time of each of their c stages (germination, sprouting and "chapola"). An effective strain (CaUAP160) was found to be applied as biofertilizers for Garcimia variety. An effective strain (CaUAP290-38) was found to be applied as biofertilizers for cultivation of caturra coffee. The largest population of Azospirillum spp was found in the rhizosphere after 180 days (https://patents.google.com). The synergistic interaction between Plant Growth-Promoting Rhizobacteria (PGPR) and Vesicular Arbuscular Mycorrhiza (VAM) has emerged as a promising strategy to enhance nutrient dynamics and plant vigor in coffee cultivation. According to findings by Ali et al. (2025) [2] , the combined use of PGPR and VAM significantly improved both biomass production and macronutrient uptake particularly nitrogen (N), phosphorus (P), and potassium (K) in coffee plants. The study evaluated six treatment regimes, including a control (P0: without PGPR and VAM), and various combinations of PGPR (10, 15, and 20 g per plant) with VAM (5 or 10 g per plant). Notably, treatments P4 (PGPR 10 g/plant + VAM 10 g/plant) and P5 (PGPR 15 g/plant + VAM 10 g/plant) produced the most substantial improvements in wet and dry biomass accumulation. Beyond nutrient acquisition, these combinations enhanced the plants' tolerance to environmental stressors, underscoring their dual role in promoting growth and resilience. The results of Ali et al. (2025) [2] support the co-application of PGPR and VAM as an ecologically sound and effective approach for sustainable coffee production under varying agro-climatic conditions. The application of rhizobacteria, specifically Bacillus nitrificans and Bacillus velezensis, has been shown to significantly enhance the growth, production, and phytochemical content of Balinese robusta coffee plants. A study conducted by Suriani, et al., (2025) [70] utilizing a randomized group approach with four treatments (control, B. nitrificans, B. velezensis, and a consortium of both) demonstrated that the consortium treatment yielded the most pronounced effects, outperforming single treatments and the control group. Both rhizobacteria strains exhibited plant growth-promoting properties, including IAA production, nitrogen fixation, and phosphorus solubilization, and effectively colonized coffee roots. These findings suggest that B. nitrificans and B. velezensis can function as effective biofertilizers and bio stimulants, enhancing coffee plant growth, yield, and phytochemical content. The use of these rhizobacteria in sustainable agriculture practices holds promise for improving coffee production while reducing reliance on synthetic fertilizers. It has been recognized that endophytic fungi have a considerable capacity to improve the nutrient up-taking ability of plants from soil both macro-elements (e.g., calcium, magnesium, nitrogen, phosphorus, potassium) and micro-elements (e.g., boron, zinc). One of the pioneering studies in this area, conducted by Jimenez-Salgado et al. (1997) [39] , identified Acetobacter diazotrophicus a nitrogen (N)-fixing bacterium-associated particularly with the root systems of coffee plants. The study suggested that an increase in populations of endophytic nitrogen-fixing bacteria can significantly enhance biological nitrogen fixation. The bacteria demonstrated a strong ability to colonize plant tissues extensively, thereby contributing positively to plant nitrogen nutrition. In addition to their presence within root tissues, A. diazotrophicus was also found to inhabit the coffee rhizosphere. This dual presence may be explained by the natural deposition of fallen coffee leaves and berries on the soil surface. These plant residues are decomposed by the soil microbiota, enriching the rhizosphere with organic matter and carbon sourcesparticularly sugars which in turn support the proliferation and activity of nitrogen-fixing bacteria like A. diazotrophicus. This interaction suggests a probable mutualistic symbiosis between coffee plants and nitrogen-fixing bacteria, although direct experimental evidence for this relationship remains limited. Further supporting this, Pratiwi et al. (2020) [61] isolated several additional nitrogen-fixing bacterial species from coffee roots, identifying Rahnella aquatilis and Pseudomonas tolaasii as particularly effective nitrogen fixers. These bacteria are capable of converting atmospheric nitrogen into ammonium, which is readily absorbed and utilized by coffee plants to support growth and development (Jha et al., 2012) [38] .Moreover, Pratiwi et al. (2020) [61] also assessed the phosphate (P) solubilizing capabilities