# Natural Substrates and Culture Conditions to Produce Pigments from Potential Microbes in Submerged Fermentation

Chatragadda Ramesh, V R Prasastha, Mekala Venkatachalam, Laurent Dufossé

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Chatragadda Ramesh, V R Prasastha, Mekala Venkatachalam, Laurent Dufossé. Natural Substrates and Culture Conditions to Produce Pigments from Potential Microbes in Submerged Fermentation. Fermentation, 2022, 8, 10.3390/fermentation8090460. [https://doi.org/10.3390/fermentation8090460](https://doi.org/10.3390/fermentation8090460)

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# Natural Substrates and Culture Conditions to Produce Pigments from Potential Microbes in Submerged Fermentation

Chatragadda Ramesh <fnref n="1" />,* ID, V. R. Prasastha <fnref n="2" />, Mekala Venkatachalam <fnref n="3" /> ID and Laurent Dufossé <fnref n="4" /> ID

**Abstract:** Pigments from bacteria, fungi, yeast, cyanobacteria, and microalgae have been gaining more demand in the food, leather, and textile industries due to their natural origin and effective bioactive functions. Mass production of microbial pigments using inexpensive and ecofriendly agro-industrial residues is gaining more demand in the current research due to their low cost, natural origin, waste utilization, and high pigment stimulating characteristics. A wide range of natural substrates has been employed in submerged fermentation as carbon and nitrogen sources to enhance the pigment production from these microorganisms to obtain the required quantity of pigments. Submerged fermentation is proven to yield more pigment when added with agro-waste residues. Hence, in this review, aspects of potential pigmented microbes such as diversity, natural substrates that stimulate more pigment production from bacteria, fungi, yeast, and a few microalgae under submerged culture conditions, pigment identification, and ecological functions are detailed for the benefit of industrial personnel, researchers, and other entrepreneurs to explore pigmented microbes for multifaceted applications. In addition, some important aspects of microbial pigments are covered herein to disseminate the knowledge.

**Keywords:** microbial pigments; submerged fermentation; natural substrates; antimicrobial and anticancer activities; dye and textile application; food colorants

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**Citation:** Ramesh, C.; Prasastha, V.R.; Venkatachalam, M.; Dufossé, L. Natural Substrates and Culture Conditions to Produce Pigments from Potential Microbes in Submerged Fermentation.

Fermentation **2022**, *8*, 460. https://doi.org/10.3390/fermentation8090460

Academic Editor: Xian Zhang

Received: 15 August 2022

Accepted: 8 September 2022

Published: 14 September 2022

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**Copyright:** © 2022 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).

## 1. Introduction

The invisible microbial world comprises both non-pigmented and an array of pigmented microbes. They are visible to the human eye when cultured on agar plates. In the microbial world, numerous pigmented bacteria [1,2], fungi [3–6], yeast [7–10], cyanobacteria [11], and microalgae [12,13] have been identified. Pigment production in these organisms is mostly taxa or species specific, and their intracellular or extracellular pigments are extracted using traditional and green methodologies [14,15]. In general, these pigments are produced by microbes to tolerate environmental stress, for survival and competition [16]. Various microbial pigments of different chemical origins have demonstrated a wide range of applications [1,17,18]. Among the numerous known microbial pigments, prodigiosin [19–21], violacein [22], carotenoids [10,23–27], melanins [28,29], azaphilones [30,31], phycocyanin [32], phycoerythrobilin [33,34], and riboflavin [35] pigments have gained more demand in the global context as value-added products and medicine [23].

Although vast literature is available on plant pigments [36–38], microbial pigments are gaining more demand due to easy cultivation, large-scale production throughout the year, and biodegradability. Another reason for microbial pigment demand is the side effects

<footnote n="1">¹ Biological Oceanography Division, CSIR-National Institute of Oceanography (CSIR-NIO), Dona Paula 403004, Goa, India</footnote>

<footnote n="2">² Division of Veterinary Public Health, Discipline of Veterinary Public Health and Epidemiology, ICAR-IVRI, Izatnagar, Bareilly 243 122, Uttar Pradesh, India</footnote>

<footnote n="3">³ Sensient BioNutrients, Hoffman Estates, IL 60016, USA</footnote>

<footnote n="4">⁴ Chemistry and Biotechnology of Natural Products (CHEMBIOPRO Lab), Ecole Supérieure d'Ingénieurs Réunion Océan Indien (ESIROI), Département Agroalimentaire, Université de La Réunion, F-97744 Saint-Denis, France</footnote>

<footnote>* Correspondence: chramesh@nio.org</footnote>
posed from synthetic colorants, such as hyperactivity disorder, cancer, allergies, and teratogenicity [39–41]. More significantly, synthetic dye effluents released from textile dyeing have been found to cause plant growth inhibition, air pollution, water contamination, and human illnesses [42]. Hence, many microbial pigments are used as food colorants [43]. The increasing demand for microbial pigments [2,44,45], mostly carotenoids, by various companies [10,23], is a sign of replacing the overuse of synthetic colorants in a wide range of applications.

The use of natural substrates to stimulate pigment production from microbes has become an important research approach in microbial biotechnology. A variety of agro-waste substrates and other natural substrates have been tested against different microbes in submerged fermentation [10,45–48]. In view of the importance of such substrates in pigment production, the search for new agro-waste substrates is still being continued globally by researchers [45]. On the other hand, the search for novel pigment genes with potential dyeing, cosmetic, drug, and food colorant applications is underway across the world, including from polar regions to deep-sea hydrothermal vents [45,49]. Large-scale screening of pigmented microbes from different environmental setups would not only unveil novel genes with different biosynthetic pathways but also delineate the evolutionary origins of pigmented microbes. Therefore, in a special way, this review is a treatise to benefit researchers and industrial personnel.

## 2. Pigmented Microbial Distribution in Evolutionary Perspective

A wide array of pigmented microbes are known to be distributed across The North Pole to The South Pole and from the Eastern to Western hemisphere [1,45]. Pigmented microbes such as bacteria, fungi, yeast, and microalgae are identified from a wide range of environments, such as marine [50,51], freshwater [16], desert [52], cryosphere [49], soil setups [1,53], and space [54] (Table 1). Their occurrence in various environments has been linked to evolutionary studies [45]. For instance, a recent review shows the distribution of prodigiosin and violacein pigment-producing bacteria from terrestrial and marine environments [45]. Similarly, *Monascus*-like pigments belonging to the azaphilone chemical class have been identified from ascomycetous fungi that originated from marine and terrestrial habitats [55,56]. These reports suggest that many other lesser known or unexplored microbial pigment molecules (across the microbial taxa) might have a specific evolutionary origin, relationships, and spread in different environments. The occurrence of pigmented bacteria in wastewaters [57,58] also indicates their function in a specific environmental setup. Therefore, exploration of novel microbial pigments, their molecular phylogeny, and chemicalomics investigations from extreme environments such as hydrothermal vents, cold springs, and glaciers are needed to shed light on evolutionary origins and their convergent and divergent pathways.

<table><caption>**Table 1.** Few examples of industrially important pigmented microbes isolated from various environments and their applications.</caption><thead><tr><th>Pigmented Microbe</th><th>Pigment</th><th>Source</th><th>Application</th><th>Reference</th></tr></thead><tbody><tr><td><strong>Bacteria</strong></td><td></td><td></td><td></td><td></td></tr><tr><td><em>Bacillus</em></td><td>Carotenoid</td><td>Different sources</td><td>Colorant</td><td>[59]</td></tr><tr><td><em>Chromobacterium violaceum</em></td><td>Violacein</td><td>River water and agricultural waste</td><td>Antimicrobial</td><td>[22]</td></tr><tr><td><em>Janthinobacterium</em> sp.</td><td>Violacein</td><td>River water</td><td>Antimicrobial</td><td>[16]</td></tr><tr><td><em>Paracoccus carotinifaciens</em></td><td>Astaxanthin</td><td>Soil</td><td>Coloring agent</td><td>[60]</td></tr><tr><td><em>Planococcus</em> sp.</td><td>Carotenoid</td><td>Wastewater</td><td>Food additive</td><td>[57]</td></tr><tr><td><em>Serratia marcescens</em></td><td>Prodigiosin</td><td>Soil</td><td>Dye, antimicrobial</td><td>[61]</td></tr><tr><td><em>Streptomyces cavourensis</em></td><td>Melanin</td><td>Sea cucumber</td><td>Antimicrobial</td><td>[62]</td></tr></tbody></table>
<table><caption>**Table 1.** *Cont.*</caption><thead><tr><th>Pigmented Microbe</th><th>Pigment</th><th>Source</th><th>Application</th><th>Reference</th></tr></thead><tbody><tr><td><strong>Bacteria</strong></td><td></td><td></td><td></td><td></td></tr><tr><td>Streptomyces sp.</td><td>4,8,13-trihydroxy-6,11-dione-trihydrogranaticins A (TDTA)</td><td>Soil</td><td>Feed additive</td><td>[63]</td></tr><tr><td><strong>Fungi</strong></td><td></td><td></td><td></td><td></td></tr><tr><td>Monascus purpureus</td><td>Monascus red pigment</td><td>Red mold rice</td><td>Food colorant</td><td>[64]</td></tr><tr><td>Monascus ruber</td><td>Monascus red pigment</td><td>Soil</td><td>Food colorant</td><td>[65]</td></tr><tr><td>Talaromyces albobiverticillius</td><td>Monascus-like</td><td>Marine</td><td>Industrial</td><td>[56]</td></tr><tr><td><strong>Yeast</strong></td><td></td><td></td><td></td><td></td></tr><tr><td>Rhodotorula glutinis</td><td>Carotenoid</td><td>Soil</td><td>Food colorant</td><td>[66]</td></tr><tr><td>Rhodotorula paludigena</td><td>Carotenoid</td><td>Mangrove</td><td>Fish feed</td><td>[67]</td></tr><tr><td>Xanthophyllomyces dendrorhous (=Phaffia rhodozyma)</td><td>Astaxanthin</td><td>Trees</td><td>Food additive</td><td>[68,69]</td></tr><tr><td><strong>Cyanobacteria</strong></td><td></td><td></td><td></td><td></td></tr><tr><td>Arthrospira maxima (=Spirulina maxima)</td><td>Phycocyanin</td><td>Freshwater</td><td>Food and drug</td><td>[70]</td></tr><tr><td>Arthrospira platensis (=Spirulina platensis)</td><td>Phycocyanin</td><td>Freshwater</td><td>Dye and food additive, fluorescent probe</td><td>[71,72]</td></tr><tr><td>Arthrospira platensis</td><td>Phycocyanin</td><td>Seawater</td><td>Food and drug</td><td>[73]</td></tr><tr><td><strong>Microalgae</strong></td><td></td><td></td><td></td><td></td></tr><tr><td>Chlorella vulgaris</td><td>Carotenoids</td><td>Freshwater</td><td>Food and drug</td><td>[74]</td></tr><tr><td>Cyanidioschyzon merolae</td><td>Phycocyanin</td><td>Hot sulfuric springs and geysers</td><td>Food colorant</td><td>[75]</td></tr><tr><td>Cyanidium caldarium</td><td>Phycocyanin</td><td>Thermal area</td><td>Food colorant</td><td>[76]</td></tr><tr><td>Cyanophora paradoxa, Dunaliella salina</td><td>Zeaxanthin and β-cryptoxanthin</td><td>Freshwater</td><td>Anticancer</td><td>[77]</td></tr><tr><td>Galdieria sulphuraria</td><td>Phycocyanin</td><td>Hot and acidic springs</td><td>Food and drug</td><td>[78]</td></tr><tr><td>Haematococcus pluvialis</td><td>Astaxanthin</td><td>Freshwater</td><td>Feed additive</td><td>[79]</td></tr><tr><td>Haslea ostrearia</td><td>Marennine</td><td>Seawater</td><td>Food colorant and drug</td><td>[80,81]</td></tr><tr><td>Phaeodactylum tricornutum</td><td>Fucoxanthin</td><td>Marine</td><td>Anti-inflammatory</td><td>[82]</td></tr></tbody></table>

### 3. Important Pigments for Submerged Fermentation

Not many pigmented microbes are reported to have food and drug applications due to some of the following reasons: (1) they are unable to grow on culture media after one or more subcultures, (2) difficulty in storing cultures alive, unlike non-pigmented microbial cultures, (3) low pigment yield, (4) inability/loss of pigment-producing nature under stress, (5) low or no bioactivity, (6) lack of dyeing and food colorant application, (7) unstable properties at various physicochemical factors, and (8) pathogenicity and toxins associated with some microbes [1]. Hence, these points need to be reckoned while screening pigments for various applications to save time and chemicals and reagents (for more details on this aspect, see Sections 7 and 8 below). The literature clearly indicates that violacein, prodigiosin from bacteria [19], azaphilones from fungi [30], and carotenoids from yeast [10] and microalgae [83] are the major pigments extensively studied in submerged fermentation for industrial applications (Figure 1). The use of these microbial dyes is highly regulated by legislation, which varies from country to country. For example, azaphilones from *Monascus* have been used in Asia for centuries but are still forbidden in Europe and the
USA. In Europe, β-carotene and lycopene from the filamentous fungus *Blakeslea trispora* are now in current use, and safety authorities concluded that α-tocopherol-containing oil suspension of the carotenoids β-carotene or lycopene, obtained from *B. trispora*, for use as an ingredient in feedstuffs or foodstuffs is not of concern from a safety point of view. There are also huge health safety issues with synthetic food colorants, and in a few years a list of safe, natural colorants coming from many sources (plants, microalgae, fungi, yeasts, bacteria) will emerge. In addition, the pigment production rate of microbes in submerged fermentation in the presence of various agro-industrial supplements gives a decision-making stage where a particular pigmented microbe is selected or not for further studies. Thus, currently, microbes with novel pigments, more bioactivity, and high pigment yield are explored by global researchers.

<figure><img src="image_5.png" /><figcaption>**Figure 1.** The 3D chemical structures of industrially important microbial pigments. Images are drawn in MolView online program (https://molview.org/, accessed on 4 July 2022).</figcaption></figure>

**4. Biosynthetic Pathways of Major Microbial Pigments**

Understanding the biosynthetic pathways of pigments is a key step to make required alterations in the pigment gene clusters and enhance the pigment yield. A variety of pigment gene cassettes found in different microbes were reviewed previously [84] and recently [45]. The biosynthetic pathways of violacein [22] and prodigiosin [20,85] have been well understood. Likewise, the biosynthetic pathways of different classes of bacterial and fungal melanins are well understood and used in a variety of applications [28]. Carotenoid biosynthesizing genes are widely investigated from several fungal species [3], yeast, *Xanthophyllomyces dendrorhous* [86], and microalgae [87], due to their importance in value-added food products. Scytonemin, a cyanobacterial pigment with cosmetic and drug value, was well studied, and its biosynthetic gene clusters (*scy*, *trp*, *ebo*) were identified [88].

