The refrigerated fresh foods tend to quickly deteriorate along its production and marketing, mainly due to the action of psychrotrophic spoilage microorganisms such as pseudomonads. These bacteria cause discolouration, texture loss and unpleasant flavours, with fatal implications for the quality and shelf life of products. Refirgerated fresh dairy products as well as fresh foods are steadly threatened by these microorganisms against which most control strategies are uneffective.
1. Introduction
The increasing global population has contributed to making food insecurity one of the global challenges; in fact, more than 820 million people in the world suffer food scarcity
[1], which negatively impacts mental, social, and physical well-being
[2]. This crucial issue has been further worsened by the COVID-19 pandemic
[3]. Thus, in response to the urgent and increasing global demand for food, several strategies and measures have been proposed by the official authorities
[4]; some of these are aimed at reducing food losses and waste at different stages of the food production and supply chains, including the prevention of food loss during processing, the transformation of perishable raw materials into shelf-stable products, the extension of the shelf-life through packaging and processing innovation, the introduction of clear date labels or storage, and the prevention of food spoilage
[5]. Spoilage is a deterioration process caused by microbiological, chemical, and physical changes that makes the food product unacceptable for the consumer and causes significant economic losses for the food industry.
In the dairy sector, the application of low temperatures has allowed the extension of the shelf-life and marketing of various fresh dairy products. However, naturally occurring bacteria, such as pseudomonads, have increasingly become a real concern for cold-stored fresh dairy products because of their ability to grow and adapt themselves to low temperatures. They are responsible for visible spoilage traits (discolorations, structure loss, rheology changes) and non-visible defects (protein breakdown, off-odours, and off-flavours), which significantly reduce the quality and shelf-life of dairy products.
Pseudomonas spp. contamination routes have been largely studied, especially for milk or milk-based beverages
[6][7]. In contrast, how these bacteria manage to contaminate cheeses even made from pasteurized milk is still much debated. Since these are environmental microorganisms generally present in the soil, the main sources of contamination are surfaces, water, and obviously, exposure to air. Pseudomonads contamination occurs at each step of the manufacturing process of dairy products and it becomes more persistent and resistant to sanification procedures when bacterial cells grow as biofilm
[8]. In addition, increasing amounts of enzymes (proteases and lipases) and the activation of metabolic pathways correlated to spoilage traits (e.g., pigments biosynthesis) have been found in biofilm rather than in the fluctuating state
[9]. Regardless of this evidence, the mechanisms responsible for the production and the activation of spoilage enzymes, metabolites, and pathways are still poorly explored. Most of them are
quorum sensing (QS) regulated, suggesting its potential role in dairy spoilage
[10][11][12]. To confirm this, different molecule signals have been detected in spoiled products, where they affect microbial biodiversity and metabolic activities
[13][14]. Thus, the most recent and innovative preservation strategies aim to intercept and inhibit this communication system, rather than to exert antimicrobial activity
[12][15]. However, to the best of researchers' knowledge, studies based on the application of QS inhibitors (QSI) to improve the shelf-life of dairy products are performed sporadically
[16][17], and most in vitro and in situ studies are focused on pseudomonads isolated from fish
[18][19][20]. This knowledge gap highlights the need to explore more deeply the metabolic activities and their regulation of dairy spoilage; this in order to identify the specific markers or novel molecular targets to apply in innovative control strategies, and in so doing reducing food losses and waste in the dairy sector.
