ABSTRACT
One of the most important ways that bacteria compete for resources and space is by producing antibiotics that inhibit competitors. Because antibiotic production is costly, the biosynthetic gene clusters coordinating their synthesis are under strict regulatory control and often require “elicitors” to induce expression, including cues from competing strains. Although these cues are common, they are not produced by all competitors, and so the phenotypes causing induction remain unknown. By studying interactions between 24 antibiotic-producing strains of streptomycetes, we show that strains commonly inhibit each other’s growth and that this occurs more frequently if strains are closely related. Next, we show that antibiotic production is more likely to be induced by cues from strains that are closely related or that share secondary metabolite biosynthetic gene clusters (BGCs). Unexpectedly, antibiotic production is less likely to be induced by competitors that inhibit the growth of a focal strain, indicating that cell damage is not a general cue for induction. In addition to induction, antibiotic production often decreases in the presence of a competitor, although this response was not associated with genetic relatedness or overlap in BGCs. Finally, we show that resource limitation increases the chance that antibiotic production declines during competition. Our results reveal the importance of social cues and resource availability in the dynamics of interference competition in streptomycetes.
IMPORTANCE Bacteria secrete antibiotics to inhibit their competitors, but the presence of competitors can determine whether these toxins are produced. Here, we study the role of the competitive and resource environment on antibiotic production in Streptomyces, bacteria renowned for their production of antibiotics. We show that Streptomyces cells are more likely to produce antibiotics when grown with competitors that are closely related or that share biosynthetic pathways for secondary metabolites, but not when they are threatened by competitor’s toxins, in contrast to predictions of the competition sensing hypothesis. Streptomyces cells also often reduce their output of antibiotics when grown with competitors, especially under nutrient limitation. Our findings highlight that interactions between the social and resource environments strongly regulate antibiotic production in these medicinally important bacteria.
INTRODUCTION
Bacteria live in diverse communities, where they compete with other microbes for resources and space. Competition between different species can be regulated by the differential uptake and use of specific nutrients. It can also be driven by secreted toxins, like antibiotics or bacteriocins, that kill or inhibit competitors. Antibiotics and bacteriocins can allow producing strains to invade established habitats or repel invasion by other strains (1, 2). However, these compounds are expected to be metabolically expensive to make and so should only be produced against genuine threats from competitors. The competition sensing hypothesis predicts that microbes should upregulate toxin production when they experience cell damage or nutrient limitation caused by competitors (3). Alternatively, bacteria can also sense competitors by detecting secreted signals that predict imminent danger, but that cause no direct harm themselves: for example, small molecule or peptide signals that are used to regulate toxin production by quorum sensing (3). Consistent with the predictions of competition sensing, several studies have observed that microbes facultatively increase antibiotic or bacteriocin production when they are grown in coculture with a competing strain (4–7). However, bacteria do not respond to all competitors in this way (7, 8). Moreover, counter to predictions of competition sensing, cocultivation can also cause strains to reduce antibiotic production (4, 6), rather than to respond aggressively to provocation. Why do bacteria respond to some competitors with aggression, but not to others? Similarly, are some cues from competitors more likely to elicit responses than others? To date, the answers to these questions have remained unknown. This shortcoming limits our ability to identify and induce cryptic antibiotic gene clusters for drug discovery and prevents a detailed understanding of the factors regulating the competitive dynamics of bacterial populations.
The aim of this article is to address these issues in the context of bacteria from the prolific antibiotic-producing family Streptomycetaceae (9). These filamentous, spore-forming bacteria are renowned for their production of secondary metabolites, including many clinically useful antibiotics, antihelminthic agents, and anticancer drugs (10). Antibiotic production in streptomycetes is associated with the developmental stage of the colony and typically coincides with the onset of sporulation (11, 12). We refer to this type of autonomous production as “constitutive” because it occurs in the absence of influence from other species. In addition, we and others have found that the presence of other strains in coculture can alter antibiotic production by increasing or reducing antibiotic output (4, 5, 13). When they occur, these changes are thought to be caused by different social cues that indicate the presence of competitors. These can include nutrient stress, such as iron depletion, or factors that cause cellular damage or predict immediate danger, like antibiotics or quorum-dependent regulators of antibiotic production, such as γ-butyrolactones (3, 14–16). However, as yet, we remain unable to predict the generality of these responses or the phenotypic or genomic factors that regulate them. Here, building on the framework of the competition sensing hypothesis, we set out to test if strains respond antagonistically to competitors that cause them harm. In addition, we investigate whether strains respond to competitive cues that we expect to be produced by strains with similar primary and secondary metabolisms due to shared resource requirements or mechanisms of antibiotic regulation. Because these traits are phylogenetically conserved (6, 17–20), this predicts that Streptomyces will be more likely to respond to social cues from closely related species.
