A novel taxonomic marker that discriminates between morphologically complex actinomycetes

The ssgB gene is required for the early stages of sporangium formation in Actinoplanes missouriensis

In Streptomyces, multiple paralogs of SsgA-like proteins (SALPs) are involved in spore formation from aerial hyphae. However, the functions of SALPs have not yet been elucidated in other actinobacterial genera. Here, we report the primary function of an SsgB ortholog (AmSsgB) in Actinoplanes missouriensis, which develops terminal sporangia on the substrate mycelia via short sporangiophores. Importantly, AmSsgB is the sole SALP in A. missouriensis. The transcription of AmssgB was upregulated during sporangium formation, consistent with our previous findings that AmssgB is a member of the AmBldD regulon. The AmssgB null mutant (ΔAmssgB) strain formed non-globose irregular structures on the substrate mycelium. Transmission electron microscopy revealed that the irregular structures contained abnormally septate hypha-like cells, without an intrasporangial matrix. These phenotypic changes were restored by complementation with AmssgB. Additionally, analysis of the heterologous expression of seven SALP-encoding genes from Streptomyces coelicolor A3(2) (ssgA-G) in the ΔAmssgB strain revealed that only ssgB could compensate for AmSsgB deficiency. This indicated that SsgB of S. coelicolor A3(2) and AmSsgB have comparable functions in A. missouriensis. In contrast to the ΔAmssgB strain, the ftsZ-disrupted strain showed a severe growth defect and produced small sporangium-like structures that swelled to some extent. These findings indicate that AmSsgB is crucial for the early stages of sporangium formation, not for spore septum formation in the late stages. We propose that AmSsgB is involved in sporangium formation by promoting the expansion of the "presporangium" structures formed on the tips of the substrate hyphae.

IMPORTANCE

SsgB has been proposed as an archetypical SsgA-like protein with an evolutionarily conserved function in the morphological development of spore-forming actinomycetes. SsgB in Streptomyces coelicolor A3(2) is involved in spore septum formation. However, it is unclear whether this is the primary function of SsgBs in actinobacteria. This study demonstrated that the SsgB ortholog (AmSsgB) in Actinoplanes missouriensis is essential for sporangium expansion, which does not seem to be related to spore septum formation. However, the heterologous expression of ssgB from S. coelicolor A3(2) restored morphological abnormalities in the ΔAmssgB mutant. We propose that the primary function of SsgB is to initiate sporulation in differentiating cells (e.g., aerial hyphae in Streptomyces and "presporangium" cells in A. missouriensis) although its molecular mechanism remains unknown.

Kitasatospora fiedleri sp. nov., a novel antibiotic-producing member of the genus Kitasatospora

Strain TÜ4103T was originally sampled from Java, Indonesia and deposited in the Tübingen strain collection under the name 'Streptomyces sp.'. The strain was found to be an antibiotic producer as strain TÜ4103T showed bioactivity against Gram-positive bacteria, such as Bacillus subtilis and Kocuria rhizophila in bioassays. Strain TÜ4103T showed 16S rRNA gene sequence similarity of 99.65 % to Kitasatospora cheerisanensis DSM 101999T and 98.82 % to Kitasatospora niigatensis DSM 44781T and Kitasatospora cineracea DSM 44780T. Genome-based phylogenetic analysis revealed that strain TÜ4103T is closely related to K. cineracea DSM 44780T and K. niigatensis DSM 44781T. The digital DNA-DNA hybridization values between the genome sequences of strain TÜ4103T and its closest phylogenomic relatives, strains DSM 44780T and DSM 44781T, were 43.0 and 42.9 %, respectively. Average nucleotide identity (ANI) values support this claim, with the highest ANI score of 91.14 % between TÜ4103T and K. niigatensis being closely followed by an ANI value of 91.10 % between K. cineracea and TÜ4103T. The genome of TÜ4103T has a size of 7.91 Mb with a G+C content of 74.05 mol%. Whole-cell hydrolysates of strain TÜ4103T are rich in meso-diaminopimelic acid, and rhamnose, galactose and mannose are characteristic as whole-cell sugars. The phospholipid profile contains phosphatidylethanolamine, diphosphatidylglycerol and glycophospholipid. The predominant menaquinones (>93.5 %) are MK-9(H8) and MK-9(H6). Based on the phenotypic, genotypic and genomic characteristics, strain TÜ4103T (=DSM 114396T=CECT 30712T) merits recognition as the type strain of a novel species of the genus Kitasatospora, for which the name Kitasatospora fiedleri sp. nov. is proposed.

Genotype-phenotype correlations within the Geodermatophilaceae

The integration of genomic information into microbial systematics along with physiological and chemotaxonomic parameters provides for a reliable classification of prokaryotes. In silico analysis of chemotaxonomic traits is now being introduced to replace characteristics traditionally determined in the laboratory with the dual goal of both increasing the speed of the description of taxa and the accuracy and consistency of taxonomic reports. Genomics has already successfully been applied in the taxonomic rearrangement of Geodermatophilaceae (Actinomycetota) but in the light of new genomic data the taxonomy of the family needs to be revisited. In conjunction with the taxonomic characterisation of four strains phylogenetically located within the family, we conducted a phylogenetic analysis of the whole proteomes of the sequenced type strains and established genotype-phenotype correlations for traits related to chemotaxonomy, cell morphology and metabolism. Results indicated that the four isolates under study represent four novel species within the genus Blastococcus. Additionally, the genera Blastococcus, Geodermatophilus and Modestobacter were shown to be paraphyletic. Consequently, the new genera Trujillonella, Pleomorpha and Goekera were proposed within the Geodermatophilaceae and Blastococcus endophyticus was reclassified as Trujillonella endophytica comb. nov., Geodermatophilus daqingensis as Pleomorpha daqingensis comb. nov. and Modestobacter deserti as Goekera deserti comb. nov. Accordingly, we also proposed emended descriptions of Blastococcus aggregatus, Blastococcus jejuensis, Blastococcus saxobsidens and Blastococcus xanthilyniticus. In silico chemotaxonomic results were overall consistent with wet-lab results. Even though in silico discriminatory levels varied depending on the respective chemotaxonomic trait, this approach is promising for effectively replacing and/or complementing chemotaxonomic analyses at taxonomic ranks above the species level. Finally, interesting but previously overlooked insights regarding morphology and ecology were revealed by the presence of a repertoire of genes related to flagellum synthesis, chemotaxis, spore production and pilus assembly in all representatives of the family. A rich carbon metabolism including four different CO₂ fixation pathways and a battery of enzymes able to degrade complex carbohydrates were also identified in Blastococcus genomes.