2. Pseudomonas spp. as Major Cause of Spoilage in Dairy Chain
Due to their metabolic versatility and adaptation,
Pseudomonas spp. are widely occurring in dairy products. Although they optimally grow at higher temperatures, some pseudomonad species are also favoured by refrigeration temperatures of fresh foods due to their ability to increase the proportion of unsaturated fatty acids in the lipid phase of their membranes, making them more fluid
[21]. This dual ability enables these bacteria to better compete with the natural microbiota of cold-stored fresh foods, and even adapt themselves under inappropriate storage conditions. Unlike other psychrotrophs, pseudomonads show a generation time at 0–7 °C shorter than at the optimal growth temperature
[22]. With regard to their need for oxygen, they can grow even in anoxic atmospheres with high percentages of CO
2 [23]. Due to the high content of nutritional compounds and water and pH neutrality, milk and fresh dairy products are optimal matrices for pseudomonads. The spoilage traits strictly depend on species, food characteristics, storage conditions, and adaptation ability
[24]; indeed,
Pseudomonas species grow and become dominant thanks to the expression of a number of determinants (such as enzymes, pigments) addressed to enhance competition and adaptation of the bacteria. In this regard,
Table 1 and
Figure 1 show some of the spoilage traits caused by
Pseudomonas spp. in dairy products under cold-storage conditions, which are better described in the following sections.
Figure 1. Spoilage traits in dairy products under cold storage conditions: (A) discolorations of dairy products contaminated by Pseudomonas spp.; (B) proteolysis of HM Mozzarella cheeses inoculated with P. fluorescens strains (Quintieri L., Caputo L., Brasca M., Fanelli F., unpublished).
Table 1. Spoilage traits on dairy products by Pseudomonas spp.
2.1. Spoilage Traits Caused by Proteolytic and Lipolytic Activities
In raw milk, psychrotrophic bacteria, such as
P. fluorescens,
P. fragi,
P. lactis,
P. putida, and
P. gessardii, are frequent
[26][31]. Although these bacteria become inactive after milk pasteurization and sterilization, their extracellular proteases are highly thermostable, and retain the ability to degrade milk proteins, causing bitterness and age gelation in ultra-high temperature (UHT) milk
[53]. The proteases released in the milk lead to the extensive breakdown of
k-casein to para-
k-casein, influencing rennet coagulation
[54]. In turn, plasminogen and plasmin are liberated from casein micelles causing additional proteolysis of
αS1-
αS2-casein and
β-casein, affecting milk texture and flavour
[55], but even cheese yield
[56]. Among the extracellular proteases produced by
Pseudomonas, the alkaline zinc metalloprotease AprX retains its activity even after boiling for 10 min, showing a high resistance to heat
[57][58].
In fresh cheeses, especially in Mozzarella cheese stored in the governing liquid, the growth of
Pseudomonas and other psychrotrophic commensal bacteria are not counteracted by any inhibiting factor; consequently, their proteases have a dramatic impact on protein structure and quality of these cheeses during cold storage
[31][59]. In these conditions, the outer part of high moisture Mozzarella cheese inoculated with a spoilage
P. fluorescens strain showed a quick hydrolysis of
α- and
β-caseins and the increase of free amino acid content in governing liquid
[60]. Casein loss results in the wrinkling of the Mozzarella skin and in the weakening of its structure, thus the cheese slowly collapses in on itself
[31].
The high content of pseudomonads in raw milk and its late pasteurization before production of pickled cheeses, such as Domiati, Feta and Turkish White cheeses, result in huge loss of protein in the brine during storage
[50][61]. In turn, catabolism of free amino acids by
Pseudomonas strains associated with the dairy environment could fuel several metabolic pathways, among which the production of volatile compounds through transaminases and other hydrolases is detrimental for the quality and shelf-life of fresh cheese
[62]. Psychrotrophic pseudomonads also synthesize lipases causing no less serious damage than those produced by proteases
[63]; the lipases of psychrotrophic pseudomonads are more active at 4–7 °C than lipases from mesophilic microorganisms and, similar to pseudomonads proteases, show a high stability at temperatures of pasteurization and UHT treatments. Based on these characteristics, the activity of lipases, regardless of the producing strains, can severely damage the quality and shelf-life of especially raw milk as well as high-fat content dairy products during their storage at low temperatures. In fact, they catalyse the hydrolysis of triglycerides to free fatty acids and glycerol
[64]. Depending on the length of the fatty acids chain, pseudomonad lipases can lead to the release of C4 and C8 fatty acids associated with rancid flavour and odours; in contrast, free medium-chain fatty acids (C10-C12) produce a soapy flavour. In milk, lipases produced by
P. fragi can create strawberry-like odour due to ethyl butyrate and ethyl hexanoate esters
[62][65].
