Question 1

I have an organic side stream from my food or agricultural process. Can fermentation turn it into something valuable?

Accepted Answer

Yes — and this is one of the most practically impactful applications of industrial fermentation. Organic side streams from food and agricultural processing contain carbohydrates, proteins, lipids, and minerals that are genuinely valuable as fermentation substrates. The conventional route for most wet organic side streams is anaerobic digestion for biogas production or aerobic biological treatment to reduce chemical oxygen demand before discharge. Both routes destroy the economic value embedded in the organic fraction. Fermentation offers an alternative: using the residual carbon, nitrogen, and mineral content of the side stream as the nutrient base for producing a higher-value product.  Deltra Labs works with a range of organic side streams in the context of bioprocess and fermentation development. Potato processing side streams — including potato steam peels, potato fruit water, and starch residues — contain significant concentrations of fermentable sugars, free amino acids, and minerals that support the growth of bacteria, yeasts, and filamentous fungi without substantial supplementation. Lactose permeate and delactosed permeate from dairy processing are well-established substrates for fermentation: lactose-fermenting yeasts such as Kluyveromyces marxianus grow efficiently on lactose permeate and can be directed toward biomass, ethanol, or other products depending on the process strategy. Manure and digestate, while more complex as substrates due to their heterogeneous composition and potential inhibitors, can support fermentations after appropriate pre-treatment, particularly for organisms tolerant of high ammonia concentrations.  The development process for a side stream valorisation project starts with substrate characterisation — establishing the carbohydrate profile, nitrogen content, mineral composition, pH, and the presence of any potential inhibitors such as organic acids, phenolics, or heavy metals that might limit microbial growth or product formation. This characterisation defines which fermentation strategies are technically feasible and which organisms are likely candidates. We then develop and validate a fermentation strategy — organism selection or isolation, media formulation, process parameters, and scale-up considerations — tailored to the specific side stream and target product combination.  Products that can be produced from organic side streams through fermentation include single-cell protein for food and feed applications, mycoprotein from filamentous fungi grown on carbohydrate-rich substrates, microbial lipids and single-cell oils from oleaginous organisms, organic acids including lactic acid, citric acid, and succinic acid, bioethanol from fermentable sugars, biosurfactants, pigments, and enzymes. The choice of target product is driven by the composition of the side stream, the organism best suited to utilise it, and the commercial value of the output relative to the cost of the process.