of various bacterial isolates. Among these, Rahnella aquatilis and Kluyvera intermedia exhibited the highest and most significant phosphate-solubilizing activity. Their findings align with those of Muleta et al. (2013) [53] , who reported several phosphate-solubilizing rhizobacterial species associated with coffee roots. In a related study, Teshome et al. (2017) further confirmed the role of phosphate-solubilizing bacteria in coffee systems. Their isolations identified Pseudomonas spp. (14.5%) as the most dominant phosphate solubilizers, followed by Rhodococcus spp. (9.1%), Stenotrophomonas spp. (7.3%), Citrobacter spp. (3.6%), Gordonia spp., and Bacillus spp. (3.6%). These results reinforce the potential application of rhizosphere and endophytic bacteria in sustainable coffee production through their roles in nitrogen fixation and phosphorus solubilization. Phosphate-solubilizing bacteria (PSB) play a pivotal role in enhancing phosphorus availability in soils, particularly in phosphorus-deficient cropping systems such as coffee plantations. In a study conducted in Kavre, Nepal, Kunwar et al. (2018) [42] isolated 26 distinct PSB strains from the rhizosphere of Coffea arabica seedlings using Pikovskaya's agar medium, where phosphate solubilization was indicated by clear halo formation. Of these, eight isolates with solubilization indices greater than 1.60 were selected for detailed evaluation. Morphological and biochemical characterization revealed that the majority were Gram-negative rods, closely resembling members of the genus Pseudomonas.The phosphate-solubilizing potential of these isolates was tested using tricalcium phosphate (TCP) and Morocco rock phosphate (RP) in both agar and brothbased media. Notably, Pseudomonas sp. PSB 10 demonstrated the highest solubilization in Pikovskaya's broth (407.5 ± 2.50 µg/ml) and NBRIP-RP broth (263.3 ± 2.92 µg/ml), while Pseudomonas sp. PSB 11 exhibited superior performance in NBRIP broth (529.17 ± 6.14 µg/ml). Furthermore, Pseudomonas sp. PSB 20 recorded the highest solubilization index (SI = 3.71 ± 0.19) on NBRIP-RP agar, suggesting strong efficacy in mobilizing poorly soluble phosphate sources. Seed germination bioassays using Coffea arabica seeds inoculated with PSB strains (PSB 1, PSB 10, PSB 11, and PSB 20) revealed significant improvements over control treatments. Among these, PSB 20 showed the most pronounced effects, significantly increasing shoot length, shoot biomass, and chlorophyll content in seedling trials. In greenhouse conditions, PSB 20 also enhanced both shoot and root biomass beyond that achieved with conventional phosphate fertilizers. These findings by Kunwar et al. (2018) [42] emphasize the potential of indigenous rhizospheric Pseudomonas spp. particularly isolate PSB 20 as effective biofertilizer candidates for sustainable Coffea arabica cultivation. Their multifunctional traits, including phosphate solubilization and plant growth promotion, support their application in low-input and organic coffee farming systems. A recent investigation by Suharjono and Yuliatin (2022) [69] into the bacterial communities of the coffee rhizosphere in Malang, East Java, provided valuable insights into microbial diversity and their functional potential in supporting coffee plant growth. Soil samples were collected from Coffea canephora (Robusta) and Coffea arabica, and analyzed using both cultureindependent and culture-dependent approaches. Genomic DNA was extracted using the Fast DNA Spin Kit and sequenced via the Illumina platform, revealing Proteobacteria as the dominant phylum, with Bradyrhizobium elkanii emerging as the most abundant species in both coffee types, showing no significant difference in relative abundance. Concurrently, culturable bacterial isolates were obtained using serial dilution methods on Tryptic Soy Agar, Pikovskaya Agar, and Nitrogen-Free Bromothymol Blue Agar to target IAA-producing, phosphatesolubilizing, and nitrogen-fixing bacteria, respectively. The selected isolates were identified through 16S rDNA sequencing. Notably, isolate S1.6.3.2 (Bacillus subtilis DSM 10) exhibited the highest IAA production at 104.46 µg/mL; isolate W3.5 (Pseudomonas putida S18) showed the greatest phosphatesolubilizing activity at 4.5 µg/mL; and isolate W1.2 (Bacillus methylotrophicus SY2) demonstrated significant ammoniafixing capability at 21.54 µg/mL. These isolates exhibit strong potential as biofertilizers Candidates, owing to their ability to enhance soil fertility and promote coffee plant growth, thereby contributing to more sustainable and productive coffee agroecosystems.