For researchers involved in experiments about microbial pigments, biosynthetic pathways have always been the core knowledge to be described as a priority. More than 30 years ago, there existed no high-throughput sequencing, synthetic biology, nor genomics, but progress was made on microbial biosynthesis of carotenoids [89]. The enzymes and genes which mediate the biosynthesis of carotenoids such as lycopene, isorenieratene, β-carotene, and phytoene were unknown up to 1990, when Misawa et al. [89] elucidated for the first time the pathway for biosynthesis of β-carotene at the level of enzyme-catalyzed reactions, using bacterial carotenoid biosynthesis genes (expression of *Erwinia uredovora* genes in the host *Escherichia coli*). Hundreds of papers are now available regarding the biosynthesis of carotenoids in microorganisms, and thousands of carotenogenic biosynthetic genes are available in databases. However, knowing the genes is not enough to obtain a large expression of these genes in the original organism or in a host [90]. Most of the current research is now dedicated to the identification of the metabolic bottleneck(s) that make(s) it
impossible to obtain commercial productions of microbial pigments. Substrate inhibition of enzymes can be a major drawback for the efficient production of valuable biochemicals in engineered microorganisms. In a recent study, Ma et al. (2022) showed that substrate inhibition of lycopene cyclase was the main limitation in carotenoid biosynthesis in the yeast *Yarrowia lipolytica* [91] and, after some genetic modifications, were able to reach 39.5 g/L β-carotene in the fermenter (a 1441-fold enhancement related to the original strain). Such advances now allow microbial pigments to outperform pigments of plant origin or from chemical synthesis.

The second example showing the crucial importance of the biosynthetic pathway studies deals with *Monascus* azaphilone pigments (MAPs), which are the fermentation products of the filamentous fungi *Monascus* spp. These MAPs are widely used in the food industry as pigments, colorants, and dyes. Despite their widespread use, efficient production of MAPs still has some challenges to address, such as the reduction in hepatotoxic mycotoxin citrinin and anti-hypercholesterolemia agent monacolin K contaminations, which are unwanted compounds in the food ingredient industry. Liu et al. (2022) sequenced the genomes of twenty-six *Monascus* species and proposed a novel classification system, consisting of sections A, B, and C, according to the biosynthetic gene cluster (BGC) distributions and phylogeny results [92]. Based on the absence of citrinin biosynthetic genes, section B species should be investigated in the near future. The biosynthesis of *Monascus* pigments has been studied for decades, and this recent publication proves that more work is still needed, as it is also requested for all classes of microbial pigments.

The third example is also about a pigment not produced by plants, specific to some microorganisms. Violacein pigment synthesis in Gram-negative bacteria is encoded by five enzymes and formed by tryptophan. Xu et al. (2022) newly discovered violacein operon *vioABCDE* in the genome of the extremophile *Janthinobacterium* sp. B9-8 [93]. Cloning of *Janthinobacterium* heterologous genes into engineered *Escherichia coli* resulted in violacein production up to 107 mg/L in a two-stage fermentation process compared to the original strain.

The last example we wanted to develop describes how microorganisms can be used to produce pigments produced only by plants up to now. Anthocyanins are phenolic molecules that give color to fruits and vegetables. Anthocyanins bring many health benefits to humans [94]. Research about anthocyanin biosynthesis regulation in heterologous hosts is currently attracting the interest of many researchers. For improving the production of microbial anthocyanins and to increase the commercial competitiveness of the microbial production, problems and questions such as low expression of genes and inappropriate balancing of genes involved in the microbial biosynthetic pathways of anthocyanins should be answered [95]. Following these steps, anthocyanin production through bacteria, yeast, and fungi will soon be a new success of microbial pigment science.

**5. High Pigment Yielding Natural Substrates**

The concentration (intensity) of microbial pigments usually varies according to species and strain. In the laboratory conditions, some pigmented microbes produce high-quantity and high-concentration pigments, while some produce low-quantity and low-intensity pigments. The use of a variety of natural/synthetic substrates to stimulate and enhance the yield of microbial pigments has been reviewed, and indicated natural substrates as a potential nutrient element in microbial pigment production [45]. Thus, the use of genetic engineering modification techniques, which are costly and time consuming, have limitations but remain an option to improve strains. However, it is not an essential step to improve pigment production unless the strain has proven to have specific bioactivity or coloring applications. In exceptional cases, mutagenesis and genetic engineering techniques are implemented for strain improvement as well as to enhance pigment production from a low pigment yielding microbe with potential application [96].

The use of natural substrates and adsorbents [45] in fermentation plays an important role in enhancing cell volume during frothing. Several studies have demonstrated
the application of natural substrates on the yield of various microbial pigments due to the presence of rich carbon-nitrogen residues [48]. However, only some substrates are demonstrated to yield more pigment [10,45–48]. Several studies have investigated a large number of agro-industrial substrates in solid-state fermentation compared to submerged fermentation [97]. Here, substrates with high pigment yielding ability used in submerged fermentation are alone detailed briefly for further implications (Table 2).

Higher prodigiosin production from *S. marcescens* was achieved using peanut broth (38.75 mg mL⁻¹) than other substrates [61]. For more substrates with a good yield of prodigiosin pigment, refer to Han et al. (2021) [20]. Among the several tested substrates, prodigiosin pigment production was enhanced greatly with cassava wastewater [98] and peanut oil cake [99].

*Monascus purpureus* culture produced more pigment yield when tested with corn cob hydrolysate [100], bakery waste hydrolysate [101], brewer's spent grain [102], and glucose fermentation medium added with rice straw hydrolysate [103] (Table 2). *Monascus ruber* produced significantly low pigment yield when supplemented with sugarcane bagasse hydrolysate [104] (Table 2). The waste extract medium made up of various peels of inedible fruit matter was reported to enhance carotenoid production from several species of *Rhodosporidium*, especially from *Rhodosporidium toruloides* [105]. Many agro-industrial residues tested were found to enhance carotenoid production from several yeast species [10,45]. Loquat kernel extract [66], sugar beet molasses [106], and sugar cane extracts [107] were the two substrates reported to enhance yeast carotenoids greatly.

<table><caption>**Table 2.** Various substrates stimulating high pigment content from industrially important microbes. Readers may refer to the corresponding references for more details about the substrate concentration and media composition.</caption><thead><tr><th>Pigment Microbe</th><th>Species</th><th>Substrate</th><th>Pigment</th><th>Production Rate</th><th>Method</th><th>Reference</th></tr></thead><tbody><tr><td rowspan="14">Bacteria</td><td>Bacillus safensis</td><td>Fruit waste of pineapple, orange, and pomegranate</td><td>Melanin</td><td>6.96 mg/mL</td><td>Shake flask</td><td>[108]</td></tr><tr><td>Bacillus subtilis</td><td>Corn steep liquor</td><td>Riboflavin</td><td>26.8 mg/L</td><td>Shake flask</td><td>[109]</td></tr><tr><td>Chromobacterium vaccinii</td><td>Rapeseed cake</td><td>Violacein</td><td>12.93 mg/L</td><td>Shake flask</td><td>[110]</td></tr><tr><td>Chromobacterium violaceum</td><td>Liquid pineapple waste</td><td>Violacein</td><td>16.25 mg/mL</td><td>1 L Bioreactor</td><td>[111]</td></tr><tr><td>Chromobacterium violaceum</td><td>Sugarcane bagasse</td><td>Violacein</td><td>820 mg/L</td><td>Shake flask</td><td>[112]</td></tr><tr><td>Chryseobacterium artocarpi</td><td>Liquid pineapple waste</td><td>Flexirubin</td><td>540 mg/L</td><td>Shake flask</td><td>[113]</td></tr><tr><td>Pseudomonas sp.</td><td>Vegetable waste</td><td>Melanin</td><td>2.79 mg/mL</td><td>Shake flask</td><td>[114]</td></tr><tr><td>Pseudomonas aeruginosa</td><td>Cotton seed meal</td><td>Pyocyanin</td><td>4 µg/mL</td><td>Shake flask</td><td>[115]</td></tr><tr><td>Pseudomonas aeruginosa</td><td>Grape seed</td><td>Pyocyanin</td><td>4 µg/mL</td><td>Shake flask</td><td>[115]</td></tr><tr><td>Sarcina sp.</td><td>Apple pomace</td><td>Carotenoid</td><td>12.87 mg/100g</td><td>Shake flask</td><td>[116]</td></tr><tr><td>Serratia marcescens</td><td>Cassava wastewater</td><td>Prodigiosin</td><td>49,500 mg/L</td><td>Shake flask</td><td>[98]</td></tr><tr><td>Serratia marcescens</td><td>Peanut oil cake</td><td>Prodigiosin</td><td>40,000 mg/L</td><td>Shake flask</td><td>[99]</td></tr><tr><td>Serratia marcescens</td><td>Tannery fleshing</td><td>Prodigiosin</td><td>33,000 mg/L</td><td>Shake flask</td><td>[117]</td></tr><tr><td>Serratia marcescens</td><td>Peanut seed broth</td><td>Prodigiosin</td><td>38.75 mg/mL</td><td>Shake flask</td><td>[61]</td></tr><tr><td>Serratia marcescens</td><td>Peanut seed oil</td><td>Prodigiosin</td><td>0.02 gm/mL</td><td>Shake flask</td><td>[118]</td></tr><tr><td>Serratia marcescens</td><td>Brown sugar</td><td>Prodigiosin</td><td>8 mg/mL</td><td>5 L Bioreactor</td><td>[119]</td></tr><tr><td>Serratia marcescens</td><td>Peanut powder and olive oil</td><td>Prodigiosin</td><td>15,420.9 mg/L</td><td>Shake flask</td><td>[120]</td></tr><tr><td>Serratia marcescens</td><td>Powdered peanut</td><td>Prodigiosin</td><td>1595.09 mg/L</td><td>Shake flask</td><td>[121]</td></tr><tr><td>Serratia marcescens</td><td>Wheat bran and sunflower oil</td><td>Prodigiosin</td><td>240 mg/L</td><td>Shake flask</td><td>[122]</td></tr></tbody></table>
<table><caption>Table 2. *Cont.*</caption><thead><tr><th>Pigment Microbe</th><th>Species</th><th>Substrate</th><th>Pigment</th><th>Production Rate</th><th>Method</th><th>Reference</th></tr></thead><tbody><tr><td rowspan="15">Fungi</td><td>Serratia marcescens</td><td>Powdered peanut</td><td>Prodigiosin</td><td>39 mg/mL</td><td>Shake flask</td><td>[61]</td></tr><tr><td>Serratia marcescens</td><td>Sesame seed</td><td>Prodigiosin</td><td>17 mg/mL</td><td>Shake flask</td><td>[61]</td></tr><tr><td>Streptomyces sp.</td><td>Dairy processing wastewater</td><td>Prodigiosin</td><td>47,000 mg/L</td><td>Shake flask</td><td>[123]</td></tr><tr><td>Aspergillus carbonarius</td><td>Apple, black carrot, pomegranate, red beet pulps</td><td>Melanin</td><td>61.84 U/gm</td><td>Shake flask</td><td>[124]</td></tr><tr><td>Blakeslea trispora</td><td>Cheese whey</td><td>Carotenoid</td><td>405 mg/L</td><td>1.4 L glass bioreactor</td><td>[125]</td></tr><tr><td>Eremothecium gossypii(=Ashbya gossypii)</td><td>Corn steep liquor</td><td>Riboflavin</td><td>13.7 gm/L</td><td>Shake flask</td><td>[126]</td></tr><tr><td>Monascus purpureus</td><td>Rice husk hydrolysate</td><td>Monascus</td><td>72.1 U/mL</td><td>Shake flask</td><td>[127]</td></tr><tr><td>Monascus purpureus</td><td>Potato pomace</td><td>Monascus</td><td>47.9 U/mL</td><td>Shake flask</td><td>[64]</td></tr><tr><td>Monascus purpureus</td><td>Whey powder</td><td>Monascus</td><td>38.4 U/mL</td><td>Shake flask</td><td>[128]</td></tr><tr><td>Monascus purpureus</td><td>Corncob hydrolysate</td><td>Monascus</td><td>25.80 U/mL</td><td>Shake flask</td><td>[100]</td></tr><tr><td>Monascus purpureus</td><td>Corncob</td><td>Monascus</td><td>133.77 U/mL</td><td>Shake flask</td><td>[129]</td></tr><tr><td>Monascus purpureus</td><td>Bakery waste hydrolysate</td><td>Monascus</td><td>24.01 U/mL</td><td>Shake flask</td><td>[101]</td></tr><tr><td>Monascus purpureus</td><td>Brewer's spent grain</td><td>Monascus</td><td>22.25 U/mL</td><td>Shake flask</td><td>[102]</td></tr><tr><td>Monascus purpureus</td><td>Soybean meal Rice straw</td><td>Monascus</td><td>21.45 U/mL</td><td>Shake flask</td><td>[46]</td></tr><tr><td>Monascus purpureus</td><td>hydrolysate with glucose</td><td>Monascus</td><td>21.20 U/mL</td><td>Shake flask</td><td>[103]</td></tr><tr><td>Monascus purpureus</td><td>Grape waste</td><td>Monascus</td><td>20-22.5 gm/L</td><td>Shake flask</td><td>[130]</td></tr><tr><td>Monascus ruber</td><td>Sugarcane bagasse hydrolysate</td><td>Monascus</td><td>18.71 U/mL</td><td>Shake flask</td><td>[104]</td></tr><tr><td>Penicillium purpurogenum</td><td>Orange peels</td><td>Monascus-like</td><td>0.58 U/mL</td><td>Shake flask</td><td>[131]</td></tr><tr><td>Sporidiobolus pararoseus</td><td>Corn steep liquor</td><td>Carotenoid</td><td>40 gm/L</td><td>Shake flask</td><td>[132]</td></tr><tr><td>Talaromyces atroroseus</td><td>Corncob hydrolysate</td><td>Monascus</td><td>16.17 U/mL</td><td>Shake flask</td><td>[133]</td></tr><tr><td>Talaromyces purpureogenus</td><td>Bengal gram husk</td><td>Monascus</td><td>0.565 U/mL</td><td>Shake flask</td><td>[134]</td></tr><tr><td>Rhodotorula achenorium</td><td>Whey ultrafiltrate</td><td>Carotenoid</td><td>262 mg/L</td><td>Shake flask</td><td>[135]</td></tr><tr><td>Rhodotorula glutinis</td><td>Brewery wastewater Mung bean waste flour and sweet potato extract</td><td>Carotenoid</td><td>1.2 mg/L</td><td>Shake flask</td><td>[136]</td></tr><tr><td>Rhodotorula glutinis</td><td>Cassava wastewater</td><td>Carotenoid</td><td>3.48 mg/L</td><td>Shake flask</td><td>[137]</td></tr><tr><td>Rhodotorula glutinis</td><td>Crude glycerol</td><td>Carotenoid</td><td>0.98 mg/L</td><td>Shake flask</td><td>[138]</td></tr><tr><td>Rhodotorula glutinis</td><td>Chicken feathers</td><td>Carotenoid</td><td>135.25 mg/L</td><td>Shake flask</td><td>[139]</td></tr><tr><td>Rhodotorula glutinis</td><td>Whey</td><td>Carotenoid</td><td>92 mg/L</td><td>Shake flask</td><td>[140]</td></tr><tr><td>Rhodotorula rubra</td><td>Sugarcane juice</td><td>Carotenoid</td><td>46 mg/L</td><td>Shake flask</td><td>[141]</td></tr><tr><td>Rhodotorula rubra</td><td>Whey ultrafiltrate</td><td>Carotenoid</td><td>30.39 mg/g</td><td>Shake flask</td><td>[107]</td></tr><tr><td>Rhodotorula rubra</td><td>Whey sugar</td><td>Carotenoid</td><td>12.1 mg/L</td><td>Shake flask</td><td>[142]</td></tr><tr><td>Rhodosporidium mucilaginosa</td><td>Potato extract</td><td>Carotenoid</td><td>0.705 OD/ml</td><td>Shake flask</td><td>[143]</td></tr><tr><td>Rhodosporidium mucilaginosa</td><td>Coffee husk extract</td><td>Carotenoid</td><td>56 mg/L</td><td>Shake flask</td><td>[141]</td></tr><tr><td>Rhodosporidium mucilaginosa</td><td>Coffee pulp extract</td><td>Carotenoid</td><td>21.35 mg/L</td><td>Shake flask</td><td>[144]</td></tr><tr><td>Rhodosporidium mucilaginosa</td><td>Coffee pulp extract</td><td>Carotenoid</td><td>16.36 mg/L</td><td>Shake flask</td><td>[144]</td></tr><tr><td>Rhodosporidium mucilaginosa</td><td>Cassava bagasse</td><td>Carotenoid</td><td>12.5 mg/L</td><td>Shake flask</td><td>[145]</td></tr><tr><td>Rhodosporidium mucilaginosa</td><td>Onion peels and mung bean husk</td><td>Carotenoid</td><td>719.69 µg/g</td><td>Shake flask</td><td>[146]</td></tr></tbody></table>
<table><caption>Table 2. *Cont.*</caption><thead><tr><th>Pigment Microbe</th><th>Species</th><th>Substrate</th><th>Pigment</th><th>Production Rate</th><th>Method</th><th>Reference</th></tr></thead><tbody><tr><td rowspan="10">Microalgae</td><td>Rhodosporidium toruloides</td><td>Waste extract</td><td>Carotenoid</td><td>62 mg/L</td><td>Shake flask</td><td>[105]</td></tr><tr><td>Rhodosporidium toruloides</td><td>Wheat straw hydrolysate</td><td>Carotenoid</td><td>24.58 mg/L</td><td>Shake flask</td><td>[147]</td></tr><tr><td>Rhodosporidium toruloides</td><td>Carob pulp syrup</td><td>Carotenoid</td><td>9.79 µg/L</td><td>Shake flask</td><td>[148]</td></tr><tr><td>Rhodotorula glutinis</td><td>Loquat kernel extract</td><td>Carotenoid</td><td>62.73-72.36 mg/L</td><td>Shake flask</td><td>[66]</td></tr><tr><td>Rhodotorula glutinis</td><td>Waste chicken feathers</td><td>Carotenoid</td><td>6.47 mg/g</td><td>Shake flask</td><td>[140]</td></tr><tr><td>Sporodiobolus pararoseus</td><td>Corn steep liquor and parboiled rice water</td><td>Carotenoid</td><td>0.84 mg/L</td><td>Shake flask</td><td>[132]</td></tr><tr><td>Sporodiobolus pararoseus</td><td>Sugarcane molasses and corn steep liquor</td><td>Carotenoid</td><td>0.52 mg/L</td><td>Shake flask</td><td>[149]</td></tr><tr><td>Sporidiobolus salmonicolor</td><td>Corn maceration and rice parboiling water</td><td>Carotenoid</td><td>7.38 mg/L</td><td>2 L Bioreactor</td><td>[150]</td></tr><tr><td>Sporidiobolus salmonicolor</td><td>Cheese whey hydrolysate</td><td>Carotenoid</td><td>590.4 µg/L</td><td>Shake flask</td><td>[151]</td></tr><tr><td>Sporidiobolus pararoseus</td><td>Corn steep liquor and par-boiled rice water</td><td>Carotenoid</td><td>843 µg/L</td><td>Shake flask</td><td>[132]</td></tr><tr><td>Xanthophyllomyces dendrorhous</td><td>Sugar beet molasses</td><td>Astaxanthin</td><td>40 mg/L</td><td>100 L Bioreactor</td><td>[106]</td></tr><tr><td>Xanthophyllomyces dendrorhous</td><td>Eucalyptus hydrolysate</td><td>Astaxanthin</td><td>30.5 mg/L</td><td>2 L Bioreactor</td><td>[152]</td></tr><tr><td>Xanthophyllomyces dendrorhous</td><td>Mustard waste</td><td>Astaxanthin</td><td>25.8 mg/L</td><td>Shake flask</td><td>[153]</td></tr><tr><td>Xanthophyllomyces dendrorhous</td><td>Date juice</td><td>Astaxanthin</td><td>23.8 mg/L</td><td>3 L Bioreactor</td><td>[154]</td></tr><tr><td>Xanthophyllomyces dendrorhous</td><td>Molasses</td><td>Astaxanthin</td><td>15.3 mg/L</td><td>Shake flask</td><td>[155]</td></tr><tr><td>Xanthophyllomyces dendrorhous</td><td>Grape juice</td><td>Astaxanthin</td><td>9.8 µg/mL</td><td>Shake flask</td><td>[156]</td></tr><tr><td>Xanthophyllomyces dendrorhous</td><td>Mesquite pods and corn steep liquor</td><td>Carotenoid</td><td>293.41 ± 31.12 µg/g</td><td>Shake flask</td><td>[157]</td></tr><tr><td>Haematococcus pluvialis</td><td>Primary-treated piggery wastewater</td><td>Astaxanthin</td><td>83.9 mg/L</td><td>Shake flask</td><td>[79]</td></tr><tr><td>Phormidium autumnale</td><td>Slaughterhouse wastewater</td><td>Carotenoid</td><td>107,902.5 kg/year</td><td>2 L Bioreactor</td><td>[158]</td></tr></tbody></table>

