Membrane-bounded nucleoid in the eubacterium Gemmata obscuriglobus

Phylogeny and Expansion of Serine/Threonine Kinases in Phagocytotic Bacteria in the Phylum Planctomycetota

The recently isolated bacterium "Candidatus Uabimicrobium amorphum" is the only known prokaryote that can engulf other bacterial cells. Its proteome contains a high fraction of proteins involved in signal transduction systems, which is a feature normally associated with multicellularity in eukaryotes. Here, we present a protein-based phylogeny which shows that "Ca. Uabimicrobium amorphum" represents an early diverging lineage that clusters with the Saltatorellus clade within the phylum Planctomycetota. A gene flux analysis indicated a gain of 126 protein families for signal transduction functions in "Ca. Uabimicrobium amorphum", of which 66 families contained eukaryotic-like Serine/Threonine kinases with Pkinase domains. In total, we predicted 525 functional Serine/Threonine kinases in "Ca. Uabimicrobium amorphum", which represent 8% of the proteome and is the highest fraction of Serine/Threonine kinases in a bacterial proteome. The majority of Serine/Threonine kinases in this species are membrane proteins and 30% contain long, tandem arrays of WD40 or TPR domains. The pKinase domain was predicted to be located in the cytoplasm, while the WD40 and TPR domains were predicted to be located in the periplasm. Such domain combinations were also identified in the Serine/Threonine kinases of other species in the Planctomycetota, although in much lower abundances. A phylogenetic analysis of the Serine/Threonine kinases in the Planctomycetota inferred from the Pkinase domain alone provided support for lineage-specific expansions of the Serine/Threonine kinases in "Ca. Uabimicrobium amorphum". The results imply that expansions of eukaryotic-like signal transduction systems are not restricted to multicellular organisms, but have occurred in parallel in prokaryotes with predatory lifestyles and phagocytotic-like behaviors.

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.

Physiological and metabolic insights into the first cultured anaerobic representative of deep-sea Planctomycetes bacteria

Planctomycetes bacteria are ubiquitously distributed across various biospheres and play key roles in global element cycles. However, few deep-sea Planctomycetes members have been cultivated, limiting our understanding of Planctomycetes in the deep biosphere. Here, we have successfully cultured a novel strain of Planctomycetes (strain ZRK32) from a deep-sea cold seep sediment. Our genomic, physiological, and phylogenetic analyses indicate that strain ZRK32 is a novel species, which we propose be named: Poriferisphaera heterotrophicis. We show that strain ZRK32 replicates using a budding mode of division. Based on the combined results from growth assays and transcriptomic analyses, we found that rich nutrients, or supplementation with NO3- or NH4+ promoted the growth of strain ZRK32 by facilitating energy production through the tricarboxylic acid cycle and the Embden-Meyerhof-Parnas glycolysis pathway. Moreover, supplementation with NO3- or NH4+ induced strain ZRK32 to release a bacteriophage in a chronic manner, without host cell lysis. This bacteriophage then enabled strain ZRK32, and another marine bacterium that we studied, to metabolize nitrogen through the function of auxiliary metabolic genes. Overall, these findings expand our understanding of deep-sea Planctomycetes bacteria, while highlighting their ability to metabolize nitrogen when reprogrammed by chronic viruses.

Essential gene complement of Planctopirus limnophila from the bacterial phylum Planctomycetes

Planctopirus limnophila belongs to the bacterial phylum Planctomycetes, a relatively understudied lineage with remarkable cell biology features. Here, we report a genome-wide analysis of essential gene content in P. limnophila. We show that certain genes involved in peptidoglycan synthesis or cell division, which are essential in most other studied bacteria, are not essential for growth under laboratory conditions in this species. We identify essential genes likely involved in lipopolysaccharide biosynthesis, consistent with the view of Planctomycetes as diderm bacteria, and highlight other essential genes of unknown functions. Furthermore, we explore potential stages of evolution of the essential gene repertoire in Planctomycetes and the related phyla Verrucomicrobia and Chlamydiae. Our results provide insights into the divergent molecular and cellular biology of Planctomycetes.

High impact of bacterial predation on cyanobacteria in soil biocrusts

Diverse bacteria lead a life as pathogens or predators of other bacteria in many environments. However, their impact on emerging ecological processes in natural settings remains to be assessed. Here we describe a novel type of obligate, intracellular predatory bacterium of widespread distribution that preys on soil cyanobacteria in biocrusts. The predator, Candidatus Cyanoraptor togatus, causes localized, cm-sized epidemics that are visible to the naked eye, obliterates cyanobacterial net primary productivity, and severely impacts crucial biocrust properties like nitrogen cycling, dust trapping and moisture retention. The combined effects of high localized morbidity and areal incidence result in decreases approaching 10% of biocrust productivity at the ecosystem scale. Our findings show that bacterial predation can be an important loss factor shaping not only the structure but also the function of microbial communities.

Some bacteria act as pathogens or predators of other bacteria, but their impact in natural settings is often unclear. Here, Bethany et al. describe a new type of obligate, intracellular predatory bacterium of widespread distribution that preys on soil cyanobacteria in biocrusts and thus severely impacts biocrust productivity.

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.

Mucisphaera calidilacus gen. nov., sp. nov., a novel planctomycete of the class Phycisphaerae isolated in the shallow sea hydrothermal system of the Lipari Islands

For extending the current collection of axenic cultures of planctomycetes, we describe in this study the isolation and characterisation of strain Pan265^T obtained from a red biofilm in the hydrothermal vent system close to the Lipari Islands in the Tyrrhenian Sea, north of Sicily, Italy. The strain forms light pink colonies on solid medium and grows as a viscous colloid in liquid culture, likely as the result of formation of a dense extracellular matrix observed during electron microscopy. Cells of the novel isolate are spherical, motile and divide by binary fission. Strain Pan265^T is mesophilic (temperature optimum 30-33 °C), neutrophilic (pH optimum 7.0-8.0), aerobic and heterotrophic. The strain has a genome size of 3.49 Mb and a DNA G + C content of 63.9%. Phylogenetically, the strain belongs to the family Phycisphaeraceae, order Phycisphaerales, class Phycisphaerae. Our polyphasic analysis supports the delineation of strain Pan265^T from the known genera in this family. Therefore, we conclude to assign strain Pan265^T to a novel species within a novel genus, for which we propose the name Mucisphaera calidilacus gen. nov., sp. nov. The novel species is the type species of the novel genus and is represented by strain Pan265^T (= DSM 100697^T = CECT 30425^T) as type strain.

