From Latin American Agro-Industrial Waste and CO₂ to High-Value Bioproducts: Fermentation-Based Production Platforms for a Regional Bioeconomy

Abstract

This focused review examines fermentation and fermentation-integrated microbial platforms that convert two regionally relevant substrate classes, Latin American agro-industrial residues and concentrated CO₂ streams, into high-value bioproducts. The review is not intended as a complete survey of all biomass valorization routes in Latin America. Instead, it evaluates platform–feedstock–product combinations with clear translational relevance for regional biorefineries, with emphasis on literature from 2020–2025 and on earlier benchmark studies only when they define current technical performance limits. Latin America and the Caribbean combine high-volume sugarcane, agave, coffee, citrus, banana, cacao, and tuber-processing residues with biogenic CO₂ from ethanol fermentation and industrial point sources from cement, lime, and oil-and-gas operations. The technical opportunity is therefore not residue abundance alone, but the rational coupling of residue chemistry, CO₂-source quality, locally isolated microbial strains, and process architectures that can be scaled under regional constraints. We compare phototrophic CO₂-fixing modules based on cyanobacteria and microalgae, chemoautotrophic gas fermentation using Cupriavidus necator and related systems, heterotrophic yeast platforms including Rhodotorula spp. and Yarrowia lipolytica, and bacterial platforms for PHAs, bacterial cellulose, and organic acids. The core technical analysis focuses on substrate conditioning, hydrolysate inhibition, oxygen- and gas-transfer constraints, light delivery, C/N control, mixed-sugar utilization, metabolic engineering, reactor configuration, downstream processing, and quantitative reporting metrics. One fermentation-integrated laboratory case study—the Synechocystis sp. PCC 6803–Rhodotorula mucilaginosa UANL-001L CO₂-to-carotenoid relay—and one explicitly defined non-fermentative boundary case on peel-extract-derived coating films are used to illustrate two different aspects of regional biorefinery design: dual-feedstock microbial conversion and low-CapEx product-fit decisions for agro-industrial residues. We conclude that Latin America’s strongest near-term position is in technically disciplined, product-specific biorefineries that integrate local feedstock chemistry with engineered or locally adapted chassis, rather than in generic biomass-to-product claims.

1. Introduction

Industrial biotechnology is being asked to deliver lower-carbon products, improved resource circularity, and more resilient supply chains for nutrients, materials, pigments, and specialty chemicals [1,2,3]. In this context, fermentation is no longer restricted to the conversion of refined sugars into ethanol or organic acids. It increasingly includes integrated microbial process trains in which phototrophic, chemolithoautotrophic, and heterotrophic modules are coupled to convert CO₂, lignocellulosic hydrolysates, pectin-rich residues, starch-rich extracts, and mixed organic side streams into higher-value products [4].

The Latin American and Caribbean (LATAM) setting is technically distinctive. Brazil processes hundreds of millions of tonnes of sugarcane per year [5], creating bagasse, straw, vinasse, and molasses streams relevant to lignocellulosic and sugar-based fermentation [6,7]. Brazilian ethanol production also creates relatively concentrated fermentation CO₂ streams [5]. Mexico concentrates agave bagasse from tequila and mezcal value chains [8,9], with AFEX/hydrolysis and solid-state enzyme routes reported for agave residues [10,11]. Coffee pulp and husk streams are especially relevant in Colombia and other coffee-producing countries [12,13,14]; citrus peel supports pectin-first and acid-fermentation cascades [15]; and cacao pod husk offers a pectin-, cellulose-, and phenolic-rich substrate [16,17]. These streams are not interchangeable feedstocks in practical fermentation design. In this context, non-interchangeability means that two streams with similar regional abundance or apparent carbon potential cannot be substituted directly without changing feedstock conditioning, microbial chassis, reactor operation, and downstream processing. For organic residues, their cellulose/hemicellulose/lignin, pectin, starch, soluble sugar, lipid, nitrogen, phenolic, caffeine, limonene, and mineral profiles determine pretreatment severity, detoxification requirements, organism choice, productivity, and downstream-processing burden. For CO₂ streams, gas purity, partial pressure, continuity of supply, impurity profile, compression requirements, and gas–liquid transfer constraints determine whether phototrophic or chemoautotrophic platforms are technically viable.

LATAM biorefineries should be designed around platform matching rather than around generic residue valorization [4,6,7]. A sugarcane-bagasse hydrolysate [6,7] requires a different microbial and process logic than citrus peel [15], coffee pulp [12,13,14], or fermentation CO₂ [4,5]. A cyanobacterial photobioreactor [18,19,20,21] has different scale-up constraints than a pressurized hydrogen-oxidizing gas fermenter [22,23,24,25]. A carotenoid process [26,27,28,29,30,31,32,33,34,35] has different reporting metrics and downstream economics than a PHA [36,37,38,39,40], bacterial cellulose [41,42,43,44], single-cell protein [4,24,25], or organic-acid process [15,18]. This focused review therefore evaluates not only which products are possible, but which combinations of substrate, chassis, reactor mode, genetic intervention, and product-recovery route are technically coherent.

1.1. Focused-Review Scope, Search Strategy, and Selection Logic

The term “fermentation-based” is used in a deliberately inclusive but technically bounded sense. Classical submerged or solid-state heterotrophic fermentation is central to the review, but phototrophic CO₂ fixation and chemoautotrophic gas fermentation are included when they are integrated with fermentative product formation, hydrolysate conversion, or sequential microbial relays. The review excludes purely thermochemical routes, stand-alone composting, anaerobic digestion without product upgrading, and residue applications that do not involve microbial conversion or a microbial-process interface. A single non-fermentative peel-extract coating-film example is retained as an explicitly labeled boundary case to clarify product-fit decisions for LATAM peel residues and is not treated as a fermentation platform.

The review prioritizes studies published between 2020 and 2025 that fall within the fermentation-based or fermentation-integrated scope defined above and meet at least one of the following criteria: (i) use of LATAM-relevant agro-industrial residues as substrates, nutrient sources, conditioning streams, or process-relevant inputs for microbial conversion or microbial-process integration; (ii) microbial conversion of CO₂, bicarbonate, syngas components, or CO₂-derived intermediates into bioproducts; (iii) fermentation of lignocellulosic, pectin-rich, starch-rich, phenolic-rich, or mixed agro-food residues into products with value density higher than fuel ethanol alone; (iv) synthetic-biology or metabolic-engineering advances in the chassis discussed here; or (v) TEA, LCA, or scale-up analyses relevant to regional deployment. Studies using LATAM-relevant residues for purposes unrelated to fermentation, microbial conversion, or bioprocess integration were not treated as core studies and were cited only narrowly as feedstock-composition, process-conditioning, or explicitly labeled boundary-case evidence. Foundational pre-2020 studies are included only where they remain benchmark references for platform performance or organism selection, such as the Synechocystis sp. PCC 6803 genome, cyanobacterial editing strategies, or hydrogen-oxidizing CO₂ fixation [22,45,46].

Literature was identified through targeted searches in Scopus, Web of Science, and Google Scholar, using search terms relevant to fermentation, industrial biotechnology, and bioprocess engineering. Search terms were combined in three Boolean blocks: (i) regional/feedstock terms, including “Latin America”, LATAM, Brazil, Mexico, Colombia, sugarcane bagasse, agave bagasse, coffee pulp, citrus peel, banana peel, cacao pod husk, agro-industrial waste, and fermentation CO₂; (ii) platform/product terms, including fermentation, biorefinery, hydrolysate, microbial conversion, CO₂ valorization, gas fermentation, cyanobacteria, microalgae, Cupriavidus necator, Rhodotorula, Yarrowia lipolytica, PHA, bacterial cellulose, carotenoids, single-cell protein, and organic acids; and (iii) translation terms, including titer, yield, productivity, downstream processing, recovery, techno-economic analysis, TEA, life-cycle assessment, LCA, scale-up, and pilot. Titles and abstracts were first screened for alignment with the fermentation-based or fermentation-integrated scope of the review. Full texts were then assessed against the selection criteria above and the technical assessment criteria described in Section 1.2. Studies were excluded from the core synthesis when they focused on purely thermochemical valorization, stand-alone composting, anaerobic digestion without product upgrading, extraction-only residue uses without microbial conversion or microbial-process integration, bulk-fuel-oriented studies without relevance to higher-value products, and reports lacking sufficient substrate, process, product, recovery, or scale-up information to support platform evaluation. The final qualitative corpus retained for synthesis consisted of 76 sources: 67 scholarly publications and 9 statistical, policy, or technical reports. Among the scholarly publications, 60 were published between 2020 and 2025, while 7 pre-2020 studies were retained as foundational or benchmark references.

Two author-derived case studies are included as local proof-of-concept illustrations, not as representative examples of all LATAM fermentation platforms and not as evidence used to rank platforms. Their inclusion follows the same platform-matching logic used throughout the review: each case makes visible a specific technical decision point that is difficult to capture through generic platform summaries alone. Box 1 is a fermentation-integrated proof-of-concept for a CO₂-to-biomass-to-heterotrophic-production relay; it illustrates the need to report measurable interfaces such as phototrophic biomass productivity, hydrolysis sugar yield, inhibitor formation, yeast growth, carotenoid profile, and carbon retained in recoverable product. Box 2 is a non-fermentative boundary case based on peel-extract-derived coating films; it is included only to clarify product-fit decisions for peel-rich residues and to distinguish fermentation-derived polymers from low-CapEx extract-based or hybrid material outputs that may coexist with fermentation modules in regional biorefineries. Thus, the case studies are used to operationalize the review framework, whereas platform-level conclusions are drawn from the wider literature synthesis and comparative tables.

Box 1. Technical case study: CO₂-to-carotenoids through a Synechocystis–Rhodotorula relay.

The UANL CO₂-to-carotenoid relay couples autotrophic carbon fixation by Synechocystis sp. PCC 6803 with heterotrophic carotenoid production by the locally isolated yeast R. mucilaginosa UANL-001L [37]. The process logic is modular: CO₂ is first converted into cyanobacterial biomass; the biomass is then hydrolyzed; the hydrolysate serves as a carbon and nutrient source for Rhodotorula cultivation; and intracellular carotenoids are recovered from the yeast biomass.

The technical value of this case is not that it already solves industrial CO₂ utilization, but that it demonstrates a testable architecture for dual-feedstock biorefineries. The measurable interfaces are cyanobacterial biomass productivity, hydrolysis sugar yield, inhibitor formation, yeast growth rate, carotenoid content, pigment profile, and carbon retained from CO₂ into recoverable product. Future optimization should compare acid, enzymatic, and biological hydrolysis; evaluate hydrolysate detoxification; and quantify the carbon and nitrogen distribution between yeast biomass, pigment, residual solids, and spent broth.