Adaptation to Endophytic Lifestyle Through Genome Reduction by Kitasatospora sp. SUK42

Endophytic actinobacteria offer great potential as a source of novel bioactive compounds. In order to investigate the potential for the production of secondary metabolites by endophytes, we recovered a filamentous microorgansism from the tree Antidesma neurocarpum Miq. After phenotypic analysis and whole genome sequencing we demonstrated that this organism, SUK42 was a member of the actinobacterial genus Kitasatospora. This strain has a small genome in comparison with other type strains of this genus and has lost metabolic pathways associated with Stress Response, Nitrogen Metabolism and Secondary Metabolism. Despite this SUK42 can grow well in a laboratory environment and encodes a core genome that is consistent with other members of the genus. Finally, in contrast to other members of Kitasatospora, SUK42 encodes saccharide secondary metabolite biosynthetic gene clusters, one of which with similarity to the acarviostatin cluster, the product of which displays α-amylase inhibitory activity. As extracts of the host plant demonstrate this inhibitory activity, it suggests that the potential medicinal properties of A. neurocarpum Miq might be provided by the endophytic partner and illustrate the potential for exploitation of endophytes for clinical or industrial uses.

Diversity and Taxonomic Distribution of Endophytic Bacterial Community in the Rice Plant and Its Prospective

Endophytic bacterial communities are beneficial communities for host plants that exist inside the surfaces of plant tissues, and their application improves plant growth. They benefit directly from the host plant by enhancing the nutrient amount of the plant’s intake and influencing the phytohormones, which are responsible for growth promotion and stress. Endophytic bacteria play an important role in plant-growth promotion (PGP) by regulating the indirect mechanism targeting pest and pathogens through hydrolytic enzymes, antibiotics, biocontrol potential, and nutrient restriction for pathogens. To attain these benefits, firstly bacterial communities must be colonized by plant tissues. The nature of colonization can be achieved by using a set of traits, including attachment behavior and motility speed, degradation of plant polymers, and plant defense evasion. The diversity of bacterial endophytes colonization depends on various factors, such as plants’ relationship with environmental factors. Generally, each endophytic bacteria has a wide host range, and they are used as bio-inoculants in the form of synthetic applications for sustainable agriculture systems and to protect the environment from chemical hazards. This review discusses and explores the taxonomic distribution of endophytic bacteria associated with different genotypes of rice plants and their origin, movement, and mechanism of PGP. In addition, this review accentuates compressive meta data of endophytic bacteria communities associated with different genotypes of rice plants, retrieves their plant-growth-promoting properties and their antagonism against plant pathogens, and discusses the indication of endophytic bacterial flora in rice plant tissues using various methods. The future direction deepens the study of novel endophytic bacterial communities and their identification from rice plants through innovative techniques and their application for sustainable agriculture systems.

Marine Actinomycetes, New Sources of Biotechnological Products

The Actinomycetales order is one of great genetic and functional diversity, including diversity in the production of secondary metabolites which have uses in medical, environmental rehabilitation, and industrial applications. Secondary metabolites produced by actinomycete species are an abundant source of antibiotics, antitumor agents, anthelmintics, and antifungals. These actinomycete-derived medicines are in circulation as current treatments, but actinomycetes are also being explored as potential sources of new compounds to combat multidrug resistance in pathogenic bacteria. Actinomycetes as a potential to solve environmental concerns is another area of recent investigation, particularly their utility in the bioremediation of pesticides, toxic metals, radioactive wastes, and biofouling. Other applications include biofuels, detergents, and food preservatives/additives. Exploring other unique properties of actinomycetes will allow for a deeper understanding of this interesting taxonomic group. Combined with genetic engineering, microbial experimental evolution, and other enhancement techniques, it is reasonable to assume that the use of marine actinomycetes will continue to increase. Novel products will begin to be developed for diverse applied research purposes, including zymology and enology. This paper outlines the current knowledge of actinomycete usage in applied research, focusing on marine isolates and providing direction for future research.

An Alternative and Conserved Cell Wall Enzyme That Can Substitute for the Lipid II Synthase MurG

Almost all bacteria are surrounded by a cell wall, which protects cells from environmental harm. Formation of the cell wall requires the precursor molecule lipid II, which in bacteria is universally synthesized by the conserved and essential lipid II synthase MurG.

The cell wall is a stress-bearing structure and a unifying trait in bacteria. Without exception, synthesis of the cell wall involves formation of the precursor molecule lipid II by the activity of the essential biosynthetic enzyme MurG, which is encoded in the division and cell wall synthesis (dcw) gene cluster. Here, we present the discovery of a cell wall enzyme that can substitute for MurG. A mutant of Kitasatospora viridifaciens lacking a significant part of the dcw cluster, including murG, surprisingly produced lipid II and wild-type peptidoglycan. Genomic analysis identified a distant murG homologue, which encodes a putative enzyme that shares only around 31% amino acid sequence identity with MurG. We show that this enzyme can replace the canonical MurG, and we therefore designated it MglA. Orthologues of mglA are present in 38% of all genomes of Kitasatospora and members of the sister genus Streptomyces. CRISPR interference experiments showed that K. viridifaciens mglA can also functionally replace murG in Streptomyces coelicolor, thus validating its bioactivity and demonstrating that it is active in multiple genera. All together, these results identify MglA as a bona fide lipid II synthase, thus demonstrating plasticity in cell wall synthesis.

