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Studying bacteria in anaerobic digestion (AD) is crucial for optimizing microbial processes. While abundant taxa are often studied, less abundant groups may harbour novel metabolic potential. This study fills the gap by focusing on the Planctomycetota phylum, known to encode diverse carbohydrate-active enzymes (CAZymes). Despite their common presence in diverse aerobic and anaerobic environments, their role in AD is relatively unexplored. We utilized both culture-dependent and culture-independent techniques to investigate the phylogenetic and metabolic diversity of Planctomycetota within AD reactors. Our findings revealed that among the diverse planctomycetotal operational taxonomic units present, only a few are prevalent and abundant community members. Planctomycetota share functional traits with e.g. Verrucomicrobiota exhibiting distinct CAZyme gene repertoires that indicates specialization in degrading algal polysaccharides and glycoproteins. To explore the planctomycetotal metabolic capabilities, we monitored their presence in algal-fed digesters. Additionally, we isolated a strain from mucin-based medium, revealing its genetic potential for a mixotrophic lifestyle. Based on the genomic analysis, we propose to introduce the Candidatus Luxemburgiella decessa gen. nov. sp. nov., belonging to the Thermoguttaceae family within the Pirellulales order of the Planctomycetia class. This study enhances our understanding of Planctomycetota in AD by highlighting their phylogenetic diversity and metabolic capabilities.

The intracellular accumulation of small organic solutes was described in the marine bacterium Rhodopirellula baltica, which belongs to the globally distributed phylum Planctomycetes whose members exhibit an intriguing lifestyle and cell morphology. Sucrose, alpha -glutamate, trehalose and mannosylglucosylglycerate (MGG) are the main solutes involved in the osmoadaptation of R. baltica. The ratio and total intracellular organic solutes varied significantly in response to an increase in salinity, temperature and nitrogen content. R. baltica displayed an initial response to both osmotic and thermal stresses that includes alpha -glutamate accumulation. This trend was followed by a rather unique and complex osmoadaptation mechanism characterized by a dual response to sub-optimal and supra-optimal salinities. A reduction in the salinity to sub-optimal conditions led primarily to the accumulation of trehalose. In contrast, R. baltica responded to salt stress mostly by increasing the intracellular levels of sucrose. The switch between the accumulation of trehalose and sucrose was by far the most significant effect caused by increasing the salt levels of the medium. Additionally, MGG accumulation was found to be salt- as well as nitrogen-dependent. MGG accumulation was regulated by nitrogen levels replacing alpha -glutamate as a K+ counterion in nitrogen-poor environments. This is the first report of the accumulation of compatible solutes in the phylum Planctomycetes and of the MGG accumulation in a mesophilic organism.

Planctomycetes are ubiquitous, environmentally and biotechnologically important bacteria that are key players in global carbon and nitrogen cycles. Ever since their first discovery in the 1920s they seemed to blur the prokaryote /eukaryote dichotomy. After initially being described as fungi and reclassified as bacteria later, they were still thought to feature a nucleus-like compartment surrounding their highly condensed DNA. Also, an endocytosis-like uptake mechanism for macromolecules was described. Besides these eukaryotic hallmark traits, Planctomycetes seemed to lack typical bacterial features such as a peptidoglycan cell wall or the universal bacterial cell division protein FtsZ, while mostly dividing by polar budding instead of binary fission. Thus, Planctomycetes were speculated to be ancestral to both, bacteria and eukaryotes. With the advent of novel microscopic techniques, along with the development of genetic tools for Planctomycetes, some of these hypotheses were revisited. Surprisingly, Planctomycetes were found to possess a peptidoglycan cell wall and to comprise a cell plan comparable to other Gram-negative bacteria as the nucleus-like structure is rather an invagination of the cytoplasmic membrane than a cohesive compartment. These finding challenge the idea of a eukaryotic ancestry of the phylum, as Planctomycetes now appear similar, yet distinct to other bacteria.

