Carl-Eric Wegner

The in situ relevance of biosynthetic gene clusters (BGCs) remains poorly understood. We apply meta-omics to characterize BGC diversity and activity along a peatland redox gradient. From seven metagenomes, we recover 9,694 BGCs, spanning diverse taxa, most lacking close relatives in reference databases, indicating extensive novelty. Only 9-27% of this potential is expressed in situ, with Acidobacteriota, despite moderate repertoires, accounting for over half of all BGC transcription. Talented producers with up to 24 clusters are largely silent, and expression is inversely related to BGCs per genome. Acidobacteriota, specialized in complex carbon processing potential express a larger proportion of their BGC repertoires than BGC-rich Pseudomonadota, which had shorter doubling times and lower potential for complex carbon processing. At the genome level, the degree of BGC expression is most strongly coupled to carbohydrate-active enzyme expression, particularly glycoside hydrolases, linking secondary metabolism to active carbon processing in peatland microbes. Thus, although BGCs are widespread, BGC expression in situ is integrated into the carbon-cycling activity of individual taxa rather than a shared physiological state.

Poorly soluble lanthanide minerals are a challenge for the sustainable extraction of lanthanides as key resources for the green energy transition and lanthanide‐dependent microbial metabolism. Lanthanide‐utilising bacteria are widespread in the environment. Their preference for light lanthanides requires differentiation mechanisms that enable downstream utilisation. Whether lanthanide discrimination occurs during access, mobilisation, uptake, or intracellular processing is mostly unknown and likely controlled by habitat and bioavailability. Using Beijerinckiaceae bacterium RH AL1 and combining transcriptomics, analytics, and electron microscopy, we studied microbial lanthanide mobilisation and uptake from different lanthanide minerals, an alloy, and pure lanthanide compounds. Strain AL1 is a facultative methylotroph that depends on light lanthanides for methanol oxidation and known for periplasmic lanthanide accumulation. We could show that strain AL1 grew with all tested lanthanide sources and selectively enriched light lanthanides independent of the source, lanthanide content, and the proportion of light lanthanides. Transcriptomics revealed that the source type significantly influenced gene expression. Lanthanide discrimination in Beijerinckiaceae bacterium RH AL1 is a multilayered process, likely rooted in the complementary action of chelation, uptake, and periplasmic storage. Strains that mobilise lanthanides and increase their bioavailability can transform mineral‐bound lanthanides into shared resources for microbial communities, with implications for sustainable lanthanide use.

The closely related M. extorquens strains PA1 and AM1 carry near-identical metallophore synthesis gene clusters, yet AM1 produces the 4-hydroxy benzoate (4HB)-capped chelator methylolanthanin (MLL), while PA1 produces mainly 3,4-dihydroxy benzoate (3,4-DHB)-capped rhodopetrobactin (RPB) siderophores. We trace this divergence to a single tandem-duplication frameshift that inactivates AsbF, the dehydratase supplying the catecholate precursor 3,4-DHB. Unable to make 3,4-DHB this way, AM1 instead caps the scaffold with the ubiquitous primary metabolite 4-HB to yield MLL (a comparatively weak iron chelator), consistent with a weaker O-CAS assay readout when comparing AM1 to PA1. We further show that PA1 produces not only micromolar RPB B (with minor RPB A) but also nanomolar amounts of MLL and mixed-cap congeners. This directly confirms the promiscuity of the biosynthetic machinery and highlights how AM1 can still assemble a chelator despite lacking the catecholate precursor. The mixed aromatic cap chelator RPB B-O was characterized by HRMS and NMR and is named methylopetrobactin B. Further, by synthesizing 13C labelled RPB B and supplying it to PA1 we ruled out by mass spectrometry that MLL is a decomposition product of or that it is produced from RPB B. Finally, a feeding experiment of 3,4-DHB and AM1, revealed that this strain can make RPB B with externally supplied precursor. Taken together, this study demonstrates, that a single loss-of-function lesion (rendering one enzyme non-functional in vivo) can redirect a conserved pathway toward an alternative chelator.

