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Baltrus, D. A.

Publications and source records attributed to Baltrus, D. A..

At least 19 recordsLinked to original sources

Independent, Ongoing Clade-Specific Expansions of IS5 Elements in Pseudomonas syringae

Insertion Sequence (IS) elements are transposable regions of DNA which are present in a majority of bacterial genomes. It has been hypothesized that differences in distributions of IS elements across bacterial strains and species may reflect underlying differences in population biology. Therefore, shifts in IS element distributions between strains may be proxies for and reflective of changes in population dynamics. Here we investigate the presence and distribution of a subclass of IS5 elements throughout genomes of Pseudomonas syringae, by querying complete genomes for the presence of InsH (the main transposase found within these IS5 elements). We report that this one subclass of IS5 elements appears to have recently undergone multiple independent expansions in P. syringae clades and find that a majority of IS5 insertion sites are not conserved across three closely related P. syringae pv. lachrymans genomes. We present further evidence, as has been shown for other members of the IS5 family in different taxa, that elements from this IS5 subclass can drive the expression of downstream genes in P. syringae. Taken together, our results highlight how dynamic IS5 elements can be within and across P. syringae genomes and point toward the potential for IS5 elements to rewire the expression of the P. syringae chromosome.

microbiology↗

Broad intraspecies killing activity in Pseudomonas syringae due to the combinatorial action of LPS-interacting bacteriocins

Bacteriocins are a diverse group of highly specific antimicrobials produced by bacteria, thought to mainly target and kill strains that are closely related to and which therefore potentially compete in the same niche space as producer cells. Single strains can produce more than one type of bacteriocin, with each usually having differing modes of action and receptors for binding, and with strain specificity for each independent bacteriocin due to the requirement for these molecules to bind to receptors in target cells prior to carrying out antibacterial functions. Here we show that Pseudomonas syringae pv. aptata DSM50252 (Ptt) displays broad intraspecific killing activity due to combinatorial and non-overlapping activities of phage derived bacteriocins (referred to as tailocins) as well as a prophage encoded lectin-like bacteriocin (aptatacin L1). These results highlight how single strains can maintain broad killing activity against a variety of potential competitors by targeting multiple conformations of a shared receptor, and provide additional evidence that tailocins and aptatacin L1 both utilize rhamnose moieties in the LPS as potential receptors for binding.

microbiology↗

Pantailocins: Phage-derived Bacteriocins from Pantoea ananatis and Pantoea stewartii subsp. indologenes

Phage-derived bacteriocins are highly specific and effective antimicrobial molecules which have successfully been used as prophylactic treatments to prevent phytopathogen infections. Given the specificity of tailocins, a necessary step for broadening the tailocin catalog and for extending applicability across systems and diseases is the screening of new clades of phytopathogens for production of molecules with tailocin-like killing activity. Here, we describe production by and sensitivity of strains to tailocins produced by Pantoea ananatis and Pantoea stewartii subsp. indologenes. Phylogenetic evidence suggests that these tailocins are derived from Myoviridae family phage like many previously described R type syringacins and R type pyocins, but also suggests that cooption from phage occurred independently of previously described tailocins. Since these tailocin encoding loci are present in the same genomic locations across multiple strains of both species and display a level of divergence that is consistent with other shared regions between the genomes and with vertical inheritance of the locus, we refer to them broadly as pantailocins.

microbiology↗

Genomic Correlates of Tailocin Sensitivity in Pseudomonas syringae

Phage derived bacteriocins, also referred to as tailocins, are structures encoded by bacterial genomes and deployed into the extracellular environment to target and kill sensitive cells. Tailocins display great potential as agricultural antimicrobials due to their durability, efficiency, and specificity of killing with prophylactic application of these molecules having been shown to prevent infection by multiple phytopathogens. Although previous reports have strongly suggested that tailocins of Pseudomonas syringae bind sugar moieties in the LipoPolySaccharide (LPS) of target cells, the molecular mechanisms and binding interactions that enable tailocins from P. syringae to kill sensitive targets remain unclear. We therefore carried out a genome-wide association study investigating tailocin sensitivity across a diverse set of P. syringae genomes. Our results demonstrate that genes strongly correlated with tailocin sensitivity are localized to one contiguous region on the P. syringae chromosome encoding LPS structures similar to the Common Polysaccharide Antigen of P. aeruginosa. We further find that enzymes involved in the biosynthesis and transport of D-rhamnose and L-rhamnose are associated with tailocin sensitivity classes A and B, respectively, with large-scale recombination of the O-antigen biosynthesis region likely underlying rapid and fundamental changes in LPS structure between strains. We identify the rfbD gene as an additional genomic indicator to predict tailocin sensitivity and use this information to test tailocin interactions with unscreened strains from across phylogroups, including some in which LPS chains have been previously characterized. Overall, our results strongly support that tailocin sensitivity across P. syringae strains is largely determined by recombination events across strains that lead to differential production of either D or L-rhamnose moieties in the main LPS chain.

