Biology subjects

Lozano-Andrade, C. N.

Publications and source records attributed to Lozano-Andrade, C. N..

10 recordsLinked to original sources

bioRxiv2026

Beyond Antimicrobial Activity: Soil Bacteria Reveal a Biotransformation Fate for the Lanthipeptide Nisin

Natural products are central mediators of microbial interactions. However, once released into the environment, they also become available for neighboring microorganisms capable of degrading and modifying them through biotransformation. These biotransformations may fundamentally reshape metabolomes and influence community behavior, yet our understanding of these processes remains limited. Ribosomally synthesized peptides are particularly compelling in this context because their structural complexity and potent antimicrobial activity coexist with the potential to yield essential nutrients and reduced bioactivity through biotransformation. Identifying the pathways underlying these biotransformations is essential for understanding mechanisms that support microbial coexistence and nutrient recycling in soil microbiomes. Here, we used nisin as a model peptide to investigate biotransformation by soil bacteria. Selective isolation under nisin-rich, carbon-limited conditions yielded two Gram-negative isolates, Burkholderia stabilis and Pseudomonas fragi. Using growth assays and liquid chromatography-mass spectrometry, we found that both isolates grow in the presence of nisin while biotransforming and depleting the peptide. Burkholderia stabilis completely converted nisin through sequential cleavage of the C-terminus, hinge region and lanthionine ring C, whereas Pseudomonas fragi showed more limited processing restricted to the C-terminal region. Although these biotransformations dismantled structural features required for nisins antimicrobial activity, the intrinsic resistance of both isolates suggests a role beyond detoxification. We further detected nisin biosynthetic genes in the source environment, supporting nisins ecological relevance and suggesting that these bacteria may participate in its turnover in soil. Together, these findings reveal extensive microbial processing of nisin and support a role for antimicrobial peptide recycling in soil microbiomes. ImportanceNatural products are often studied through the lens of their biological activities, but much less attention has been paid to what happens to these molecules after they enter complex microbial communities. Using the lantibiotic nisin as a model system, we show that soil bacteria can extensively biotransform and deplete an antimicrobial peptide through extracellular enzymatic activity. The presence of both nisin-producing and nisin-biotransforming microorganisms in the same soil environment suggests that antimicrobial peptides may be continuously produced and recycled in nature. Our findings highlight biotransformation as an important but underexplored process governing the persistence, turnover, and ecological roles of microbial natural products.

microbiology↗

bioRxiv2025

Penicillium hordei acidification precipitates Bacillus subtilis lipopeptides to evade inhibition

Interkingdom interactions are crucial for community and ecosystem functioning, however secondary metabolites mediating interactions between plant beneficial bacteria and fungi remain understudied. Penicillium and Bacillus species can individually suppress soilborne phytopathogens and promote plant growth. Here, we showed that Penicillium hordei and Bacillus subtilis co-culture led to precipitation of B. subtilis lipopeptides, observed as white line in agar. Metabolomic analysis revealed B. subtilis triggered enhanced production of fungal terrestric acid and its biosynthetic intermediates, which induced lipopeptide precipitation to prevent P. hordei inhibition by chemical inactivation and physical barrier formation. Besides lipopeptide precipitation, terrestric acid-mediated acidification progressively reduced production of antifungal plipastatins. The lack of lipopeptide production permitted P. hordei to invade and overgrow B. subtilis colony. We demonstrated that the white line phenomenon was conserved among closely related fungi via secretion of terrestric, fulvic or barceloneic acids. Furthermore, terrestric acid at specific concentrations acted as a universal metabolite that drives B. subtilis lipopeptide precipitation even in distantly related fungi. This study provides new insights into acidification as a fungal defensive strategy that may promote co-existence with beneficial bacteria exhibiting strong antagonistic potential, thereby contributing to the formation of a stable rhizosphere community.

