Mass Spectrometry Uncovers the Role of Surfactin as an Interspecies

Feb 14, 2019 - ... products that serve as territorial markers. This new attribute as an attractant of selected microbes and the conversion into a dete...
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Mass spectrometry uncovers the role of surfactin as an interspecies recruitment factor Tal Luzzatto-Knaan, Alexey V. Melnik, and Pieter C. Dorrestein ACS Chem. Biol., Just Accepted Manuscript • DOI: 10.1021/acschembio.8b01120 • Publication Date (Web): 14 Feb 2019 Downloaded from http://pubs.acs.org on February 15, 2019

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Graphical abstract 78x42mm (300 x 300 DPI)

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Mass spectrometry uncovers the role of surfactin as an interspecies

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recruitment factor

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Tal Luzzatto-Knaan1*, Alexey V. Melnik1 and Pieter C. Dorrestein1*

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1Collaborative

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Pharmaceutical Sciences, University of California San Diego, CA 92093, USA.

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*Address correspondence to Tal Luzzatto-Knaan, [email protected] or Pieter

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Dorrestein, [email protected]

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Keywords: Mass spectrometry, Bacillus subtilis, Surfactin, Paenibacillus dendritiformis,

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Microbial ecology

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Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and

ABSTRACT Microbes use metabolic exchange to sense and respond to their changing environment.

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Surfactins, produced by Bacillus subtilis are extensively studied for its attributed role in biofilm

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formation, biosurfactant properties and antimicrobial activity, affecting the surrounding

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microbial consortia. Using mass spectrometry, we reveal that Paenibacillus dendritiformis,

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originally isolated with B. subtilis, is not antagonized by the presence of surfactins, and is

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actually attracted to it. We demonstrate here for the first time, that P. dendritiformis is also

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actively degrading surfactins produced by B. subtilis, and accumulating the degradation products

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that serve as territorial marker. This new attribute as an attractant of selected microbes and the

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conversion it into a deterrent, highlights the diverse role natural products have in shaping the

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environment and establishing mixed communities.

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INTRODUCTION Microbes often must respond and react to neighboring organisms. For this reason,

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microbes have evolved to produce niche specific chemistries to interact with their ecological

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environment such as soil, ocean water, or hosts such as plants, animal or even human cells 1.

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Humans have taken advantage of these molecules produced by microbes. They form our

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treatments for excessive iron accumulation (e.g. desferrioxamine) 2, prevent organs from being

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rejected during transplants (e.g. rapamycin) 3, we use them as antibiotics (e.g. erythromycin) 4, to

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treat insect pests of crops (e.g. bialaphos) 5, and as industrial biosurfactant (e.g. surfactin) 6 Such

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potent bioactivities have revolutionized medicine, biotechnology and agriculture 7, 8. Therefore,

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exploring the chemistry behind microbial interactions are of great interest. However, it is clear

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that these molecules, in the context of their ecological niche, must serve different and diverse

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functions. Such molecules are produced as a way to interact and influence the behavior and

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phenotype of self and neighboring cells or create an environmental niche favorable for

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supporting their life cycle 9. This metabolic exchange, the release of chemical cues and active

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natural products, may vary based on specific interactions 1.

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In this study, we focused on the chemical interplay between two Firmicutes by advanced

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mass spectrometry techniques, in order to unravel the diverse functionality of molecules in a

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defined ecological niche (Supplemental table S1). Bacillus subtilis, a well-studied and wide

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spared microbe, is also the eminent producer of surfactins 10. Surfactins are cyclic lipopeptides

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attributed with the natural functions in antagonism towards other organisms, motility on

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semisolid surfaces, attachment to surfaces and triggering biofilm formation 11-15. The other

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organism is the pattern forming Peanibacillus dendritiformis that considered to be highly

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responsive to small changes in the environment, which are expressed by visible changes in its 2 ACS Paragon Plus Environment

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social motility, known as swarming patterns 16. As a single colony, P. dendritiformis forms radial

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dendritic swarming patterns on solid surfaces 17-20. This extraordinary swarming capability

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makes P. dendritiformis an ideal model for characterizing interactions with its surrounding.