microbiology↗

Interspecies Killing Activity of Pseudomonas syringae Tailocins

Tailocins are ribosomally synthesized bacteriocins, encoded by bacterial genomes, but originally derived from bacteriophage tails. As with both bacteriocins and phage, tailocins are largely thought to be species-specific with killing activity often assumed to be directed against closely-related strains. Previous investigations into interactions between tailocin host range and sensitivity across phylogenetically diverse isolates of the phytopathogen Pseudomonas syringae have demonstrated that many strains possess intraspecific tailocin activity and that this activity is highly precise and specific against subsets of strains. However, here we demonstrate that at least one strain of P. syringae, USA011R, defies both expectations and current overarching dogma because tailocins from this strain possess broad killing activity against other agriculturally significant phytopathogens such as Erwinia amylovora and Xanthomonas perforans as well as against the clinical human pathogen Salmonella choleraesuis. Moreover, we show that the full spectrum of this interspecific killing activity is not conserved across closely related strains with data suggesting that even if tailocins can target different species, they do so with different efficiencies. Our results reported herein highlight the potential for and phenotypic divergence of interspecific killing activity of P. syringae tailocins and establish a platform for further investigations into the evolution of tailocin host range and strain specificity.

microbiology↗

The 16S rRNA Gene Is Not a Precise Classifier for Luteibacter Species

Luteibacter species are found throughout agricultural and plant associated microbial communities, and have largely been identified and classified through comparisons of the 16S rRNA genes. Through comparisons of 16S classifications with whole genome phylogenies and ANI, we highlight a somewhat unique situation whereby Luteibacter pinisoli and Luteibacter sp. 9143 would be classified as the same species using 16S rRNA sequences but are clearly differentiated by these other metrics. We present this case as an outlier, but also as an example for the challenges of classification solely using 16S rRNA gene sequences.

microbiology↗

Convergent Gene Expression Patterns During Compatible Interactions Between Two Pseudomonas syringae Pathovars and a Common Host (Nicotiana benthamiana)

Summary/Abstract Pseudomonas syringae is a diverse phytopathogenic species complex, and includes strains that can cause disease across a wide variety of plant species. Much previous research into the molecular basis of immunity and infection has focused on pathogen and plant responses in a handful of model strains and hosts, and with a tacit assumption that early steps in infection and host resistance are generalizable to the species complex and across plant hosts as a whole. Here, we provide a test of this assumption by measuring the dual pathogen and host transcriptomes of two distinct pathogenic lineages of P. syringae during compatible infection of a shared model host (Nicotiana benthamiana). Our results demonstrate that, with a handful of exceptions, host plants largely respond in a similar way to both pathogenic lineages and both bacterial pathogens possess highly similar transcriptional responses at 5 hours post inoculation. However, we also highlight that subsets of genes with differential expression patterns in both bacteria and host which likely represent strain-specific responses.

plant biology↗

Transcriptional profiles of a foliar fungal endophyte (Pestalotiopsis, Ascomycota) and its endohyphal bacterium (Luteibacter, Gammaproteobacteria) in co-culture support sulfur exchange and growth regulation