Methylorubrum species are prominent members of the plant phyllosphere, where they are exposed to fluctuating environmental conditions, including intense ultraviolet (UV) radiation. To mitigate such stressors, these bacteria commonly synthesise carotenoids as an oxidative protection. In this study, we investigated the carotenoid production of two closely related methylotrophic strai ns, Methylorubrum extorquens PA1 and AM1 (short PA1 & AM1), with a particular focus on the influence of iron availability. We identified and comprehensively structurally characterised the main carotenoid produced by both strains by using ultraviolet–visible (UV– Vis ) spectroscopy, high-performance liquid chromatography (HPLC), high-resolution mass spectrometry (HRMS) with collision-induced dissociation (CID), ion mobility–mass spectrometry (IM–MS), nuclear magnetic resonance (NMR) spectroscopy, and ultrafast transient absorption (TA) spectroscopy. We show that both strains produce, unaffected by the iron availability, the same carotenoid, identified as 4-[2-O-11Z-octadecenoyl-β-D-glucopyranosyl]-4,4′-diapo-Ψ,Ψ-carotene-4,4′-dioate. However, the iron availability strongly influenced the carotenoid production making it a tuneable parameter for boosting bacterial carotenogenis in biotechnological settings.

Poorly soluble lanthanide minerals pose challenges for both a sustainable extraction of lanthanides as key resources for decarbonization and lanthanide-dependent microbial metabolism. Microbial use of lanthanides is widespread, yet bacteria’s preference for light lanthanides requires differentiation mechanisms that enable downstream utilization. Whether lanthanide discrimination occurs during access, mobilization, uptake, or intracellular processing is mostly unknown and likely controlled by habitat and bioavailability. We studied microbial lanthanide mobilization and uptake from different lanthanide minerals, an alloy, and pure lanthanide compounds. Beijerinckiaceae bacterium RH AL1 served as a model organism for an integrated approach combining transcriptomics, analytics, and electron microscopy. This facultative methylotroph depends on light lanthanides for methanol oxidation and forms periplasmic lanthanide deposits. AL1 grew with all tested lanthanide sources and selectively enriched light lanthanides independent of source type, overall lanthanide content, and the proportion of light lanthanides. Transcriptomics revealed that the type of lanthanide source significantly influenced gene expression beyond lanthanide utilization. Lanthanide discrimination in Beijerinckiaceae bacterium RH AL1 is a multilayered process rooted in the complementary action of chelation, uptake mechanisms, and periplasmic storage. Adaptations that increase lanthanide bioavailability transform mineral-bound lanthanides into shared resources within microbial communities, with implications for sustainable lanthanide use.

The in situ relevance of biosynthetic gene clusters (BGCs) remains poorly understood. We applied meta-omics to characterize BGC diversity and activity along a peatland redox gradient. From seven metagenomes, we recovered 9,694 BGCs spanning diverse taxa, most lacking close relatives in reference databases, indicating extensive novelty. Only 9-27% of this potential was expressed in situ, with Acidobacteriota, despite moderate repertoires, accounting for over half of all BGC transcription. Talented producers with up to 24 clusters were largely silent, and expression was inversely related to BGCs per genome. Acidobacteriota and other oligotrophic taxa expressed most of their BGCs, whereas copiotrophic Pseudomonadota expressed a few, suggesting that life-history and stress-responsive regulation govern activation. PKS and terpene BGCs expression was enriched in genomes expressing markers of aerobic respiration and stress, whereas RiPPs were associated with antimicrobial resistance, stationary phase and stress. Thus, although BGCs are widespread, environmental constraints determine which are realized.