Ectopic positioning of the cell division plane is associated with single amino acid substitutions in the FtsZ-recruiting SsgB in Streptomyces

In most bacteria, cell division begins with the polymerization of the GTPase FtsZ at mid-cell, which recruits the division machinery to initiate cell constriction. In the filamentous bacterium Streptomyces, cell division is positively controlled by SsgB, which recruits FtsZ to the future septum sites and promotes Z-ring formation. Here, we show that various amino acid (aa) substitutions in the highly conserved SsgB protein result in ectopically placed septa that sever spores diagonally or along the long axis, perpendicular to the division plane. Fluorescence microscopy revealed that between 3.3% and 9.8% of the spores of strains expressing SsgB E120 variants were severed ectopically. Biochemical analysis of SsgB variant E120G revealed that its interaction with FtsZ had been maintained. The crystal structure of Streptomyces coelicolor SsgB was resolved and the key residues were mapped on the structure. Notably, residue substitutions (V115G, G118V, E120G) that are associated with septum misplacement localize in the α2-α3 loop region that links the final helix and the rest of the protein. Structural analyses and molecular simulation revealed that these residues are essential for maintaining the proper angle of helix α3. Our data suggest that besides altering FtsZ, aa substitutions in the FtsZ-recruiting protein SsgB also lead to diagonally or longitudinally divided cells in Streptomyces.

Ecosystem Functions of Microbial Consortia in Sustainable Agriculture

Knowledge of the agricultural soil microbiota, of the microbial consortia that comprise it, and the promotion of agricultural practices that maintain and encourage them, is a promising way to improve soil quality for sustainable agriculture and to provide food security. Although numerous studies have demonstrated the positive effects of beneficial soil microorganisms on crop yields and quality, the use of microbial consortia in agriculture remains low. Microbial consortia have more properties than an individual microbial inoculum, due to the synergy of the microorganisms that populate them. This review describes the main characteristics, ecosystem functions, crop benefits, and biotechnological applications of microbial consortia composed of arbuscular mycorrhizal fungi (AMF), plant growth-promoting rhizobacteria (PGPR), and Actinobacteria, to promote the restoration of agricultural soils and, consequently, the quality and health of agricultural crops. The aim is to provide knowledge that will contribute to the development of sustainable and sufficiently productive agriculture, which will adapt in a good way to the pace of the growing human population and to climate change.

Differential transcription of expanded gene families in central carbon metabolism of Streptomyces coelicolor A3(2)

Background

Streptomycete bacteria are prolific producers of specialized metabolites, many of which have clinically relevant bioactivity. A striking feature of their genomes is the expansion of gene families that encode the same enzymatic function. Genes that undergo expansion events, either by horizontal gene transfer or duplication, can have a range of fates: genes can be lost, or they can undergo neo-functionalization or sub-functionalization. To test whether expanded gene families in Streptomyces exhibit differential expression, an RNA-Seq approach was used to examine cultures of wild-type Streptomyces coelicolor grown with either glucose or tween as the sole carbon source.

Results

RNA-Seq analysis showed that two-thirds of genes within expanded gene families show transcriptional differences when strains were grown on tween compared to glucose. In addition, expression of specialized metabolite gene clusters (actinorhodin, isorenieratane, coelichelin and a cryptic NRPS) was also influenced by carbon source.

Conclusions

Expression of genes encoding the same enzymatic function had transcriptional differences when grown on different carbon sources. This transcriptional divergence enables partitioning to function under different physiological conditions. These approaches can inform metabolic engineering of industrial Streptomyces strains and may help develop cultivation conditions to activate the so-called silent biosynthetic gene clusters.

Regulation of antibiotic production in Actinobacteria: new perspectives from the post-genomic era

Covering: 2000 to 2018 The antimicrobial activity of many of their natural products has brought prominence to the Streptomycetaceae, a family of Gram-positive bacteria that inhabit both soil and aquatic sediments. In the natural environment, antimicrobial compounds are likely to limit the growth of competitors, thereby offering a selective advantage to the producer, in particular when nutrients become limited and the developmental programme leading to spores commences. The study of the control of this secondary metabolism continues to offer insights into its integration with a complex lifecycle that takes multiple cues from the environment and primary metabolism. Such information can then be harnessed to devise laboratory screening conditions to discover compounds with new or improved clinical value. Here we provide an update of the review we published in NPR in 2011. Besides providing the essential background, we focus on recent developments in our understanding of the underlying regulatory networks, ecological triggers of natural product biosynthesis, contributions from comparative genomics and approaches to awaken the biosynthesis of otherwise silent or cryptic natural products. In addition, we highlight recent discoveries on the control of antibiotic production in other Actinobacteria, which have gained considerable attention since the start of the genomics revolution. New technologies that have the potential to produce a step change in our understanding of the regulation of secondary metabolism are also described.

Polyphasic classification of the gifted natural product producer Streptomyces roseifaciens sp. nov

A polyphasic study was designed to establish the taxonomic status of a Streptomyces strain isolated from soil from the QinLing Mountains, Shaanxi Province, China, and found to be the source of known and new specialized metabolites. Strain MBT76^T was found to have chemotaxonomic, cultural and morphological properties consistent with its classification in the genus Streptomyces. The strain formed a distinct branch in the Streptomyces16S rRNA gene tree and was closely related to the type strains of Streptomyces hiroshimensis and Streptomycesmobaraerensis. Multi-locus sequence analyses based on five conserved house-keeping gene alleles showed that strain MBT76^T is closely related to the type strain of S. hiroshimensis, as was the case in analysis of a family of conserved proteins. The organism was also distinguished from S. hiroshimensis using cultural and phenotypic features. Average nucleotide identity and digital DNA-DNA hybridization values between the genomes of strain MBT76^T and S. hiroshimensis DSM 40037^T were 88.96 and 28.4±2.3%, respectively, which is in line with their assignment to different species. On the basis of this wealth of data it is proposed that strain MBT76^T (=DSM 106196^T=NCCB 100637^T), be classified as a new species, Streptomycesroseifaciens sp. nov.

