General Neuroscience


Publications (15)

First report of ‘Candidatus Phytoplasma asteris’ associated with yellowing, scorching and decline of almond trees in India

Citation
Gupta et al. (2023). PeerJ 11
Names (2)
Ca. Phytoplasma asteris Ca. Phytoplasma
Subjects
General Agricultural and Biological Sciences General Biochemistry, Genetics and Molecular Biology General Medicine General Neuroscience
Abstract
The almond, a commercially important tree nut crop worldwide, is native to the Mediterranean region. Stone fruit trees are affected by at least 14 ‘Candidatus Phytoplasma’ species globally, among which ‘Candidatus Phytoplasma asteris’ is one of the most widespread phytoplasma infecting Prunus dulcis, causing aster yellows disease. Recently, almond plantations of Nauni region were consistently affected by phytoplasma, as evidenced by visible symptoms, fluorescent microscopic studies and molecular characterization. During several surveys from May to September 2020–2022, almond aster yellows phytoplasma disease showing symptoms such as chlorosis, inward rolling, reddening, scorching and decline with an incidence as high as 40%. Leaf samples were collected from symptomatic almond trees and the presence of phytoplasma was confirmed through fluorescent microscopic studies by employing DAPI (4, 6-diamino-2-phenylindole) that showed distinctive light blue flourescent phytoplasma bodies in phloem sieve tube elements. The presence of phytoplasma in symptomatic almond trees was further confirmed using nested PCR with specific primer pairs followed by amplification of 16S rDNA and 16S-23S rDNA intergenic spacer (IS) fragments. Sequencing and BLAST analysis of expected amplicon of the 16S rDNA gene confirmed that the almond phytoplasma in Himachal Pradesh was identical to the aster yellows group phytoplasma. Phylogenetic analysis of 16S rDNA almond phytoplasma also grouped ‘Prunus dulcis’ aster yellows phytoplasma within 16SrI-B subgroup showed 94% nucleotide identity with ‘Prunus dulcis’ phytoplasma PAEs3 and ‘Prunus dulcis’ phytoplasma PAE28 from Iran. This research presents the first host report of ‘Candidatus Phytoplasma asteris’ infecting almonds in India, expanding the knowledge of the diversity and distribution of phytoplasma strains affecting almond trees globally.

Extensive microbial diversity within the chicken gut microbiome revealed by metagenomics and culture