To examine the social factors that regulate antibiotic production in streptomycetes, we studied antagonistic interactions between 24 different strains across a broad phylogenetic range in two nutrient environments. First, in each nutrient environment, we tested all possible pairwise interactions between these strains (24 × 24 = 576) by growing them as colonies and then testing if they could inhibit the growth of each other strain by inoculating these on top of the focal colony (Fig. 1). Next, we tested if growth in coculture with a second strain altered the inhibitory behaviors we recorded during pairwise interactions. These three-way interactions consisted of 24 × 24 interactions, which we measured against 24 target strains to score 13,824 combinations in each nutrient environment. This allowed us to compare the inhibitory capacity of strains during solitary growth, reflecting constitutive expression, to their behavior after interacting with a competitor during coculture (Fig. 1). These approaches allowed us to directly test if altered antibiotic production during growth in coculture could be predicted as a function of the phenotype or genotype of the competitor.
Schematic of constitutive and facultative inhibition assays. Focal strains (orange) were tested for their capacity to inhibit each target strain (gray) inoculated on top of the focal colony in a soft agar overlay. Inhibition was detected as a zone of clearance surrounding the colony. All 24 strains were tested as both focal and target strains, leading to 576 possible assays for constitutive antibiotic production. For the facultative assays, a second colony was inoculated 1 cm away, designated the competitor, that could interact with the focal strain through diffusible molecules. All 24 strains were tested each as the focal, competitor, and target strain, resulting in 24 × 24 × 24 = 13,824 assays. All assays were conducted under both high- and low-resource conditions. Comparison of the ability of the focal strain to inhibit the target in the constitutive and facultative assays revealed whether antibiotic production was induced, suppressed, or unchanged.
RESULTS
Constitutive antagonism.We first measured constitutive antibiotic production by growing each strain on a defined minimal medium (MM) and then testing if it could inhibit an overlay of each target strain (Fig. 1). These results formed the baseline against which we examined facultative responses. Similar to antagonistic interactions in Streptomyces and other microbes (4, 6, 21), these assays revealed that approximately half of all possible pairwise interactions were inhibitory (47.7%) (Fig. 2A, top left triangles). We used multilocus sequence typing (MLST) to infer the phylogeny of the strains. Next, we identified the biosynthetic gene clusters (BGCs) in the complete genomes of these strains by using the bioinformatics tool antiSMASH (22). This revealed considerable variability in the number of secondary metabolite BGCs within each genome (mean ± standard error [SE] = 34 ± 1.85; range = 22 to 64) (see Fig. S2 in the supplemental material).
Constitutive antagonism. (A) Inhibition matrix sorted by multilocus sequence typing (MLST) relatedness. Triangles indicate whether a target strain showed growth (white) or was inhibited (black) by the focal strain. Each square is divided into two triangles: the upper triangle shows the results under high-resource conditions, while the lower triangle shows the results under low-resource conditions. Self-inhibition is denoted in blue. Missing data due to inconsistent results are shown in gray. Panels B to D show results of assays conducted at high resource levels. (B) Correlation between inhibition phenotype dissimilarity (Euclidian distance determined by calculating the dissimilarity between focal strain inhibition phenotypes) and phylogenetic distance (Mantel test, P < 0.001, r = 0.27, n = 552) or (C) biosynthetic gene cluster (BGC) distance (Mantel test, P < 0.001, r = 0.43, n = 552). Dots are semitransparent: darker areas represent overlapping data points. (D) Logistic regression between the probability of inhibition and phylogenetic and biosynthetic gene cluster (BGC) distance (Pphylogenetic distance < 0.001, PBGC distance = 0.046, McFadden R2 = 0.02, n = 536).