Stress-induced formation of cell wall-deficient cells in filamentous actinomycetes

The cell wall is a shape-defining structure that envelopes almost all bacteria and protects them from environmental stresses. Bacteria can be forced to grow without a cell wall under certain conditions that interfere with cell wall synthesis, but the relevance of these wall-less cells (known as L-forms) is unclear. Here, we show that several species of filamentous actinomycetes have a natural ability to generate wall-deficient cells in response to hyperosmotic stress, which we call S-cells. This wall-deficient state is transient, as S-cells are able to switch to the normal mycelial mode of growth. However, prolonged exposure of S-cells to hyperosmotic stress yields variants that are able to proliferate indefinitely without their cell wall, similarly to L-forms. We propose that formation of wall-deficient cells in actinomycetes may serve as an adaptation to osmotic stress.

Bacteria can be forced to grow without cell wall if cell wall synthesis is inhibited. Here Ramijan et al. show that, in filamentous actinomycetes, hyperosmotic stress induces formation of wall-deficient cells that can switch to normal mycelial growth, or mutate and proliferate indefinitely as wall-less forms.

High-Resolution Analysis of the Peptidoglycan Composition in Streptomyces coelicolor

The bacterial cell wall maintains cell shape and protects against bursting by turgor. A major constituent of the cell wall is peptidoglycan (PG), which is continuously modified to enable cell growth and differentiation through the concerted activity of biosynthetic and hydrolytic enzymes. Streptomycetes are Gram-positive bacteria with a complex multicellular life style alternating between mycelial growth and the formation of reproductive spores. This involves cell wall remodeling at apical sites of the hyphae during cell elongation and autolytic degradation of the vegetative mycelium during the onset of development and antibiotic production. Here, we show that there are distinct differences in the cross-linking and maturation of the PGs between exponentially growing vegetative hyphae and the aerial hyphae that undergo sporulation. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis identified over 80 different muropeptides, revealing that major PG hydrolysis takes place over the course of mycelial growth. Half of the dimers lacked one of the disaccharide units in transition-phase cells, most likely due to autolytic activity. The deacetylation of MurNAc to MurN was particularly pronounced in spores and strongly reduced in sporulation mutants with a deletion of bldD or whiG, suggesting that MurN is developmentally regulated. Altogether, our work highlights the dynamic and growth phase-dependent changes in the composition of the PG in StreptomycesIMPORTANCE Streptomycetes are bacteria with a complex lifestyle and are model organisms for bacterial multicellularity. From a single spore, a large multigenomic multicellular mycelium is formed, which differentiates to form spores. Programmed cell death is an important event during the onset of morphological differentiation. In this work, we provide new insights into the changes in the peptidoglycan composition and over time, highlighting changes over the course of development and between growing mycelia and spores. This revealed dynamic changes in the peptidoglycan when the mycelia aged, with extensive peptidoglycan hydrolysis and, in particular, an increase in the proportion of 3-3 cross-links. Additionally, we identified a muropeptide that accumulates predominantly in the spores and may provide clues toward spore development.

Genome-Based Taxonomic Classification of the Phylum Actinobacteria

The application of phylogenetic taxonomic procedures led to improvements in the classification of bacteria assigned to the phylum Actinobacteria but even so there remains a need to further clarify relationships within a taxon that encompasses organisms of agricultural, biotechnological, clinical, and ecological importance. Classification of the morphologically diverse bacteria belonging to this large phylum based on a limited number of features has proved to be difficult, not least when taxonomic decisions rested heavily on interpretation of poorly resolved 16S rRNA gene trees. Here, draft genome sequences of a large collection of actinobacterial type strains were used to infer phylogenetic trees from genome-scale data using principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families, and genera, as well as many species and a few subspecies were shown to be in need of revision leading to proposals for the recognition of 2 orders, 10 families, and 17 genera, as well as the transfer of over 100 species to other genera. In addition, emended descriptions are given for many species mainly involving the addition of data on genome size and DNA G+C content, the former can be considered to be a valuable taxonomic marker in actinobacterial systematics. Many of the incongruities detected when the results of the present study were compared with existing classifications had been recognized from 16S rRNA gene trees though whole-genome phylogenies proved to be much better resolved. The few significant incongruities found between 16S/23S rRNA and whole genome trees underline the pitfalls inherent in phylogenies based upon single gene sequences. Similarly good congruence was found between the discontinuous distribution of phenotypic properties and taxa delineated in the phylogenetic trees though diverse non-monophyletic taxa appeared to be based on the use of plesiomorphic character states as diagnostic features.

Isolation of β-1,3-Glucanase-Producing Microorganisms from Poria cocos Cultivation Soil via Molecular Biology

β-1,3-Glucanase is considered as a useful enzymatic tool for β-1,3-glucan degradation to produce (1→3)-linked β-glucan oligosaccharides with pharmacological activity properties. To validly isolate β-1,3-glucanase-producing microorganisms, the soil of Wolfiporia extensa, considered an environment rich in β-1,3-glucan-degrading microorganisms, was subjected to high throughput sequencing. The results demonstrated that the genera Streptomyces (1.90%) and Arthrobacter (0.78%) belonging to the order Actinomycetales (8.64%) in the phylum Actinobacteria (18.64%) were observed in soil for P. cocos cultivation (FTL₁). Actinomycetes were considered as the candidates for isolation of glucan-degrading microorganisms. Out of 58 isolates, only 11 exhibited β-1,3-glucan-degrading activity. The isolate SYBCQL belonging to the genus Kitasatospora with β-1,3-glucan-degrading activity was found and reported for the first time and the isolate SYBC17 displayed the highest yield (1.02 U/mg) among the isolates. To check the β-1,3-glucanase contribution to β-1,3-glucan-degrading activity, two genes, 17-W and 17-Q, encoding β-1,3-glucanase in SYBC17 and one gene QLK1 in SYBCQL were cloned and expressed for verification at the molecular level. Our findings collectively showed that the isolates able to secrete β-1,3-glucanase could be obtained with the assistance of high-throughput sequencing and genes expression analysis. These methods provided technical support for isolating β-1,3-glucanase-producing microorganisms.