For this fermentation review, this case is a local proof-of-concept and illustrative process module, not a representative benchmark for all CO₂-to-product platforms. It demonstrates the broad focused-review thesis: LATAM can generate distinctive bioprocess concepts by coupling CO₂-fixing chassis with locally isolated heterotrophic organisms adapted to regional substrate conditions.

Schematic representation of the relay in which CO₂-fixed cyanobacterial biomass is hydrolyzed and redirected to heterotrophic carotenoid production by R. mucilaginosa UANL-001L.

Box 2. Boundary case study: non-fermentative peel-extract coating films as low-CapEx outputs of residue-based biorefineries.

This case is not presented as a fermentation-based polymer-production process. The UANL peel-extract coating-film study used banana peel, orange peel, potato peel, and combinations at 100 g/L extract concentration, with spin-coating used to fabricate thin films [24]. Orange peel extract generated the highest reported yield among the tested formulations [24], consistent with the role of pectin and soluble-sugar balance in film-forming matrices.

Its relevance to this review is as a local boundary case for platform matching. In contrast to PHAs or bacterial cellulose, where microbial conversion and fermentation performance define process feasibility, peel-extract films depend mainly on residue composition, extraction conditions, film formation, and application-specific material metrics. Including this case helps distinguish fermentation-derived biopolymers from low-CapEx residue-derived coatings that may be integrated alongside fermentation modules in a regional biorefinery.

Thus, the case supports the broader argument that LATAM residues should not be forced into a single fermentation pathway. Some streams may be better routed to microbial polymer production, whereas others may be more technically coherent as extract-based coatings, hybrid materials, or downstream coproducts, provided that quality metrics and regulatory use cases are clearly defined.

Schematic representation of the agro-industrial peel-extract coating-film workflow, in which banana, orange, and potato peel extracts are prepared at defined concentration, processed by spin-coating into thin bioplastic films, and evaluated through yield, surface morphology, thickness, structural signatures, mechanical properties, water-vapor permeability, biodegradation, and application fit.

1.2. Technical Assessment Criteria

Each platform is evaluated against six technical criteria: carbon-entry mode, substrate specificity, achievable titer/yield/productivity, reactor and mass-transfer constraints, genetic tractability, and downstream-processing intensity. This framing is important because many LATAM residue streams are available at low or negative cost, but low feedstock cost does not compensate for poor hydrolysis, low titer, high water content, inhibitor carryover, unstable mixed cultures, or expensive product extraction. For high-value products, technical feasibility is often determined less by theoretical pathway availability than by whether the process can reach reproducible volumetric productivity and recoverable product concentration under non-ideal substrate conditions.

To harmonize performance indicators across product classes, this review uses four common metric families: production intensity, yield or carbon efficiency, productivity, and recovery burden. Production intensity refers to the amount of product formed, but the appropriate unit depends on product form: g/L or mg/L for extracellular or soluble products, mg/g DCW or %DCW for intracellular products, g/L or g/m² for bacterial cellulose, and film mass or thickness-normalized performance for coating materials. Yield or carbon efficiency should be anchored to a defined input, such as g product/g substrate consumed, product per kg dry residue, mol C retained in product/mol C fed, or product per kg CO₂ fixed or supplied. Productivity should be reported as a time-normalized rate, preferably under controlled reactor conditions. Recovery burden refers to the downstream-processing effort needed to obtain a usable product, including extraction or purification efficiency, solvent or energy demand, product purity, and application-specific quality metrics. Therefore, cross-platform comparisons in this review do not rely on maximum titer alone, but on whether each route reports production, yield/carbon use, productivity, and recoverable product quality in a comparable manner.

Accordingly, here we treat residue analysis and policy context as enabling conditions rather than as the principal content. Residue volumes justify regional relevance and policy and innovation ecosystems affect deployment, but the central object of analysis is the microbial production platform and its process-engineering envelope.

Dual feedstock refers to the two major carbon-input classes used to organize this review: (i) LATAM agro-industrial residues, which provide organic carbon, nutrients, and residue-specific conditioning challenges, and (ii) captured CO₂ streams, which provide inorganic carbon for phototrophic or chemoautotrophic microbial platforms. The term is used at the process-architecture level and does not imply that both feedstocks must be supplied simultaneously to every microorganism. Depending on the platform, residues and CO₂ can be converted in independent modules, used in parallel within the same biorefinery, or coupled sequentially, as in a CO₂-to-biomass-to-heterotrophic-fermentation relay. This dual-feedstock architecture is summarized in Figure 1, which links LATAM agro-industrial residues and captured CO₂ streams to feedstock conditioning, microbial conversion platforms, high-value product families, and cross-cutting technical constraints.

Agro-industrial residues and captured CO₂ streams are integrated through feedstock-conditioning, gas-conditioning, and microbial-conversion modules. Phototrophic CO₂-fixing platforms, chemoautotrophic gas fermentation, and heterotrophic fermentation/bioprocessing can operate as independent or coupled routes to produce carotenoids, PHAs, bacterial cellulose, lipids, organic acids, nutraceuticals, and bioplastic coatings. The biomass–hydrolysate relay represents a dual-feedstock strategy in which CO₂-derived biomass feeds downstream heterotrophic production. Cross-cutting requirements include synthetic biology, bioreactor scale-up, downstream processing, TEA, and LCA, while major bottlenecks include feedstock variability, inhibitor formation, gas–liquid mass transfer, strain robustness, and purification cost.

2. Boundary Conditions: LATAM Feedstock and CO₂-Source Context

The most useful way to classify LATAM residues for fermentation is not by crop name but by process chemistry. Lignocellulosic residues such as sugarcane and agave bagasse require fractionation, enzyme accessibility, and inhibitor control [6,7,10,47]. Pectin-rich citrus residues support pectin recovery, organic-acid fermentation, and exopolysaccharide-forming platforms but require limonene management [15,48]. Starch- and pectin-containing banana and potato peels can support yeast and bacterial growth after mild extraction or hydrolysis [26,49]. Phenolic- and caffeine-rich coffee residues require detoxification or stress-tolerant organisms [12,13,14,50], while cacao pod husk combines pectin, cellulose, hemicellulose, minerals, and phenolics [16,17].

CO₂-source quality is equally important. Ethanol fermentation CO₂ is comparatively concentrated and low in NOx, SOx, and oxygen relative to flue gas, which reduces conditioning requirements for phototrophic or chemoautotrophic bioprocessing [5]. Cement and lime CO₂ streams have higher contaminant and temperature challenges and therefore require gas cleanup or robust bioreactor interfaces [4,23]. In process design, the critical variables are not only annual CO₂ tonnes, but partial pressure, continuity of supply, impurity profile, compression cost, on-site water and power, and distance to biomass aggregation nodes [23,51].

To make this non-interchangeability operational, and to avoid treating regional residues and CO₂ sources as generic carbon inputs, the main LATAM feedstock and CO₂ streams are classified in

Table 1. LATAM feedstock and CO₂ streams classified by fermentation-relevant chemistry rather than by residue identity alone.

Stream	Dominant Fermentation-Relevant Chemistry	Main Technical Constraint	Best-Matched Microbial Route	Key Reporting Metrics
Sugarcane bagasse/straw + ethanol CO2 [5]	Cellulose/hemicellulose/lignin residues [6,7]; molasses sugars; concentrated biogenic CO2 [5]	Pretreatment severity, enzyme loading, furans/phenolics, ash and moisture [21,25]; gas capture/compression [26]	SSF/SSCF yeasts [6,7]; PHA bacteria [28,29,30,31,32]; C. necator gas fermentation [4,20,26,33,34,35,36]; cyanobacterial biomass-to-product relays [37,38]	Sugar release; inhibitor profile; titer/yield/productivity; carbon balance; kLa or CO2 transfer rate
Agave bagasse [8,9]	Crystalline cellulose, hemicellulose, residual soluble sugars/fructan-derived components [9,10]	Variable moisture, lignin accessibility, hydrolysate standardization [10,11]	Oleaginous yeasts; cellulase/xylanase SSF [11]; ethanol or lipid/carotenoid routes [10]	Reducing sugars after pretreatment; enzyme units; yeast growth; product per g dry residue
Coffee pulp/husk [12,13,14]	Pectin, cellulose, nitrogen, caffeine, tannins, chlorogenic acids, phenolics [12,13,14]	Phenolic toxicity, caffeine stress, variable solids and moisture [12,13,14,25]	Fungal or LAB conditioning [14]; Rhodotorula-type stress-tolerant yeasts [23,39,40]; bioactive recovery [12,13]	Detoxification index; phenolic retention or removal; biomass/product yield
Citrus peel [15]	Pectin, soluble sugars, essential oils, limonene, flavonoids [15,22]	Limonene inhibition, pectin-extraction vs. fermentation sequencing [15,22]	Pectin-first cascade [22]; succinic/lactic acid [15]; EPS or coating materials [24]	Pectin yield; limonene removal; acid titer; polymer/coating properties
Banana/potato/vegetable peels [23,24]	Starch, pectin, soluble sugars, minerals, phenolics [23,24]	Batch variability, sterilization load, low-solids extracts [24]	Rhodotorula metabolites [23]; BC/EPS; coating-film precursors [24]	Extract solids; C/N ratio; carotenoids/EPS; film yield and surface metrics
Cacao pod husk [16,17]	Pectin, cellulose/hemicellulose, minerals, antioxidants, phenolics [16,17]	High mineral load, phenolic inhibition, collection logistics [16,17]	LAB/fungal SSF [17]; organic acids; antioxidant-rich extracts [16,17]; PHA after hydrolysis [28,29]	Lactic acid; antioxidant capacity; sugar release; detoxification
Cement/lime/oil-and-gas CO2 [4,26]	CO2 with variable O2, NOx/SOx, particulates, water vapor and heat [4,26]	Gas cleanup, intermittency, pressure, bioreactor compatibility [26]	C. necator and other gas fermenters [4,20,26,33,34,35,36]; microalgae where light and water allow [41,42,43]	CO2 purity; gas utilization efficiency; safety window; power-to-product efficiency

by fermentation-relevant chemistry, dominant technical constraint, best-matched microbial route, and key reporting metrics.

Building on this classification, Figure 2 provides a feedstock-chemistry-to-platform decision tree that connects residue or CO₂-stream class with conditioning strategy, compatible microbial platform, likely product family, and major bottleneck.

The figure maps major Latin American residue and CO₂-stream classes to their required conditioning steps, compatible microbial platforms, likely high-value products, and dominant technical bottlenecks. Lignocellulosic, pectin-rich, starch-rich, phenolic-rich, and gaseous CO₂ feedstocks require different pretreatment, detoxification, hydrolysis, or gas-conditioning strategies before conversion by yeast, bacterial, phototrophic, chemoautotrophic, or consortium-based platforms. The scheme emphasizes that platform selection should be based on feedstock chemistry, inhibitor burden, organism tolerance, reactor constraints, and downstream-processing feasibility rather than residue abundance alone.