Symbiosis with bacteria is widespread among eukaryotes, including fungi. Bacteria that live within fungal mycelia (endohyphal bacteria) occur in many plant-associated fungi, including diverse Mucoromycota and Dikarya. Pestalotiopsis sp. 9143 is a filamentous ascomycete isolated originally as a foliar endophyte of Platycladus orientalis (Cupressaceae). It is infected naturally with the endohyphal bacterium Luteibacter sp. 9143, which influences auxin and enzyme production by its fungal host. Previous studies have used transcriptomics to examine similar symbioses between endohyphal bacteria and root-associated fungi such as arbuscular mycorrhizal fungi and plant pathogens. However, currently there are no gene expression studies of endohyphal bacteria of Ascomycota, the most species-rich fungal phylum. We developed methods for assessing gene expression by Pestalotiopsis sp. and Luteibacter sp. when grown in co-culture and when each was grown axenically. Our assays showed that the density of Luteibacter sp. in co-culture was greater than in axenic culture, but the opposite was true for the Pestalotiopsis sp. Dual RNA-seq data demonstrate that growing in co-culture modulates developmental and metabolic processes in both the fungus and bacterium, potentially through changes in the balance of organic sulfur via methionine acquisition. Our analyses also suggest an unexpected, potential role of the bacterial type VI secretion system in symbiosis establishment, expanding current understanding of the scope and dynamics of fungal-bacterial symbioses. TWEETWhen in co-culture, Luteibacter downregulates motility and upregulates a T6SS. Gene expression changes in its host, Pestalotiopsis, suggest the bacterium impacts fungal cell structure and methionine availability. IMPORTANCEInteractions between microbes and their hosts have important outcomes for host- and environmental health. Foliar fungal endophytes that infect healthy plants can harbor facultative endosymbionts called endohyphal bacteria, which can influence the outcome of plant-fungus interactions. These bacterial-fungal interactions can be influential but are poorly understood, particularly from a transcriptome perspective. Here, we report on a comparative, dual RNA-seq study examining the gene expression patterns of a foliar fungal endophyte and a facultative endohyphal bacterium when cultured together vs. separately. Our findings support a role for the fungus in providing organic sulfur to the bacterium, potentially through methionine acquisition, and potential involvement of a bacterial type VI secretion system in symbiosis establishment. This work adds to the growing body of literature characterizing endohyphal bacterial-fungal interactions, with a focus on a model facultative bacterial-fungal symbiosis in two species-rich lineages, the Ascomycota and Proteobacteria.

microbiology↗

Genome context influences evolutionary flexibility of nearly identical type III effectors in two phytopathogenic Pseudomonads

Integrative Conjugative Elements (ICEs) are replicons that can insert and excise from chromosomal locations in a site specific manner, can conjugate across strains, and which often carry a variety of genes useful for bacterial growth and survival under specific conditions. Although ICEs have been identified and vetted within certain clades of the agricultural pathogen Pseudomonas syringae, the impact of ICE carriage and transfer across the entire P. syringae species complex remains underexplored. Here we identify and vet an ICE (PmaICE-DQ) from P. syringae pv. maculicola ES4326, a strain commonly used for laboratory virulence experiments, demonstrate that this element can excise and conjugate across strains, and contains loci encoding multiple type III effector proteins. Moreover, genome context suggests that another ICE (PmaICE-AOAB) is highly similar in comparison with and found immediately adjacent to PmaICE-DQ within the chromosome of strain ES4326, and also contains multiple type III effectors. Lastly, we present passage data from in planta experiments that suggests that genomic plasticity associated with ICEs may enable strains to more rapidly lose type III effectors that trigger R-gene mediated resistance in comparison to strains where nearly isogenic effectors are not present in ICEs. Taken together, our study sheds light on a set of ICE elements from P. syringae pv. maculicola ES4326 and highlights how genomic context may lead to different evolutionary dynamics for shared virulence genes between strains.

microbiology↗

Prophylactic Application of Tailocins Prevents Infection by Pseudomonas syringae

Tailocins are phage-derived bacteriocins that demonstrate great potential as agricultural antimicrobials given their high killing efficiency and their precise strain-specific targeting ability. Our group has recently categorized and characterized tailocins produced by and tailocin sensitivities of the phytopathogen Pseudomonas syringae, and here we extend these experiments to test whether prophylactic tailocin application can prevent infection of Nicotiana benthamiana by P. syringae pv. syringae B728a. Specifically, we demonstrate that multiple strains can produce tailocins that prevent infection by strain B728a and engineer a deletion mutant to prove that tailocin targeting is responsible for this protective effect. Lastly, we provide evidence that heritable resistance mutations do not explain the minority of cases where tailocins fail to prevent infection. Our results extend previous reports of prophylactic use of tailocins against phytopathogens, and establish a model system with which to test and optimize tailocin application for prophylactic treatment to prevent phytopathogen infection.