Streptomyces Differentiation in Liquid Cultures as a Trigger of Secondary Metabolism

Streptomyces is a diverse group of gram-positive microorganisms characterised by a complex developmental cycle. Streptomycetes produce a number of antibiotics and other bioactive compounds used in the clinic. Most screening campaigns looking for new bioactive molecules from actinomycetes have been performed empirically, e.g., without considering whether the bacteria are growing under the best developmental conditions for secondary metabolite production. These screening campaigns were extremely productive and discovered a number of new bioactive compounds during the so-called “golden age of antibiotics” (until the 1980s). However, at present, there is a worrying bottleneck in drug discovery, and new experimental approaches are needed to improve the screening of natural actinomycetes. Streptomycetes are still the most important natural source of antibiotics and other bioactive compounds. They harbour many cryptic secondary metabolite pathways not expressed under classical laboratory cultures. Here, we review the new strategies that are being explored to overcome current challenges in drug discovery. In particular, we focus on those aimed at improving the differentiation of the antibiotic-producing mycelium stage in the laboratory.

Sporulation-specific cell division defects in ylmE mutants of Streptomyces coelicolor are rescued by additional deletion of ylmD

Cell division during the reproductive phase of the Streptomyces life-cycle requires tight coordination between synchronous formation of multiple septa and DNA segregation. One remarkable difference with most other bacterial systems is that cell division in Streptomyces is positively controlled by the recruitment of FtsZ by SsgB. Here we show that deletion of ylmD (SCO2081) or ylmE (SCO2080), which lie in operon with ftsZ in the dcw cluster of actinomycetes, has major consequences for sporulation-specific cell division in Streptomyces coelicolor. Electron and fluorescence microscopy demonstrated that ylmE mutants have a highly aberrant phenotype with defective septum synthesis, and produce very few spores with low viability and high heat sensitivity. FtsZ-ring formation was also highly disturbed in ylmE mutants. Deletion of ylmD had a far less severe effect on sporulation. Interestingly, the additional deletion of ylmD restored sporulation to the ylmE null mutant. YlmD and YlmE are not part of the divisome, but instead localize diffusely in aerial hyphae, with differential intensity throughout the sporogenic part of the hyphae. Taken together, our work reveals a function for YlmD and YlmE in the control of sporulation-specific cell division in S. coelicolor, whereby the presence of YlmD alone results in major developmental defects.

Expanding Primary Metabolism Helps Generate the Metabolic Robustness To Facilitate Antibiotic Biosynthesis in Streptomyces

The expansion of the genetic repertoire of an organism by gene duplication or horizontal gene transfer (HGT) can aid adaptation. Streptomyces bacteria are prolific producers of bioactive specialized metabolites that have adaptive functions in nature and have found extensive utility in human medicine. While the biosynthesis of these specialized metabolites is directed by dedicated biosynthetic gene clusters, little attention has been focused on how these organisms have evolved robustness in their genomes to facilitate the metabolic plasticity required to provide chemical precursors for biosynthesis during the complex metabolic transitions from vegetative growth to specialized metabolite production and sporulation. Here, we examine genetic redundancy in actinobacteria and show that specialized metabolite-producing bacterial families exhibit gene family expansion in primary metabolism. Focusing on a gene duplication event, we show that the two pyruvate kinases in the genome of Streptomyces coelicolor arose by an ancient duplication event and that each has evolved altered enzymatic kinetics, with Pyk1 having a 20-fold-higher kcat than Pyk2 (4,703 s-1 compared to 215 s-1, respectively), and yet both are constitutively expressed. The pyruvate kinase mutants were also found to be compromised in terms of fitness compared to wild-type Streptomyces These data suggest that expanding gene families can help maintain cell functionality during metabolic perturbation such as nutrient limitation and/or specialized metabolite production.IMPORTANCE The rise of antimicrobial-resistant infections has prompted a resurgence in interest in understanding the production of specialized metabolites, such as antibiotics, by Streptomyces The presence of multiple genes encoding the same enzymatic function is an aspect of Streptomyces biology that has received little attention; however, understanding how the metabolic expansion influences these organisms can help enhance production of clinically useful molecules. Here, we show that expanding the number of pyruvate kinases enables metabolic adaptation, increases strain fitness, and represents an excellent target for metabolic engineering of industrial specialized metabolite-producing bacteria and the activation of cryptic specialized metabolites.

SParticle, an algorithm for the analysis of filamentous microorganisms in submerged cultures

Streptomycetes are filamentous bacteria that produce a plethora of bioactive natural products and industrial enzymes. Their mycelial lifestyle typically results in high heterogeneity in bioreactors, with morphologies ranging from fragments and open mycelial mats to dense pellets. There is a strong correlation between morphology and production in submerged cultures, with small and open mycelia favouring enzyme production, while most antibiotics are produced mainly in pellets. Here we describe SParticle, a Streptomyces Particle analysis method that combines whole slide imaging with automated image analysis to characterize the morphology of submerged grown Streptomyces cultures. SParticle allows the analysis of over a thousand particles per hour, offering a high throughput method for the imaging and statistical analysis of mycelial morphologies. The software is available as a plugin for the open source software ImageJ and allows users to create custom filters for other microbes. Therefore, SParticle is a widely applicable tool for the analysis of filamentous microorganisms in submerged cultures.

Inter- and intracellular colonization of Arabidopsis roots by endophytic actinobacteria and the impact of plant hormones on their antimicrobial activity

Many actinobacteria live in close association with eukaryotes such as fungi, insects, animals and plants. Plant-associated actinobacteria display (endo)symbiotic, saprophytic or pathogenic life styles, and can make up a substantial part of the endophytic community. Here, we characterised endophytic actinobacteria isolated from root tissue of Arabidopsis thaliana (Arabidopsis) plants grown in soil from a natural ecosystem. Many of these actinobacteria belong to the family of Streptomycetaceae with Streptomyces olivochromogenes and Streptomyces clavifer as well represented species. When seeds of Arabidopsis were inoculated with spores of Streptomyces strain coa1, which shows high similarity to S. olivochromogenes, roots were colonised intercellularly and, unexpectedly, also intracellularly. Subsequent exposure of endophytic isolates to plant hormones typically found in root and shoot tissues of Arabidopsis led to altered antibiotic production against Escherichia coli and Bacillus subtilis. Taken together, our work reveals remarkable colonization patterns of endophytic streptomycetes with specific traits that may allow a competitive advantage inside root tissue.