The LATAM-specific interpretation should therefore be read as a set of regional deployment archetypes rather than as a uniform continental model. Brazil represents a high-density sugarcane–ethanol context in which bagasse, straw, molasses/vinasse, and relatively concentrated fermentation CO₂ can be co-located with existing industrial utilities; this favors lignocellulosic hydrolysate fermentation, residue-to-VFA-to-PHA cascades, and CO₂-linked gas or phototrophic modules, but the decisive filters are residue moisture, mill radius, bagasse energy integration, product logistics, and downstream-processing capacity [5,6,7,51]. Mexico represents an agave-bagasse and semi-arid industrial context in which tequila/mezcal residues can support yeast-, enzyme-, lipid/carotenoid-, or PHA-oriented hydrolysate routes, while water demand, hydrolysate standardization, and access to controlled pilot infrastructure constrain deployment [8,9,10,11,26,51]. Colombia and other coffee-producing regions present more dispersed, often wet, phenolic- and caffeine-rich residues, making decentralized fungal/LAB conditioning, stress-tolerant yeasts, bioactive transformation, and low-CapEx preprocessing more realistic than capital-intensive gas-fermentation infrastructure unless aggregation nodes exist [12,13,14,50]. Citrus-producing regions are better interpreted as pectin- and limonene-constrained systems, where pectin-first cascades, organic-acid fermentation, EPS/BC, or coating-material outlets may be more coherent than generic sugar fermentation [15,48,49]. Cacao-producing regions require a different logic because pod husk contains pectin, minerals, lignocellulose, and phenolics, so SSF, detoxification, antioxidant enrichment, organic acids, or downstream PHA substrates may be more appropriate than direct high-titer monoculture fermentation [16,17,37]. Finally, industrial CO₂ routes near cement, lime, oil-and-gas, or ethanol facilities should be assessed by gas purity, continuity, compression, water and power availability, renewable-H₂ access, and proximity to product markets rather than by CO₂ tonnage alone [4,5,23,51]. Thus, country-level or subregional deployment should be evaluated as a combination of residue density, energy and water constraints, infrastructure maturity, and market access, not as a generic LATAM opportunity.

3. Technical Platform Matching for CO₂- and Waste-Fed Bioproduction

3.1. Phototrophic CO₂-Fixing Modules

3.1.1. Cyanobacteria: Synechocystis sp. PCC 6803 as a CO₂-to-Intermediate Chassis

Synechocystis sp. PCC 6803 is technically attractive because it combines oxygenic photosynthesis and a sequenced, extensively annotated genome [45] with natural transformability and a long history of molecular-tool development [46,52,53,54]. In the context of this review, its most relevant role is not to compete directly with sugar-fed heterotrophic fermentation for every product class, but to serve as a CO₂-to-intermediate module. The intermediate can be biomass, glycogen-rich material, PHB [55], organic acids such as citramalate [18], terpenoid precursors [56,57,58], or hydrolysable cell material that is then routed to a heterotrophic production organism.

The technical bottlenecks are delivery of photosynthetically active light throughout the reactor volume, culture density, self-shading, CO₂ transfer, oxygen stripping, and the energy cost of harvesting dilute biomass. Here, light delivery refers to the engineering challenge of providing sufficient and spatially distributed photon flux to the cells through appropriate reactor geometry, light-path length, illumination regime, and mixing. It is closely linked to, but distinct from, self-shading: as biomass concentration increases, cells absorb and scatter incident light, creating illuminated and dark zones that reduce photosynthetic productivity. The most informative performance metrics are areal productivity, volumetric productivity, carbon-fixation rate, product fraction of dry cell weight, photosynthetic efficiency, and productivity under scale-relevant light-path lengths. Recent process optimization has demonstrated that citramalate production from CO₂ in Synechocystis can reach 6.35 g/L and 1.59 g/L/day in 2 L photobioreactors, showing that process-parameter control can be as important as genetic intervention for cyanobacterial production [18].

Genetic-tool development is accelerating. New cyanobacterial toolkits include strain-tailored vectors [52], base-editing approaches that introduce mutations without relying only on slow serial homologous recombination [53], and CRISPR activation for targeted gene upregulation [54]. These tools are directly relevant to LATAM CO₂-to-product concepts because they allow engineering around three practical constraints: increasing carbon flux into a product sink, reducing competing storage or photorespiratory pathways, and improving stress tolerance under high light, variable CO₂, and fluctuating outdoor cultivation conditions.

3.1.2. Microalgae: High-Value Biomass Under Light-, Nutrient-, and Stress-Controlled Regimes

Microalgae such as Chlorella, Nannochloropsis, and Haematococcus pluvialis are relevant when product value justifies photobioreactor complexity or when wastewater/nutrient recycling reduces input costs [19,20,21]. Their main product classes are proteins, lipids, polyunsaturated fatty acids, pigments, and antioxidant-rich biomass [19,20,21]. Haematococcus remains the reference organism for natural astaxanthin [29,30], but the process is technically demanding because astaxanthin accumulation requires stress induction after biomass generation [29,30]. This creates a two-phase process with distinct optimal regimes: growth under nutrient-replete conditions and product accumulation under high light, salinity, nutrient limitation, or other stressors.

For LATAM, the advantage of solar irradiance must be balanced against evaporation, contamination, water availability, and cooling. Open ponds reduce CapEx but increase contamination and productivity variability. Closed tubular, flat-panel, or hybrid photobioreactors improve containment and CO₂ use but impose higher CapEx, cleaning, heat-removal, and pumping requirements. For a focused technical comparison, microalgal studies should report not only pigment or lipid content, but also incident-light normalization, areal productivity, CO₂ utilization, nitrogen/phosphorus inputs, dewatering energy, extraction solvent, and product stability.

3.1.3. Design Rules for Phototroph-to-Fermenter Coupling

A phototrophic module becomes biorefinery-relevant when its output can enter a second microbial process without excessive dewatering, drying, or sterilization. Three configurations are most plausible. First, harvested phototrophic biomass can be hydrolyzed and used as a carbon/nitrogen source for yeasts or bacteria. Second, engineered cyanobacteria can secrete organic acids, sucrose, or other soluble intermediates that are consumed by heterotrophs. Third, phototrophic biomass can be fractionated, recovering one product from the phototroph and routing residual biomass to a second fermenter.

The coupling problem is therefore a mass-transfer and separation problem as much as a microbiology problem. A sequential relay reduces direct co-culture instability but adds harvesting and hydrolysis steps. A co-culture reduces unit operations but introduces light competition, oxygen and pH gradients, and species-ratio control. A practical LATAM design should report the carbon fraction retained across the relay, the nitrogen value of the phototrophic biomass, the hydrolysis sugar yield, the inhibitory by-products generated by hydrolysis, and the product recovered per kg CO₂ fed.

3.2. Chemoautotrophic Gas Fermentation

Chemoautotrophic gas fermentation is the most direct route for converting concentrated CO₂ into microbial biomass or intracellular products where light delivery is not practical [4]. Cupriavidus necator H16 is the central model because it grows lithoautotrophically on H₂, O₂, and CO₂ [22,25,59,60] and naturally accumulates PHB under nutrient limitation [22,59]. The platform is attractive for LATAM ethanol-CO₂ and industrial CO₂ streams only if the process is integrated with low-carbon H₂, controlled oxygen dosing, high gas-transfer efficiency, and credible safety engineering [4,23,24].

The biochemical logic is straightforward but the reactor engineering is not. H₂ oxidation supplies reducing power and ATP, CO₂ is assimilated primarily through the Calvin–Benson–Bassham cycle, and carbon is routed to biomass, PHB, or engineered products [22,25,59]. However, H₂/O₂ mixtures create flammability risks; gas–liquid mass transfer often limits productivity; pressure increases gas solubility but raises equipment cost; and cell-density targets must be balanced against heat removal and foam control [23]. Recent gas-fermentation scale-up guidance emphasizes the need for hydrodynamic and kinetic models, CFD-informed scale-down experiments, and careful selection of pneumatically agitated or pressurized systems rather than simple geometric scaling of stirred tanks [23].

Recent pilot-scale work illustrates the trajectory of the field: a 300 L pressurized deep-jet gas bioreactor for C. necator SCP production reached high cell densities and highlighted the importance of chemolithoautotrophic inoculum adaptation [24]. This matters for LATAM implementation because the most likely early applications are not only PHB, but also single-cell protein, feed ingredients, and hybrid CO₂-to-biomass-to-product routes. For PHB, nutrient limitation and carbon excess remain key, but downstream extraction, cell disruption, solvent or non-solvent recovery, and polymer purity determine commercial feasibility [36,38,39].

3.3. Heterotrophic Yeast Platforms

3.3.1. Rhodotorula spp. and Locally Isolated Red Yeasts

Rhodotorula spp. are technically relevant candidate platforms for LATAM residue-fed processes because available studies support three features needed for crude agro-industrial substrates: growth on non-refined carbon sources, production of carotenoids/lipids/enzymes, and tolerance to stressors associated with complex media [26,27,28]. In a LATAM-relevant example, an autochthonous R. mucilaginosa strain converted banana peel into several valuable metabolites [26]. More broadly, R. mucilaginosa has been reviewed as an alternative source of natural carotenoids, lipids, and enzymes for industrial use [27], and recent work has evaluated agro-industrial biowaste as low-cost substrates for carotenoid production by R. mucilaginosa [28]. Thus, the relevance of Rhodotorula is not based on geographic origin alone, but on the match between residue-fed process requirements and yeast physiology. However, broader deployment across LATAM residues still requires residue-specific validation, particularly for agave, citrus, coffee, and cacao streams. Their product portfolio includes torularhodin, torulene, beta-carotene, single-cell oils, extracellular polysaccharides, and enzymes [26,27,28]. Recent synthetic-biology and host-development work further supports the view that Rhodotorula can move from wild-type screening toward engineered microbial-cell-factory use [61,62,63]. The technical attractiveness is linked to the use of low-cost hydrolysates and extracts; the constraint is that carotenoid titers and productivities are usually much lower than those of engineered Yarrowia systems on defined media. Therefore, Rhodotorula-based processes should be evaluated by different metrics: product per unit waste input, tolerance to inhibitors, extractability of intracellular pigments, and performance under minimal supplementation.