The Subcellular Proteome of a Planctomycetes Bacterium Shows That Newly Evolved Proteins Have Distinct Fractionation Patterns

The Planctomycetes bacteria have unique cell architectures with heavily invaginated membranes as confirmed by three-dimensional models reconstructed from FIB-SEM images of Tuwongella immobilis and Gemmata obscuriglobus. The subcellular proteome of T. immobilis was examined by differential solubilization followed by LC-MS/MS analysis, which identified 1569 proteins in total. The Tris-soluble fraction contained mostly cytoplasmic proteins, while inner and outer membrane proteins were found in the Triton X-100 and SDS-soluble fractions, respectively. For comparisons, the subcellular proteome of Escherichia coli was also examined using the same methodology. A notable difference in the overall fractionation pattern of the two species was a fivefold higher number of predicted cytoplasmic proteins in the SDS-soluble fraction in T. immobilis. One category of such proteins is represented by innovations in the Planctomycetes lineage, including unique sets of serine/threonine kinases and extracytoplasmic sigma factors with WD40 repeat domains for which no homologs are present in E. coli. Other such proteins are members of recently expanded protein families in which the newly evolved paralog with a new domain structure is recovered from the SDS-soluble fraction, while other paralogs may have similar domain structures and fractionation patterns as the single homolog in E. coli. The expanded protein families in T. immobilis include enzymes involved in replication-repair processes as well as in rRNA and tRNA modification and degradation. These results show that paralogization and domain shuffling have yielded new proteins with distinct fractionation characteristics. Understanding the molecular intricacies of these adaptive changes might aid in the development of a model for the evolution of cellular complexity.

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.

Identification of Evolutionarily Conserved Nuclear Matrix Proteins and Their Prokaryotic Origins

Compared to prokaryotic cells, a typical eukaryotic cell is much more complex along with its endomembrane system and membrane-bound organelles. Although the endosymbiosis theories convincingly explain the evolution of membrane-bound organelles such as mitochondria and chloroplasts, very little is understood about the evolutionary origins of the nucleus, the defining feature of eukaryotes. Most studies on nuclear evolution have not been able to take into consideration the underlying structural framework of the nucleus, attributed to the nuclear matrix (NuMat), a ribonucleoproteinaceous structure. This can largely be attributed to the lack of annotation of its core components. Since NuMat has been shown to provide a structural platform for facilitating a variety of nuclear functions such as replication, transcription, and splicing, it is important to identify its protein components to better understand these processes. In this study, we address this issue using the developing embryos of Drosophila melanogaster and Danio rerio and identify 362 core NuMat proteins that are conserved between the two organisms. We further compare our results with publicly available Mus musculus NuMat dataset and Homo sapiens cellular localization dataset to define the core homologous NuMat proteins consisting of 252 proteins. We find that of them, 86 protein groups have originated from pre-existing proteins in prokaryotes. While 36 were conserved across all eukaryotic supergroups, 14 new proteins evolved before the evolution of the last eukaryotic common ancestor and together, these 50 proteins out of the 252 core conserved NuMat proteins are conserved across all eukaryotes, indicating their indispensable nature for nuclear function for over 1.5 billion years of eukaryotic history. Our analysis paves the way to understand the evolution of the complex internal nuclear architecture and its functions.

Rosistilla oblonga gen. nov., sp. nov. and Rosistilla carotiformis sp. nov., isolated from biotic or abiotic surfaces in Northern Germany, Mallorca, Spain and California, USA

Planctomycetes are ubiquitous bacteria with fascinating cell biological features. Strains available as axenic cultures in most cases have been isolated from aquatic environments and serve as a basis to study planctomycetal cell biology and interactions in further detail. As a contribution to the current collection of axenic cultures, here we characterise three closely related strains, Poly24T, CA51T and Mal33, which were isolated from the Baltic Sea, the Pacific Ocean and the Mediterranean Sea, respectively. The strains display cell biological features typical for related Planctomycetes, such as division by polar budding, presence of crateriform structures and formation of rosettes. Optimal growth was observed at temperatures of 30-33 °C and at pH 7.5, which led to maximal growth rates of 0.065-0.079 h-1, corresponding to generation times of 9-11 h. The genomes of the novel isolates have a size of 7.3-7.5 Mb and a G + C content of 57.7-58.2%. Phylogenetic analyses place the strains in the family Pirellulaceae and suggest that Roseimaritima ulvae and Roseimaritima sediminicola are the current closest relatives. Analysis of five different phylogenetic markers, however, supports the delineation of the strains from members of the genus Roseimaritima and other characterised genera in the family. Supported by morphological and physiological differences, we conclude that the strains belong to the novel genus Rosistilla gen. nov. and constitute two novel species, for which we propose the names Rosistilla carotiformis sp. nov. and Rosistilla oblonga sp. nov. (the type species). The two novel species are represented by the type strains Poly24T (= DSM 102938T = VKM B-3434T = LMG 31347T = CECT 9848T) and CA51T (= DSM 104080T = LMG 29702T), respectively.

Description of Polystyrenella longa gen. nov., sp. nov., isolated from polystyrene particles incubated in the Baltic Sea

Planctomycetes occur in almost all aquatic ecosystems on earth. They have a remarkable cell biology, and members of the orders Planctomycetales and Pirellulales feature cell division by polar budding, perform a lifestyle switch from sessile to motile cells and have an enlarged periplasmic space. Here, we characterise a novel planctomycetal strain, Pla110T, isolated from the surface of polystyrene particles incubated in the Baltic Sea. After phylogenetic analysis, the strain could be placed in the family Planctomycetaceae. Strain Pla110T performs cell division by budding, has crateriform structures and grows in aggregates or rosettes. The strain is a chemoheterotroph, grows under mesophilic and neutrophilic conditions, and exhibited a doubling time of 21 h. Based on our phylogenetic and morphological characterisation, strain Pla110T (DSM 103387T = LMG 29693T) is concluded to represent a novel species belonging to a novel genus, for which we propose the name Polystyrenella longa gen. nov., sp. nov.

Lignipirellula cremea gen. nov., sp. nov., a planctomycete isolated from wood particles in a brackish river estuary

A novel planctomycetal strain, designated Pla85_3_4T, was isolated from the surface of wood incubated at the discharge of a wastewater treatment plant in the Warnow river near Rostock, Germany. Cells of the novel strain have a cell envelope architecture resembling that of Gram-negative bacteria, are round to pear-shaped (length: 2.2 ± 0.4 µm, width: 1.2 ± 0.3 µm), form aggregates and divide by polar budding. Colonies have a cream colour. Strain Pla85_3_4T grows at ranges of 10-30 °C (optimum 26 °C) and at pH 6.5-10.0 (optimum 7.5), and has a doubling time of 26 h. Phylogenetically, strain Pla85_3_4T (DSM 103796T = LMG 29741T) is concluded to represent a novel species of a novel genus within the family Pirellulaceae, for which we propose the name Lignipirellula cremea gen. nov., sp. nov.