Genome-based classification of micromonosporae with a focus on their biotechnological and ecological potential

There is a need to clarify relationships within the actinobacterial genus Micromonospora, the type genus of the family Micromonosporaceae, given its biotechnological and ecological importance. Here, draft genomes of 40 Micromonospora type strains and two non-type strains are made available through the Genomic Encyclopedia of Bacteria and Archaea project and used to generate a phylogenomic tree which showed they could be assigned to well supported phyletic lines that were not evident in corresponding trees based on single and concatenated sequences of conserved genes. DNA G+C ratios derived from genome sequences showed that corresponding data from species descriptions were imprecise. Emended descriptions include precise base composition data and approximate genome sizes of the type strains. antiSMASH analyses of the draft genomes show that micromonosporae have a previously unrealised potential to synthesize novel specialized metabolites. Close to one thousand biosynthetic gene clusters were detected, including NRPS, PKS, terpenes and siderophores clusters that were discontinuously distributed thereby opening up the prospect of prioritising gifted strains for natural product discovery. The distribution of key stress related genes provide an insight into how micromonosporae adapt to key environmental variables. Genes associated with plant interactions highlight the potential use of micromonosporae in agriculture and biotechnology.

Analysis of Spo0M function in Bacillus subtilis

Spo0M has been previously reported as a regulator of sporulation in Bacillus subtilis; however, little is known about the mechanisms through which it participates in sporulation, and there is no information to date that relates this protein to other processes in the bacterium. In this work we present evidence from proteomic, protein-protein interaction, morphological, subcellular localization microscopy and bioinformatics studies which indicate that Spo0M function is not necessarily restricted to sporulation, and point towards its involvement in other stages of the vegetative life cycle. In the current study, we provide evidence that Spo0M interacts with cytoskeletal proteins involved in cell division, which suggest a function additional to that previously described in sporulation. Spo0M expression is not restricted to the transition phase or sporulation; rather, its expression begins during the early stages of growth and Spo0M localization in B. subtilis depends on the bacterial life cycle and could be related to an additional proposed function. This is supported by our discovery of homologs in a broad distribution of bacterial genera, even in non-sporulating species. Our work paves the way for re-evaluation of the role of Spo0M in bacterial cell.

New natural products identified by combined genomics-metabolomics profiling of marine Streptomyces sp. MP131-18

Marine actinobacteria are drawing more and more attention as a promising source of new natural products. Here we report isolation, genome sequencing and metabolic profiling of new strain Streptomyces sp. MP131-18 isolated from marine sediment sample collected in the Trondheim Fjord, Norway. The 16S rRNA and multilocus phylogenetic analysis showed that MP131-18 belongs to the genus Streptomyces. The genome of MP131-18 isolate was sequenced, and 36 gene clusters involved in the biosynthesis of 18 different types of secondary metabolites were predicted using antiSMASH analysis. The combined genomics-metabolics profiling of the strain led to the identification of several new biologically active compounds. As a result, the family of bisindole pyrroles spiroindimicins was extended with two new members, spiroindimicins E and F. Furthermore, prediction of the biosynthetic pathway for unusual α-pyrone lagunapyrone isolated from MP131-18 resulted in foresight and identification of two new compounds of this family – lagunapyrones D and E. The diversity of identified and predicted compounds from Streptomyces sp. MP131-18 demonstrates that marine-derived actinomycetes are not only a promising source of new natural products, but also represent a valuable pool of genes for combinatorial biosynthesis of secondary metabolites.

Genome Sequence of the Filamentous Actinomycete Kitasatospora viridifaciens

The vast majority of antibiotics are produced by filamentous soil bacteria called actinomycetes. We report here the genome sequence of the tetracycline producer “Streptomyces viridifaciens” DSM 40239. Given that this species has the hallmark signatures characteristic of the Kitasatospora genus, we previously proposed to rename this organism Kitasatospora viridifaciens.

SepG coordinates sporulation-specific cell division and nucleoid organization in Streptomyces coelicolor

Bacterial cell division is a highly complex process that requires tight coordination between septum formation and chromosome replication and segregation. In bacteria that divide by binary fission a single septum is formed at mid-cell, a process that is coordinated by the conserved cell division scaffold protein FtsZ. In contrast, during sporulation-specific cell division in streptomycetes, up to a hundred rings of FtsZ (Z rings) are produced almost simultaneously, dividing the multinucleoid aerial hyphae into long chains of unigenomic spores. This involves the active recruitment of FtsZ by the SsgB protein, and at the same time requires sophisticated systems to regulate chromosome dynamics. Here, we show that SepG is required for the onset of sporulation and acts by ensuring that SsgB is localized to future septum sites. Förster resonance energy transfer imaging suggests direct interaction between SepG and SsgB. The beta-lactamase reporter system showed that SepG is a transmembrane protein with its central domain oriented towards the cytoplasm. Without SepG, SsgB fails to localize properly, consistent with a crucial role for SepG in the membrane localization of the SsgB-FtsZ complex. While SsgB remains associated with FtsZ, SepG re-localizes to the (pre)spore periphery. Expanded doughnut-shaped nucleoids are formed in sepG null mutants, suggesting that SepG is required for nucleoid compaction. Taken together, our work shows that SepG, encoded by one of the last genes in the conserved dcw cluster of cell division and cell-wall-related genes in Gram-positive bacteria whose function was still largely unresolved,coordinates septum synthesis and chromosome organization in Streptomyces.

