1,721,100 research outputs found
First high-quality draft genome of Ochrobactrum haematophilum P6BS-III, a highly glyphosate-tolerant strain isolated from agricultural soil in Argentina
No full textWe report here on a high-quality draft genome sequence of Ochrobactrum haematophilum strain P6BS-III (DSM 106071), a Gram negative, non-sporulating bacterium isolated from a pastureland (Buenos Aires province, Argentina) which had been chronically exposed to the herbicide glyphosate. The genome of 5.25 Mb with a DNA G+C content of 56.63% size was estimated to contain 5,291 protein coding genes and 57 RNA genes. Genome analysis revealed the presence of the phn operon, which is involved in the phosphonate degradation pathway, and a class II 5-enolpyruvylshikimate-3-phosphate synthase (EPSP) that confers tolerance to glyphosate. Genes related to plant growth promotion traits are also present, and include genes for phosphorus metabolism, calcium phosphate and phytate solubilization, siderophore production, organic acid biosynthesis and indole acetic acid (IAA) production.Fil: Massot, Francisco. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Nanobiotecnología. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Instituto de Nanobiotecnología; Argentina. Hasselt University; BélgicaFil: Gkorezis, Panagiotis. Hasselt University; BélgicaFil: McAmmond, Breanne. Thompson Rivers University; CanadáFil: d´Haen, Jan. Hasselt University; BélgicaFil: Van Hamme, Jonathan. Thompson Rivers University; CanadáFil: Merini, Luciano Jose. Instituto Nacional de Tecnología Agropecuaria. Centro Regional La Pampa-San Luis. Estación Experimental Agropecuaria Anguil; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Vangronsveld, Jaco. Hasselt University; BélgicaFil: Thijs, Sofie. Hasselt University; Bélgic
Diversity and plant growth-promoting potential of (un)culturable bacteria in the Hedera helix phylloplane
No full textBackground: A diverse community of microbes naturally exists on the phylloplane, the surface of leaves. It is one of the most prevalent microbial habitats on earth and bacteria are the most abundant members, living in communities that are highly dynamic. Today, one of the key challenges for microbiologists is to develop strategies to culture the vast diversity of microorganisms that have been detected in metagenomic surveys.
Results: We isolated bacteria from the phylloplane of Hedera helix (common ivy), a widespread evergreen, using five growth media: Luria–Bertani (LB), LB01, yeast extract–mannitol (YMA), yeast extract–flour (YFlour), and YEx. We also included a comparison with the uncultured phylloplane, which we showed to be dominated by Proteobacteria, Actinobacteria, Bacteroidetes, and Firmicutes. Inter-sample (beta) diversity shifted from LB and LB01 containing the highest amount of resources to YEx, YMA, and YFlour which are more selective. All growth media equally favoured Actinobacteria and Gammaproteobacteria, whereas Bacteroidetes could only be found on LB01, YEx, and YMA. LB and LB01 favoured Firmicutes and YFlour was most selective for Betaproteobacteria. At the genus level, LB favoured the growth of Bacillus and Stenotrophomonas, while YFlour was most selective for Burkholderia and Curtobacterium. The in vitro plant growth promotion (PGP) profile of 200 isolates obtained in this study indicates that previously uncultured bacteria from the phylloplane may have potential applications in phytoremediation and other plant-based biotechnologies.
Conclusions: This study gives first insights into the total bacterial community of the H. helix phylloplane, including an evaluation of its culturability using five different growth media. We further provide a collection of 200 bacterial isolates underrepresented in current databases, including the characterization of PGP profiles. Here we highlight the potential of simple strategies to obtain higher microbial diversity from environmental samples and the use of high-throughput sequencing to guide isolate selection from a variety of growth media.Funding
This work was supported by the Hasselt University Methusalem project 08M03VGRJ, by the project G0D0916N (“Plant–microbe associations to reduce particulate matter concentration and toxicity in urban areas: a multidisciplinary approach”) financed by the Research Foundation – Flanders (FWO) and by a personal grant of VS provided by the Research Foundation – Flanders (FWO). The funding bodies had no role in the design of the study and collection, analysis, interpretation of data, or manuscript preparation.