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Though some of these patterns have been widely described 16, 18, only little is known about the

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chemistry affecting its motility 17.

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Both species are ubiquitous and are commonly found in soil, plants and rhizosphere,

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insects, and many other environments 21. In fact, P. dendritiformis was initially isolated with B.

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subtilis and classified as such - meaning they are naturally interacting 22. Here we demonstrate a

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new interpretation for the chemical “give and take” between these two co-occurring microbes.

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RESULTS AND DISCUSSION

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P. dendritiformis is chemo-attracted to B. subtillis

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We observed that when P. dendritiformis is co-inoculated with Bacillus subtilis NCIB

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3610 at various distances (three colonies of each microbe at 1, 2, 3 cm apart), a distinct change in

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the swarming pattern of P. dendritiformis occurs. The first P. dendritiformis colony that senses

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the presence of B. subtilis, changed its swarming phenotype towards and around the B. subtilis

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colony forming tight dendrites (Figure 1A). In this case, the unusual phenotype was only

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detected for the closest P. dendritiformis colonies (1 cm apart) while the more distant colonies,

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that were 2 and 3 cm apart were halted, and did not exhibit this phenotype. Not only attracted

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and accelerated movement of P. dendritiformis around the adjacent colony of B. subtilis, the

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same P. dendritiformis colony enclosed the more distant B. subtilis colonies, preventing

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additional P. dendritiformis sibling colonies to engage in interaction (Fig 1A). Interactions

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among kin-species were recently reported, relating the various phenotypes to phylogeny 23. 3 ACS Paragon Plus Environment

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While B. subtilis sibling colony swarms merge, other non-kin strains form distinct boundaries

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between swarms often affected by the release of antimicrobial compounds 23. Conversely, kin-

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recognition has been investigated for P. dendritiformis in great detail and this kin-inhibition, as

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we see here by halting the more distant sibling colonies (Fig 1A), is attributed to the production

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of a sibling lethal factor that prevents swarms from merging and restricting colonial territory 24,

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25.

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response to non-kin-neighboring microbial interactions 23-25. Previous work with Paenibacillus

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vortex suggested airborne substances as inducers of motility, benefiting the non-motile microbe

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Xanthomonas perforans 26. However, the increased motility phenotype of P. dendritiformis was

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not a result of volatile molecules, as co-inoculation on partitioned plates cultured under identical

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conditions presented no such swarming (Fig 1B). This indicated that the attractive chemical

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signal is more likely transferring through the media.

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Figure 1: Paenibacillus dendritiformis (Pd) and Bacillus subtilis NCIB 3610 (Bs3610) grown in

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co-culture. (A) Colonies inoculated at 1,2,3 cm apart on peptone media and (B) on a partitioned

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plate.

Yet, the attraction of P. dendritiformis as shown here, has not been reported before in

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Targeting chemo-attractive molecules by mass spectrometry To understand the nature of the attraction of P. dendritiformis towards B. subtilis at the

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chemical level, we employed orthogonal mass spectrometry-based methods, imaging mass

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spectrometry (IMS) and molecular networking (Figure 2) 8. To visualize the molecules that are

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present in the agar, the co-culture was transferred onto a matrix assisted laser

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desorption/ionization (MALDI) target plate, covered with an organic matrix to assist in the

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desorption and ionization of the molecules and subjected to MALDI-IMS. Imaging mass

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spectrometry enabled the visualization of the spatial distribution of molecules associated with

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this interaction. In IMS, the selected parent mass ions of the molecules are displayed by pseudo-

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color, based on their intensity in each pixel creating a spatial image 27, 28. Optical images are then

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overlaid by such ion image distributions to understand the relationships between molecules with

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respect to the observed phenotypes. The IMS experiments also included the following controls;

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growth medium alone, culture of P. dendritiformis, two adjacent sibling cultures of P.

