scholarly journals Insights into the taxonomic and functional characterization of agricultural crop core rhizobiomes and their potential microbial drivers

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Antonio Castellano-Hinojosa ◽  
Sarah L. Strauss
Keyword(s):  
Plant Growth ◽  
Functional Traits ◽  
Functional Characterization ◽  
Soil Health ◽  
Soil Nutrient ◽  
Rrna Gene ◽  
Agricultural Crop ◽  
Limited Information ◽  
The Core

AbstractWhile our understanding of plant–microbe interactions in the rhizosphere microbiome (rhizobiome) has increased, there is still limited information on which taxa and functions drive these rhizobiome interactions. Focusing on the core rhizobiome (members common to two or more microbial assemblages) of crops may reduce the number of targets for determining these interactions, as they are expected to have greater influence on soil nutrient cycling and plant growth than the rest of the rhizobiome. Here, we examined whether the characterization of a core rhizobiome on the basis of only taxonomic or functional traits rather than the combined analysis of taxonomic and functional traits provides a different assessment of the core rhizobiome of agricultural crops. Sequences of the bacterial 16S rRNA gene from six globally important crops were analyzed using two different approaches in order to identify and characterize the taxonomic and functional core rhizobiome. For all crops examined, we found significant differences in the taxonomic and functional composition between the core rhizobiomes, and different phyla, genera, and predicted microbial functions were dominant depending on the core rhizobiome type. Network analysis indicated potentially important taxa were present in both taxonomic and functional core rhizobiomes. A subset of genera and predicted functions were exclusively or predominately present in only one type of core rhizobiome while others were detected in both core rhizobiomes. These results highlight the necessity of including both taxonomy and function when assessing the core rhizobiome, as this will enhance our understanding of the relationships between microbial taxa and soil health, plant growth, and agricultural sustainability.

scholarly journals Molecular characterization of a ceftriaxone-resistant Neisseria gonorrhoeae strain found in Switzerland: a case report

2021 ◽  
Vol 20 (1) ◽  
Author(s):  
Konrad Egli ◽  
Anna Roditscheff ◽  
Ursula Flückiger ◽  
Martin Risch ◽  
Lorenz Risch ◽  
...  
Keyword(s):  
Neisseria Gonorrhoeae ◽  
23S Rrna ◽  
Rrna Gene ◽  
Limited Information ◽  
Specific Pcr ◽  
Appropriate Treatment ◽  
23S Rrna Gene ◽  
Allele Type ◽  
Ciprofloxacin Resistance

Abstract Background The resistance of Neisseria gonorrhoeae to ceftriaxone is unusual in Switzerland. The underlying genotype responsible for resistance is suspected to be novel. Generally, resistance in Neisseria gonorrhoeae (Ng) involves a comprehensive set of genes with many different mutations leading to resistance to different β-lactams and fluoroquinolones. Case presentation A patient had a positive result from specific PCR for Ng. We routinely culture all clinical specimens with a positive NG-PCR. In this particular case, we isolated a strain with resistance to ceftriaxone in Switzerland. A total of seven different genes (penA, ponA, porinB, mtr, gyrA, parC, 23S rRNA gene) in this strain were partially sequenced for comparison with phenotypic susceptibility testing. Interestingly, two different mutations in the porinB gene were observed, and data on this gene are limited. Information on the identified allele type of the penA gene is very limited as well. Three different mutations of parC and gyrA that correlate with ciprofloxacin resistance were found. The combination of ceftriaxone and ciprofloxacin resistance makes an appropriate treatment difficult to obtain due to multidrug resistance. Conclusion The combined results for all genes show the appearance of new mutations in central Europe either due to worldwide spread or the emergence of new genetic combinations of mutations.

Cloning of the 5′ regulatory regions and functional characterization of the core promoters of ovine PLAU (u-PA) and SERPIN1 (PAI-1)

Gene ◽  
2011 ◽  
Vol 489 (1) ◽  
pp. 11-20 ◽  
Author(s):  
A.D. Lampidonis ◽  
G. Theodorou ◽  
C. Pecorini ◽  
R. Rebucci ◽  
A. Baldi ◽  
...  
Keyword(s):  
Functional Characterization ◽  
Regulatory Regions ◽  
Core Promoters ◽  
The Core ◽  
Pai 1

scholarly journals Diversity and Function of the Eastern Oyster (Crassostrea virginica) Microbiome