A systematic study of the whole genome sequence of Amycolatopsis methanolica strain 239T provides an insight into its physiological and taxonomic properties which correlate with its position in the genus

The complete genome of methanol-utilizing Amycolatopsis methanolica strain 239^T was generated, revealing a single 7,237,391 nucleotide circular chromosome with 7074 annotated protein-coding sequences (CDSs). Comparative analyses against the complete genome sequences of Amycolatopsis japonica strain MG417-CF17^T, Amycolatopsis mediterranei strain U32 and Amycolatopsis orientalis strain HCCB10007 revealed a broad spectrum of genomic structures, including various genome sizes, core/quasi-core/non-core configurations and different kinds of episomes. Although polyketide synthase gene clusters were absent from the A. methanolica genome, 12 gene clusters related to the biosynthesis of other specialized (secondary) metabolites were identified. Complete pathways attributable to the facultative methylotrophic physiology of A. methanolica strain 239^T, including both the mdo/mscR encoded methanol oxidation and the hps/hpi encoded formaldehyde assimilation via the ribulose monophosphate cycle, were identified together with evidence that the latter might be the result of horizontal gene transfer. Phylogenetic analyses based on 16S rDNA or orthologues of AMETH_3452, a novel actinobacterial class-specific conserved gene against 62 or 18 Amycolatopsis type strains, respectively, revealed three major phyletic lineages, namely the mesophilic or moderately thermophilic A. orientalis subclade (AOS), the mesophilic Amycolatopsis taiwanensis subclade (ATS) and the thermophilic A. methanolica subclade (AMS). The distinct growth temperatures of members of the subclades correlated with corresponding genetic variations in their encoded compatible solutes. This study shows the value of integrating conventional taxonomic with whole genome sequence data.

Taxonomy, Physiology, and Natural Products of Actinobacteria

Actinobacteria are Gram-positive bacteria with high G+C DNA content that constitute one of the largest bacterial phyla, and they are ubiquitously distributed in both aquatic and terrestrial ecosystems. Many Actinobacteria have a mycelial lifestyle and undergo complex morphological differentiation. They also have an extensive secondary metabolism and produce about two-thirds of all naturally derived antibiotics in current clinical use, as well as many anticancer, anthelmintic, and antifungal compounds. Consequently, these bacteria are of major importance for biotechnology, medicine, and agriculture. Actinobacteria play diverse roles in their associations with various higher organisms, since their members have adopted different lifestyles, and the phylum includes pathogens (notably, species of Corynebacterium, Mycobacterium, Nocardia, Propionibacterium, and Tropheryma), soil inhabitants (e.g., Micromonospora and Streptomyces species), plant commensals (e.g., Frankia spp.), and gastrointestinal commensals (Bifidobacterium spp.). Actinobacteria also play an important role as symbionts and as pathogens in plant-associated microbial communities. This review presents an update on the biology of this important bacterial phylum.

Diversity and functions of volatile organic compounds produced by Streptomyces from a disease-suppressive soil

In disease-suppressive soils, plants are protected from infections by specific root pathogens due to the antagonistic activities of soil and rhizosphere microorganisms. For most disease-suppressive soils, however, the microorganisms and mechanisms involved in pathogen control are largely unknown. Our recent studies identified Actinobacteria as the most dynamic phylum in a soil suppressive to the fungal root pathogen Rhizoctonia solani. Here we isolated and characterized 300 isolates of rhizospheric Actinobacteria from the Rhizoctonia-suppressive soil. Streptomyces species were the most abundant, representing approximately 70% of the isolates. Streptomyces are renowned for the production of an exceptionally large number of secondary metabolites, including volatile organic compounds (VOCs). VOC profiling of 12 representative Streptomyces isolates by SPME-GC-MS allowed a more refined phylogenetic delineation of the Streptomyces isolates than the sequencing of 16S rRNA and the house-keeping genes atpD and recA only. VOCs of several Streptomyces isolates inhibited hyphal growth of R. solani and significantly enhanced plant shoot and root biomass. Coupling of Streptomyces VOC profiles with their effects on fungal growth, pointed to VOCs potentially involved in antifungal activity. Subsequent assays with five synthetic analogs of the identified VOCs showed that methyl 2-methylpentanoate, 1,3,5-trichloro-2-methoxy benzene and the VOCs mixture have antifungal activity. In conclusion, our results point to a potential role of VOC-producing Streptomyces in disease suppressive soils and show that VOC profiling of rhizospheric Streptomyces can be used as a complementary identification tool to construct strain-specific metabolic signatures.

Socially mediated induction and suppression of antibiosis during bacterial coexistence

Despite their importance for humans, there is little consensus on the function of antibiotics in nature for the bacteria that produce them. Classical explanations suggest that bacteria use antibiotics as weapons to kill or inhibit competitors, whereas a recent alternative hypothesis states that antibiotics are signals that coordinate cooperative social interactions between coexisting bacteria. Here we distinguish these hypotheses in the prolific antibiotic-producing genus Streptomyces and provide strong evidence that antibiotics are weapons whose expression is significantly influenced by social and competitive interactions between competing strains. We show that cells induce facultative responses to cues produced by competitors by (i) increasing their own antibiotic production, thereby decreasing costs associated with constitutive synthesis of these expensive products, and (ii) by suppressing antibiotic production in competitors, thereby reducing direct threats to themselves. These results thus show that although antibiotic production is profoundly social, it is emphatically not cooperative. Using computer simulations, we next show that these facultative strategies can facilitate the maintenance of biodiversity in a community context by converting lethal interactions between neighboring colonies to neutral interactions where neither strain excludes the other. Thus, just as bacteriocins can lead to increased diversity via rock-paper-scissors dynamics, so too can antibiotics via elicitation and suppression. Our results reveal that social interactions are crucial for understanding antibiosis and bacterial community dynamics, and highlight the potential of interbacterial interactions for novel drug discovery by eliciting pathways that mediate interference competition.

Transcriptional analysis of the cell division-related ssg genes in Streptomyces coelicolor reveals direct control of ssgR by AtrA

SsgA-like proteins are a family of actinomycete-specific regulatory proteins that control cell division and spore maturation in streptomycetes. SsgA and SsgB together activate sporulation-specific cell division by controlling the localization of FtsZ. Here we report the identification of novel regulators that control the transcription of the ssgA-like genes. Transcriptional regulators controlling ssg gene expression were identified using a DNA-affinity capture assay. Supporting transcriptional and DNA binding studies showed that the ssgA activator gene ssgR is controlled by the TetR-family regulator AtrA, while the γ-butyrolactone-responsive AdpA (SCO2792) and SlbR (SCO0608) and the metabolic regulator Rok7B7 (SCO6008) were identified as candidate regulators for the cell division genes ssgA, ssgB and ssgG. Transcription of the cell division gene ssgB depended on the sporulation genes whiA and whiH, while ssgR, ssgA and ssgD were transcribed independently of the whi genes. Our work sheds new light on the mechanisms by which sporulation-specific cell division is controlled in Streptomyces.