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dendritiformis, and B. subtilis alone (Figure 2A). The interaction and controls were all placed on

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the same target plate so that the relative intensities can be directly compared. Representative

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signals not found in the background agar are shown in Figure 2B. Some signals were observed in

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only one of the mono-cultures, while others were found only when interacting. Of these m/z

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248.5 and 659.5 were only detected on the P. dendritiformis colonies themselves and decreased

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or even disappeared to below detectable levels when P. dendritiformis was co-cultured adjacent

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to B. subtilis. The signal at m/z 427.6, although present in the background media, was also

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observed to increase around the colony of P. dendritiformis, while m/z 615.8 was B. subtilis

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colony associated and m/z 714.2 was observed most intensely at the outer edges of the B. subtilis

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colony. The m/z 1058.9 was associated with the B. subtilis colony as well as secreted into the 5 ACS Paragon Plus Environment

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agar but depleted as this signal gets closer to P. dendritiformis. At the same time there were

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several signals observed only in the interaction and not in any of the controls. Examples include

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m/z 622.4, and 658.4. The ions at m/z 615.8, 714.2 and 1058.9 are consistent with polyglutamates

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and the surfactin, previously detected in B. subtilis by imaging mass spectrometry 29. None of the

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other ions had been previously investigated.

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Figure 2: Bacillus subtilis NCIB 3610 (Bs3610) and Paenibacillus dendritiformis (Pd)

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interactions investigated by mass spectrometry-based approach combining IMS and tandem MS. 6 ACS Paragon Plus Environment

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(A) Experimental setup of interactions includes: media blank, Pd single colony and Pd vs. Pd

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sibling interaction, Bs3610 single colony and Bs3610 vs. Pd co-culture interaction. (B) Matrix

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assisted laser desorption/ionization imaging mass spectrometry (MALDI-IMS) demonstrating the

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spatial distribution of selected ions of Pd and Bs3610 in mono and co-culture. (C) Tandem mass

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spectrometry of corresponding samples analyzed by GNPS molecular networking. Node fill

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color represents the sample origin: Red= Bs3610, Blue/Cyan= Pd, Pd vs. Pd, Purple= Bs3610 vs.

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Pd, Gray> 2 groups.

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Surfactin and associated products are involved in P. dendritiformis attraction to B.

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subtilis

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Because parent masses provide little structural insight, microbial IMS was complemented

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with liquid chromatography based untargeted tandem mass spectrometry (LC-MS/MS). For this

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experiment, the corresponding interaction and controls (growth medium alone, P. dendritiformis

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and B. subtilis) were extracted with EtOAc/MeOH (1:1) and subjected to LC-MS/MS analysis.

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During the elution, the ions were subjected to fragmentation in a data dependent fashion. The

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untargeted mass spectrometry was followed by molecular networking in the crowd-sourced

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analysis infrastructure called Global Natural Products Social (GNPS) molecular networking

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(Figure 2C) 30. Molecular networking clusters the spectral relationships of the fragmented ions

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that were detected by mass spectrometry from which one can infer the structural relationships of

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the molecules and enables direct dereplication against public reference spectra 8, 30-32. We set out

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to inspect the molecular families -a cluster of related spectra- in this molecular network in more

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detail (Figure 3). For most ions, no spatial information was available due to the different

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ionization methods of MALDI and electron spray ionization (ESI). However, one of the families

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was linked to two different surfactins (m/z 1022.6767, 1036.6944, corresponding to C14, C15,

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[M+H]+ surfactins) (Figure 3A-C), based on manual inspection of all the neighboring nodes, for

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which no spectral references were matched. These nodes were found to be related by CH2

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additions or deletions, resulting from substitutions seen by promiscuous adenylation domain

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specificities of the surfactin synthetases, and were annotated as C13-C17 surfactins and

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derivatives (Supplemental figure S1) 9-11, 29. Spatial mapping of the surfactins observed in the B.

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subtilis control sample by IMS revealed they have the same distributions (Figure 3B). This

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molecular family also had four purple nodes (representing mainly [M+H2O+2H]+2), indicating

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that these derivatives were observed at interaction (Figure 3). The possibility is that by

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interaction, surfactin is altered in some fashion such as hydrolysis, as similarly reported before

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when B. subtilis was cultured with a Streptomyces sp. 29.

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An additional molecular family was found associated with the interaction between P.