Growing evidence has shown that, apart from local environmental factors, changes in landscape-level factors by accelerated land-use change can also shape soil pathogenic fungal diversity. However, the global representativeness of such patterns remains unclear. Here, we assess how pathogenic fungal diversity in 511 soil samples worldwide responds to landscape factors, including landscape complexity index based on eight landscape metrics and quantity of different land cover types across six spatial scales (i.e., surrounding landscape, 250 m to 10,000 m radii from the sampling coordinate). We find that while soil variables explain over half of the variance, pathogenic fungal alpha diversity increases with landscape complexity and crop cover proportion, but decreases with grass and tree cover proportion, together explaining 23.4% of the total variance. Landscape factors have weaker impacts on beta diversity, explaining 13.0% of the variance. Across spatial scales, grassland ecosystems exhibit increasingly stronger responses to landscape variables compared to forest ecosystems. Landscape factors have a higher relative contribution to root-associated fungi than leaf/fruit/seed-associated fungi. Our results emphasize the importance of local factors and the complementary role of landscape patterns in shaping global soil pathogenic fungal distributions, highlighting scale-dependent effects across ecosystems and fungal functional groups.

Pseudomonas alloputida KT2440 is a ubiquitous, soil-dwelling bacterium that metabolizes recalcitrant and volatile carbon sources. The latter is utilized by two redundant, Ca- and lanthanide (Ln)-dependent, pyrroloquinoline quinone-dependent alcohol dehydrogenases (PQQ ADH), PedE and PedH, whose expression is regulated by Ln availability. P. alloputida KT2440 is the best-studied non-methylotroph in the context of Ln-utilization. Combined with microfluidic cultivation and single-cell elemental analysis, we studied the impact of light and heavy Ln on transcriptome-wide gene expression when growing P. alloputida KT2440 with 2-phenylethanol as the carbon and energy source. Light Ln (La, Ce, and Nd) and a mixture of light and heavy Ln (La, Ce, Nd, Dy, Ho, Er, and Yb) had a positive effect on growth, whereas supplementation with heavy Ln (Dy, Ho, Er, and Yb) exerted fitness costs. These were likely a consequence of mismetallation and non-utilizable Ln interfering with Ln sensing and signaling. The measured amounts of cell-associated Ln varied between elements. Gene expression analysis suggested that the Ln sensing and signaling machinery, the two-component system PedS2R2 and PedH, responds differently to (non-)utilizable Ln. We expanded our understanding of the lanthanide (Ln) switch in P. alloputida KT2440, demonstrating that it adjusts the levels of pedE and pedH transcripts based on the availability of Ln. We propose that the usability of Ln influences the bacterium’s response to different Ln elements. IMPORTANCE: The Ln switch, the inverse regulation of Ca- and Ln-dependent PQQ ADH in response to Ln availability in organisms featuring both, is central to our understanding of Ln utilization. Although the preference of bacteria for light Ln is well known, the effect of different Ln, light and heavy, on growth and gene expression has rarely been studied. We provide evidence for a fine-tuning mechanism of Ca- and Ln-dependent PQQ ADH in P. alloputida KT2440 on the transcriptome level. The response to (non-)utilizable Ln differs depending on the element. Ln commonly co-occur in nature. Our findings underline that Ln-utilizing microbes must be able to discriminate between Ln to use them effectively. Considering the prevalence of Ln-dependent proteins in many microbial taxa, more work addressing Ln sensing and signaling is needed. Ln availability likely necessitates different adaptations regarding Ln utilization.

