1,720,991 research outputs found
Revised systematics of Holospora-like bacteria and characterization of “Candidatus Gortzia infectiva”, a novel macronuclear symbiont of Paramecium jenningsi
No full textThe genus Holospora (Rickettsiales) includes highly
infectious nuclear symbionts of the ciliate Paramecium with
unique morphology and life cycle. To date, nine species have
been described, but a molecular characterization is lacking for
most of them. In this study, we have characterized a novel
Holospora-like bacterium (HLB) living in the macronuclei of
a Paramecium jenningsi population. This bacterium was morphologically
and ultrastructurally investigated in detail, and its
life cycle and infection capabilities were described. We also
obtained its 16S rRNA gene sequence and developed a specific
probe for fluorescence in situ hybridization experiments. A new
taxon, “Candidatus Gortzia infectiva”, was established for this
HLB according to its unique characteristics and the relatively
low DNA sequence similarities shared with other bacteria. The
phylogeny of the order Rickettsiales based on 16S rRNA gene
sequences has been inferred, adding to the available data the
sequence of the novel bacterium and those of two Holospora
species (Holospora obtusa and Holospora undulata) characterized
for the purpose. Our phylogenetic analysis provided molecular
support for the monophyly of HLBs and showed a
possible pattern of evolution for some of their features. We
suggested to classify inside the family Holosporaceae only
HLBs, excluding other more distantly related and phenotypically
different Paramecium endosymbionts
Characterization of "Candidatus nebulobacter yamunensis" from the cytoplasm of Euplotes aediculatus (Ciliophora, Spirotrichea) and emended description of the family Francisellaceae
No full textOur knowledge of ciliate endosymbionts occurrence and diversity greatly expanded in the last decades, due to the development of characterization methods for uncultivable bacteria. Symbionts related to human pathogens such as rickettsiae and francisellae have been detected inside the cytoplasm of different ciliate species. In the present work, we have characterized a novel Francisella-related bacterium inside the rich prokaryotic community harbored by a population of Euplotes aediculatus (Ciliophora, Spirotrichea). Following the “Full-Cycle rRNA Approach” we obtained the almost full-length 16S rRNA gene sequence of this bacterium, and developed probes for diagnostic fluorescence in situ hybridizations. Attempts to culture the endosymbiont outside of its host failed. We classified this novel organism in a new taxon for which we propose the name “Candidatus Nebulobacter yamunensis”. In order to investigate its evolutionary relationships, we have also performed phylogenetic analyses on the class Gammaproteobacteria and the order Thiotrichales, which include the monogeneric family Francisellaceae. We found highly supported evidences for the establishment of a new monophyletic taxon including Francisella species, other organisms currently incertae sedis, and “Candidatus Nebulobacter yamunensis”. These organisms form a clade sharing a signature sequence not present in other Thiotrichales bacteria. Moreover, most of them have developed an intracellular life cycle inside eukaryotic organisms. We emended the original description of family Francisellaceae in order to encompass all members of the described clade
"Candidatus Defluviella procrastinata" and Candidatus Cyrtobacter zxanobii", two novel ciliate endosymbionts belonging to the"Midichloria clade"
No full textThe “Midichloria clade” is a recently discovered
but well-established evolutionary lineage clustering inside
the order Rickettsiales (Alphaproteobacteria). Not much is
known about the biology of these organisms. The best
characterized ones are endocellular symbionts of very different
eukaryotic hosts, ranging from arthropods to protists.
“Candidatus Midichloria mitochondrii”, the most studied
organism of the group, is an interesting object of study
because of its unique capability to infect metazoans’ mitochondria
and the presence of flagellar genes in its genome.
With this work, we aim at increasing the knowledge on the
biodiversity and phylogeny of the “Midichloria group”. We
characterized according to the “full cycle rRNA approach”
two novel endosymbionts of ciliated protozoa, i.e.
Paramecium nephridiatum and Euplotes aediculatus.
According to the nomenclatural rules for uncultivated prokaryotes,
we established the novel taxa “Candidatus
Defluviella procrastinata” and “Candidatus Cyrtobacter
zanobii” for the two bacterial symbionts. Our phylogenetic
analysis based on 16S rRNA gene sequences confirms that
the evolutionary histories of “Midichloria clade” representatives
and of their hosts are very different. This suggests that
the symbiotic processes arose many times independently,
perhaps through ways of transmission still not described in
Rickettsiales
Summer holidays as break-point in shaping a tannery sludge microbial community around a stable core microbiota
Full text linkRecently, several investigations focused on the discovery of a bacterial consortium shared among different wastewater treatment plants (WWTPs). Nevertheless, the definition of a core microbiota over time represents the necessary counterpart in order to unravel the dynamics of bacterial communities in these environments. Here we performed a monthly survey on the bacterial community of a consortial industrial plant. Objectives of this study were: (1) to identify a core microbiota constant over time; (2) to evaluate the temporal dynamics of the community during one year. A conspicuous and diversified core microbiota is constituted by operational taxonomic units which are present throughout the year in the plant. Community composition data confirm that the presence and abundance of bacteria in WWTPs is highly consistent at high taxonomic level. Our results indicate however a difference in microbial community structure between two groups of samples, identifying the summer holiday period as the break-point. Changes in the structure of the microbial community occur otherwise gradually, one month after another. Further studies will clarify how the size and diversity of the core microbiota could affect the observed dynamics
Survey of Paramecium duboscqui using three markers and assessment of the molecular variability in the genus Paramecium.