Alienimonas californiensis gen. nov. sp. nov., a novel Planctomycete isolated from the kelp forest in Monterey Bay

Planctomycetes are environmentally and biotechnologically important bacteria and are often found in association with nutrient-rich (marine) surfaces. To allow a more comprehensive understanding of planctomycetal lifestyle and physiology we aimed at expanding the collection of axenic cultures with new isolates. Here, we describe the isolation and genomic and physiological characterisation of strain CA12T obtained from giant bladder kelp (Macrocystis pyrifera) in Monterey Bay, California, USA. 16S rRNA gene sequence and whole genome-based phylogenetic analysis showed that strain CA12T clusters within the family Planctomycetaceae and that it has a high 16S rRNA sequence similarity (82.3%) to Planctomicrobium piriforme DSM 26348T. The genome of strain CA12T has a length of 5,475,215 bp and a G+C content of 70.1%. The highest growth rates were observed at 27 °C and pH 7.5. Using different microscopic methods, we could show that CA12T is able to divide by consecutive polar budding, without completing a characteristic planctomycetal lifestyle switch. Based on our data, we suggest that the isolated strain represents a novel species within a novel genus. We thus propose the name Alienimonas gen. nov. with Alienimonas californiensis sp. nov. as type species of the novel genus and CA12T as type strain of the novel species.

Maioricimonas rarisocia gen. nov., sp. nov., a novel planctomycete isolated from marine sediments close to Mallorca Island

Planctomycetes are ubiquitous bacteria with environmental and biotechnological relevance. Axenic cultures of planctomycetal strains are the basis to analyse their unusual biology and largely uncharacterised metabolism in more detail. Here, we describe strain Mal4T isolated from marine sediments close to Palma de Mallorca, Spain. Strain Mal4T displays common planctomycetal features, such as division by polar budding and the presence of fimbriae and crateriform structures on the cell surface. Cell growth was observed at ranges of 10-39 °C (optimum at 31 °C) and pH 6.5-9.0 (optimum at 7.5). The novel strain shows as pear-shaped cells of 2.0 ± 0.2 × 1.4 ± 0.1 µm and is one of the rare examples of orange colony-forming Planctomycetes. Its genome has a size of 7.7 Mb with a G+C content of 63.4%. Phylogenetically, we conclude that strain Mal4T (= DSM 100296T = LMG 29133T) is the type strain representing the type species of a novel genus, for which we propose the name Maioricimonas rarisocia gen. nov., sp. nov.

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.

Rubinisphaera italica sp. nov. isolated from a hydrothermal area in the Tyrrhenian Sea close to the volcanic island Panarea

Planctomycetes is a fascinating phylum of mostly aquatic bacteria, not only due to the environmental importance in global carbon and nitrogen cycles, but also because of a unique cell biology. Their lifestyle and metabolic capabilities are not well explored, which motivated us to study the role of Planctomycetes in biofilms on marine biotic surfaces. Here, we describe the novel strain Pan54T which was isolated from algae in a hydrothermal area close to the volcanic island Panarea in the Tyrrhenian Sea, north of Sicily in Italy. The strain grew best at pH 9.0 and 26 °C and showed typical characteristics of planctomycetal bacteria, e.g. division by polar budding, formation of aggregates and presence of stalks and crateriform structures. Phylogenetically, the strain belongs to the genus Rubinisphaera. Our analysis suggests that Pan54T represents a novel species of this genus, for which we propose the name Rubinisphaera italica sp. nov. We suggest Pan54T (= DSM 29369 = LMG 29789) as the type strain of the novel species.

Three Planctomycetes isolated from biotic surfaces in the Mediterranean Sea and the Pacific Ocean constitute the novel species Symmachiella dynata gen. nov., sp. nov. and Symmachiella macrocystis sp. nov

Planctomycetes is a phylum of environmentally important bacteria, which also receive significant attention due to their fascinating cell biology. Access to axenic Planctomycete cultures is crucial to study cell biological features within this phylum in further detail. In this study, we characterise three novel strains, Mal52T, Pan258 and CA54T, which were isolated close to the coasts of the islands Mallorca (Spain) and Panarea (Italy), and from Monterey Bay, CA, USA. The three isolates show optimal growth at temperatures between 22 and 24 °C and at pH 7.5, divide by polar budding, lack pigmentation and form strong aggregates in liquid culture. Analysis of five phylogenetic markers suggests that the strains constitute two novel species within a novel genus in the family Planctomycetaceae. The strains Mal52T (DSM 101177T = VKM B-3432T) and Pan258 were assigned to the species Symmachiella dynata gen nov., sp. nov., while strain CA54T (DSM 104301T = VKM B-3450T) forms a separate species of the same genus, for which we propose the name Symmachiella macrocystis sp. nov.

Increased WD40 motifs in Planctomycete bacteria and their evolutionary relevance

Species of the family Planctomycetes have a complex intracellular structure, which is distinct from that of the majority of non-Planctomycetes bacteria. At present, genomic evidence of the evolution of intracellular complexity is lacking, cognitions of Planctomycetes's intracellular structure mainly rely on electron microscope observation. As the presence of WD40 motifs in eukaryotic proteins probably links to intracellular complexity, bioinformatic studies were conducted to detect and enumerate WD40 motifs, WD40 domains, and WD40 motif-bearing proteins in the genomes of 11 Planctomycetes species, 2775 non-Planctomycetes bacteria, and 63 representative eukaryotes. Compared to non-Planctomycetes bacteria (average 5 WD40 motifs and 1 WD40 motif-bearing protein per genome), a large increase in the number of WD40 motifs in Planctomycetes species (average 116 WD40 motifs and 26 WD40 motif-bearing proteins per genome) was observed. However, the average number of WD40 motifs in Planctomycetes species was significantly lower than that of eukaryotes (average 584 WD40 motifs and 193 WD40 motif-bearing proteins per genome). The number of WD40 motif-bearing proteins was found to correlate with genome size and gene number. Most WD40 motif-bearing proteins of Planctomycetes species belonged to the categories of 'ribosome assembly protein 4' and 'eukaryotic-like serine/threonine protein kinase.' Collinearity analysis of amino acid compositions of Planctomycetes and eukaryotic WD40 motifs revealed that the sequences of the four anti-parallel β-sheets of WD40 motifs were conserved. However, a number of Planctomycetes WD40 motifs had increased size of the interval region of β-sheets D and A. Taken together, results of this study suggest a positive correlation between the number of WD40 motif-bearing proteins and the evolution of Planctomycetes species toward a complex intracellular structure similar to that of eukaryotes.