Pseudomonas alloputida KT2440 is a ubiquitous, soil-dwelling bacterium that metabolizes recalcitrant and volatile carbon sources. The latter are utilized by two redundant, Ca- and lanthanide (Ln)-dependent, pyrroloquinoline quinone-dependent alcohol dehydrogenases (PQQ ADH), PedE and PedH, whose expression is regulated by Ln availability. P. alloputida KT2440 is the best-studied, non-methylotroph in the context of Ln-utilization. We report the most comprehensive differential gene expression analysis, to date, for any Ln-utilizing microbe. Combined with microfluidic cultivation and single-cell elemental analysis, we studied the impact of light and heavy Ln when growing P. alloputida KT2440 with 2-phenylethanol as the carbon and energy source. Light Ln (La, Ce, Nd) and a mixture of light and heavy Ln (La, Ce, Nd, Dy, Ho, Er, Yb) had a positive effect on growth, while supplementation with heavy Ln (Dy, Ho, Er, Yb) exerted fitness costs. These were likely a consequence of mismetallation and oxidative stress. Gene expression analysis showed that the Ln sensing and signaling machinery, the two-component system PedS2R2 and PedH, responds differently to (non-)utilizable Ln. We broadened the understanding of the Ln switch in P. alloputida KT2440 and could show that it operates as a dimmer switch, modulating the pool of PQQ ADH dependent on Ln availability. Determined quantities of cell-associated Ln suggest a role for Ln beyond alcohol oxidation. The usability of Ln governs the response of P. alloputida KT2440 to different Ln elements. Importance: The Ln switch, the inverse regulation of Ca- and Ln-dependent PQQ ADH dependent on Ln availability in organisms featuring both, is central to our understanding of Ln utilization. Although the preference of bacteria for light Ln is well known, the effect of different Ln, light and heavy, on growth and gene expression has rarely been studied. We provide evidence for a dimmer switch-like regulation of Ca- and Ln-dependent PQQ ADH in P. alloputida KT2440, and could show that the response to (non-)utilizable Ln differs depending on the element. Ln commonly co-occur in nature. Our findings underline that Ln-utilizing microbes must be able to discriminate between Ln to use them effectively. Considering the prevalence of Ln-dependent proteins in many microbial taxa, more work addressing Ln sensing and signaling is needed. Ln availability likely necessitates different adaptations regarding Ln utilization.

Lanthanides (Ln) are the most recently described life metals and are central to methylotrophy (type of metabolism in which organic substrates without carbon-carbon bonds serve as carbon and energy source) in diverse taxa. We recently characterized a novel, Ln-dependent, and Ln-accumulating methylotroph, Beijerinckiaceae bacterium RH AL1, which requires lighter Ln (La, Ce, Nd) for methanol oxidation. Starting from two sets of incubations, one with different La concentrations (50 nM and 1 µM) and one with different Ln elements [La, Nd, or an Ln cocktail (containing Ce, Nd, Dy, Ho, Er, Yb)], we could show that La concentration and different Ln elements strongly affect gene expression and intracellular Ln accumulation. Differential gene expression analysis revealed that up to 41% of the encoded genes were differentially expressed. The effects of La concentration and Ln elements were not limited to Ln-dependent methanol oxidation but reached into many aspects of metabolism. We observed that Ln influence the flagellar and chemotactic machinery and that they affect polyhydroxyalkanoate biosynthesis. The most differentially expressed genes includedlanM, coding for the well-characterized lanthanide-binding protein lanmodulin, and a glucose dehydrogenase gene linked to the conversion of β-D-glucose to D-glucono-1,5-lactone, a known potential metal chelator. Electron microscopy, together with RNAseq, suggested that Beijerinckiaceae bacterium RH AL1 can discriminate between Ln elements and that they are differently taken up and accumulated. The discrimination of Ln and links between Ln and various aspects of metabolism underline a broader physiological role for Ln in Beijerinckiaceae bacterium RH AL1.IMPORTANCE: Since its discovery, Ln-dependent metabolism in bacteria attracted a lot of attention due to its bio-metallurgical application potential regarding Ln recycling and circular economy. The physiological role of Ln is mostly studied dependent on presence and absence. Comparisons of how different (utilizable) Ln affect metabolism have rarely been done. We noticed unexpectedly pronounced changes in gene expression caused by different Ln supplementation. Our research suggests that strain RH AL1 distinguishes different Ln elements and that the effect of Ln reaches into many aspects of metabolism, for instance, chemotaxis, motility, and polyhydroxyalkanoate metabolism. Our findings regarding Ln accumulation suggest a distinction between individual Ln elements and provide insights relating to intracellular Ln homeostasis. Understanding comprehensively how microbes distinguish and handle different Ln elements is key for turning knowledge into application regarding Ln-centered biometallurgy.