Butter is one of the dairy products most sensitive to the activity of lipases and phospholipases by psychrotrophic pseudomonads (
P. putrefaciens,
P. nigrificans,
P. fragi, and
P. fluorescens)
[61], which can cause a colour change on the surface (surface stain) and rancidity:
P. putrefaciens and
P. nigrificans are able to grow on the surface of butter and produce a black discoloration and a putrid odour within 7–10 days of storage at refrigeration temperature
[42]; a skunk-like smell is also developed in butter by
P. mephitica [66], while
P. fragi and, rarely,
P. fluorescens can turn the butter rancid
[48].
2.2. Discoloration as a Spoilage Trait
Among all the spoilage defects recorded on cold-stored dairy products, the one concerning discoloration is certainly the most studied in the last decade. Indeed, several cases of anomalous discoloration on Mozzarella cheese were due to the contamination by
P. putida (reddish discoloration
[67]),
P. fluorescens biovar IV and
P. libanensis (bluish discoloration
[40]),
P. gessardii (yellow and purple spots
[40]), and
P. fluorescens (greenish and fluorescent discoloration
[68]), thanks to the production of different pigments (pyoverdine, pyocyanin, pyorubin, and pyomelanin
[69]).
In 2010, starting from the European outbreak reported by RASFF’s (Rapid Alert System for Food and Feed), alerting to hundreds of different Mozzarella cheese lots with blue discoloration
[70], the concern related to the risk of coloured taints on cheese surface has grown in importance, mostly for dairy companies that need to prevent or trace these spoilage events
[71][72]. A method to screen and counteract the synthesis of blue-pigmenting strains was developed by Caputo et al.
[60]; the authors also identified the strain (
P. lactis ITEM17298) and pigment (leucoindigoidine that oxides to blue indigoidine) responsible for the cheese defects
[60][73][74]. The work of Caputo and colleagues
[60] also proved that the entry into the production cycle of pigmenting pseudomonads leads to the appearance of anomalous taints on Mozzarella cheese even after 2 days of storage. The spoiled product was immediately withdrawn from the market in accordance with current legislation, since it negatively impacts the consumer’s choice and compliance with the original characteristics of the product
[75].
In milk and fresh cheeses, pseudomonads synthesize and secrete siderophores to overcome iron starvation; these molecules (pyoverdine, pyochelin, pseudomonine, quinolobactin, etc.) work as low-molecular-weight iron chelators causing the appearance of diffusible yellow greenish or fluorescent pigmentation in milk and fresh dairy products
[68].
3. QS-Regulated Spoilage Traits in Dairy-Borne Pseudomonas spp.
The advances in technological methodologies used to study the evolution of QS systems in the different growth conditions and time of incubation allowed researchers to shed a light on several spoilage activities in QS-regulated biofilms: several AHLs have been indeed detected in foods spoiled by psychrotrophic bacteria; in addition, AHLs concentration was proved to increase with the degree of food spoilage
[13][14]. A deep analysis of the QS spoilage-related genes and pathways is reported below and for
P. fluorescens and
P. lactis also displayed in
Figure 2a,b.