Question 2

Mycoprotein from side streams

Accepted Answer

Mycoprotein is a high-protein, high-fibre food and feed ingredient produced by cultivating filamentous fungi on carbohydrate-containing substrates under fermentation conditions. The most commercially established example is the Quorn product, produced from Fusarium venenatum, but a range of other filamentous fungi including species of Aspergillus, Rhizopus, Neurospora, and Trichoderma are also capable of producing edible fungal biomass with comparable nutritional properties. The mycelial biomass of filamentous fungi has a protein content of approximately 40 to 50 percent of dry weight, a fibre content in the form of chitin and beta-glucan, and a texture that is inherently fibrous due to the hyphal growth morphology. These properties make mycoprotein an attractive meat analogue and protein ingredient for food applications, and also a high-value ingredient for aquafeed, poultry feed, insect feed, and other animal nutrition applications where digestible, high-quality protein sources are in increasing demand.One of the most practically important and underappreciated advantages of fungal fermentation for mycoprotein production is that many filamentous fungi do not require strict aseptic conditions in the way that bacterial fermentations typically do. The low pH that develops naturally during fungal growth, combined with the robust competitive advantage of fast-growing filamentous fungi on complex substrates, means that non-aseptic or low-aseptic fungal fermentation is technically feasible for many side stream applications. This is a significant practical and economic advantage when working with large-volume, low-value organic side streams, where the cost of full aseptic processing would make the economics unworkable. It means that side streams with high biological oxygen demand, complex organic composition, and significant microbial contamination loads can be processed directly or with minimal pre-treatment.A further advantage specific to filamentous fungi is their metabolic versatility with respect to organic acids and other impurities commonly present in food and agricultural side streams. Organic acids including lactic acid, acetic acid, citric acid, and short-chain fatty acids — which are present in many fermented or partially degraded side streams and would inhibit many bacterial or yeast fermentations — are readily consumed by filamentous fungi as carbon sources. Rather than acting as inhibitors, they become part of the substrate that the fungus converts into biomass. This means that side streams containing residual organic acids, off-flavours, or partial fermentation products from upstream processing can often be used directly without acid neutralisation or removal steps that would add cost and complexity.The economic logic of mycoprotein production from side streams is straightforward: organic waste streams with a high biological oxygen demand represent a disposal cost for the generating company. Wastewater treatment, discharge fees, COD penalties, and the cost of running aerobic digesters or biological treatment plants are real operational costs that scale with the volume and organic load of the stream. Fungal fermentation converts the same organic load — the BOD that is currently a liability — into fungal biomass with positive commercial value as a protein ingredient. The net economic benefit is therefore not just the value of the protein produced but also the reduction or elimination of the disposal and treatment costs associated with the side stream.The range of organic side streams that are technically relevant for mycoprotein production through non-aseptic or low-aseptic fungal fermentation is broad and covers many of the largest-volume waste streams in the European food and agricultural processing sector.Acid whey, the liquid byproduct of Greek yogurt and strained cheese production, is one of the most problematic food industry side streams in terms of disposal cost and regulatory pressure. It has a high organic acid content — primarily lactic acid — a low pH of approximately 4 to 4.5, and a significant lactose concentration. Filamentous fungi capable of consuming both lactose and lactic acid can grow directly on acid whey without pH adjustment, converting two of the primary disposal problem components into fungal biomass.Ice cream and dairy plant wastewater streams contain residual sugars, fats, proteins, and cleaning agent residues from production and cleaning cycles. The sugar and protein fraction of these streams can support fungal growth, and the periodic nature of the stream — matching production schedules — is manageable in a fed-batch fermentation context.Olive pomace and olive mill wastewater are among the most environmentally problematic side streams in Mediterranean agriculture. Olive mill wastewater has a very high COD — typically 40 to 220 grams of oxygen per litre — contains phenolic compounds that are toxic to most microorganisms, and is generated in very large volumes during the olive pressing season. Certain filamentous fungi, particularly white-rot fungi and some Aspergillus species, are capable of growing on olive mill wastewater and degrading the phenolic fraction while accumulating biomass. This makes fungal fermentation one of the few biological treatment routes that can both remediate olive mill wastewater and produce a valuable product simultaneously.Palm oil mill effluent, known as POME, is generated in very large volumes in South-East Asian palm oil processing and has a COD of 15,000 to 100,000 milligrams per litre — one of the highest of any food processing side stream. It contains residual palm oil, suspended solids, and a complex mixture of organic compounds. Fungal fermentation on POME has been evaluated as a route to produce fungal biomass for feed applications, simultaneously reducing the organic load before discharge.Distillery stillage — also called thin stillage or vinasse — is the liquid fraction remaining after ethanol distillation from grain, molasses, or sugarcane fermentation. It is rich in residual organic matter, yeast cell debris, unfermented carbohydrates, and minerals. The composition varies significantly depending on the feedstock, but the high organic content and large volumes generated at distilleries make it an economically attractive substrate for fungal biomass production if the economics of protein recovery are competitive with existing stillage disposal routes.Winery pomace and winery wastewater contain grape skin residues, seeds, tartaric acid, ethanol residues, polyphenols, and sugars from grape pressing and winemaking operations. The polyphenol content can inhibit some organisms but is tolerated or metabolised by specific fungal species, and the seasonal availability of winery waste matches the grape harvest calendar.Potato processing waste — including potato peel streams, potato fruit water from starch production, and potato washing water — is one of the most relevant side streams in the Netherlands and northern Europe given the scale of the Dutch potato processing industry. Potato fruit water contains significant concentrations of fermentable carbohydrates, amino acids, and minerals, and has been demonstrated as a viable substrate for fungal biomass production. The starch content of potato peel streams can be hydrolysed enzymatically or by acidic pre-treatment to release fermentable glucose before fungal fermentation.Sugar beet and sugarcane processing wastewater and molasses are large-volume, carbohydrate-rich streams that have historically been used as fermentation substrates. Vinasse from sugarcane ethanol production is the residue after distillation and contains residual sugars, amino acids, minerals, and organic acids. Beet molasses is one of the most established non-sterile fermentation substrates in industrial biotechnology, and fungal species capable of growing on molasses in non-aseptic conditions are well-documented.The technical challenge in mycoprotein production from side streams is not primarily the biology — filamentous fungi are genuinely robust on complex, contaminated substrates — but the process design: characterising the substrate sufficiently to design a reliable fermentation, selecting the right organism for the specific substrate composition, managing the fermentation to produce mycelium with consistent protein content and safety profile, and developing a downstream processing route that separates and concentrates the fungal biomass efficiently. The absence of mycotoxins in the product must be confirmed through appropriate strain selection and validated production conditions, and this is a non-negotiable requirement for any food or feed application.Deltra Labs evaluates the technical and economic feasibility of mycoprotein production for specific side stream compositions, selects or screens for appropriate fungal strains, develops the fermentation strategy and process parameters, and supports the downstream processing design needed to deliver fungal biomass at the quality required for the intended food, feed, or aquafeed application.