Microorganisms as biocontrol agents against plant diseases and pests in coffee

The microbiota associated with coffee plants have emerged as valuable resources for the development of biologically based disease and pest management strategies. Numerous bacterial and fungal taxa isolated from the rhizosphere, phyllosphere, and endosphere of Coffea species have demonstrated antagonistic activities against key phytopathogens and nematodes affecting coffee cultivation. Prominent bacterial genera include Pseudomonas, Bacillus, Burkholderia, and Streptomyces, while fungal genera such as Trichoderma and Verticillium have also shown promise in biocontrol applications.

Mechanisms of Action

Several microbial isolates exhibit biocontrol activity through the production of hydrolytic enzymes, secondary metabolites, and volatile compounds. Enzymes such as chitinases, proteases, and lipases contribute to the degradation of fungal cell walls, while metabolites like hydrogen cyanide (HCN), siderophores, and various antibiotics have been implicated in the suppression of pathogen growth (Muleta et al., 2009; Kejela et al., 2016; Duong et al., 2021) [54,40,24] .

In Vitro Antagonism

The antagonistic potential of coffee-associated microorganisms has been widely demonstrated through dual culture and agar diffusion assays. These assays revealed strong inhibitory effects against major coffee pathogens, including Hemileia vastatrix (the causal agent of coffee leaf rust, CLR), Gibberella xylarioides (responsible for coffee wilt disease, CWD), as well as species of Colletotrichum and Fusarium (Silva et al., 2012; Haddad et al., 2013) [66,32] .

In Plant Validation

Greenhouse and growth chamber experiments have corroborated in vitro results, showing that microbial inoculants can significantly reduce disease severity. For instance, pre-or coinoculation of Bacillus subtilis and Pseudomonas fluorescens was effective in managing CLR symptoms (Shiomi et al., 2006; Silva et al., 2012; Haddad et al., 2014) [66,65,33] . Similarly, antagonistic strains of Streptomyces and Burkholderia were shown to suppress CWD in controlled conditions.

Nematode Suppression

Beyond fungal pathogens, coffee-associated microorganisms have shown activity against plant-parasitic nematodes. Endophytic bacteria such as Paenibacillus spp. and arbuscular mycorrhizal fungi (AMF) have demonstrated efficacy against Meloidogyne incognita (root-knot nematode) and Pratylenchus coffeae (root lesion nematode), reducing galling and improving plant tolerance (Vaast et al., 1997a; Mekete et al., 2009; Asyiah et al., 2018) [77,49,3].

Field Applications

Although most studies have been conducted under controlled conditions, a few field trials have demonstrated the practical potential of microbial biocontrol. In one such study, application of Verticillium lecanii resulted in delayed CLR symptom development, though its overall efficacy was limited (Vélez and Rosillo, 1995) [80] . Daivasikamani and Rajanaika (2009) [14] . Evaluated biocontrol agents over a two-year period, reporting disease incidence reductions of 36% with Bacillus subtilis and 28% with Pseudomonas fluorescens. Despite these reductions being lower than those achieved with chemical fungicides, the results support the potential of biocontrol agents as complementary tools in integrated pest management strategies. The application of plant growth-promoting bacteria (PGPB) offers a sustainable solution for enhancing coffee health and productivity. Several bacterial strains isolated from the phyllosphere, endosphere, and rhizosphere exhibited multiple beneficial traits, including disease suppression, phytohormone production, and growth stimulation in coffee seedlings. In particular, Pseudomonas gozinkensis (MN1F), Paraburkholderia caribensis (BEca88), and Enterobacter cloacae (RBca5) demonstrated consistent effectiveness in reducing the severity of coffee leaf rust, brown eye spot, and brown leaf blight, while also improving seed germination and seedling vigor. In a recent study, De Souza et al. (2025) [21] reported that these strains produced key metabolites such as indole-3-acetic acid (IAA), hydrogen cyanide (HCN), and antifungal compounds, and may also contribute to induced systemic resistance. These results highlight the potential of native PGPB strains as biotechnological tools for integrated disease management and growth enhancement in coffee production systems. Their consistent performance under controlled conditions supports their further development into commercial bioinoculants for sustainable agriculture. [21]

Role of microbes in post-harvest processing of coffee

In recent years, increasing attention has been directed toward the role of microorganisms in enhancing coffee quality during postharvest processing. Following the harvest of ripe coffee cherries, the beans undergo a series of processing steps to yield green (raw) coffee beans. Three principal methods wet, dry, and semidry processing are widely employed for this purpose. Microorganisms, particularly yeasts and bacteria, play a critical role during the fermentation stage by breaking down the mucilage layer through the secretion of pectinolytic enzymes, organic acids, and alcohols. The development of defined microbial starter cultures has become a focus of research, aiming to identify strains with desirable characteristics such as efficient mucilage degradation, stress tolerance, antifungal activity, and the potential to enhance the sensory attributes of the final product. As a result, the use of selected microbial inoculants during fermentation is gaining prominence for improving the flavour, aroma, and overall quality of green coffee beans (Haile and Kang, 2019) [34] .

