Profiling 16S bacterial DNA and RNA: Difference between community structure and transcriptional activity in phenanthrene polluted sand in the vicinity of plant roots

2006 ◽  
Vol 38 (7) ◽  
pp. 1545-1553 ◽  
Author(s):  
Stéphane C. Corgié ◽  
Thierry Beguiristain ◽  
Corinne Leyval
2021 ◽  
Vol 11 (1) ◽  
Author(s):  
José Mariano Amabis ◽  
Eduardo Gorab

AbstractMicronucleoli are among the structures composing the peculiar scenario of the nucleolus in salivary gland nuclei of dipterans representative of Sciaridae. Micronucleolar bodies contain ribosomal DNA and RNA, are transcriptionally active and may appear free in the nucleoplasm or associated with specific chromosome regions in salivary gland nuclei. This report deals with an extreme case of nucleolar fragmentation/dispersion detected in the salivary gland of Schwenkfeldina sp. Such a phenomenon in this species was found to be restricted to cell types undergoing polyteny and seems to be differentially controlled according to the cell type. Furthermore, transcriptional activity was detected in virtually all the micronucleolar bodies generated in the salivary gland. The relative proportion of the rDNA in polytene and diploid tissues showed that rDNA under-replication did not occur in polytene nuclei suggesting that the nucleolar and concomitant rDNA dispersion in Schwenkfeldina sp. may reflect a previously hypothesised process in order to counterbalance the rDNA loss due to the under-replication. The chromosomal distribution of epigenetic markers for the heterochromatin agreed with early cytological observations in this species suggesting that heterochromatin is spread throughout the chromosome length of Schwenkfeldina sp. A comparison made with results from another sciarid species argues for a role played by the heterochromatin in the establishment of the rDNA topology in polytene nuclei of Sciaridae.


Microbiome ◽  
2014 ◽  
Vol 2 (1) ◽  
pp. 19 ◽  
Author(s):  
Agata Wesolowska-Andersen ◽  
Martin Bahl ◽  
Vera Carvalho ◽  
Karsten Kristiansen ◽  
Thomas Sicheritz-Pontén ◽  
...  

2019 ◽  
Vol 26 (3) ◽  
pp. 165-171
Author(s):  
Jean-Marc Cavaillon

André Boivin (1895–1949) started his career in Marseille as a biochemist. Soon after the discovery of insulin, he worked on its purification, allowing for the treatment of local patients. He later moved to Strasbourg and set-up a microtitration technique of small carbon molecules and a method for quantifying purine and pyrimidine bases. His main scientific contribution occurred in Bucharest, where he was recruited to organize the teaching of medicinal chemistry. Together with Ion and Lydia Mesrobeanu, at the Cantacuzene Institute, they were the first to characterize the biochemical nature of endotoxins, which he termed the “glucido-lipidic antigen.” After joining the Institut Pasteur annex near Paris, he worked with Gaston Ramon pursuing his research on smooth and rough LPS. Additionally, with Albert Delaunay, he researched the formation of exotoxins and antibodies (Abs). He was nominated assistant-director of the Institut Pasteur in 1940. He initiated research on bacterial DNA and RNA, and was the first to hypothesize on how RNA fits into gene function. In 1947 he moved for a second time to Strasbourg, accepting a position as a Professor of Biological Chemistry. After his premature death at the age of 54, the French academies mourned his loss and recognized him as one of their outstanding masters of biochemistry, microbiology, immunology, and molecular biology.


mSystems ◽  
2020 ◽  
Vol 5 (6) ◽  
pp. e00929-20
Author(s):  
Jiachao Zhou ◽  
Xiaofen Chai ◽  
Lin Zhang ◽  
Timothy S. George ◽  
Fei Wang ◽  
...  