Question 3

Lactose permeate and delactosed permeate

Accepted Answer

Yes. Lactose permeate — the liquid fraction remaining after ultrafiltration of whey or milk that contains lactose, minerals, and small amounts of protein — and delactosed permeate — the residual liquid after crystallisation or enzymatic hydrolysis of most of the lactose — are among the most well-characterised and practically important organic side streams in the European food industry. The EU dairy sector generates substantial volumes of these streams annually, and their disposal or processing is a significant operational cost for dairy companies. Fermentation offers a route to convert these streams into products with positive economic value.  Lactose permeate contains approximately 70 to 80 grams per litre of lactose, making it a rich fermentation substrate for organisms capable of metabolising this disaccharide. Kluyveromyces marxianus is the most industrially relevant lactose-fermenting yeast and can be cultivated on lactose permeate to produce biomass for feed applications, ethanol, or other products depending on fermentation conditions. Candida pseudotropicalis and several other yeast species also utilise lactose efficiently. Lactic acid bacteria including Lactobacillus and Lactococcus species ferment lactose to lactic acid under anaerobic or microaerobic conditions, producing a product with applications in food acidification, preservation, bioplastics, and green chemistry. The galactose fraction remaining after glucose utilisation in mixed sugar fermentations or after lactase treatment can present a challenge for some organisms that preferentially consume glucose before galactose, and process development must account for this diauxic behaviour.  Delactosed permeate has a lower residual lactose content but retains minerals — particularly calcium, phosphorus, potassium, and sodium — and can serve as a mineral source or partial medium component in fermentations using other primary substrates. The mineral composition of dairy permeate streams is often well-suited to bacterial fermentations that would otherwise require supplementation with inorganic salts. Deltra Labs evaluates the use of lactose permeate and delactosed permeate as primary or supplementary substrates in fermentation development projects, characterises their composition, identifies appropriate producing organisms, and develops process strategies that convert this cost centre into a product with positive value.

Question 4

Producing a specific compound by fermentation

Accepted Answer

Yes — and this is precisely the situation where early-stage feasibility work has the most value, because the decisions made at the beginning of a fermentation development project define the scope and cost of everything that follows. Deltra Labs supports clients at exactly this stage: when the target compound has been identified and the desire to produce it through fermentation has been established, but the producing organism, the fermentation route, and the process strategy are still open questions.  The starting point for any novel biological production concept is a technical feasibility assessment. This involves establishing whether the target compound can be produced biologically and, if so, which biological systems are capable of producing it. For compounds with established biosynthetic routes in known microorganisms — fatty acids and lipids produced by oleaginous yeasts such as Yarrowia lipolytica, pigments such as carotenoids and lycopene produced by bacteria and yeasts, organic acids produced by fungi and bacteria, vitamins such as riboflavin produced by Ashbya gossypii or vitamin B12 produced by Propionibacterium freudenreichii, or nutraceuticals such as ergosterol, coenzyme Q10, or polyunsaturated fatty acids — the first question is whether classical strain improvement or process optimisation can achieve the required productivity, or whether the existing literature provides a viable starting point for process development. For these cases, Deltra Labs develops or adapts the fermentation strategy based on the available scientific and patent literature and translates it into a practical, experimental process.  For target compounds where no established biological production route exists, or where the client wants to explore whether a naturally occurring organism might produce the compound more efficiently than engineering an existing host, we conduct strain screening campaigns. This involves screening a collection of environmental isolates or culture collection strains for natural production of the target compound or a biosynthetic precursor, identifying candidates with detectable production, and then developing those candidates as production strains through classical improvement and process optimisation. This approach is particularly relevant for speciality lipids and oils with unusual fatty acid profiles, novel pigments, bioactive secondary metabolites, and antimicrobial or crop-protective compounds where natural producers may exist but have not yet been characterised for industrial production.

