Production of a Dibrominated Aromatic Secondary Metabolite by a Planctomycete Implies Complex Interaction with a Macroalgal Host

Planctoellipticum variicoloris gen. nov., sp. nov., a novel member of the family Planctomycetaceae isolated from wastewater of the aeration lagoon of a sugar processing plant in Northern Germany

In the present study, we characterise a strain isolated from the wastewater aeration lagoon of a sugar processing plant in Schleswig (Northern Germany) by Heinz Schlesner. As a pioneer in planctomycetal research, he isolated numerous strains belonging to the phylum Planctomycetota from aquatic habitats around the world. Phylogenetic analyses show that strain SH412T belongs to the family Planctomycetaceae and shares with 91.6% the highest 16S rRNA gene sequence similarity with Planctopirus limnophila DSM 3776T. Its genome has a length of 7.3 Mb and a G + C content of 63.6%. Optimal growth of strain SH412T occurs at pH 7.0-7.5 and 28 °C with its pigmentation depending on sunlight exposure. Strain SH412T reproduces by polar asymmetric division ("budding") and forms ovoid cells. The cell size determination was performed using a semi-automatic pipeline, which we first evaluated with the model species P. limnophila and then applied to strain SH412T. Furthermore, the data acquired during time-lapse analyses suggests a lifestyle switch from flagellated daughter cells to non-flagellated mother cells in the subsequent cycle. Based on our data, we suggest that strain SH412T represents a novel species within a novel genus, for which we propose the name Planctoellipticum variicoloris gen. nov., sp. nov., with strain SH412T (= CECT 30430T = STH00996T, the STH number refers to the Jena Microbial Resource Collection JMRC) as the type strain of the new species.

A type III polyketide synthase cluster in the phylum Planctomycetota is involved in alkylresorcinol biosynthesis

Members of the bacterial phylum Planctomycetota have recently emerged as promising and for the most part untapped sources of novel bioactive compounds. The characterization of more than 100 novel species in the last decade stimulated recent bioprospection studies that start to unveil the chemical repertoire of the phylum. In this study, we performed systematic bioinformatic analyses based on the genomes of all 131 described members of the current phylum focusing on the identification of type III polyketide synthase (PKS) genes. Type III PKSs are versatile enzymes involved in the biosynthesis of a wide array of structurally diverse natural products with potent biological activities. We identified 96 putative type III PKS genes of which 58 are encoded in an operon with genes encoding a putative oxidoreductase and a methyltransferase. Sequence similarities on protein level and the genetic organization of the operon point towards a functional link to the structurally related hierridins recently discovered in picocyanobacteria. The heterologous expression of planctomycetal type III PKS genes from strains belonging to different families in an engineered Corynebacterium glutamicum strain led to the biosynthesis of pentadecyl- and heptadecylresorcinols. Phenotypic assays performed with the heterologous producer strains and a constructed type III PKS gene deletion mutant suggest that the natural function of the identified compounds differs from that confirmed in other bacterial alkylresorcinol producers. KEY POINTS: • Planctomycetal type III polyketide synthases synthesize long-chain alkylresorcinols. • Phylogenetic analyses suggest an ecological link to picocyanobacterial hierridins. • Engineered C. glutamicum is suitable for an expression of planctomycete-derived genes.

Stratiformator vulcanicus gen. nov., sp. nov., a marine member of the family Planctomycetaceae isolated from a red biofilm in the Tyrrhenian Sea close to the volcanic island Panarea

A novel planctomycetal strain, designated Pan189T, was isolated from biofilm material sampled close to Panarea Island in the Tyrrhenian Sea. Cells of strain Pan189T are round grain rice-shaped, form pink colonies and display typical planctomycetal characteristics including asymmetric cell division through polar budding and presence of crateriform structures. Cells bear a stalk opposite to the division pole and fimbriae cover the cell surface. Strain Pan189T has a mesophilic (optimum at 24 °C) and neutrophilic (optimum at pH 7.5) growth profile, is aerobic and heterotrophic. Under laboratory-scale cultivation conditions, it reached a generation time of 102 h (µmax = 0.0068 h-1), which places the strain among the slowest growing members of the phylum Planctomycetota characterized so far. The genome size of the strain is with 5.23 Mb at the lower limit among the family Planctomycetaceae (5.1-8.9 Mb). Phylogenetically, the strain represents a novel genus and species in the family Planctomycetaceae, order Planctomycetales, class Planctomycetia. We propose the name Stratiformator vulcanicus gen. nov., sp. nov. for the novel taxon, that is represented by the type strain Pan189T (= DSM 101711 T = CECT 30699 T).