For locally isolated strains such as R. mucilaginosa UANL-001L, the defensible scientific claim is not that local origin guarantees superiority, but that local isolates may contain tolerance traits useful for regional substrates. A technical development pipeline should include genome sequencing, karyotype or ploidy assessment if relevant, carbon-source profiling, inhibitor tolerance panels, carotenoid/lipid coproduction mapping, and transformation-method development. Recent demonstration of heterologous terpenoid production in R. mucilaginosa indicates that the species is no longer only a wild-type pigment producer; it can be treated as an emerging non-model yeast chassis [61].

3.3.2. Yarrowia Lipolytica as an Engineered Benchmark Chassis

Yarrowia lipolytica is the strongest engineered yeast benchmark for lipid- and acetyl-CoA-derived products because of its high acetyl-CoA flux, lipid metabolism, robust growth on glycerol and other substrates, and mature synthetic-biology toolkit [31,32,33,62]. It is particularly relevant for carotenoids, apocarotenoids, terpenoids, specialty lipids, and nutraceutical molecules [32,33,34,35]. Recent engineering strategies include hybrid promoter tuning, gene-copy optimization, pathway compartmentalization, cofactor balancing, temperature-shift fermentation, and biosensor-aided screening [33,34,35].

For LATAM waste integration, the key question is whether engineered Y. lipolytica strains that perform well on glucose, glycerol, or defined media can maintain productivity on agave, citrus, sugarcane, or mixed peel hydrolysates. This requires rigorous substrate-conditioning studies: sugar spectrum, acetic acid, furfural, HMF, phenolics, limonene, minerals, nitrogen, pH buffering capacity, and osmotic pressure should be reported. In many cases, a two-stage process will be more realistic than one-pot conversion of raw hydrolysate. In a two-stage process, biomass formation and product formation are deliberately separated. In the first stage, the yeast is grown on a robust and reproducible carbon source or conditioned hydrolysate to establish sufficient cell density. In the second stage, the culture is shifted through controlled C/N ratio, nitrogen limitation, dissolved-oxygen control, or feed composition to redirect metabolism toward carotenoid, lipid, or terpenoid accumulation. This strategy can be implemented as fed-batch induction or medium/feed shift in the same bioreactor, or as a sequential transfer between reactors, and it reduces the risk that inhibitors or variable nutrients in raw hydrolysates compromise both growth and production.

3.3.3. Fermentation Modes for Yeasts on Residue-Derived Substrates

The most relevant operating modes are batch screening, fed-batch production, two-stage growth/product formation, and, for robust strains, repeated-batch or continuous operation. For lipid- and carotenoid-producing yeasts, dissolved oxygen should be treated as a primary process-control variable, particularly for lipid pathways. Oxygen availability affects respiratory metabolism, redox balance, acetyl-CoA routing, oxygen-dependent fatty-acid desaturation, and oxidative stress; therefore, the production phase should define and optimize the dissolved-oxygen setpoint rather than refer generically to oxygen limitation. C/N ratio and nitrogen limitation remain central triggers for lipid accumulation in oleaginous yeasts, whereas nitrogen source, trace metals, and oxygen availability can influence pigment formation. In residue-fed systems, the best practice is to decouple feedstock conditioning from organism evaluation: first define a hydrolysate specification, and then test strain performance across controlled gradients of inhibitors and nutrients.

3.4. Bacterial Platforms for Polymers, Cellulose, and Organic Acids

Bacterial platforms are strongest when the product is an intracellular polymer, extracellular matrix, or organic acid. PHA-producing bacteria include Cupriavidus, Pseudomonas, Halomonas, and mixed microbial cultures [36,37,38,39,40]. The technical advantage of pure cultures is product consistency and easier pathway engineering; the advantage of mixed cultures is the ability to use variable waste streams and volatile fatty acids generated by acidogenic fermentation [37,40]. For LATAM, the most important PHA routes are not only direct sugar-to-PHB, but also residue-to-VFA-to-PHA cascades, because food-processing residues and peel hydrolysates can be acidified in a first stage and then used for PHA accumulation [37,40].

Komagataeibacter and related acetic-acid bacteria produce bacterial cellulose (BC), a high-purity extracellular nanofibrillar material [41,42,43,44]. BC processes are oxygen-transfer-limited and morphology-sensitive [43,44]. Static cultures produce pellicles useful for some applications but are slow and area-intensive; agitated cultures can improve volumetric productivity but may generate cellulose-negative mutants or altered morphology. Waste-derived substrates reduce medium cost but introduce color, minerals, phenolics, and fouling, which can complicate purification and application-specific performance [41,42,43,44].

Lactic acid bacteria, Bacillus, filamentous fungi, and mixed consortia are important for residue conditioning and organic-acid production. Their role in LATAM should be functional: detoxification of phenolics, enzyme generation, pectin or starch hydrolysis, acidification to VFAs, production of lactic/succinic/acetic acids, or preparation of hydrolysates for a downstream production chassis. This avoids treating every fermentative organism as a separate platform and instead places each organism in a defined process module.

3.5. Designed Consortia and Sequential Microbial Relays

Designed consortia are attractive for LATAM residues because the feedstocks are chemically complex and often inhibitory [12,13,14,15,16,17,50], and consortia can distribute conversion tasks across different organisms through division of labor, cross-feeding, or sequential metabolic functions [64,65]. However, the technical burden is higher than in monoculture because population structure, nutrient partitioning, oxygen gradients, pH drift, cross-feeding, product toxicity, contamination susceptibility, and long-term stability must be controlled [64,65]. In this context, the less conservative alternative to a sequential relay is a highly integrated process, such as a simultaneous co-culture or consolidated one-pot bioprocess, in which substrate conditioning, hydrolysis or detoxification, intermediate generation, and high-value product formation occur in the same reactor or in tightly coupled reactors without an intermediate stabilization, sterilization, or pasteurization step [64,65,66]. Relevant examples include mixed-culture residue-to-VFA-to-PHA systems [37,40] and consolidated lignocellulosic residue fermentations in which enzyme production, saccharification, and product formation occur in the same process environment [66]. These architectures can reduce unit operations, transfer losses, and processing time, but they increase the control burden because species ratios, cross-feeding, oxygen or light gradients, pH, inhibitors, product toxicity, contamination, and variable feedstock composition must be managed simultaneously [64,65,66]. Sequential relays are therefore lower-risk modular designs: one organism or process module prepares the substrate, and another performs high-value product formation. For many first-generation LATAM implementations, we propose that sequential relays are more realistic because they are easier to troubleshoot, sterilize or pasteurize between steps, and assign performance metrics to each module.

The major microbial platforms reviewed in this section are compared in

Table 2. Platform comparison for LATAM-relevant fermentation and fermentation-integrated bioprocesses.

Platform	Feed-Mode Requirement/Dual-Feed Compatibility	Carbon Input	Engineering Levers	Reactor/Process Bottleneck	Best Product Fit
Synechocystis sp. PCC 6803	Single autotrophic CO2/bicarbonate module; can participate in dual-feedstock relays when its biomass or secreted intermediates feed a downstream heterotroph.	CO2/bicarbonate; light; mineral nutrients	Organic-acid/process optimization and carbon-sink engineering [38]; strain-customized tools and promoter tuning [44]; base editing [45]; CRISPRa [46]; terpenoid modules [50]	Light path, self-shading, O2 removal, dilute-biomass harvesting	Organic acids, PHB, terpenoids, hydrolysable biomass intermediates
Chlorella/Nannochloropsis/Haematococcus	Single phototrophic CO2-based module; dual-feedstock use is optional when biomass is routed to a second process or when wastewater nutrients are integrated.	CO2 + light; optional wastewater nutrients	Microalgal CO2 capture, nutrient limitation, strain selection and PBR design [41,42,43]; stress induction for Haematococcus astaxanthin [51,52]	Dewatering, contamination, heat removal, extraction	Astaxanthin, lipids, PUFAs, protein-rich biomass
Cupriavidus necator	Single carbon feed as CO2 under lithoautotrophic gas fermentation; H2 and O2 are required process gases, not additional carbon feedstocks. Hybrid or mixotrophic modes with formate or organic substrates are possible but not mandatory.	H2/O2/CO2; formate possible in hybrid systems	Native CO2 fixation and PHB basis [20]; gas-fermentation scale-up and inoculum adaptation [26,35]; product diversification [33,34,36]	Gas–liquid mass transfer, flammability, pressure, H2 cost	PHB, SCP, isopropanol, chemicals, engineered products
Rhodotorula spp.	Single heterotrophic organic-feed module using hydrolysates, peel extracts, glycerol, or mixed sugars; does not directly fix CO2. Dual-feedstock use occurs only when CO2-derived biomass hydrolysate is used as feed.	Hydrolysates, peel extracts, glycerol, mixed sugars	Local-strain screening and waste-substrate use [23,39,40]; pathway engineering, inhibitor tolerance and MVA flux [53,54,55]	Low pigment titers, intracellular extraction, substrate variability	Carotenoids, lipids, EPS, enzymes
Yarrowia lipolytica	Single heterotrophic organic-feed module using glucose, glycerol, acetate, or conditioned hydrolysates; dual-feedstock operation is optional through staged or blended organic feeds.	Glucose, glycerol, acetate, conditioned hydrolysates	CRISPR and promoter/copy-number tuning [56,57,58]; compartmentalization and biosensors [59,60]	Translation from defined media to real hydrolysates	Carotenoids, apocarotenoids, lipids, terpenoids
PHA bacteria/MMC	Usually single organic-feed operation using sugars, glycerol, or VFAs; C. necator is the main exception because it can operate autotrophically on CO2/H2/O2. Residue-to-VFA-to-PHA cascades are sequential rather than inherently dual-feed.	Sugars, VFAs, glycerol, CO2/H2 for C. necator	PHA platform control [28]; nutrient-limitation and C/N/P control [28,30,31,67]; mixed-culture feast–famine selection [29,32,67]; halophilic/non-sterile selection [68,69,70]; DSP and polymer-quality optimization [28,30,31]	Nutrient-limitation control, DO/kLa, VFA variability, feast–famine selection for MMCs, culture stability, DSP, solvent use, polymer purity	PHB, PHBV, medium-chain-length PHAs
Komagataeibacter spp.	Single organic-feed operation using sugars, molasses, fruit residues, or peel extracts; oxygen transfer is the main process requirement.	Sugars, molasses, fruit residues, peel extracts	Medium optimization and waste substrates [61,62]; oxygen control and cultivation method [63,64]	Oxygen transfer, pellicle morphology, purification	Bacterial cellulose, BC composites, coatings
LAB/fungal conditioning modules	Single residue-derived feed or solid-state fermentation modules; typically used as upstream conditioning steps in sequential relays.	Pectin/starch/phenolic residues	Enzyme production, acidification, detoxification, SSF	Moisture, contamination, process reproducibility	Lactic/succinic acids, detoxified hydrolysates, bioactives

Note: Feed mode refers to the main carbon source supplied to the microbial module. Light, oxygen, hydrogen, mineral nutrients, aeration, and pH-control agents are considered process inputs unless they contribute carbon to the product. In this review, “dual feedstock” refers mainly to process-level integration of CO₂-derived and residue-derived streams, not to a universal physiological requirement of all microorganisms. SSF, solid-state fermentation; SSCF, simultaneous saccharification and co-fermentation; PHA, polyhydroxyalkanoate; SCP, single-cell protein; EPS, extracellular polysaccharide; MMC, mixed microbial culture.