ABSTRACTPlant roots are usually colonized by various arbuscular mycorrhizal (AM) fungal species, which vary in morphological, physiological, and genetic traits. This colonization constitutes the mycorrhizal nutrient uptake pathway (MP) and supplements the pathway through roots. Simultaneously, the extraradical hyphae of each AM fungus is associated with a community of bacteria. However, whether the community structure and function of the microbiome on the extraradical hyphae differ between AM fungal species remains unknown. In order to understand the community structure and the predicted functions of the microbiome associated with different AM fungal species, a split-root compartmented rhizobox cultivation system, which allowed us to inoculate two AM fungal species separately in two root compartments, was used. We inoculated two separate AM fungal species combinations, (i) Funneliformis mosseae and Gigaspora margarita and (ii) Rhizophagus intraradices and G. margarita, on a single root system of cotton. The hyphal exudate-fed, active microbiome was measured by combining 13C-DNA stable isotope probing with MiSeq sequencing. We found that different AM fungal species, which were simultaneously colonizing a single root system, hosted active microbiomes that were distinct from one another. Moreover, the predicted potential functions of the different microbiomes were distinct. We conclude that the arbuscular mycorrhizal fungal component of the system is responsible for the recruitment of distinct microbiomes in the hyphosphere. The potential significance of the predicted functions of the microbial ecosystem services is discussed.IMPORTANCE Arbuscular mycorrhizal (AM) fungi form tight symbiotic relationships with the majority of terrestrial plants and play critical roles in plant P acquisition, adding a further dimension of complexity. The plant-AM fungus-bacterium system is considered a continuum, with the bacteria colonizing not only the plant roots, but also the associated mycorrhizal hyphal network, known as the hyphosphere microbiome. Plant roots are usually colonized by different AM fungal species which form an independent phosphorus uptake pathway from the root pathway, i.e., the mycorrhizal pathway. The community structure and function of the hyphosphere microbiome of different AM species are completely unknown. In this novel study, we found that arbuscular mycorrhizal fungi cocolonizing on single plant roots recruit their own specific microbiomes, which should be considered in evaluating plant microbiome form and function. Our findings demonstrate the importance of understanding trophic interactions in order to gain insight into the plant-AM fungus-bacterium symbiosis.


Microbiome ◽  
2019 ◽  
Vol 7 (1) ◽  
Author(s):  
Shuaimin Chen ◽  
Tatoba R. Waghmode ◽  
Ruibo Sun ◽  
Eiko E. Kuramae ◽  
Chunsheng Hu ◽  
...  

Abstract Background Plant roots assemble microbial communities both inside the roots and in the rhizosphere, and these root-associated microbiomes play pivotal roles in plant nutrition and productivity. Although it is known that increased synthetic fertilizer input in Chinese farmlands over the past 50 years has resulted in not only increased yields but also environmental problems, we lack a comprehensive understanding of how crops under elevated nutrient input shape root-associated microbial communities, especially through adjusting the quantities and compositions of root metabolites and exudates. Methods The compositions of bacterial and fungal communities from the roots and rhizosphere of wheat (Triticum aestivum L.) under four levels of long-term inorganic nitrogen (N) fertilization were characterized at the tillering, jointing and ripening stages. The root-released organic carbon (ROC), organic acids in the root exudates and soil organic carbon (SOC) and soil active carbon (SAC) in the rhizosphere were quantified. Results ROC levels varied dramatically across wheat growth stages and correlated more with the bacterial community than with the fungal community. Rhizosphere SOC and SAC levels were elevated by long-term N fertilization but varied only slightly across growth stages. Variation in the microbial community structure across plant growth stages showed a decreasing trend with N fertilization level in the rhizosphere. In addition, more bacterial and fungal genera were significantly correlated in the jointing and ripening stages than in the tillering stage in the root samples. A number of bacterial genera that shifted in response to N fertilization, including Arthrobacter, Bacillus and Devosia, correlated significantly with acetic acid, oxalic acid, succinic acid and tartaric acid levels. Conclusions Our results indicate that both plant growth status and N input drive changes in the microbial community structure in the root zone of wheat. Plant growth stage demostrated a stronger influence on bacterial than on fungal community composition. A number of bacterial genera that have been described as plant growth-promoting rhizobacteria (PGPR) responded positively to N fertilization, and their abundance correlated significantly with the organic acid level, suggesting that the secretion of organic acids may be a strategy developed by plants to recruit beneficial microbes in the root zone to cope with high N input. These results provide novel insight into the associations among increased N input, altered carbon availability, and shifts in microbial communities in the plant roots and rhizosphere of intensive agricultural ecosystems.


2020 ◽  
Vol 51 (6) ◽  
pp. 593-604
Author(s):  
Maja Zakošek Pipan ◽  
Janko Mrkun

The long-standing hypothesis that the neonatal microbiome is acquired during and after birth has been challenged by recent studies in humans using advanced molecular technologies, which identified bacteria and bacterial DNA and RNA in amniotic fluid, placenta, and meconium. Similar studies have recently been conducted on canine neonates, giving a description of the gut microbiota of newborn puppies and a comparison of different types of parturition on theirdevelopment. In this review, we summarize the current knowledge of microbiome and microbial alterations in the canine gut, vagina and oral cavity throughout pregnancy, and their effects on the microbiome of the placenta and the meconium in neonatal puppies. We further compare the microbiome knowledge gained in the last decade on human neonates and draw parallels with canine pregnancy and the neonatal microbiome.


Sign in / Sign up

Export Citation Format

Share Document