Blastopirellula sediminis sp. nov. a new member of Pirellulaceae isolated from the Andaman and Nicobar Islands

Two cream-coloured strains (JC732^T, JC733) of Gram-stain negative, mesophilic, catalase and oxidase positive, aerobic bacteria which divide by budding, form crateriform structures, and cell aggregates were isolated from marine habitats of Andaman and Nicobar Islands, India. Both strains had genome size of 7.1 Mb and G + C content of 58.9%. Both strains showed highest 16S rRNA gene-based similarity with Blastopirellula retiformator Enr8^T (98.7%). Strains JC732^T and JC733 shared 100% identity of 16S rRNA gene and genome sequences. The coherence of both strains with the genus Blastopirellula was supported by the 16S rRNA gene based and the phylogenomic trees. Further, the chemo-taxonomic characters and the genome relatedness indices [ANI (82.4%), AAI (80.4%) and dDDH (25.2%)] also support the delineation at the species level. Both strains have the capability to degrade chitin and genome analysis shows the ability to fix N₂. Based on the phylogenetic, phylogenomic, comparative genomic, morphological, physiological, and biochemical characteristics, strain JC732^T is described as a new species of the genus Blastopirellula for which the name Blastopirellula sediminis sp. nov. is proposed, with strain JC733 as an additional strain.

Stieleria sedimenti sp. nov., a Novel Member of the Family Pirellulaceae with Antimicrobial Activity Isolated in Portugal from Brackish Sediments

The phylum Planctomycetota is known for having uncommon biological features. Recently, biotechnological applications of its members have started to be explored, namely in the genus Stieleria. Here, we formally describe a novel Stieleriaisolate designated as strain ICT_E10.1T, obtained from sediments collected in the Tagus estuary (Portugal). Strain ICT_E10.1T is pink-pigmented, spherical to ovoid in shape, and 1.7 µm ± 0.3 × 1.4 µm ± 0.3 in size. Cells cluster strongly in aggregates or small chains, divide by budding, and have prominent fimbriae. Strain ICT_E10.1T is heterotrophic and aerobic. Growth occurs from 20 to 30 °C, from 0.5 to 3% (w/v) NaCl, and from pH 6.5 to 11.0. The analysis of the 16S rRNA gene sequence placed strain ICT_E10.1T into the genus Stieleria with Stieleria neptunia Enr13T as the closest validly described relative. The genome size is 9,813,311 bp and the DNA G+C content is 58.8 mol%. Morphological, physiological, and genomic analyses support the separation of this strain into a novel species, for which we propose the name Stieleria sedimenti represented by strain ICT_E10.1T as the type of strain (=CECT 30514T= DSM 113784T). Furthermore, this isolate showed biotechnological potential by displaying relevant biosynthetic gene clusters and potent activity against Staphylococcus aureus.

Isolation, diversity and antimicrobial activity of planctomycetes from the Tejo river estuary (Portugal)

The discovery of new bioactive compounds is an invaluable aid to the development of new drugs. Strategies for finding novel molecules can focus on the exploitation of less studied organisms and ecosystems such as planctomycetes and brackish habitats. The unique cell biology of the underexplored Planctomycetota mean it is of particular interest. In this study, we aimed to isolate planctomycetes from the estuary of the Tejo river (Portugal). To reach this goal, macroalgae, water and sediments were sampled and diverse media and isolation techniques applied. Sixty-nine planctomycetal strains were brought into pure culture. An analysis of the 16S rRNA genes found that the majority of the isolates were affiliated to the genus Rhodopirellula. Putative novel taxa belonging to genera Stieleria and Rhodopirellula were also isolated and characterized morphologically. Enterobacterial Repetitive Intergenic Consensus fingerprinting analyses showed higher diversity and different genotypes within close strains. Relevant biosynthetic gene clusters were found in most isolates and acetone extracts from representative strains exhibited mild antimicrobial activities against Escherichia coli and Staphylococcus aureus. Our work has not only enlarged the number and diversity of cultured planctomycetes but also shown the potential for the discovery of bioactive compounds from the novel taxa.