Citation
Gilroy et al. (2021). PeerJ 9
Names (94)
“Mediterraneibacter excrementigallinarum” “Ruthenibacterium merdavium” “Gemmiger stercoravium” “Eisenbergiella intestinipullorum” “Merdibacter merdavium” “Enterocloster excrementipullorum” “Borkfalkia stercoripullorum” “Gemmiger stercoripullorum” “Merdibacter merdigallinarum” “Intestinimonas stercoravium” “Limosilactobacillus intestinipullorum” “Mediterraneibacter pullistercoris” “Faecalibacterium gallistercoris” “Borkfalkia excrementigallinarum” “Mediterraneibacter stercoripullorum” “Anaerotignum merdipullorum” “Fusicatenibacter merdavium” “Anaerostipes excrementavium” “Blautia pullistercoris” “Hungatella pullicola” “Borkfalkia faecipullorum” “Acetatifactor stercoripullorum” “Mediterraneibacter vanvlietii” “Eisenbergiella stercoravium” “Butyricicoccus avistercoris” “Blautia stercorigallinarum” “Acutalibacter stercorigallinarum” “Mediterraneibacter excrementavium” “Corynebacterium faecigallinarum” “Phocaeicola excrementigallinarum” “Blautia merdavium” “Anaerostipes avistercoris” “Dietzia intestinigallinarum” “Mediterraneibacter faecigallinarum” “Mediterraneibacter faecipullorum” “Dietzia intestinipullorum” “Alistipes stercoravium” “Eisenbergiella merdavium” “Ligilactobacillus avistercoris” “Eisenbergiella merdigallinarum” “Nosocomiicoccus stercorigallinarum” “Mailhella merdavium” “Fournierella excrementigallinarum” “Fournierella merdavium” “Desulfovibrio gallistercoris” “Blautia merdipullorum” “Phocaeicola faecigallinarum” “Alistipes avicola” “Bariatricus faecipullorum” “Desulfovibrio intestinavium” “Brachybacterium merdavium” “Brevibacterium intestinavium” “Agathobaculum intestinipullorum” “Limosilactobacillus excrementigallinarum” “Mediterraneibacter merdigallinarum” “Fournierella merdigallinarum” “Mediterraneibacter pullicola” “Mediterraneibacter merdipullorum” “Microbacterium stercoravium” “Collinsella stercoripullorum” “Ligilactobacillus excrementavium” “Mucispirillum faecigallinarum” “Janibacter merdipullorum” “Lactobacillus pullistercoris” “Atopostipes pullistercoris” “Gemmiger excrementavium” “Fournierella merdipullorum” “Ruania gallistercoris” “Tidjanibacter faecipullorum” “Companilactobacillus pullicola” “Rothia avicola” “Rubneribacter avistercoris” “Sphingobacterium stercorigallinarum” “Intestinimonas merdavium” “Luteimonas excrementigallinarum” “Alistipes intestinigallinarum” “Tetragenococcus pullicola” “Eisenbergiella pullistercoris” “Agathobaculum merdavium” “Evtepia faecavium” “Barnesiella excrementavium” “Acutalibacter pullistercoris” “Anaerofilum excrementigallinarum” “Evtepia faecigallinarum” “Gemmiger excrementipullorum” “Anaerobiospirillum pullistercoris” “Acinetobacter avistercoris” “Limosilactobacillus merdigallinarum” “Desulfovibrio intestinigallinarum” “Blautia stercoravium” “Barnesiella excrementigallinarum” “Gemmiger faecavium” “Alectryobacillus” “Alectryobacillus merdavium”
Subjects
General Agricultural and Biological Sciences General Biochemistry, Genetics and Molecular Biology General Medicine General Neuroscience
Abstract
Background The chicken is the most abundant food animal in the world. However, despite its importance, the chicken gut microbiome remains largely undefined. Here, we exploit culture-independent and culture-dependent approaches to reveal extensive taxonomic diversity within this complex microbial community. Results We performed metagenomic sequencing of fifty chicken faecal samples from two breeds and analysed these, alongside all (n = 582) relevant publicly available chicken metagenomes, to cluster over 20 million non-redundant genes and to construct over 5,500 metagenome-assembled bacterial genomes. In addition, we recovered nearly 600 bacteriophage genomes. This represents the most comprehensive view of taxonomic diversity within the chicken gut microbiome to date, encompassing hundreds of novel candidate bacterial genera and species. To provide a stable, clear and memorable nomenclature for novel species, we devised a scalable combinatorial system for the creation of hundreds of well-formed Latin binomials. We cultured and genome-sequenced bacterial isolates from chicken faeces, documenting over forty novel species, together with three species from the genus Escherichia, including the newly named species Escherichia whittamii. Conclusions Our metagenomic and culture-based analyses provide new insights into the bacterial, archaeal and bacteriophage components of the chicken gut microbiome. The resulting datasets expand the known diversity of the chicken gut microbiome and provide a key resource for future high-resolution taxonomic and functional studies on the chicken gut microbiome.