Evolutionary Remodeling of the Cell Envelope in Bacteria of the Planctomycetes Phylum

Bacteria of the Planctomycetes phylum have many unique cellular features, such as extensive membrane invaginations and the ability to import macromolecules. These features raise intriguing questions about the composition of their cell envelopes. In this study, we have used microscopy, phylogenomics, and proteomics to examine the composition and evolution of cell envelope proteins in Tuwongella immobilis and other members of the Planctomycetes. Cryo-electron tomography data indicated a distance of 45 nm between the inner and outer membranes in T. immobilis. Consistent with the wide periplasmic space, our bioinformatics studies showed that the periplasmic segments of outer-membrane proteins in type II secretion systems are extended in bacteria of the order Planctomycetales. Homologs of two highly abundant cysteine-rich cell wall proteins in T. immobilis were identified in all members of the Planctomycetales, whereas genes for peptidoglycan biosynthesis and cell elongation have been lost in many members of this bacterial group. The cell wall proteins contain multiple copies of the YTV motif, which is the only domain that is conserved and unique to the Planctomycetales. Earlier diverging taxa in the Planctomycetes phylum contain genes for peptidoglycan biosynthesis but no homologs to the YTV cell wall proteins. The major remodeling of the cell envelope in the ancestor of the Planctomycetales coincided with the emergence of budding and other unique cellular phenotypes. The results have implications for hypotheses about the process whereby complex cellular features evolve in bacteria.

Formation and function of bacterial organelles

Advances in imaging technologies have revealed that many bacteria possess organelles with a proteomically defined lumen and a macromolecular boundary. Some are bound by a lipid bilayer (such as thylakoids, magnetosomes and anammoxosomes), whereas others are defined by a lipid monolayer (such as lipid bodies), a proteinaceous coat (such as carboxysomes) or have a phase-defined boundary (such as nucleolus-like compartments). These diverse organelles have various metabolic and physiological functions, facilitating adaptation to different environments and driving the evolution of cellular complexity. This Review highlights that, despite the diversity of reported organelles, some unifying concepts underlie their formation, structure and function. Bacteria have fundamental mechanisms of organelle formation, through which conserved processes can form distinct organelles in different species depending on the proteins recruited to the luminal space and the boundary of the organelle. These complex subcellular compartments provide evolutionary advantages as well as enabling metabolic specialization, biogeochemical processes and biotechnological advances. Growing evidence suggests that the presence of organelles is the rule, rather than the exception, in bacterial cells.

Diversity of sediment associated Planctomycetes and its related phyla with special reference to anammox bacterial community in a high Arctic fjord

The fjords of west Spitsbergen Svalbard, Arctic Norway, are undergoing a transformation as the impact of nutrient rich warmer Atlantic water is significantly altering the primary production and subsequently the carbon pool. Members of the phylum Planctomycetes are ubiquitous in marine systems and are important in the mineralization of organic matter. Hence, the phylogenetic diversity and distribution pattern of Planctomycetes in the surface sediments of a high Arctic fjord, the Kongsfjorden were studied. Further, considering the release of ammonium as a part of mineralization, the diversity of bacterial community involved in anaerobic ammonium oxidation (anammox) was also evaluated. The highly diverse Planctomycetes community, which consisted mainly of uncultivated and uncharacterized Planctomycetes, was observed in the study area with a total of 162 OTUs. The major genera observed were Blastopirellula (13.3%), Gimesia (13%), Rhodopirellula (10%), Planctomicrobium (2%) and Thermogutta (1.6%). Functional prediction revealed the dominance of carbohydrate metabolism genes and the presence of gene clusters for production of secondary metabolites and xenobiotic degradation. Anammox bacterial sequences were detected from all the samples with a total of 52 OTUs. Most of the OTUs belonged to the genus Candidatus Scalindua and three distinct clusters were observed in the phylogenetic tree, (a) Ca. Scalindua brodae (49%), (b) Ca. Scalindua wagneri (31%) and (c) Ca. Scalindua marina (12%) based on their phylogenic distance. Our findings suggest the existence of highly diverse Planctomycetes and anammox bacterial community with regional variants in the sediments of Kongsfjorden.

Response Characteristics of Nitrifying Bacteria and Archaea Community Involved in Nitrogen Removal and Bioelectricity Generation in Integrated Tidal Flow Constructed Wetland-Microbial Fuel Cell

This study explores nitrogen removal performance, bioelectricity generation, and the response of microbial community in two novel tidal flow constructed wetland-microbial fuel cells (TFCW-MFCs) when treating synthetic wastewater under two different chemical oxygen demand/total nitrogen (COD/TN, or simplified as C/N) ratios (10:1 and 5:1). The results showed that they achieved high and stable COD, NH₄ ⁺-N, and TN removal efficiencies. Besides, TN removal rate of TFCW-MFC was increased by 5-10% compared with that of traditional CW-MFC. Molecular biological analysis revealed that during the stabilization period, a low C/N ratio remarkably promoted diversities of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in the cathode layer, whereas a high one enhanced the richness of nitrite-oxidizing bacteria (NOB) in each medium; the dominant genera in AOA, AOB, and NOB were Candidatus Nitrosotenuis, Nitrosomonas, and Nitrobacter. Moreover, a high C/N ratio facilitated the growth of Nitrosomonas, while it inhibited the growth of Candidatus Nitrosotenuis. The distribution of microbial community structures in NOB was separated by space rather than time or C/N ratio, except for Nitrobacter. This is caused by the differences of pH, dissolved oxygen (DO), and nitrogen concentration. The response of microbial community characteristics to nitrogen transformations and bioelectricity generation demonstrated that TN concentration is significantly negatively correlated with AOA-shannon, AOA-chao, 16S rRNA V4-V5-shannon, and 16S rRNA V4-V5-chao, particularly due to the crucial functions of Nitrosopumilus, Planctomyces, and Aquicella. Additionally, voltage output was primarily influenced by microorganisms in the genera of Nitrosopumilus, Nitrosospira, Altererythrobacter, Gemmata, and Aquicella. This study not only presents an applicable tool to treat high nitrogen-containing wastewater, but also provides a theoretical basis for the use of TFCW-MFC and the regulation of microbial community in nitrogen removal and electricity production.

Three marine strains constitute the novel genus and species Crateriforma conspicua in the phylum Planctomycetes

Planctomycetes is a ubiquitous phylum of mostly aquatic bacteria that have a complex lifestyle and an unusual cell biology. Here, we describe three strains of the same novel genus and species isolated from three different environments; from a red biofilm at a hydrothermal vent in the Mediterranean Sea, from sediment in a salt-water fish tank, and from the surface of algae at the coast of the Balearic island Mallorca. The three strains Mal65^T (DSM 100706^T = LMG 29792^T, Pan14r (DSM 29351 = LMG 29012), and V7 (DSM 29812 = CECT 9853 = VKM B-3427) show typical characteristics of the Planctomycetaceae family, such as cell division by budding, crateriform structures and growth in aggregates or rosettes.  The strains are mesophilic, neutrophilic to alkaliphilic as well as chemoheterotrophic and exhibit doubling times between 12 and 35 h. Based on our phylogenetic analysis, the three strains represent a single novel species of a new genus, for which we propose the name Crateriforma conspicua gen. nov. sp. nov.