No full textThe genus Paramecium (phylum Ciliophora) is one of the best-known among protozoa. Nevertheless, the
knowledge on the diversity and distribution of species within this genus was remarkably scarce until
recent times. In the last years a constantly growing amount of data has formed, especially on the distribution
of species and the characterization of molecular markers. Much effort has been made on detecting
clades inside each morphospecies, which could suggest the presence of sibling species complexes as in
the famous case of Paramecium aurelia. In this work we present new data on Paramecium duboscqui,
one of the morphospecies that have not yet been surveyed employing DNA sequences as markers. We
obtained data from nine strains sampled around the world, using the three most commonly employed
markers (18S rRNA gene, ITS1-5.8S-ITS2 and COI gene sequences). Moreover, we compared our results
with those already available for other Paramecium species, and performed phylogenetic analyses for
the entire genus. We also expanded the knowledge on the ITS2 secondary structure and its usefulness
in studies on Paramecium. Our approach, that considers the data of all the species together, highlighted
some characteristic patterns as well as some ambiguities that should be further investigated
Strengths and Biases of High-Throughput Sequencing Data in the Characterization of Freshwater Ciliate Microbiomes
No full textMolecular surveys of eukaryotic microbial communities employing high-throughput sequencing (HTS) techniques are rapidly supplanting traditional morphological approaches due to their larger data output and reduced bench work time. Here, we directly compare morphological and Illumina data obtained from the same samples, in an effort to characterize ciliate faunas from sediments in freshwater environments. We show how in silico processing affects the final outcome of our HTS analysis, providing evidence that quality filtering protocols strongly impact the number of predicted taxa, but not downstream conclusions such as biogeography patterns. We determine the abundance distribution of ciliates, showing that a small fraction of abundant taxa dominates read counts. At the same time, we advance reasons to believe that biases affecting HTS abundances may be significant enough to blur part of the underlying biological picture. We confirmed that the HTS approach detects many more taxa than morphological inspections, and highlight how the difference varies among taxonomic groups. Finally, we hypothesize that the two datasets actually correspond to different conceptions of “diversity,” and consequently that neither is entirely superior to the other when investigating environmental protists
Detecting Associations Between Ciliated Protists and Prokaryotes with Culture-Independent Single-Cell Microbiomics: a Proof-of-Concept Study
No full textSymbioses between prokaryotes and microbial eukaryotes, particularly ciliated protists, have been studied for a long time. Nevertheless, researchers have focused only on a few host genera and species, mainly due to difficulties in cultivating the hosts, and usually have considered a single symbiont at a time. Here, we present a pilot study using a single-cell microbiomic approach to circumvent these issues. Unicellular ciliate isolation followed by simultaneous amplification of eukaryotic and prokaryotic markers was used. Our preliminary test gave reliable and satisfactory results both on samples collected from different habitats (marine and freshwater) and on ciliates belonging to different taxonomic groups. Results suggest that, as already assessed for many macro-organisms like plants and metazoans, ciliated protists harbor distinct microbiomes. The applied approach detected new potential symbionts as well as new hosts for previously described ones, with relatively low time and cost effort and without culturing. When further developed, single-cell microbiomics for ciliates could be applied to a large number of studies aiming to unravel the evolutionary and ecological meaning of these symbiotic systems
Ciliate communities and hidden biodiversity in freshwater biotopes of the Pistoia province (Tuscany, Italy)
No full textCiliates are essential components of aquatic environments, playing a pivotal role in microbial loops. Thus, the composition and dynamics of ciliate communities have been subjected to intense studying. Morphological methods have been traditionally employed, until the development of next-generation sequencing recently allowed to explore the topic with exclusively molecular techniques. However, the results of the two approaches are hardly comparable, and the pictures they offer can be quite different. This may be due, among other reasons, to two factors: (1) morphological descriptions may miss a large portion of “hidden biodiversity” (including rare species and resistance forms) that is detected instead by molecular methods; (2) identification errors may arise due to difficulties in recognizing microbial taxa without in-depth analyses. In this survey of freshwater systems of the Pistoia province (Tuscany, Italy) we address both issues, trying to quantify the hidden diversity through prolonged observations of differentially treated sample aliquots, combining morphological identification with Sanger sequencing. We provide the first insights into the ciliate fauna of this area presenting results that are suitable for future comparisons thanks to their multidisciplinary origin, and supply the first molecular data on well-known taxa such as Linostomella and Disematostoma
At the threshold of symbiosis: the genome of obligately endosymbiotic ‘Candidatus Nebulobacter yamunensis’ is almost indistinguishable from that of a cultivable strain
Full text linkComparing obligate endosymbionts with their free-living relatives is a powerful approach to investigate the evolution of symbioses, and it has led to the identification of several genomic traits consistently associated with the establishment of symbiosis. 'Candidatus Nebulobacter yamunensis' is an obligate bacterial endosymbiont of the ciliate Euplotes that seemingly depends on its host for survival. A subsequently characterized bacterial strain with an identical 16S rRNA gene sequence, named Fastidiosibacter lacustris, can instead be maintained in pure culture. We analysed the genomes of 'Candidatus Nebulobacter' and Fastidiosibacter seeking to identify key differences between their functional traits and genomic structure that might shed light on a recent transition to obligate endosymbiosis. Surprisingly, we found almost no such differences: the two genomes share a high level of sequence identity, the same overall structure, and largely overlapping sets of genes. The similarities between the genomes of the two strains are at odds with their different ecological niches, confirmed here with a parallel growth experiment. Although other pairs of closely related symbiotic/free-living bacteria have been compared in the past, 'Candidatus Nebulobacter' and Fastidiosibacter represent an extreme example proving that a small number of (unknown) factors might play a pivotal role in the earliest stages of obligate endosymbiosis establishment
Biodiversità delle comunità di ciliati di ambienti dulciacquicoli naturali ed antropizzati della provincia di Pistoia: uno studio multidisciplinare
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