The study area is one of the most ecologically heterogeneous stretches of the Mediterranean. It spans rocky shores, sandy beaches, seagrass meadows, busy commercial and fishing ports, and the Mar Menor, one of Europe’s largest hypersaline lagoons, protected under the Ramsar Convention, Natura 2000, and Special Protection Area frameworks. It also includes the Salt Ponds of San Pedro del Pinatar, where active salt exploitation pushes salinity to an extraordinary 70.4 grams per liter — more than double typical seawater. Sampling ran from autumn 2024 through summer 2025, with triplicate water and sediment collections at each site in every season, accompanied by in situ measurements of temperature, pH, dissolved oxygen, salinity, conductivity, and nutrients, plus laboratory analyses of chlorophyll-a, sediment granulometry, and elemental composition.

Recovering yeasts from marine environments is technically demanding because their densities in seawater are typically very low. The team used a membrane filtration approach, concentrating 1-liter water samples and suspended sediment through sterile nitrocellulose membranes, then plating the concentrates onto five different culture media prepared with filtered seawater or supplemented with sodium chloride. An enrichment protocol was added for sediments to boost recovery of rare viable cells. Colonies were grouped into morphotypes based on color, size, shape, and texture, and a stratified selection strategy preserved the relative representation of each morphotype while reducing redundancy. Species identification relied on sequencing the internal transcribed spacer (ITS) region and the D1/D2 domain of the large subunit rRNA gene, with pragmatic similarity thresholds of at least 98.4 percent for ITS and 99.5 percent for LSU used to assign species proxies. Isolates falling below these thresholds were conservatively treated as potentially novel species pending formal description.

The taxonomic picture that emerged is dominated by the phylum Ascomycota, which accounted for 62 percent of identified species, distributed mainly among the classes Pichiomycetes, Dothideomycetes, Saccharomycetes, and Dipodascomycetes. Basidiomycota made up the remaining 38 percent, chiefly Tremellomycetes and Microbotryomycetes. The genera Rhodotorula and Candida were the most represented in both seawater and sediment. Rhodotorula mucilaginosa was the single most abundant species overall — 25 percent of water isolates and 10 percent of sediment isolates — and the only taxon detected at all ten sampling sites. Candida parapsilosis, a species better known as a human commensal, ranked second, a pattern the authors link to substantial anthropogenic influence along the coast.

Perhaps the most eye-catching component of the dataset is the prevalence of pigmented and melanized fungi. Roughly 10 percent of isolates were stress-tolerant black yeast-like fungi, including Aureobasidium pullulans, Aureobasidium melanogenum, Hortaea werneckii, Exophiala oligosperma, and Zalaria alba. Hortaea werneckii, one of the most halotolerant eukaryotes known, dominated both water and sediment at the hypersaline Salt Ponds site, where it co-occurred with various Debaryomyces species. Red-pigmented carotenoid-producing taxa such as Rhodotorula, Cystobasidium, Sporobolomyces, Symmetrospora, and Rhodosporidiobolus were also abundant. The researchers argue that intense solar radiation, hypersalinity, and seasonal thermal stress characteristic of the semi-arid Murcian coast select for these melanized and carotenoid-rich organisms, whose pigments protect against ultraviolet exposure and oxidative damage.

Diversity was not evenly distributed. Gamma diversity — total species richness pooled across all sites and seasons — was significantly higher in seawater than in sediment, with 77 species detected in the water column versus 44 in the benthos. The authors suggest the water column acts as a dynamic reservoir of yeast diversity, favored by greater dispersal potential, while sediments impose selective pressures that limit which species persist. Spatially, the Port of Cartagena, one of the most important harbors in the western Mediterranean, showed the highest richness of all: 26 species from the water column and 17 from sediments, with the top diversity indices across every metric measured. In contrast, sandy sediments at Portmán, Calblanque, and La Manga supported the lowest diversity, consistent with the constant reworking of unconsolidated substrates by waves, which leaves little organic matter and few stable surfaces for microbial colonization.

Beta diversity analyses revealed just how different these communities are from place to place. Jaccard distances between sites ranged from 0.69 to 0.96, indicating pronounced taxonomic differentiation. Sørensen-based partitioning showed that species turnover accounted for nearly 95 percent of total beta diversity, meaning the coastal gradient hosts largely distinct yeast assemblages rather than nested subsets of a single community. Seasonally, richness stayed remarkably stable — 37 species in autumn, 36 in winter, 40 in spring, and 30 in summer — but community composition shifted dramatically, with only six species, including Candida parapsilosis, Filobasidium magnum, Hortaea werneckii, and Rhodotorula mucilaginosa, present across all four seasons. PERMANOVA confirmed significant seasonal differences in assemblage structure, and among the environmental variables tested, temperature was the only significant individual factor, explaining 13.6 percent of the variance.

Beyond their ecological roles in organic matter recycling and nutrient cycling, the yeasts displayed impressive functional versatility. Screening of 90 representative strains showed that about 40 percent produced at least one extracellular lytic enzyme, with many producing several. Six activities were tested on agar plates: amylase, cellulase, pectinase, xylanase, chitinase, and protease. Aureobasidium pullulans was positive for all six, while Symmetrospora marina and Sampaiozyma vanillica showed notable amylase and chitinase activity. The standardized API-ZYM micromethod, which probes 19 enzymatic activities, confirmed broad repertoires in the black yeast-like fungi, with several species expressing more than half of the activities tested. Stress tolerance assays added to the picture: all isolates grew at 5 percent sodium chloride, roughly 40 percent tolerated 10 to 15 percent, and about 90 percent resisted oxidative stress induced by 1 millimolar hydrogen peroxide, with the melanized species showing the highest resistance.

These traits matter for biotechnology. Marine yeasts are known to produce robust enzymes, ferment in seawater, accumulate lipids, synthesize antimicrobials and anticancer compounds, and degrade environmental pollutants. Their resilience stems from complex physiological machinery, including mitogen-activated protein kinase signaling pathways that orchestrate adaptive transcriptional responses to salinity, temperature, pH, and oxidative stress. The enzymatic repertoire documented in the Murcian isolates also signals a central ecological function: degrading complex polymers such as cellulose, chitin, and pectin within coastal ecosystems, thereby feeding carbon and nutrients back into the microbial food web. Strains with this level of enzymatic breadth and stress tolerance are promising candidates for industrial bioprospecting, bioremediation of contaminated coastal sites, and bioconversion processes.

The survey carries a clinical warning as well. Opportunistic pathogens of potential human concern — Candida parapsilosis, Exophiala oligosperma, Nakaseomyces glabratus, and Diutina catenulata — were predominantly detected at anthropogenically impacted sites, supporting their proposed value as bioindicators of marine contamination. Candida parapsilosis, which peaked at 25 percent relative abundance in summer, has been designated a high-priority fungal pathogen by the World Health Organization, underscoring the need to connect environmental monitoring with public health surveillance. The authors conclude that marine yeasts emerge from this study as both sensitive gauges of ecosystem health and reservoirs of robust strains with significant biotechnological potential, and they call for future work combining cultivation-based and culture-independent approaches to fully capture the diversity and metabolic capacities of this underexplored microbial frontier.

Subject of Research: Microbiology

Article Title: Unveiling the diversity, ecology, and biotechnological potential of culturable marine yeasts in Western Mediterranean coastal ecosystems

Article References: Martínez-Rodrigo, A., Núñez, A., Franco, A., Madrid, M., Vicente-Soler, J., Cansado, J., & Soto, T. (2026). Unveiling the diversity, ecology, and biotechnological potential of culturable marine yeasts in Western Mediterranean coastal ecosystems. IMA Fungus, 17, Article e182209. https://doi.org/10.3897/imafungus.17.182209

Image Credits: AI Generated

DOI: 10.3897/imafungus.17.182209

Keywords: marine yeasts, Mediterranean Sea, mycology, biotechnology, microbiology, biodiversity, Mar Menor, black yeast fungi, enzymes, bioprospecting, Unveiling, diversity

The research, led by Muhammad Sarfaraz Iqbal and Hairong Cheng of Shanghai Jiao Tong University together with collaborators in Pakistan, Afghanistan and Saudi Arabia, took a transcriptome-guided approach to a problem that has long frustrated metabolic engineers. The central issue is NADPH, the reduced form of nicotinamide adenine dinucleotide phosphate. Erythrose reductase, the enzyme that performs the final step of converting erythrose into erythritol, consumes NADPH to do its job. But Yarrowia lipolytica carries a large repertoire of other NADPH-dependent oxidoreductases, enzymes that also bind and consume this cofactor for their own unrelated reactions. When erythritol production is pushed to industrial levels, these competing enzymes become silent drains on the NADPH pool, and the yields suffer. The specific contributors to this cofactor competition, however, had remained poorly defined.