Functional Microorganisms and Enzymes in Coffee Bean Fermentation

Numerous studies, including the comprehensive review by Haile and Kang (2019) [34] , have identified a diverse range of microbial species involved in coffee fermentation, with over 50 species of yeasts and bacteria reported to be active during the process. These microorganisms contribute significantly to the biochemical transformations that occur during fermentation, including the production of ethanol and various organic acids such as lactic, butyric, acetic, and higher carboxylic acids through the metabolism of pectin-rich substrates. In particular, cellulolytic species of Bacillus are known to secrete a variety of extracellular enzymes that facilitate the degradation of structural polysaccharides such as cellulose and pectin found in the skin, pulp, and mucilage of coffee cherries. According to Haile and Kang (2019) [34] , among the microbial enzymes involved in pectin degradation, three are considered particularly important: pectin lyase, polygalacturonase, and pectin methyl esterase. Pectin lyase catalyses the cleavage of pectin via a β-elimination mechanism, resulting in the formation of unsaturated galacturonic acid derivatives. Polygalacturonase, the primary enzyme involved in pectin hydrolysis during coffee fermentation, breaks down the α-1, 4 glycosidic linkages in polygalacturonic acid. Pectin methyl esterase initiates deesterification by removing methoxyl groups from pectin, thereby generating pectic acid and methanol. These enzymatic activities collectively facilitate the efficient removal of mucilage, thereby influencing the physical properties and quality of the final coffee product.

Starter Cultures for Coffee Fermentation

A starter culture refers to a defined microbiological preparation used to initiate and accelerate the fermentation process. In the food fermentation industry, starter cultures are well established in the production of cheese, yogurt, beer, and wine (Steinkraus, 2004; Schwan et al., 2014) [68,27]. Similarly, the application of starter cultures in controlled coffee fermentation has shown potential to enhance coffee quality and provide greater economic benefits to producers. As highlighted by Corsetti et al. (2012) [13] , microorganisms selected for starter cultures should exhibit key characteristics such as being non-pathogenic, non-toxigenic, and well-adapted to the raw substrate and processing conditions. Additionally, they should contribute to desirable sensory attributes, extend product shelf life, reduce processing time, and inhibit the growth of food-borne pathogens. Despite the promising potential, research on the use of defined starter cultures in coffee fermentation remains limited. The first notable study by Agate and Bhat (1996) [1] successfully introduced a starter culture composed of a mixture of three Saccharomyces species (S. marxianus, S. bayanus, and S. cerevisiae var. ellipsoideus), which enhanced fermentation efficiency by accelerating mucilage degradation. Further work by Avallone et al. (2002) [4] evaluated the microbial and physicochemical characteristics of coffee fermentation using pectinolytic microorganisms isolated from spontaneous fermentations, including Lactobacillus brevis L166, Erwinia herbicola C26, Bacillus subtilis C12, and Kluyveromyces fragilis K211. However, the study reported that these inoculants did not significantly enhance polysaccharide degradation or improve the organoleptic qualities of the final beverage. The authors suggested that employing lactic acid bacteria may better replicate natural fermentation processes and deliver improved outcomes. More recently, the use of aromatic yeast strains has been explored to enhance flavour development during dry, semidry, and wet processing methods (Evangelista et al., 2014) [27] . Although coffee fermentation typically involves a diverse indigenous microbiota, most native microorganisms are presumed to lack specific traits necessary for enhancing the sensory quality of the final product. As such, only a select few species have been identified and utilized based on their positive impact on coffee flavour and aroma.

