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Heterogeneity in Respiratory Electron Transfer and Adaptive Iron Utilization in a Bacterial Biofilm

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Heterogeneity in Respiratory Electron Transfer and Adaptive Iron Utilization in a Bacterial Biofilm ARTICLE https://doi.org/10.1038/s41467-019-11681-0 OPEN Heterogeneity in respiratory electron transfer and adaptive iron utilization in a bacterial biofilm Yuxuan Qin 1,2, Yinghao He 2, Qianxuan She 2, Philip Larese-Casanova3, Pinglan Li1 & Yunrong Chai2 In Bacillus subtilis, robust biofilm formation requires large quantities of ferric iron. Here we show that this process requires preferential production of a siderophore precursor, 2,3- dihydroxybenzoate, instead of the siderophore bacillibactin. A large proportion of iron is fi fi 1234567890():,; associated extracellularly with the bio lm matrix. The bio lms are conductive, with extra- cellular iron potentially acting as electron acceptor. A relatively small proportion of ferric iron is internalized and boosts production of iron-containing enzymes involved in respiratory electron transfer and establishing strong membrane potential, which is key to biofilm matrix production. Our study highlights metabolic diversity and versatile energy generation strate- gies within B. subtilis biofilms. 1 Beijing Advanced Innovation Center for Food Nutrition and Human Health, Key Laboratory of Functional Dairy, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China. 2 Department of Biology, Northeastern University, Boston, MA 02115, USA. 3 Department of Civil and Environmental Engineering, Northeastern University, Boston, MA 02115, USA. Correspondence and requests for materials should be addressed to P.L. (email: [email protected]) or to Y.C. (email: [email protected]) NATURE COMMUNICATIONS | (2019) 10:3702 | https://doi.org/10.1038/s41467-019-11681-0 | www.nature.com/naturecommunications 1 ARTICLE NATURE COMMUNICATIONS | https://doi.org/10.1038/s41467-019-11681-0 ost bacteria are capable of forming surface-associated, and Δpps, Fig. 1a, b). Surprisingly, a ΔdhbA mutant deficient in architecturally complex communities, known as the siderophore bacillibactin production was very defective in M fi 1,2 fi bio lms . The Gram-positive bacterium Bacillus sub- bio lm formation (Fig. 1b). Bacillibactin is a catechol siderophore tilis forms morphologically complex colony biofilms on solid that binds to ferric iron with an extremely high affinity22. The surface and pellicle biofilms at the air/liquid interface, in spe- role of bacillibactin in iron acquisition is well known, but its role cialized biofilm-inducing media3,4. Cell differentiation occurs in in biofilm formation has not been studied in B. subtilis until very the B. subtilis biofilm both spatially and temporally, and is recently23. regulated by integrative signaling pathways and influenced by Bacillibactin biosynthesis relies on the dhbA-F operon encod- various environmental factors4–6. Cell differentiation generates ing enzymes that carry out four sequential reactions converting 3- phenotypically distinct cell types within the biofilm, such as chorismate to bacillibactin (Fig. 1a, c)24. Since dhbF encodes the matrix producers, swimmers, competent cells, antibiotic produ- most important enzyme involved in the final reaction in cers, and so on. Each cell type possesses unique features and bacillibactin biosynthesis (Fig. 1c), a deletion mutant of dhbF functionality, yet different cell types complement with each other (ΔdhbF) was constructed and the biofilm phenotype of the in that the entire community shows synergy and cooperation6,7. mutant was examined. To our surprise, the mutant did not In summary, complexity and heterogeneity is a hallmark feature exhibit any noticeable biofilm defect (Fig. 1d). Puzzled by this of the B. subtilis biofilm. observation, non-polar in-frame deletion mutations for each Iron is an essential nutrient element for growth and a cofactor individual genes in the dhbA-F operon were constructed and for various enzymes and proteins involved in key biological biofilm phenotypes by those in-frame deletion mutants were processes in the bacteria, in particular cellular metabolism and examined. As shown in Fig. 1d, ΔdhbA, ΔdhbB, and ΔdhbC all energy generation8. In the natural environments, iron availability had a very severe biofilm defect. In contrast, ΔdhbE formed is very limited due to extremely low solubility of ferric iron (Fe3+) robust pellicle biofilms, similar to that of ΔdhbF. Since DhbE and under neutral pH (10−18 M)8. Bacteria thus developed various DhbF are known to be only involved in the last step of strategies to uptake iron from the environment. When intracel- bacillibactin biosynthesis, which (together with DhbB) converts lular levels of iron are low, bacteria turn on multiple iron uptake 2,3-dihydroxybenzoate (DHB) to bacillibactin, a trimeric ester of systems