Multidisciplinary


Publications (135)

The inside scoop: Comparative genomics of two intranuclear bacteria, “Candidatus Berkiella cookevillensis” and “Candidatus Berkiella aquae”

Citation
Kidane et al. (2022). PLOS ONE 17 (12)
Names
Ca. Berkiella cookevillensis Ca. Berkiella aquae
Subjects
Multidisciplinary
Abstract
“Candidatus Berkiella cookevillensis” (strain CC99) and “Candidatus Berkiella aquae” (strain HT99), belonging to the Coxiellaceae family, are gram-negative bacteria isolated from amoebae in biofilms present in human-constructed water systems. Both bacteria are obligately intracellular, requiring host cells for growth and replication. The intracellular bacteria-containing vacuoles of both bacteria closely associate with or enter the nuclei of their host cells. In this study, we analyzed the genome sequences of CC99 and HT99 to better understand their biology and intracellular lifestyles. The CC99 genome has a size of 2.9Mb (37.9% GC) and contains 2,651 protein-encoding genes (PEGs) while the HT99 genome has a size of 3.6Mb (39.4% GC) and contains 3,238 PEGs. Both bacteria encode high proportions of hypothetical proteins (CC99: 46.5%; HT99: 51.3%). The central metabolic pathways of both bacteria appear largely intact. Genes for enzymes involved in the glycolytic pathway, the non-oxidative branch of the phosphate pathway, the tricarboxylic acid pathway, and the respiratory chain were present. Both bacteria, however, are missing genes for the synthesis of several amino acids, suggesting reliance on their host for amino acids and intermediates. Genes for type I and type IV (dot/icm) secretion systems as well as type IV pili were identified in both bacteria. Moreover, both bacteria contain genes encoding large numbers of putative effector proteins, including several with eukaryotic-like domains such as, ankyrin repeats, tetratricopeptide repeats, and leucine-rich repeats, characteristic of other intracellular bacteria.

Reclassification of eight Akkermansia muciniphila strains and description of Akkermansia massiliensis sp. nov. and Candidatus Akkermansia timonensis, isolated from human feces

Citation
Ndongo et al. (2022). Scientific Reports 12 (1)
Names
Ca. Akkermansia timonensis
Subjects
Multidisciplinary
Abstract
AbstractAkkermansiamuciniphila is a human intestinal tract bacterium that plays an important role in the mucus layer renewal. Several studies have demonstrated that it is a modulator for gut homeostasis and a probiotic for human health. The Akkermansia genus contains two species with standing in nomenclature but their genomic diversity remains unclear. In this study, eight new Akkermansia sp. strains were isolated from the human gut. Using the digital DNA-DNA hybridization (dDDH), average nucleotide identity (ANI) and core genome-based phylogenetic analysis applied to 104 A.muciniphila whole genomes sequences, strains were reclassified into three clusters. Cluster I groups A.muciniphila strains (including strain ATCC BAA-835T as type strain), whereas clusters II and III represent two new species. A member of cluster II, strain Marseille-P6666 differed from A.muciniphila strain ATCC BAA-835T and from A.glycaniphila strain PytT in its ability to grow in microaerophilic atmosphere up to 42 °C, to assimilate various carbon sources and to produce acids from a several compounds. The major fatty acids of strain Marseille-P6666 were 12-methyl-tetradecanoic and pentadecanoic acids. The DNA G + C content of strain Marseille-P6666 was 57.8%. On the basis of these properties, we propose the name A.massiliensis sp. nov. for members of cluster II, with strain Marseille-P6666T (= CSUR P6666 = CECT 30548) as type strain. We also propose the name “Candidatus Akkermansia timonensis” sp. nov. for the members of cluster III, which contains only uncultivated strains, strain Akk0196 being the type strain.