Paralogization and New Protein Architectures in Planctomycetes Bacteria with Complex Cell Structures

Bacteria of the phylum Planctomycetes have a unique cell plan with an elaborate intracellular membrane system, thereby resembling eukaryotic cells. The origin and evolution of these remarkable features is debated. To study the evolutionary genomics of bacteria with complex cell architectures, we have resequenced the 9.2-Mb genome of the model organism Gemmata obscuriglobus and sequenced the 10-Mb genome of G. massiliana Soil9, the 7.9-Mb genome of CJuql4, and the 6.7-Mb genome of Tuwongella immobilis, all of which belong to the family Gemmataceae. A gene flux analysis of the Planctomycetes revealed a massive emergence of novel protein families at multiple nodes within the Gemmataceae. The expanded protein families have unique multidomain architectures composed of domains that are characteristic of prokaryotes, such as the sigma factor domain of extracytoplasmic sigma factors, and domains that have proliferated in eukaryotes, such as the WD40, leucine-rich repeat, tetratricopeptide repeat and Ser/Thr kinase domains. Proteins with identifiable domains in the Gemmataceae have longer lengths and linkers than proteins in most other bacteria, and the analyses suggest that these traits were ancestrally present in the Planctomycetales. A broad comparison of protein length distribution profiles revealed an overlap between the longest proteins in prokaryotes and the shortest proteins in eukaryotes. We conclude that the many similarities between proteins in the Planctomycetales and the eukaryotes are due to convergent evolution and that there is no strict boundary between prokaryotes and eukaryotes with regard to features such as gene paralogy, protein length, and protein domain composition patterns.

Answers to naysayers regarding microbial extracellular vesicles

It is now over 30 years since the discovery of extracellular vesicles (EVs) in Gram-negative bacteria. However, for cell-walled microbes such as fungi, mycobacteria and Gram-positive bacteria it was thought that EV release would be impossible, since such structures were not believed to cross the thick cell wall. This notion was disproven 10 years ago with the discovery of EVs in fungi, mycobacteria, and gram-positive bacteria. Today, EVs have been described in practically every species tested, ranging from Fungi through Bacteria and Archaea, suggesting that EVs are a feature of every living cell. However, there continues to be skepticism in some quarters regarding EV release and their biological significance. In this review, we list doubts that have been verbalized to us and provide answers to counter them. In our opinion, there is no doubt as to existence and physiological function of EVs and we take this opportunity to highlight the most pressing topics in our understanding of the biological processes underlying these structures.

Organelle Formation in Bacteria and Archaea

Uncovering the mechanisms that underlie the biogenesis and maintenance of eukaryotic organelles is a vibrant and essential area of biological research. In comparison, little attention has been paid to the process of compartmentalization in bacteria and archaea. This lack of attention is in part due to the common misconception that organelles are a unique evolutionary invention of the "complex" eukaryotic cell and are absent from the "primitive" bacterial and archaeal cells. Comparisons across the tree of life are further complicated by the nebulous criteria used to designate subcellular structures as organelles. Here, with the aid of a unified definition of a membrane-bounded organelle, we present some of the recent findings in the study of lipid-bounded organelles in bacteria and archaea.

Development of simultaneous nitrification-denitrification (SND) in biofilm reactors with partially coupled a novel biodegradable carrier for nitrogen-rich water purification

Development of simultaneous nitrification-denitrification (SND) is a promising approach for nitrogen-rich water purification. Coupling biofilm reactors with novel biodegradable carrier of Pumelo Peel (PP) and various conventional plastic fillers (polyurethane filler, SPR-1 suspension filler, TA-II elastic filler and sphere filler) were examined to achieve SND in this study. Results represented that partially coupled with PP could achieve highly efficient SND. Optimal performance appealed in a bioreactor of coupling PP and SPR-1filler with ammonia and total nitrogen removal efficiencies of 96.8±4.0% and 78.9±9.5%, respectively, as well as low effluent COD_Mn of 1.85±0.86mgL^-1. Notably, PP and conventional plastic filler played obviously different roles in combined bioreactor system. Microbial analysis suggested that dominant genera were Thiothrix, Gemmata, unclassified comanonadaceae, unclassified Rhizobiales, Salipiger, Chloronema and Klebsiella in optimal combined bioreactor, which indicated novel co-existence of heterotrophic nitrification, solid-phase, non-solid-phase heterotrophic and sulfur-based autotrophic denitrification for achieving efficient SND.

The Paradigms They Are a-Changin': past, present and future of PVC bacteria research

These are exciting times for PVC researchers! The PVC superphylum is composed of the bacterial phyla Planctomycetes, Verrucomicrobia, Chlamydiae (those three founders giving it its name), Lentisphaerae and Kirimatiellaeota as well as some uncultured candidate phyla, such as the Candidatus Omnitrophica (previously known as OP3). Despite early debates, most of the disagreements that surround this group of bacteria have been recently resolved. In this article, we review the history of the study of PVC bacteria, with a particular focus on the misinterpretations that emerged early in the field and their resolution. We begin with a historical perspective that describes the relevant facts of PVC research from the early times when they were not yet termed PVC. Those were controversial times and we refer to them as the “discovery age” of the field. We continue by describing new discoveries due to novel techniques and data that combined with the reinterpretations of old ones have contributed to solve most of the discordances and we refer to these times as the “illumination age” of PVC research. We follow by arguing that we are just entering the “golden age” of PVC research and that the future of this growing community is looking bright. We finish by suggesting a few of the directions that PVC researches might take in the future.

Determining the bacterial cell biology of Planctomycetes

Bacteria of the phylum Planctomycetes have been previously reported to possess several features that are typical of eukaryotes, such as cytosolic compartmentalization and endocytosis-like macromolecule uptake. However, recent evidence points towards a Gram-negative cell plan for Planctomycetes, although in-depth experimental analysis has been hampered by insufficient genetic tools. Here we develop methods for expression of fluorescent proteins and for gene deletion in a model planctomycete, Planctopirus limnophila, to analyse its cell organization in detail. Super-resolution light microscopy of mutants, cryo-electron tomography, bioinformatic predictions and proteomic analyses support an altered Gram-negative cell plan for Planctomycetes, including a defined outer membrane, a periplasmic space that can be greatly enlarged and convoluted, and an energized cytoplasmic membrane. These conclusions are further supported by experiments performed with two other Planctomycetes, Gemmata obscuriglobus and Rhodopirellula baltica. We also provide experimental evidence that is inconsistent with endocytosis-like macromolecule uptake; instead, extracellular macromolecules can be taken up and accumulate in the periplasmic space through unclear mechanisms.