## 6. Submerged Culture Conditions for Pigment Production

Usually, pigmented bacteria, fungi, and yeast are highly sensitive to physicochemical parameters. Thus, these microbes require a variety of in vitro culture conditions to yield more pigments in either solid-state or submerged fermentation. It is necessary to investigate the optimized culture conditions for each species or strain. Therefore, optimization of experimental design studies using artificial neural networks, Box-Behnken design, central composite design, Plackett-Burman design, and response surface modeling have been used to identify the key physicochemical factors that trigger high pigment production in microbes. Regardless of species, a review of the literature suggests that most pigmented microbes, except few cases, produce pigments at temperatures ranging between 22-28 °C, pH 5-6, and agitation at 100-150 rpm [1,10] (Table 3).

The maximum prodigiosin pigment production from *S. marcescens* was observed at 28 °C (38.75 mg/mL) compared to 30 °C (25.98 mg/mL) when cultured in peanut seed broth but not with other substrates tested [61]. Many species of fungi and yeast were
observed to produce carotenoid pigments under various parameters such as temperature, pH, agitation, and light availability [10]. *Monascus purpureus*, when cultured with whey powder [128], bakery waste hydrolysate [101], and corncob hydrolysate [100], was able to produce more pigments at 30 °C. Numerous yeast species have been observed to yield more carotenoid pigments at pH 5 and temperature below 30 °C [10]. On the other hand, carotenoid production from microalgae *Haematococcus pluvialis* and *Phormidium autumnale* have demonstrated the maximum yield at 23 °C [79] and 26 °C [158], respectively. The pigment yield levels from microbes depends on the type of substrate used in submerged fermentation (Table 3).

<table><caption>**Table 3.** Culture conditions set along with various agro-waste to produce different microbial pigments in submerged fermentation. Readers may refer to the respective reference for more details about the concentration of each substrate used in submerged fermentation.</caption><thead><tr><th>Pigment</th><th>Substrate</th><th>Temperature</th><th>pH</th><th>Reference</th></tr></thead><tbody><tr><td rowspan="10">Carotenoid</td><td>Wheat straw hydrolysate</td><td>30 °C</td><td>5.3</td><td>[147]</td></tr><tr><td>Coffee husk media</td><td>28 °C</td><td>5.7</td><td>[144]</td></tr><tr><td>Corn maceration and rice parboiling water</td><td>25 °C</td><td>4.0</td><td>[150]</td></tr><tr><td>Cassava bagasse</td><td>25 °C</td><td>6.0</td><td>[145]</td></tr><tr><td>Corn steep liquor and parboiled rice water</td><td>25 °C</td><td>4.0</td><td>[132]</td></tr><tr><td>Rice powder</td><td>35 °C</td><td>7.0</td><td>[159]</td></tr><tr><td>Mesquite pods and corn steep liquor</td><td>20 °C</td><td>5.5</td><td>[157]</td></tr><tr><td>Cheese whey</td><td>26 °C</td><td>7.3</td><td>[125]</td></tr><tr><td>Primary-treated piggery wastewater</td><td>23 °C</td><td>7.5</td><td>[79]</td></tr><tr><td rowspan="2">Flexirubin</td><td>Slaughterhouse wastewater</td><td>26 °C</td><td>7.6</td><td>[158]</td></tr><tr><td>Liquid pineapple waste</td><td>30 °C</td><td>7.0</td><td>[113]</td></tr><tr><td rowspan="5">Melanin</td><td>Fruit pulp</td><td>25 °C</td><td>6.5</td><td>[124]</td></tr><tr><td>Fruit waste</td><td>30.7 °C</td><td>6.8</td><td>[108]</td></tr><tr><td>Vegetable waste</td><td>25 °C</td><td>7.0</td><td>[114]</td></tr><tr><td>Potato pomace</td><td>28 °C</td><td>5.0</td><td>[64]</td></tr><tr><td>Glucose fermentation media</td><td>30 °C</td><td>5.5</td><td>[103]</td></tr><tr><td rowspan="2">Monascus</td><td>Whey medium</td><td>30 °C</td><td>6.0</td><td>[128]</td></tr><tr><td>Grape waste</td><td>30 °C</td><td>6.5</td><td>[46]</td></tr><tr><td rowspan="5">Monascus-like</td><td>Brewer's spent grain media</td><td>30 °C</td><td>5.5-7.5</td><td>[102]</td></tr><tr><td>Rice powder</td><td>32 °C</td><td>3.5</td><td>[160]</td></tr><tr><td>Potato dextrose broth</td><td>24 °C</td><td>6.4</td><td>[161]</td></tr><tr><td>Orange peels</td><td>24 °C</td><td>5.0</td><td>[131]</td></tr><tr><td>Brown sugar</td><td>25 °C</td><td>7.0</td><td>[119]</td></tr><tr><td rowspan="4">Prodigiosin</td><td>Cassava wastewater</td><td>28 °C</td><td>7.0</td><td>[98]</td></tr><tr><td>Peanut oil</td><td>28 °C</td><td>-</td><td>[118]</td></tr><tr><td>Peanut powder and olive oil</td><td>26 °C</td><td>7.0</td><td>[120]</td></tr><tr><td>Powdered peanut broth</td><td>28 °C</td><td>7.0</td><td>[61]</td></tr><tr><td rowspan="3">Pyocyanin</td><td>Peanut oil cake</td><td>30 °C</td><td>7.0</td><td>[99]</td></tr><tr><td>Wheat bran medium</td><td>30 °C</td><td>-</td><td>[122]</td></tr><tr><td>Cotton seed meal media</td><td>37 °C</td><td>-</td><td>[115]</td></tr><tr><td rowspan="2">Riboflavin</td><td>Corn steep liquor</td><td>37 °C</td><td>7.2</td><td>[109]</td></tr><tr><td>Corn steep liquor</td><td>28 °C</td><td>6.8</td><td>[126]</td></tr><tr><td rowspan="2">Violacein</td><td>Liquid pineapple waste</td><td>30 °C</td><td>7.0</td><td>[111]</td></tr><tr><td>Sugarcane bagasse</td><td>30 °C</td><td>7.0</td><td>[112]</td></tr></tbody></table>

## 7. Rapid Identification of Microbial Pigments

The identification of pigments from microbes is easier compared to non-pigmented microbial compounds. Identification of non-pigmented compounds on thin-layer chromatography (TLC) requires additional tests and UV visualization. However, rapid extraction, purification, and identification of pigments has become easy due to color appearance. For
instance, the TLC technique, a simple and cost-effective method, was quick and effective to purify and identify red pigments [162] (Figure 2). TLC is a cheaper technique compared to other chromatographic techniques such as high-performance liquid chromatography (HPLC) and high-performance thin-layer chromatography (HPTLC), which are basically costly instruments that require more maintenance and costly consumables to process samples. Hence, TLC outstands as the cheapest and most efficient method to purify pigments. It is not clear whether or not pigmented microbes display cellular vitiligo (a condition in which the bacterial cell wall may display patchy loss of pigmentation) condition. However, it is easier to purify extracted pigments (intra- and extracellular) of any microbe using TLC. Some wild fungal species and some cultured species on agar plates release droplets of concentrated pigmented molecules on their filaments' surface. These compounds are collected using a syringe (Figure 3) and mixed (authors' unpublished data) in methanol (because methanol has high polarity and better extractive yield) to test their bioactivity and colorant properties. It is not possible to obtain enough quantity of pigment droplets to test a large number of cytotoxicity and antimicrobial assays using this approach. Thus, this approach serves as a simple and rapid technique to determine the bioactive nature of pigment droplets using fewer bioassays. Thereby, this rapid method allows researchers to decide whether or not to choose a pigmented microbe that releases pigment droplets for submerged fermentation. Upon confirming the biological properties, pigment droplets can be purified easily using TLC, as shown in Figure 2. After obtaining clear, distinct pigment bands with TLC;TLC plates are allowed to dry at room temperature to evaporate the solvents on the silica gel. Then those bands are scraped using sterile pointed blades, and the eluted pigments are collected in a micro-vial to identify the pigments using HPLC, Fourier-transform infrared spectroscopy (FT-IR), liquid chromatography-mass spectrometry (LC-MS), and nuclear magnetic resonance (NMR) analyses.

<figure><img src="image_6.png" /><figcaption>**Figure 2.** Illustration depicting the TLC technique as the easiest, rapid, effective, cheap, and time saving method to isolate and purify pigment molecules over non-pigmented compounds.</figcaption></figure>
<figure><img src="image_7.png" /><figcaption>**Figure 3.** Isolation of concentrated pigment droplets (authors’ unpublished data) released by fungi on their mycelia surfaces and testing them directly for biological properties in a simple and rapid way. Before or after confirming the bioactivity, these pigment droplets can be purified with TLC as shown in Figure 2.</figcaption></figure>

## 8. Need for Targeted Drug Research on Microbial Pigments

Numerous studies have widely studied the potential biological properties of microbial pigments as antimicrobial and anticancer agents. The antimicrobial activities of microbial pigments against common pathogens and/or using strains that are available in their laboratory have been reported very often. However, the current research need is to find the molecules that combat multidrug-resistant microbes (MDRM) and a variety of cancer cells. Therefore, a routine antimicrobial investigation using pathogens (which are not of current interest) may be useful only for documentation but not in drug development research if considering the following reasons: (1) to find an effective pigment molecule against targeted MDRM and currently emerging pathogens, and (2) to develop a potential anticancer pigment molecule. Research work merely focusing on routine antibacterial properties for documentation and publications may no longer support the rapid development of drugs and help public health. Therefore, it is urgent to realize that the targeted research on the above two points using microbial pigments is very important to save time, research budgets, and hard work. In addition, one of the important notes is finding effective pigment molecules for rapid development of food colorant drug applications without repeating or duplicating the works performed before. The literature review has indicated the photodynamic photopigment therapy (i.e., the activation of photosensitizing pigments by light energy to treat a variety of diseases and infections) as an effective method to treat cancer and several microbial infections [45,163]. Therefore, studies that deal with microbial pigments need to perform photopigment therapy based on antimicrobial and other biological properties to understand the bioactive nature of microbial pigments in the presence and absence of light treatments.