To find the culprits, the team ran time-resolved RNA sequencing across 96 hours of fermentation, watching how every gene in the yeast genome changed its expression as erythritol accumulated. Two genes stood out with strikingly different temporal profiles. YALI0_F02013g, annotated as a putative pyridoxine 4-dehydrogenase, was progressively induced 3.4-fold over the course of the run, peaking at 5040 FPKM at 72 hours, precisely when erythritol production is typically at its most intense. YALI0_A19910g, annotated as a putative glycerol 2-dehydrogenase, moved in the opposite direction, being repressed 920-fold by the 96-hour mark. The fact that one candidate ramps up exactly when the product is being made, while the other is switched off as the process matures, suggested that both are functionally connected to erythritol metabolism, though in very different ways.

The expression trends were not left to stand on sequencing data alone. The researchers validated them by quantitative real-time PCR, achieving Pearson correlation coefficients greater than 0.94 between the RNA-seq and qRT-PCR measurements, a level of agreement that gives confidence the temporal profiles are real rather than artifacts of library preparation. The correlation analysis also revealed something more provocative. YALI0_A19910g expression correlated strongly negatively with erythritol titre, with a Pearson r of −0.858, meaning that as this gene’s expression fell, erythritol levels rose. YALI0_F02013g, by contrast, showed only a weak positive correlation with the product. The negative correlation for YALI0_A19910g is the kind of signal that immediately suggests a repressive relationship, as if the cell itself is trying to shut down this enzyme when erythritol production matters most.

But correlation alone cannot prove that an enzyme competes for NADPH. The team therefore turned to molecular docking, computationally fitting NADPH into the predicted three-dimensional structures of both enzymes to measure how tightly each would bind the cofactor. The results were unambiguous. YALI0_F02013g showed a predicted binding affinity of −9.8 kcal per mole for NADPH, while YALI0_A19910g came in at −8.6 kcal per mole, both figures indicating high affinity in the range typical of genuine NADPH-dependent enzymes. The docking analysis also identified conserved catalytic triads in both proteins, the characteristic arrangements of amino acids that oxidoreductases use to shuttle hydride ions from NADPH onto their substrates. In other words, both enzymes look structurally competent to grab NADPH and use it, exactly the property that would make them competitors in the cofactor economy of an erythritol-producing cell.

To rank the two candidates against each other, the researchers built an integrated prioritisation model that weighed expression dynamics, correlation with product titre, docking scores and functional annotations. The model scored YALI0_F02013g at 5.6 out of 10 and YALI0_A19910g at 5.0 out of 10, naming the putative pyridoxine 4-dehydrogenase as the higher-priority engineering target. The ranking may seem counterintuitive given the strong negative correlation of YALI0_A19910g with erythritol titre, but the logic becomes clear when flux is considered. YALI0_F02013g is induced precisely during the production window, meaning its enzyme is present and active exactly when NADPH is most precious, so its cofactor demand is the one that actually drains the pool in real time.

The team then used in silico metabolic modelling to estimate what would happen if YALI0_F02013g were repressed. The flux estimates suggest that knocking down this single gene could conserve approximately 67 percent of the competing NADPH demand, potentially increasing erythritol yield by around 14 percent. A 14 percent yield improvement may sound modest in the abstract, but in industrial biotechnology, where margins on commodity products are razor thin, a double-digit gain achieved by repressing one gene rather than rebuilding an entire pathway is the kind of result that gets attention. The authors are careful to note that these projections require experimental validation, and the modelling is presented as a hypothesis-generating exercise rather than a demonstrated outcome.

The broader significance of the study lies in its methodology. Rather than blindly overexpressing erythrose reductase or deleting genes at random, the researchers combined transcriptomics, correlation analysis, molecular docking and metabolic modelling into a single pipeline that converges on specific, testable targets. This is the kind of rational cofactor engineering that is increasingly seen as the next frontier in industrial strain development. NADPH is not just a currency for erythritol; it is required for fatty acid synthesis, for amino acid biosynthesis, for oxidative stress defence and for a host of other anabolic reactions. Every metabolic engineer who has tried to boost a NADPH-dependent product knows the frustration of raising cofactor supply only to watch competing enzymes absorb the gain. Identifying which enzymes are the biggest absorbers is the prerequisite for fixing the problem, and this study offers a template for doing exactly that.

There are also caveats worth keeping in mind. The study was conducted in a specific strain background of Yarrowia lipolytica, and the authors explicitly frame YALI0_F02013g as a candidate metabolic bottleneck in the strain examined, not a universal law of erythritol fermentation. Different industrial strains may carry different complements of oxidoreductases, and the relative importance of these two genes could shift with the carbon source, the fermentation conditions or the genetic modifications already present in a production strain. The annotations themselves are putative, based on sequence similarity rather than purified enzyme assays, so the actual substrates of YALI0_F02013g and YALI0_A19910g in vivo remain to be confirmed experimentally.

Even so, the study delivers something the field has lacked: named, ranked, structurally characterised candidates for the NADPH competition that limits erythritol yields. If experimental follow-up confirms the in silico projections, repressing YALI0_F02013g could become a standard engineering move in industrial Yarrowia strains, a single-gene edit that redirects roughly two-thirds of a competing cofactor demand toward the product. And if the pipeline itself proves robust, the same transcriptome-guided strategy could be applied to other NADPH-dependent products, from xylitol to lipids, in microbes across the industrial biotechnology landscape. The sweetest result of all may be the demonstration that the path to higher yields sometimes runs not through adding more enzyme, but through finding and silencing the quiet competitors that have been there all along.

Subject of Research: Metabolic Engineering

Article Title: Transcriptome-guided identification of YALI0_F02013g and YALI0_A19910g as candidate NADPH-dependent oxidoreductases associated with enhanced erythritol production in Yarrowia lipolytica

Article References: Iqbal, M. S., Iqbal, M. H., Babakarkhil, T., Alkhanani, A. F., Alsubhi, W. A., Anwar, Y., & Cheng, H. (2026). Transcriptome-guided identification of YALI0_F02013g and YALI0_A19910g as candidate NADPH-dependent oxidoreductases associated with enhanced erythritol production in Yarrowia lipolytica. Biotechnology for Biofuels and Bioproducts. https://doi.org/10.1186/s13068-026-02827-6

Image Credits: AI Generated

DOI: 10.1186/s13068-026-02827-6

Keywords: Yarrowia lipolytica, erythritol, NADPH, oxidoreductase, transcriptomics, molecular docking, metabolic engineering, biotechnology, YALI0_F02013g, cofactor efficiency, Transcriptome-guided, identification

The paper, authored by Jamiu Adeniyi Yusuf and Ibrahim Ayodele Yusuf of the National Institute for Legislative and Democratic Studies in Abuja, Nigeria, introduces what the authors call a Sequential Gate Framework. Its central claim is deceptively simple: one-size-fits-all funding is ineffective because the risks facing a biotechnological venture change fundamentally as it matures. A policy instrument that works brilliantly for early-stage research can be useless, or even harmful, at the commercialization stage. By matching specific financial tools to three distinct development gates, the framework aims to give green biotech the kind of de-risked investment pathway that has historically propelled other deep-technology sectors to industrial scale.

To understand why the framework is needed, it helps to grasp what makes biotechnology financially unusual. The authors distinguish two intertwined categories of risk. Technical risk asks whether a technology will work reliably; market risk asks whether it will be profitable and adopted. In biotechnology, both are amplified because the core of the technology is living. Digital products, once proven, can often be replicated and distributed at almost no additional cost. Biotechnology operates in what scientists sometimes call wetware, systems built on living organisms, enzymes, and biological processes that respond unpredictably to changes in temperature, contamination, or raw material quality. Engineered microbes designed to break down waste or capture carbon may perform beautifully in a controlled laboratory environment and then lose efficiency when fed impure, real-world feedstock.

From an investor’s perspective, that unpredictability reads as unreliability, and unreliability raises the cost of capital. The problem is compounded by the dominance of existing grey infrastructure. Economies have been built over decades around conventional chemical, mechanical, and fossil-fuel-based systems that enjoy established supply chains, regulatory familiarity, and often direct subsidies. This creates what economists call path dependency, where past investments constrain present choices. Biotechnological alternatives must also overcome the green premium, the extra cost of choosing environmentally friendly technologies when their benefits, such as cleaner ecosystems or reduced emissions, are not fully reflected in market prices. Society gains, but the investor does not always see an immediate return. Worse, biotechnology lacks standardized benchmarks for measuring bio-risk, which makes institutional due diligence difficult and pushes capital toward safer, more familiar sectors.