Yeast and Fungal Fermentation for Enhancing Green Coffee Bean Quality

A study by Kwak et al. (2018) [43] investigated the effects of yeast fermentation on the antioxidant activity and consumer acceptability of green coffee beans. The results showed that a 24-hour yeast fermentation significantly increased antioxidant activity, total polyphenol, and flavonoid contents. Although consumer acceptance of the fermented coffee was generally lower than that of the non-fermented control, one particular fermentation using Saccharomyces species received approximately 39.4% preference over the control, indicating potential for sensory improvement through targeted yeast inoculation. Rhizopus oligosporus, a filamentous fungus commonly used as a starter in the production of fermented foods such as tempeh, also holds potential in coffee processing. During fermentation, R. oligosporus secretes a variety of extracellular enzymes, including proteases (Lee et al., 2016) [46] and polysaccharidedegrading enzymes such as xylanase, polygalacturonase, cellulase, arabinase, β-D-glucosidase, and α-D-galactosidase (De Reu et al., 1997) [20] . In a study by Lee et al. (2016) [46] , solidstate fermentation of green coffee beans with R. oligosporus altered both volatile and non-volatile compound profiles. The metabolism of aroma precursors during fermentation resulted in the breakdown of some volatiles and the generation of others, which contributed to improved aroma precursor profiles. These precursors are crucial for the development of key odorant compounds such as pyrazines, thiols, furanones, and guaiacol, which are responsible for the characteristic coffee aroma after roasting. Given coffee's widespread global demand, even marginal improvements in its quality can significantly enhance marketability. The use of green coffee beans rather than parchment coffee as a substrate for fermentation presents an opportunity for coffee-processing industries to directly implement microbial fermentation strategies. However, further research is needed to isolate and characterize microorganisms that meaningfully enhance sensory attributes. Future studies should also explore the commercial potential of microbial fermentation for modulating the aroma and flavour of green coffee beans.

Conclusion

The exploration of coffee-associated microorganisms has revealed numerous beneficial roles across both cultivation and postharvest stages. These microbes contribute significantly to plant health by enhancing nutrient uptake, promoting growth, and suppressing pathogens, while also playing a central role in fermentation by influencing the sensory quality of the final product through enzymatic and metabolic activities. Advances in microbial characterization through both culture-dependent methods and high-through put sequencing have enriched our understanding of microbial diversity and functionality in coffee ecosystems. Despite these promising developments, the practical application of these microorganisms under field conditions remains limited. Future research should prioritize in situ validation of microbial inoculants, especially considering the long growth cycle and environmental variability associated with coffee cultivation. Additionally, integrating omics-based tools with culturomics approaches will be essential for isolating and deploying robust, functionally relevant strains. Harnessing the full potential of the coffee microbiome offers a sustainable path forward, reducing dependency on chemical inputs and enhancing the quality, resilience, and environmental compatibility of coffee production systems.