This study reports the characterization of three novel species belonging to the two newly established genera Njordella gen. nov. and Rania gen. nov. in the family Pirellulaceae within the phylum Planctomycetota . The three investigated strains SH302 T , SH451 T and SH573 T were isolated from water samples originating from distinct locations across Northern Germany: Lägerdorf (a municipality close to Hamburg), Fjord Schlei (a 42 km estuary of the Baltic Sea) and Fehmarn Island in the Baltic Sea. All strains form (light) pink colonies, reproduce asymmetrically by polar budding and display an acorn-shaped cell morphology typical in the family Pirellulaceae . Rosette formation was only observed for strains SH302 T and SH573 T . The three strains are mesophilic with a temperature optimum at 28 °C, aerobic and heterotrophic, but differ in their pH preference. While strains SH302 T and SH573 T are neutrophilic (pH optimum at 7.0 and 7.5, respectively), strain SH451 T is slightly alkaliphilic (optimal growth at pH 8.0). The genome sizes of strains SH302 T , SH451 T and SH573 T are 7.2 Mb, 6.6 Mb and 9.4 Mb, respectively. Based on phylogenetic, morphological and physiological analyses, we conclude that the novel strains belong to three novel species of two novel genera. For the novel taxa, we introduce the names Njordella aestuarii gen. nov., sp. nov., represented by strain SH451 T (= CECT 30907 T  = KCTC 102089 T ) as the type strain and Njordella calcicola sp. nov. with type strain SH302 T (= DSM 116728 T  = KCTC 102091 T ). For the third taxon, we chose the name Rania fehmarnensis gen. nov., sp. nov. represented by the type strain SH573 T (= DSM 116763 T  = CECT 31080 T  = KCTC 102135 T ).

The family Pirellulaceae (phylum Planctomycetota ) is known for its environmental versatility, with members isolated from marine habitats, algal surfaces, soil and lakes; yet, no member has been isolated from terrestrial subsurface habitats. Here, we describe the planctomycetal strain NA78 T that was discovered in percolates from fractured limestone in ca. 0.6 m depth at the Hainich Critical Zone Exploratory (CZE) in central Germany. Cells of the isolated strain are pear-shaped, measuring approximately 1.1 × 1.8 μm, and divide by asymmetrical cell division (“polar budding”). Liquid cultures have a whitish color and cells of the strain form aggregates. Colonies are rigid, round and of whitish to beige color. Strain NA78 T grows under oxic conditions and thrives at temperatures between 18 and 24 °C, with an optimum at 18 °C. The strain tolerates pH values from 6.0 to 9.0, with optimal growth at pH 7.5, and matches the pH range of the bedrock percolate. Its genome has a size of 7.97 Mbp and a DNA G + C content of 58.2%. From combined results of phylogenetic analyses and phenotypic and genomic characterization, we conclude that strain NA78 T belongs to a novel species of the genus Anatilimnocola . We thus introduce the name Anatilimnocola aquadivae sp. nov., represented by NA78 T (= CECT 30429 T  = STH00992 T ; the STH number refers to the Jena Microbial Resource collection JMRC) as the type strain.

Interactions between microalgae and bacteria can directly influence the global biogeochemical cycles but the majority of such interactions remain unknown. 16S rRNA gene-based co-occurrence networks have potential to help identify microalgal-bacterial interactions. Here, we used data from 10 Earth microbiome projects to identify potential microalgal-bacterial associations in aquatic ecosystems. A high degree of clustering was observed in microalgal-bacterial modules, indicating densely connected neighbourhoods. Proteobacteria and Bacteroidetes predominantly co-occurred with microalgae and represented hubs of most modules. Our results also indicated that species-specificity may be a global characteristic of microalgal associated microbiomes. Several previously known associations were recovered from our network modules, validating that biologically meaningful results can be inferred using this approach. A range of previously unknown associations were recognised such as co-occurrences of Bacillariophyta with uncultured Planctomycetes OM190 and Deltaproteobacteria order NB1-j . Planctomycetes and Verrucomicrobia were identified as key associates of microalgae due to their frequent co-occurrences with several microalgal taxa. Despite no clear taxonomic pattern, bacterial associates appeared functionally similar across different environments. To summarise, we demonstrated the potential of 16S rRNA gene-based co-occurrence networks as a hypothesis-generating framework to guide more focused research on microalgal-bacterial associations.