The Sequential Gate Framework responds by dividing the biotechnological lifecycle into three gates, each with a defined risk profile, a targeted set of policy instruments, and measurable exit criteria tied to Technology Readiness Levels. The first is the R&D gate, where the dominant challenge is fundamental technical uncertainty. Private investors are typically reluctant to fund experiments that may take years to show any commercial promise, yet this is precisely where transformative ideas need the most support. The authors recommend direct public R&D subsidies to cover experiments, equipment, and skilled personnel, alongside patent box tax regimes that reduce taxes on income generated from intellectual property. A technology exits this gate only when it reaches a laboratory proof of concept, roughly TRL 3 to 4, and secures its intellectual property through patent filings.

The second gate is where most technologies die. At the demonstration stage, the challenge shifts from whether an idea works to whether it can be scaled. A bioreactor process proven in one-liter laboratory flasks may fail catastrophically at 10,000-liter pilot scale, where temperature fluctuations, shear stress, and unrefined feedstock introduce severe operational risks. The authors call the required tools public-private partnerships and first-loss guarantees. Under a first-loss arrangement, a public institution such as a government agency or development bank agrees to absorb the initial portion of any losses, which dramatically lowers the barrier for private investors. The exit criterion here is what the authors term technical bankability: stable, repeatable production at pilot scale, more than a hundred times laboratory volume, reaching TRL 6 to 7, with biological variance reduced to a margin acceptable to institutional underwriters.

The third and final gate confronts market risk. Even a proven technology must survive competition against cheap, fossil-fuel incumbents protected by decades of infrastructure and subsidy. The framework’s centerpiece instrument here is the Contract for Difference, or CfD, a mechanism already used in renewable energy markets. The government guarantees a strike price for the product; if the market price falls below that level, the government pays the difference, and if it rises above, the producer pays back the surplus. This delivers the revenue stability needed to secure long-term commercial loans. The authors also endorse Advanced Market Commitments, in which governments or large organizations pledge in advance to purchase a specified volume of bio-based materials or carbon capture services, creating guaranteed demand that justifies scale-up investment. Exit from this gate comes at TRL 8 to 9, when a technology achieves commercial price parity with fossil-fuel incumbents and sustains market demand without direct subsidies.

The paper illustrates the mechanics with a concrete case study: the commercialization of engineered microbes for enzymatic degradation of PET plastic waste. At the R&D gate, public grants fund genetic sequencing and initial bioreactor assays until the strains demonstrate a repeatable rate of plastic depolymerization. At the demonstration gate, a public-private partnership backed by a first-loss guarantee shields investors from a pilot bioreactor crash caused by feedstock contamination, and the technology achieves technical bankability once it shows steady, high-yield enzymatic throughput over a continuous operational cycle. At the market gate, a CfD establishes a guaranteed price for bio-recycled PET monomers, protecting the firm if virgin fossil-derived PET prices plummet and enabling the long-term borrowing required for true industrial scale.

Notably, the authors do not ignore the critiques of such interventionism. They engage directly with the crowding-out hypothesis, which warns that accessible public financing may displace private venture capital and misallocate resources toward inefficient technologies. Their mitigation is structural: public instruments must be designed as strict co-investments, acting as a catalyst rather than a replacement for private equity. They also acknowledge that long-term price guarantees are vulnerable to policy capture and rent-seeking, in which entrenched industrial actors lock in government support and shift technological risk onto taxpayers. Their remedy is time-bound sunset clauses and performance-based metrics, ensuring that state support decays predictably as technologies mature and functions as a temporary bridge rather than a permanent subsidy.

Looking forward, the authors highlight two cutting-edge accelerants. Digital Twins, virtual models that replicate real bioprocesses, combined with artificial intelligence, allow firms to predict scaling behavior before committing capital, turning what was once a black box into what they describe as something closer to a glass box. This directly attacks the information asymmetry between biotechnologists and institutional investors, lowering perceived risk and speeding commercialization. For emerging economies, where deep-tech venture capital markets are nearly absent and fiscal space is constrained, the framework pivots toward multilateral development banks, blended finance, sovereign green bonds, and facilities such as the Green Climate Fund, with regional demand aggregation through mechanisms like the African Continental Free Trade Area. The broader vision is a unified global bioeconomy taxonomy that would let projects be bundled into green bonds for institutional investors. If the authors are right, the fate of green biotechnology will be decided not in the laboratory but in the architecture of finance itself, and a synchronized, sequential de-risking strategy may be the missing blueprint that turns biological promise into planetary impact.

Subject of Research: A sequential policy framework for de-risking biotechnological investments in environmental sustainability

Article Title: From lab to ledger: a sequential policy framework for de-risking biotechnological investments in environmental sustainability

Article References: Yusuf, J. A., & Yusuf, I. A. (2026). From lab to ledger: a sequential policy framework for de-risking biotechnological investments in environmental sustainability. Frontiers in Environmental Engineering, 5, Article 1844952. https://doi.org/10.3389/fenve.2026.1844952

Image Credits: AI Generated

DOI: 10.3389/fenve.2026.1844952

Keywords: biotechnology, circular bioeconomy, Valley of Death, green finance, de-risking, Contracts for Difference, public-private partnerships, Digital Twins, technology readiness levels, environmental sustainability, first-loss guarantees, policy framework

Agrobacterium is the workhorse of plant transformation, ferrying foreign DNA into plant cells through a process that has been harnessed for decades in laboratories worldwide. Dozens of engineered strains exist, each with distinct genotypes and phenotypes suited to different plant species, yet the molecular details of how the bacterium infects plants and integrates T-DNA into host genomes remain incompletely understood. Screening mutant strains and deliberately constructing engineered variants are considered key routes to unraveling these mechanisms, but the tools for doing so have been cumbersome.

Traditional Agrobacterium gene editing relies on plasmids carrying suicide genes, such as the widely used pK18mobSacB system, and typically demands two rounds of homologous recombination. In the first round, an antibiotic like kanamycin forces a tool plasmid that cannot replicate autonomously in Agrobacterium to integrate into the bacterium’s endogenous Ti or Ri plasmid through homologous recombination. In the second round, the SacB suicide gene enables negative selection against cells still carrying the plasmid, allowing researchers to isolate products of the second recombination event. The problem is that these steps yield large numbers of unmodified bacteria, driving overall modification efficiency down to very low levels.

The new method, described for the first time in detail by Yu Liu, Geng Sun, and colleagues, sidesteps much of this complexity by requiring only a single round of homologous recombination. The trick lies in turning the bacterium’s own biology against itself, so to speak: instead of relying solely on an introduced template, the researchers induce the production of endogenous T-DNA within the Agrobacterium cell and use this single-stranded DNA as the homologous repair template. Because single-stranded DNA is known to be a more effective substrate for homologous recombination than double-stranded DNA, this endogenous supply of T-DNA provides a ready-made molecular scaffold for precise editing.

Getting tool plasmids into Agrobacterium has historically been its own bottleneck, often requiring triparental mating, a three-strain conjugation dance, or expensive electroporation equipment. The Bozhou team showed that a simple freeze-thaw method suffices for introducing their plasmids into competent GV3101 cells, a convenience that could make the protocol accessible to laboratories without specialized transformation apparatus. The researchers constructed a backbone vector called pSG-SacB05, combining pBBR1 origin and replication sequences from pBBR1MCS-2, the SacB gene from pK18mobSacB, a pBR322 origin for easier plasmid preparation, a kanamycin resistance gene, and T-DNA repeat sequences with multiple cloning sites for inserting template sequences.

To demonstrate the method, the team targeted VirD2, a crucial protein in Agrobacterium-mediated genetic transformation that plays a pivotal role in transferring T-DNA from bacterium to plant cell and is essential for integrating T-DNA into the host genome. Using a tool plasmid called pSG-SacB10, they engineered simultaneous modifications at both the N-terminal and C-terminal ends of VirD2, which resides on the Ti plasmid of GV3101. The design inserted a 72-base-pair SpyTag sequence flanked by a 487-base-pair left homology arm derived from VirD1, and deleted 714 base pairs of the VirD2 C-terminus while inserting 152 base pairs of VirF sequence, all flanked by a 574-base-pair right homology arm from VirD3. A 630-base-pair N-terminal segment of VirD2 was preserved and could act as a middle homology arm.

The modification protocol unfolds across eleven carefully defined steps, beginning with vector construction using homologous arms longer than 400 base pairs, followed by freeze-thaw transformation onto plates containing rifampicin, streptomycin, and kanamycin. The critical induction phase involves culturing kanamycin-resistant clones in liquid medium adjusted to pH 5.5 with 20 milligrams per liter kanamycin and 300 micromolar acetosyringone, a phenolic compound that triggers Agrobacterium’s virulence machinery, at 25 degrees Celsius for three days. An optional extended culture step can push modification efficiency higher, and dual PCR detection with specific primer pairs confirms whether edits occurred at both target sites before the bacteria are plated on sucrose-containing medium to eliminate cells still carrying the tool plasmid.