References

1. De Melo Pereira GV, Neto E, Soccol VT, Medeiros ABP, Woiciechowski AL, Soccol CR. Conducting starter culturecontrolled fermentations of coffee beans during on-farm wet processing: growth, metabolic analyses and sensorial effects. Food Res Int. 2015;75:348-356.
2. De Oliveira Junqueira AC, de Melo Pereira GV, Coral Medina JD, Alvear MC, Rosero R, de Carvalho Neto DP, et al. First description of bacterial and fungal communities in Colombian coffee beans fermentation analysed using Illumina-based amplicon sequencing. Sci Rep. 2019;9(1):8794.
3. De Reu JC, Linssen VA, Rombouts FM, Nout MR. Consistency, polysaccharidase activities and non-starch polysaccharides content of soya beans during tempe fermentation. J Sci Food Agric. 1997;73(3):357-363.
4. De Souza MPP, Cipriano MAP, Braghini MT, De Sousa LP, Mondego JMC, Patrício FRA, et al. Beneficial bacteria improve seedling growth and nutrition and promote biological control of coffee diseases. J Appl Microbiol. 2025;136(3):lxaf050.
5. De Zelicourt A, Al-Yousif M, Hirt H. Rhizosphere microbes as essential partners for plant stress tolerance. Mol Plant. 2013;6(2):242-245.
6. Duong B, Marraccini P, Maeght JL, Vaast P, Lebrun M, Duponnois R. Coffee microbiota and its potential use in sustainable crop management: a review. Front Sustain Food Syst. 2020;4:607935.
7. Duong B, Nguyen HX, Phan HV, Colella S, Trinh PQ, Hoang GT, et al. Identification and characterization of Vietnamese coffee bacterial endophytes displaying in vitro antifungal and nematicidal activities. Microbiol Res. 2021;242:126613.
8. Elhalis H, Cox J, Zhao J. Ecological diversity, evolution and metabolism of microbial communities in the wet fermentation of Australian coffee beans. Int J Food Microbiol. 2020;321:108544.
9. Elhalis H, Cox J, Frank D, Zhao J. The crucial role of yeasts in the wet fermentation of coffee beans and quality. Int J Food Microbiol. 2020;333:108796.
10. Evangelista SR, Miguel MGDCP, de Souza Cordeiro C, Silva CF, Pinheiro ACM, Schwan RF. Inoculation of starter cultures in a semi-dry coffee (Coffea arabica) fermentation process. Food Microbiol. 2014;44:87-95.
11. Fierer N. Embracing the unknown: disentangling the complexities of the soil microbiome. Nat Rev Microbiol. 2017;15(10):579-90.
12. Frank AC, Saldierna Guzmán JP, Shay JE. Transmission of bacterial endophytes. Microorganisms. 2017;5(4):70.
13. Genre A, Lanfranco L, Perotto S, Bonfante P. Unique and common traits in mycorrhizal symbioses. Nat Rev Microbiol. 2020;18(11):649-660.
14. Gevers D, Knight R, Petrosino JF, Huang K, McGuire AL, Birren BW, et al. The human microbiome project: A community resource for the healthy human microbiome. PLoS Biol. 2012;10(8):e1001377.
15. Haddad F, Saraiva RM, Mizubuti ES, Romeiro RS, Maffia LA. Antifungal compounds as a mechanism to control Hemileia vastatrix by antagonistic bacteria. Trop Plant Pathol. 2013;38:398-405.
16. Haddad F, Saraiva RM, Mizubuti ES, Romeiro RS, Maffia LA. Isolation and selection of Hemileia vastatrix antagonists. Eur J Plant Pathol. 2014;139:763-72.
17. Haile M, Kang WH. The role of microbes in coffee fermentation and their impact on coffee quality. J Food Qual. 2019;2019:4836709.
18. Hardoim PR, Van Overbeek LS, Berg G, Pirttilä AM, Compant S, Campisano A, et al. The hidden world within plants: Ecological and evolutionary considerations for defining functioning of microbial endophytes. Microbiol Mol Biol Rev. 2015;79(3):293-320.
19. Hartmann A, Rothballer M, Schmid M. Lorenz Hiltner: A pioneer in rhizosphere microbial ecology and soil bacteriology research. Plant Soil. 2008;312:7-14.
20. James TY, Marino JA, Perfecto I, Vandermeer J. Identification of putative coffee rust mycoparasites via single-molecule DNA sequencing of infected pustules. Appl Environ Microbiol. 2016;82(2):631-9.
21. Jha CK, Patel B, Saraf M. Stimulation of the growth of Jatropha curcas by the plant growth promoting bacterium Enterobacter cancerogenus MSA2. World J Microbiol Biotechnol. 2012;28:891-899.
22. Jimenez-Salgado T, Fuentes-Ramirez LE, Tapia-Hernandez A, Mascarua-Esparza MA, Martinez-Romero E, CaballeroMellado J, et al. Coffea arabica L., a new host plant for Acetobacter diazotrophicus, and isolation of other nitrogenfixing Acetobacteria. Appl Environ Microbiol. 1997;63:3676-3683.