, with emphasis on carbon input, engineering levers, reactor or process bottlenecks, and best product fit.

To make the platform comparison more transparent and less descriptive,

Table 3. Structured platform extraction matrix used for cross-platform comparison of LATAM-relevant fermentation and fermentation-integrated bioprocesses.

Platform/Route	Representative References	Feedstock or Carbon Source	Organism/Chassis	Reactor Mode	Reported Titer or Content	Reported Yield	Reported Productivity	Recovery/DSP Strategy	Main Scale-up Constraint
Cyanobacterial CO2-to-intermediate module	[38,47,48,49,50]	CO2 or bicarbonate; light; mineral nutrients	Synechocystis sp. PCC 6803	Photobioreactor; 2 L benchmark for citramalate	6.35 g/L citramalate reported in 2 L photobioreactors [38]; other products often reported as intracellular content or product-specific titer	Product-specific; carbon recovery from CO2 often not fully reported	1.59 g/L/day citramalate [38]	Extracellular organic-acid recovery or biomass harvesting followed by product-specific extraction	Light delivery, self-shading, CO2 transfer, O2 stripping, dilute-biomass harvesting
Microalgal pigment/lipid/SCP platforms	[41,42,43,51,52]	CO2 + light; mineral nutrients; optional wastewater nutrients	Chlorella, Nannochloropsis, Haematococcus pluvialis	Open ponds, closed photobioreactors, or two-stage stress cultivation	Often reported as mg/g DCW, %DCW, or pigment/lipid content rather than only g/L	NC across product classes	Areal and volumetric productivity required; not uniformly reported	Harvesting, dewatering, cell disruption, solvent extraction, pigment stabilization	Contamination, evaporation, heat removal, dewatering energy, stress induction, outdoor seasonal variability
Chemoautotrophic gas fermentation	[20,26,33,34,35,36]	H2/O2/CO2; formate possible in hybrid systems	Cupriavidus necator H16 and related hydrogen-oxidizing bacteria	Pressurized or gas-transfer-intensive bioreactors; 300 L deep-jet benchmark for SCP [35]	Product-specific; CDW, PHB %DCW, SCP biomass, or engineered-product titer	Gas-to-product or substrate-to-product yield as reported	Volumetric productivity and gas conversion as reported	Biomass drying for SCP; cell disruption and polymer extraction for PHB; product-specific DSP for engineered products	H2/O2 safety, gas–liquid mass transfer, pressure operation, H2 cost, gas recycling, heat removal
Rhodotorula residue-fed platform	[23,39,40,53,54,55]	Banana peel extract, agro-industrial hydrolysates, glycerol, mixed sugars, non-refined carbon sources	Rhodotorula mucilaginosa and related red yeasts	Submerged batch or fed-batch fermentation	Carotenoids, lipids, EPS, and enzymes reported as product-specific titer or content; often lower than engineered Yarrowia benchmarks	Product per substrate or product per dry residue when available	Often underreported in residue-fed studies	Biomass harvesting, cell disruption, solvent extraction, pigment stabilization	Low pigment titer, intracellular extraction, feedstock variability, supplementation needs, limited genetic standardization
Engineered Yarrowia benchmark platform	[56,57,58,59,60]	Glucose, glycerol, acetate, defined media, or conditioned hydrolysates	Yarrowia lipolytica	Batch, fed-batch, or two-stage growth/production induction	High engineered titers reported for carotenoids, apocarotenoids, terpenoids, lipids, and nutraceuticals in defined or conditioned media	Product/substrate yield as reported	Fed-batch or two-stage productivity as reported	Biomass harvesting, intracellular extraction, oil or pigment recovery, product purification	Translation from defined media to real LATAM hydrolysates, oxygen control, strain stability, substrate inhibition
PHA-producing bacteria and mixed microbial cultures	[28,29,30,31,32,67,68,69,70]	Sugars, glycerol, VFAs from food-waste fermentation, residue hydrolysates, or CO2/H2 for C. necator	Cupriavidus, Pseudomonas, Halomonas, and MMCs	Pure-culture fed-batch, halophilic/non-sterile systems, or feast–famine mixed-culture operation	g/L PHA and %DCW commonly reported	YP/S, VFA-to-PHA yield, or gas-to-PHA yield as reported	g/L/h or g/L/day when reported	Cell disruption, solvent or non-solvent extraction, polymer purification, residual biomass/endotoxin removal	DSP cost, polymer purity, monomer consistency, Mw/PDI control, mixed-culture stability
Bacterial-cellulose platform	[61,62,63,64]	Sugars, molasses, fruit residues, acidic food by-products, peel extracts	Komagataeibacter spp. and related acetic-acid bacteria	Static, agitated, or modified aerobic cultivation	g/L BC or pellicle yield as reported	Substrate-to-BC yield when available	g/L/day or surface/volume productivity when available	Washing, alkali purification, depigmentation, water removal, application-specific conditioning	Oxygen transfer, pellicle morphology, cellulose-negative mutants, slow static cultivation, purification burden
LAB/fungal conditioning and organic-acid modules	[11,14,15,17]	Pectin-rich, starch-rich, phenolic, or lignocellulosic residues	LAB, Bacillus, filamentous fungi, mixed consortia	Solid-state fermentation, submerged fermentation, acidogenic conditioning	Organic acids, enzymes, detoxified hydrolysates, or bioactives reported in product-specific units	Product/substrate or enzyme yield when reported	Acid or enzyme productivity when reported	Acid recovery, neutralization, enzyme extraction, conditioned hydrolysate transfer	Moisture control, contamination, pH/product inhibition, substrate heterogeneity, reproducibility
Non-fermentative boundary case: peel-extract coating films	[24]	Banana, orange, potato, and mixed peel extracts	No microbial production chassis; included as boundary case	Extract preparation and spin-coating	Film yield, thickness, roughness, FTIR/XRD signatures, tensile properties, WVTR, biodegradation	NA for fermentation yield	NA for fermentation productivity	Film formation, drying, surface and mechanical characterization, application-fit testing	Batch composition, adhesion, permeability, reproducibility, biodegradation, regulatory use case

NR, not reported; NC, not directly comparable; NA, not applicable; DCW, dry cell weight; DSP, downstream processing; MMC, mixed microbial culture; PHA, polyhydroxyalkanoate; SCP, single-cell protein; EPS, extracellular polysaccharide; WVTR, water-vapor transmission rate. The matrix summarizes representative platform-level evidence and reporting structure; it is not intended to rank organisms by maximum titer because the reviewed platforms differ in carbon-entry mode, product class, reactor configuration, and downstream-processing burden.

provides a structured extraction matrix summarizing the study-level variables used to compare the main fermentation and fermentation-integrated platforms discussed in this review. The matrix includes the feedstock or carbon source, organism or chassis, reactor mode, reported titer or content, yield, productivity, recovery or downstream-processing strategy, and main scale-up constraint. When titer, yield, or productivity were not reported, or were reported in non-comparable formats across studies, the field is indicated as NR (not reported) or NC (not directly comparable). Table 3 should be interpreted as a platform-level extraction matrix, not as a ranking by maximum reported titer.

4. Technical Engineering Pipeline for LATAM-Relevant Chassis

4.1. Pretreatment and Hydrolysate Specification

Residue-fed fermentation should begin with hydrolysate specification, not organism screening. For lignocellulosic feedstocks, pretreatment must increase cellulose accessibility and hemicellulose solubilization while limiting furfural, HMF, acetic acid, formic acid, and phenolic inhibitor formation [47,50]. For pectin-rich residues, extraction conditions affect degree of esterification, molecular weight, and downstream film or gel behavior [48]. For coffee and cacao residues, phenolic and alkaloid composition can be either inhibitory or product-relevant depending on the process objective [12,13,14,15,16,17].

A minimum hydrolysate dataset for technical comparability should include total solids, soluble solids, monomeric sugars, oligomeric sugars, total nitrogen, C/N ratio, pH, buffering capacity, ash, major minerals, organic acids, furfural, HMF, total phenolics, specific inhibitory compounds when relevant (caffeine, limonene), and sterilization or pasteurization regime. Without these data, productivity comparisons across residues are not interpretable. For LATAM biorefineries, this point is central because seasonal and geographic variability can be larger than the differences between microbial strains.

4.2. Local-Strain Development: From Isolate to Production Chassis

A locally isolated strain becomes a platform only after a technical development sequence: phenotypic screening, genome sequencing, genome annotation, pathway reconstruction, substrate and inhibitor profiling, transformation method development, omics-guided bottleneck identification, and fermentation validation. For Rhodotorula and other non-conventional yeasts, the gap is often not product potential but genetic tractability. The development of tools for non-conventional yeasts, including promoters, terminators, CRISPR systems, and modular pathway assembly, provides a template for adapting local strains into usable production chassis [62,63].

For LATAM laboratories, the highest-leverage near-term activity is the creation of annotated local-strain libraries linked to substrate metadata. A yeast isolated from agave bagasse, coffee pulp, desert soils, or fruit residues should be deposited with genome sequence, substrate-utilization profile, inhibitor tolerance, temperature range, pH range, and product profile. This would convert biodiversity claims into engineering resources and would make local-strain arguments more credible to international reviewers.

4.3. CRISPR, Base Editing, CRISPRi/a, and Pathway Control

In cyanobacteria, recent advances such as strain-customized molecular tools [52], multiplex base editing [53], and CRISPR activation [54] directly address the slow and laborious editing cycles that have historically limited photosynthetic cell factories. For CO₂-to-product routes, the relevant edits include strengthening CO₂ fixation and precursor pathways, increasing product-sink capacity, repressing competing sinks such as glycogen or PHB when appropriate, tuning transporter expression, and improving tolerance to high light or product toxicity. Because many cyanobacteria are polyploid, editing tools must also be evaluated by segregation completeness and genetic stability under production conditions.