The results revealed a striking dependence on culture conditions. When five independent modification cultures were grown at pH 5.5 with acetosyringone, four produced clear 572-base-pair and 793-base-pair electrophoretic bands indicating edits at both the upstream and downstream regions. Among 22 monoclonal colonies tested from each culture, 13.6 percent carried the downstream modification, 22.7 percent carried the upstream modification, and 4.5 percent carried both simultaneously. After secondary colony purification and SacB residue testing, all 27 sucrose-surviving colonies were SacB negative, and Sanger sequencing of four candidate modified strains confirmed their sequences matched the designed target with perfect fidelity. Kanamycin sensitivity tests further verified that no residual antibiotic resistance from the tool plasmid remained in the successfully edited bacteria.

In contrast, parallel cultures grown at pH 7.0 without acetosyringone told a different story. While 39.1 percent of colonies showed the upstream modification, not a single colony among 110 tested displayed the downstream edit, despite weak 793-base-pair signals in liquid culture. This opposite trend, with upstream modification rising while downstream modification vanished, suggests that small-fragment and long-fragment recombination operate through fundamentally different mechanisms. The researchers propose that the medium-copy-number pSG-SacB10 plasmid provides enough template for short-fragment recombination on its own, but long-fragment modification depends on the abundance of single-stranded endogenous T-DNA, which is only produced under the acidic, acetosyringone-induced conditions that activate Vir gene expression and promote T-DNA processing and stability.

The authors acknowledge that the method’s efficiency, while promising, remains modest, and they point to several contributing factors. High concentrations of streptomycin and kanamycin may suppress Vir gene expression, and more importantly, commonly used Agrobacterium strains including GV3101 carry a function-less recA mutation, removing a key enzyme in DNA repair that would normally boost recombination. The team suggests that introducing a functional recA gene will be crucial for improving efficiency and expanding the host range of the technique in future work. Even so, with nine Sanger-confirmed colonies across multiple experiments all showing 100 percent sequence accuracy, the precision of the method is clear, and given how rapidly bacteria grow, the researchers argue the approach can meet practical demands. They position the protocol as a straightforward, reproducible tool for Agrobacterium genome engineering with potential applications across biotechnology and agricultural sciences, from creating integration-less strains for cleaner plant transformation to building custom variants that illuminate the still-mysterious mechanics of nature’s own genetic engineer.

Subject of Research: A one-step homologous recombination method for precise Agrobacterium genome editing using induced endogenous T-DNA

Article Title: Precise genome modification of agrobacterium based on one-step homologous recombination via endogenous transfer DNA

Article References: Liu, Y., Sun, G., Gao, C., Gao, R., Tang, J., Wang, M., Guo, J., & Guo, R. (2026). Precise genome modification of agrobacterium based on one-step homologous recombination via endogenous transfer DNA. Acta Biochimica Polonica, 73, Article 16599. https://doi.org/10.3389/abp.2026.16599

Image Credits: AI Generated

DOI: 10.3389/abp.2026.16599

Keywords: Agrobacterium, genome editing, T-DNA, homologous recombination, VirD2, SacB, acetosyringone, plant transformation, biotechnology, GV3101, genetic engineering, homology-directed repair

Coccolithophores are unusual among microalgae because they partition captured carbon into two distinct reservoirs. Like other photosynthetic microorganisms, they fix CO2 into organic tissues through photosynthesis. But they also precipitate carbon into micrometric plates of calcium carbonate (CaCO3) called coccoliths, which together form an exoskeleton known as the coccosphere. Because the carbon locked in the mineral phase corresponds to roughly 12 percent of the CaCO3 mass, these organisms have the potential to sequester more carbon than microalgae lacking this calcifying strategy. In nature, coccolithophores account for approximately 20 percent of oceanic primary productivity and contribute up to half of the roughly 1.6 petagrams of calcite produced annually in the pelagic zone.

What makes coccolithophores especially attractive for carbon capture and storage (CCUS) is the fate of their mineral carbon. In most microalgal systems, CO2 captured during growth is eventually released back to the atmosphere when biomass degrades or is consumed. By contrast, a substantial fraction of carbon in coccolithophores precipitates as CaCO3 and is stored over long timescales in deep-sea sediments, providing a unique form of carbon sequestration among microalgae. Their complex coccolith architecture also offers potential for nanotechnology, biomedicine, and sustainable materials, promoting reuse within a circular economy.

Despite this promise, comprehensive knowledge of coccolithophore biotechnological potential remains limited. These algae typically thrive in oligotrophic ocean waters, which may have constrained research into their response to nutrient-rich conditions. However, some opportunistic taxa—such as Chrysotila roscoffensis and Gephyrocapsa huxleyi (formerly Emiliania huxleyi)—are well adapted to turbulent, eutrophic environments and seasonally form large oceanic blooms. The research team selected one strain of G. huxleyi and two strains of C. roscoffensis, chosen based on published evidence of successful cultivation in bioreactors, reports of intense natural blooms in high-nutrient environments, and high calcification capacity.

The experimental design tested three conditions: a slightly modified f/2 medium as a baseline, an enhanced macronutrient supply (N70) with nitrogen raised to 70 mg/L and phosphorus to 8 mg/L, and a carbon-replete condition (N70 + C) that added daily spikes of sodium bicarbonate (NaHCO3) delivering approximately 13 mg of carbon per liter per day. The researchers chose bicarbonate addition rather than continuous CO2 bubbling because coccolithophores are sensitive to bubbling, and bicarbonate offers a more stable dissolved inorganic carbon pool while avoiding rapid CO2 outgassing. At the observed pH values above 8, bicarbonate ions dominate the medium’s carbonate chemistry.

The results revealed a striking pattern. For all three strains, nutrient enrichment alone (N70) did not increase total mass, confirming that carbon availability remained the pivotal limiting factor. But adding bicarbonate changed everything. One C. roscoffensis strain (CS2) proved the most promising overall, exhibiting the highest dry weight of 1,172.7 ± 42.2 mg/L and total CO2 absorption of 1,210.7 ± 3.1 mg/L, compared to G. huxleyi at 569.4 ± 20.5 mg/L and 329.9 ± 11.9 mg/L respectively. The CS2 strain also maintained a stable ratio between particulate inorganic carbon (PIC) and particulate organic carbon (POC) during cultivation—an attractive trait for future large-scale applications.

The two species responded to carbon supplementation in fundamentally different ways. G. huxleyi preferentially increased calcification, producing a PIC:POC ratio of 2.1 ± 1.1 under enhanced carbon supply—unusually high compared with the maximum of 1.38 previously reported in the literature. This means the optical density increases in G. huxleyi cultures primarily reflected coccolith production rather than organic biomass growth. The researchers verified this through a clever decalcification experiment: when they dissolved the calcium carbonate from G. huxleyi cultures using acid, the measured optical density dropped from 1.75 to 0.45, confirming that detached coccoliths had biased optical readings. In contrast, C. roscoffensis strains showed substantial gains in both organic and inorganic fractions, with CS2 recording the highest organic biomass accumulation of 480.8 ± 17.3 mg/L.

Nutrient consumption data reinforced these interpretations. The C. roscoffensis strains consumed far more nitrogen than G. huxleyi under carbon-replete conditions—up to 47.4 ± 1.7 mg/L for CS2 compared to just 7.4 ± 2.2 mg/L for G. huxleyi. Phosphorus was almost completely depleted (approximately 100 percent) for both C. roscoffensis strains under N70 + C, consistent with the onset of phosphorus limitation for further growth. Statistical analysis using two-way ANOVA confirmed that organic biomass was strongly affected by strain, nutrient condition, and their interaction (all p < 0.001), with only the C. roscoffensis strains exhibiting marked biomass increases under carbon supplementation.

Notably, CS2 stored approximately 311 mg/L of CO2 in its inorganic fraction—more than the 225 mg/L calculated for G. huxleyi despite G. huxleyi’s higher PIC:POC ratio and greater coccolith production. This finding suggests that C. roscoffensis combined higher organic yield with stable inorganic carbon storage, producing the greatest overall CO2 capture among the tested strains. The researchers emphasize that their CO2 estimates are conservative, particularly for species that actively shed coccoliths like G. huxleyi, since detached plates remaining in the culture medium were not explicitly quantified.