“Candidatus Trichorickettsia mobilis”, a Rickettsiales bacterium, can be transiently transferred from the unicellular eukaryote Paramecium to the planarian Dugesia japonica

Citation
Modeo et al. (2020). PeerJ 8
Names (1)
Ca. Trichorickettsia mobilis
Subjects
General Agricultural and Biological Sciences General Biochemistry, Genetics and Molecular Biology General Medicine General Neuroscience
Abstract
Most of the microorganisms responsible for vector-borne diseases (VBD) have hematophagous arthropods as vector/reservoir. Recently, many new species of microorganisms phylogenetically related to agents of VBD were found in a variety of aquatic eukaryotic hosts; in particular, numerous new bacterial species related to the genus Rickettsia (Alphaproteobacteria, Rickettsiales) were discovered in protist ciliates and other unicellular eukaryotes. Although their pathogenicity for humans and terrestrial animals is not known, several indirect indications exist that these bacteria might act as etiological agents of possible VBD of aquatic organisms, with protists as vectors. In the present study, a novel strain of the Rickettsia-Like Organism (RLO) endosymbiont “Candidatus (Ca.) Trichorickettsia mobilis” was identified in the macronucleus of the ciliate Paramecium multimicronucleatum. We performed transfection experiments of this RLO to planarians (Dugesia japonica) per os. Indeed, the latter is a widely used model system for studying bacteria pathogenic to humans and other Metazoa. In transfection experiments, homogenized paramecia were added to food of antibiotic-treated planarians. Treated and non-treated (i.e. control) planarians were investigated at day 1, 3, and 7 after feeding for endosymbiont presence by means of PCR and ultrastructural analyses. Obtained results were fully concordant and suggest that this RLO endosymbiont can be transiently transferred from ciliates to metazoans, being detected up to day 7 in treated planarians’ enterocytes. Our findings might offer insights into the potential role of ciliates or other protists as putative vectors for diseases caused by Rickettsiales or other RLOs and occurring in fish farms or in the wild.

Differing responses of red abalone (Haliotis rufescens) and white abalone (H. sorenseni) to infection with phage-associated Candidatus Xenohaliotis californiensis

Citation
Vater et al. (2018). PeerJ 6
Names (1)
Ca. Xenohaliotis californiensis
Subjects
General Agricultural and Biological Sciences General Biochemistry, Genetics and Molecular Biology General Medicine General Neuroscience
Abstract
The Rickettsiales-like prokaryote and causative agent of Withering Syndrome (WS)—Candidatus Xenohaliotis californiensis (Ca. Xc)—decimated black abalone populations along the Pacific coast of North America. White abalone—Haliotis sorenseni—are also susceptible to WS and have become nearly extinct in the wild due to overfishing in the 1970s. Candidatus Xenohaliotis californiensis proliferates within epithelial cells of the abalone gastrointestinal tract and causes clinical signs of starvation. In 2012, evidence of a putative bacteriophage associated with Ca. Xc in red abalone—Haliotis rufescens—was described. Recently, histologic examination of animals with Ca. Xc infection in California abalone populations universally appear to have the phage-containing inclusions. In this study, we investigated the current virulence of Ca. Xc in red abalone and white abalone at different environmental temperatures. Using a comparative experimental design, we observed differences over time between the two abalone species in mortality, body condition, and bacterial load by quantitative real time PCR (qPCR). By day 251, all white abalone exposed to the current variant of Ca. Xc held in the warm water (18.5 °C) treatment died, while red abalone exposed to the same conditions had a mortality rate of only 10%, despite a relatively heavy bacterial burden as determined by qPCR of posterior esophagus tissue and histological assessment at the termination of the experiment. These data support the current status of Ca. Xc as less virulent in red abalone, and may provide correlative evidence of a protective phage interaction. However, white abalone appear to remain highly susceptible to this disease. These findings have important implications for implementation of a white abalone recovery program, particularly with respect to the thermal regimes of locations where captively-reared individuals will be outplanted.