Evolutionary gradient of predicted nuclear localization signals (NLS)-bearing proteins in genomes of family Planctomycetaceae

BACKGROUND

The nuclear envelope is considered a key classification marker that distinguishes prokaryotes from eukaryotes. However, this marker does not apply to the family Planctomycetaceae, which has intracellular spaces divided by lipidic intracytoplasmic membranes (ICMs). Nuclear localization signal (NLS), a short stretch of amino acid sequence, destines to transport proteins from cytoplasm into nucleus, and is also associated with the development of nuclear envelope. We attempted to investigate the NLS motifs in Planctomycetaceae genomes to demonstrate the potential molecular transition in the development of intracellular membrane system.

RESULTS

In this study, we identified NLS-like motifs that have the same amino acid compositions as experimentally identified NLSs in genomes of 11 representative species of family Planctomycetaceae. A total of 15 NLS types and 170 NLS-bearing proteins were detected in the 11 strains. To determine the molecular transformation, we compared NLS-bearing protein abundances in the 11 representative Planctomycetaceae genomes with them in genomes of 16 taxonomically varied microorganisms: nine bacteria, two archaea and five fungi. In the 27 strains, 29 NLS types and 1101 NLS-bearing proteins were identified, principal component analysis showed a significant transitional gradient from bacteria to Planctomycetaceae to fungi on their NLS-bearing protein abundance profiles. Then, we clustered the 993 non-redundant NLS-bearing proteins into 181 families and annotated their involved metabolic pathways. Afterwards, we aligned the ten types of NLS motifs from the 13 families containing NLS-bearing proteins among bacteria, Planctomycetaceae or fungi, considering their diversity, length and origin. A transition towards increased complexity from non-planctomycete bacteria to Planctomycetaceae to archaea and fungi was detected based on the complexity of the 10 types of NLS-like motifs in the 13 NLS-bearing proteins families.

CONCLUSION

The results of this study reveal that Planctomycetaceae separates slightly from the members of non-planctomycete bacteria but still has substantial differences from fungi, based on the NLS-like motifs and NLS-bearing protein analysis.

Identification of constraints influencing the bacterial genomes evolution in the PVC super-phylum

BACKGROUND

Horizontal transfer plays an important role in the evolution of bacterial genomes, yet it obeys several constraints, including the ecological opportunity to meet other organisms, the presence of transfer systems, and the fitness of the transferred genes. Bacteria from the Planctomyctetes, Verrumicrobia, Chlamydiae (PVC) super-phylum have a compartmentalized cell plan delimited by an intracytoplasmic membrane that might constitute an additional constraint with particular impact on bacterial evolution. In this investigation, we studied the evolution of 33 genomes from PVC species and focused on the rate and the nature of horizontally transferred sequences in relation to their habitat and their cell plan.

RESULTS

Using a comparative phylogenomic approach, we showed that habitat influences the evolution of the bacterial genome's content and the flux of horizontal transfer of DNA (HT). Thus bacteria from soil, from insects and ubiquitous bacteria presented the highest average of horizontal transfer compared to bacteria living in water, extracellular bacteria in vertebrates, bacteria from amoeba and intracellular bacteria in vertebrates (with a mean of 379 versus 110 events per species, respectively and 7.6% of each genomes due to HT against 4.8%). The partners of these transfers were mainly bacterial organisms (94.9%); they allowed us to differentiate environmental bacteria, which exchanged more with Proteobacteria, and bacteria from vertebrates, which exchanged more with Firmicutes. The functional analysis of the horizontal transfers revealed a convergent evolution, with an over-representation of genes encoding for membrane biogenesis and lipid metabolism, among compartmentalized bacteria in the different habitats.

CONCLUSIONS

The presence of an intracytoplasmic membrane in PVC species seems to affect the genome's evolution through the selection of transferred DNA, according to their encoded functions.

Nuclear Pore-Like Structures in a Compartmentalized Bacterium

Planctomycetes are distinguished from other Bacteria by compartmentalization of cells via internal membranes, interpretation of which has been subject to recent debate regarding potential relations to Gram-negative cell structure. In our interpretation of the available data, the planctomycete Gemmata obscuriglobus contains a nuclear body compartment, and thus possesses a type of cell organization with parallels to the eukaryote nucleus. Here we show that pore-like structures occur in internal membranes of G.obscuriglobus and that they have elements structurally similar to eukaryote nuclear pores, including a basket, ring-spoke structure, and eight-fold rotational symmetry. Bioinformatic analysis of proteomic data reveals that some of the G. obscuriglobus proteins associated with pore-containing membranes possess structural domains found in eukaryote nuclear pore complexes. Moreover, immunogold labelling demonstrates localization of one such protein, containing a β-propeller domain, specifically to the G. obscuriglobus pore-like structures. Finding bacterial pores within internal cell membranes and with structural similarities to eukaryote nuclear pore complexes raises the dual possibilities of either hitherto undetected homology or stunning evolutionary convergence.

Ancient, highly conserved proteins from a LUCA with complex cell biology provide evidence in support of the nuclear compartment commonality (NuCom) hypothesis

The nuclear compartment commonality (NuCom) hypothesis posits a complex last common ancestor (LUCA) with membranous compartments including a nuclear membrane. Such a LUCA then evolved to produce two nucleated lineages of the tree of life: the Planctomycetes-Verrucomicrobia-Chlamydia superphylum (PVC) within the Bacteria, and the Eukarya. We propose that a group of ancient essential protokaryotic signature proteins (PSPs) originating in LUCA were incorporated into ancestors of PVC Bacteria and Eukarya. Tubulins, ubiquitin system enzymes and sterol-synthesizing enzymes are consistent with early origins of these features shared between the PVC superphylum and Eukarya.

The S-Layer Protein of the Anammox Bacterium Kuenenia stuttgartiensis Is Heavily O-Glycosylated

Anaerobic ammonium oxidation (anammox) bacteria are a distinct group of Planctomycetes that are characterized by their unique ability to perform anammox with nitrite to dinitrogen gas in a specialized organelle. The cell of anammox bacteria comprises three membrane-bound compartments and is surrounded by a two-dimensional crystalline S-layer representing the direct interaction zone of anammox bacteria with the environment. Previous results from studies with the model anammox organism Kuenenia stuttgartiensis suggested that the protein monomers building the S-layer lattice are glycosylated. In the present study, we focussed on the characterization of the S-layer protein glycosylation in order to increase our knowledge on the cell surface characteristics of anammox bacteria. Mass spectrometry (MS) analysis showed an O-glycan attached to 13 sites distributed over the entire 1591-amino acid S-layer protein. This glycan is composed of six monosaccharide residues, of which five are N-acetylhexosamine (HexNAc) residues. Four of these HexNAc residues have been identified as GalNAc. The sixth monosaccharide in the glycan is a putative dimethylated deoxyhexose. Two of the HexNAc residues were also found to contain a methyl group, thereby leading to an extensive degree of methylation of the glycan. This study presents the first characterization of a glycoprotein in a planctomycete and shows that the S-layer protein Kustd1514 of K. stuttgartiensis is heavily glycosylated with an O-linked oligosaccharide which is additionally modified by methylation. S-layer glycosylation clearly contributes to the diversification of the K. stuttgartiensis cell surface and can be expected to influence the interaction of the bacterium with other cells or abiotic surfaces.