The study underscores two practical lessons for coccolithophore cultivation: raising macronutrients alone is insufficient without concurrent increases in bioavailable carbon, and careful control of carbonate chemistry and pH is essential to balance photosynthesis against calcification. The findings also illustrate the value of strain selection within a species—CS2 showed higher nutrient conversion efficiency and greater PIC:POC stability across conditions, making it a promising candidate for forthcoming experiments. Coupled with literature reports showing promising results for related species in photobioreactors and outdoor raceway ponds, the research corroborates that the genus Chrysotila deserves further study as a candidate for large-scale applications where permanent inorganic carbon sequestration is the desired outcome. Beyond carbon storage, optimized coccolithophore productivity could unlock applications in biomedicine, construction, nanotechnology, and sustainable materials—turning these microscopic ocean architects into versatile tools for a circular economy.

Subject of Research: Coccolithophore strain screening for carbon capture and storage applications

Article Title: Harnessing coccolithophores for carbon capture and storage: exploring nutrient enrichment for future biotechnological applications

Article References: Palandri, E., Sforza, E., Ait Abbas, S., Relitti, F., De Vittor, C., Carrara, A., & Bordiga, M. (2026). Harnessing coccolithophores for carbon capture and storage: exploring nutrient enrichment for future biotechnological applications. Frontiers in Photobiology, 4, Article 1742840. https://doi.org/10.3389/fphbi.2026.1742840

Image Credits: AI Generated

DOI: 10.3389/fphbi.2026.1742840

Keywords: coccolithophores, carbon capture, microalgae, CCUS, biotechnology, calcium carbonate, Chrysotila roscoffensis, Gephyrocapsa huxleyi, Harnessing, carbon, capture, storage

The fellowship provides up to $50,000 per year for a maximum of two years, a level of support that places it among the more substantial non-federal funding options available to early-career life scientists. Since its establishment in 2015, the program has advanced SLAS’s mission to promote laboratory science and technology by giving graduate researchers the flexibility and resources to pursue impactful discoveries. More than a decade after its launch, the fellowship continues to function as a bridge between academic training and the industrial-scale automation technologies that now drive modern drug discovery and biological research.

Eligibility is defined around the core technical domains that SLAS represents. Applicants must be enrolled in a graduate degree program related to high-throughput screening, quantitative biosciences and/or drug discovery. These fields sit at the intersection of engineering, biology and data science: high-throughput screening relies on robotic liquid handling, automated microscopy and miniaturized assay formats to test thousands to millions of compounds against biological targets; quantitative biosciences apply mathematical modeling and rigorous statistical frameworks to extract reproducible insight from complex biological systems; and drug discovery integrates both approaches to identify and optimize candidate molecules that can progress toward clinical development.

The evaluation criteria reflect the society’s emphasis on both scientific merit and institutional infrastructure. Applications are assessed on the quality and originality of the proposed research, its relevance to laboratory automation and screening, and the institution’s ability to support the student’s work. That third criterion matters in practice: cutting-edge automation research requires access to robotic workstations, plate readers, liquid handlers, imaging systems and the computational pipelines needed to process large experimental datasets. A well-designed proposal paired with a laboratory that can actually execute the work is what the review process is built to identify.

For the selected fellow, the structure of the award offers a kind of scientific freedom that is increasingly rare in a constrained funding environment. Benjamin David, a past recipient from the University of Michigan, highlighted the flexibility the fellowship provided throughout his research journey. As he described it, if he found an interesting aspect of the research while progressing through his project, he had the freedom to pause and explore that new area, something he noted would not be possible with other types of grants tied to specific work. That flexibility is significant because exploratory detours in graduate research often produce unexpected findings, yet rigid grant structures typically penalize deviations from pre-specified aims.

The timing of the 2027 cycle carries particular weight. As the scientific research community faces volatility related to future research funding, this longstanding program remains an important source of support for emerging scientists. Across the life sciences, early-career researchers have watched traditional funding streams tighten and shift, making fellowship awards like this one a meaningful hedge against uncertainty. A two-year commitment of up to $100,000 can cover stipend support, research supplies, instrumentation access and conference travel, allowing a graduate student to focus on the science rather than on assembling a patchwork of short-term funding.

The technical scope of eligible research is broad within its defined boundaries. A proposal might involve developing new microfluidic devices that miniaturize assays to conserve reagents and increase throughput, or machine-learning pipelines that mine high-content imaging data for subtle phenotypic signatures of drug activity. It could address assay development for previously undruggable protein targets, automation of cell culture workflows, or novel biosensors that translate biological signals into quantifiable outputs. What unites these possibilities is the fellowship’s focus on laboratory technology as an enabling discipline: the tools and methods that let researchers ask bigger questions faster and with greater precision.

SLAS itself occupies a distinctive position in the scientific ecosystem. The society brings together academic researchers, industry scientists and technology providers around laboratory automation and screening, a community that has historically driven innovations such as 384-well and 1536-well microplate formats, acoustic droplet ejection for precise liquid transfer, and automated high-content imaging platforms. By channeling fellowship support into graduate training, SLAS invests directly in the pipeline of scientists who will design and operate the next generation of automated laboratories, where artificial intelligence, robotics and biology increasingly converge.

Graduate students, faculty members and educational institutions are encouraged to share the opportunity and apply before the deadline. Because the award is made to the institution on behalf of the student, interested applicants should coordinate early with their departments and research advisors to prepare a competitive submission that demonstrates both the originality of the proposed research and the institutional capacity to carry it out. With applications due November 9, 2026, the window for assembling proposals, securing institutional endorsement and refining research plans is now open, and for one graduate student, the 2027 fellowship could provide the resources and latitude to turn an ambitious idea into a discovery.

Subject of Research: Graduate fellowship funding for laboratory automation, quantitative biosciences and drug discovery research

Article Title: Applications accepted until November 9 for the 2027 SLAS Graduate Education Fellowship Grant

Article References: Applications accepted until November 9 for the 2027 SLAS Graduate Education Fellowship Grant. (n.d.). Original publication

Image Credits: AI Generated

DOI: Not provided

Keywords: SLAS, graduate fellowship, laboratory automation, drug discovery, high-throughput screening, quantitative biosciences, research funding, science education, fellowship grant, early-career scientists, life sciences, biotechnology

Destruxins are cyclic hexadepsipeptides, ring-shaped molecules assembled from amino acids and hydroxy acids, that more than forty known analogs call home. They are the chemical weapons that Metarhizium fungi deploy against insect hosts, disrupting immune cells and muscle function, and they also mediate the fungus’s interactions with plants. Beyond agriculture, destruxins have attracted attention in medical research for antiviral, antimicrobial, anticancer, antiangiogenic, and immunosuppressive properties. Yet the environmental triggers that switch their biosynthesis on or off have remained murky, with reports in the literature sometimes contradicting one another.

The research team, led by Pamela Vrabl at the University of Innsbruck’s Institute of Microbiology, hypothesized that light might act not as a simple trigger but as a modulator whose effects depend on the nutritional state of the culture. This idea rests on a growing body of evidence from other fungi, including Aspergillus nidulans and Penicillium species, where the same wavelength can either boost or suppress secondary metabolite production depending on the medium. To test this in Metarhizium, the team grew the production strain M. brunneum BIPESCO 5 in 4.5-liter stirred-tank bioreactors under two radically different diets: a nutrient-rich Sabouraud medium with 4 percent glucose, and a defined minimal medium in which nitrogen was the limiting nutrient.

Each medium was subjected to five illumination regimes: complete darkness, red light centered at 660 nanometers, green light at 528 nanometers, and blue light at 455 nanometers, all delivered at an intensity of 1.4 milliwatts per square centimeter, plus ultraviolet-A irradiation at 340 and 375 nanometers at 1.1 milliwatts per square centimeter. LED panels were mounted in front of the glass bioreactor vessels and shrouded in light-tight fabric to prevent cross-contamination between treatments. Irradiance was verified with calibrated photodiode power sensors and spectrometers, ensuring that differences in output could not be attributed to sloppy light measurement.

Across 21 independent bioreactor batch cultivations, each run for 90 hours with triplicate sampling at ten time points, the fungus followed the classic growth pattern of filamentous fungi under carbon excess: a lag phase, exponential growth terminated by depletion of the first essential nutrient, a prolonged deceleration phase, and finally stationary phase. In the nutrient-rich medium, phosphate ran out first; in the minimal medium, ammonium did. Destruxin production began only after exponential growth had ended, consistent with the general principle that secondary metabolites accumulate once primary growth stalls.