Acknowledgements
We thank Prof. Jonathan Van Hamme for proofreading the language in this manuscript. We thank the VSC (Flemish Supercomputer Center), funded by the Research Foundation – Flanders (FWO) and the Flemish Government – department EWI for providing the computational resources and services used in this work
Habitat and feeding behaviour influence microbiome composition in Rhabdocoela ('Turbellaria')
No full textMicrobiome studies in Platyhelminthes have predominantly focused on a limited number of taxa, overlooking the vast diversity of turbellarian hosts. Here, we aimed to expand our understanding of microbial associations in a selection of free-living representatives of Rhabdocoela, a group of turbellarian flatworms that is very species-rich and ecologically diverse. Using 16S rRNA sequencing, we characterised the microbiomes of three species of Rhabdocoela, representing the two major lineages within this taxon: Dalytphloplanida and Kalyptorhynchia. The specimens were captured in the wild and obtained from marine or freshwater habitats. Gyratrix hermaphroditus (Kalyptorhynchia) and Mesostoma ehrenbergii (Dalytphloplanida) were both dominated by Proteobacteria, while Phaenocora evelinae (Dalytphloplanida) was predominantly associated with Cyanobacteria, more specific Oxyphytobacteria (chloroplasts). Based on the observed genera, our analysis revealed distinct microbial patterns, possibly associated with the habitat and lifestyle of the studied species. We could not exclude the presence of a phylosymbiotic signal as a limited core microbiome was present for each rhabdocoel species, although no set of bacteria common in all three rhabdocoel species was found. This explorative study contributes to the expanding knowledge of invertebrate microbiomes, providing new insights into the microbial associations of a selection of turbellarians. The descriptive results presented here open up several promising avenues for future research, including the search for functional roles of turbellarian bacterial symbionts and exploring potential correlations between microbiome compositions, turbellarian phylogeny and environmental parameters
The planarian microbiome in response to external stressors - focus on silvernanoparticles
No full textMany animals live in close association with complex microbial communities. The so-called microbiomes include bacteria, bacteriophages, fungi and viruses and are believed to have a beneficial effect on the hosts physiology. However, little is known about the invertebrate microbiome and its composition, how it is influenced by external factors and its stability as well as its function for the host physiology and health. In this study, we characterized the microbiome of a freshwater predator, the planarian Schmidtea mediterranea. Bacteria were found in the mucus and gut and sequencing results indicate mainly the association of proteobacteria with lab cultivated Schmidtea mediterranea. In addition, we investigated how environmental changes influence the planarian microbiome by a combination of ARISA fingerprinting and 16S rRNA sequencing. Of the studied compounds (Cd, MMS and silver nanoparticles) and other external changes (different foods and antibiotics exposure), silver nanoparticles had the highest impact on the planarian microbiome. Future research will reveal if and how an altered microbiome is important for the planarian physiology
More than a gut feeling? The composition, diversity and variability of the planarian microbiome
No full textMany animals live in close association with complex microbial communities. The so-called microbiome includes bacteria, fungi and viruses, which often contribute to the hosts physiology and health. Recently a functional link between endogenous bacteria, planarian physiology and the regeneration process was described. Disturbances of the microbiome resulted in tissue lesions and degeneration, although the exact function of the associated bacteria for planarian physiology remains unknown. Therefore, in this study, we investigated the planarian microbiome more in detail to gain insight into the composition, diversity and variability. We found that bacteria were present at the epidermis and in the gut of Schmidtea mediterranea. Via 16S rRNA sequencing, we showed an overall abundance of Betaproteobacteriales in diverse conditions, although at lower taxonomic levels variation between individuals and conditions was observed. The microbiome was sensitive to external stressors, especially after exposure to silver nanoparticles. Finally, our results also suggested fluctuations in the planarian microbiomes during the different phases of the regeneration process. Together, these findings form a solid basis to understand the nature and variability of microorganism associations to further elucidate their role in planarian physiology
The planarian microbiome in response to external stressors
No full textMany animals live in close association with complex microbial communities. The so-called microbiomes include bacteria, fungi and viruses and are believed to have a beneficial effect on the hosts physiology. An altered microbial composition in humans is associated with adverse health outcomes such as diabetes, inflammatory bowel diseases and allergies. Also invertebrates, such as fruitflies and earth worms, have associated bacteria that are linked with beneficial traits in fitness, immune responses and metabolic processes. Recently a functional link between endogenous bacteria and the planarian physiology and regeneration process was demonstrated.
We further investigated the planarian microbiome and its response to external stressors. Bacteria were present at the epidermis and in the gut of the worms. Alterations in Schmidtea mediterranea’s bacterial communities, as a response to environmental changes, were identified by a combination of ARISA fingerprinting and 16S rRNA sequencing. Of the studied compounds (Cd, MMS, AgNPs, …) and other external changes such as different food, silver nanoparticles had the highest impact on planarian microbiomes. In addition, microbiomes were studied in different phases of the regeneration process
Habitat and Feeding Behaviour Influence Microbiome Composition in Rhabdocoela ('Turbellaria')
No full text1. Microbiome studies in Platyhelminthes have predominantly focused on a limited number of taxa, overlooking the vast diversity of turbellarian hosts. Here, we aimed to expand our understanding of microbial associations in a selection of free-living representatives of Rhabdocoela, a group of turbellarian flatworms that is very species rich and ecologically diverse. 2. Using 16S rRNA sequencing, we characterised the microbiomes of three species of Rhabdocoela, representing the two most speciose lineages within this taxon: Dalytyphloplanida and Kalyptorhynchia. The specimens were captured in the wild and obtained from marine or freshwater habitats. 3. The microbiomes of Gyratrix hermaphroditus (Kalyptorhynchia) and Mesostoma ehrenbergii (Dalytyphloplanida) were both dominated by Proteobacteria, while Phaenocora evelinae (Dalytyphloplanida) was predominantly associated with Cyanobacteria, more specifically Oxyphytobacteria (chloroplasts). 4. Based on the observed genera, our analysis revealed distinct microbial patterns, possibly associated with the habitat and lifestyle of the studied species. We could not exclude the presence of a phylosymbiotic signal as a limited core microbiome was present for each rhabdocoel species, although no set of bacteria common to all three rhabdocoel species was found. 5. This explorative study contributes to the expanding knowledge of invertebrate microbiomes, providing new insights into the microbial associations of a selection of turbellarians. The descriptive results presented here open up several promising avenues for future research, including the search for functional roles of turbellarian bacterial symbionts and exploring potential correlations between microbiome compositions, turbellarian phylogeny and environmental variables.This work was supported by the Research Foundation Flanders (FWO) (G.0B83.17N, N1522719 and 1522015N), the Bijzonder OnderzoeksFonds of Hasselt University (BOF16NI03) and the Hasselt University Methusalem project (08M03VGRJ). The research leading to results presented in this publication was carried out with infrastructure funded by The European Marine Biological Resource Centre (EMBRC) Belgium—FWO project GOH3817N.