Screening for Biofilm-Stimulating Factors in the Freshwater Planctomycete Planctopirus limnophila to Improve Sessile Growth in a Chemically Defined Medium

Planctomycetes such as Planctopirus limnophila offer a promising source of bioactive molecules, particularly when they switch from planktonic to sessile growth, but little is known about the corresponding biosynthetic gene clusters and how they are activated. We therefore screened for factors that promote sessile growth and biofilm formation to enable the cultivation of P. limnophila in a fixed-bed reactor. We carried out screening in microtiter plates focusing on biofilm formation and changes in optical density in response to various C:N ratios, metal ions, and oxidative stress. We used MTT assays and crystal violet staining to quantify biofilm formation. Positive factors were then validated in a fixed-bed bioreactor. The initial screen showed that D1ASO medium supplemented with NH4Cl to achieve a C:N ratio of 5.7:1, as well as 50 µM FeSO4 or CuSO4, increased the biofilm formation relative to the control medium. Exposure to H2O2 did not affect cell viability but stimulated biofilm formation. However, the same results were not replicated in the fixed-bed bioreactor, probably reflecting conditions that are unique to this environment such as the controlled pH and more vigorous aeration. Although we were able to cultivate P. limnophila in a fixed-bed bioreactor using a chemically defined medium, the factors that stimulate biofilm formation and inhibit planktonic growth were only identified in microtiter plates and further evaluation is required to establish optimal growth conditions in the bioreactor system.

Beyond Soil-Dwelling Actinobacteria: Fantastic Antibiotics and Where to Find Them

Bacterial secondary metabolites represent an invaluable source of bioactive molecules for the pharmaceutical and agrochemical industries. Although screening campaigns for the discovery of new compounds have traditionally been strongly biased towards the study of soil-dwelling Actinobacteria, the current antibiotic resistance and discovery crisis has brought a considerable amount of attention to the study of previously neglected bacterial sources of secondary metabolites. The development and application of new screening, sequencing, genetic manipulation, cultivation and bioinformatic techniques have revealed several other groups of bacteria as producers of striking chemical novelty. Biosynthetic machineries evolved from independent taxonomic origins and under completely different ecological requirements and selective pressures are responsible for these structural innovations. In this review, we summarize the most important discoveries related to secondary metabolites from alternative bacterial sources, trying to provide the reader with a broad perspective on how technical novelties have facilitated the access to the bacterial metabolic dark matter.

The bacterial phylum Planctomycetes as novel source for bioactive small molecules

Extensive knowledge and methodological expertise on the bacterial cell biology have been accumulated over the last decades and bacterial cells have now become an integral part of several (bio-)technological processes. While it appears reasonable to focus on a relatively small number of fast-growing and genetically easily manipulable model bacteria as biotechnological workhorses, the for the most part untapped diversity of bacteria needs to be explored when it comes to bioprospecting for natural product discovery. Members of the underexplored and evolutionarily deep-branching phylum Planctomycetes have only recently gained increased attention with respect to the production of small molecules with biomedical activities, e.g. as a natural source of novel antibiotics. Next-generation sequencing and metagenomics can provide access to the genomes of uncultivated bacteria from sparsely studied phyla, this, however, should be regarded as an addition rather than a substitute for classical strain isolation approaches. Ten years ago, a large sampling campaign was initiated to isolate planctomycetes from their varied natural habitats and protocols were developed to address complications during cultivation of representative species in the laboratory. The characterisation of approximately 90 novel strains by several research groups in the recent years opened a detailed in silico look into the coding potential of individual members of this phylum. Here, we review the current state of planctomycetal research, focusing on diversity, small molecule production and potential future applications. Although the field developed promising, the time frame of 10 years illustrates that the study of additional promising bacterial phyla as sources for novel small molecules needs to start rather today than tomorrow.

Analysis of Bacterial Communities on North Sea Macroalgae and Characterization of the Isolated Planctomycetes Adhaeretor mobilis gen. nov., sp. nov., Roseimaritima multifibrata sp. nov., Rosistilla ulvae sp. nov. and Rubripirellula lacrimiformis sp. nov

Planctomycetes are bacteria that were long thought to be unculturable, of low abundance, and therefore neglectable in the environment. This view changed in recent years, after it was shown that members of the phylum Planctomycetes can be abundant in many aquatic environments, e.g., in the epiphytic communities on macroalgae surfaces. Here, we analyzed three different macroalgae from the North Sea and show that Planctomycetes is the most abundant bacterial phylum on the alga Fucus sp., while it represents a minor fraction of the surface-associated bacterial community of Ulva sp. and Laminaria sp. Especially dominant within the phylum Planctomycetes were Blastopirellula sp., followed by Rhodopirellula sp., Rubripirellula sp., as well as other Pirellulaceae and Lacipirellulaceae, but also members of the OM190 lineage. Motivated by the observed abundance, we isolated four novel planctomycetal strains to expand the collection of species available as axenic cultures since access to different strains is a prerequisite to investigate the success of planctomycetes in marine environments. The isolated strains constitute four novel species belonging to one novel and three previously described genera in the order Pirellulales, class Planctomycetia, phylum Planctomycetes.