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dendritiformis and B. subtilis. The corresponding IMS spatial distribution of m/z 608.4, 622.4,

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636.4, 650.4 ions suggest that they are related to P. dendritiformis (Figure 3D-F). Notably,

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neither one of these masses are detected in monoculture swarming and sibling colony interaction

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controls of P. dendritiformis, nor detected in the monoculture of B. subtilis. Further examination

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of the fragmentation pattern generated by tandem MS showed two putative Leu/Ile mass shifts

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and an additional fragment differing by 14Da between the four compounds, suggesting a

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lipopeptidic nature. A deeper analysis uncovered a perfect match of these structures to the

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lipopeptidic tails of surfactins produced by B. subtilis (C13, C14, C15, C16) differing by the

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variable length of the acyl chain (Figure 3F,) 11. 8 ACS Paragon Plus Environment

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Figure 3: Annotation and spatial pattern of surfactin and surfactin-like lipopeptidic tail

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molecular families in Bacillus subtilis NCIB 3610 and Paenibacillus dendritiformis interactions.

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Upper panel: (A) Molecular network of detected molecules and annotation of surfactins by

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match to the GNPS spectral library. (B) Spatial distribution of surfactin ions [M+Na]+ by

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MALDI IMS. (C) Tandem MS spectra and structure of surfactins C14, C15. Selected nodes

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highlighted in colored circle corresponding to the spatial pattern pseudo color. Lower panel: (D)

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A molecular family of molecules detected in co-culture from LC-MS/MS molecular network (E)

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Spatial distribution of selected ions (m/z 608.4,622.4, 636.4 and 650.4 [M+Na]+) by MALDI

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IMS. (F) Detected tandem MS spectra and structure of surfactins-like lipopeptidic tail. Selected

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nodes highlighted in colored circle corresponding to the spatial pattern and annotated lipid tail.

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Node fill color represents the sample origin: Red= Bs3610, Blue/Cyan= Pd, Pd vs. Pd, Purple=

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Bs3610 vs. Pd, Gray> 2 groups.

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The IMS image overlay of surfactin C15 produced by B. subtilis and the corresponding

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lipopeptide tail (m/z 636.4 [M+Na]+ ) provides a complementary image (Figure 4A) suggesting

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that these molecules are anticorrelated. The residual peptidic fragment of the breakdown m/z

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459.28 [M+H]+ that is common among the four surfactins was annotated by b and y ions of the

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MS spectrum (Figure 4B/C). The IMS spatial distribution of the peptidic product m/z 481.3

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[M+Na]+ correlated with degradation of the lipopeptidic tails (Supplemental figure S2). The

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overlap of the surfactin degradation products with the region of increased motility led us to ask

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the following two questions: First, is surfactin involved in the increased motility and the

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attraction of P. dendritiformis when it is adjacent to B. subtilis? and secondly, can P.

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Figure 4: Complementary analysis of surfactin C15 degradation products. (A) IMS

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complementary image of surfactin C15 as produced by Bacillus subtilis and its lipopeptidic m/z

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636.42 [M+Na]+ and peptidic m/z 459.28 [M+H]+ degradation products. (B) Extracted ion

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chromatogram of the four lipopeptidic tails and the common peptidic product. (C) Annotation of

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the peptidic product by b and y ions.

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Surfactin act as an attractant and is modified by P.dendritiformis To test the hypothesis that surfactins are involved in the increased motility phenotype, we

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examined the swarming response of P. dendritiformis towards the wild type strain B. subtilis

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NCIB 3610 versus the mutated B. subtilis NCIB 3610 strain that lacks surfactin synthetase

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capabilities (∆srfAA). ∆srfAA is deficient in the first loading domain of the biosynthetic pathway

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of surfactins disabling the production of all structurally related surfactins 28, 33. Our results reveal

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an attraction of P. dendritiformis to the wild type Bs3610 and no attraction to the non-producing

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mutant (Figure 5A, Supplemental figure S3A, B). These results are consistent with the

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interpretation that surfactin is a key molecule required for this phenotype. However, mutation

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may result in additional effects on other molecules that are present. Therefore, we set out to

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determine if surfactin on its own is able to induce the motility behavior in P. dendritiformis. A

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disc diffusion assay with commercially available B. subtilis surfactin C15 (Sigma-Aldrich CAS#

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24730-31-2, 0.01mg used based on previous reports for effective dose 17, 34, 35) and a dose-

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response assay (Supplemental figure S3C-E), recapitulated the P. dendritiformis’s motility

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phenotype (Figure 5B,C). To verify that P. dendritiformis was responsible for the degradation of

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surfactin, we extracted disc diffusion assay plates and found the corresponding degradation

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products as in Figure 4 (by parent mass and MS/MS) to be present only when P. dendritiformis

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was present (Supplemental figure S4). These results support our hypothesis, confirming the

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necessity of surfactin for enhanced motility and its active degradation by P. dendritiformis.