Acknowledgements
The authors thank Natascha Steffanie and Ria Vanderspikken for their skilful technical assistance. We also thank Breanne McAmmond and Jonathan Van Hamme for performing the Ion Torrent sequencing run. Bioinformatics analyses were made possible thanks to the Flemish Supercomputer Centre (VSC) infrastructure, supported by the FWO. Bart Tessens and Albrecht Houben are thanked for their collecting efforts, which yielded the rhabdocoel specimens included in this work. Sampling in France was facilitated by the staff members of the marine station in Roscoff. The Brazilian expedition was supported by Ana Maria Leal-Zanchet and João Braccini
More than a gut feeling? The composition, diversity and variability of the planarian microbiome
No full textMany animals live in close association with complex microbial communities. The so-called microbiome includes bacteria, fungi and viruses, which often contribute to the hosts physiology and health. Recently a functional link between endogenous bacteria, planarian physiology and the regeneration process was described. Disturbances of the microbiome resulted in tissue lesions and degeneration, although the exact function of the associated bacteria for planarian physiology remains unknown. Therefore, in this study, we investigated the planarian microbiome more in detail to gain insight into the composition, diversity and variability. We found that bacteria were present at the epidermis and in the gut of Schmidtea mediterranea. Via 16S rRNA sequencing, we showed an overall abundance of Betaproteobacteriales in diverse conditions, although at lower taxonomic levels variation between individuals and conditions was observed. The microbiome was sensitive to external stressors, especially after exposure to silver nanoparticles. Finally, our results also suggested fluctuations in the planarian microbiomes during the different phases of the regeneration process. Together, these findings form a solid basis to understand the nature and variability of microorganism associations to further elucidate their role in planarian physiology
The planarian microbiome in response to external stressors - focus on silvernanoparticles
No full textMany animals live in close association with complex microbial communities. The so-called microbiomes include bacteria, bacteriophages, fungi and viruses and are believed to have a beneficial effect on the hosts physiology. However, little is known about the invertebrate microbiome and its composition, how it is influenced by external factors and its stability as well as its function for the host physiology and health. In this study, we characterized the microbiome of a freshwater predator, the planarian Schmidtea mediterranea. Bacteria were found in the mucus and gut and sequencing results indicate mainly the association of proteobacteria with lab cultivated Schmidtea mediterranea. In addition, we investigated how environmental changes influence the planarian microbiome by a combination of ARISA fingerprinting and 16S rRNA sequencing. Of the studied compounds (Cd, MMS and silver nanoparticles) and other external changes (different foods and antibiotics exposure), silver nanoparticles had the highest impact on the planarian microbiome. Future research will reveal if and how an altered microbiome is important for the planarian physiology
The planarian microbiome in response to external stressors
No full textMany animals live in close association with complex microbial communities. The so-called microbiomes include bacteria, fungi and viruses and are believed to have a beneficial effect on the hosts physiology. An altered microbial composition in humans is associated with adverse health outcomes such as diabetes, inflammatory bowel diseases and allergies. Also invertebrates, such as fruitflies and earth worms, have associated bacteria that are linked with beneficial traits in fitness, immune responses and metabolic processes. Recently a functional link between endogenous bacteria and the planarian physiology and regeneration process was demonstrated.
We further investigated the planarian microbiome and its response to external stressors. Bacteria were present at the epidermis and in the gut of the worms. Alterations in Schmidtea mediterranea’s bacterial communities, as a response to environmental changes, were identified by a combination of ARISA fingerprinting and 16S rRNA sequencing. Of the studied compounds (Cd, MMS, AgNPs, …) and other external changes such as different food, silver nanoparticles had the highest impact on planarian microbiomes. In addition, microbiomes were studied in different phases of the regeneration process
- …