The antagonistic behavior of each strain against the 24 possible targets generated a unique inhibition fingerprint, which we designate the inhibition phenotype. We calculated the dissimilarity in inhibition phenotypes to quantify whether strains inhibit the same or different targets and found a significant correlation between inhibition phenotype dissimilarity and phylogenetic distance (Fig. 2B) (Mantel test, P < 0.001, r = 0.27). This result indicates that closely related strains inhibit the same targets. We then tested if this was due to the possibility that related strains produce similar antagonistic compounds. To address this, we grouped all BGCs identified in the genomes into gene cluster families by using BiG-SCAPE (23) and calculated Jaccard distances between the strains based on their shared BGCs. This analysis revealed that BGC distance is significantly correlated with inhibition phenotype (Mantel test, P < 0.001, r = 0.43) (Fig. 2C), supporting the idea that related strains produce similar secondary metabolites.
Consistent with the idea that closely related strains are more likely competitors, strains showed a stronger tendency to inhibit closely related targets (logistic regression, P < 0.001, McFadden R2 = 0.02, n = 536). As BGCs often also provide resistance against the product they encode, we expected that strains with a high degree of BGC similarity would not inhibit each other. Indeed, strains were most likely to inhibit targets that are closely related but have dissimilar BGCs (logistic regression, Pphylogenetic distance < 0.001, PBGC distance = 0.046, McFadden R2 = 0.02, n = 536) (Fig. 2D). In contrast to another study that examined inhibitory interactions between phylogenetically diverse bacteria (21), we found no association between the probability of inhibition and the metabolic overlap between strains, assessed as the ability to grow on 95 different carbon sources by using Biolog plates.
Altered inhibition during coculture.Our results show that streptomycetes constitutively produce antibiotics that inhibit closely related strains. However, constitutive antibiotic production does not account for facultative changes that are caused by cues from other strains. We measured facultative responses by inoculating each strain next to a competitor and then assessing if it could inhibit the growth of the different target strains, as described above. This allowed us to directly compare the inhibitory capacity of each focal strain in the presence and absence of each competitor (Fig. 1). A focal-competitor interaction was scored as “induced” if the focal strain was able to inhibit any of the target strains that it was unable to inhibit when it was grown on its own and “suppressed” if the opposite occurred. By this approach, a focal strain could be both induced and suppressed by the same competitor against different target strains. The results of these assays, shown in Fig. 3A, confirm that facultative responses are extremely widespread. The inhibition phenotype was changed by a competitor in approximately half of the focal-competitor interactions (48%), meaning that the focal strain was induced or suppressed against at least one target strain in the presence of a given competitor. These changes dramatically altered the inhibition phenotype of the focal strain and changed the total number of strains that each focal strain could inhibit (Fig. 3B). Strains also changed their inhibition phenotype in response to a competitor colony of the same strain (58% [diagonal in Fig. 3A]). Overall, we observed induction in 33% of all tested focal-competitor interactions and suppression in 45%. There was considerable variability in the responsiveness of strains to competitors; whereas some strains responded to none of the competitors, others responded to nearly all of them (induced, 0 to 20; suppressed, 0 to 22) (Fig. 3C). On average each focal strain was induced by 7.4 ± 1.5 (mean ± SE) competitors and suppressed by 9.6 ± 1.7. In many cases, a given strain was both induced and suppressed by the same competitor against different targets (Fig. 3A). Although this led to a distinct inhibition phenotype, compared to the focal strain grown alone, it may not have changed the total number of inhibited targets.
Altered antagonism during coculture under high-resource conditions. (A) Interaction heat map showing changes to target strain inhibition when a focal strain is grown in coculture with a competitor. Each square is divided into two triangles: the upper triangle shows induction in red, while the lower triangle shows suppression in blue. Gray triangles indicate that either induction or suppression was not possible for this focal strain, due to the result in the constitutive assay. (A strain that does not inhibit any targets cannot be suppressed, while a strain that inhibits all targets cannot be induced.) (B) Gray bars indicate the number of target strains inhibited by the focal strain when grown alone. Black dots indicate the net number of target strains inhibited by the same focal strain if it was induced and/or suppressed during coculture with one of the 24 possible competitors. Dots showing the same number of inhibited target strains as the gray bar indicate that a competitor strain causes an equal level of induction and suppression against targets, resulting in no net change. (C) Number of competitors that induce or suppress each focal strain. Cases where suppression is not possible due to the absence of constitutive inhibition are denoted as “NA.”