microbiology↗

bioRxiv2024

Coupling of secondary metabolite production in Bacillus subtilis

Although not essential for their growth, the production of secondary metabolites increases the fitness of the producing microorganisms in their natural habitat by enhancing establishment, competition and nutrient acquisition. The Gram-positive soil-dwelling bacterium, Bacillus subtilis produces a variety of secondary metabolites. Here, we investigated the regulatory relationship between the non-ribosomal peptide surfactin and the sactipeptide bacteriocin subtilosin A. We discovered that B. subtilis mutants lacking surfactin production exhibited higher production of subtilosin A compared to their parental wild-type strain. Additionally, spatial visualization of B. subtilis production of metabolites demonstrated that surfactin secreted by a wild-type colony could suppress subtilosin A production in an adjacent mutant colony lacking surfactin production. Reporter assays were performed using mutants in specific transcriptional regulators that confirmed the role of ResD as an activator of the subtilosin A encoding BGC, while removal or Rok and AbrB repressors increased expression of the BGC that was further enhanced by additional deletion of surfactin, suggesting that a so far unidentified regulator might mediate the influence of surfactin on production of subtilosin A. Our study reveals a regulatory influence of one secondary metabolite on another, highlighting that the function of secondary metabolites could be more complex than its influence on other organisms and interactions among secondary metabolites could also contribute to their ecological significance. ImportanceSecondary metabolites play an important role in the life of microorganisms facilitating their fitness in the environment, including competing against other microorganisms, interacting with their host or environment, and allowing expansion in their environment. However, secondary metabolites also function as cue molecules influencing gene expression between and within species. Here, we describe that the non-ribosomally synthesized peptide surfactin repress the production of ribosomally synthesized and post translationally modified peptide, subtilosin A in Bacillus subtilis, revealing an ecological interaction between two secondary metabolites that could potentially influence the biocontrol efficiency of B. subtilis strain that depends on the production of these secondary metabolites against plant pathogen microorganisms.

microbiology↗

bioRxiv2024

Surfactin facilitates the establishment of Bacillus subtilis in synthetic communities

Soil bacteria are prolific producers of a myriad of biologically active secondary metabolites. These natural products play key roles in modern society, finding use as anti-cancer agents, as food additives, and as alternatives to chemical pesticides. As for their original role in interbacterial communication, secondary metabolites have been extensively studied under in vitro conditions, revealing a multitude of roles including antagonism, effects on motility, niche colonization, signaling, and cellular differentiation. Despite the growing body of knowledge on their mode of action, biosynthesis, and regulation, we still do not fully understand the role of secondary metabolites on the ecology of the producers and resident communities in situ. Here, we specifically examine the influence of Bacillus subtilis-produced cyclic lipopeptides (LPs) during the assembly of a bacterial synthetic community (SynCom), and simultaneously, explore the impact of LPs on B. subtilis establishment success in a SynCom propagated in an artificial soil microcosm. We found that surfactin production facilitates B. subtilis establishment success within multiple SynComs. Surprisingly, while neither a wild type nor a LP non-producer mutant had major impact on the SynCom composition over time, the B. subtilis and the SynCom metabolomes are both altered during co-cultivation. Overall, our work demonstrates the importance of surfactin production in microbial communities, suggesting a broad spectrum of action of this natural product.

microbiology↗

bioRxiv2023

Resistance towards and biotransformation of Pseudomonas-produced secondary metabolites during community invasion

The role of antagonistic secondary metabolites produced by Pseudomonas protegens in suppression of soil-borne phytopathogens has been clearly documented. However, their contribution to the ability of P. protegens to establish in soil and rhizosphere microbiomes remains ambiguous. Here, we use a four-species synthetic community to determine how antibiotic production contributes to P. protegens community invasion and identify community traits that alter the abundance of key P. protegens antimicrobial metabolites (DAPG, pyoluteorin and orfamide A). Surprisingly, mutants deficient in antimicrobial production caused similar perturbations in community composition compared to invasion by wildtype P. protegens. Intriguingly, while pyoluteorin and orfamide A are secreted at levels toxic to individual bacterial strains, community-level resistance circumvents toxicity. Here, we identify the underlying mechanism by which the cyclic lipopeptide, orfamide A, is inactivated and degraded by Rhodococcus globerulus D757 and Stenotrophomonas indicatrix D763. Altogether, the demonstration that the synthetic community constrains P. protegens invasion by detoxifying its antibiotics may provide a mechanistic explanation to inconsistencies in biocontrol effectiveness in situ.

microbiology↗

bioRxiv2023

Competition for iron shapes metabolic antagonism between Bacillus subtilis and Pseudomonas

Siderophores have long been implicated in sociomicrobiology as determinants of bacterial interrelations. For plant-associated genera like Bacillus and Pseudomonas, siderophores are well known for their biocontrol functions. Here, we explored the functional role of the Bacillus subtilis siderophore bacillibactin in an antagonistic interaction with Pseudomonas marginalis. The presence of bacillibactin strongly influenced the outcome of the interaction in an iron-dependent manner. The bacillibactin producer B. subtilis restricts colony spreading of P. marginalis by repressing the transcription of histidine kinase-encoding gene gacS, thereby abolishing production of secondary metabolites such as pyoverdine and viscosin. By contrast, lack of bacillibactin restricted B. subtilis colony growth in a mechanism reminiscent of a siderophore tug-of-war for iron. Our analysis revealed that the Bacillus-Pseudomonas interaction is conserved across fluorescent Pseudomonas spp., expanding our understanding of the interplay between two genera of the most well-studied soil microbes.

microbiology↗

bioRxiv2023

Enhanced niche colonisation and competition during bacterial adaptation to a fungus