Compartmentalization in PVC super-phylum: evolution and impact

BACKGROUND

The PVC super-phylum gathers bacteria from seven phyla (Planctomycetes, Verrucomicrobiae, Chlamydiae, Lentisphaera, Poribacteria, OP3, WWE2) presenting different lifestyles, cell plans and environments. Planctomyces and several Verrucomicrobiae exhibit a complex cell plan, with an intracytoplasmic membrane inducing the compartmentalization of the cytoplasm into two regions (pirellulosome and paryphoplasm). The evolution and function of this cell plan is still subject to debate. In this work, we hypothesized that it could play a role in protection of the bacterial DNA, especially against Horizontal Genes Transfers (HGT). Therefore, 64 bacterial genomes belonging to seven different phyla (whose four PVC phyla) were studied. We reconstructed the evolution of the cell plan as precisely as possible, thanks to information obtained by bibliographic study and electronic microscopy. We used a strategy based on comparative phylogenomic in order to determine the part occupied by the horizontal transfers for each studied genomes.

RESULTS

Our results show that the bacteria Simkania negevensis (Chlamydiae) and Coraliomargarita akajimensis (Verrucomicrobiae), whose cell plan were unknown before, are compartmentalized, as we can see on the micrographies. This is one of the first indication of the presence of an intracytoplasmic membrane in a Chlamydiae. The proportion of HGT does not seems to be related to the cell plan of bacteria, suggesting that compartmentalization does not induce a protection of bacterial DNA against HGT. Conversely, lifestyle of bacteria seems to impact the ability of bacteria to exchange genes.

CONCLUSIONS

Our study allows a best reconstruction of the evolution of intracytoplasmic membrane, but this structure seems to have no impact on HGT occurrences.

REVIEWERS

This article was reviewed by Mircea Podar and Olivier Tenaillon.

Paleomicrobiology: a Snapshot of Ancient Microbes and Approaches to Forensic Microbiology

Paleomicrobiology, or the study of ancient microorganisms, has raised both fascination and skepticism for many years. While paleomicrobiology is not a recent field, the application of emerging techniques, such as DNA sequencing, is proving essential and has provided novel information regarding the evolution of viruses, antibiotic resistance, saprophytes, and pathogens, as well as ancient health and disease status, cultural customs, ethnic diets, and historical events. In this review, we highlight the importance of studying ancient microbial DNA, its contributions to current knowledge, and the role that forensic paleomicrobiology has played in deciphering historical enigmas. We also discuss the emerging techniques used to study the microbial composition of ancient samples as well as major concerns that accompany ancient DNA analyses.

Gemmata species: Planctomycetes of medical interest

The Planctomycetes genus Gemmata is represented by both uncultured organisms and cultured Gemmata obscuriglobus and 'Gemmata massiliana' organisms. Their plasmidless 9.2 Mb genomes encode a complex cell plan, cell signaling capacities, antibiotic and trace metal resistance and multidrug resistance efflux pumps. As they lack iron metabolism pathways, they are fastidious. Gemmata spp. are mainly found in aquatic and soil environments but have also been found in hospital water networks in close proximity to patients, in animals, on human skin, the gut microbiota and in the blood of aplastic leukemic patients. Due to their panoply of attack and defense mechanisms and their recently demonstrated association with humans, the potential of Gemmata organisms to behave as opportunistic pathogens should be more widely recognized.

The origin and evolution of the acidocalcisome and its interactions with other organelles

Acidocalcisomes are acidic calcium stores that have been found from bacteria to human cells. They are rich in phosphorus compounds in the form of orthophosphate (P_i), pyrophosphate (PP_i), and polyphosphate (polyP) and their acidity is maintained by proton pumps such as the vacuolar proton pyrophosphatase (V-H⁺-PPase, or VP1), the vacuolar proton ATPase (V-H⁺-ATPase), or both. Recent studies in trypanosomatids and in other species have revealed their role in phosphate metabolism, and cation and water homeostasis, as suggested by the presence of novel pumps, transporters, and channels. An important role in autophagy has also been described. The study of the biogenesis of acidocalcisomes as well as of the interactions of these lysosome-related organelles with other organelles have uncovered important roles in calcium signaling and osmoregulation. Significantly, despite conservation of acidocalcisomes across all of cellular life, there is evidence for intimate integration of these organelles with eukaryotic cellular functions, and which are directly relevant to parasites.

Global and Targeted Lipid Analysis of Gemmata obscuriglobus Reveals the Presence of Lipopolysaccharide, a Signature of the Classical Gram-Negative Outer Membrane

Planctomycete bacteria possess many unusual cellular properties, contributing to a cell plan long considered to be unique among the bacteria. However, data from recent studies are more consistent with a modified Gram-negative cell plan. A key feature of the Gram-negative plan is the presence of an outer membrane (OM), for which lipopolysaccharide (LPS) is a signature molecule. Despite genomic evidence for an OM in planctomycetes, no biochemical verification has been reported. We attempted to detect and characterize LPS in the planctomycete Gemmata obscuriglobus. We obtained direct evidence for LPS and lipid A using electrophoresis and differential staining. Gas chromatography-mass spectrometry (GC-MS) compositional analysis of LPS extracts identified eight different 3-hydroxy fatty acids (3-HOFAs), 2-keto 3-deoxy-d-manno-octulosonic acid (Kdo), glucosamine, and hexose and heptose sugars, a chemical profile unique to Gram-negative LPS. Combined with molecular/structural information collected from matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) MS analysis of putative intact lipid A, these data led us to propose a heterogeneous hexa-acylated lipid A structure (multiple-lipid A species). We also confirmed previous reports of G. obscuriglobus whole-cell fatty acid (FA) and sterol compositions and detected a novel polyunsaturated FA (PUFA). Our confirmation of LPS, and by implication an OM, in G. obscuriglobus raises the possibility that other planctomycetes possess an OM. The pursuit of this question, together with studies of the structural connections between planctomycete LPS and peptidoglycans, will shed more light on what appears to be a planctomycete variation on the Gram-negative cell plan.

IMPORTANCE

Bacterial species are classified as Gram positive or negative based on their cell envelope structure. For 25 years, the envelope of planctomycete bacteria has been considered a unique exception, as it lacks peptidoglycan and an outer membrane (OM). However, the very recent detection of peptidoglycan in planctomycete species has provided evidence for a more conventional cell wall and raised questions about other elements of the cell envelope. Here, we report direct evidence of lipopolysaccharide in the planctomycete G. obscuriglobus, suggesting the presence of an OM and supporting the proposal that the planctomycete cell envelope is an extension of the canonical Gram-negative plan. This interpretation features a convoluted cytoplasmic membrane and expanded periplasmic space, the functions of which provide an intriguing avenue for future investigation.