Competition sensing predicts that bacteria will change their behavior in response to antagonistic competitors that they detect by sensing cell damage (3). We define a competitor as antagonistic if it inhibits the focal strain during the constitutive assay. Although we found that induction of the focal strain was significantly related to whether or not its competitor was antagonistic (logistic regression, P < 0.001, McFadden R2 = 0.06, n = 354), the direction of this result did not match our expectations (Fig. 4A, black bars). Unexpectedly, antibiotic production in the focal strain was nearly twice as likely to be induced by a nonantagonistic competitor (probability of induction of 0.41 versus 0.22). This indicates that cell damage was not a strong cue for antibiotic induction. Other ways that focal cells could sense competitors is if they detect compounds they produce, such as antibiotics and quorum sensing signals, or by experiencing nutrient stress due to resource competition. Since both primary metabolism and secondary metabolism are correlated with phylogenetic distance, we examined if induction was correlated with phylogenetic distance. As predicted, focal strains are more frequently induced by a closely related competitor (logistic regression, P < 0.001, McFadden R2 = 0.02, n = 487) (Fig. 4B, solid line). To examine if this effect was associated with the production of similar secondary metabolites, we tested if differences in induction could be explained by BGC similarity. Indeed, focal strains are more likely induced by competitors with which they share more BGCs (logistic regression, P < 0.001, McFadden R2 = 0.04, n = 487) (Fig. 4C, solid line). This suggests that cues for induction rely more on the detection of secreted compounds, rather than the damage these compounds cause. This makes cases of self-induction, where the focal and competitor colonies are of the same strain, also likely due to a local increase in the concentration of autoinducers, such as γ-butyrolactones.
Induction during coculture. (A) The probability that a focal strain is induced is lower when the competitor is antagonistic to the focal strain under both high-resource (logistic regression, P < 0.001, McFadden R2 = 0.06, n = 354) and low-resource (logistic regression, P < 0.001, McFadden R2 = 0.12, n = 419) conditions. (B) Logistic regressions between the probability of induction and phylogenetic distance under high-resource (black line) and low-resource (dashed line) conditions (P < 0.001, McFadden R2 = 0.02, n = 487 and P = 0.205, McFadden R2 = 0.00292, n = 445, respectively) or (C) logistic regressions between the probability of induction and BGC distance under high-resource (black line) and low-resource (dashed line) conditions (P < 0.001, McFadden R2 = 0.04, n = 487 and P = 0.174, McFadden R2 = 0.003, n = 445, respectively). Shaded areas indicate SE.
In addition to induction, we found that antibiotic production was also commonly suppressed in the presence of competitors. Although this strategy can be perceived as benefiting the competitor strain if it prevents a focal strain from producing a potentially harmful antibiotic, it could also benefit the suppressed strain by allowing it to redirect energy toward other functions. However, we found no relationship between suppression and the competitor’s ability to inhibit the focal strain (logistic regression, P = 0.83, McFadden R2 = 0.025). Suppression was also not associated with phylogenetic or BGC distance (logistic regression, P = 0.94, McFadden R2 < 0.001, n = 366, and P = 0.202, McFadden R2 = 0.003, n = 366, respectively).
Effect of resource stress on inhibition.To address the role of nutrient limitation in antibiotic production, we tested whether constitutive or facultative inhibition changed if the carbon source concentration was reduced by 10-fold (Fig. 2A, bottom right triangles). The frequency of constitutive inhibition was marginally higher under these conditions: 49.2% versus 47.7% of all pairwise interactions were inhibitory on low- versus high-resource medium, and only 6.7% of pairwise interactions differed between the two resource conditions (McNemar’s χ2 = 0, df = 1, P = 1). Likewise, we found a strong correlation between the inhibition phenotypes of the strains at both resource concentrations (Mantel test, r = 0.93, P < 0.001), with phylogenetic and BGC distances both significantly correlated with inhibition phenotype and in the same direction as in the high-resource concentration (Mantel test, P < 0.001, r = 0.30, and P < 0.001, r = 0.39, respectively) (see Fig. S1 in the supplemental material). As at the higher glycerol concentration, strains are more likely to inhibit closely related targets with dissimilar BGCs (logistic regression, Pphylogenetic distance < 0.001, PBGC distance = 0.019, McFadden R2 = 0.02, n = 526) (Fig. S1).
FIG S1
Copyright © 2021 Westhoff et al.This content is distributed under the terms of the Creative Commons Attribution 4.0 International license.
FIG S2
Copyright © 2021 Westhoff et al.This content is distributed under the terms of the Creative Commons Attribution 4.0 International license.