Tailoring specialized metabolite production in streptomyces

Streptomycetes are prolific producers of a plethora of medically useful metabolites. These compounds are made by complex secondary (specialized) metabolic pathways, which utilize primary metabolic intermediates as building blocks. In this review we discuss the evolution of specialized metabolites and how expansion of gene families in primary metabolism has lead to the evolution of diversity in these specialized metabolic pathways and how developing a better understanding of expanded primary metabolic pathways can help enhance synthetic biology approaches to industrial pathway engineering.

Morphogenesis of Streptomyces in submerged cultures

Members of the genus Streptomyces are mycelial bacteria that undergo a complex multicellular life cycle and propagate via sporulation. Streptomycetes are important industrial microorganisms, as they produce a plethora of medically relevant natural products, including the majority of clinically important antibiotics, as well as a wide range of enzymes with industrial application. While development of Streptomyces in surface-grown cultures is well studied, relatively little is known of the parameters that determine morphogenesis in submerged cultures. Here, growth is characterized by the formation of mycelial networks and pellets. From the perspective of industrial fermentations, such mycelial growth is unattractive, as it is associated with slow growth, heterogeneous cultures, and high viscosity. Here, we review the current insights into the genetic and environmental factors that determine mycelial growth and morphology in liquid-grown cultures. The genetic factors include cell-matrix proteins and extracellular polymers, morphoproteins with specific roles in liquid-culture morphogenesis, with the SsgA-like proteins as well-studied examples, and programmed cell death. Environmental factors refer in particular to those dictated by process engineering, such as growth media and reactor set-up. These insights are then integrated to provide perspectives as to how this knowledge can be applied to improve streptomycetes for industrial applications.

Eliciting antibiotics active against the ESKAPE pathogens in a collection of actinomycetes isolated from mountain soils

The rapid emergence of multidrug-resistant (MDR) bacterial pathogens poses a major threat for human health. In recent years, genome sequencing has unveiled many poorly expressed antibiotic clusters in actinomycetes. Here, we report a well-defined ecological collection of >800 actinomycetes obtained from sites in the Himalaya and Qinling mountains, and we used these in a concept study to see how efficiently antibiotics can be elicited against MDR pathogens isolated recently from the clinic. Using 40 different growth conditions, 96 actinomycetes were identified - predominantly Streptomyces - that produced antibiotics with efficacy against the MDR clinical isolates referred to as ESKAPE pathogens: Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa and/or Enterobacter cloacae. Antimicrobial activities that fluctuated strongly with growth conditions were correlated with specific compounds, including borrelidin, resistomycin, carbomethoxy-phenazine, and 6,7,8- and 5,6,8-trimethoxy-3-methylisocoumarin, of which the latter was not described previously. Our work provided insights into the potential of actinomycetes as producers of drugs with efficacy against clinical isolates that have emerged recently and also underlined the importance of targeting a specific pathogen.

Streptomyces leeuwenhoekii sp. nov., the producer of chaxalactins and chaxamycins, forms a distinct branch in Streptomyces gene trees

A polyphasic study was carried out to establish the taxonomic status of an Atacama Desert isolate, Streptomyces strain C34(T), which synthesises novel antibiotics, the chaxalactins and chaxamycins. The organism was shown to have chemotaxonomic, cultural and morphological properties consistent with its classification in the genus Streptomyces. Analysis of 16S rRNA gene sequences showed that strain C34(T) formed a distinct phyletic line in the Streptomyces gene tree that was very loosely associated with the type strains of several Streptomyces species. Multilocus sequence analysis based on five house-keeping gene alleles underpinned the separation of strain C34(T) from all of its nearest phylogenetic neighbours, apart from Streptomyces chiangmaiensis TA-1(T) and Streptomyces hyderabadensis OU-40(T) which are not currently in the MLSA database. Strain C34(T) was distinguished readily from the S. chiangmaiensis and S. hyderabadensis strains by using a combination of cultural and phenotypic data. Consequently, strain C34(T) is considered to represent a new species of the genus Streptomyces for which the name Streptomyces leeuwenhoekii sp. nov. is proposed. The type strain is C34(T) (= DSM 42122(T) = NRRL B-24963(T)). Analysis of the whole-genome sequence of S. leeuwenhoekii, with 6,780 predicted open reading frames and a total genome size of around 7.86 Mb, revealed a high potential for natural product biosynthesis.

Bacterial solutions to multicellularity: a tale of biofilms, filaments and fruiting bodies

Although bacteria frequently live as unicellular organisms, many spend at least part of their lives in complex communities, and some have adopted truly multicellular lifestyles and have abandoned unicellular growth. These transitions to multicellularity have occurred independently several times for various ecological reasons, resulting in a broad range of phenotypes. In this Review, we discuss the strategies that are used by bacteria to form and grow in multicellular structures that have hallmark features of multicellularity, including morphological differentiation, programmed cell death and patterning. In addition, we examine the evolutionary and ecological factors that lead to the wide range of coordinated multicellular behaviours that are observed in bacteria.

Streptacidiphilus hamsterleyensis sp. nov., isolated from a spruce forest soil

Three acidophilic actinobacteria, isolates LSCA2, FGG8 and HSCA14(T), recovered from spruce litter were examined using a polyphasic approach. Chemotaxonomic and morphological properties of the isolates were found to be consistent with their classification in the genus Streptacidiphilus. The isolates were shown to have identical 16S rRNA gene sequences and were most closely related to Streptacidiphilus neutrinimicus DSM 41755(T) (99.9 % similarity). However, DNA:DNA relatedness between isolate HSCA14(T) and the type strain of S. neutrinimicus was found to be low at 44.0 (±14.1) %. A combination of phenotypic features, including degradative and nutritional characteristics were shown to distinguish the isolates from their nearest phylogenetic neighbours. Data from this study show that the isolates form a novel species in the genus for which the name S. hamsterleyensis sp. nov. is proposed. The type strain is HSCA 14(T) (=DSM 45900(T) = KACC 17456(T) = NCIMB 14865(T)).