The first major result concerned nutrition alone. Cultures grown under nitrogen limitation produced roughly twice as much destruxin A and B in absolute terms as those in the rich medium—up to 42.9 milligrams per liter of destruxin A and 22.7 milligrams per liter of destruxin B in darkness, compared with 19.1 and 8.6 milligrams per liter respectively in the rich medium. When normalized to fungal dry mass, the gap widened dramatically: nitrogen-limited cultures produced up to five times more destruxin A and nearly seven times more destruxin B per gram of biomass than their well-fed counterparts. This aligns with the long-standing observation that reduced nitrogen availability tends to elevate secondary metabolite levels in fungi, although the authors note that the regulatory role of nitrogen in destruxin biosynthesis remains incompletely understood and that published reports on the topic vary considerably.

The second and more striking result was that light did matter—but its direction flipped with the diet. In the nutrient-rich medium, shorter wavelengths enhanced production: cultures exposed to ultraviolet-A, blue, or green light produced significantly more destruxin A than those kept in darkness or under red light, and biomass-normalized destruxin B also rose significantly with shorter wavelengths. In the nitrogen-limited medium, the same short-wavelength treatments had the opposite effect, significantly reducing destruxin A and B levels relative to darkness and red light. Red light, by contrast, behaved much like darkness in both media. Destruxin E, the third analog measured, showed no significant light response in either medium, though its concentrations fluctuated wildly between replicate cultures—possibly because the molecule hydrolyzes into a related form called destruxin E-diol.

Perhaps the most telling detail lay in the ratios. Although light exposure swung the absolute concentrations of destruxins A and B up and down, the ratio between the two remained essentially constant within each medium—roughly 70:30 in the rich medium and 60:40 under nitrogen limitation—regardless of wavelength. Statistical analysis confirmed strong positive correlations between the two metabolites across all light treatments, with Pearson correlation coefficients reaching 0.94 in the minimal medium and 0.97 when data from both media were pooled. This pattern suggests that the biosynthetic pathway for destruxins A and B, whose genes are known to be clustered in the Metarhizium genome, is governed primarily by nutritional status, while light modulates the total flux running through it rather than rerouting it toward one product or the other.

The findings place destruxin regulation alongside a broader phenomenon in fungal physiology: nutrient-dependent light responses, in which the same photic signal produces different metabolic outcomes depending on carbon and nitrogen availability. Similar crosstalk has been documented for sterigmatocystin production in Aspergillus nidulans, where changing the carbon source could reverse whether light or darkness favored toxin synthesis, and for the antibiotic xanthoepocin in Penicillium ochrochloron. For Metarhizium, whose ecological repertoire spans insect pathogen, soil saprotroph, and plant-associated endophyte, such flexibility makes evolutionary sense: the fungus encounters everything from absolute darkness underground to green-light-dominated leaf surfaces and full sun, and its chemistry presumably adapts accordingly.

For biotechnologists, the practical implications are immediate. Destruxin yields in fermentation could potentially be increased by co-optimizing nutrient formulation and illumination regime rather than treating light as an afterthought, and shifting the product profile toward a preferred analog might become feasible by tuning the two variables in concert. The authors caution that mechanistic and scale-up studies will be needed before such strategies reach the production floor, and they emphasize that rigorous standardization of both cultivation and light conditions—wavelength and intensity alike—will be essential for untangling the molecular machinery underneath. What the study establishes beyond doubt is that destruxin biosynthesis is not a simple on/off switch but a finely tuned adaptive system, one that listens to both the menu and the light before deciding what to make.

Subject of Research: Nutrient-dependent effects of light wavelength on destruxin biosynthesis in the entomopathogenic fungus Metarhizium brunneum

Article Title: Nutrient-dependent influence of red, green, blue, and UV-A light on the production of destruxin A, B, and E in Metarhizium brunneum bioreactor batch cultures

Article References: Schobert, J., Erckert, S. A., Schinagl, C. W., Schöbel, H., Strasser, H., & Vrabl, P. (2026). Nutrient-dependent influence of red, green, blue, and UV-A light on the production of destruxin A, B, and E in Metarhizium brunneum bioreactor batch cultures. Frontiers in Photobiology, 4, Article 1753405. https://doi.org/10.3389/fphbi.2026.1753405

Image Credits: AI Generated

DOI: 10.3389/fphbi.2026.1753405

Keywords: Metarhizium brunneum, destruxins, fungal photobiology, secondary metabolism, bioreactor cultivation, nitrogen limitation, light wavelength, entomopathogenic fungi, biological pest control, UV-A irradiation, biotechnology, fungal physiology

The work builds on a well-known fact of microbial life: microorganisms in nature rarely live alone. In the human gut, the Human Microbiome Project identified roughly 3,000 bacterial species coexisting in a single ecological niche, and their stability depends on constant chemical conversation. When antibiotics or dietary shifts disturb this balance, cross-feeding structures and nutrient competition shift with them, sometimes with severe health consequences. Understanding and eventually engineering such communication is therefore not just an academic curiosity — it is a prerequisite for designing stable synthetic microbial communities for industry, agriculture, and medicine.

Previous efforts had already pushed the boundaries of artificial cross-species signaling. In 2013, researchers showed that Escherichia coli could be made to talk to Bacillus megaterium using quorum-sensing peptides borrowed from Staphylococcus aureus. More recently, the Dresden group demonstrated communication in the opposite direction: yeast engineered to produce bacterial quorum-sensing peptides CSF and PhrF successfully activated reporter responses in B. subtilis. What remained missing was the reverse channel — bacteria signaling to yeast — and that is precisely what the new study delivers.

The engineering strategy exploited one of the most thoroughly characterized signaling systems in eukaryotic biology: the yeast mating pheromone pathway. Haploid Saccharomyces cerevisiae cells exist as one of two mating types, a or α, and each secretes a small peptide pheromone that binds to a specific receptor on cells of the opposite type. Receptor activation triggers a signaling cascade that induces morphological changes, cell-cycle arrest, and the expression of mating-specific genes. Among these, the FIG1 gene is switched on roughly 100-fold within just 20 minutes of receptor activation — a speed and dynamic range that makes it an ideal handle for synthetic biologists.

To turn B. subtilis into a yeast-language speaker, the team built on a signal peptide toolbox they had developed previously. The codon-optimized α-factor gene was inserted into an evaluation vector, preceded by the secretion signal peptide of the bacterial protein YfkD to route the peptide through B. subtilis’s native Sec secretion system. Expression was placed under the control of P_liaI, a promoter inducible by the antibiotic bacitracin. The final construct was integrated into the amyE locus of the protease-deficient strain WB800N, yielding the producer strain TMB6428. When induced with bacitracin, this strain secreted α-pheromone at concentrations of up to 8 nanomolar — modest by industrial standards, but consistent and robust, and sufficient for the task at hand.

On the receiving end, the researchers used a haploid yeast strain carrying deletions in BAR1 and FAR1. BAR1 encodes an aspartyl protease that degrades and inactivates α-factor, so its removal prevents the secreted signal from being destroyed before it can act. FAR1 encodes a cyclin-dependent kinase inhibitor responsible for the G1 growth arrest that normally follows pheromone exposure; deleting it keeps the sensor cells alive and dividing rather than frozen in mating mode. Into this background, the team integrated a single genomic copy of the fluorescent protein mNeongreen under control of the α-inducible FIG1 promoter. Genomic integration was necessary because B. subtilis cannot grow properly in yeast minimal medium, which would have made plasmid selection by auxotrophy impractical. The choice of mNeongreen over standard GFP was deliberate: originally discovered in the lancelet Branchiostoma lanceolatum, mNeongreen is the brightest green fluorescent protein known, resists photobleaching better than GFP, and matures faster — all advantages when the expected signal is weak.

Getting the two organisms to grow together posed its own challenges. B. subtilis doubles roughly every 30 minutes, while haploid yeast needs about 90 minutes in rich medium, so the team had to balance starting densities carefully. They settled on a ratio of approximately 1:6, with yeast at an OD600 of 0.1 and bacteria at 0.6 — a bias toward the bacterial producer that compensates for the fact that the engineered strain secretes only a single copy of α-factor, whereas yeast’s native MFα gene encodes four tandem copies processed into four separate peptides. The cultivation medium also required compromise: standard LB broth supplemented with 2% glucose satisfied the nutritional needs of both organisms at a shared incubation temperature of 31.5 °C.

The proof of principle came when mid-exponential co-cultures were induced with bacitracin. Within two hours, Western blot analysis detected mNeongreen protein in co-cultures containing the α-factor-producing bacteria, and the signal intensified at four and twenty-two hours as pheromone accumulated. Flow cytometry of 20,000 cells per sample confirmed statistically significant fluorescence in induced co-cultures, while negative controls — uninduced cultures and co-cultures with wild-type B. subtilis W168, which cannot produce α-factor — showed no detectable signal. The positive control, yeast treated with 250 nanomolar synthetic α-factor, produced brighter fluorescence than the co-culture, consistent with the bacterial secretion rate being lower than the bolus concentration used artificially. Under physiological conditions, 100 nanomolar synthetic α-factor is sufficient to induce mating in BAR1-deleted yeast, so the bacterial output, though modest, falls within a biologically meaningful range.