In yeasts, the engineering logic is different. Y. lipolytica benefits from relatively mature CRISPR and modular-cloning systems, allowing copy-number tuning, promoter libraries, pathway compartmentalization, and Design–Build–Test–Learn (DBTL) cycles for carotenoids and nutraceuticals [31,32,33,34,35]. A DBTL cycle refers to an iterative metabolic-engineering workflow in which a pathway or strain design is built, experimentally tested, evaluated for product formation and bottlenecks, and then refined using the resulting data to guide the next optimization round. Rhodotorula spp. are less standardized but are increasingly accessible to engineering, including recent work demonstrating terpenoid biosynthesis in R. mucilaginosa through manipulation of endogenous mevalonate flux [61]. For LATAM-focused chassis, an important next step is not simply importing Yarrowia toolkits, but adapting equivalent methods to local Rhodotorula isolates and stress-tolerant bacteria.

4.4. Dynamic Regulation, Biosensors, and Process-Responsive Circuits

Static overexpression is rarely optimal for waste-fed fermentation. Real hydrolysates vary in sugar ratio, nitrogen, inhibitors, and trace elements. Dynamic regulation can separate growth from product formation, reduce accumulation of toxic intermediates, and redirect flux after biomass establishment. In cyanobacteria, process-responsive CRISPR activation, base editing, and strain-customized toolsets are relevant to carbon-sink control [52,53,54,58]. In non-conventional yeasts, recent synthetic-biology tool development provides the basis for biosensors, modular control, and high-throughput screening [33,62]. Examples include nitrogen-responsive lipid accumulation, oxygen-responsive pigment production, quorum-linked PHA accumulation, inducible promoter systems, metabolite biosensors for high-throughput screening, and CRISPRi/a-based repression or activation at selected process stages.

For carotenoids and terpenoids, dynamic control should focus on balancing IPP/DMAPP generation, geranylgeranyl pyrophosphate supply, downstream cyclization/desaturation, and oxidative stress. For PHAs, the relevant switch is growth-to-storage metabolism under carbon excess and nutrient limitation. For BC, dynamic strategies are less mature, but oxygen availability, gluconic acid accumulation, and cellulose synthase expression are key control points. For organic acids, pH tolerance, product export, redox balance, and by-product suppression define the engineering targets.

4.5. Reactor and Process-Control Variables

The technical maturity of a platform cannot be judged from shake-flask titers alone. Phototrophic systems require reporting of light intensity, light path, optical density, areal productivity, CO₂ sparging rate, pH control, and dewatering method. Gas fermentations require gas composition, pressure, safety envelope, gas-flow rate, kLa or equivalent gas-transfer metric, gas conversion, heat removal, and inoculum history [23,24]. Yeast and bacterial fermentations require dissolved oxygen, agitation, aeration, pH control, antifoam, feeding regime, C/N ratio, and substrate sterilization method. Solid-state fermentation requires moisture, water activity, particle size, bed temperature, aeration, and enzyme diffusion metrics.

For LATAM deployment, low-capital-expenditure (low-CapEx) design should not be confused with the absence of process control. Rather, the goal is fit-for-purpose control: a regionally appropriate process may use simpler or lower-cost equipment, but it must still maintain reproducible critical variables such as substrate specification, temperature, pH, aeration or dissolved oxygen, feeding regime, contamination control, and product-quality endpoints. Small and medium enterprises are more likely to adopt fermentation technologies if process designs reduce unnecessary equipment complexity while preserving the minimum controls required for reproducible performance.

4.6. Downstream Processing as the Decisive Economic Bottleneck

Downstream processing (DSP) is often the hidden bottleneck in high-value products. Intracellular carotenoids require biomass harvesting, drying or wet extraction, cell disruption, solvent selection, antioxidant protection, purification, and stability testing. PHAs require cell separation, cell disruption, polymer recovery, solvent or surfactant processes, residual endotoxin or biomass removal, molecular-weight control, and thermal characterization [38,39]. BC requires washing, alkali treatment, depigmentation when waste substrates are used, water removal, and application-specific functionalization [43,44].

Downstream processing should therefore be treated as a platform-selection criterion rather than as a terminal polishing step. For intracellular products such as carotenoids, lipids, and PHAs, low broth titer or low intracellular content increases the amount of biomass that must be harvested, disrupted, extracted, and purified, which can offset the apparent advantage of low-cost residues. In microalgal and cyanobacterial routes, dilute cultures make dewatering and drying major energy and cost drivers, especially when pigment or lipid extraction requires cell disruption and solvent handling [29,30,71]. For carotenoids, solvent selection, wet versus dry extraction, oxidative protection, pigment stability, and extraction efficiency determine whether a reported pigment content becomes a recoverable product [26,27,28,71]. For PHAs, polymer accumulation as %DCW is insufficient unless the process also reports cell-disruption strategy, recovery yield, solvent or non-solvent recovery, residual biomass or endotoxin removal, polymer purity, monomer composition, and molecular-weight preservation [36,38,39]. For bacterial cellulose, the extracellular nature of the product avoids cell disruption, but shifts the burden to washing, alkali treatment, depigmentation, water removal, sterilization or biocompatibility requirements, and application-specific material performance [41,42,43,44]. Organic-acid routes face a different DSP penalty because pH control, neutralization salts, acid recovery, and by-product removal can dominate process cost and environmental burden [15]. Thus, a LATAM platform should not be considered scalable only because fermentation occurs on a low-cost residue; it should also demonstrate a DSP mass balance that includes recovery yield, product purity or grade, solvent and water use, energy demand, and waste-stream management.

Every production claim should be linked to a recovery and product-quality claim [38,39,43,44,71,72]. A reported carotenoid content without extraction efficiency, pigment profile, extraction method, and stability information is incomplete [26,27,28,29,30,71]. A PHA cell content without polymer recovery yield, purity, monomer composition, molecular weight, and thermal or mechanical characterization is incomplete [36,38,39]. A BC yield without purification, crystallinity, morphology, mechanical properties, water-holding capacity, and barrier performance such as water-vapor transmission is incomplete [41,42,43,44]. A coating film without composition, thickness, surface roughness, mechanical or barrier performance, adhesion or application-fit testing, and biodegradation metrics remains a material observation rather than a validated biorefinery product module [49,72].

5. High-Value Bioproduct Classes and Technical Readiness

To avoid treating all reviewed routes as equally deployable, we distinguish mature or near-pilot options from infrastructure-intensive, emerging, and mainly conceptual routes. Here, “mature” does not imply immediate commercial readiness in LATAM; it denotes platform families with established reactor logic, repeated product-class validation, defined downstream-processing requirements, and clear quality metrics. Residue-to-organic-acid fermentations, residue-to-VFA-to-PHA cascades, selected halophilic or pure-culture PHA systems, and bacterial-cellulose production are the most mature fermentation-derived routes, although each remains constrained by feedstock conditioning, DSP cost, and application-specific product quality [15,36,37,38,39,40,41,42,43,44,73,74,75]. Microalgal/Haematococcus pigment production and C. necator gas fermentation are not merely conceptual, but they are infrastructure-intensive: their scalability depends on photobioreactor/dewatering systems or renewable H₂ supply, gas-transfer capacity, pressure operation, and safety engineering [19,20,21,23,24,29,30]. Rhodotorula residue-fed carotenoid/lipid production and engineered Y. lipolytica routes are best classified as emerging and translation-limited: the former is attractive for crude substrates but requires improved titer, extraction efficiency, and strain standardization, whereas the latter has stronger engineered performance on defined media but still requires validation on real LATAM hydrolysates [26,27,28,31,32,33,34,35,47,50,61,62,63]. Cyanobacterial terpenoid production, CO₂-to-biomass-to-heterotroph relays, designed consortia, and other dual-feedstock prototypes should be treated as early-stage or proof-of-concept routes until integrated carbon balances, recovery yields, TEA/LCA, and pilot-relevant operation are demonstrated [18,52,53,54,55,56,57,58,64,65,66,76]. The peel-extract coating-film example is not assigned fermentation readiness because it is retained only as a non-fermentative boundary case for product-fit decisions [49].

5.1. Carotenoids and Terpenoid-Derived Pigments

Carotenoids are technically attractive because their value density can justify more complex processing than bulk fuels. The main LATAM-relevant production routes are: (i) microalgal astaxanthin under two-stage stress cultivation [29,30]; (ii) Rhodotorula-derived torularhodin, torulene, and beta-carotene from waste substrates [26,27,28]; (iii) engineered Y. lipolytica for beta-carotene, lycopene, zeaxanthin, astaxanthin, crocetin, or related products [31,32,33,34,35]; and (iv) cyanobacterial terpenoid or carotenoid precursor production from CO₂ [56,57,58].

The technical comparison should not simply rank organisms by maximum titer [26,27,28,29,30,31,32,33,34,35]. Rhodotorula-based routes may show lower reported carotenoid titers than highly engineered yeast platforms, but they can be attractive for crude or non-refined substrates and for processes based on wild-type, locally isolated, or minimally engineered strains [26,27,28,61,62,63]. Y. lipolytica may reach higher engineered titers for carotenoids, apocarotenoids, terpenoids, and nutraceutical molecules, but these results are often obtained with defined or well-conditioned feedstocks, and translation to real hydrolysates requires additional substrate-conditioning and inhibitor-management studies [31,32,33,34,35,47,50]. Haematococcus pluvialis can accumulate high astaxanthin contents, but its process requires stress induction after biomass generation and faces harvesting, dewatering, extraction, and stability constraints [29,30]. Cyanobacteria offer direct CO₂ conversion to terpenoid or carotenoid-related products, but their productivity is limited by photobioreactor constraints such as light delivery, self-shading, CO₂ transfer, oxygen accumulation, areal productivity, and dilute-biomass harvesting [18,19,20,21,56,57,58].