The ‘Candidatus Phytoplasma mali’ effector protein SAP11CaPm interacts with MdTCP16, a class II CYC/TB1 transcription factor that is highly expressed during phytoplasma infection

Citation
Mittelberger et al. (2022). PLOS ONE 17 (12)
Names
Ca. Phytoplasma mali Ca. Phytoplasma asteris
Subjects
Multidisciplinary
Abstract
’Candidatus Phytoplasma mali’, is a bacterial pathogen associated with the so-called apple proliferation disease in Malus × domestica. The pathogen manipulates its host with a set of effector proteins, among them SAP11CaPm, which shares similarity to SAP11AYWB from ’Candidatus Phytoplasma asteris’. SAP11AYWB interacts and destabilizes the class II CIN transcription factors of Arabidopsis thaliana, namely AtTCP4 and AtTCP13 as well as the class II CYC/TB1 transcription factor AtTCP18, also known as BRANCHED1 being an important factor for shoot branching. It has been shown that SAP11CaPm interacts with the Malus × domestica orthologues of AtTCP4 (MdTCP25) and AtTCP13 (MdTCP24), but an interaction with MdTCP16, the orthologue of AtTCP18, has never been proven. The aim of this study was to investigate this potential interaction and close a knowledge gap regarding the function of SAP11CaPm. A Yeast two-hybrid test and Bimolecular Fluorescence Complementation in planta revealed that SAP11CaPm interacts with MdTCP16. MdTCP16 is known to play a role in the control of the seasonal growth of perennial plants and an increase of MdTCP16 gene expression has been detected in apple leaves in autumn. In addition to this, MdTCP16 is highly expressed during phytoplasma infection. Binding of MdTCP16 by SAP11CaPm might lead to the induction of shoot proliferation and early bud break, both of which are characteristic symptoms of apple proliferation disease.

New globally distributed bacterial phyla within the FCB superphylum

Citation
Gong et al. (2022). Nature Communications 13 (1)
Names
“Blakebacteria” “Joyebacteria” “Arandabacterum” “Blakebacterales” “Joyebacterales” “Orphanbacterota” “Blakebacteraceae” “Joyebacteraceae” “Orphanbacteria” “Blakebacterum” “Joyebacterum” “Orphanbacterales” “Blakebacterum guaymasense” “Joyebacterum haimaense” “Orphanbacteraceae” “Blakebacterota” “Arandabacterum bohaiense” “Orphanbacterum” “Arandabacteria” “Arandabacterales” “Arandabacterota” “Arandabacteraceae” “Joyebacterota” “Orphanbacterum longqiense”
Subjects
General Biochemistry, Genetics and Molecular Biology General Chemistry General Physics and Astronomy Multidisciplinary
Abstract
AbstractMicrobes in marine sediments play crucial roles in global carbon and nutrient cycling. However, our understanding of microbial diversity and physiology on the ocean floor is limited. Here, we use phylogenomic analyses of thousands of metagenome-assembled genomes (MAGs) from coastal and deep-sea sediments to identify 55 MAGs that are phylogenetically distinct from previously described bacterial phyla. We propose that these MAGs belong to 4 novel bacterial phyla (Blakebacterota, Orphanbacterota, Arandabacterota, and Joyebacterota) and a previously proposed phylum (AABM5-125-24), all of them within the FCB superphylum. Comparison of their rRNA genes with public databases reveals that these phyla are globally distributed in different habitats, including marine, freshwater, and terrestrial environments. Genomic analyses suggest these organisms are capable of mediating key steps in sedimentary biogeochemistry, including anaerobic degradation of polysaccharides and proteins, and respiration of sulfur and nitrogen. Interestingly, these genomes code for an unusually high proportion (~9% on average, up to 20% per genome) of protein families lacking representatives in public databases. Genes encoding hundreds of these protein families colocalize with genes predicted to be involved in sulfur reduction, nitrogen cycling, energy conservation, and degradation of organic compounds. Our findings advance our understanding of bacterial diversity, the ecological roles of these bacteria, and potential links between novel gene families and metabolic processes in the oceans.