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Figure 5: Paenibacillus dendritiformis (Pd)

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attraction to surfactin produced by Bacillus

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subtilis NCIB 3610 (Bs3610). (A) Mono and

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co-inoculation of Pd with the wild type

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Bs3610 and the surfactin deficient mutant

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(∆srfAA). (B) Disc diffusion assay of Pd with

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Bacillus subtilis commercial surfactin (Sigma-

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Aldrich CAS# 24730-31-2). (C) Co-

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inoculation of Pd with Bs3610 vs. commercial

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surfactin. Scale bar represent 5mm.

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The role of surfactin and its degradation products IMS experiments, show that the degradation products of surfactins are incorporated into

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the P. dendritiformis colony (Figure 3E) and not accumulated at the interaction zone 29 nor

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directly consumed as a carbon source 36. Therefore, we wondered how these molecules affect P.

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dendritiformis, and if they are associated with the enhanced motility as seen with the intact

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surfactin. By MS guided purification we have isolated both the lipopeptidic product (m/z

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614.4364 [M+H]+ , 636.4199 [M+Na]+ ) and the peptidic residue m/z 459.2830 [M+H]+ and

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tested the effect of these products on P. dendritiformis colonies response. The two degradation

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products had different affects on the swarming pattern of P. dendritiformis. While the peptidic

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tail showed no change in pattern similar to the negative control, the lipopeptidic tail restricted the

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growth around the applied area (Growth inhibition p value of p=0.000303 measured based on

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inhibition diameter by pairwise t-test) (Figure 6). Because we see no evidence of bactericidal or

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bacterial growth effects and see these exact molecules incorporated into the colonies, it is not

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expected to be toxic to P. dendritiformis. Initially, we suspected that these lipopeptide products

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might be assisting with swarming of P. dendritiformis, therefore, introducing these products

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would be attractive as well. However, the “pre-cut” product (i.e. the lipopeptidic tail) seem to

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lose its attractive properties following degradation and is not an attractive agent on its own and is

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not promoting swarming. Thus, it appears that modification of the attractant (surfactin) becomes

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a restricting territorial marker (lipopeptidic degradation product) for P. dendritiformis colonies.

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Figure 6: The effect of surfactin degradation products on the swarming of Paenibacillus

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dendritiformis (Pd). (A) Diffusion assay with purified degradation products of surfactin and (B)

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solvent and commercial surfactin C15 (Sigma-Aldrich CAS# 24730-31-2) as reference control.

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Assay was performed in triplicates. Swarm inhibition measured based on inhibition diameter, p

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value of p=0.000303 by pairwise t-test.

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Bacillus subtilis, though studied for decades, is still considered a treasure trove for the

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potential of its antimicrobial chemical arsenal 37. Surfactins are a great example of these vastly

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explored molecules, due to their biosurfactant and antimicrobial properties attributed to their

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ability to interact with membranes 10, 34, 38. These attributes are essential for the plant growth

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promoting rhizobacteria (PGPR) properties of B. subtilis that shape the microbial communities in

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the rhizosphere 10, 11, 39. Modification of antimicrobial agents have been described before by

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enzymatic inactivation of specific functional groups such as in β-lactamases resistance 40, 41. 15 ACS Paragon Plus Environment

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Modification of B. subtilis surfactins was also proposed as part of a defense mechanism of

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Streptomyces sp. Mg1 to detoxify the antimicrobial effect of surfactin, by secreting hydrolyzing

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enzymes, while the inactivated product was detected at the inhibition zone by IMS 29. In contrast,

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our findings show that surfactins produced by B. subtilis are the source of attraction for P.