23. Kejela T, Thakkar VR, Thakor P. Bacillus species (BT42) isolated from Coffea arabica L. rhizosphere antagonizes Colletotrichum gloeosporioides and Fusarium oxysporum and also exhibits multiple plant growth promoting activity. BMC Microbiol. 2016;16:1-13.
24. Kloepper JW. Plant growth-promoting rhizobacteria on radishes. In: Proc 4 th Int Conf Plant Pathogenic Bacter. Angers, France: Station de Pathologie Végétale et Phytobactériologie, INRA; 1978. p. 879-882.
25. Kunwar VS, Chimouriya S, Lamichhane J, Gauchan DP. Isolation and characterization of phosphate solubilizing bacteria from rhizosphere of coffee plant and evaluating their effects on growth and development of coffee seedlings. Biotechnol Ind J. 2018;14(5):173.
26. Kwak HS, Jeong Y, Kim M. Effect of yeast fermentation of green coffee beans on antioxidant activity and consumer acceptability. J Food Qual. 2018;2018:5967130.
27. Lee LW, Cheong MW, Curran P, Yu B, Liu SQ. Modulation of coffee aroma via the fermentation of green coffee beans with Rhizopus oligosporus: I. Green coffee. Food Chem. 2016;211:916-24.
28. Lamelas A, Desgarennes D, López-Lima D, Villain L, Alonso-Sánchez A, Artacho A, et al. The bacterial microbiome of Meloidogyne-based disease complex in coffee and tomato. Front Plant Sci. 2020;11:136.
29. Lee LW, Cheong MW, Curran P, Yu B, Liu SQ. Modulation of coffee aroma via the fermentation of green coffee beans with Rhizopus oligosporus: I. Green coffee. Food Chem. 2016;211:916-924.
30. Mahdhi M, Tounekti T, Al-Turki TA, Khemira H. Composition of the root mycorrhizal community associated with Coffea arabica in Fifa Mountains (Jazan region, Saudi Arabia). J Basic Microbiol. 2017;57(8):691-698.
31. Meena VS, Meena SK, Verma JP, Kumar A, Aeron A, Mishra PK, et al. Plant beneficial rhizospheric microorganism (PBRM) strategies to improve nutrient use efficiency: A review. Ecol Eng. 2017;107:8-32.
32. Mekete T, Hallmann J, Kiewnick S, Sikora R. Endophytic bacteria from Ethiopian coffee plants and their potential to antagonise Meloidogyne incognita. Nematology. 2009;11(1):117-127.
33. Mendes R, Garbeva P, Raaijmakers JM. The rhizosphere microbiome: Significance of plant beneficial, plant pathogenic, and human pathogenic microorganisms. FEMS Microbiol Rev. 2013;37(5):634-663.
34. Mina D, Pereira JA, Lino-Neto T, Baptista P. Epiphytic and endophytic bacteria on olive tree phyllosphere: Exploring tissue and cultivar effect. Microb Ecol. 2020;80:145-157.
35. Mithöfer D, Méndez VE, Bose A, Vaast P. Harnessing local strength for sustainable coffee value chains in India and Nicaragua: Reevaluating certification to global sustainability standards. Int J Biodivers Sci Ecosyst Serv Manag. 2017;13(1):471-496.
36. Muleta D, Assefa F, Börjesson E, Granhall U. Phosphatesolubilising rhizobacteria associated with Coffea arabica L. in natural coffee forests of southwestern Ethiopia. J Saudi Soc Agric Sci. 2013;12:73-84.
37. Muleta D, Assefa F, Hjort K, Roos S, Granhall U. Characterization of rhizobacteria isolated from wild Coffea arabica L. Eng Life Sci. 2009;9(2):100-108.
38. Nadaf SA, Shivaprasad P, Babou C, Hariyappa N, Chandrashekar N, Kumari P, et al. Coffee (Coffea spp.). In: Soil Health Management for Plantation Crops: Recent Advances and New Paradigms. 2024. p. 337-89.
39. Ndayambaje JB, Nsabimana A, Dushime S, Ishimwe F, Janvier H, Ongol MP. Microbial identification of potato taste defect from coffee beans. Food Sci Nutr. 2019;7(1):287-92.
40. Nogales A, Nobre T, Valadas V, Ragonezi C, Döring M, Polidoros A, Arnholdt-Schmitt B. Can functional hologenomics aid tackling current challenges in plant breeding? Brief Funct Genomics. 2016;15(4):288-97.
41. Orozco-Mosqueda M, del Rocha-Granados MC, Glick BR, Santoyo G. Microbiome engineering to improve biocontrol and plant growth-promoting mechanisms. Microbiol Res. 2018;208:25-31.
42. Patel JS, Singh A, Singh HB, Sarma BK. Plant genotype, microbial recruitment and nutritional security. Front Plant Sci. 2015;6:608.