Question 5

Specialty oils, fats and lipids

Accepted Answer

Yes. The fermentative production of microbial lipids — often referred to as single-cell oil production — is an established and growing area of industrial biotechnology with applications in food, feed, nutraceuticals, oleochemicals, and biobased materials. A range of microorganisms are capable of accumulating lipids to high percentages of their dry cell weight under appropriate fermentation conditions, and the fatty acid profile of the accumulated oil can vary significantly between organisms and can be influenced by fermentation conditions, making microbial fermentation an attractive route to specialty oils with profiles that are difficult or expensive to obtain from plant or animal sources.  Oleaginous yeasts are among the most practically relevant lipid producers for industrial fermentation. Yarrowia lipolytica is the most extensively studied oleaginous yeast and can accumulate lipids to 30 to 60 percent of dry cell weight under nitrogen-limited conditions, with a fatty acid profile dominated by oleic acid, palmitic acid, and linoleic acid. The lipid content and fatty acid composition of Yarrowia lipolytica can be shifted by adjusting the carbon source, the carbon-to-nitrogen ratio, the fermentation temperature, and the dissolved oxygen profile during the production phase. Lipomyces starkeyi, Rhodotorula glutinis, Trichosporon oleaginosus, and Cryptococcus curvatus are other oleaginous yeasts with industrial relevance, each with characteristic lipid yields and fatty acid profiles.  For specialty fatty acids with high commercial value — including gamma-linolenic acid (GLA), arachidonic acid (ARA), docosahexaenoic acid (DHA), eicosapentaenoic acid (EPA), and other polyunsaturated fatty acids with nutraceutical or pharmaceutical applications — filamentous fungi and microalgae are the primary biological producers. Mortierella alpina produces arachidonic acid and has been used commercially for ARA production for infant formula applications. Schizochytrium and Thraustochytrid species produce DHA at high concentrations. Microalgae including Nannochloropsis, Isochrysis, and Phaeodactylum produce EPA and DHA under photoautotrophic or mixotrophic conditions. Deltra Labs evaluates the technical and commercial feasibility of producing target lipids and fatty acids through fermentation, selects the most appropriate producing organism for the specific fatty acid profile required, and develops the fermentation and downstream processing strategy — including cell disruption, extraction, and concentration — to deliver the target oil at the required quality and scale.  Strain screening for novel lipid producers is also a service we offer for clients looking for natural organisms that produce a specific fatty acid profile without the need for genetic engineering. Environmental isolates from oleaginous substrates, soil, and aquatic environments sometimes produce unusual fatty acids or lipid profiles not represented in existing culture collections, and screening these isolates can identify natural producers that are both effective and non-GMO.

Question 6

Specialty chemicals, nutraceuticals, pigments, antioxidants, vitamins

Accepted Answer

Yes. The biobased production of specialty chemicals, functional ingredients, nutraceuticals, pigments, antioxidants, and vitamins through microbial fermentation is one of the most active areas of industrial biotechnology, driven by increasing consumer and regulatory preference for naturally derived ingredients over petrochemical or synthetic alternatives, and by the cost and sustainability advantages of fermentation over chemical synthesis or plant extraction for many compounds.  Pigments represent a well-developed area where fermentation offers a practical and scalable production route. Carotenoids including beta-carotene, lycopene, astaxanthin, and zeaxanthin are produced by a range of bacteria and yeasts including Blakeslea trispora for beta-carotene, Lycopersicon-derived bacterial strains for lycopene, and Phaffia rhodozyma and Haematococcus pluvialis for astaxanthin. Riboflavin (vitamin B2) is produced commercially by fermentation using Ashbya gossypii and Bacillus subtilis. The red pigment monascin and related compounds are produced by Monascus purpureus, though safety considerations limit their food applications in some regulatory contexts. Violacein, indigoidine, and other microbially produced pigments are receiving increasing research attention as alternatives to synthetic dyes for food and textile applications.  Nutraceuticals and functional food ingredients produced by fermentation include coenzyme Q10 (ubiquinone), produced by Agrobacterium tumefaciens and several other bacterial species; ergosterol (provitamin D2), produced by Saccharomyces cerevisiae and other yeasts; gamma-aminobutyric acid (GABA), produced by lactic acid bacteria; and a range of exopolysaccharides including hyaluronic acid, xanthan gum, and levan that have applications in food, cosmetics, and biomedicine. Antioxidants produced by fermentation include ergothioneine, glutathione, and various phenolic compounds produced by fungi and bacteria.  For specialty chemicals with applications in materials, green chemistry, or industrial processing — including biobased plasticisers, monomers for bioplastics, lubricants, and surface-active agents — fermentation routes are increasingly being developed as alternatives to petrochemical production. Succinic acid, itaconic acid, glucaric acid, and muconic acid are biobased platform chemicals produced by fermentation that serve as precursors for polymers, coatings, and other materials applications. Deltra Labs develops fermentation processes for target compounds in all of these categories, starting from organism selection and strain development through to process optimisation and downstream processing strategy. The approach is always feasibility-first: we establish whether the target can be produced at relevant concentrations before committing to a full process development programme.