Endosymbiotic theories for eukaryote origin

For over 100 years, endosymbiotic theories have figured in thoughts about the differences between prokaryotic and eukaryotic cells. More than 20 different versions of endosymbiotic theory have been presented in the literature to explain the origin of eukaryotes and their mitochondria. Very few of those models account for eukaryotic anaerobes. The role of energy and the energetic constraints that prokaryotic cell organization placed on evolutionary innovation in cell history has recently come to bear on endosymbiotic theory. Only cells that possessed mitochondria had the bioenergetic means to attain eukaryotic cell complexity, which is why there are no true intermediates in the prokaryote-to-eukaryote transition. Current versions of endosymbiotic theory have it that the host was an archaeon (an archaebacterium), not a eukaryote. Hence the evolutionary history and biology of archaea increasingly comes to bear on eukaryotic origins, more than ever before. Here, we have compiled a survey of endosymbiotic theories for the origin of eukaryotes and mitochondria, and for the origin of the eukaryotic nucleus, summarizing the essentials of each and contrasting some of their predictions to the observations. A new aspect of endosymbiosis in eukaryote evolution comes into focus from these considerations: the host for the origin of plastids was a facultative anaerobe.

18 GHz electromagnetic field induces permeability of Gram-positive cocci

The effect of electromagnetic field (EMF) exposures at the microwave (MW) frequency of 18 GHz, on four cocci, Planococcus maritimus KMM 3738, Staphylococcus aureus CIP 65.8(T), S. aureus ATCC 25923 and S. epidermidis ATCC 14990(T), was investigated. We demonstrate that exposing the bacteria to an EMF induced permeability in the bacterial membranes of all strains studied, as confirmed directly by transmission electron microscopy (TEM), and indirectly via the propidium iodide assay and the uptake of silica nanospheres. The cells remained permeable for at least nine minutes after EMF exposure. It was shown that all strains internalized 23.5 nm nanospheres, whereas the internalization of the 46.3 nm nanospheres differed amongst the bacterial strains (S. epidermidis ATCC 14990(T) ~  0%; Staphylococcus aureus CIP 65.8(T) S. aureus ATCC 25923, ~40%; Planococcus maritimus KMM 3738, ~ 80%). Cell viability experiments indicated that up to 84% of the cells exposed to the EMF remained viable. The morphology of the bacterial cells was not altered, as inferred from the scanning electron micrographs, however traces of leaked cytosolic fluids from the EMF exposed cells could be detected. EMF-induced permeabilization may represent an innovative, alternative cell permeability technique for applications in biomedical engineering, cell drug delivery and gene therapy.

Exploring bacterial organelle interactomes: a model of the protein-protein interaction network in the Pdu microcompartment

Bacterial microcompartments (MCPs) are protein-bound organelles that carry out diverse metabolic pathways in a wide range of bacteria. These supramolecular assemblies consist of a thin outer protein shell, reminiscent of a viral capsid, which encapsulates sequentially acting enzymes. The most complex MCP elucidated so far is the propanediol utilizing (Pdu) microcompartment. It contains the reactions for degrading 1,2-propanediol. While several experimental studies on the Pdu system have provided hints about its organization, a clear picture of how all the individual components interact has not emerged yet. Here we use co-evolution-based methods, involving pairwise comparisons of protein phylogenetic trees, to predict the protein-protein interaction (PPI) network governing the assembly of the Pdu MCP. We propose a model of the Pdu interactome, from which selected PPIs are further inspected via computational docking simulations. We find that shell protein PduA is able to serve as a “universal hub” for targeting an array of enzymes presenting special N-terminal extensions, namely PduC, D, E, L and P. The varied N-terminal peptides are predicted to bind in the same cleft on the presumptive luminal face of the PduA hexamer. We also propose that PduV, a protein of unknown function with remote homology to the Ras-like GTPase superfamily, is likely to localize outside the MCP, interacting with the protruding β-barrel of the hexameric PduU shell protein. Preliminary experiments involving a bacterial two-hybrid assay are presented that corroborate the existence of a PduU-PduV interaction. This first systematic computational study aimed at characterizing the interactome of a bacterial microcompartment provides fresh insight into the organization of the Pdu MCP.

Many bacteria produce giant proteinaceous structures within their cells, which they use to carry out special metabolic reactions in their interior. Much has been learned recently about the individual components—shell proteins and encapsulated enzymes—that assemble together, thousands of subunits in all, to make these bacterial microcompartments or MCPs. However, in order to carry out their biological functions, these systems must be highly organized through specific protein-protein interactions, and such a higher level understanding of organization in MCP systems is lacking. In this study, we use genomic data and phylogenetic analysis to predict the network of interactions between the approximately 20 different kinds of proteins and enzymes present in the Pdu MCP. Then, we use computational docking to examine a subset of those that are predicted to involve enzymes bound to the interior surface of the shell proteins, and show that the results are consistent with recent experimental data. We further provide new experimental evidence for one of the predicted protein-protein interactions. This study expands our understanding of a complex system of proteins serving as a metabolic organelle in bacterial cells, and provides a foundation for further experimental investigations.

A statistical anomaly indicates symbiotic origins of eukaryotic membranes

We report a remarkable statistical paradox from a compositional analysis of membrane lipids of archaea, eubacteria, and eukaryotes. The presence of Simpson's paradox in the analysis of lipids common to plasma membranes of all domains provides the first evidence based on the compositional analysis of lipidomics data for the symbiotic origins of eukaryotic cells.

Compositional analyses of nucleic acids and proteins have shed light on possible origins of living cells. In this work, rigorous compositional analyses of ∼5000 plasma membrane lipid constituents of 273 species in the three life domains (archaea, eubacteria, and eukaryotes) revealed a remarkable statistical paradox, indicating symbiotic origins of eukaryotic cells involving eubacteria. For lipids common to plasma membranes of the three domains, the number of carbon atoms in eubacteria was found to be similar to that in eukaryotes. However, mutually exclusive subsets of same data show exactly the opposite—the number of carbon atoms in lipids of eukaryotes was higher than in eubacteria. This statistical paradox, called Simpson's paradox, was absent for lipids in archaea and for lipids not common to plasma membranes of the three domains. This indicates the presence of interaction(s) and/or association(s) in lipids forming plasma membranes of eubacteria and eukaryotes but not for those in archaea. Further inspection of membrane lipid structures affecting physicochemical properties of plasma membranes provides the first evidence (to our knowledge) on the symbiotic origins of eukaryotic cells based on the “third front” (i.e., lipids) in addition to the growing compositional data from nucleic acids and proteins.