Recovery of Lutacidiplasmatales archaeal order genomes suggests convergent evolution in Thermoplasmatota

Citation
Sheridan et al. (2022). Nature Communications 13 (1)
Names
“Lutacidiplasmataceae” “Lutacidiplasma” “Lutacidiplasma silvani” “Lutacidiplasmatales”
Subjects
General Biochemistry, Genetics and Molecular Biology General Chemistry General Physics and Astronomy Multidisciplinary
Abstract
AbstractThe Terrestrial Miscellaneous Euryarchaeota Group has been identified in various environments, and the single genome investigated thus far suggests that these archaea are anaerobic sulfite reducers. We assemble 35 new genomes from this group that, based on genome analysis, appear to possess aerobic and facultative anaerobic lifestyles and may oxidise rather than reduce sulfite. We propose naming this order (representing 16 genera) “Lutacidiplasmatales” due to their occurrence in various acidic environments and placement within the phylum Thermoplasmatota. Phylum-level analysis reveals that Thermoplasmatota evolution had been punctuated by several periods of high levels of novel gene family acquisition. Several essential metabolisms, such as aerobic respiration and acid tolerance, were likely acquired independently by divergent lineages through convergent evolution rather than inherited from a common ancestor. Ultimately, this study describes the terrestrially prevalent Lutacidiciplasmatales and highlights convergent evolution as an important driving force in the evolution of archaeal lineages.

An essential role for tungsten in the ecology and evolution of a previously uncultivated lineage of anaerobic, thermophilic Archaea

Citation
Buessecker et al. (2022). Nature Communications 13 (1)
Names
Wolframiiraptor allenii Wolframiiraptor sinensis Terraquivivens tikiterensis Ts Terraquivivens Geocrenenecus Benthortus Terraquivivens yellowstonensis Terraquivivens tengchongensis Terraquivivens ruidianensis Geocrenenecus huangii Geocrenenecus arthurdayi Geocrenenecus dongiae Ts Benthortus lauensis Ts Wolframiiraptoraceae Wolframiiraptor Wolframiiraptor gerlachensis Ts
Subjects
General Biochemistry, Genetics and Molecular Biology General Chemistry General Physics and Astronomy Multidisciplinary
Abstract
AbstractTrace metals have been an important ingredient for life throughout Earth’s history. Here, we describe the genome-guided cultivation of a member of the elusive archaeal lineage Caldarchaeales (syn. Aigarchaeota), Wolframiiraptor gerlachensis, and its growth dependence on tungsten. A metagenome-assembled genome (MAG) of W. gerlachensis encodes putative tungsten membrane transport systems, as well as pathways for anaerobic oxidation of sugars probably mediated by tungsten-dependent ferredoxin oxidoreductases that are expressed during growth. Catalyzed reporter deposition-fluorescence in-situ hybridization (CARD-FISH) and nanoscale secondary ion mass spectrometry (nanoSIMS) show that W. gerlachensis preferentially assimilates xylose. Phylogenetic analyses of 78 high-quality Wolframiiraptoraceae MAGs from terrestrial and marine hydrothermal systems suggest that tungsten-associated enzymes were present in the last common ancestor of extant Wolframiiraptoraceae. Our observations imply a crucial role for tungsten-dependent metabolism in the origin and evolution of this lineage, and hint at a relic metabolic dependence on this trace metal in early anaerobic thermophiles.

Identification of three new ‘Candidatus Liberibacter solanacearum’ haplotypes in four psyllid species (Hemiptera: Psylloidea)

Citation
Grimm et al. (2022). Scientific Reports 12 (1)
Names
“Liberibacter solanacearum”
Subjects
Multidisciplinary
Abstract
AbstractEleven haplotypes of the bacterium, ‘Candidatus Liberibacter solanacearum’, have been identified worldwide, several of which infect important agricultural crops. In the United States, haplotypes A and B are associated with yield and quality losses in potato, tomato, and other crops of the Solanaceae. Both haplotypes are vectored by potato psyllid, Bactericera cockerelli. Recently, a third haplotype, designated F, was identified in southern Oregon potato fields. To identify the vector of this haplotype, psyllids of multiple species were collected from yellow sticky cards placed near potato fields during two growing seasons. Over 2700 specimens were tested for ‘Ca. L. solanacearum’ by polymerase chain reaction. Forty-seven psyllids harbored the bacterium. The infected specimens comprised four psyllid species in two families, Aphalaridae and Triozidae (Hemiptera: Psylloidea). Nucleic acid and/or amino acid sequence analysis of the ‘Ca. L. solanacearum’ 16S ribosomal RNA, 50S ribosomal proteins L10/L12, and outer membrane protein identified three new haplotypes of the bacterium, designated as Aph1, Aph2 and Aph3, including two variants of Aph2 (Aph2a and Aph2b). The impact of these new haplotypes on solanaceous or other crops is not known. The vector of ‘Ca. L. solanacearum’ haplotype F was not detected in this study.