The need to innovate sample collection and library generation in microbial drug discovery: a focus on academia

The question of whether culturable microorganisms will continue to be a viable source of new drug leads is inherently married to the strategies used to collect samples from the environment, the methods used to cultivate microorganisms from these samples, and the processes used to create microbial libraries. An academic microbial natural products (NP) drug discovery program with the latest innovative chromatographic and spectroscopic technology, high-throughput capacity, and bioassays will remain at the mercy of the quality of its microorganism source library. This viewpoint will discuss limitations of sample collection and microbial strain library generation practices. Additionally, it will offer suggestions to innovate these areas, particularly through the targeted cultivation of several understudied bacterial phyla and the untargeted use of mass spectrometry and bioinformatics to generate diverse microbial libraries. Such innovations have potential to impact downstream therapeutic discovery, and make its front end more informed, efficient, and less reliant on serendipity. This viewpoint is not intended to be a comprehensive review of contributing literature and was written with a focus on bacteria. Strategies to discover NPs from microbial libraries, including a variety of genomics and "OSMAC" style approaches, are considered downstream of sample collection and library creation, and thus are out of the scope of this viewpoint.

Analysis of bacterial communities in a municipal duck pond during a phytoplankton bloom and isolation of Anatilimnocola aggregata gen. nov., sp. nov., Lacipirellula limnantheis sp. nov. and Urbifossiella limnaea gen. nov., sp. nov. belonging to the phylum Planctomycetes

Waterbodies such as lakes and ponds are fragile environments affected by human influences. Suitable conditions can result in massive growth of phototrophs, commonly referred to as phytoplankton blooms. Such events benefit heterotrophic bacteria able to use compounds secreted by phototrophs or their biomass as major nutrient source. One example of such bacteria are Planctomycetes, which are abundant on the surfaces of marine macroscopic phototrophs; however, less data are available on their ecological roles in limnic environments. In this study, we followed a cultivation-independent deep sequencing approach to study the bacterial community composition during a cyanobacterial bloom event in a municipal duck pond. In addition to cyanobacteria, which caused the bloom event, members of the phylum Planctomycetes were significantly enriched in the cyanobacteria-attached fraction compared to the free-living fraction. Separate datasets based on isolated DNA and RNA point towards considerable differences in the abundance and activity of planctomycetal families, indicating different activity peaks of these families during the cyanobacterial bloom. Motivated by the finding that the sampling location harbours untapped bacterial diversity, we included a complementary cultivation-dependent approach and isolated and characterized three novel limnic strains belonging to the phylum Planctomycetes.

Tautonia plasticadhaerens sp. nov., a novel species in the family Isosphaeraceae isolated from an alga in a hydrothermal area of the Eolian Archipelago

A novel planctomycetal strain, designated ElPT, was isolated from an alga in the shallow hydrothermal vent system close to Panarea Island in the Tyrrhenian Sea. Cells of strain ElPT are spherical, form pink colonies and display typical planctomycetal characteristics including division by budding and presence of crateriform structures. Strain ElPT has a mesophilic (optimum at 30 °C) and neutrophilic (optimum at pH 7.5) growth profile, is aerobic and heterotrophic. It reaches a generation time of 29 h (µmax = 0.024 h-1). The strain has a genome size of 9.40 Mb with a G + C content of 71.1% and harbours five plasmids, the highest number observed in the phylum Planctomycetes thus far. Phylogenetically, the strain represents a novel species of the recently described genus Tautonia in the family Isosphaeraceae. A characteristic feature of the strain is its tendency to attach strongly to a range of plastic surfaces. We thus propose the name Tautonia plasticadhaerens sp. nov. for the novel species, represented by the type strain ElPT (DSM 101012T = LMG 29141T).