43. Prates Júnior P, Moreira BC, da Silva MDCS, Veloso TGR, Stürmer SL, Fernandes RBA, et al. Agroecological coffee management increases arbuscular mycorrhizal fungi diversity. PLoS One. 2019;14(1):e0209093.
44. Pratiwi ER, Ardyati T, Suharjono S. Plant growth promoting endophytic bacteria of Coffea canephora and Coffea arabica L. in UB Forest. J Exp Life Sci. 2020;10:119-126.
45. Rodríguez A, Trejo-Calzada R, García-De la Peña C, Arreola-Ávila JG, Nava-Reyna E, Vaca-Paniagua F, et al. A metagenomic approach in the evaluation of the soil microbiome in coffee plantations under organic and conventional production in tropical agroecosystems. Emirates J Food Agric. 2020;32(4):263-270.
46. Santoyo G, Moreno-Hagelsieb G, Orozco-Mosqueda MC, Glick BR. Plant growth-promoting bacterial endophytes. Microbiol Res. 2016;183:92-99.
47. Schwan RF, Pereira GDM, Fleet GH. Microbial activities during cocoa fermentation. In: Cocoa and coffee fermentations. 2014. p. 129-192.
48. Shiomi HF, Silva HSA, de Melo IS, Nunes FV, Bettiol W. Bioprospecção de bactérias endofíticas como agentes de biocontrole da ferrugem do cafeeiro. Sci Agric. 2006;63(1):32-39.
49. Silva HSA, Tozzi JP, Terrasan CR, Bettiol W. Endophytic microorganisms from coffee tissues as plant growth promoters and biocontrol agents of coffee leaf rust. Biol Control. 2012;63(1):62-67.
50. Spatafora JW, Chang Y, Benny GL, Lazarus K, Smith ME, Berbee ML, et al. A phylum-level phylogenetic classification of zygomycete fungi based on genome-scale data. Mycologia. 2016;108(5):1028-1046.
51. Steinkraus K. Industrialization of indigenous fermented foods. 2 nd ed. Boca Raton: CRC Press; 2004.
52. Suharjono, Yuliatin E. Bacteria communities of coffee plant rhizosphere and their potency as plant growth promoting. 2022.
53. Suriani NI, Alzahrani M, Nasr F, Alneghery LM, Suprapta DN, Suarsana IN, et al. Rhizobacteria consortium improves growth, yield, and phytochemicals in robusta coffee (Coffea canephora L.). Front Microbiol. 2025;16:1602940.
54. Jiménez-Salgado T, Gutierrez-Contreras FL, García-Torres A, Mauricio-Gutierrez A, Tapia-Hernández RA. Coffeeassociated nitrogen-fixing microorganisms. Patent WO2017037500A1. 2017. https://patents.google.com/patent/WO2017037500A1/en
55. Teshome B, Wassie M, Abatneh E. Isolation, screening and biochemical characterization of phosphate-solubilizing rhizobacteria associated with Coffea arabica L. J Fert Pestic. 2017;8:188.
56. Melkamu MT, Muleta DM, Berecha G, Adugna G. Antagonistic effects of rhizobacteria against coffee wilt disease caused by Gibberella xylarioides. 2013.
57. Tkacz A, Bestion E, Bo Z, Hortala M, Poole PS. Influence of plant fraction, soil, and plant species on microbiota: A multikingdom comparison. mBio. 2020;11(1):e0278502719.
58. Urbano GR, Taniwaki MH, Leitao MDF, Vicentini MC. Occurrence of ochratoxin A-producing fungi in raw Brazilian coffee. J Food Prot. 2001;64(8):1226-1230.
59. Urgiles-Gómez N, Avila-Salem ME, Loján P, Encalada M, Hurtado L, Araujo S, et al. Plant growth-promoting microorganisms in coffee production: From isolation to field application. Agronomy. 2021;11(8):1531.
60. Vaast P, Caswell-Chen EP, Zasoski RJ. Influences of a rootlesion nematode, Pratylenchus coffeae, and two arbuscular mycorrhizal fungi, Acaulospora mellea and Glomus clarum, on coffee (Coffea arabica L.). Biol Fertil Soils. 1997;26:130-135.
61. Vallejos-Torres G, Arévalo L, Iliquin I, Solis R. Respuesta en campo de clones de café a la inoculación con consorcios de hongos micorrízicos arbusculares en la región Amazonas, Perú. Inf Tecnol. 2019;30(6):73-84.
62. Vandenkoornhuyse P, Quaiser A, Duhamel M, Le Van A, Dufresne A. The importance of the microbiome of the plant holobiont. New Phytol. 2015;206(4):1196-1206.
63. Vélez PE, Rosillo AG. Evaluación del antagonismo del hongo Verticillium lecanii sobre Hemileia vastatrix en condiciones de invernadero y de campo. 1995.
64. Veloso TGR, da Silva MDCS, Cardoso WS, Guarçoni RC, Kasuya MCM, Pereira LL. Effects of environmental factors on microbiota of fruits and soil of Coffea arabica in Brazil. Sci Rep. 2020;10(1):14692.
65. Venkatesha MG. Sustainable coffee cultivation in India: Challenges and management. In: Proc 16 th Asian Agric Symp & 1 st Int Symp Agric Technol. 2010;19-21.