Perhaps the most visually striking evidence came from epifluorescence microscopy. Beyond the green glow of mNeongreen, the microscope revealed yeast cells undergoing shmoo formation — the characteristic pear-shaped morphological change that haploid cells adopt in response to authentic mating pheromone. Shmoo formation appeared about four hours after induction and increased over the following eighteen hours, demonstrating that the α-factor secreted by B. subtilis was not merely recognized at the receptor level but was fully functional, capable of driving the complete physiological differentiation program of yeast mating. The bacterial cells, meanwhile, showed no morphological changes, confirming that the signal flowed in one direction only.

The study also revealed a manageable imperfection: the P_liaI promoter exhibits slight leakiness, producing faint fluorescence in uninduced co-cultures after four and twenty-two hours. The researchers attribute this to known intrinsic transition-state induction of the LiaRS system, and note that the yeast-only positive control did not show this time-dependent increase because synthetic α-factor was added only once at the start rather than continuously. Looking ahead, the team envisions a synthetic sensor-actuator circuit in which engineered B. subtilis cells detect environmental signals — antibiotics, for example — and respond by secreting yeast pheromones that trigger the production of degradation enzymes in yeast. Since engineered S. cerevisiae capable of degrading β-lactam antibiotics in response to α-pheromone has already been described, the two pieces of such a self-regulating loop already exist. With accumulation of degradation end products potentially serving as a built-in negative feedback to shut the circuit down, the prospect of autonomous, self-contained microbial consortia — communicating across kingdoms to clean up pollutants or produce chemicals sustainably — has moved measurably closer to reality.

Subject of Research: Engineered interkingdom pheromone signaling between Bacillus subtilis and Saccharomyces cerevisiae

Article Title: Interkingdom communication 2.0: pheromone-based control between Bacillus subtilis and Saccharomyces cerevisiae

Article References: Döring, J., Vološen, T., Ostermann, K., & Wolf, D. (2026). Interkingdom communication 2.0: pheromone-based control between Bacillus subtilis and Saccharomyces cerevisiae. Applied Microbiology and Biotechnology, 110(1), Article 310. https://doi.org/10.1007/s00253-026-14069-5

Image Credits: AI Generated

DOI: 10.1007/s00253-026-14069-5

Keywords: interkingdom communication, Bacillus subtilis, Saccharomyces cerevisiae, pheromone signaling, synthetic biology, quorum sensing, mNeongreen, co-culture, FIG1 promoter, microbial consortia, biotechnology, signal transduction

The microbial workhorse at the center of the study is Methylorubrum extorquens PA1, a facultative methylotroph that naturally grows on methanol and can also assimilate ethanol. Methylotrophs have long fascinated metabolic engineers because they can consume cheap, non-food carbon sources that do not compete with agriculture. Methanol, in particular, can be generated from methane, carbon dioxide and biomass, making it an attractive platform molecule for industrial biotechnology. Ethanol, too, is produced at enormous scale from fermentation and is easy to store, transport and handle. If a robust microbial chassis could be engineered to funnel these two-carbon and one-carbon molecules into complex aromatics, the result would be a flexible carbon-recycling platform suited to a circular economy.

Yet turning that vision into reality has proven difficult, and the new study illustrates precisely why. When the researchers profiled the metabolism of M. extorquens PA1 growing on ethanol, they discovered a critical bottleneck: the bacterium was inefficiently converting acetate into acetyl-CoA, the universal metabolic currency that fuels biosynthesis. As a result, acetate accumulated outside the cells and growth on ethanol suffered. In essence, the microbe was letting a large fraction of the carbon it consumed leak out of its metabolic network before that carbon could be routed toward anything useful. Identifying this choke point was the first major insight of the work, and it framed every engineering decision that followed.

The team’s solution was to overexpress an endogenous enzyme called acetyl-CoA synthase, known as MeACS1, which directly activates acetate into acetyl-CoA. This single intervention suppressed the wasteful extracellular acetate accumulation and measurably improved the bacterium’s growth on ethanol. The result underscores a broader principle in metabolic engineering: before a production pathway can be installed, the native assimilation routes feeding it must be able to keep up with demand. In methylotrophs engineered for methanol utilization, the analogous challenge often lies in formaldehyde detoxification and the serine cycle; for ethanol, the study suggests that relieving the acetyl-CoA bottleneck is likely the critical step for efficient assimilation of this C2 feedstock.

With the entry point strengthened, the researchers turned to the synthetic part of the project: building a biosynthetic module that could deliver cinnamic acid. Cinnamic acid is produced in plants from the amino acid L-phenylalanine by phenylalanine ammonia-lyase enzymes, which catalyze the non-oxidative deamination that strips the amino group and releases the aromatic acid. The team imported the gene for one such enzyme, EncP from the marine bacterium Streptomyces maritimus, into M. extorquens PA1. Heterologous phenylalanine ammonia-lyases have been deployed in engineered microbes before, but never in this methylotrophic context, and the enzyme gave the bacterium a direct route from its own phenylalanine pool to the target product.

Supplying enough L-phenylalanine then became the next rate-limiting problem. Phenylalanine is synthesized through the shikimate pathway, a seven-step route that connects central carbon metabolism to the aromatic amino acids. Its entry substrates are phosphoenolpyruvate, drawn from glycolysis, and erythrose-4-phosphate, drawn from the pentose phosphate pathway. The researchers attacked both sides of the precursor question. They co-expressed two feedback-resistant enzymes from Escherichia coli: a mutant version of 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase, the first and most heavily regulated enzyme of the shikimate pathway, and a fusion of chorismate mutase with prephenate dehydrogenase that pushes flux from chorismate toward phenylalanine. By using feedback-resistant variants, the engineers ensured that accumulating aromatic intermediates could not slam the brakes on the very pathway they were trying to boost.

On the erythrose-4-phosphate side, the team overexpressed the endogenous transketolase of M. extorquens, MeTkt, an enzyme that helps channel carbon through the sugar-phosphate rearrangements that generate this key precursor. Together, these layered interventions shunted more carbon from ethanol assimilation through the shikimate pathway and into L-phenylalanine, and from there through the bacterial ammonia-lyase into cinnamic acid. The resulting strain, designated PAc1/pTE102-CA3, produced 1.75 milligrams per liter of cinnamic acid from ethanol in simple test-tube cultures. That figure may sound modest by industrial standards, but it represents 2.6 times the yield the same engineered network could achieve from methanol, an important demonstration that ethanol is a superior feedstock for this particular chassis.

The team then moved from test tubes to controlled fed-batch cultivation, the standard workhorse format of industrial fermentation, in which ethanol was supplied incrementally to avoid overwhelming the cells. Under these conditions the engineered bacterium accumulated 52.34 milligrams per liter of cinnamic acid, roughly a thirty-fold improvement over the tube cultures, while maintaining stable growth and without notable acetate accumulation. That combination of productivity and physiological stability is significant: many engineered strains collapse under the metabolic burden of aromatic overproduction, or excrete organic acids that poison the culture. Here, the early repair of the acetyl-CoA bottleneck appears to have paid dividends, keeping the carbon balanced as the production pathway drew heavily on central metabolism.

Why does cinnamic acid matter? The compound and its derivatives sit at the base of a large family of plant phenylpropanoids, including p-coumaric acid, caffeic acid, ferulic acid, cinnamaldehyde and a suite of polymers and pharmaceutical intermediates. A microbial route from ethanol to cinnamic acid could be extended, in principle, by adding downstream enzymes to reach these higher-value molecules. The study therefore positions M. extorquens PA1 not merely as a curiosity of methylotrophic metabolism but as a credible chassis for ethanol-based aromatic biosynthesis more broadly. It also provides a foundation for engineering other C2-assimilating bacteria, an emerging class of platform organisms that can feed on acetate and ethanol generated from gas fermentation and electrochemical carbon capture.

The work, supported by the RIKEN Center for Sustainable Resource Science, RIKEN’s Special Postdoctoral Researcher Program and a JST ACT-X grant, remains at an early stage, and the authors are candid that further engineering will be needed to push titers toward commercial relevance. Even so, the study delivers a clear technical roadmap: fix the acetyl-CoA entry point, install a proven ammonia-lyase, deregulate and amplify the shikimate and phenylalanine branches, and reinforce erythrose-4-phosphate supply. Each step is modular, and each can be iterated as new tools for editing methylotroph genomes mature. As biorefineries search for routes that decouple chemical manufacturing from fossil carbon, this small soil bacterium, now taught to drink ethanol and exude an aromatic acid, offers a compelling proof of principle for the carbon-recycling economy of the future.