Question 7

Can you screen for a natural biological compound to protect crops against pathogens or pests — a natural biopesticide or biostimulant?

Accepted Answer

Yes. The search for natural, biologically produced alternatives to synthetic pesticides and crop protection chemicals is one of the most practically important areas in agricultural biotechnology, driven by regulatory pressure to reduce synthetic pesticide use across Europe, consumer demand for residue-free produce, and the resistance of many pathogens and pests to established chemical treatments. Microorganisms produce a vast diversity of bioactive secondary metabolites with antifungal, antibacterial, insecticidal, nematicidal, and herbicidal activities, and many of these compounds — or the microorganisms that produce them — can be developed into biological crop protection products or biostimulants.  Deltra Labs approaches this through two complementary strategies. The first is microbial screening — identifying from environmental samples or culture collections microorganisms that produce bioactive compounds with the desired protective activity against a specific target pathogen or pest. This involves isolating and cultivating candidate microorganisms under defined conditions, screening the cultures or fermentation extracts for inhibitory activity against the target organism using bioassay methods, and identifying and developing the most active producers as fermentation strains for scale-up. Soil bacteria from the genus Bacillus, Pseudomonas, and Streptomyces are prolific producers of antifungal and antibacterial compounds and are well-established sources of biocontrol agents. Trichoderma species produce a range of antifungal metabolites and are widely used as biocontrol agents in agriculture. Actinomycetes are the most prolific known producers of bioactive secondary metabolites and are a logical starting point for screening campaigns targeting novel antifungal or antibacterial compounds.  The second strategy is developing a fermentation and formulation process for a bioactive compound or producing organism that has already been identified as effective. Producing a biocontrol compound at relevant concentrations, harvesting it efficiently, and formulating it in a way that maintains activity on the crop requires process development work that is distinct from the initial discovery work. Deltra Labs develops the fermentation strategy for the producing organism, optimises the production conditions for the bioactive compound, and can support the development of a downstream recovery process appropriate to the stability and physical properties of the compound.  In addition to protective compounds, we also develop cultivation processes for plant growth-promoting rhizobacteria (PGPR) — including nitrogen-fixing bacteria such as Rhizobium, Azospirillum, and Azotobacter, and phosphate-solubilising bacteria — that improve nutrient availability and crop productivity when applied to soil or seed. The fermentation and formulation of rhizobacterial inoculants involves specific challenges around maintaining cell viability, storage stability, and effective colonisation of the rhizosphere, all of which require process development expertise to address at production scale.

Question 8

Novel microorganism isolation

Accepted Answer

Yes. The isolation of novel microorganisms from environmental samples — soil, water, plant material, food production environments, fermentation residues, and other substrates — is a valuable starting point for applications where existing culture collection strains do not perform adequately, where a natural organism is preferred over an engineered one, or where the target activity or tolerance is rare enough that it requires active enrichment and selection to find.  The principle behind targeted environmental isolation is simple but powerful: organisms that naturally thrive in conditions related to your problem are more likely to possess the biological capabilities needed to solve it than organisms selected from a general-purpose culture collection. A microorganism isolated from a high-acid environment is more likely to be acid-tolerant than a standard laboratory strain. An organism isolated from an environment rich in a specific carbon source is more likely to utilise that carbon source efficiently. An organism isolated from a site contaminated with a specific compound is more likely to tolerate or degrade that compound. Deltra Labs designs isolation campaigns around this logic — identifying environmental niches relevant to the target application, collecting and processing samples, and using selective enrichment and screening to identify organisms with the desired properties.  For side stream valorisation projects, for example, we can isolate organisms from composting environments, silage, fermented food substrates, or the microbiome associated with the side stream itself — these environments naturally select for organisms capable of efficiently metabolising complex organic substrates at relevant pH and temperature ranges. For crop protection applications, soil samples from the rhizosphere of healthy plants in environments where the target pathogen is present can be a source of natural biocontrol organisms that have co-evolved with the pathogen. For high-temperature fermentation processes, thermophilic organisms can be isolated from compost, hot springs, or industrial warm-water environments.  The deliverable from a novel microorganism isolation project is a characterised isolate — identified to species or strain level by 16S rRNA sequencing (for bacteria) or ITS sequencing (for fungi), characterised for growth requirements, substrate utilisation, relevant tolerances, and the target activity — that is ready for development as a production strain or application organism. The isolated organism is your property and, if it possesses genuinely novel properties, may be a patentable asset.