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dendritiformis and not an antimicrobial threat, while the degradation products of surfactin are

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incorporated into the P. dendritiformis colony and not restricted to the interaction zone, as

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uncovered by IMS. Hence, one of the questions that should be asked is, what is the effect of the

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degradation of surfactins on the PGPR ability of B. subtilis? On the other hand, it was proposed

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that members of the Paenibacillus family also possess PGPR characteristics 42. Therefore, if P.

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dendritiformis is attracted to B. subtilis surfactins, that highlight their potential role in recruiting

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additional beneficial bacteria to the rhizosphere. Indeed, P. dendritiformis initially isolated with

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B. subtilis, highlighting their natural co-occurrence 22.

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The unique motility of P. dendritiformis colonies was carefully studied, concluding that

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the main factor affecting colonial growth is the presence or production of surface active

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(surfactants) molecules 17. One possible hypothesis is the exploitation of public goods, in this

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case, secreted surfactins produced by B. subtilis utilized by the non-producing P. dendritiformis

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community 23, 43. That can explain the rapid colonial growth of P. dendritiformis that does not

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pay the metabolic costs of surfactin production. In evolutionary terms, P. dendritiformis could

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create dependency on surfactin production by B. subtilis compatible with the emerging Black

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Queen Hypothesis 44. Meaning that an organism is capable of losing traits that are energetically

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expensive, yet still thrive in the compatible neighboring consortia. In that sense, it could be that

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while diverging phylogenetically from B. subtilis, P. dendritiformis had already lost the ability to

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produce surfactins (while able to produce other biosurfactants) but kept the ability to degrade and 16 ACS Paragon Plus Environment

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utilize them if provided as public goods, hence the attraction 23. It should be noted here, that

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while P. dendritiformis is enclosing B. subtilis and restricting its growth, B. subtilis is kept alive

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and vital, still producing surfactins.

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CONCLUSIONS

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Recent literature show that the plant microbiome assembly varies depending of the plant

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species and the soil conditions in what is termed “plant-soil feedbacks” (PSF) affected by the

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plants’ ability to recruit soil microbes to its rhizosphere 45. It was also suggested that addition of

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B. subtilis to tomato plant’s rhizosphere results in transient impact on the microbiome

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composition 46. Therefore, as we suggested here, some of these bacteria are able to recruit

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additional microbial species to form compatible assemblages. This behavior has vast potential

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applications in agriculture, biotechnology, and human health and are the inspiration of the

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emerging field of synthetic ecology of microbes, that predicts potential chemical interactions

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among microbes based on their genomic information 47. Predictions can be made by

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mathematical modeling to generate hypotheses that may be further studied with the various

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genomic and transcriptomic methods that are currently available. However, the application of

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spatial metabolomics, as used in this study, highlights microbial interactions that could not be

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explored by molecular approaches alone. The active degradation of surfactins as shown here, is

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an important example of metabolic exchange and the various utilities of different microbes. The

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chemical interplay shown by these two laboratory model systems is a clever strategy of one

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microbe sends out a signal to recruit other organisms to its ecological niche to establish favorable

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mixed communities. Such give and take of chemical signals among complex microbial

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communities are critical in understanding the interactions of microbial ecology and encourages

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multidisciplinary synergistic collaborations. 17 ACS Paragon Plus Environment

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METHODS

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Bacterial Strains and Media

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The strains used for this study were Paenibacillus dendritiformis, Bacillus subtilis NCIB 3610,

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∆srfAA (see Supplemental table S1). Peptone media reagents were used unless otherwise

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indicated. All chemical reagents were purchased from Sigma-Aldrich unless stated otherwise.

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All solvents used were LCMS grade. Bacteria suspension (5µl) inoculated from overnight

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cultures in LB liquid media for microbial interactions on 0.5% peptone/1% agar, incubated at

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30oC. Plates were incubated at 30oC for 24 hours before recording.

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MALDI IMS

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Samples were transferred onto a MALDI target plate and mounted with universal matrix as

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described by Yang et al. 27. Samples were analyzed by Autoflex speed MALDI ToF (Bruker

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Daltonics) instrument in 300um raster for selected regions with 55% laser and 12.0 gain. Data

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visualized using the FlexImaging software 4.1 (Bruker Daltonics) normalized to RMS.