Streptomyces focal strains responded differently to the presence of a competitor under different resource conditions (Fig. 5) (McNemar's χ2 = 5.43, df = 1, P < 0.05), with a change in inhibition phenotype in 56.1% versus 49.1% under low- versus high-resource conditions, respectively (Fig. 6). While we expected more induction due to resource stress, in accordance with the competition sensing hypothesis, the incidence of induction was slightly lower at lower resource levels (30.2% versus 33.0%). In contrast we observed a dramatic increase in suppression, from 45.0% to 59.1% (Fig. 6). Just as at the higher resource level, strains were more likely to be induced by competitors that did not inhibit them (Fig. 4A, gray bars) (logistic regression, P < 0.001, McFadden R2 = 0.12, n = 419). In contrast to the higher-resource conditions, neither phylogenetic nor BGC similarity was associated with induction in the low-resource environment (Fig. 4B and C, dashed lines) (logistic regression, P = 0.205, McFadden R2 = 0.00292, n = 445 and P = 0.174, McFadden R2 = 0.003, n = 445, respectively). Suppression was still not associated with any of the factors that we tested, suggesting that antibiotic suppression may be a general reaction to resource stress in streptomycetes.
Altered antagonism during coculture under low-resource conditions. (A) Interaction heat map showing change in target strain inhibition when a focal strain is grown in coculture with a competitor. Each square is divided into two triangles: the upper triangle shows induction in red, while the lower triangle shows suppression in blue. Gray triangles indicate that either induction or suppression was not possible for this focal strain, due to the result in the constitutive assay. (A strain that does not inhibit any targets cannot be suppressed, while a strain that inhibits all targets cannot be induced.) (B) Gray bars indicate the number of strains inhibited by the focal strain when grown alone. Black dots indicate the net number of target strains inhibited by the same focal strain if it was induced and/or suppressed during coculture with one of the 24 possible competitors. Dots showing the same number of inhibited target strains as the gray bar indicate that a competitor strain causes an equal level of induction and suppression against targets, resulting in no net change. (C) Number of competitors that induce or suppress each focal strain. Cases where suppression is not possible due to the absence of constitutive inhibition are denoted as “NA.”
Constitutive and facultative inhibition under high- and low-resource conditions. Shown are comparisons of the total amount of inhibition, change in inhibition due to competition, and induction and suppression found under low- and high-resource conditions.
DISCUSSION
Competitive and social interactions between neighboring microbial cells in soil are common as different species vie for space and resources. One of the ways that bacteria compete is by secreting toxins like antibiotics or bacteriocins, but the production of these compounds is typically studied without consideration of this biotic context. Both theory and experiments have shown that this perspective is limited because it neglects factors that induce or suppress toxins and fails to identify toxins whose production is dependent on competitive interactions (4, 5, 24–27). In this context, the aims of our work were two-fold: first to establish to what extent the role of social interactions affect antibiotic production in common soil microbes of the Streptomycetaceae, and second to identify factors that are predictive of competition-mediated responses.
By comparing levels of antibiotic production in the absence and presence of another species in coculture, termed constitutive production and facultative production, respectively, we found that production was induced in ∼1/3 of cocultures, under both high- and low-resource conditions. These results considerably expand on results from earlier studies that describe changes in secondary metabolite production and inhibition in a smaller set of actinomycetes or against a smaller set of target species (4–6). The latter aspect is especially important because susceptibility varies markedly between strains; studies with fewer targets may therefore underestimate the frequency of facultative changes to antibiotic production. Induction was strongly predicted by phylogenetic distance in our study, with closely related strains more likely to inhibit each other. Previous studies also identified a correlation between phylogenetic distance and inhibition in Streptomyces (6, 13). However, one of these pointed in the opposite direction, showing closely related strains as less likely to inhibit each other, which could possibly be due to the differences in the method of determining growth inhibition (13). The weak significant relationships identified in the present study suggest that other untested factors, beside the parameters tested here, may be important. An earlier study linked the association between induction and phylogenetic distance to nutrient use, as closely related strains compete for the same resources, but did not test for overlap in secondary metabolites (6). The same study found that streptomycetes increase antibiotic production when grown with susceptible competitors, without assessing the impact of whether or not the competitor could reciprocally inhibit the focal strain. Unexpectedly, we found that a focal strain was less likely to be induced during coculture if it was grown with an inhibitory competitor. In other words, while coculture frequently