Rapid visual Candidatus Liberibacter asiaticus detection (citrus greening disease) using simple alkaline heat DNA lysis followed by loop-mediated isothermal amplification coupled hydroxynaphthol blue (AL-LAMP-HNB) for potential local use

Citation
Thoraneenitiyan et al. (2022). PLOS ONE 17 (10)
Names
Ca. Liberibacter asiaticus
Subjects
Multidisciplinary
Abstract
An outbreak of citrus greening or Huanglongbing disease bacteria occurs in many areas. We sampled and identified an ongoing ~year 2020 orange tree endemic in northern Thailand as Candidatus Liberibacter asiaticus. We thereby developed a plant greening disease (C. Liberibacter asiaticus) detection assay using simple alkaline heat DNA lysis and loop-mediated isothermal amplification coupled hydroxynaphthol blue (AL-LAMP-HNB), and evaluated the developed assay for its feasibility as point-of-care detection on 65 plant leaf samples with 100–1×104 copies of C. Liberibacter asiaticus or mocked injection compared with commercial DNA lysis kit and PCR-GE. Our assay is sensitive to 5–8.9 copies of omp (equaling 0.0056–0.01 fg) compatible with PCR-GE limit of detection. This ultra sensitive limit of detection could allow the disease detection before clinical apparent state of disease when C. Liberibacter asiaticus infection number is few, i.e. fewer than 100 copies of C. Liberibacter asiaticus. The assay is also specific with 6 degenerate primers targeting every strain of C. Liberibacter asiaticus omp from GenBank database, rapid (40 min total assay time), inexpensive (~2–3 USD/reaction), does not require sophisticated instrumentation, and has comparable assay accuracy (93.85–100% accuracy, 100% specificity, and 89.74–100% sensitivity) to bacterial DNA extraction by a commercial kit followed by PCR and gel electrophoresis (92.31% accuracy, 100% specificity, and 87.18% sensitivity) based on the real sample tests. Hence, the technique could be used in local or laboratory resource-restricted settings. The test result could be read by naked eyes through the color change from violet (negative) to sky blue (positive) for a C. Liberibacter asiaticus-infected specimen. Furthermore, this assay uses safe chemical reagents and, thus, is safe for the users.

Biosynthetic potential of the global ocean microbiome

Citation
Paoli et al. (2022). Nature 607 (7917)
Names
Ca. Eudoremicrobiaceae “Eudoremicrobium malaspinii”
Subjects
Multidisciplinary
Abstract
AbstractNatural microbial communities are phylogenetically and metabolically diverse. In addition to underexplored organismal groups1, this diversity encompasses a rich discovery potential for ecologically and biotechnologically relevant enzymes and biochemical compounds2,3. However, studying this diversity to identify genomic pathways for the synthesis of such compounds4 and assigning them to their respective hosts remains challenging. The biosynthetic potential of microorganisms in the open ocean remains largely uncharted owing to limitations in the analysis of genome-resolved data at the global scale. Here we investigated the diversity and novelty of biosynthetic gene clusters in the ocean by integrating around 10,000 microbial genomes from cultivated and single cells with more than 25,000 newly reconstructed draft genomes from more than 1,000 seawater samples. These efforts revealed approximately 40,000 putative mostly new biosynthetic gene clusters, several of which were found in previously unsuspected phylogenetic groups. Among these groups, we identified a lineage rich in biosynthetic gene clusters (‘Candidatus Eudoremicrobiaceae’) that belongs to an uncultivated bacterial phylum and includes some of the most biosynthetically diverse microorganisms in this environment. From these, we characterized the phospeptin and pythonamide pathways, revealing cases of unusual bioactive compound structure and enzymology, respectively. Together, this research demonstrates how microbiomics-driven strategies can enable the investigation of previously undescribed enzymes and natural products in underexplored microbial groups and environments.