Figure 2. Major spoilage traits regulated by quorum sensing systems reported for (a) P. fluorescens and (b) P. lactis. N-(3-Hydroxybutanoyl)-L-homoserine lactone (C4-HSL); N-hexanoyl-homoserine lactone (C6-HSL); N-3-oxo-octanoyl-L-Homoserine lactone (C8-HSL); N-decanoylhomoserine lactone (C10-AHL); N-dodecanoyl-L-Homoserine lactone (C12-HSL); N-(3-hydroxy-7-cis-tetradecenoyl)-Homoserine lactone (3-OH-C14:1-AHL); 3′,5′ Cyclic diguanylic acid (c-di-GMP); two-component system GacA/two-component system GacS (gacA/gacS); RNA polymerase sigma factor RpoS (RpoS); acyl-homoserine-lactone synthase/transcriptional activator protein PhzR (phzI/phzR); acyl homoserine lactone synthase/LuxR family transcriptional regulator (luxI/luxR); acyl-homoserine-lactone synthase/transcriptional regulatory protein PcoR (pcoI/pcoR); triacylglycerol lipase (lipS); periplasmic serine endoprotease DegP-like (mucD); Metalloprotease AprX (aprX); two-componenent system BarA/UvrY-regulatory subunit (barA/uvrY); acyl-homoserine-lactone synthase esaR (esaR); cyl-homoserine-lactone synthase/transcriptional activator protein LasR (lasI/lasR); acyl-homoserine-lactone synthase/regulatory protein RhlR (rh/I/rh/R); lipoyl synthase (lipA); exopolysaccharide (EPS).
3.1. Proteases, Lipases and Phospholipases
Hydrolytic enzymes are usually produced in the late exponential/early stationary growth phase when the organisms have reached comparatively high cell densities (>10
6 cfu/mL) and can be released from the biofilms into the milk without bacterial detachment.
[76]
Recently, RNA-sequencing was employed to explore the involvement of QS in dairy spoilage caused by
P. azotoformans. Fifteen pathways among those analysed were significantly affected by C6-HSL
[13]; these latter included cell division, energy metabolism, and nutrient uptake, which are crucial for bacterial survival and adaptation in the food processing environment. Some of the genes upregulated by C6-HSL were elongation factors and
sec/yajC/
yidC, responsible for protein synthesis and secretion, respectively; the type VI secretion system T4SS used for the transport of proteins and DNA across the cell envelope; and
lipS,
mucD, and the probable periplasmic serine endoprotease DegP-like (PputW619_1070). In Gram-negative bacteria (e.g.,
E. coli), DegP serine endoproteases are involved in regulated intramembrane proteolysis (RIP) cleaving transmembrane proteins to liberate a cytosolic domain of proteins able to modify gene transcription, such as the two-component regulatory system CpxA/CpxR, which responds to envelope stress response
[77].
In milk, the AHLs signal molecules (C4-HSL and 3OC8-HSL) from
Pseudomonas species, such as
P. azotoformans, were found to change their particle size distribution, and lead to the destabilization of UHT milk during storage; this feature, as well as off taste and off odour, was putatively attributed to the production of QS-regulated heat-resistant proteases and lipases produced by psychrotrophic bacteria
[13][78]. Indeed, AHLs and other AHL-related products from
Pseudomonas species have been shown to increase the activity of the
aprX promoter; the activity was instead repressed in presence of the enzyme AHL lactonase hydrolysing AHLs
[35][57]. Post-transcriptional regulation, under the control of the GacS/GacA two-component regulatory system, was also suggested to take place in the expression and secretion of protease in this system
[57]. AprX is mainly secreted by the species
P. fluorescens, but it has also been detected in various other species found in raw milk such as
P. fragi, P. tolaasii, P. rhodesiae, P. gessardii, P. proteolytica, P. brenneri, or
P. chlororaphis. Recently, the genomic analysis of three
P. lactis individuals isolated from dairy products identified several protease genes (
aprA,
prsDE,
prtAB), positioned in a QS-regulated operon previously associated with milk spoilage by
P. fluorescens [73];
aprA was described as 98% similar to the peptidase
aprX
[79]. AprA and AprX hydrolyse the four types of casein (
αs1,
αs2,
β, and
κ) with a large activity spectrum, and generally exhibit activity in a large range of pH (4.5–10), with optimum activity between 7.5 and 9, as well as across temperatures (0–55 °C), with optimal activity between 37 and 47 °C
[80].
Liu et al.