Furthermore, the use of animal models in in vivo studies has constraints such as finance and ethics. In this regard, *Galleria mellonella* has been identified as a widely used, cheaper, and alternative model to study the cytotoxicity effect of a candidate drug. This invertebrate model requires no ethical approvals, is significantly cheaper, and its short lifespan enables it to be an ideal invertebrate model for high-throughput research [164].
The response of *G. mellonella*, which shares some similarities with the mammalian in-
nate immune system, is the most crucial feature that makes it a useful preclinical in vivo
model [165–167]. In comparison to mammals, this mini-host has economic and ethical
benefits, and its short lifespan makes it an ideal model for high-throughput investigations
of a variety of compounds [168,169]. They can readily be cultivated at 37°C in an incubator,
giving researchers more control over the experimental situation and allowing them to
examine clinically relevant human pathogens at a temperature similar to the human host,
resulting in precise and reliable data [170]. Therefore, alternative invertebrate models such
as *G. mellonella* larva may be used as an effective and rapid preclinical in vivo model to
determine the cytotoxicity of pigments.

9. Role of Pigmented Microbes in Climate Change

The global temperature has been increasing in recent years due to anthropogenic gases released from industrialization, automobiles, and the enormous use of greenhouse-gas-releasing systems [171]. Therefore, the current research trend has turned towards green energy, green chemistry, and green earth concepts. The toxic gases and water discharges released from the synthetic colorant manufacturing industries and textile industries using synthetic colorants are entering the atmosphere [39,42,172]. Therefore, the use of microbial pigments over synthetic colorants would eliminate toxic gases and other pollutants emitted from parties manufacturing and utilizing synthetic colorants. Therefore, efforts in this direction to implement natural pigments in every industry that uses pigments are needed urgently to arrest industrial emissions and to overcome environmental pollution, global warming, and climate change. The combination of green-energy-based industries and pigmented microbes could pave the way to reducing the industrial-based atmospheric and liquid chemical effluents. It is the need of the hour to understand the importance of the ecosystem rather than showing interest in color-appealing things (originated from industries) without knowing their (toxic emissions released from an attractive product that uses synthetic colorants) negative impacts on the environment and health. In addition, utilizing natural substrates over synthetic chemical substrates in any fermentation system may indirectly reduce the industrial emissions (by reducing synthetic chemical demand and emissions released from chemical manufacturing industries) into the atmosphere.

Light-harvesting primary pigments are known to capture CO₂ from the atmosphere. It is evident that many bacterial and fungal species found in agroecosystems [173] as well as aquatic microbes, especially marine microbes [174–176], are directly involved in carbon sequestration. However, little is known about the role of pigmented bacteria, fungi, and yeast in CO₂ sequestration, indicating the research gap to be studied. Nevertheless, pigments originating from microbes, especially bacteria (pigmented fungi and yeast are the least studied in this context), could indirectly help CO₂ capture by acting as potential growth promoters of plants [177,178] and biocontrol agents of phytopathogens [177–179] and insects [180]. Prodiginein obtained via mutasynthesis in *Pseudomonas putida* was reported to enhance the root growth of *Arabidopsis thaliana* at low concentrations [178]. *Serratia marcescens* isolated from cattle manure vermicompost [177] and halotolerant bacteria *Bacillus* and *Halobacillus* isolated from groundnut plants’ rhizosphere [180] showed growth-promoting abilities [177,181] and inhibited phytopathogenic fungi [177]. The prodigiosin pigment of *S. marcescens* isolated from *Digitaria decumbens* grass compost [179] and the rhizosphere of *Bacopa monnieri* acted as a biocontrol agent to phytopathogens [182]. Cell-free culture filtrates of pink pigmented *Methylobacterium* strains when added with 1.09 to 9.89 µg·mL⁻¹ of cytokinins showed a seed germination effect on wheat *Triticum aestivum* [183]. Liquid extracts from *Spirulina platensis* showed a seed germination effect on the groundnut *Arachis hypogaea* [184]. These studies indicate that microbial pigments could protect plants from phytopathogens, promote plant growth, and indirectly facilitate CO₂ capture by protecting plants from chloroplast damage and photosynthesis arrest.

Fungal species have also been shown to be involved in CO₂ sequestration, in particular,
soil fungi dramatically benefit the environment and ecosystem in a positive way [185].
Numerous research studies have shown that arbuscular mycorrhizal fungi (AMF) play a role as climate change warriors. The mycorrhizal fungi have a symbiotic relationship with plants by colonizing the root cells, where they form a large hyphal network and exert major control on transporting carbon [186-188]. In addition, the symbiotic association of fungi with plants has fundamental effects on the plant physiology and growth, and especially helps to utilize phosphorus and nitrogen, thus aiding in stimulating plant growth. For example, hyphae of AMF produce a glycoprotein called glomalin, which protects hyphae against nutrient or water losses, glues together soil aggregates, and improves nutrient cycling as well as nutrient uptake in plants [189,190]. Similarly, AMF of the phylum Glomeromycota boost water and nutrient exchange in plant roots through their hyphae [191,192]. Many *Rhizobium* spp., colonize the plant root cells of some plants of the legume family, which helps in nitrogen fixation [193].

Ectomycorrhizal fungal (EMF) species of *Suillus*, *Piloderma*, and *Cortinarius* are pre-dominant in boreal forests and are likely to play a crucial role in storing soil carbon in mycorrhizal forests [194,195]. Furthermore, species of *Suillus* and *Cortinarius* are involved in forest restoration and are linked to rapid turnover of microbial biomass and efficient nitrogen utilization in the forest plants [196]. In addition to these benefits, it was reported that several species of *Trichoderma* have been used as successful biocontrol agents owing to this potential action against phytopathogens. In a study by Lombardi et al., it was found that *Trichoderma* spp. stimulated strawberry plant growth, improved fruit yield, and improved the accumulation of anthocyanins and antioxidants in red ripened fruits [197]. *Piriformospora indica* also exhibited a multifunctional role in diverse plant species mainly by regulating plant metabolism and improving plant tolerance to various biotic and abiotic stresses [198]. Considering the role of fungal pigments in carbon sequestration and their influence on ecosystem function, little is known. However, it was demonstrated that the highly melanized fungus *Cenococcum geophilum* is drought-tolerant in water-stressed habitats. It is suggested that melanin is an important functional trait that allowed the hyphae to penetrate deeper into the soil to access water, and it is considered that melanin production helps with this function [199]. Hence, by closely working together with plants, fungal communities can potentially strengthen their defense mechanisms, improve resilience to plant diseases, enhance nutrient uptake through well-developed roots, store soil carbon, and so on.

Although several species of yeast have demonstrated plant-growth-promoting ability [200], the ability of pigmented yeast to promote plant growth has not been studied, whereas, similar to macroalgal culture beds [201], several investigations found that large-scale culture of microalgae in open systems, bioreactors [202-209], and integrated culture systems [210] play an important role in the mitigation of atmospheric CO2. In this way, bacteria, fungi, and microalgae offer multifaceted applications to society and protect the environment by regulating CO2 levels.

## 10. Current Applications of Microbial Pigments

The numerous applications of microbial pigments in food, textile, leather, cosmetic, and drug industries have been reviewed very often in the last five years by various authors [1,2,114,164,211-214]. Here, we detail the selected and recent applications of microbial pigments in various areas. Undecylprodigiosin, a prodigiosin pigment derivative, was reported to have dyeing, food colorant, and antimicrobial properties [162,215]. Particularly, undecylprodigiosin and other unidentified pigment molecules have been demonstrated to show a high affinity to staining transverse sections of *Tridax procumbens* [162], indicating the application of these pigments as natural stains in laboratory studies. Recently, the prodigiosin pigment extracted from *Serratia plymuthica* has been used to develop an antibacterial (against *S. aureus* and *P. aeruginosa*) food packaging system in combination with bacterial cellulose and a chitosan composite [216]. Similarly, the development of antimicrobial textiles for hospital-acquired infections has been demonstrated using prodigiosin extracted from *Serratia rubidaea* [217]. The flexirubin pigment extracted from *Chryseobac-
*terium artocarp* i was used to make soaps [113]. Tyrian purple indigoid (originated from *Murex*) synthesized from *E. coli* has potential dye applications [218]. Indigoid pigments are reported to have chemosensory and semiconductor properties [219]. Phycocyanin ex- tracted from *Arthrospira platensis* is used as a fluorescent probe in medical, food safety, and environmental research [71,220]. Microalgae is one of the major sources of nutraceuticals, pharmaceuticals, and biogases [84], especially having anticancer properties [27,221,222]. Thus, microalgae-based pigments have also been gaining more attraction in the industry compared to bacterial and fungal pigments.

**11. Future Directions of Microbial Pigments**

Pigmented microbes have been widely explored for multifaceted applications in various industries. However, the evolutionary importance of microbial pigments is least understood. Therefore, the origin of pigmented genes and pigment molecules from a wide range of microbes (bacteria, fungi, yeast, cyanobacteria, and microalgae) distributed in different environments such as marine, aerobic, terrestrial, and estuarine are needed to be explored intensively to understand their convergent and divergent evolutionary patterns in the tree of life. On the other hand, pigmented microbes are known to be abundant in the marine environment and have demonstrated potential biological properties. Nevertheless, marine pigmented microbes have largely remained unexplored. Furthermore, the use of various agro-wastes, poultry waste, and fish waste need to be utilized in submerged fermentation to test the stimulation efficiency of these substrates to yield high pigment production from microbes. Thus, further research on these less-studied research gaps is essential to explore the ecological, evolutionary, and societal benefits of microbial pigments.

**12. Conclusions**

Microbial pigments have proven to offer multifaceted applications to a wide range of industries, including biomedical, textile, leather, food, and drug industries. It is evident that synthetic pigments pose toxic effects on the environment and biota, including humans. Therefore, the production of pigments from potential microbes needs to be implemented intensively in submerged fermentation. The use of natural agro-industrial residues in submerged fermentation has proven to yield more pigments and reduced the production costs of pigments in various industries. Therefore, submerged fermentation is inferred as a convenient and effective method to understand the synergetic effect of substrates and culture conditions on pigment production from potential microbes. This strategy would undoubtedly fulfill the industrial needs and eliminate risks posed by synthetic pigments used in food and drugs.

**Author Contributions:** Conceptualization, C.R. and V.R.P.; writing—original draft preparation, C.R., V.R.P., L.D. and M.V.; writing—review and editing, C.R., V.R.P., M.V. and L.D.; visualization, C.R. and V.R.P. All authors have read and agreed to the published version of the manuscript.

**Funding:** This research received no external funding.

**Institutional Review Board Statement:** Not applicable.

**Informed Consent Statement:** Not applicable.

**Data Availability Statement:** Not applicable.

**Acknowledgments:** CR thanks the CSIR-NIO for institutional support. This is the CSIR-NIO's contribution: 6970 under the projects MLP2019 and OLP2005.

**Conflicts of Interest:** The authors declare no conflict of interest. The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript, or in the decision to publish the results.
## References

1. Ramesh, C.; Vinithkumar, N.V.; Kirubagaran, R.; Venil, C.K.; Dufossé, L. Multifaceted applications of microbial pigments: Current knowledge, challenges and future directions for public health implications. *Microorganisms* **2019**, *7*, 186. [CrossRef]

2. Venil, C.K.; Zakaria, Z.A.; Ahmad, W.A. Bacterial pigments and their applications. *Process Biochem.* **2013**, *48*, 1065–1079. [CrossRef]

3. Sandmann, G. Carotenoids and their biosynthesis in fungi. *Molecules* **2022**, *27*, 1431. [CrossRef]

4. Kalra, R.; Conlan, X.A.; Goel, M. Fungi as a potential source of pigments: Harnessing filamentous fungi. *Front. Chem.* **2020**, *8*, 369. [CrossRef]

5. Lagashetti, A.C.; Dufossé, L.; Singh, S.K.; Singh, P.N. Fungal pigments and their prospects in different industries. *Microorganisms* **2019**, *7*, 604. [CrossRef] [PubMed]

6. Hyde, K.D.; Xu, J.; Rapior, S.; Jeewon, R.; Lumyong, S.; Niego, A.G.T.; Abeywickrama, P.D.; Aluthmuhandiram, J.V.S.; Brahaman- age, R.S.; Brooks, S.; et al. The amazing potential of fungi: 50 ways we can exploit fungi industrially. *Fungal Divers.* **2019**, *97*, 1–136. [CrossRef]

7. Mata-Gómez, L.C.; Montañez, J.C.; Méndez-Zavala, A.; Aguilar, C.N. Biotechnological production of carotenoids by yeasts: An overview. *Microb. Cell Fact.* **2014**, *13*, 12. [CrossRef] [PubMed]

8. Kanamoto, H.; Nakamura, K.; Misawa, N. Carotenoid production in oleaginous yeasts. *Adv. Exp. Med. Biol.* **2021**, *1261*, 153–163.

9. Chreptowicz, K.; Mierzejewska, J.; Tkácová, J.; Młyniec, M.; Certik, M. Carotenoid-producing yeasts: Identification and character- istics of environmental isolates with a valuable extracellular enzymatic activity. *Microorganisms* **2019**, *7*, 653. [CrossRef]

10. Igreja, W.S.; Maia, F.d.A.; Lopes, A.S.; Chisté, R.C. Biotechnological production of carotenoids using low cost-substrates is influenced by cultivation parameters: A review. *Int. J. Mol. Sci.* **2021**, *22*, 8819. [CrossRef]

11. Lopes, G.; Clarinha, D.; Vasconcelos, V. Carotenoids from cyanobacteria: A biotechnological approach for the topical treatment of psoriasis. *Microorganisms* **2020**, *8*, 302. [CrossRef] [PubMed]

12. Barkia, I.; Saari, N.; Manning, S.R. Microalgae for high-value products towards human health and nutrition. *Mar. Drugs* **2019**, *17*, 304. [CrossRef] [PubMed]

13. Saha, S.K.; Murray, P. Exploitation of microalgae species for nutraceutical purposes: Cultivation aspects. *Fermentation* **2018**, *4*, 46. [CrossRef]

14. Pailliè-Jiménez, M.E.; Stincone, P.; Brandelli, A. Natural pigments of microbial origin. *Front. Sustain. Food Syst.* **2020**, *4*, 590439. [CrossRef]

15. Nemer, G.; Louka, N.; Vorobiev, E.; Salameh, D.; Nicaud, J.-M.; Maroun, R.G.; Koubaa, M. Mechanical cell disruption technologies for the extraction of dyes and pigments from microorganisms: A review. *Fermentation* **2021**, *7*, 36. [CrossRef]

16. Lyakhovchenko, N.S.; Abashina, T.N.; Polivtseva, V.N.; Senchenkov, V.Y.; Pribylov, D.A.; Chepurina, A.A.; Nikishin, I.A.; Avakova, A.A.; Goyanov, M.A.; Gubina, E.D.; et al. A blue-purple pigment-producing bacterium isolated from the Vezelka river in the city of Belgorod. *Microorganisms* **2021**, *9*, 102. [CrossRef]

17. Sen, T.; Barrow, C.J.; Deshmukh, S.K. Microbial pigments in the food industry—Challenges and the way forward. *Front. Nutr.* **2019**, *6*, 7. [CrossRef]

18. Celedón, R.S.; Díaz, L.B. Natural pigments of bacterial origin and their possible biomedical applications. *Microorganisms* **2021**, *9*, 739. [CrossRef]