Genetic analysis of ‘Candidatus Phytoplasma aurantifolia’ associated with witches’ broom on acid lime trees

Citation
Al-Ghaithi et al. (2018). PeerJ 6
Names (1)
Ca. Phytoplasma aurantifolia
Subjects
General Agricultural and Biological Sciences General Biochemistry, Genetics and Molecular Biology General Medicine General Neuroscience
Abstract
“Candidatus Phytoplasma aurantifolia” is associated with witches’ broom disease of lime in Oman and the UAE. A previous study showed that an infection by phytoplasma may not necessarily result in the physical appearance of witches’ broom symptoms in some locations in Oman and the UAE. This study investigated whether phytoplasma strains belonging to “Ca. P. aurantifolia” (based on the 16S rRNA gene analysis) in locations where disease symptoms are expressed are different from phytoplasma in locations where disease symptoms are not expressed. About 21 phytoplasma strains (15 from areas and trees with disease symptoms and six from areas and trees without disease symptoms) were included in the analysis. The study utilized sequences of the imp and SAP11 genes to characterize the 21 strains. Phylogenetic analysis of both genes showed that the 21 strains are similar to each other and to reference strains in GenBank. The study shows that there is a low level of diversity among all phytoplasma strains. In addition, it shows that phytoplasma in places where witches’ broom symptoms are not expressed are similar to phytoplasma in places where disease symptoms are expressed. This may suggest that disease expression is not linked to the presence of different phytoplasma strains, but may be due to other factors such as weather conditions.

Genomic comparisons of a bacterial lineage that inhabits both marine and terrestrial deep subsurface systems

Citation
Jungbluth et al. (2017). PeerJ 5
Names (3)
Desulforudis audaxviator Ts “Desulfopertinax cowenii” “Desulfopertinax”
Subjects
General Agricultural and Biological Sciences General Biochemistry, Genetics and Molecular Biology General Medicine General Neuroscience
Abstract
It is generally accepted that diverse, poorly characterized microorganisms reside deep within Earth’s crust. One such lineage of deep subsurface-dwelling bacteria is an uncultivated member of the Firmicutes phylum that can dominate molecular surveys from both marine and continental rock fracture fluids, sometimes forming the sole member of a single-species microbiome. Here, we reconstructed a genome from basalt-hosted fluids of the deep subseafloor along the eastern Juan de Fuca Ridge flank and used a phylogenomic analysis to show that, despite vast differences in geographic origin and habitat, it forms a monophyletic clade with the terrestrial deep subsurface genome of “Candidatus Desulforudis audaxviator” MP104C. While a limited number of differences were observed between the marine genome of “Candidatus Desulfopertinax cowenii” modA32 and its terrestrial relative that may be of potential adaptive importance, here it is revealed that the two are remarkably similar thermophiles possessing the genetic capacity for motility, sporulation, hydrogenotrophy, chemoorganotrophy, dissimilatory sulfate reduction, and the ability to fix inorganic carbon via the Wood-Ljungdahl pathway for chemoautotrophic growth. Our results provide insights into the genetic repertoire within marine and terrestrial members of a bacterial lineage that is widespread in the global deep subsurface biosphere, and provides a natural means to investigate adaptations specific to these two environments.

Comparative genomics ofSynechococcusand proposal of the new genusParasynechococcus

Citation
Coutinho et al. (2016). PeerJ 4
Names (1)
“Parasynechococcus”
Subjects
General Agricultural and Biological Sciences General Biochemistry, Genetics and Molecular Biology General Medicine General Neuroscience
Abstract
Synechococcusis among the most important contributors to global primary productivity. The genomes of several strains of this taxon have been previously sequenced in an effort to understand the physiology and ecology of these highly diverse microorganisms. Here we present a comparative study ofSynechococcusgenomes. For that end, we developed GenTaxo, a program written in Perl to perform genomic taxonomy based on average nucleotide identity, average amino acid identity and dinucleotide signatures, which revealed that the analyzed strains are drastically distinct regarding their genomic content. Phylogenomic reconstruction indicated a division ofSynechococcusin two clades (i.e. Synechococcus and the new genus Parasynechococcus), corroborating evidences that this is in fact a polyphyletic group. By clustering protein encoding genes into homologue groups we were able to trace the Pangenome and core genome of both marine and freshwaterSynechococcusand determine the genotypic traits that differentiate these lineages.