microbiology↗

Pantoea ananatis defeats Allium chemical defenses with a plasmid-borne virulence gene cluster

Onion (Allium. cepa L), garlic (A. sativum L.), and other members of the Allium genus produce volatile antimicrobial thiosulfinates upon cellular damage. Allicin has been known since the 1950s as the primary antimicrobial thiosulfinate compound and odorant produced by garlic. However, the roles of endogenous thiosulfinate production in host-bacterial pathogen interactions have not been described. The bacterial onion pathogen Pantoea ananatis, which lacks both the virulence Type III and Type II Secretion Systems, induces necrotic symptoms and extensive cell death in onion tissues dependent on a proposed secondary metabolite synthesis chromosomal gene cluster. We found strong correlation between the genetic requirements for P. ananatis to colonize necrotized onion tissue and its capacity for tolerance to the thiosulfinate allicin based on the presence of an eleven gene, plasmid-borne, virulence cluster of sulfur/redox genes. We have designated them alt genes for allicin tolerance. We show that allicin and onion thiosulfinates restrict bacterial growth with similar kinetics. The alt gene cluster is sufficient to confer allicin tolerance and protects the glutathione pool during allicin treatment. Independent alt genes make partial phenotypic contributions indicating that they function as a collective cohort to manage thiol stress. Our work implicates endogenous onion thiosulfinates produced during cellular damage as mediators of interactions with bacteria. The P. ananatis-onion pathosystem can be modeled as a chemical arms race of pathogen attack, host chemical counter-attack, and pathogen resistance. Significance StatementAlliums (e.g. onion and garlic), after sustaining cellular damage, produce potent antimicrobial thiosulfinates that react with cellular thiols. The bacterial onion pathogen Pantoea ananatis, which lacks the virulence Type III and Type II Secretion Systems, induces cell death and necrotic symptoms on onions. We have identified a plasmid-borne cluster of sulfur/redox virulence genes that 1) are required for P. ananatis to colonize necrotized onion tissue, 2) are sufficient for tolerance to the thiosulfinates, and, 3) protect the glutathione pool during thiosulfinate treatment. We propose that the thiosulfinate production potential of Allium spp. governs Allium-bacterial interaction outcomes and that the P. ananatis-onion pathosystem can be modeled as a chemical arms race of attack and counterattack between the pathogen and host.

plant biology↗

Genomic Background Governs Opposing Responses to Nalidixic Acid Upon Megaplasmid Acquisition in Pseudomonas

Horizontal gene transfer is a significant driver of evolutionary dynamics across microbial populations. Although the benefits of the acquisition of new genetic material are often quite clear, experiments across systems have demonstrated that gene transfer events can cause significant phenotypic changes and entail fitness costs in a way that is dependent on the genomic and environmental context. Here we test for the generality of one previously identified cost, sensitization of cells to the antibiotic nalidixic acid after acquisition of a [~]1Mb megaplasmid, across Pseudomonas strains and species. Overall, we find that the presence of this megaplasmid sensitizes many different Pseudomonas strains to nalidixic acid, but that this same horizontal gene transfer event increases resistance of Pseudomonas putida KT2440 to nalidixic acid across assays as well as to ciprofloxacin under competitive conditions. These phenotypic results are not easily explained away as secondary consequences of overall fitness effects and appear to occur independently of another cost associated with this megaplasmid, sensitization to higher temperatures. Lastly, we draw parallels between these reported results and the phenomenon of sign epistasis for de novo mutations and explore how context dependence of effects of plasmid acquisition could impact overall evolutionary dynamics and the evolution of antimicrobial resistance. ImportanceNumerous studies have demonstrated that gene transfer events (e.g. plasmid acquisition) can entail a variety of costs that arise as byproducts of the incorporation of foreign DNA into established physiological and genetic systems. These costs can be ameliorated through evolutionary time by the occurrence of compensatory mutations, which stabilize presence of a horizontally transferred region within the genome but which also may skew future adaptive possibilities for these lineages. Here we demonstrate another possible outcome, that phenotypic changes arising as a consequence of the same horizontal gene transfer event are costly to some strains but may actually be beneficial in other genomic backgrounds under the right conditions. These results provide new a new viewpoint for considering conditions that promote plasmid maintenance and highlight the influence of genomic and environmental contexts when considering amelioration of fitness costs after HGT events.