19. Choi, S.Y.; Lim, S.; Yoon, K.; Lee, J.I.; Mitchell, R.J. Biotechnological activities and applications of bacterial pigments violacein and prodigiosin. *J. Biol. Eng.* **2021**, *15*, 10. [CrossRef]

20. Han, R.; Xiang, R.; Li, J.; Wang, F.; Wang, C. High-level production of microbial prodigiosin: A review. *J. Basic Microbiol.* **2021**, *61*, 506–523. [CrossRef]

21. Paul, T.; Bandyopadhyay, T.K.; Mondal, A.; Tiwari, O.N.; Muthuraj, M.; Bhunia, B. A comprehensive review on recent trends in production, purification, and applications of prodigiosin. *Biomass Convers. Biorefinery* **2022**, *12*, 1409–1431. [CrossRef]

22. Durán, N.; Justo, G.Z.; Durán, M.; Brocchi, M.; Cordi, L.; Tasic, L.; Castro, G.R.; Nakazato, G. Advances in *Chromobacterium violaceum* and properties of violacein-its main secondary metabolite: A review. *Biotechnol. Adv.* **2016**, *34*, 1030–1045. [CrossRef] [PubMed]

23. Foong, L.C.; Loh, C.W.L.; Ng, H.S.; Lan, J.C. Recent development in the production strategies of microbial carotenoids. *World J. Microbiol. Biotechnol.* **2021**, *37*, 12. [CrossRef] [PubMed]

24. Martínez-Cámara, S.; Ibañez, A.; Rubio, S.; Barreiro, C.; Barredo, J.-L. Main carotenoids produced by microorganisms. *Encyclopedia* **2021**, *1*, 1223–1245. [CrossRef]

25. Nelis, H.J.; Leenheer, A.P. De Microbial sources of carotenoid pigments used in foods and feeds. *J. Appl. Biotechnol.* **1991**, *70*, 181–191. [CrossRef]

26. Eman, M.M. Fungal and yeast carotenoids. *J. Yeast Fungal Res.* **2019**, *10*, 30–44. [CrossRef]

27. Ávila-Román, J.; García-Gil, S.; Rodríguez-Luna, A.; Motilva, V.; Talero, E. Anti-inflammatory and anticancer effects of microalgal carotenoids. *Mar. Drugs* **2021**, *19*, 531. [CrossRef]

28. Singh, S.; B.Nimse, S.; Mathew, D.E.; Dhimmar, A.; Sahastrabudhe, H.; Gajjar, A.; A.Ghadge, V.; Kumar, P.; B.Shinde, P. Microbial melanin: Recent advances in biosynthesis, extraction, characterization, and applications. *Biotechnol. Adv.* **2021**, *53*, 107773. [CrossRef]

29. Tran-Ly, A.N.; Reyes, C.; Schwarze, F.W.M.R.; Ribera, J. Microbial production of melanin and its various applications. *World J. Microbiol. Biotechnol.* **2020**, *36*, 170. [CrossRef]
30. Vendruscolo, F.; Bühler, R.M.M.; de Carvalho, J.C.; de Oliveira, D.; Moritz, D.E.; Schmidell, W.; Ninow, J.L. *Monascus*: A reality on the production and application of microbial pigments. *Appl. Biochem. Biotechnol.* **2016**, *178*, 211–223. [CrossRef]

31. Chaudhary, V.; Katyal, P.; Puniya, A.K.; Panwar, H. Natural pigment from *Monascus*: The production and therapeutic significance. *J. Appl. Microbiol.* **2021**, *133*, 18–38. [CrossRef] [PubMed]

32. de Morais, M.G.; Prates, D.d.F.; Moreira, J.B.; Duarte, J.H.; Costa, J.A.V. Phycocyanin from microalgae: Properties, extraction and purification, with some recent applications. *Ind. Biotechnol.* **2018**, *14*, 30–37. [CrossRef]

33. Sonani, R.R. Recent advances in production, purification and applications of phycobiliproteins. *World J. Biol. Chem.* **2016**, *7*, 100–109. [CrossRef] [PubMed]

34. Puzorjov, A.; McCormick, A.J. Phycobiliproteins from extreme environments and their potential applications. *J. Exp. Bot.* **2020**, *71*, 3827–3842. [CrossRef]

35. Averianova, L.A.; Balabanova, L.A.; Son, O.M.; Podvolotskaya, A.B.; Tekutyeva, L.A. Production of vitamin B2 (riboflavin) by microorganisms: An overview. *Front. Bioeng. Biotechnol.* **2020**, *8*, 570828. [CrossRef]

36. Sharma, M.; Usmani, Z.; Gupta, V.K.; Bhat, R. Valorization of fruits and vegetable wastes and by-products to produce natural pigments. *Crit. Rev. Microbiol.* **2021**, *41*, 535–563. [CrossRef]

37. Pargai, D.; Jahan, S.; Gahlot, M. Functional properties of natural dyed textiles. In *Chemistry and Technology of Natural and Synthetic Dyes and Pigments*; Samanta, A.K., Awwad, N., Algarni, H.M., Eds.; IntechOpen: London, UK, 2020; pp. 1–19.

38. Newsome, A.G.; Culver, C.A.; van Breemen, R.B. Nature's palette: The search for natural blue colorants. *J. Agric. Food Chem.* **2014**, *62*, 6498–6511. [CrossRef]

39. Yadav, A.K.; Jain, C.K.; Malik, D.S. Toxic characterization of textile dyes and effluents in relation to human health hazards. *J. Sustain. Environ. Res.* **2014**, *3*, 95–102.

40. Babitha, S. Microbial pigments. In *Biotechnology for Agro-Industrial Residues Utilisation: Utilisation of Agro-Residues*; Nigam, P.S., Pandey, A., Eds.; Springer: Berlin/Heidelberg, Germany, 2009; pp. 147–162. ISBN 9781402099410.

41. Dey, S.; Nagababu, B.H. Applications of food color and bio-preservatives in the food and its effect on the human health. *Food Chem. Adv.* **2022**, *1*, 100019. [CrossRef]

42. Slama, H.B.; Bouket, A.C.; Pourhassan, Z.; Alenezi, F.N.; Silini, A.; Cherif-Silini, H.; Oszako, T.; Luptakova, L.; Golinska, P.; Belbahri, L. Diversity of synthetic dyes from textile industries, discharge impacts and treatment methods. *Appl. Sci.* **2021**, *11*, 6255. [CrossRef]

43. Dufossé, L. Current and potential natural pigments from microorganisms (bacteria, yeasts, fungi, microalgae). In *Handbook on Natural Pigments in Food and Beverages Industrial Applications for Improving Food Color*; Carle, R., Schweiggert, R.M., Eds.; Woodhead Publishing: Sawston, UK, 2016; pp. 337–354.

44. Venil, C.K.; Dufossé, L.; Devi, P.R. Bacterial pigments: Sustainable compounds with market potential for pharma and food industry. *Front. Sustain. Food Syst.* **2020**, *4*, 100. [CrossRef]

45. Ramesh, C.H.; Dufossé, L. Ecological and biotechnological aspects of pigmented Microbes: A way forward in development of food and pharmaceutical grade pigments. *Microorganisms* **2021**, *9*, 637. [CrossRef]

46. Lopes, F.C.; Tichota, D.M.; Pereira, J.Q.; Segalin, J.; Rios, A.d.O.; Brandelli, A. Pigment production by filamentous fungi on agro-industrial byproducts: An eco-friendly alternative. *Appl. Biochem. Biotechnol.* **2013**, *171*, 616–625. [CrossRef] [PubMed]

47. De Medeiros, T.D.M.; Dufossé, L.; Bicas, J.L. Lignocellulosic substrates as starting materials for the production of bioactive biopigments. *Food Chem. X.* **2022**, *13*, 100223. [CrossRef]

48. Lopes, F.C.; Ligabue-Braun, R. Agro-industrial residues: Eco-friendly and inexpensive substrates for microbial pigments production. *Front. Sustain. Food Syst.* **2021**, *5*, 589414. [CrossRef]

49. Sajjad, W.; Din, G.; Rafiq, M.; Iqbal, A.; Khan, S.; Zada, S.; Ali, B.; Kang, S. Pigment production by cold-adapted bacteria and fungi: Colorful tale of cryosphere with wide range applications. *Extremophiles* **2020**, *24*, 447–473. [CrossRef]

50. Nawaz, A.; Chaudhary, R.; Shah, Z.; Dufossé, L.; Fouillaud, M.; Mukhtar, H.; ul Haq, I. An overview on industrial and medical applications of bio-pigments synthesized by marine bacteria. *Microorganisms* **2021**, *9*, 11. [CrossRef]

51. Ramesh, C.; Vinithkumar, N.V.; Kirubagaran, R. Marine pigmented bacteria: A prospective source of antibacterial compounds. *J. Nat. Sci. Biol. Med.* **2019**, *10*, 104–113. [CrossRef]

52. Liu, M.; Peng, F.; Wang, Y.; Zhang, K.; Chen, G.; Fang, C. *Cineococcus xinjiangensis* sp. nov., isolated from desert sand. *Int. J. Syst. Evol. Microbiol.* **2009**, *59*, 1090–1093. [CrossRef]

53. Mumtaz, R.; Bashir, S.; Numan, M.; Shinwari, Z.K.; Ali, M. Pigments from soil bacteria and their therapeutic properties: A mini review. *Curr. Microbiol.* **2019**, *76*, 783–790. [CrossRef]

54. Daudu, R.; Parker, C.W.; Singh, N.K.; Wood, J.M.; Debieu, M.; O'Hara, N.B.; Mason, C.E.; Venkateswaran, K. Draft genome sequences of *Rhodotorula mucilaginosa* strains isolated from the international space station. *Microbiol. Resour. Announc.* **2020**, *9*, e00570-20. [CrossRef] [PubMed]

55. Lebeau, J.; Venkatachalam, M.; Fouillaud, M.; Petit, T.; Vinale, F.; Dufossé, L.; Caro, Y. Production and new extraction method of polyketide red pigments produced by ascomycetous fungi from terrestrial and marine habitats. *J. Fungi* **2017**, *3*, 34. [CrossRef] [PubMed]

56. Venkatachalam, M.; Magalon, H.; Dufossé, L.; Fouillaud, M. Production of pigments from the tropical marine-derived fungi *Talaromyces albobiverticillius*: New resources for natural red-colored metabolites. *J. Food Compos. Anal.* **2018**, *70*, 35–48. [CrossRef]
57. Majumdar, S.; Priyadarshinee, R.; Kumar, A.; Mandal, T.; Mandal, D.D. Exploring *Planococcus* sp. TRC1, a bacterial isolate, for carotenoid pigment production and detoxification of paper mill effluent in immobilized fluidized bed reactor. *J. Clean. Prod.* **2019**, *211*, 1389–1402. [CrossRef]

58. Padhan, B.; Poddar, K.; Sarkar, D.; Sarkar, A. Production, purification, and process optimization of intracellular pigment from novel psychrotolerant *Paenibacillus* sp. BPW19. *Biotechnol. Rep.* **2021**, *29*, e00592. [CrossRef]

59. Khaneja, R.; Perez-Fons, L.; Fakhry, S.; Baccigalupi, L.; Steiger, S.; To, E.; Sandmann, G.; Dong, T.C.; Ricca, E.; Fraser, P.D.; et al. Carotenoids found in *Bacillus*. *J. Appl. Microbiol.* **2010**, *108*, 1889–1902. [CrossRef]

60. Hayashi, M.; Ishibashi, T.; Kuwahara, D.; Hirasawa, K. Commercial production of astaxanthin with *Paracoccus carotinifaciens*. *Adv. Exp. Med. Biol.* **2021**, *1261*, 11–20.

61. Giri, A.V.; Anandkumar, N.; Muthukumaran, G.; Pennathur, G. A novel medium for the enhanced cell growth and production of prodigiosin from *Serratia marcescens* isolated from soil. *BMC Microbiol.* **2004**, *4*, 11. [CrossRef]

62. Wibowo, J.T.; Kellermann, M.Y.; Petersen, L.-E.; Alfiansah, Y.R.; Lattyak, C.; Schupp, P.J. Characterization of an insoluble and soluble form of melanin produced by *Streptomyces cavourensis* SV 21, a sea cucumber associated bacterium. *Mar. Drugs* **2022**, *20*, 54. [CrossRef]

63. Zhu, Y.; Shang, X.; Yang, L.; Zheng, S.; Liu, K.; Lia, X. Purification, identification and properties of a new blue pigment produced from *Streptomyces* sp. A1013Y. *Food Chem.* **2020**, *308*, 125600. [CrossRef]

64. Chen, X.; Gui, R.; Li, N.; Wu, Y.; Chen, J.; Wu, X.; Qin, Z.; Yang, S.-T.; Li, X. Production of soluble dietary fibers and red pigments from potato pomace in submerged fermentation by *Monascus purpureus*. *Process Biochem.* **2021**, *111*, 159–166. [CrossRef]

65. Darwesh, O.M.; Matter, I.A.; Almoallim, H.S.; Alharbi, S.A.; Oh, Y.-K. Isolation and optimization of *Monascus ruber* OMNRC45 for red pigment production and evaluation of the pigment as a food colorant. *Appl. Sci.* **2020**, *10*, 8867. [CrossRef]

66. Taskin, M.; Erdal, S. Production of carotenoids by *Rhodotorula glutinis* MT-5 in submerged fermentation using the extract from waste loquat kernels as substrate. *J. Sci. Food Agric.* **2011**, *91*, 1440–1445. [CrossRef] [PubMed]

67. Rekha, R.; Nimsi, K.A.; Manjusha, K.; Sirajudheen, T.K. Marine yeast *Rhodotorula paludigena* VA 242 a pigment enhancing feed additive for the ornamental fish koi carp. *Aquac. Fish.* **2022**. [CrossRef]

68. Libkind, D.; Moliné, M.; Tognetti, C. Isolation and selection of new astaxanthin producing strains of *Xanthophyllomyces den-drorhous*. In *Microbial Carotenoids from Fungi: Methods and Protocols, Methods in Molecular Biology*; Barredo, J.-L., Ed.; Springer Science+Business Media: New York, NY, USA, 2012; Volume 898, pp. 183–194.

69. Libkind, D.; Moliné, M.; Colabella, F. Isolation and selection of new astaxanthin-producing strains of *Phaffia rhodozyma*. In *Microbial Carotenoids from Fungi: Methods and Protocols, Methods in Molecular Biology*; Barreiro, C., Barredo, J.-L., Eds.; Humana Press: New York, NY, USA, 2018; Volume 1852, pp. 297–310.