5.2. PHAs, Bacterial Cellulose, and Bioplastic Coating Films

PHAs are the most mature microbial biopolymer class for fermentation-based waste valorization, but they remain cost-sensitive because raw materials, fermentation productivity, and downstream recovery dominate economics [36,37,38,39]. Volatile-fatty-acid routes from food-waste fermentation are especially relevant for residue-to-VFA-to-PHA cascades [40]. The most relevant LATAM designs are likely to be cascades: residue hydrolysis or acidogenic fermentation generates sugars or VFAs; a PHA-producing pure culture or mixed microbial culture converts these intermediates into polymer; and recovery is optimized for the target application [37,40]. Operationally, PHA platforms should be distinguished as pure-culture accumulation processes or mixed-microbial-culture enrichment processes. In pure cultures such as Cupriavidus, Pseudomonas, and Halomonas, polymer accumulation is typically driven by carbon excess combined with limitation of nitrogen, phosphorus, or another growth-limiting nutrient; however, oxygen availability must be controlled rather than treated as a simple limitation variable because insufficient oxygen can reduce respiration, redox balance, cell-density formation, and volumetric productivity [36,38,39,73,74,75]. In gas-fed C. necator systems, oxygen control is additionally coupled to H₂/O₂ safety, gas–liquid mass transfer, pressure operation, gas recycling, and heat removal [23,24]. In mixed-microbial-culture PHA routes, feast–famine selection is the central operational strategy: short feast periods with excess VFAs select organisms that rapidly store carbon as PHA, while famine periods favor populations that can survive by using intracellular reserves [37,40,68]. Importantly, nutrient limitation should not be treated as a “more severe is better” variable. In VFA-fed sequencing batch reactors, moderate phosphate limitation provided the best balance between PHA productivity, microbial selection, and reactor stability, whereas excessive phosphate limitation compromised productivity and sludge settleability [68]. Therefore, the VFA spectrum, organic loading rate, feast/famine ratio, solids or hydraulic retention time, pH, dissolved oxygen, C/N/P balance, salinity, and temperature influence not only PHA content and productivity, but also monomer composition, molecular weight, and microbial-community stability [37,38,39,40,68]. For LATAM residue-to-VFA systems, microbial stability should therefore be evaluated over repeated operating cycles and changing residue batches, rather than inferred from a single batch result. Minimum scalable reporting should include C/N/P ratio, VFA profile, feeding regime, dissolved oxygen or kLa, feast/famine timing for mixed cultures, PHA titer and %DCW, productivity, YP/S or carbon retained in polymer, monomer composition, Mw/PDI, polymer recovery yield, and stability over sequential runs.

Halophilic or seawater-based PHA-producing platforms may be attractive for selected water-constrained or coastal deployment contexts because high-salinity media can reduce freshwater demand and create a selective environment that lowers the need for strict sterilization [73,74,75]. However, non-sterile or low-sterility operation should not be equated with product purity. In pure or engineered Halomonas-type systems, culture stability, strain identity, PHA content, monomer composition, molecular weight, residual biomass or endotoxin content, and polymer recovery yield must still be verified [38,39,73,74,75]. In mixed-microbial-culture PHA routes, non-sterile operation can generate community-dependent polymers and possible coproducts; therefore, product quality must be controlled through enrichment strategy, feed composition, feast–famine selection, salinity or pH selection, and downstream purification [37,40]. Thus, for LATAM deployment, non-sterile operation should be framed as a cost-, water-, and robustness-oriented strategy for selected halophilic or mixed-culture PHA systems, not as a general route to high-purity products.

Bacterial cellulose is technically distinct because the product is extracellular and highly pure [41,42], but production is oxygen-intensive and morphology-sensitive [43,44]. Waste substrates can reduce medium cost [41,42], but color, phenolics, minerals, and variable sugar composition can alter pellicle quality [43,44]. Applications in food, wound dressings, composites, packaging, and electronics require different quality metrics. A food coating requires barrier and sensory performance; a wound dressing requires biocompatibility and sterility; an electronic substrate requires uniformity and mechanical/thermal stability.

Although PHAs and bacterial cellulose are the fermentation-derived polymer routes central to this review, not all residue-derived materials should be forced into a fermentation framework. Some peel-rich streams may be more technically coherent as direct extract-based coatings or hybrid materials. Box 2 is therefore included as a boundary case, not as a fermentation platform, to illustrate how platform matching can distinguish microbial polymer production from low-CapEx material routes that may be integrated as coproduct outlets in broader LATAM biorefineries.

5.3. Lipids, Single-Cell Oils, PUFAs, SCP, and Bioactives

Oleaginous yeasts and microalgae can accumulate lipids relevant to oleochemicals, biodiesel precursors, and specialty nutrition. The technical challenge is product positioning. Bulk biodiesel will rarely justify expensive fermentation unless integrated with coproducts or waste treatment. Specialty lipids, PUFAs, and nutraceutical fractions are more compatible with controlled bioprocessing. For single-cell protein, hydrogen-oxidizing bacteria are increasingly relevant where renewable H₂ and gas-transfer infrastructure are available [4,24,25], while microalgae remain relevant where light, water, nutrients, and dewatering economics are favorable [21]. Amino-acid profile, nucleic-acid reduction, digestibility, safety, and regulatory acceptance become decisive for either route.

Coffee, cacao, citrus, and peel residues also contain bioactive compounds that can be released, transformed, or enriched through fermentation. The technical distinction is between extraction and microbial transformation. We here emphasize cases where microorganisms modify bioactivity, reduce toxicity, generate peptides, release bound phenolics, synthesize vitamins, or produce new metabolites, not merely solvent extraction from residues.

The product families discussed above are summarized in

Table 4. Product classes, harmonized performance indicators, downstream-processing requirements, and near-term LATAM deployment rationale for focused evaluation.

Product Class	Main Platform Routes	Production Intensity	Yield/Carbon-Efficiency Metric	Productivity Metric	Recovery Burden/Product-Quality Metric	Readiness/Near-Term LATAM Deployment Rationale
Carotenoids/pigments	Rhodotorula, Yarrowia, Haematococcus, cyanobacteria	mg/L and mg/g DCW; pigment profile	Product per g substrate, per kg dry residue, or carbon retained in pigment for CO2-linked relays	mg/L/day, mg/g DCW/day, or areal productivity for phototrophs	Extraction efficiency, cell-disruption method, solvent compatibility, oxidation stability, purity	High-value nutraceutical/colorant markets; local yeast strains
PHAs	C. necator, Pseudomonas, Halomonas, MMC	g/L PHA and %DCW; monomer composition	YP/S, VFA-to-PHA yield, gas-to-PHA yield, or carbon retained in polymer	g/L/h or g/L/day; feast/famine ratio for MMCs when applicable	Polymer recovery yield, purity, Mw/PDI, thermal/mechanical behavior, residual biomass/endotoxin control, solvent recovery	Residue-to-VFA-to-PHA cascades; sugarcane/agro-waste clusters; selected halophilic or mixed-culture routes when stability and product quality are demonstrated
Bacterial cellulose	Komagataeibacter spp. and consortia	g/L, g/m2, or pellicle mass	BC per g sugar, per g residue-derived carbon, or carbon retained in cellulose	g/L/day or g/m2/day	Washing/alkali burden, crystallinity, morphology, tensile strength, WHC, WVTR, sterility or biocompatibility depending on application	Food coatings, wound dressings, packaging composites
Organic acids	LAB, engineered yeasts/bacteria, cyanobacteria for selected acids	g/L acid titer	g acid/g substrate, mol acid/mol carbon source, or CO2-to-acid carbon efficiency where applicable	g/L/h or g/L/day	Acid-recovery yield, neutralization salts, by-products, final purity, pH-control cost	Citrus/cacao/peel hydrolysates; platform intermediates
Single-cell protein	C. necator, microalgae, yeasts	g/L CDW and protein fraction	Biomass yield per substrate or gas input; nitrogen-to-protein efficiency; gas utilization for CO2/H2 routes	g CDW/L/h or g CDW/L/day; areal productivity for microalgae	Drying energy, nucleic-acid reduction, amino-acid profile, digestibility, safety, regulatory approval	CO2/H2 routes near renewable power; feed applications
Lipids/PUFAs	Yarrowia, Rhodotorula, Chlorella, Nannochloropsis	Lipid g/L, lipid %DCW, fatty-acid profile	Lipid per g substrate, per kg dry residue, or carbon retained in lipid fraction	g/L/day or mg/g DCW/day	Oil extraction efficiency, fractionation, oxidative stability, solvent use, purity	Specialty oils rather than bulk fuels
Bioplastic coatings/films	Fermentation-derived BC/EPS; peel-extract and starch/pectin blends as non-fermentative boundary or hybrid material routes	Film yield, thickness, and solids-normalized film mass	Film mass per g extract or dry residue; not applicable as fermentation carbon yield for non-fermentative boundary cases	Batch production rate or coating throughput when available	Composition, adhesion, roughness, WVTR, tensile properties, biodegradation, food-contact or agricultural-use testing	Low-CapEx packaging/agricultural films

DCW, dry cell weight; YP/S, product yield per substrate consumed; Mw, molecular weight; PDI, polydispersity index; WHC, water-holding capacity; WVTR, water-vapor transmission rate; MMC, mixed microbial culture. Production intensity, yield/carbon efficiency, productivity, and recovery burden are used as harmonized metric families. Product-specific units are retained because intracellular pigments, intracellular polymers, extracellular cellulose, soluble acids, biomass products, oils, and coating films cannot be meaningfully compared using one universal unit. For PHAs, C/N/P ratio, VFA profile, DO/kLa, and feast/famine timing are considered operational-control variables that should accompany production metrics, especially in mixed-microbial-culture systems. “Near-term LATAM deployment rationale” refers to product–platform combinations that may be prioritized for first-generation pilot-scale or early translational development under current regional constraints; it does not imply commercial maturity. The near-term deployment designation should not be interpreted as a sustainability claim; environmental superiority requires product-specific LCA with explicit energy, transport, water, chemical-input, avoided-product, coproduct-allocation, and end-of-life assumptions.

, which harmonizes the comparison around four metric families: production intensity, yield or carbon efficiency, productivity, and recovery burden. Because carotenoids, PHAs, bacterial cellulose, organic acids, SCP, lipids, and coating films differ in physical form and downstream-processing requirements, the table does not force a single numerical unit across all products. Instead, it specifies product-specific indicators needed to make each platform technically comparable and translationally interpretable, while also summarizing platform routes, downstream-processing bottlenecks, and the near-term LATAM deployment rationale for each class. In this table, “near-term” is used as a qualitative deployment-prioritization criterion, not as a claim of immediate commercial readiness. It refers to product–platform combinations that appear suitable for first-generation regional pilot validation because they combine available LATAM feedstocks or CO₂ streams, an established or emerging microbial platform, product value density sufficient to justify downstream-processing and quality-control costs, compatibility with existing or realistically accessible regional infrastructure, and measurable product-quality endpoints. Table 4 should therefore be read together with the readiness distinction above: some routes are mature but DSP-limited, others are scalable only with substantial infrastructure, and others remain proof-of-concept until integrated pilot validation is available.

6. TEA, LCA, and Scale-up as Technical Filters

6.1. Quantitative Gates for Platform Progression

For LATAM, not all bench-scale demonstrations have equal translational attention. A practical stage-gate framework is needed. At screening scale, the question is substrate compatibility and product identity. At lab bioreactor scale, the question is reproducible titer/yield/productivity with controlled pH, oxygen, feeding, and substrate specification. At pilot scale, the question is mass transfer, contamination tolerance, feedstock logistics, DSP recovery, and product-quality consistency. At demonstration scale, the question is unit economics and regulatory acceptance.