altered antibiotic production, this was not evidently driven by cellular damage caused by the second strain, as specifically predicted by the competition sensing hypothesis (3). Instead, our results suggest that cells are more likely to induce antibiotic production in response to cues that are correlated with phylogenetic distance, rather than direct harm itself. For example, under high-resource conditions strains that share BGCs are more likely to induce each other. This suggests two possible sources for cues. First, antibiotic intermediates or antibiotics themselves, can serve as inducers of antibiotic production or resistance (16). These responses can prevent autotoxicity or killing by neighboring clonemates and also act as regulators of the expression of their own biosynthetic gene cluster (26, 28). Because resistance is often encoded in the antibiotic biosynthetic gene cluster, self-inhibition, which was observed in few instances, could be due to not-yet-expressed resistance in spores during challenge with a high dose of antibiotic, or alternatively by the production of germination inhibitors, such as germicidin, that inhibit the germination of conspecific spores (29). Second, related strains that share one or more BGCs may be more likely to utilize the same, or similar, secreted factors that induce antibiotic production: e.g., the quorum-dependent γ-butyrolactone signals. Streptomyces cells contain multiple receptors for cognate and noncognate γ-butyrolactones, thereby allowing them to detect these signals as a precursor of the antibiotics another strain might produce (15, 30, 31). Similar eavesdropping of quorum-dependent signals has been observed for bacteriocins in Streptococcus pneumoniae, which leads to cross-induction of strain-specific antimicrobials (7). Testing this idea in Streptomyces using chemically synthesized signals and reporter strains remains an important objective for future work.
When we repeated our assays at 1/10 the glycerol concentration, constitutive expression was only marginally changed; however, these lower resource concentrations led to slightly reduced induction rates and a marked increase in suppression. Moreover, the associations between induction and phylogenetic distance and BGC distance disappeared. These results indicate that antibiotic regulation integrates information about the competitive environment as well as environmental resource availability, leading strains to respond differently when exposed to a combination of competitive cues and resource stress than when exposed to only one of these. Links between nutrient sensing or carbon catabolite repression and antibiotic production in streptomycetes are well established. For example, under nutrient-rich conditions N-acetylglucosamine blocks morphogenesis and antibiotic production, while it has the opposite effect under nutrient-poor conditions (32, 33). A second possibility may be that competition exacerbates nutrient stress overall, leading to a general suppressive response that does not depend on the particulars of the competitor. By this view, suppression is best considered a generic response to nutrient stress, rather than the result of a specific action by the second strain. Other possibilities exist, such as degradation of exogenous enzymes or coercion or manipulation by the competitor colony. These strategies could be amplified by lowered nutrients to reflect a switch from offense to defense. This result indicates that further work will need to consider responses other than antibiotic production when examining the behavior of cells in coculture. For example, strains may respond to nutrient stress from competitors by redirecting energy used for antagonism toward functions that help them to avoid competition: e.g., hyphal growth in the direction opposite the competing strain or increased sporulation. Whereas the first possibility would contribute to an escape in space, the latter would allow an escape in time, leaving spores to germinate when nutrient stress is relieved. These alternative responses, which are equivalent to a “fight or flight” decision, might be anticipated if there are trade-offs between antibiotic production and other aspects of development, as we have found in Streptomyces coelicolor (34).
In summary, our results provide strong evidence that antibiotic production by streptomycetes is highly responsive to their social and resource environment. We establish the importance of BGC similarity on antibiotic induction, suggesting a role for shared regulatory compounds, and show that suppression and possibly escape, as a means of “flight,” should be more thoroughly examined as a response to interference competition. This is equally important for many of the other mechanisms that bacteria use to regulate inter- and intraspecific warfare (35). It will also be crucial to examine these responses in experiments that more closely approximate the natural environment, including environments with increased spatial heterogeneity and decreased diffusion, and where local interactions are maintained over longer periods of time. Similarly, an important next step is to determine how these social interactions influence competitive outcomes, as has been done for constitutive antibiotic production between competing species (1, 2, 36). Together, these approaches will lead to a fuller understanding of the role of antibiotic production in natural soils and the factors that maintain microbial diversity. In addition, they will help to identify factors that can be used to induce cryptic antibiotic BGCs in Streptomyces as potential drug leads.