70. Ruiz-Domínguez, M.C.; Jáuregui, M.; Medina, E.; Jaime, C.; Cerezal, P. Rapid green extractions of C-phycocyanin from *Arthrospira maxima* for functional applications. *Appl. Sci.* **2019**, *9*, 1987. [CrossRef]

71. Zheng, Y.; Mo, L.; Zhang, W.; Duan, Y.; Huang, J.; Chen, C.; Gao, Y.; Shi, X.; Li, F.; Yang, J.; et al. Phycocyanin fluorescent probe from *Arthrospira platensis*: Preparation and application in LED-CCD fluorescence density strip qualitative detection system. *J. Appl. Phycol.* **2019**, *31*, 1107–1115. [CrossRef]

72. Kissoudi, M.; Sarakatsianos, I.; Samanidou, V. Isolation and purification of food-grade C-phycocyanin from *Arthrospira platensis* and its determination in confectionery by HPLC with diode array detection. *J. Sep. Sci.* **2018**, *41*, 975–981. [CrossRef]

73. Leema, J.T.M.; Kirubagaran, R.; Vinithkumar, N.V.; Dheenan, P.S.; Karthikayulu, S. High value pigment production from *Arthrospira (Spirulina) platensis* cultured in seawater. *Bioresour. Technol.* **2010**, *101*, 9221–9227. [CrossRef]

74. Ru, I.T.K.; Sung, Y.Y.; Jusoh, M.; Wahid, M.E.A.; Nagappan, T. *Chlorella vulgaris*: A perspective on its potential for combining high biomass with high value bioproducts. *Appl. Phycol.* **2020**, *1*, 2–11. [CrossRef]

75. Rahman, D.Y.; Sarian, F.D.; van Wijk, A.; Martinez-Garcia, M.; van der Maarel, M.J.E.C. Thermostable phycocyanin from the red microalga *Cyanidioschyzon merolae*, a new natural blue food colorant. *J. Appl. Phycol.* **2017**, *29*, 1233–1239. [CrossRef]

76. Eisele, L.E.; Bakhru, S.H.; Liu, X.; MacColl, R.; Edwards, M.R. Studies on C-phycocyanin from *Cyanidium caldarium*, a eukaryote at the extremes of habitat. *Biochim. Biophys. Acta.* **2000**, *1456*, 99–107. [CrossRef]

77. Baudelet, P-H.; Gagez, A.-L.; Bérard, J.-B.; Juin, C.; Bridiau, N.; Kaas, R.; Thiéry, V.; Cadoret, J.-P.; Picot, L. Antiproliferative activity of *Cyanophora paradoxa* pigments in melanoma, breast and lung cancer cells. *Mar. Drugs* **2013**, *11*, 4390–4406. [CrossRef] [PubMed]

78. Sørensen, L.; Hantke, A.; Eriksen, N.T. Purification of the photosynthetic pigment C-phycocyanin from heterotrophic *Galdieria sulphuraria*. *J. Sci. Food Agric*. *Food Agric.* **2013**, *93*, 2933–2938. [CrossRef]

79. Kang, C.D.; An, J.Y.; Park, T.H.; Sim, S.J. Astaxanthin biosynthesis from simultaneous N and P uptake by the green alga *Haematococcus pluvialis* in primary-treated wastewater. *Biochem. Eng. J.* **2006**, *31*, 234–238. [CrossRef]

80. Francezon, N.; Herbaut, M.; Bardeau, J.-F.; Cougnon, C.; Bélanger, W.; Tremblay, R.; Jacquette, B.; Dittmer, J.; Pouvreau, J.-B.; Mouget, J.-L.; et al. Electrochromic properties and electrochemical behavior of marennine, a bioactive blue-green pigment produced by the marine diatom *Haslea ostrearia*. *Mar. Drugs* **2021**, *19*, 231. [CrossRef] [PubMed]

81. Gabed, N.; Verret, F.; Peticca, A.; Kryvoruchko, I.; Gastineau, R.; Bosson, O.; Séveno, J.; Davidovich, O.; Davidovich, N.; Witkowski, A.; et al. What was old is new again: The pennate diatom *Haslea ostrearia* (Gaillon) Simonsen in the multi-omic age. *Mar. Drugs* **2022**, *20*, 234. [CrossRef]
82. Lee, A.H.; Shin, H.Y.; Park, J.H.; Koo, S.Y.; Kim, S.M.; Yang, S.H. Fucoxanthin from microalgae *Phaeodactylum tricornutum* inhibits pro-inflammatory cytokines by regulating both NF-κB and NLRP3 inflammasome activation. *Sci. Rep.* **2021**, *11*, 543. [CrossRef]

83. Udayan, A.; Pandey, A.K.; Sirohi, R.; Sreekumar, N.; Sang, B.-I.; Sim, S.J.; Kim, S.H.; Pandey, A. Production of microalgae with high lipid content and their potential as sources of nutraceuticals. *Phytochem. Rev.* **2022**, *23*, 1–28. [CrossRef]

84. Margalith, P.Z. *Pigment Microbiology*; Chapman & Hall: London, UK, 1992.

85. Williamson, N.R.; Fineran, P.C.; Leeper, F.J.; Salmond, G.P.C. The biosynthesis and regulation of bacterial prodigines. *Nat. Rev. Microbiol.* **2006**, *4*, 887–899. [CrossRef]

86. Barredo, J.L.; García-Estrada, C.; Kosalkova, K.; Barreiro, C. Biosynthesis of astaxanthin as a main carotenoid in the heterobasidiomycetous yeast *Xanthophyllomyces dendrorhous*. *J. Fungi* **2017**, *3*, 44. [CrossRef]

87. Ren, Y.; Sun, H.; Deng, J.; Huang, J.; Chen, F. Carotenoid production from microalgae: Biosynthesis, salinity responses and novel biotechnologies. *Mar. Drugs* **2021**, *19*, 713. [CrossRef] [PubMed]

88. Gao, X.; Jing, X.; Liu, X.; Lindblad, P. Biotechnological production of the sunscreen pigment scytonemin in cyanobacteria: Progress and strategy. *Mar. Drugs* **2021**, *19*, 129. [CrossRef] [PubMed]

89. Misawa, N.; Nakagawa, M.; Kobayashi, K.; Yamano, S.; Izawa, Y.; Nakamura, K.; Harashima, K. Elucidation of the *Erwinia uredovora* carotenoid biosynthetic pathway by functional analysis of gene products expressed in *Escherichia coli*. *J. Bacteriol.* **1990**, *172*, 6704–6712. [CrossRef]

90. Sankari, M.; Rao, P.R.; Hemachandran, H.; Pullela, P.K.; George, P.D.C.; Tayubi, I.A.; Subramanian, B.; Gothandam, K.M.; Singh, P.; Ramamoorthy, S. Prospects and progress in the production of valuable carotenoids: Insights from metabolic engineering, synthetic biology, and computational approaches. *J. Biotechnol.* **2018**, *266*, 89–101. [CrossRef] [PubMed]

91. Ma, Y.; Liu, N.; Greisen, P.; Li, J.; Qiao, K.; Huang, S.; Stephanopoulos, G. Removal of lycopene substrate inhibition enables high carotenoid productivity in *Yarrowia lipolytica*. *Nat. Commun.* **2022**, *13*, 572. [CrossRef]

92. Liu, A.; Chen, A.J.; Liu, B.; Wei, Q.; Bai, J.; Hu, Y. Investigation of citrinin and monacolin K gene clusters variation among pigment producer *Monascus* species. *Fungal Genet. Biol.* **2022**, *160*, 103687. [CrossRef]

93. Xu, X.; Chu, X.; Du, B.; Huang, C.; Xie, C.; Zhang, Z.; Jiang, L. Functional characterization of a novel violacein biosynthesis operon from *Janthinobacterium* sp. B9-8. *Appl. Microbiol. Biotechnol.* **2022**, *106*, 2903–2916. [CrossRef]

94. Sunil, L.; Shetty, N.P. Biosynthesis and regulation of anthocyanin pathway genes. *Appl. Microbiol. Biotechnol.* **2022**, *106*, 1783–1798. [CrossRef]

95. Zha, J.; Koffas, M.A.G. Production of anthocyanins in metabolically engineered microorganisms: Current status and perspectives. *Synth. Syst. Biotechnol.* **2017**, *2*, 259–266. [CrossRef]

96. Sánchez-Muñoz, S.; Mariano-Silva, G.; Leite, M.O.; Mura, F.B.; Verma, M.L.; Silva, S.S.d.; Chandel, A.K. Production of fungal and bacterial pigments and their applications. In *Biotechnological Production of Bioactive Compounds*; Verma, M.L., Chandel, A.K., Eds.; Elsevier: Amsterdam, The Netherlands, 2020; pp. 327–361.

97. Soccol, C.R.; da Costa, E.S.F.; Letti, L.A.J.; Karp, S.G.; Woiciechowski, A.L.; Vandenberghe, L.P.d.S. Recent developments and innovations in solid state fermentation. *Biotechnol. Res. Innov.* **2017**, *1*, 52–71. [CrossRef]

98. de Araújo, H.W.C.; Fukushima, K.; Takaki, G.M.C. Prodigiosin production by *Serratia marcescens* UCP 1549 using renewable-resources as a low cost substrate. *Molecules* **2010**, *15*, 6931–6940. [CrossRef] [PubMed]

99. Naik, C.; Srisevita, J.M.; Shushma, K.N.; Farah, N.; Shilpa, A.C.; Muttanna, C.D.; Darshan, N.; Sannadurgappa, D. Peanut oil cake: A novel substrate for enhanced cell growth and prodigiosin production from *Serratia marcescens* CF-53. *J. Res. Biol.* **2012**, *2*, 549–557.

100. Zhou, Z.; Yin, Z. Corn cob hydrolysate, an efficient substrate for *Monascus* pigment production through submerged fermentation. *Biotechnol. Appl. Biochem.* **2014**, *61*, 716–723. [CrossRef]

101. Haque, M.A.; Kachrimanidou, V.; Koutinas, A.; Lin, C.S.K. Valorization of bakery waste for biocolorant and enzyme production by *Monascus purpureus*. *J. Biotechnol.* **2016**, *231*, 55–64. [CrossRef] [PubMed]

102. Silbir, S.; Goksungur, Y. Natural red pigment production by *Monascus purpureus* in submerged fermentation systems using a food industry waste: Brewer's spent grain. *Foods* **2019**, *8*, 161. [CrossRef] [PubMed]

103. Liu, J.; Luo, Y.; Guo, T.; Tang, C.; Chai, X.; Zhao, W.; Bai, J.; Lin, Q. Cost-effective pigment production by *Monascus purpureus* using rice straw hydrolysate as substrate in submerged fermentation. *J. Biosci. Bioeng.* **2020**, *129*, 229–236. [CrossRef]

104. Hilares, R.T.; de Souza, R.A.; Marcelino, P.F.; da Silva, S.S.; Dragone, G.; Mussatto, S.I.; Santos, J.C. Sugarcane bagasse hydrolysate as a potential feedstock for red pigment production by *Monascus ruber*. *Food Chem.* **2018**, *245*, 786–791. [CrossRef]

105. Sinha, S.; Singh, G.; Arora, A.; Paul, D. Carotenoid production by red yeast isolates grown in agricultural and "mandi" waste. *Waste Biomass Valorization* **2021**, *12*, 3939–3949. [CrossRef]

106. An, G.H.; Jang, B.G.; Cho, M.H. Cultivation of the carotenoid- hyperproducing mutant 2A2N of the red yeast *Xanthophyllomyces dendrorhous* (*Phaffia rhodozyma*) with molasses. *J. Biosci. Bioeng.* **2001**, *92*, 121–125. [CrossRef]

107. Bonadio, M.d.P.; de Freita, L.A.; Mutton, M.J.R. Carotenoid production in sugarcane juice and synthetic media supplemented with nutrients by *Rhodotorula rubra* 102. *Braz. J. Microbiol.* **2018**, *49*, 872–878. [CrossRef]

108. Tarangini, K.; Mishra, S. Production of melanin by soil microbial isolate on fruit waste extract: Two step optimization of key paramete. *Biotechnol. Rep.* **2014**, *4*, 139–146. [CrossRef] [PubMed]

109. Lee, K.H.; Park, Y.H.; Han, J.K.; Park, J.H.; Lee, K.H.; Kyung, H.; Choi, H. Microorganism for Producing Rboflavin and Method for Producing Riboflavin using the Same 2004. U.S. Patent 20040110248A1, 23 January 2007.
110. Cassarini, M.; Crônier, D.; Besaury, L.; Rémond, C. Protein-rich agro-industrial co-products are key substrates for growth of *Chromobacterium vaccinii* and its violacein bioproduction. *Waste Biomass Valorization* **2022**, *1–10*. [CrossRef]

111. Aruldass, C.A.; Rubiyatno; Venil, C.K.; Ahmad, W.A. Violet pigment production from liquid pineapple waste by *Chromobacterium violaceum* UTM5 and evaluation of its bioactivity. *RSC Adv.* **2015**, *5*, 51524–51536. [CrossRef]

112. Ahmad, W.A.; Yusof, N.Z.; Nordin, N.; Zakaria, Z.A.; Rezali, M.F. Production and characterization of violacein by locally isolated *Chromobacterium violaceum* grown in agricultural wastes. *Appl. Biochem. Biotechnol.* **2012**, *167*, 1220–1234. [CrossRef]

113. Aruldass, C.A.; Dufosse, L.; Ahmad, W.A. Current perspective of yellowish-orange pigments from microorganisms-a review. *J. Clean. Prod.* **2018**, *180*, 168–182. [CrossRef]

114. Tarangini, K.; Mishra, S. Production, characterization and analysis of melanin from isolated marine *Pseudomonas* sp. using vegetable waste. *Res. J. Eng. Sci.* **2013**, *2*, 40–46.

115. El-Fouly, M.Z.; Sharaf, A.M.; Shahin, A.A.M.; El-Bialy, H.A.; Omara, A.M.A. Biosynthesis of pyocyanin pigment by *Pseudomonas aeruginosa*. *J. Radiat. Res. Appl. Sci.* **2015**, *8*, 36–48. [CrossRef]

116. Joshi, V.K.; Attri, D.; Rana, M.S. Optimization of apple pomace based medium and fermentation conditions for pigment production by *Sarcina* sp. *Indian J. Nat. Prod. Resour.* **2011**, *2*, 421–427.

117. Sumathi, C.; Mohanapriya, D.; Swarnalatha, S.; Dinesh, M.G.; Sekaran, G. Production of prodigiosin using tannery fleshing and evaluating its pharmacological effects. *Sci. World J.* **2014**, *2014*, 290–327. [CrossRef]

118. Hernandez-Velasco, P.; Morales-Atilano, I.; Rodríguez-Delgado, M.; Rodríguez-Delgado, J.M.; Luna-Moreno, D.; Avalos-Alanís, F.G.; Villarreal-Chiu, J.F. Photoelectric evaluation of dye-sensitized solar cells based on prodigiosin pigment derived from *Serratia marcescens* 11E. *Dye. Pigment.* **2020**, *177*, 108278. [CrossRef]

119. Aruldass, C.A.; Venil, C.K.; Zakaria, Z.A.; Ahmad, W.A. Brown sugar as a low-cost medium for the production of prodigiosin by locally isolated *Serratia marcescens* UTM1. *Int. Biodeterior. Biodegrad.* **2014**, *95*, 19–24. [CrossRef]

120. Lin, C.; Jia, X.; Chen, L.; Zhang, H.; Lin, R.; Chen, J. Enhanced production of prodigiosin by *Serratia marcescens* FZSF02 in the form of pigment pellets. *Electron J. Biotechnol.* **2019**, *40*, 58–64. [CrossRef]

121. Picha, P.; Kale, D.; Dave, I.; Pardeshi, S. Comparative studies on prodigiosin production by *Serratia marcescens* using various crude fatty acid sources its characterization and applications. *J. Int. J. Curr. Microbiol. Appl. Sci.* **2015**, *2*, 254–267.