microbiology↗

Identifying transposon insertions in bacterial genomes through nanopore sequencing

Transposon mutagenesis is a widely used tool for carrying out forward genetic screens across systems, but in some cases it can be difficult to identify transposon insertion points after successful phenotypic screens. As an alternative to traditional methods, we report on the efficacy of using an Oxford Nanopores MinION to identify transposon insertions through whole genome sequencing. We also report experiments using CRISPR-Cas to selectively target regions of the genome where a transposon has integrated. Our experiments provide a framework for understanding the efficiency of such techniques for carrying out forward genetic screens and point towards the ability to use CRISPR-based sequence capture to identify the insertion of particular regions of DNA across all genomes, which may enable Tn-Seq experiments using Nanopore based sequencing.

microbiology↗

Evidence of Tailocin Persistence and Resistance in Pseudomonas

Phage tail-like bacteriocins (tailocins) are bacterially-produced protein toxins that can mediate competitive interactions between co-colonizing bacteria. Both theoretical and empirical research has shown there are intransitive interactions between bacteriocin-producing, bacteriocin-sensitive, and bacteriocin-resistant populations, whereby producers outcompete sensitive, sensitive outcompete resistant, and resistant outcompete producers. These so-called rock-paper-scissor dynamics explain how all three populations can be maintained in the same environment, without one genotype driving the others extinct. Using Pseudomonas syringae as a model system, we demonstrate that otherwise sensitive bacterial cells have the ability to survive bacteriocin exposure through a physiological mechanism. This mechanism is similar to the persister phenotype that allows cells to survive antibiotic exposure, without acquiring antibiotic resistance. We show that a significant fraction of the target cells that survive a lethal dose of tailocin did not exhibit any detectable increase in survival in subsequent exposure (i.e. they survived through a persistence-like mechanism). Tailocin persister cells were more prevelant in stationary rather than log phase cultures. Of the fraction of cells that gained detectable tailocin resistance, there was a range of resistance from complete (insensitive) to incomplete (partially sensitive). By genomic sequencing and genetic engineering we showed that a mutation in a hypothetical gene containing 8-10 transmembrane domains causes tailocin high-persistence and genes of various glycosyl transferases cause incomplete and complete tailocin resistance. Importantly, of the several classes of mutations, only those causing complete tailocin resistance compromised host fitness. This result, combined with previous research, indicates that bacteria likely utilize persistence as a means to survive bacteriocin-mediated killing without suffering the costs associated with resistance. This research provides important insight into how bacteria can escape the trap of fitness trade-offs associated with gaining de novo tailocin resistance, and expands our understanding of how sensistive bacterial populations can persist in the presence of lethal competitors.

microbiology↗

Conditionally Redundant Bacteriocin Targeting by Pseudomonas syringae

The widespread use of antimicrobials under clinical and agricultural settings has resulted in the evolution of resistance to these compounds. To combat the emergence of resistance, current research efforts are focusing on designing treatments to exploit combinations of antimicrobials, where the evolution of resistance confers sensitivity to alternative compounds. In this work we demonstrate that strains of Pseudomonas syringae possess a natural analogue to this strategy. Specifically, we demonstrate that a single strain produces multiple bacteriocins that can target another strain, but antimicrobial activity of the second bacteriocin is manifest only after resistance to the first emerges. The evolution of resistance also sensitizes the target strain to bacteriocins from a variety of other strains. Strains of P. syringae therefore encode multiple bacteriocins that can act in a conditionally redundant manner. It is possible that combinations of bacteriocins could be applied as a cocktail or sequentially, to potentially achieve durable pathogen control.

microbiology↗

Variation in the oxidative burst in response to wounding and bacterial infection among native and invading genotypes of yellow starthistle (Centaurea solstitialis)