Question 9

Setting up a biotech lab

Accepted Answer

Yes. Timo van Roosmalen has direct practical experience in setting up biotechnology research and production laboratories from scratch — including the specification of equipment, the establishment of analytical methods, the development of standard operating procedures, and the practical commissioning and validation of fermentation systems from bench scale to pilot scale. This experience is available to clients as an interim R&D service alongside contract research projects.  The practical challenges of establishing a new biotech laboratory or fermentation facility are different from those of running one. Equipment specification requires knowledge of what each piece of equipment actually needs to do in practice — not just in the supplier's datasheet — and of how different instruments and systems interact in a functioning laboratory workflow. Fermentation equipment in particular requires careful specification of bioreactor type, control system capabilities, sensor integration, aeration and agitation design, and steam sterilisation or autoclave requirements, all of which depend on the organisms to be cultivated and the products to be produced. Analytical method development and validation, media preparation workflows, strain banking protocols, and contamination control procedures are all necessary before productive experimental work can begin and all benefit from experience of what works in practice rather than what looks good on paper.  For organisations building a new internal fermentation or bioprocess capability — whether a food company moving into fermentation-based production, a start-up transitioning from contract research to in-house development, or a research institution adding industrial-scale fermentation to its capabilities — Deltra Labs can provide interim scientific leadership for the setup phase, including equipment specification, supplier selection support, laboratory design input, SOPdevelopment, and the training of in-house personnel on fermentation operation and process troubleshooting. This is available as a standalone interim engagement or as a complement to an ongoing contract research relationship.

Question 10

Fermentation vs anaerobic digestion

Accepted Answer

Anaerobic digestion is the most widely used biological treatment for wet organic side streams, and for many applications it is appropriate. It handles complex and heterogeneous organic waste efficiently, is well-established at large scale, and produces biogas that can be used for heat and power generation. However, anaerobic digestion optimises for the destruction of organic matter — the goal is to reduce chemical oxygen demand (COD) as completely as possible, converting the organic carbon content of the side stream into methane and carbon dioxide. In doing so, it destroys the economic value embedded in the carbohydrates, proteins, and other biologically useful compounds present in the side stream.  Fermentation-based valorisation takes the opposite perspective: it treats the organic content of the side stream not as waste to be treated but as a resource to be converted into a higher-value product. The residual sugars in potato processing water, the lactose in dairy permeate, the fermentable carbohydrates in vegetable processing side streams — these are genuine fermentation substrates that can support the growth of microorganisms and the production of valuable compounds. By using a targeted fermentation strategy, the same organic fraction that would enter an aerobic or anaerobic digester can instead be converted into single-cell protein, mycoprotein, microbial oil, lactic acid, ethanol, or another product with positive commercial value.  The practical choice between anaerobic digestion and fermentation-based valorisation depends on several factors: the composition and variability of the side stream, the volume generated, the available infrastructure, the target product market, and the economics of the fermentation process relative to the value of the product. For high-volume, low-value side streams with heterogeneous composition and significant inhibitor loads, anaerobic digestion may remain the most practical route. For streams with a defined, fermentable carbohydrate fraction — such as lactose permeate, starch-containing potato side streams, or sugar beet pulp — fermentation can produce a product worth significantly more per tonne than the energy recovered through digestion. Deltra Labs evaluates this trade-off for specific side stream compositions and helps clients make technically and economically informed decisions about the most appropriate valorisation route before committing to process development.

Question 11

Can biotechnology and microorganisms be used to improve soil health, and can Deltra Labs help develop such a solution?