122. Luti, K.J.K.; Yonis, R.W.; Mahmoud, S.T. An application of solid state fermentation and elicitation with some microbial cells for the enhancement of prodigiosin production by *Serratia marcescens*. *J. Al-Nairain Univ.* **2018**, *21*, 98–105. [CrossRef]

123. El-Bondkly, A.M.A.; El-Gendy, M.M.A.; Bassyouni, R.H. Overproduction and biological activity of prodigiosin-like pigments from recombinant fusant of endophytic marine *Streptomyces* species. *Antonie Van Leeuwenhoek* **2012**, *102*, 719–734. [CrossRef]

124. Arikan, E.B.; Canli, O.; Caro, Y.; Dufossé, L.; Dizge, N. Production of bio-based pigments from food processing industry by-products (apple, pomegranate, black carrot, red beet pulps) using *Aspergillus carbonarius*. *J. Fungi* **2020**, *6*, 240. [CrossRef]

125. Roukas, T.; Varzakakou, M.; Kotzekidou, P. From cheese whey to carotenes by *Blakeslea trispora* in a bubble column reactor. *Appl. Biochem. Biotechnol.* **2015**, *175*, 182–193. [CrossRef]

126. Park, E.Y.; Ito, Y.; Nariyama, M.; Sugimoto, T.; Lies, D.; Kato, T. The improvement of riboflavin production in *Ashbya gossypii* via disparity mutagenesis and DNA microarray analysis. *Appl. Microbiol. Biotechnol.* **2011**, *91*, 1315–1326. [CrossRef]

127. Zhang, S.; Zhao, W.; Nkechi, O.; Lu, P.; Bai, J.; Lin, Q.; Liu, J. Utilization of low-cost agricultural by-product rice husk for *Monascus* pigments production via submerged batch-fermentation. *J. Sci. Food Agric.* **2022**, *102*, 2454–2463. [CrossRef]

128. Mehri, D.; Perendeci, N.A.; Goksungur, Y. Utilization of whey for red pigment production by *Monascus purpureus* in submerged fermentation. *Fermentation* **2021**, *7*, 75. [CrossRef]

129. Embaby, A.M.; Hussein, M.N.; Hussein, A. *Monascus* orange and red pigments production by *Monascus purpureus* ATCC16436 through co-solid state fermentation of corn cob and glycerol: An eco-friendly environmental low cost approach. *PLoS ONE* **2018**, *13*, e0207755. [CrossRef] [PubMed]

130. Silveira, S.T.; Daroit, D.J.; Brandelli, A. Pigment production by *Monascus purpureus* in grape waste using factorial design. *Food Sci. Technol.* **2008**, *41*, 170–174. [CrossRef]

131. Kantifedaki, A.; Kachrimanidou, V.; Mallouchos, A.; Papanikolaou, S.; Koutinas, A.A. Orange processing waste valorisation for the production of bio-based pigments using the fungal strains *Monascus purpureus* and *Penicillium purpurogenum*. *J. Clean. Prod.* **2018**, *185*, 882–890. [CrossRef]

132. Valduga, E.; Ribeiro, A.H.R.; Cence, K.; Colet, R.; Tiggemann, L.; Zeni, J.; Toniazzo, G. Carotenoids production from a newly isolated *Sporidiobolus pararoseus* strain using agroindustrial substrates. *Biocatal. Agric. Biotechnol.* **2014**, *3*, 207–213. [CrossRef]

133. Morales-Oyervides, L.; Ruiz-Sánchez, J.P.; Oliveira, J.C.; Sousa-Gallagher, M.J.; Morales-Martínez, T.K.; Albergamo, A.; Salvo, A.; Giuffrida, D.; Dufossé, L.; Montañez, J. Medium design from corncob hydrolyzate for pigment production by *Talaromyces atroroseus* GH2: Kinetics modeling and pigments characterization. *Biochem. Eng. J.* **2020**, *161*, 107698. [CrossRef]

134. Pandit, S.G.; Ramesh, K.P.M.; Puttananjaiah, M.H.; Dhale, M.A. *Cicer arietinum* (Bengal gram) husk as alternative for *Talaromyces purpureogenus* CFRM02 pigment production: Bioactivities and identification. *LWT—Food Sci. Technol.* **2019**, *116*, 108499. [CrossRef]

135. Nasrabadi, M.; Razavi, S. Optimization of β-carotene production by a mutant of the lactose-positive yeast *Rhodotorula achenorium* from whey ultrafiltrate. *Food Sci. Biotech.* **2011**, *20*, 445–454. [CrossRef]

136. Schneider, T.; Graeff-Hönninger, S.; French, W.T.; Hernandez, R.; Merkt, N.; Claupein, W.; Hetrick, M.; Pham, P. Lipid and carotenoid production by oleaginous red yeast *Rhodotorula glutinis* cultivated on brewery effluents. *Energy* **2013**, *61*, 34–43. [CrossRef]
137. Tinoi, J.; Rakariyatham, N.; Deming, R.L. Simplex optimization of carotenoid production by *Rhodotorula glutinis* using hydrolyzed mung bean waste flour as substrate. *Process Biochem.* **2005**, *40*, 2551–2557. [CrossRef]

138. Ribeiro, J.E.S.; Sant'Ana, A.M.d.S.; Martini, M.; Sorce, C.; Andreucci, A.; de Melo, D.J.N.; da Silva, F.L.H. *Rhodotorula glutinis* cultivation on cassava wastewater for carotenoids and fatty acids generation. *Biocatal. Agric. Biotechnol.* **2019**, *22*, 101419. [CrossRef]

139. Saenge, C.; Cheirsilp, B.; Suksaroge, T.T.; Bourtoom, T. Potential use of oleaginous red yeast *Rhodotorula glutinis* for the bioconversion of crude glycerol from biodiesel plant to lipids and carotenoids. *Process Biochem.* **2011**, *46*, 210–218. [CrossRef]

140. Taskin, M.; Sisman, T.; Erdal, S.; Kurbanoglu, E.B. Use of waste chicken feathers as peptone for production of carotenoids in submerged culture of *Rhodotorula glutinis* MT-5. *Eur. Food Res. Technol.* **2011**, *233*, 657–665. [CrossRef]

141. Marova, I.; Carnecka, M.; Halienova, A.; Certik, M.; Dvorakova, T.; Haronikova, A. Use of several waste substrates for carotenoid-rich yeast biomass production. *J. Environ. Manag.* **2011**, *95*, 338–342. [CrossRef] [PubMed]

142. Frengova, G.I.; Emilina, S.D.; Beshkova, D.M. Carotenoid production by lactoso-negative yeasts co-cultivated with lactic acid bacteria in whey ultrafiltrate. *Z. Naturforsch. C. J. Biosci.* **2003**, *58*, 562–567. [CrossRef]

143. Kaur, B.; Chakraborty, D.; Kaur, H. Production and stability analysis of yellowish pink pigments from *Rhodotorula rubra* MTCC 1446. *Int. J. Microbiol.* **2012**, *7*, 1–7. [CrossRef]

144. Moreira, M.D.; Melo, M.M.; Coimbra, J.M.; Dos Reis, K.C.; Schwan, R.F.; Silva, C.F. Solid coffee waste as alternative to produce carotenoids with antioxidant and antimicrobial activities. *Waste Manag.* **2018**, *82*, 93–99. [CrossRef]

145. Manimala, M.R.A.; Murugesan, R. Studies on carotenoid pigment production by yeast *Rhodotorula mucilaginosa* using cheap materials of agro-industrial origin. *Pharma Innov.* **2017**, *6*, 80.

146. Sharma, R.; Ghoshal, G. Optimization of carotenoids production by *Rhodotorula mucilaginosa* (MTCC-1403) using agro-industrial waste in bioreactor: A statistical approach. *Biotechnol. Rep.* **2020**, *25*, e00407. [CrossRef]

147. Liu, Z.; Feist, A.M.; Dragone, G.; Mussatto, S.I. Lipid and carotenoid production from wheat straw hydrolysates by different oleaginous yeasts. *J. Clean. Prod.* **2020**, *249*, 119308. [CrossRef]

148. Freitas, C.; Parreira, T.M.; Roseiro, J.; Reis, A.; da Silva, T.L. Selecting low-cost carbon sources for carotenoid and lipid production by the pink yeast *Rhodosporidium toruloides* NCYC 921 using flow cytometry. *Bioresour. Technol.* **2014**, *158*, 355–359. [CrossRef]

149. Machado, W.R.C.; de Medeiros Burkert, J.F. Optimization of agroindustrial medium for the production of carotenoids by wild yeast *Sporidiobolus pararoseus*. *Afr. J. Microbiol. Res.* **2015**, *9*, 209–219.

150. Colet, R.; Urnau, L.; Bampi, J.; Zeni, J.; Dias, B.B.; Rodrigues, E.; Jacques, R.A.; Di Luccio, M.; Valduga, E. Use of low-cost agro products as substrate in semi-continuous process to obtain carotenoids by *Sporidiobolus salmonicolor*. *Biocatal. Agric. Biotechnol.* **2017**, *11*, 268–274. [CrossRef]

151. Valduga, E.; Tatsch, P.; Vanzo, L.; Rauber, F.; Di Luccio, M.; Treichel, H. Assessment of hydrolysis of cheese whey and use of hydrolysate for bioproduction of carotenoids by *Sporidiobolus salmonicolor* CBS 2636. *J. Sci. Food Agric.* **2009**, *89*, 1060–1065. [CrossRef]

152. Vázquez, M.; Santos, V.; Parajó, J.C. Fed-batch cultures of *Phaffia rhodozyma* in xylose-containing media made from wood hydrolysates. *Food Biotechnol. Lett.* **1998**, *12*, 43–55. [CrossRef]

153. Tinoi, J.; Rakariyatham, N.; Deming, R.L. Utilization of mustard waste isolates for improved production of astaxanthin by *Xanthophyllomyces dendrorhous*. *J. Ind. Microbiol. Biotechnol.* **2006**, *33*, 309–314. [CrossRef]

154. Ramírez, J.; Obledo, N.; Arellano, M.; Herrera, E. Astaxanthin production by *Phaffia rhodozyma* in a fed-batch culture using a low cost medium feedin. *e-Gnosis* **2006**, *4*, 1–9.

155. Haard, N.F. Astaxanthin formation by the yeast *Phaffia rhodozyma* on molasses. *Biotechnol. Lett.* **1988**, *10*, 609–614. [CrossRef]

156. Meyer, P.S.; du Preez, J.C. Astaxanthin production by a *Phaffia rhodozyma* mutant on grape juice. *World J. Microbiol. Biotechnol.* **1994**, *10*, 178–183. [CrossRef] [PubMed]

157. Villegas-Méndez, M.Á.; Aguilar-Machado, D.E.; Balagurusamy, N.; Montañez, J.; Morales-Oyervides, L. Agro-industrial wastes for the synthesis of carotenoids by *Xanthophyllomyces dendrorhous*: Mesquite pods- based medium design and optimization. *Biochem. Eng. J.* **2019**, *150*, 107260. [CrossRef]

158. Rodrigues, D.B.; Flores, É.M.M.; Barin, J.S.; Mercadante, A.Z.; Jacob-Lopes, E.; Zepka, L.Q. Production of carotenoids from microalgae cultivated using agroindustrial wastes. *Food Res. Int.* **2014**, *65*, 144–148. [CrossRef]

159. Korumilli, T.; Mishra, S. Carotenoid production by *Bacillus clausii* using rice powder as the sole substrate pigment analyses and optimization of key pro- duction parameters. *J. Biochem. Technol.* **2014**, *5*, 788–794.

160. Lian, X.; Wang, C.; Guo, K. Identification of new red pigments produced by *Monascus ruber*. *Dye. Pigment.* **2007**, *73*, 121–125. [CrossRef]

161. Venkatachalam, M.; Shum-Chéong-Sing, A.; Dufossé, L.; Fouillaud, M. Statistical optimization of the physico-chemical parameters for pigment production in submerged fermentation of *Talaromyces albobiverticillius* 30548. *Microorganisms* **2020**, *8*, 711. [CrossRef] [PubMed]

162. Ramesh, C.; Vinithkumar, N.V.; Kirubagaran, R.; Venil, C.K.; Dufosse, L. Applications of prodigiosin extracted from marine red pigmented bacteria *Zooshikella* sp. and actinomycete *Streptomyces* sp. *Microorganisms* **2020**, *8*, 556. [CrossRef] [PubMed]

163. Orlandi, V.T.; Martegani, E.; Giaroni, C.; Baj, A.; Bolognese, F. Bacterial pigments: A colorful palette reservoir for biotechnological applications. *Biotechnol. Appl. Biochem.* **2021**, *69*, 981–1001. [CrossRef]
164. Prasastha, V.R.; Yasur, J.; Abishad, P.; Unni, V.; Gourkhede, D.P.; Nishanth, M.A.D.; Niveditha, P.; Vergis, J.; Malik, S.V.S.; Byrappa, K.; et al. Antimicrobial efficacy of green synthesized nanosilver with entrapped cinnamaldehyde against multi-drug-resistant enteroaggregative *Escherichia coli* in *Galleria mellonella*. *Pharmaceutics* **2022**, *14*, 1924. [CrossRef]

165. Pereira, M.F.; Rossi, C.C. Overview of rearing and testing conditions and a guide for optimizing *Galleria mellonella* breeding and use in the laboratory for scientific purposes. *J. Pathol. Microbiol. Immunol.* **2020**, *128*, 607–620. [CrossRef]

166. Pereira, M.F.; Rossi, C.C.; da Silva, G.C.; Rosa, J.N.; Bazzolli, D.M.S. *Galleria mellonella* as an infection model: An in-depth look at why it works and practical considerations for successful application. *Pathog. Dis.* **2020**, *78*, ftaa056. [CrossRef]

167. Tsai, C.J.-Y.; Loh, J.M.S.; Proft, T. *Galleria mellonella* infection models for the study of bacterial diseases and for antimicrobial drug testing. *Virulence* **2016**, *7*, 214–229. [CrossRef]

168. Andrea, A.; Krogfelt, K.A.; Jenssen, H. Methods and challenges of using the greater wax moth (*Galleria mellonella*) as a model organism in antimicrobial compound discovery. *Microorganisms* **2019**, *7*, 85. [CrossRef]

169. Cutuli, M.A.; Petronio Petronio, G.; Vergalito, F.; Magnifico, I.; Pietrangelo, L.; Venditti, N.; Di Marco, R. *Galleria mellonella* as a consolidated in vivo model hosts: New developments in antibacterial strategies and novel drug testing. *Virulence* **2019**, *10*, 527–541. [CrossRef] [PubMed]

170. Wojda, I. Immunity of the greater wax moth *Galleria mellonella*. *Insect Sci.* **2017**, *24*, 342–357. [CrossRef]

171. Abas, N.; Kalair, A.R.; Khan, N.; Haider, A.; Saleem, Z.; Saleem, M.S. Natural and synthetic refrigerants, global warming: A review. *Renew. Sustain. Energy Rev.* **2018**, *90*, 557–569. [CrossRef]

172. Khan, S.; Malik, A. Toxicity evaluation of textile effluents and role of native soil bacterium in biodegradation of a textile dye. *Environ. Sci. Pollut. Res.* **2018**, *25*, 4446–4458. [CrossRef]

173. Six, J.; Frey, S.D.; Thiet, R.K.; Batten, K.M. Bacterial and fungal contributions to carbon sequestration in agroecosystems. *Soil Sci. Soc. Am. J.* **2006**, *70*, 555–569. [CrossRef]

174. Tanet, L.; Martini, S.; Casalot, L.; Tamburini, C. Reviews and syntheses: Bacterial bioluminescence-ecology and impact in the biological carbon pump. *Biogeosciences Discuss.* **2020**, *17*, 3757–3778. [CrossRef]