Bacterial-fungal interactions (BFIs) influence microbial community performance of most ecosystems and elicit specific microbial behaviours, including stimulating specialised metabolite production. Using a simple BFI system encompassing the Gram-positive bacterium Bacillus subtilis and the black mould fungus Aspergillus niger, we established a co-culture experimental evolution method to investigate bacterial adaptation to the presence of a fungus. In the evolving populations, B. subtilis was rapidly selected for enhanced production of the lipopeptide surfactin and accelerated surface spreading ability, leading to inhibition of fungal expansion and acidification of the environment. These phenotypes were explained by specific mutations in the DegS-DegU two-component system. In the presence of surfactin, fungal hyphae exhibited bulging cells with delocalised secretory vesicles and RlmA-dependent cell wall stress induction. Increased surfactin production typically enhances the competitive success of bacteria against fungi, which likely explains the primary adaption path in the presence of A. niger. Significance statementExperimental evolution and co-cultivation of different microbes are important and useful techniques for discovering new traits and unravelling cryptic regulatory connections. We combined these methods by evolving the Gram-positive bacterium Bacillus subtilis in the presence of the black mould fungus Aspergillus niger that were previously shown to engage in an intricate and physical interaction. Both are ubiquitous, environmentally and industrially relevant model microbes in the colonisation of rhizo- and endosphere and in the production of enzymes. Our results demonstrate how laboratory adaptation can be exploited to improve biocontrol properties of bacteria.

microbiology↗

bioRxiv2022

Establishment of a transparent soil system to study Bacillus subtilis chemical ecology

Bacterial secondary metabolites are structurally diverse molecules that drive microbial interaction by altering growth, cell differentiation, and signaling. Bacillus subtilis, a Gram-positive soil-dwelling bacterium, produces a wealth of secondary metabolites, among them, lipopeptides have been vastly studied by their antimicrobial, antitumor, and surfactant activities. However, the natural functions of secondary metabolites in the lifestyles of the producing organism remain less explored under natural conditions, i.e. in soil. Here, we describe a hydrogel-based transparent soil system to investigate B. subtilis chemical ecology under controllable soil-like conditions. The transparent soil matrix allows the growth of B. subtilis and other isolates gnotobiotically and under nutrient-controlled conditions. Additionally, we show that transparent soil allows the detection of lipopeptides production and dynamics by HPLC-MS and MALDI-MS imaging, along with fluorescence imaging of 3-dimensional bacterial assemblages. We anticipate that this affordable and highly controllable system will promote bacterial chemical ecology research and help to elucidate microbial interactions driven by secondary metabolites.

microbiology↗

bioRxiv2020

Phages weaponize their bacteria with biosynthetic gene clusters

Bacteria produce many different specialized metabolites, which are encoded by biosynthetic gene clusters (BGCs). Despite high industrial relevance owing to broad bioactive potential of these metabolites, their ecological roles remain largely unexplored. We analyze all available genomes for BGCs of phage origin. The BGCs predominantly reside within temperate phages infecting certain commensal and pathogenic bacteria. Nearly all phage BGCs encode bacteriocins, which appear to serve as a strong proxy for phage specificity. Using the gut-associated bacterium Bacillus subtilis, we demonstrate how a temperate phage equips its host with a functional BGC, providing it with a competitive fitness advantage over close relatives. Therefore, certain temperate phages use BGCs to weaponize their bacteria against close relatives, leading to evolutionary benefits from lysogeny to the infected host, and hence, to the phage itself. Our study is a large step towards understanding the natural role of specialized metabolites, as well as mutualistic phage-host relationships.

microbiology↗

bioRxiv2020

Secondary metabolites of Bacillus subtilis impact soil-derived semi-synthetic bacterial community assembly

Secondary metabolites provide Bacillus subtilis with increased competitiveness towards other microorganisms. In particular nonribosomal peptides (NRPs) have an enormous antimicrobial potential by causing cell lysis, perforation of fungal membranes, enzyme inhibition or disruption of bacterial protein synthesis. This knowledge was primarily acquired in vitro when B. subtilis was competing with other microbial monocultures. However, our understanding of the true ecological role of these small molecules is limited. In this study, we have established soil-derived semi-synthetic mock communities containing 13 main genera and supplemented them with B. subtilis P5_B1 WT, its NRP deficient strain sfp or single NRP mutants incapable of producing surfactin, plipastatin or bacillaene. 16S amplicon sequencing revealed that the invasion of NRP-producing B. subtilis strains had no major impact on the bacterial communities. Still, the abundances of the two genera Lysinibacillus and Viridibacillus were reduced. Interestingly, this effect was diminished in communities supplemented with the NRPs deficient strain. Growth profiling of Lysinibacillus fusiformis M5 exposed to either spent media of the B. subtilis strains or pure surfactin indicates the sensitivity of this strain towards the biosurfactant surfactin. Our study provides a more in-depth insight into the influence of B. subtilis NRPs on semi-synthetic bacterial communities and helps to understand their ecological role.

microbiology↗