Thalassoglobus polymorphus sp. nov., a novel Planctomycete isolated close to a public beach of Mallorca Island

Access to axenic cultures is crucial to extend the knowledge of the biology, lifestyle or metabolic capabilities of bacteria from different phyla. The phylum Planctomycetes is an excellent example since its members display an unusual cell biology and complex lifestyles. As a contribution to the current collection of axenic planctomycete cultures, here we describe strain Mal48T isolated from phytoplankton material sampled at the coast of S'Arenal close to Palma de Mallorca (Spain). The isolated strain shows optimal growth at pH 7.0-7.5 and 30 °C and exhibits typical features of Planctomycetes. Cells of the strain are spherical to pear-shaped, divide by polar budding with daughter cells showing the same shape as the mother cell, tend to aggregate, display a stalk and produce matrix or fimbriae. Strain Mal48T showed 95.8% 16S rRNA gene sequence similarity with the recently described Thalassoglobus neptunius KOR42T. The genome sequence of the novel isolate has a size of 6,357,355 bp with a G+C content of 50.3%. A total of 4874 protein-coding genes, 41 tRNA genes and 2 copies of the 16S rRNA gene are encoded in the genome. Based on phylogenetic, morphological and physiological analyses, we conclude that strain Mal48T (= DSM 100737T = LMG 29019T) should be classified as the type strain of a new species in the genus Thalassoglobus, for which the name Thalassoglobus polymorphus sp. nov. is proposed.

Stieleria varia sp. nov., isolated from wood particles in the Baltic Sea, constitutes a novel species in the family Pirellulaceae within the phylum Planctomycetes

Species belonging to the bacterial phylum Planctomycetes are ubiquitous members of the microbial communities in aquatic environments and are frequently isolated from various biotic and abiotic surfaces in marine and limnic water bodies. Planctomycetes have large genomes of up to 12.4 Mb, follow complex lifestyles and display an uncommon cell biology; features which motivate the investigation of members of this phylum in greater detail. As a contribution to the current collection of axenic cultures of Planctomycetes, we here describe strain Pla52^T isolated from wood particles in the Baltic Sea. Phylogenetic analysis places the strain in the family Pirellulaceae and suggests two species of the recently described genus Stieleria as current closest neighbours. Strain Pla52n^T shows typical features of members of the class Planctomycetia, including division by polar budding and the presence of crateriform structures. Colonies of strain Pla52n^T have a light orange colour, which is an unusual pigmentation compared to the majority of members in the phylum, which show either a pink to red pigmentation or entirely lack pigmentation. Optimal growth of strain Pla52n^T at 33 °C and pH 7.5 indicates a mesophilic (i.e. with optimal growth between 20 and 45 °C) and neutrophilic growth profile. The strain is an aerobic heterotroph with motile daughter cells. Its genome has a size of 9.6 Mb and a G + C content of 56.0%. Polyphasic analyses justify delineation of the strain from described species within the genus Stieleria. Therefore, we conclude that strain Pla52n^T = LMG 29463^T = VKM B-3447^T should be classified as the type strain of a novel species, for which we propose the name Stieleria varia sp. nov.

Stieleriacines, N-Acyl Dehydrotyrosines From the Marine Planctomycete Stieleria neptunia sp. nov

Bacteria of the phylum Planctomycetes occur ubiquitously in marine environments and play important roles in the marine nitrogen- and carbon cycle, for example as scavengers after phototrophic blooms. Here, we describe the isolation and characterization of the planctomycetal strain Enr13^T isolated from a Posidonia sp. biofilm obtained from seawater sediment close to Panarea Island, Italy. Phylogenetic tree reconstruction based on 16S rRNA gene sequences and multi-locus sequence analysis supports the delineation of strain Enr13^T from characterized species part of the phylum of Planctomycetes. HPLC-MS analysis of culture broth obtained from strain Enr13^T revealed the presence of lipophilic metabolites, of which the major compound was isolated by preparative reversed-phase HPLC. The structure of this compound, named stieleriacine D (1), was elucidated utilizing HRESIMS, 1D- and 2D-NMR data as a new N-acylated dehydrotyrosine derivative. Its biosynthesis was proposed based on an in silico gene cluster analysis. Through analysis of the MS/MS spectrum of 1 and its minor derivative, stieleriacine E (2), it was possible to assign the structure of 2 without isolation. 1 showed antibacterial activity, however, the wide distribution of structurally related compounds indicates a potential role as a signaling molecule.