Carotenoids are isoprenoid lipids found across the tree of life with important implications in oxidative stress adaptations, photosynthetic metabolisms, as well as in membrane dynamics. The canonical view is that C40 carotenoids are synthesized from phytoene and C30 carotenoids from diapophytoene. Squalene is mostly associated with the biosynthesis of polycyclic triterpenes, although there have been suggestions that it could also be involved in the biosynthesis of C30 carotenoids. However, demonstration of the existence of this pathway in nature is lacking. Here, we demonstrate that C30 carotenoids are synthesized from squalene in the Planctomycetes bacteria and that this squalene route to C30 carotenoids is the most widespread in prokaryotes. Using the evolutionary history of carotenoid and squalene amino oxidases, we propose an evolutionary scenario to explain the origin and diversification of the different carotenoid and squalene-related pathways. We show that carotenoid biosynthetic pathways have been constantly transferred and neofunctionalized during prokaryotic evolution. One possible origin of the squalene pathway connects it with the one of C40 carotenoid synthesis of Cyanobacteria. The widespread occurrence of the squalene route to C30 carotenoids in Bacteria increases the functional repertoire of squalene, establishing it as a general hub of carotenoids and polycyclic triterpenes synthesis.

Plant roots and soil microorganisms interact with each other mainly in the rhizosphere. Changes in the community structure of the rhizosphere microbiome are influenced by many factors. In this study, we determined the community structure of rhizosphere bacteria in cotton, and studied the variation of rhizosphere bacterial community structure in different soil types and developmental stages using TM-1, an upland cotton cultivar ( Gossypium hirsutum L.) and Hai 7124, a sea island cotton cultivar ( G. barbadense L.) by high-throughput sequencing technology. Six bacterial phyla were found dominantly in cotton rhizosphere bacterial community including Acidobacteria, Actinobacteria, Bacteroidetes, Planctomycetes, Proteobacteria, and Verrucomicrobia. The abundance of Acidobacteria, Cyanobacteria, Firmicutes, Planctomycetes and Proteobacteria were largely influenced by cotton root. Bacterial α-diversity in rhizosphere was lower than that of bulk soil in nutrient-rich soil, but higher in cotton continuous cropping field soil. The β-diversity in nutrient-rich soil was greater than that in continuous cropping field soil. The community structure of the rhizosphere bacteria varied significantly during different developmental stages. Our results provided insights into the dynamics of cotton rhizosphere bacterial community and would facilitate to improve cotton growth and development through adjusting soil bacterial community structure artificially.

The phylum Planctomycetes comprises bacteria with uncommon features among prokaryotes, such as cell division by budding, absence of the bacterial tubulin-homolog cell division protein FtsZ and complex cell plans with invaginations of the cytoplasmic membrane. Although planctomycetes are ubiquitous, the number of described species and isolated strains available as axenic cultures is still low compared to the diversity observed in metagenomes or environmental studies. An increasing interest in planctomycetes is reflected by the recent description of a large number of new species and their increasing accessibility in terms of pure cultures. In this review, data from all taxonomically described species belonging to Planctomycetia, the class with the currently highest number of characterized members within the phylum Planctomycetes, is summarized. Phylogeny, morphology, physiology, ecology and genomic traits of its members are discussed. This comprehensive overview will help to acknowledge several aspects of the biology of these fascinating bacteria.

Phagocytosis is a key eukaryotic feature, conserved from unicellular protists to animals, that enabled eukaryotes to feed on other organisms. It could also be a driving force behind endosymbiosis, a process by which α-proteobacteria and cyanobacteria evolved into mitochondria and plastids, respectively. Here we describe a planctomycete bacterium, ‘ Candidatus Uab amorphum’, which is able to engulf other bacteria and small eukaryotic cells through a phagocytosis-like mechanism. Observations via light and electron microscopy suggest that this bacterium digests prey cells in specific compartments. With the possible exception of a gene encoding an actin-like protein, analysis of the ‘ Ca . Uab amorphum’ genomic sequence does not reveal any genes homologous to eukaryotic phagocytosis genes, suggesting that cell engulfment in this microorganism is probably not homologous to eukaryotic phagocytosis. The discovery of this “phagotrophic” bacterium expands our understanding of the cellular complexity of prokaryotes, and may be relevant to the origin of eukaryotic cells. Phagocytosis is a typically eukaryotic feature that could be behind the origin of eukaryotic cells. Here, the authors describe a bacterium that can engulf other bacteria and small eukaryotic cells through a phagocytosis-like mechanism.