O_LIPremise of the study: Invasive plants may leave enemies behind when they colonize a new habitat, allowing selection to favor increased investment in growth and/or reproduction over defensive traits. Previous studies have identified reduced diversity of potential bacterial pathogens and evolutionary increases in growth and reproduction in invading populations of yellow starthistle (Centaurea solstitialis). This study leverages a recently developed high-throughput assay of immune function to test for evidence of a trade-off between increased growth and defense against bacterial pathogens in yellow starthistles invasion of California (USA).\nC_LIO_LIMethods: Seven bacterial strains were cultured from infected leaf tissue in the native range. Healthy leaf tissue from five native European collections and six invading collections were exposed to these native bacterial strains. A standardized assay of peroxidase activity was used measure the oxidative burst immune response to pathogen recognition by the leaf. Immune responses were compared to plant growth within and between ranges to assess evidence for a trade-off.\nC_LIO_LIKey Results: Plant genotypes from the native range demonstrated a higher immune response to bacterial strains than did invading genotypes, consistent with a trade-off with plant growth across regions. The same trade-off was also apparent across genotypes from the native range, but not across genotypes from the invaded range.\nC_LIO_LIConclusions: Our results provide evidence that increased growth in a highly invasive plant species may come at a cost to immune function, consistent with the hypothesis that escape from enemies can provide opportunities for shifts in resource allocation that favor the proliferation of non-native species.\nC_LI

plant biology↗

Unusual Sulfur Requirements During Laboratory Growth of Leutibacter

Many terrestrial bacteria are assumed to utilize sulfate transport and metabolism as a means for fulfilling cellular sulfur requirements. As such, many defined minimal media for bacterial growth under laboratory conditions contain sulfate as their sulfur source. Herein, an exception to this assumption is described as sulfate transport capabilities have been lost at least once in a lineage of Luteibacter associated with plants and fungi. However, a representative of this lineage (an endohyphal species, Luteibacter sp. 9143) can grow in minimal media when sulfur is supplemented with organic (cysteine and methionine) or inorganic (thiosulfate) compounds, and when co-cultured with its fungal host. A related strain of Luteibacter (UNC366Tsa5.1, isolated from the rhizosphere of Arabidopsis) potentially possesses more limited sulfur acquisition pathways than Luteibacter sp. 9143. These results highlight the surprising sulfur requirements of Luteibacter, which may be illustrative of close associations between these strains and eukaryotes, as well as a need for caution when inferring auxotrophies in a focal strain based on differential growth in minimal versus rich media.\n\nImportanceSulfate is often used as the sulfur source in minimal media. Here we show that some Luteibacter strains cannot utilize sulfate as a sulfur source, likely due to loss of genes encoding transport proteins. As sulfur requirements for Luteibacter can be met through co-culture with their fungal partner, this knowledge could provide a means to engineer better symbiotic relationships between bacteria and fungi that may be relevant for agriculture. Because growth in minimal media can be restored by supplementation with either cysteine or methionine, and in some cases only methionine, this result highlights how unexpected growth requirements could masquerade as auxotrophy for certain strains and conditions.

microbiology↗

Adaptation, Specialization, and Coevolution within Phytobiomes

Growth patterns of individual plants and evolutionary trajectories of plant communities are intimately linked with and are critically affected by host-associated microbiomes. Research across systems has begun to shed light on how these phytobiomes are established and under laboratory and natural conditions, and have cultivated hope that a better understanding of the governing principles for host-microbe interactions can guide attempts to engineer microbiomes to boost agricultural yields. One important, yet relatively understudied, parameter in regards to phytobiome membership is the degree to which specialization and coevolution between plant species and microbial strains structures these communities. In this article, I provide an broad overview about current knowledge concerning mechanisms enabling adaptation and specialization of phytobiome communties to host plants as well as the potential for plants themselves to recruit and cultivate interactions with beneficial microbes. I further explore the possibility of host-beneficial microbe coevolution and suggest interactions that could promote the evolution of such close-knit partnerships. It is my hope that this overview will encourage future experiments that can begin to fill in this black box of ecological and evolutionary interactions across phytobiomes.\n\n\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=155 SRC=\"FIGDIR/small/120493_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (26K):\norg.highwire.dtl.DTLVardef@16c5315org.highwire.dtl.DTLVardef@c298d7org.highwire.dtl.DTLVardef@1c073a6org.highwire.dtl.DTLVardef@1e8bd1d_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