Subject of Research: Metabolic engineering of Methylorubrum extorquens PA1 for cinnamic acid production from ethanol

Article Title: Metabolic engineering of Methylorubrum extorquens PA1 for cinnamic acid production from ethanol

Article References: Fujiwara, R., Mitsui, R., Akai, G., Tanaka, Y., & Shirai, T. (2026). Metabolic engineering of Methylorubrum extorquens PA1 for cinnamic acid production from ethanol. Biotechnology for Biofuels and Bioproducts. https://doi.org/10.1186/s13068-026-02833-8

Image Credits: AI Generated

DOI: 10.1186/s13068-026-02833-8

Keywords: Methylorubrum extorquens, metabolic engineering, cinnamic acid, ethanol, methylotroph, shikimate pathway, acetyl-CoA synthase, phenylalanine ammonia-lyase, biorefinery, biotechnology, RIKEN, renewable chemicals

Between 2023 and 2024, researchers collected dead and decaying twigs bearing fungal fruiting bodies from macadamia plantations in Yunnan Province in southwestern China and Chiang Mai Province in northern Thailand. These two regions are significant for different reasons. China first introduced macadamia in the 1970s and now accounts for more than 60 percent of the world’s cultivated macadamia area, with Yunnan alone representing 88 percent of that national footprint, making it the largest macadamia-growing region on Earth. Thailand, where the crop was trialed experimentally as early as 1953, has seen rapid expansion of plantations in the north, particularly around Chiang Mai, as domestic consumption and export potential have grown.

Back in the laboratory, the team combined classical morphological examination with modern molecular systematics to work out exactly what they had collected. Under compound and stereomicroscopes they documented the fine details of fungal anatomy: the size and shape of the flask-like fruiting bodies known as ascomata, the layered structure of their walls, the form of spore-producing sacs called asci, and the dimensions, septation, and surface texture of the ascospores themselves. For the molecular work, DNA was extracted from pure cultures, and six genetic loci were amplified and sequenced, including the internal transcribed spacer region (ITS), the nuclear large and small ribosomal subunits (nrLSU and nrSSU), and the protein-coding genes tef1-α, tub2, and rpb2. These sequences were aligned, combined, and analyzed using maximum likelihood and Bayesian inference methods, generating phylogenetic trees for each fungal genus with strong statistical support at the critical nodes.

The results were striking. Eighteen fungal taxa were identified across ten genera and seven families, all within the phylum Ascomycota. Five of these proved to be new to science: Dothiorella lignicola, Lasiodiplodia macadamiae, Palmiascoma macadamiae, Xylochrysis macadamiae, and Xylochrysis yunnanensis. Each was formally described and named according to the International Code of Nomenclature for algae, fungi, and plants, with type specimens deposited in herbaria in China and Thailand and living cultures preserved in culture collections. In several cases, the new species were separated from their closest relatives by a combination of subtle morphological differences and substantial genetic distances. Xylochrysis macadamiae, for example, differs from its nearest known relatives in having larger, semi-immersed fruiting bodies and rough-walled ascospores, along with nucleotide differences of around 7 to 12 percent in key gene regions.

Thirteen previously described species were also recorded from macadamia for the first time, spanning genera such as Sporidesmium, Crassiparies, Chromolaenicola, Montagnula, Pseudochaetosphaeronema, and Helminthosporium. Several of these records were also new geographic findings, extending known distributions across national borders. Perhaps most intriguingly, the sexual reproductive structures of three species, Chromolaenicola ananasi, Pseudochaetosphaeronema siamense, and Helminthosporium nanjingense, had never been observed before; this study documented them for the first time, filling significant gaps in mycological knowledge. Eight of the ten genera encountered had never previously been reported from macadamia anywhere in the world.

One species had a tangled taxonomic backstory. Dothiorella lignicola had been described earlier under a different name, but that earlier name was formally rejected because its original description was based on an incorrect host, species name, etymology, and DNA sequences, a violation of Article 52.1 of the nomenclatural code. The replacement name D. lignicola, referring to the fungus’s wood-dwelling habit, now stands, anchored by a Thai collection whose tef1-α gene sequences differ from its closest relatives by more than 20 base pairs, alongside consistent morphological distinctions such as larger, ovoid conidia.

Identifying the fungi was only half of the study. Because saprobic fungi survive by secreting enzymes that dismantle tough plant polymers, the researchers wanted to know what these macadamia colonizers could actually digest. Twenty pure cultures representing the 18 species were screened on agar plates for four lignocellulolytic enzymes: cellulase, xylanase, mannanase, and laccase. For the first three enzymes, plates containing carboxymethyl cellulose, xylan, or locust bean gum were flooded with Congo red after incubation; where enzymes had broken down the substrate, a clear halo appeared around the fungal colony. Laccase activity was detected instead on guaiacol agar, where the enzyme oxidizes the compound to produce a brownish-red color change. Enzyme output was quantified with an enzyme potency index, calculated from the difference between the halo diameter and the colony diameter, and all experiments were run in triplicate with statistical analysis by one-way ANOVA and Duncan’s multiple range test.

The enzyme screening revealed a community of capable biomass degraders, but with clear patterns of specialization. Xylanase was the most frequently detected activity, produced by 17 isolates representing 15 species, followed by cellulase, found in 14 isolates from 12 species, and mannanase, found in 10 isolates from nine species. Laccase, the oxidative enzyme needed to attack the chemically stubborn lignin fraction of plant cell walls, appeared in only five isolates. The single strongest xylanase producer was the newly described Xylochrysis macadamiae, with an enzyme potency index of 3.50, followed by Sporidesmium tropicale at 3.10. In the cellulase category, two Helminthosporium species dominated, with H. puerense reaching an index of 2.25. Mannanase activity peaked in Pseudochaetosphaeronema puerense at 1.98, while Sporidesmium tropicale led laccase production at 2.20. Only three isolates, Dothiorella lignicola and two Lasiodiplodia species, showed no detectable activity for any enzyme, possibly because their enzyme production fell below the assay’s detection limit or because they preferentially consumed simple sugars available in the medium.

The predominance of xylanase makes ecological sense. Hemicellulose, the xylan-rich matrix that surrounds cellulose fibers in plant cell walls, is less crystalline and more chemically accessible than cellulose itself, so decomposer fungi typically attack it first, gaining access to the more recalcitrant components afterward. Lignin, encrusted around the cellulose in hardwood twigs, requires specialized oxidative enzymes such as laccases and peroxidases, which relatively few ascomycetes produce in quantity. The observed enzyme profile of the macadamia community mirrors this well-known decomposition sequence, and the four isolates that produced all four enzymes tested, including Crassiparies quadrisporus, Pseudochaetosphaeronema chiangraiense, and Sporidesmium tropicale, stand out as particularly versatile degraders.

Beyond their ecological role in recycling carbon, nitrogen, and phosphorus through decaying orchard wood, these fungi have potential commercial value. Lignocellulolytic enzymes are workhorses of industrial biotechnology, used in converting plant biomass to biofuels, in food and feed processing, in pulp and paper manufacture, in textile production, and in environmental bioremediation. The authors suggest that the next steps should include quantitative enzyme assays, optimization of culture conditions, and purification and biochemical characterization of the most promising enzymes. For now, the study’s core message is clear: even beneath one of the world’s most intensively studied nut crops, entire communities of fungi, including species unknown to science, have been quietly waiting on dead twigs, and some of them carry enzymatic toolkits worth far more than their weight in nuts.

Subject of Research: Diversity, taxonomy, and lignocellulolytic enzyme production of saprobic microfungi associated with macadamia in China and Thailand

Article Title: New species and additional records of saprobic microfungi associated with Macadamia in China and Thailand and their lignocellulitic enzyme production

Article References: Zhang, X., Karunarathna, S. C., Tibpromma, S., Senwanna, C., Kumla, J., Du, T.-Y., Elgorban, A. M., Alfagham, A. T., Filimban, F. Z., Dai, D.-Q., & Suwannarach, N. (2026). New species and additional records of saprobic microfungi associated with Macadamia in China and Thailand and their lignocellulitic enzyme production. MycoKeys, 141, 217-281. https://doi.org/10.3897/mycokeys.141.209886

Image Credits: AI Generated

DOI: 10.3897/mycokeys.141.209886

Keywords: macadamia, saprobic fungi, new species, taxonomy, phylogenetics, lignocellulolytic enzymes, xylanase, cellulase, laccase, biotechnology, China, Thailand