Accepted Answer

Yes — and this is one of the fastest-growing areas at the intersection of industrial biotechnology and sustainable agriculture. Soil health is increasingly recognised as the foundation of productive and resilient farming systems, and the role of the soil microbiome in driving nutrient cycling, organic matter decomposition, plant disease suppression, and crop productivity is now well-established in both the scientific literature and mainstream agricultural practice. The challenge for most farmers, agronomists, and agricultural companies exploring this space is translating the science into a practical, scalable, and consistent biological product or management practice. That translation — from biological concept to working fermentation process and applicable product — is exactly what Deltra Labs develops.Why soil health matters and where microbiology fitsHealthy soil is not simply a mineral substrate for plant roots. It is a complex, living ecosystem in which bacteria, fungi, archaea, protozoa, nematodes, and a vast diversity of other organisms interact continuously with each other, with plant roots, and with the soil mineral and organic fraction. These interactions drive processes that are fundamental to crop productivity: the decomposition of organic matter and the release of plant-available nutrients, the fixation of atmospheric nitrogen into plant-available ammonium, the solubilisation of phosphate and other minerals from forms that are chemically bound in the soil, the suppression of soilborne plant pathogens through competition, antibiosis, and induced systemic resistance in the plant, and the formation and stabilisation of soil aggregates that determine water retention, aeration, and resistance to erosion.Intensive agricultural management over decades — including high rates of synthetic fertiliser application, fungicide and herbicide use, frequent tillage, and the removal of crop residues — has in many cases reduced the diversity and functional capacity of the soil microbiome. This degradation of soil biology is directly connected to the increasing fertiliser requirements, declining organic matter content, reduced water-holding capacity, and increased disease pressure that many growers are observing in their fields. Restoring and maintaining a functional soil microbiome is therefore not simply an environmental goal but a practical agronomic necessity for sustainable productivity.Plant growth-promoting rhizobacteria and nitrogen fixationAmong the most practically relevant and commercially established groups of soil microorganisms for agriculture are the plant growth-promoting rhizobacteria (PGPR) — a diverse functional group of bacteria that colonise the plant root system and directly or indirectly improve plant growth and health. Nitrogen-fixing PGPR are of particular importance in the context of reducing synthetic nitrogen fertiliser use. Biological nitrogen fixation — the conversion of atmospheric dinitrogen into ammonium by the enzyme nitrogenase — is carried out by a range of bacteria, and the efficiency of this process under field conditions depends critically on the producing organism and its compatibility with the host plant and soil environment.Symbiotic nitrogen fixers including Rhizobium, Bradyrhizobium, Mesorhizobium, and Sinorhizobium species form specific associations with leguminous crops — including soya, clover, alfalfa, peas, and beans — and fix nitrogen within root nodules at rates that can substantially reduce or eliminate the need for synthetic nitrogen fertiliser for those crops. The effectiveness of commercial Rhizobium inoculants depends strongly on the match between the bacterial strain and the specific host legume variety, the competitiveness of the inoculant strain with resident soil rhizobia, and the viability of the bacterial cells at the point of application. Producing a rhizobial inoculant with consistent cell viability, competitive colonisation capacity, and demonstrated nitrogen fixation efficacy under realistic field conditions requires fermentation process development work that is distinct from laboratory-scale production.Associative and free-living nitrogen fixers — including Azospirillum brasilense, Azotobacter vinelandii, Gluconacetobacter diazotrophicus, Herbaspirillum seropedicae, and Paenibacillus polymyxa — associate with the roots of non-leguminous crops including wheat, maize, rice, and sugarcane and fix atmospheric nitrogen at rates that are lower than symbiotic fixation but agronomically meaningful when the producing organisms are present in sufficient numbers and in the right physiological state. Brazilian sugarcane production has demonstrated that biological nitrogen fixation by associative diazotrophs can supply a significant fraction of the nitrogen requirement of sugarcane varieties bred for this association. The fermentation and formulation of associative nitrogen fixers for consistent performance across diverse soil and climate conditions is an active area of product development in the biostimulant and biofertiliser industry.Phosphate solubilising bacteria and mineral nutrient cyclingPhosphate is the second most frequently limiting macronutrient for crop production after nitrogen, and unlike nitrogen it cannot be obtained from the atmosphere. A large fraction of the phosphate in agricultural soils — often 70 to 80 percent — exists in forms that are chemically unavailable to plants, bound to iron, aluminium, and calcium as insoluble precipitates, or locked in organic matter as phytate and other organic phosphate esters. Phosphate-solubilising bacteria (PSB) including Bacillus megaterium, Pseudomonas putida, Burkholderia cepacia, Penicillium bilaii, and Aspergillus niger release these bound forms through the production of organic acids — gluconic acid, citric acid, oxalic acid — that acidify the rhizosphere and dissolve insoluble phosphate minerals, and through the production of phytase enzymes that hydrolyse organic phosphate esters. The net effect is an increase in plant-available phosphate in the rhizosphere without additional synthetic phosphate fertiliser input.Similarly, potassium-solubilising bacteria including Bacillus mucilaginosus, Frateuria aurantia, and