Nicolai Kallscheuer

Bacterial signals control the development of marine algae, yet the molecular basis of these cross-kingdom interactions remains largely unknown. Thallusin is the paradigmatic case: isolated in 2005, it induces rhizoid and cell wall formation in the green seaweed Ulva at picomolar concentrations, but its biosynthesis has remained elusive for two decades. Comparative genomics across five bacterial phyla identifies a conserved set of genes - the eustigmatophyte bacterial operon ( ebo ) - as determinants of thallusin biosynthesis. Isotope labeling, heterologous expression, and gene deletion in Stieleria maiorica show that the aromatic scaffold derives from a cyclitol precursor and L-aspartate, with subsequent prenylation and cyclization. Searching 124,295 prokaryotic genomes identifies producers in eleven bacterial lineages, including soil cyanobacteria, establishing thallusin as a widespread cross-kingdom signal reaching beyond the ocean.

The majority of characterized members of the phylum Planctomycetota were isolated from marine habitats. To expand the open collection of limnic planctomycetes, we here characterize three isolates from the strain collection of Heinz Schlesner (Kiel University), a pioneer in the research on budding planctomycetes and other bacteria with uncommon morphologies. The three strains SH203, SH248 ^T and SH280 were isolated from two municipal ponds in Kiel and from a nature reserve close to a gypsum mine in the surroundings of Hamburg, Northern Germany. The three isolates share an identical 16S rRNA gene sequence over the analyzed sequence of ca. 1300 bp. Cells are pear-shaped, motile, non-pigmented and show the typical asymmetrical division mode through polar budding observed in most other members of the family Planctomycetaceae . Phylogenetic analyses identified the three described species of the genus Rubinisphaera as the current closest relatives. The comparison of five phylogenetic markers along with differences in phenotypic and genomic features together delineate the novel strains from the genus Rubinisphaera . Hence, we introduce Lacunimicrobium album gen. nov., sp. nov., a novel taxon in the family Planctomycetaceae . The novel species is represented by the type strain SH248 ^T (= CECT 30703 ^T = STH01007 ^T ; the STH number refers to the Jena Microbial Resource Collection JMRC). It has a heterotrophic, mesophilic and neutrophilic profile and a genome with a length of 5.42 Mbp and a DNA G + C content of 54.6%.

N-acyl tyrosines, a prominent class of N-acyl amino acid biomolecules, are produced by selected species in at least three bacterial phyla: Pseudomonadota, Actinomycetota and Planctomycetota. Long-chain N-acyl tyrosines with a characteristic 2,3-dehydrotyrosine core structure and additional taxon-specific chemical modifications were previously reported under the names thalassotalic acids, kyonggic acids and stieleriacines. However, the underlying pathway for their biosynthesis in the different bacterial taxa remains largely unexplored. Here, we focused on the identification of biosynthetic enzymes in the two known stieleriacine-producing planctomycetal strains of the eponymous genus Stieleria. Comparative genome analyses of stieleriacine-, thalassotalic acid- and kyonggic acid producers suggest a common pathway for N-acyl dehydrotyrosine biosynthesis based on conserved genes encoding a putative adenylyltransferase/cyclase, nitroreductase and the hallmark protein N-acyl amino acid synthase (NasY). The targeted deletion of three predicted nasY genes in Stieleria neptunia indicates that one of the three encoded enzymes predominantly produces stieleriacines. We also confirmed the absolute structure of stieleriacine C by synthesis of its epimer and structural derivatives, which serve as the basis for the future investigation of the biological function of N-acyl tyrosines.