[81] reported that the sigma factor RpoS, a positive regulator of two AHL synthase genes and three coding for LuxR-like transcription factors, is a key regulator of spoilage activity by
P. fluorescens. Under food-processing conditions (exposure to heat, cold, salt, acid, and preservatives), it positively regulates the extracellular protease activities and the total volatile basic nitrogen production; thus, its monitoring during food processing and storage is considered a useful strategy to ensure the quality and safety of the final food.
In several species of
Pseudomonas spp. (e.g.,
P. fluorescens and
P. psychrophila) the production of lipases were regulated by C4-HSLs; these latter increased the proteases and lipases production in pasteurized milk after incubation at 48 °C for 18 h and caused milk spoilage
[11]; moreover, the occurrence of AHLs in heat-treated milk demonstrated that they retained all or at least part of their activities, including the modulation of
Pseudomonas spp. growth
[82].
Few studies report the regulation of lipase genes and include
P. aeruginosa; in this strain the expression of the lipase genes was controlled by the RhlR/I system and Gac system
[83]. In
P. lactis and
P. fluorescens [35][79], isolated by dairy products, the activity of lipase included in
aprX-
lipA operon were by the homologue of the
E. coli envZ-
ompR affected by environmental osmolarity and regulating biofilm formation
[84].
The phospholipase C of
P. fluorescens is a heat-stable enzyme, presenting high residual activity after pasteurization and UHT treatment; it is able to hydrolyse intact milk fat globules by increasing the lipase activity. Similar to lipases and proteases, phospholipase C activity is highest in the stationary growth phase and is regulated by the Gac system
[85].
3.2. Pigments
Dairy products often appear discoloured due to the biosynthesis of pigments (pyoverdine or fluorescein, pyorubin, pyomelanin, pyocyanin, and indigoidine) by some
Pseudomonas species
[86]; pigment synthesis is putatively orchestrated to counteract the increased oxidative stress that pseudomonads undergo at low temperatures
[86], as well as to modulate the transition to planktonic to biofilm state, to act as antimicrobials against other microorganisms or as signalling molecules and virulence factors
[35].
By combining different omics approaches, it was possible to identify the genomic locus unique to blue pigmenting
Pseudomonas spp.
[9][73]. The “blue branch” of the
P. fluorescens phylogenetic tree include strains harbouring a genomic locus, indicated by Andreani et al.
[72] as the c4_BAR (Contig 4 Blue Accessory Region); this region was described as containing 16 genes (16 Kb), including those coding for the
trp accessory genes
trpD,
trpF,
trpA,
and trpC. Quintieri et al.
[73] identified this region also in other pseudomonads; the analysis of the genomic context of the flanking regions suggested this region as a hotspot for genomic island integration. Quintieri’s group revealed the pathway related to the blue indigoidine synthesis by its inhibition in the presence of lactoferrin-derived antibiofilm peptides
[9][35]. In Gram-negative bacteria, such as
Roseobacter spp., indigoidine synthesis was modulated by C8-HSLs
[87] through a multi-layered control exercised by a LuxRI-like system integrated with c-di-GMP
[88][89]; pigment production was found to confer a competitive advantage to this strain when grown in co-culture with other microorganisms
[88].
In addition to leucoindigoidine, the
P. lactis ITEM 17298 harboured genes associated with the synthesis of the dark pigment pyomelanin from homogentisate (HGA)
[35][73]. The metabolic route correlated to pyomelanin synthesis crossed the QS-regulated shikimate pathway, producing chorismate from D-erythrose 4-phosphate, a pentose phosphate intermediate; then, chorismate was converted to tryptophan. This latter pathway was recently associated with indigo derivate pigments by Andreani et al.
[72][90].
In
P. aeruginosa, Lan et al.
[89] identified the oxidative stress sensing and response
ospR (oxidative stress response and pigment production Regulator) gene, which binds to the promoter region of homogentisate 1,2-dioxygenase (
hmgA) and affects its expression; the
hmgA gene is involved in pyomelanin production. Orthologues of
ospR are also present in
P. fluorescens strains while they are absent in other pseudomonads such as
P. putida,
P. syringae, and
P. entomophila. In addition to protection against oxidative stress,
ospR plays multiple regulatory roles as a transcriptional regulator of
β-lactam-resistant and QS-related genes (e.g.,
phzM,
phzS)
[89].