MATERIALS AND METHODS
Strains and culturing conditions.The panel of 24 Streptomycetaceae strains used in this study (see Table S1 in the supplemental material) included 21 strains isolated from a single soil sample from the Himalayan Mountains collected at 5,000 m near a hot water spring (37). These 21 strains were selected due to their consistent phenotypes and the ability to sporulate under our lab growth conditions. The remaining three strains were well-characterized lab strains: Streptomyces coelicolor A3(2) M145, Streptomyces griseus IFO13350, and Streptomyces venezuelae ATCC 10712.
TABLE S1
Copyright © 2021 Westhoff et al.This content is distributed under the terms of the Creative Commons Attribution 4.0 International license.
High-density spore stocks were generated by culturing on soy flour-mannitol (SFM) agar (20 g soy flour, 20 g mannitol, 20 g agar per liter) or on R5 agar {103 g sucrose, 0.42 g K2SO4, 10.1 g MgCl2, 50 g glucose, 0.1 g Casamino Acids, 5 g yeast extract, 5.7 g TES [N-tris(hydroxymethyl)methyl-2-aminoethanesulfonic acid], 2 ml R5 trace element solution, and 22 g agar per liter}. After 3 to 4 days of growth, spores were harvested with a cotton disc soaked in 3 ml 20% glycerol, and spores were extracted from the cotton by passing the liquid through an 18-gauge syringe to remove the vegetative mycelium. Titers of the resulting spore stocks were determined and stored at −20°C.
Multiwell master plates were prepared by diluting the high-density spore stocks to 1 × 106 spores ml−1 in deionized water, and these plates were stored at –20°C. The glycerol concentration after the dilution of stocks was always lower than the concentration of glycerol added as a carbon source to the medium.
To perform the interaction assays, approximately 1 μl of the focal strain (and when indicated 1 μl of the competitor strain) was replicated on a 25-grid plate (Thermo Fisher Scientific, Newport, United Kingdom) using a custom-built multipin replicator (EnzyScreen BV, Heemstede, The Netherlands) from a frozen master plate. Each well of the 25-grid plate contained 2 ml minimal medium (MM) (500 mg l-asparagine [Duchefa Biochemie, The Netherlands], 500 mg KH2PO4 [Duchefa Biochemie], 200 mg MgSO4·7H2O [Duchefa Biochemie], 10 mg Fe2SO4·7H2O [Sigma-Aldrich, St. Louis, MO], and 20 g agar [TM Duché & Sons Ltd, Wilmslow, Cheshire, UK] per liter [pH 7.2] supplemented with either 0.05 or 0.5% glycerol). After 4 days of growth at 30°C, a 1-ml overlay (0.8% agar MM) containing 1.6 × 105 spores/ml was added on top. After 24 to 48 h of incubation at 30°C (depending on the growth speed of the target strain), 1 ml of the dye resazurin (Cayman Chemical Company, Ann Arbor, MI) was added to each well at a concentration of 50 mg liter−1, and then the mixture was incubated for half an hour before the surplus was removed. Change in color of this redox dye from blue to pink was used as a measure of growth of the target strain, as resazurin (blue) is changed to resorufin (pink) by metabolically active cells. Pictures were taken of every plate, and these were scored for the presence or absence of inhibition zones around the colony/colonies. Every interaction was assessed at least in duplicate. When the results of assays were inconsistent, the particular interaction was repeated. In some cases, it was impossible to score assay results due to spreading of the spores from a colony into the overlay agar with the target strain. This resulted in an easily recognizable “swirl” of growth coming from a colony, and as such, we excluded these results (designated “missing data”).
Whole-genome sequencing.Whole-genome sequencing was performed for all strains for which a full genome sequence was not yet available to perform genome mining and to generate a phylogenetic tree. As described before (38), strains were grown in liquid culture containing 50% YEME–50% TSBS with 5 mM MgCl2 and 0.5% glycine at 30°C and with centrifugation at 250 rpm for 2 days. After centrifugation, the pellet was resuspended in TEG buffer with 1.5 mg ml−1 lysozyme, and after 1 h of incubation at 30°C, the reaction was stopped by adding 0.5 volume of 2 M NaCl. DNA was extracted using a standard phenol-chloroform extraction, followed by DNA precipitation and washing in isopropanol and 96% ethanol. Dried DNA was resuspended in Milli-Q water and then treated with 50 μg ml−1 of RNase and incubated at 37°C for 1 h. Following RNase treatment, the mixture was purified and cleaned as described above, after which the purified DNA was washed with 70% ethanol and resuspended in Milli-Q water. Paired-end sequence reads were generated using the Illumina HiSeq2500 system at BaseClear. De novo assembly was performed using the “De novo assembly” option of the CLC Genomics Workbench version 9.5.1, and the genome was annotated using the BaseClear annotation pipeline based on the Prokka Prokaryotic Genome Annotation System (version 1.6).