Members of the phylum Planctomycetota are ubiquitous bacteria that play important roles in the global carbon and nitrogen cycle. In this study, we sampled the shallow-sea hydrothermal vent system close to Panarea Island, Italy, and analyzed the bacterial diversity in this habitat using a cultivation-independent amplicon sequencing approach. Motivated by the observed abundance of members of the phylum Planctomycetota , we employed cultivation conditions that facilitate the enrichment of planctomycetes and isolated strain Pan216 ^T . This strain shows a rarely observed type of cell division—lateral budding. Based on 16S rRNA gene- and multi-locus sequence analyses, its phylogenetic position in the phylum Planctomycetota appears vague. Strain Pan216 ^T clustered between the different described families in the class Planctomycetia . The novel isolate shares the highest sequence identity (85.4%) of the 16S rRNA gene with Thermostilla marina SVX8 ^T , indicating that this strain belongs to a novel family. In addition to its uncommon cell division mode, Pan216 ^T cells are pill-shaped and covered by a putative outer surface layer. Genomic analyses of strain Pan216 ^T revealed many giant genes, putative S-layer protein-encoding genes, and only a limited set of canonical cell division genes. Based on the results of the polyphasic analysis, we conclude that strain Pan216 ^T constitutes a novel family within the phylum Planctomycetota , for which we propose the name Kolteriaceae fam. nov. The novel species Kolteria novifilia gen. nov., sp. nov. is represented by the type strain Pan216 ^T (= DSM 100414 ^T = CECT 9536 ^T ). IMPORTANCE: We describe a novel family of the underrepresented bacterial phylum Planctomycetota that divides by unusual lateral budding. Our strain is the only validly described species that uses this mode of cell division. Furthermore, it represents the only planctomycete outside of the anammox bacteria that has an S-layer-like structure. Taken together, the novel family shows a novel mechanism of cell division that could only be studied in this species.

The phylum Planctomycetota is changing our understanding of bacterial metabolism, driving critical biogeochemical processes through the transformation of complex polymeric substrates into valuable bioactive compounds. Sophisticated methods for cultivation, genome sequencing and genetic strain engineering developed in the last two decades have stimulated detailed studies on cell propagation, metabolic capabilities and potential applications of phylum members beyond the mere isolation and characterization of novel taxa. This review synthesizes recent advances in understanding the Planctomycetota physiology with a focus on the degradation of phototroph-derived polysaccharides, anaerobic ammonium oxidation (anammox) and biosynthesis of secondary metabolites. New data especially collected over the last 5 years justifies more intensive research of the yet uncharacterized pathways of substrate uptake and utilization, as well as genome mining-assisted bioprospection to exploit the phylum's chemical repertoire. Key points: • Planctomycetes can degrade high-molecular-weight sugars produced by algae • Anaerobic ammonium oxidation (anammox) is used in technical applications • The first secondary metabolites were discovered in the last 5 years

Members of the phylum Planctomycetota possess a plethora of intriguing and hitherto underexplored features including an enlarged periplasmic space, asymmetric cell division (“budding”), and a mostly undiscovered small molecule portfolio. Due to the large phylogenetic distance to frequently used and easily genetically accessible model bacteria, most of the established genetic tools are not readily applicable for the here-investigated bacterial phylum. However, techniques for targeted gene inactivation and the introduction of heterologous genes are crucial to investigate the cell biology in the phylum in greater detail. In this study, the targeted genomic modification of model planctomycetes was achieved by enforcing two types of homologous recombination events: simultaneous double homologous recombination for the deletion of coding regions and insertion-duplication mutagenesis for the introduction of foreign DNA into the chromosome. Upon testing the expression of commonly used fluorescent protein-encoding genes, many of the tested native promoters could not be harnessed for variation of the expression strength. Since also four commonly used inducible gene expression systems did not work in the tested model strain Planctopirus limnophila , a native rhamnose-dependent transcriptional regulator/promoter pair was established as an inducible expression system. The expanded molecular toolbox will allow the future characterization of genome-encoded features in the understudied phylum. Key points: • Two recombination methods were used for the genetic modification of planctomycetes • Commonly used fluorescent proteins are functional in model planctomycetes • A rhamnose-dependent regulator was turned into an inducible expression system