For gas fermentation, stage-gate metrics should include gas utilization efficiency, power-to-product efficiency, H₂ consumption per kg product, safety controls, gas recycling, and representative scale-down models [23,24]. For phototrophs, the gates should include areal productivity, annualized outdoor productivity, dewatering energy, contamination risk, and seasonal robustness [19,20,21,29,30]. For waste-fed heterotrophs, gates should include hydrolysate specification, fed-batch productivity, inhibitor tolerance, substrate logistics, and DSP cost. For polymers and films, performance metrics must be application-specific, not only mass yield [38,39,40,43,44].

Based on these quantitative progression criteria, Figure 3 proposes a stage-gate roadmap for advancing LATAM fermentation biorefineries from feedstock intelligence and platform selection to integrated pilot validation and deployment.

The figure outlines a staged development pathway from feedstock and CO₂-source characterization to pilot-scale deployment of dual-feedstock bioprocesses. Sequential gates connect feedstock intelligence, platform selection, strain/pathway engineering, bench validation, integrated pilot-module development, and translation. Cross-cutting tracks highlight the parallel maturation of feedstock analytics, synthetic biology, reactor engineering, downstream processing, and TEA/LCA–market fit. The lower panels indicate the minimum evidence required before pilot investment, major scale-up risks, and the expected output of a pilot-ready biorefinery module for high-value bioproducts.

6.2. TEA Structure for Dual-Feedstock Biorefineries

A credible TEA should allocate cost across feedstock collection, pretreatment, hydrolysis or conditioning, fermentation, utilities, downstream processing, waste treatment, labor, depreciation, and quality control. LATAM-relevant sensitivity analyses should include feedstock radius, residue moisture, enzyme cost, electricity price, renewable H₂ price, bioreactor productivity, product selling price, solvent recovery, and capacity factor. For dual-feedstock systems, CO₂ capture and compression should not be treated as free unless the CO₂ stream is already captured for another process.

In TEA terms, fermentation productivity and DSP recovery are multiplicative rather than independent: the economically relevant output is not only product formed in the reactor, but product recovered at the required purity and quality grade. Therefore, TEA sensitivity analyses should include extraction or purification yield, dewatering and drying energy, cell-disruption cost, solvent price and recycle efficiency, acid/base consumption, polymer or pigment losses during recovery, and the cost of treating DSP-derived waste streams [29,30,36,38,39,71,72].

The key TEA distinction is between low-value, high-volume products and high-value, low-volume products. Organic acids and SCP require high productivity and tight cost control. Carotenoids and specialty nutraceuticals can tolerate lower volumes but require strict product identity and quality. PHAs sit between these extremes: feedstock savings help, but DSP and polymer properties determine market access. Bacterial cellulose and coating films require application-specific techno-economic analysis because food, biomedical, packaging, and agricultural uses have different quality and regulatory costs.

6.3. LCA Boundaries and Carbon Accounting

LCA should distinguish biogenic CO₂ recycling from durable carbon storage. A CO₂-to-carotenoid or CO₂-to-SCP process can reduce fossil feedstock demand but does not necessarily store carbon long-term [4]. PHAs and cellulose-based materials may store carbon for longer, but end-of-life assumptions—biodegradation, composting, recycling, incineration, or landfill—strongly affect results. For residue-fed processes, avoided waste treatment, avoided methane generation, and displaced products can dominate the impact category. For gas fermentation, renewable H₂ production can dominate the footprint if electricity is carbon-intensive [4,23,51].

LATAM LCA studies should therefore treat residue availability and CO₂ use as inventory inputs, not as proof of sustainability. Any sustainability claim should be linked to an explicit functional unit and counterfactual scenario: what would have happened to the residue in the absence of the bioprocess, what product is being displaced, and how coproducts, avoided waste treatment, avoided methane emissions, or carbon storage are allocated. The electricity grid mix, defined here as the composition and emission intensity of the electricity used by the process, should be reported together with renewable-power assumptions, residue baseline use, transport distances, residue moisture, water source and recycling, nutrient inputs, chemical inputs, enzyme loading, acid/base consumption, solvent use and recovery, product-recovery yield, waste-stream treatment, and end-of-life scenario. This is important because electricity- and utility-intensive operations such as CO₂ capture or compression, H₂ electrolysis, aeration, agitation, pumping, cooling, dewatering, drying, cell disruption, extraction, purification, and downstream processing can dominate the environmental footprint. Similarly, wet or dispersed residues can lose their apparent sustainability advantage if long transport distances, high moisture content, chemical pretreatment, sterilization, or solvent-intensive recovery are required. Avoided-product assumptions should be product-specific and conservative: carotenoids should be compared with the relevant pigment source, PHAs with the target polymer grade and end-of-life pathway, SCP with the displaced feed-protein source, organic acids with the corresponding industrial acid route, and bacterial cellulose or coating films with their intended packaging, biomedical, or agricultural material function. A process that is attractive in Brazil under sugarcane-bagasse energy integration may not have the same footprint in northern Mexico unless electricity source, water demand, residue logistics, chemical inputs, and avoided-product assumptions are included explicitly [4,23,29,30,36,38,39,51,71,72]. Consequently, TEA/LCA results should not be transferred across LATAM countries without recalculating residue collection radius, residue moisture, electricity grid mix, heat and power integration, water demand, chemical inputs, transport distance, pilot-infrastructure availability, and target-market access.

6.4. Pilot-Scale Validation Protocol

This review recommends a common pilot-validation package for LATAM fermentation biorefineries: (i) feedstock characterization over at least three seasonal or supplier batches; (ii) bench-to-bioreactor transfer with pH/DO/feeding control; (iii) stress testing with realistic inhibitor ranges; (iv) DSP mass balance; (v) product-quality characterization against target application; (vi) preliminary TEA/LCA sensitivity analysis; and (vii) a reproducibility run using a second residue batch. This package would make LATAM studies more comparable and more visible in international review literature.

7. Policy and Innovation Ecosystem as Enabling Constraints

Regional policy matters because fermentation scale-up requires aggregation infrastructure, pilot facilities, regulatory clarity, public–private financing, and standards for product approval. IRENA analyses support the view that Latin America has strong biomass and renewable-energy potential [51]. IICA documents the formation and guiding principles of a regional bioeconomy network [69,70], while WIPO highlights uneven innovation infrastructure and commercialization capacity across Latin America [67].

These deployment constraints are not uniform across the region: countries or subregions with dense agro-industrial clusters may justify centralized pilot facilities, whereas dispersed wet-residue systems may require decentralized conditioning, mobile preprocessing, or shared characterization hubs; market access for pigments, SCP, PHAs, BC, or biomedical materials will also depend on regulatory and commercialization capacity [67,69,70].

The most actionable policy-linked technical need is shared pilot infrastructure. Many LATAM laboratories can generate strong bench-scale data but lack access to controlled 10–300 L fermentation, gas-fermentation rigs, photobioreactors, downstream-processing equipment, and standardized product-characterization platforms. Shared regional facilities would allow researchers to validate strain and feedstock claims under comparable conditions and would reduce the gap between academic publications and investable bioprocesses.

8. Research Priorities for a Focused LATAM Fermentation Program

The following priorities were selected using the same technical assessment criteria applied throughout this review: carbon-entry mode, substrate specificity, achievable titer/yield/productivity, reactor and mass-transfer constraints, genetic tractability, and downstream-processing intensity. They were also aligned with the stage-gate logic proposed for LATAM biorefinery progression, in which a platform must move from feedstock characterization and bench validation to integrated pilot testing, TEA/LCA, and product-quality verification. Priority was assigned to research actions that meet five conditions: (i) direct relevance to major LATAM residue or CO₂ streams; (ii) ability to address a recurrent translational bottleneck, such as feedstock variability, hydrolysate inhibition, gas/light transfer, strain robustness, DSP cost, or product-quality validation; (iii) generation of measurable and comparable data across laboratories; (iv) feasibility as a near-term action in regional laboratories or shared pilot facilities; and (v) applicability to more than one high-value product class. Thus, the priorities are organized as a development sequence rather than as a strict ranking: define the substrate, characterize the chassis, build integrated prototypes with mass balances, adapt engineering tools, report scale-relevant metrics, and align TEA/LCA with the target product class.

First, build residue-specific hydrolysate specifications. Each major feedstock should have a compositional envelope, inhibitor profile, and recommended conditioning route. This is more useful than another general statement that residues are abundant.

Second, convert local isolates into characterized chassis. UANL-type Rhodotorula isolates, bagasse-associated consortia, halophiles, thermotolerant yeasts, and pigment-producing strains should be sequenced, phenotyped, and linked to engineering workflows.

Third, develop dual-feedstock prototypes with explicit mass balances. CO₂-to-biomass-to-product relays, residue-to-VFA-to-PHA cascades, and pectin-first citrus biorefineries should be evaluated by carbon recovery, energy use, DSP burden, and product quality.

Fourth, adapt synthetic-biology tools to local chassis. CRISPR, base editing, promoters, terminators, transformation protocols, biosensors, and modular cloning frameworks should be translated from model organisms into regionally useful strains.

Fifth, report fermentation in scale-relevant terms. Studies should include titer, yield, productivity, product identity, substrate specification, process controls, DSP recovery, and application-specific quality metrics.

Sixth, align TEA/LCA with product class. A carotenoid process, PHA process, BC process, SCP process, and organic-acid process do not share the same economic gate. Each should be assessed against its own market, regulatory, and downstream-processing requirements.

9. Conclusions

Latin America has a credible opportunity in fermentation-based and fermentation-integrated bioproduction, but the opportunity should be framed technically rather than rhetorically. Residue abundance and CO₂-source availability are necessary boundary conditions; they are not sufficient. The decisive questions are whether a defined substrate can be converted reproducibly by a suitable microbial platform, whether the product can be recovered at acceptable cost and quality, and whether the process survives scale-up, TEA, LCA, and regulatory scrutiny.

This focused review of LATAM fermentation platforms is therefore centered on platform matching. Phototrophic systems are strongest where light, land, water, and CO₂-source quality support integrated CO₂-to-intermediate production. Chemoautotrophic C. necator systems are strongest where concentrated CO₂, renewable H₂, and gas-transfer expertise are available. Rhodotorula and other local yeasts are strongest where crude substrates and stress tolerance matter. Y. lipolytica is the engineered benchmark for acetyl-CoA-derived products. PHA and bacterial-cellulose systems are strongest when product-quality and downstream-processing requirements are defined from the beginning. The UANL case studies illustrate how regional strains and residues can support distinctive process concepts, but their greatest value is as modules within a broader technical roadmap.

The strongest version of the regional argument is not that LATAM can valorize many wastes into many products. It is that LATAM can design technically coherent dual-feedstock biorefineries in which residue chemistry, CO₂-source quality, locally adapted microorganisms, synthetic biology, reactor design, and downstream processing are matched to specific high-value product classes. That is the focused research frontier this review identifies.