175. Jiao, N.; Robinson, C.; Azam, F.; Thomas, H.; Baltar, F.; Dang, H.; Hardman-Mountford, N.J.; Johnson, M.; Kirchman, D.L.; Koch, B.P.; et al. Mechanisms of microbial carbon sequestration in the ocean—Future research directions. *Biogeosciences* **2014**, *11*, 5285–5306. [CrossRef]

176. Zhang, C.; Dang, H.; Azam, F.; Benner, R.; Legendre, L.; Passow, U.; Polimene, L.; Robinson, C.; Suttle, C.A.; Jiao, N. Evolving paradigms in biological carbon cycling in the ocean. *Natl. Sci. Rev.* **2018**, *5*, 481–499. [CrossRef]

177. Matteoli, F.P.; Passarelli-Araujo, H.; Reis, R.J.A.; da Rocha, L.O.; de Souza, E.M.; Aravind, L.; Olivares, F.L.; Venancio, T.M. Genome sequencing and assessment of plant growth-promoting properties of a *Serratia marcescens* strain isolated from vermicompost. *BMC Genom.* **2018**, *19*, 750. [CrossRef]

178. Habash, S.S.; Brass, H.U.C.; Klein, A.S.; Klebl, D.P.; Weber, T.M.; Classen, T.; Pietruszka, J.; Grundler, F.M.W.; Schleker, A.S.S. Novel prodiginein derivatives demonstrate bioactivities on plants, nematodes, and fungi. *Front. Plant Sci.* **2020**, *11*, 579807. [CrossRef]

179. Gutiérrez-Román, M.I.; Holguín-Meléndez, F.; Bello-Mendoza, R.; Guillén-Navarro, K.; Dunn, M.F.; Huerta-Palacios, G. Production of prodigiosin and chitinases by tropical *Serratia marcescens* strains with potential to control plant pathogens. *World J. Microbiol. Biotechnol.* **2012**, *28*, 145–153. [CrossRef]

180. Suryawanshi, R.K.; Patil, C.D.; Borase, H.P.; Narkhede, C.P.; Salunke, B.K.; Patil, S.V. Mosquito larvicidal and pupaeccidal potential of prodigiosin from *Serratia marcescens* and understanding its mechanism of action. *Pestic. Biochem. Physiol.* **2015**, *123*, 49–55. [CrossRef] [PubMed]

181. Banik, A.; Pandya, P.; Patel, B.; Rathod, C.; Dangar, M. Characterization of halotolerant, pigmented, plant growth promoting bacteria of groundnut rhizosphere and its in-vitro evaluation of plant-microbe protocooperation to withstand salinity and metal stress. *Sci. Total Environ.* **2018**, *630*, 231–242. [CrossRef] [PubMed]

182. Jimtha, C.J.; Jishma, P.; Sreelekha, S.; Chithra, S.; Radhakrishnan, E.K. Antifungal properties of prodigiosin producing rhizospheric *Serratia* sp. *Rhizosphere* **2017**, *3*, 105–108. [CrossRef]

183. Meena, B.; Anburajan, L.; Sathish, T.; Das, A.K.; Vinithkumar, N.V.; Kirubagaran, R.; Dharani, G. Studies on diversity of Vibrio sp. and the prevalence of *hapA*, *tcpI*, *st*, *rtxA* & *C*, *acfB*, *hlyA*, *ctxA*, *ompU* and *toxR* genes in environmental strains of Vibrio cholerae from Port Blair bays of South Andaman, India. *Mar. Pollut. Bull.* **2019**, *144*, 105–116.

184. Sivalingam, K.M. Isolation, identification and evaluation of *Spirulina platensis* for its effect on seed germination of groundnut (*Arachis hypogaea* L.), Wolaita Sodo, Southern Ethiopia. *J. Algal Biomass Utln.* **2020**, *11*, 34–42.

185. Oyanedel, R.; Hinsley, A.; Dentinger, B.T.M.; Milner-Gulland, E.J.; Furci, G. A way forward for wild fungi in international sustainability policy. *Conserv. Lett.* **2022**, *15*, e12882. [CrossRef]

186. Rillig, M.C.; Mummey, D.L. Mycorrhizas and soil structure. *New Phytol.* **2006**, *171*, 41–53. [CrossRef]

187. Chahal, K.; Gupta, V.; Verma, N.K.; Chaurasia, A.; Rana, B. Arbuscular mycorrhizal (AM) fungi as a tool for sustainable agricultural system. In *Mycorrhizal Fungi-Utilization in Agriculture and Forestry*; Radhakrishnan, R., Ed.; IntechOpen: London, UK, 2020; pp. 1–12.

188. Kiers, E.T.; Duhamel, M.; Beesetty, Y.; Mensah, J.A.; Franken, O.; Verbruggen, E.; Fellbaum, C.R.; Kowalchuk, G.A.; Hart, M.M.; Bago, A.; et al. Reciprocal rewards stabilize cooperation in the mycorrhizal symbiosis. *Science* **2011**, *333*, 880–882. [CrossRef]
189. Liang, T.; Shi, X.; Guo, T.; Peng, S. Arbuscular mycorrhizal fungus mediate changes in mycorrhizosphere soil aggregates. *Agric. Sci.* **2015**, *6*, 1455–1463. [CrossRef]

190. Mohammadi, K.; Khalesro, S.; Sohrabi, Y.; Heidari, G. A review: Beneficial effects of the mycorrhizal fungi for plant growth. *J. Appl. Environ. Biol. Sci.* **2011**, *1*, 310–319.

191. French, K.E. Engineering mycorrhizal symbioses to alter plant metabolism and improve crop health. *Front Microbiol.* **2017**, *8*, 1403. [CrossRef] [PubMed]

192. Prasad, K.; Khare, A.; Rawat, P. Glomalin arbuscular mycorrhizal fungal reproduction, lifestyle and dynamic role in global sustainable agriculture for future generation. In *Fungal Reproduction and Growth*; Sultan, S., Singh, G.K.S., Eds.; IntechOpen: London, UK, 2022; pp. 1–22.

193. Hause, B.; Fester, T. Molecular and cell biology of arbuscular mycorrhizal symbiosis. *Planta* **2005**, *221*, 184–196. [CrossRef] [PubMed]

194. Lindahl, B.D.; Kyaschenko, J.; Varenius, K.; Clemmensen, K.E.; Dahlberg, A.; Karltun, E.; Stendahl, J. A group of ectomycorrhizal fungi restricts organic matter accumulation in boreal forest. *Ecol. Lett.* **2021**, *24*, 1341–1351. [CrossRef] [PubMed]

195. Qu, Z.-L.; Santalahti, M.; Köster, K.; Berninger, F.; Pumpanen, J.; Heinonsalo, J.; Sun, H. Soil fungal community structure in boreal pine forests: From southern to subarctic areas of Finland. *Front. Microbiol.* **2021**, *12*, 653896. [CrossRef] [PubMed]

196. Clemmensen, K.E.; Finlay, R.D.; Dahlberg, A.; Stenlid, J.; Wardle, D.A.; Lindahl, B.D. Carbon sequestration is related to mycorrhizal fungal community shifts during long-term succession in boreal forests. *New Phytol.* **2015**, *205*, 1525–1536. [CrossRef]

197. Lombardi, N.; Caira, S.; Troise, A.D.; Scaloni, A.; Vitaglione, P.; Vinale, F.; Marra, R.; Salzano, A.M.; Lorito, M.; Woo, S.L. *Trichoderma* applications on strawberry plants modulate the physiological processes positively affecting fruit production and quality. *Front. Microbiol.* **2020**, *11*, 1364. [CrossRef]

198. Gill, S.S.; Gill, R.; Trivedi, D.K.; Anjum, N.A.; Sharma, K.K.; Ansari, M.W.; Ansari, A.A.; Johri, A.K.; Prasad, R.; Pereira, E.; et al. *Piriformospora indica*: Potential and significance in plant stress tolerance. *Front. Microbiol.* **2016**, *7*, 332. [CrossRef]

199. Fernandez, C.W.; Koide, R.T. The function of melanin in the ectomycorrhizal fungus *Cenococcum geophilum* under water stress. *Fungal Ecol.* **2013**, *6*, 479–486. [CrossRef]

200. Kapoor, D.; Karnwal, A. Yeast as plant growth promoter and biocontrol agent. In *Fungi Bio-Prospects in Sustainable Agriculture, Environment and Nano-Technology Volume 1: Fungal Diversity of Sustainable Agriculture*; Sharma, V.K., Shah, M., Parmar, S., Kumar, A., Eds.; Elsevier: Amsterdam, The Netherlands, 2020; pp. 429–457.

201. Sondak, C.F.; Ang, P.O.; Beardall, J.; Bellgrove, A.; Boo, S.M.; Gerung, G.S.; Hepburn, C.D.; Hong, D.D.; Hu, Z.; Kawai, H.; et al. Carbon dioxide mitigation potential of seaweed aquaculturebeds (SABs). *J. Appl. Phycol.* **2017**, *29*, 2363–2373. [CrossRef]

202. Zhao, B.; Su, A. Macro assessment of microalgae-based CO₂ sequestration: Environmental and energy effects. *Algal Res.* **2020**, *51*, 102066. [CrossRef]

203. Oncel, S.S.; Kose, A.; Oncel, D.S. Carbon sequestration in microalgae photobioreactors building integrated. In *Start-Up Creation The Smart Eco-Efficient Built Environment*; Pacheco-Torgal, F., Rasmussen, E., Granqvist, C.-G., Ivanov, V., Kaklauskas, A., Makonin, S., Eds.; Elsevier: Amsterdam, The Netherlands, 2020; pp. 161–200.

204. Vale, M.A.; Ferreira, A.; Pires, J.C.M.; Gonçalves, A.L. CO₂ capture using microalgae. In *Advances in Carbon Capture Methods, Technologies and Applications*; Rahimpour, M.R., Farsi, M., Makarem, M.A., Eds.; Elsevier: Duxford, UK, 2020; pp. 381–405.

205. Pavlik, D.; Zhong, Y.; Daiek, C.; Liao, W.; Morgan, R.; Clary, W.; Liu, Y. Microalgae cultivation for carbon dioxide sequestration and protein production using a high-efficiency photobioreactor system. *Algal Res.* **2017**, *25*, 413–420. [CrossRef]

206. Xu, X.; Gu, X.; Wang, Z.; Shatner, W.; Wang, Z. Progress, challenges and solutions of research on photosynthetic carbon sequestration efficiency of microalgae. *Renew. Sustain. Energy Rev.* **2019**, *110*, 65–82. [CrossRef]

207. Narala, R.R.; Garg, S.; Sharma, K.K.; Thomas-Hall, S.R.; Deme, M.; Li, Y.; Schenk, P.M. Comparison of microalgae cultivation in photobioreactor, open raceway pond, and a two-stage hybrid system. *Front. Energy Res.* **2016**, *4*, 29. [CrossRef]

208. Onyeaka, H.; Miri, T.; Obileke, K.; Hart, A.; Anumudu, C.; Al-Sharify, Z.T. Minimizing carbon footprint via microalgae as a biological capture. *Carbon Capture Sci. Technol.* **2021**, *1*, 100007. [CrossRef]

209. Jerney, J.; Spilling, K. Large Scale Cultivation of Microalgae: Open and Closed Systems. *Methods Mol. Biol.* **2020**, *1980*, 1–8.

210. Viswanaathan, S.; Perumal, P.K.; Sundaram, S. Integrated approach for carbon sequestration and wastewater treatment using algal-bacterial consortia: Opportunities and challenges. *Sustainability* **2022**, *14*, 1075. [CrossRef]

211. Vishnupriya, S.; Bhavaniramya, S.; Baskaran, D.; Karthiayani, A. Microbial pigments and their application. In *Microbial Polymers*; Vaishnav, A., Choudhary, D.K., Eds.; Springer Nature: Singapore, 2021; pp. 197–214.

212. Numan, M.; Bashir, S.; Mumtaz, R.; Tayyab, S.; Rehman, N.U.; Khan, A.L.; Shinwari, Z.K.; Al-Harrasi, A. Therapeutic applications of bacterial pigments: A review of current status and future opportunities. *3 Biotech* **2018**, *8*, 207. [CrossRef]

213. Mohammadi, M.A.; Ahangari, H.; Mousazadeh, S.; Hosseini, S.M.; Dufossé, L. Microbial pigments as an alternative to synthetic dyes and food additives: A brief review of recent studies. *Bioprocess Biosyst. Eng.* **2022**, *45*, 1–12. [CrossRef]

214. Kaur, P.; Singh, S.; Ghoshal, G.; Ramamurthy, P.C.; Parihar, P.; Singh, J.; Singh, A. Valorization of agri-food industry waste for the production of microbial pigments: An eco-friendly approach. In *Advances in Agricultural and Industrial Microbiology*; Nayak, S.K., Baliyarsingh, B., Mannazzu, I., Singh, A., Mishra, B.B., Eds.; Springer: Singapore, 2022; pp. 137–166.

215. Ramesh, C.H.; Anwesh, M.; Vinithkumar, N.V.; Kirubagaran, R.; Dufossé, L. Complete genome analysis of undecylprodigiosin pigment biosynthesizing marine *Streptomyces* species displaying potential bioactive applications. *Microorganisms* **2021**, *9*, 2249. [CrossRef]
216. Amorim, L.F.A.; Mouro, C.; Riool, M.; Gouveia, I.C. Antimicrobial food packaging based on prodigiosin-incorporated double-layered bacterial cellulose and chitosan composites. *Polymers* **2022**, *14*, 315. [CrossRef] [PubMed]

217. Metwally. R.A.; El Sikaily, A.; El-Sersy, N.A.; A.Ghozlan, H.; Sabry, S.A. Antimicrobial activity of textile fabrics dyed with prodigiosin pigment extracted from marine *Serratia rubidaea* RAM_Alex bacteria. *Egypt. J. Aquat. Res.* **2021**, *47*, 301–305. [CrossRef]

218. Lee, J.; Kim, J.; Song, J.E.; Song, W.-S.; Kim, E.-J.; Kim, Y.-G.; Jeong, H.-J.; Kim, H.R.; Choi, K.-Y.; Kim, B.-G. Production of tyrian purple indigoid dye from tryptophan in *Escherichia coli*. *Nat. Chem. Biol.* **2021**, *17*, 104–112. [CrossRef] [PubMed]

219. Choi, K.-Y. A review of recent progress in the synthesis of bio-indigoids and their biologically assisted end-use applications. *Dye. Pigment.* **2020**, *181*, 108570. [CrossRef]

220. Hou, Y.; Yan, M.; Wang, Q.; Wang, Y.; Xu, Y.; Wang, Y.; Li, H.; Wang, H. C-phycocyanin from *Spirulina maxima* as a green fluorescent probe for the highly selective detection of Mercury(II) in seafood. *Food Anal. Methods* **2017**, *10*, 1931–1939. [CrossRef]

221. Patel, A.K.; Albarico, F.P.J.B.; KrishnaPerumal, P.; Vadrale, A.P.; Nian, C.T.; Chau, H.T.B.; Anwar, C.; Wani, H.M.; Pal, A.; Saini, R.; et al. Algae as an emerging source of bioactive pigments. *Bioresour. Technol.* **2022**, *351*, 126910. [CrossRef]

222. Srivastava, A.; Kalwani, M.; Chakdar, H.; Pabbi, S.; Shukla, P. Biosynthesis and biotechnological interventions for commercial production of microalgal pigments: A review. *Bioresour. Technol.* **2022**, *352*, 127071. [CrossRef]