Pseudomonas spp. also produced fluorescent pigments on the cheese surface
[91], putatively correlated to the synthesis of fluorescent siderophores, well known as pyoverdines (Pvds) or pseudobactins, which are involved in iron uptake and storage
[9]; providing iron to the cell is especially important during the lag phase of growth, when the total siderophore concentration could be low. After binding its specific receptor, iron-bound pyoverdines act as signalling molecules that trigger the expression of several genes, e.g., those involved in the secretion of toxins responsible for virulence in pathogenic strains or for competitive advantage in the presence of other
Pseudomonas spp. Moreover, pseudomonads pyoverdines can mediate proteases and lipases activities during spoilage
[10][92][93].
As described by Machado et al.
[80], who reported the inhibition of pyoverdine synthesis and proteases by applying a natural plant extract able to intercept the QS systems (
las and
rhl) involved in their expression, the identification and application of QS inhibitors to counteract pseudomonads growth, spoilage, or pathogenesis represents a promising preservation technique to improve the shelf-life of foods.
3.3. Off Flavours
Both milk fats and proteins release the elements responsible for the off flavours associated with dairy products. In particular, milk fats and triglycerides release short-chain fatty acids and keto and hydroxy acids that can react, leading to a bitter, soapy taste in fluid milk
[64]; in addition, unsaturated fatty acids and phospholipids are substrates for autoxidation reactions. In contrast, proteins are a source of sulphur compounds and amino acids; the first ones are responsible for the cooked flavour in heated milk, whereas the second ones react with reducing sugars through the non-enzymatic browning reaction that produces caramel-like flavours
[94]. As discussed above, fats and proteins hydrolysis occur thanks to the activity of protease and lipases, positively affected by QS; the kind and amount of released off-flavour compounds depend on the activated enzyme and substrate.
For example, the presence of exogenous C6-HSL in milk inoculated with
P. azotoformans increased the lipolysis of fat in milk with a consequent higher content of volatile compounds (acetone, 2-heptanone, 2-butanone, and 2-pentanone) and acids (acetic acid, hexanoic acid, and octanoic acid)
[13]. Likewise, hydrophobic peptides, derived by the hydrolysis of casein and responsible for the bitter off flavours, were released by QS-regulated AprX
[9][95], as previously described.
Free amino acids are also substrates for the production, by pseudomonads decarboxylases, of biogenic amines (BAs, e.g., monoamines tyramine, histamine, cadaverine, and putrescine), a group of toxic compounds that can negatively affect the sensory properties of dairy products during storage; e.g., cadaverine and histamine impart a putrid and pungent flavour to milk
[96]. It has been reported that in
Pseudomonas spp. some BAs (such as putrescine) act as signalling molecules, triggering the attachment and biofilm formation; they also protect bacteria against radiation and oxidative stress and contribute to the development of antibiotic resistance and pathogenesis
[97]. The effect of exogenous C4-HSL, C6-HSL, C8-HSL, C12-HSL, and C14-HSL on total volatile basic nitrogen (TVB-N), which reflect the accumulation of biogenic amines, was demonstrated by Li et al.
[14] in aquatic products inoculated with
P. fluorescens.
4. Conclusion
Food spoilage causes losses of billions of dollars worldwide every year with severe economic and social impacts. In dairy sector new and sustanable strategies are needed to control spoilage of fresh dairy products during their storg at low temperatures. With the evidence of Pseudomonas spp. contamination as a major cause of dairy decay, this entry has deeply investigated all the well-known issues, focusing for the first time on the role of microbial cross-talk in the evolution of spoilage events. Indeed, recently, molecule signals involved in QS have been detected in spoiled products where they affect microbial biodiversity and metabolic activities; these could be exploited as useful markers to monitor the quality of dairy products under storage and prevent spoilage events using natural antimicrobials and QS inhibitors.