Using the complete genomes, multilocus sequence typing (MLST) was performed as described by Guo et al. (39). For this purpose, we used the sequences of six housekeeping genes (atpD, gyrB, recA, rpoB, trpB, and 16S rRNA) that were shown to give good resolution for the S. griseus clade. For the already available sequenced genomes, the sequences for S. coelicolor (strain V) were downloaded from StrepDB (http://strepdb.streptomyces.org.uk) and used to BLAST search against the genome sequences of S. venezuelae ATCC 10712 (txid 54571) (strain W), S. griseus subsp. griseus NBRC 13350 (txid 455632), and MBT66 (strain P) in the NCBI database. For all sequenced genomes, the genes of interest were located from the annotated genome or were searched in a database constructed with the genomes in Geneious (Geneious 9.1.4). Each gene was aligned and trimmed before the six sequences for each strain were concatenated in frame and used to construct a neighbor-joining tree using Geneious to reveal the phylogenetic distances between the strains.
Analysis of biosynthetic gene clusters.Biosynthetic gene clusters were identified within each genome with antiSMASH version 4.0 run with default parameters (22). BiG-SCAPE was used to calculate the pairwise distances between all BGCs, using default parameters and a cutoff of 0.5 as a threshold for similarity (23). This generated a BGC presence/absence matrix that we used to calculate a Jaccard distance between each pair of genomes to define the BGC distance between the strains.
Resource use.Carbon source utilization of each strain was tested using Biolog SFP2 plates (Biolog, Hayward, CA), on which growth on 95 carbon sources can be assessed. Plates were inoculated as described by Schlatter et al. (40). Briefly, strains were grown on MM with 0.5% glycerol for 7 days before spores were swabbed into a 0.2% carrageenan solution and adjusted to an optical density at 590 nm (OD590) of 0.2 to 0.24. This solution was diluted 10 times in 0.2% carrageenan, and 100 μl of this dilution was added to each well. Plates were incubated at 30°C for 3 days before the absorbance of each well at 590 nm was measured using a Spark 10M plate reader (Tecan, Switzerland). All strains were assessed in triplicate. For the analysis, the absorbance of the water control was subtracted for each well and the mean was taken. If the sample mean was not significantly different from 0 (one-sample t test, α = 0.05), the value was adjusted to 0. The Pearson correlation coefficient was calculated between all possible pairwise combinations of the strains, and the metabolic distance was calculated as 1 − correlation coefficient. Strain P showed extremely poor growth on the Biolog plates and was therefore excluded.
Statistics.All statistics were performed in R. Correlation between phylogenetic distance, metabolic dissimilarity, secondary metabolite distance, and inhibition and resistance phenotype was determined using Mantel tests. To establish whether antagonism and inhibition and induction and suppression are dependent, logistic regressions were performed. Logistic regression was also used to test for association between inhibition, induction or suppression and phylogenetic distance, and metabolic distance or BGC distance. For the logistic regressions, we excluded all self-self interactions, as these confound the analyses by having zero distance between the strains or test for self-inhibition.
Data availability.The data generated in this study are deposited in Dryad (https://doi.org/10.5061/dryad.wpzgmsbkw) and the genome sequences are deposited in GenBank under the corresponding MBT names.
FIG S3
Copyright © 2021 Westhoff et al.This content is distributed under the terms of the Creative Commons Attribution 4.0 International license.
FIG S4
Copyright © 2021 Westhoff et al.This content is distributed under the terms of the Creative Commons Attribution 4.0 International license.
ACKNOWLEDGMENTS
This work was financially supported by grants 824.02.003 and 731.014.206 from the Dutch National Science Foundation (NWO) to D.E.R. and to G.P.v.W., respectively.
The authors contributed in the following ways. S.W. and D.E.R. designed the experiments. S.W. performed the experiments and analyzed the data. A.K. and S.F.A.v.H. assisted with the (bio)informatics. S.W., D.E.R., and G.P.v.W. wrote the manuscript.
We declare there is no conflict of interest.
FOOTNOTES
- Received 24 September 2020
- Accepted 14 December 2020
- Published 9 February 2021
- Copyright © 2021 Westhoff et al.
This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.