Aspergillus species release potassium from silicate minerals and organic potassium forms through acid and enzyme production. Sulphur-oxidising bacteria including Thiobacillus species convert elemental sulphur to sulphate that plants can absorb. The combined activity of multiple functional groups of nutrient-cycling bacteria in the rhizosphere constitutes what is sometimes described as a biological fertiliser system — one that reduces dependence on synthetic mineral inputs while maintaining or improving crop nutrition.Biocontrol and soil-borne disease suppressionSoil-borne plant pathogens — including Fusarium oxysporum, Rhizoctonia solani, Sclerotinia sclerotiorum, Verticillium dahliae, Pythium species, and Phytophthora species — cause significant yield losses in a wide range of crops worldwide and are becoming increasingly difficult to manage with synthetic fungicides due to the development of resistance and regulatory restrictions on active substances. Soil microorganisms that suppress these pathogens through direct antagonism, competition for resources, or induction of systemic resistance in the plant are receiving increasing attention as components of integrated disease management strategies.Bacillus subtilis, Bacillus amyloliquefaciens, and Bacillus velezensis produce iturin, surfactin, fengycin, and other lipopeptide antibiotics with potent antifungal activity that suppress a range of soil-borne pathogens. Pseudomonas fluorescens and Pseudomonas putida produce phenazines, pyoluteorin, 2,4-diacetylphloroglucinol, and hydrogen cyanide that are antagonistic to fungal and bacterial pathogens. Trichoderma harzianum, Trichoderma asperellum, and related species are direct mycoparasites that colonise and destroy the hyphae and sclerotia of soilborne fungal pathogens, and also produce lytic enzymes and volatile compounds with broad-spectrum antifungal activity. Streptomyces lydicus and other actinomycetes produce antifungal compounds including natamycin and candicin that are active against a range of soilborne pathogens.The effectiveness of biocontrol agents under field conditions depends on their ability to survive in the soil, compete with the resident microbiome, and colonise the rhizosphere at sufficient population densities to exert meaningful suppressive activity. Producing these organisms at the right cell density, in the right physiological state, and in a formulation that protects viability from production through storage to field application requires fermentation and formulation expertise.Mycorrhizal fungi and fungal soil networksArbuscular mycorrhizal fungi (AMF) — including species of Rhizophagus, Glomus, Funneliformis, and Claroideoglomus — form obligate symbioses with the roots of the majority of terrestrial plant species, extending the effective root surface area by orders of magnitude through their extensive extraradical mycelial networks. These networks facilitate the transfer of phosphate, zinc, copper, and water from soil volumes inaccessible to the root hair system into the plant, in exchange for photosynthetically fixed carbon from the host. AMF also improve soil aggregate stability through the production of glomalin-related soil proteins, contribute to soil water retention, and in some plant-pathogen combinations provide significant disease protection. The reduction of AMF diversity and colonisation rates in intensively managed arable soils — driven by tillage, synthetic fertiliser use, and fungicide application — is widely associated with reduced soil structural stability and increased crop dependence on external inputs.Ectomycorrhizal fungi including Pisolithus tinctorius, Suillus species, and Laccaria bicolor form associations with forest trees including pine, oak, birch, and beech and play a central role in nutrient cycling and carbon storage in forest ecosystems. The production of mycorrhizal inoculants for reforestation, agroforestry, and horticultural applications requires specific fermentation and substrate development approaches because AMF are obligate biotrophs that cannot be cultivated in the absence of a host plant root, while ectomycorrhizal fungi can be produced on defined substrates under controlled fermentation conditions.How Deltra Labs approaches soil health projectsProjects in the soil health and agricultural microbiology space typically start with a clear definition of the agronomic problem or objective — nitrogen reduction, phosphate efficiency, soilborne disease management, soil structure improvement, or a combination — and an identification of the biological mechanism most likely to address it. From there, Deltra Labs evaluates which organisms are most relevant, whether they need to be isolated from the target environment or can be sourced from culture collections, and what fermentation and formulation strategy will deliver consistent performance under realistic field conditions.For clients who want to develop a proprietary biological product for a specific crop, soil type, or climate zone, we conduct targeted isolation campaigns — collecting soil samples from relevant environments, enriching for organisms with the desired functional properties, and characterising the most promising isolates for development as production strains. For clients who want to produce an established biological with a defined organism, we develop the fermentation process, optimise the production conditions for cell density and physiological state, and support the formulation strategy — liquid, wettable powder, granule, or seed coating — that best suits the application method and shelf-life requirement.The market for biological soil amendments, biofertilisers, and biocontrol agents is growing rapidly across Europe and globally, driven by Farm to Fork strategy targets for synthetic pesticide and fertiliser reduction, consumer demand for sustainably produced food, and the agronomic evidence that functional soil biology reduces input costs and improves long-term productivity. If you are exploring whether biotechnology can address a specific soil health challenge in your farming system, your crop, or your product portfolio — a feasibility call is the right starting point.

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