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LCMS analysis

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Samples extracted from solid media with EtOAc /MeOH (1:1) sonicated for 10 min. Samples

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were dried out and re-suspended in MeOH. Liquid Chromatography High Resolution tandem

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Mass Spectrometry (LC-HRMS/MS): Samples were analyzed using an LC system Dionex

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UltiMate 3000 (Thermo) using a Phenomenex Kinetex C-18 column (1.7 µm, 50 × 2.1 mm) A=

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98%H2O/2%ACN/0.1%FA, B=98%ACN/2%H2O/0.1%FA in the following method:

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Chromatographic separation performed by a linear gradient: 0–1 min 5% B, 1–2 min 5–50% B,

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2–4 min 50-55% B, 4–10 min 50-100% B, 10–11.5 min 100% B, 11.5-12 min 100-5%B and 12-

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12.5 min 5%B. MS spectra were acquired in a positive ion mode on a Maxis QTOF mass

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spectrometer (Bruker Daltonics), equipped with ESI source as described by Bouslimani et al. 48.

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Molecular networking

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A molecular network was created using the online workflow at GNPS. The data was filtered by

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removing all MS/MS peaks within +/- 17 Da of the precursor m/z. MS/MS spectra were window

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filtered by choosing only the top 6 peaks in the +/- 50Da window throughout the spectrum. The

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data was then clustered with MS-Cluster with a parent mass tolerance of 1.0 Da and a MS/MS

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fragment ion tolerance of 0.5 Da to create consensus spectra. Further, consensus spectra that

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contained less than 2 spectra were discarded. A network was then created where edges were

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filtered to have a cosine score above 0.6 and more than 4 matched peaks. Further edges between

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two nodes were kept in the network if and only if each of the nodes appeared in each other's

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respective top 10 most similar nodes. The spectra in the network were then searched against

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GNPS' spectral libraries. The library spectra were filtered in the same manner as the input data.

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All matches kept between network spectra and library spectra were required to have a score

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above 0.6 and at least 4 matched peaks 30.

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Mutant assay/ Disc diffusion assay

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Five microliters of an overnight bacterial culture were inoculated as co-cultures on a

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peptone/agar media 1cm apart. For surfactin disc assay, gradual concentration of commercial

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surfactin C15 (Sigma-Aldrich CAS# 24730-31-2) was tested (in MeOH, supplemental figure

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S3C). Selected concentration of 0.01mg was plated on a Whatman paper disc. Plates were

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incubated at 30oC for 24 hours before recording.

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MS guided purification 19 ACS Paragon Plus Environment

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The isolation of degradation products (lipopeptidic tails combined / peptidic product) carried out

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on a semi-preparative column Luna C18, 5µM, 100Å, 250 x 4.6 mm (Phenomenex) with guard

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column of the same stationary phase attached with chromatographic method as mentioned above

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at a flow rate of 1 mL min-1. 30 fractions were collected. All fractions were combined and dried

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to roughly 1mL volume in a rotary evaporator then transferred to pre-weighed and dried

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microcentrifuge tubes and lyophilized to dryness. The resultant powder of purified sample was

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solubilized in MeOH at 1mg mL-1 for further experiments.

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Acknowledgments

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Authors would like to thank the Ben-Jacob Lab for kindly providing Paenibacillus

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dendritiformis strain. This work was supported by BARD, the United States - Israel Binational

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Agricultural Research and Development Fund, Vaadia-BARD Postdoctoral Fellowship Award

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no. FI-494–13.

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Competing interests

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The authors declare no competing interests.

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Supporting Information Available: This material is available free of charge via the internet

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at http://pubs.acs.org. Files include:

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Table of strains, Annotation of surfactins, IMS of peptidic product, Mutant and disc diffusion

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assay, Degradation of commercial surfactin, Link to data on GNPS.

381

Author Contributions

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TLK and PCD designed the project

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TLK and AVM performed the research

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TLK and AVM analyzed data

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TLK, AVM and PCD wrote the paper

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