The unique cell biology presented by members of the phylum Planctomycetota has puzzled researchers ever since their discovery. Initially thought to have eukaryotic-like features, their traits are now recognized as exceptional but distinctly bacterial. However, recently discovered strains again added novel and stunning aspects to the planctomycetal cell biology—shapeshifting by members of the “ Saltatorellus ” clade to an extent that is unprecedented in any other bacterial phylum, and phagocytosis-like cell engulfment in the bacterium “ Candidatus Uabimicrobium amorphum.” These recent additions to the phylum Planctomycetota indicate hitherto unexplored members with unique cell biology, which we aimed to make accessible for further investigations. Targeting bacteria with features like “ Ca. U. amorphum”, we first studied both the morphology and behavior of this microorganism in more detail. While similar to eukaryotic amoeboid organisms at first sight, we found “ Ca. U. amorphum” to be rather distinct in many regards. Presenting a detailed description of “ Ca. U. amorphum,” we furthermore found this organism to divide in a fashion that has never been described in any other organism. Employing the obtained knowledge, we isolated a second “bacterium of prey” from the harbor of Heligoland Island (North Sea, Germany). Our isolate shares key features with “ Ca. U. amorphum”: phagocytosis-like cell engulfment, surface-dependent motility, and the same novel mode of cell division. Being related to “ Ca. U. amorphum” within genus thresholds, we propose the name “ Ca. Uabimicrobium helgolandensis” for this strain. IMPORTANCE: “ Candidatus Uabimicrobium helgolandensis” HlEnr_7 adds to the explored bacterial biodiversity with its phagocytosis-like uptake of prey bacteria. Enrichment of this strain indicates that there might be “impossible” microbes out there, missed by metagenomic analyses. Such organisms have the potential to challenge our understanding of nature. For example, the origin of eukaryotes remains enigmatic, with a contentious debate surrounding both the mitochondrial host entity and the moment of uptake. Currently, favored models involve a proteobacterium as the mitochondrial progenitor and an Asgard archaeon as the fusion partner. Models in which a eukaryotic ancestor engulfed the mitochondrial ancestor via phagocytosis had been largely rejected due to bioenergetic constraints. Thus, the phagocytosis-like abilities of planctomycetal bacteria might influence the debate, demonstrating that prey engulfment is possible in a prokaryotic cellular framework.

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.

Axenic cultures of two strains, JC673^T and JC717, both belonging to the phylum Planctomycetota, were isolated from distinct geographical locations in India. Strain JC673^T was obtained from algal mats of a wetland situated in the state of Kerala, India, while strain JC717 originated from the Central Marine Fisheries Research Institute (CMFRI), state of Tamil Nadu, India. The two strains share 99.9% 16S rRNA gene sequence similarity and are most closely related to Gemmata obscuriglobus UQM 2246^T (99.3% 16S rRNA gene sequence identity). The newly isolated strains are Gram-negative, grow aerobically and tolerate up to 4% (w/v) NaCl and a pH of up to 9.0. Cells are spherical and form pink-pigmented colonies. The respiratory quinone is MK-6. Major fatty acids are C_18:0, C_16:1ω5c and C_16:0. Polar lipids include phosphatidylcholine, phosphatidylethanolamine, several unidentified amino lipids, unidentified phospholipids, additional unidentified lipids, and an unidentified choline lipid. The polyamine spermidine is produced by the two strains. The strains have a genome size of about 8.2 Mb with a DNA G+C content of 67.6%. Solvent-based culture extracts of the isolates showed antimicrobial activity against three bacterial test strains. Their phylogenetic position along with differences in morphological, physiological, and genomic features support the classification as a new species of the genus Gemmata, for which we propose the name Gemmata algarum sp. nov. Strain JC673^T (=KCTC 72851^T = NBRC 114340^T) and JC717 are the type and non-type strain of the new species, respectively.