for iron acquisition. In B. subtilis, those iron acquisition 2,3-dihydroxybenzoate-glycine-threonine (Fig. 1c), these results systems are composed of transporters for the import of elemental suggest that bacillibactin is not important; rather, the precursor iron, ferric citrate, ferrioxamine, ferrichrome, and petrobactin9.A DHB plays an essential role in biofilm formation. To further test key regulator, Ferric uptake regulator (Fur), is responsible for the this idea, a chemical complementation was performed by regulation and derepression of the above iron acquisition systems supplementing pure DHB (1 μgml−1) to the biofilm media. This when iron is limited10,11. Fur also regulates genes involved in the time, ΔdhbA, ΔdhbB, and ΔdhbC all formed robust, wild-type-like biosynthesis of a B. subtilis siderophore, bacillibactin (DhbA- pellicle biofilms (MSgg + DHB, Fig. 1d). We also noticed that in CEBF), and a cognate uptake system (FeuABC-YusV)12,13. order to completely rescue the biofilm defect of ΔdhbA, ΔdhbB, Bacillibactin is a catechol siderophore and binds iron with an and ΔdhbC to the wild-type level, supplementation of about extremely high affinity, allowing B. subtilis cells to acquire very 60 μM (equals to about 1 μgml−1) DHB was needed, implying low amounts of iron from the environment. In most pathogens, that wild-type cells produced and secreted DHB sufficiently. This siderophores are essential for the bacteria to survive in the host or implication was also supported by a recent study, in which environment14–16. On the other hand, excessive intracellular iron secreted DHB amounts were directly measured23. DHB is able to could be toxic due to its involvement in the Fenton’s reaction, bind ferric ion, albeit at a lower binding affinity compared to that which generates non-selective free radicals that can damage of bacillibactin9. A similar DHB, 3,4-dihydroxybenzoate, or various biological molecules such as protein, lipid, and DNA17. protocatechuic acid, produced by Corynebacterium glutamicum, Thus, in bacteria, iron homeostasis plays an important role in is a well-studied iron chelator25,26. maintaining an appropriate range of intracellular iron levels to satisfy the normal need for metabolism and growth8,15. Recent studies indicate importance of iron not only in free- dhbA-F genes are differentially expressed in biofilm cells.To living bacteria but also in biofilm formation18–20. In biofilm- learn more about DHB biosynthesis, we decided to investigate the forming bacteria such as Pseudomonas aeruginosa and Staphy- regulation of the dhbA-F operon under biofilm conditions by lococcus aureus, high levels of iron were shown to be important quantitative real-time PCR (RT-qPCR). To do so, a pair of pri- for robust biofilm formation18,19, suggesting a common and mers were designed to probe transcription for each of the dhbA, important role of iron in biofilm development. In B. subtilis, dhbB, dhbC, and dhbE genes, while three pairs were designed to robust biofilm formation also demands unusually high levels of probe dhbF transcription since the size of dhbF (~7.13 kb) is ferric iron, hundreds fold higher than needed for normal growth3, almost 60% of the entire operon (Fig. 2a). Results from RT-qPCR yet the exact reason is less clear. In this study, we aim to address showed that in cells collected from pellicle biofilms, expression of the above question. We provide mechanistic details of why all genes in the dhbA-F operon was detected except for dhbF excessive iron is needed for robust biofilm formation in B. subtilis (black bars, Fig. 2b). In fact, all three pairs of primers failed to and uncover an adaptive strategy for acquisition and utilization of detect the transcription of dhbF (# indicates below detection limit, large amounts of iron during B. subtilis biofilm development. Fig. 2b). This result was quite interesting to us for two reasons. First, differential expression of the genes within the dhbA-F operon was observed, which could provide genetic basis for Results strong production of DHB (over bacillibactin) during biofilm 2,3-Dihydroxybenzoate is essential for biofilm formation.Ina formation. In a recent study, Rizzi et al.23 quantified the pro- previous study21, we investigated the role of various non- duction of DHB and bacillibactin during pellicle biofilm forma- ribosomal peptides (NRPs) in B. subtilis in biofilm formation. tion in B. subtilis and found that DHB was produced about 10- Many of those NRPs had dispensable roles in biofilm formation fold higher than bacillibactin. Second, the dhbA-F operon was fi 21 fi μ as assessed by the bio lm phenotypes of the mutants . For readily expressed in the iron-rich bio lm medium (50 M FeCl3). instance, two mutants deficient in either bacillaene or fengycin This seemed to contradict to the knowledge that the dhbA-F biosynthesis showed little noticeable biofilm phenotypes (Δpks
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