2020 ◽  
Author(s):  
Zachary T. Pimentel ◽  
Keith Dufault-Thompson ◽  
Kayla T. Russo ◽  
Abigail K. Scro ◽  
Roxanna M. Smolowitz ◽  
...  
Keyword(s):  
Crassostrea Virginica ◽  
Functional Characterization ◽  
Eastern Oyster ◽  
High Variability ◽  
Metabolic Reconstruction ◽  
Rrna Gene ◽  
Shotgun Metagenomics ◽  
Community Profiling ◽  
Genome Scale

ABSTRACTMarine invertebrate microbiomes play important roles in various host and ecological processes. However, a mechanistic understanding of host-microbe interactions is so far only available for a handful of model organisms. Here, an integrated taxonomic and functional analysis of the microbiome of the eastern oyster, Crassostrea virginica, was performed using 16S rRNA gene amplicon profiling, shotgun metagenomics, and genome-scale metabolic reconstruction. A relatively low number of amplicon sequence variants (ASVs) were observed in oyster tissues compared to water samples, while high variability was observed across individual oysters and among different tissue types. Targeted metagenomic sequencing of the gut microbiota led to further characterization of a dominant bacterial taxon, the class Mollicutes, which was captured by the reconstruction of a metagenome-assembled genome (MAG). Genome-scale metabolic reconstruction of the oyster Mollicutes MAG revealed a reduced set of metabolic functions and a high reliance on the uptake of host-derived nutrients. A chitin degradation and an arginine deiminase pathway were unique to the MAG as compared to other closely related Mycoplasma genomes, indicating a distinct mechanism of carbon and energy acquisition by the oyster- associated Mollicutes. A systematic reanalysis of public eastern oyster-derived microbiome data revealed the Mollicutes as a ubiquitous taxon among adult oysters despite their general absence in larvae and biodeposit samples, suggesting potential horizontal transmission via an unknown mechanism.IMPORTANCEDespite well-documented biological significance of invertebrate microbiomes, a detailed taxonomic and functional characterization is frequently missing from many non-model marine invertebrates. By using 16S rRNA gene-based community profiling, shotgun metagenomics, and genome-scale metabolic reconstruction, this study provides an integrated taxonomic and functional analysis of the microbiome of the eastern oyster, Crassostrea virginica. Community profiling revealed a surprisingly low richness, as compared to surrounding seawater, and high variability among different tissue types and individuals. Reconstruction of a Mollicutes MAG enabled the phylogenomic positioning and functional characterization of the oyster-associated Mollicutes. Comparative analysis of the adult oyster gut, biodeposits, and oyster larvae samples indicated the potentially ubiquitous associations of the Mollicutes taxon with adult oysters. To the best of our knowledge, this study represented the first metagenomics derived functional inference of the eastern oyster microbiome. An integrated analytical procedure was developed for the functional characterization of microbiomes in other non-model host species.

scholarly journals Functional Characterization of MigA and WapR: Putative Rhamnosyltransferases Involved in Outer Core Oligosaccharide Biosynthesis of Pseudomonas aeruginosa

2008 ◽  
Vol 190 (6) ◽  
pp. 1857-1865 ◽  
Author(s):  
Karen K. H. Poon ◽  
Erin L. Westman ◽  
Evgeny Vinogradov ◽  
Shouguang Jin ◽  
Joseph S. Lam
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Functional Characterization ◽  
Outer Core ◽  
Resonance Spectroscopy ◽  
Core Oligosaccharide ◽  
Strain Pao1 ◽  
The Core ◽  
O Antigen ◽  
Knockout Mutants

ABSTRACT Pseudomonas aeruginosa lipopolysaccharide (LPS) contains two glycoforms of core oligosaccharide (OS); one form is capped with O antigen through an α-1,3-linked l-rhamnose (l-Rha), while the other is uncapped and contains an α-1,6-linked l-Rha. Two genes in strain PAO1, wapR (PA5000) and migA (PA0705), encode putative glycosyltransferases associated with core biosynthesis. We propose that WapR and MigA are the rhamnosyltransferases responsible for the two linkages of l-Rha to the core. Knockout mutants with mutations in both genes were generated. The wapR mutant produced LPS lacking O antigen, and addition of wapR in trans complemented this defect. The migA mutant produced LPS with a truncated outer core and showed no reactivity to outer core-specific monoclonal antibody (MAb) 5C101. Complementation of this mutant with migA restored reactivity of the LPS to MAb 5C101. Interestingly, LPS from the complemented migA strain was not reactive to MAb 18-19 (specific for the core-plus-one O repeat). This was due to overexpression of MigA in the complemented strain that caused an increase in the proportion of the uncapped core OS, thereby decreasing the amount of the core-plus-one O repeat, indicating that MigA has a regulatory role. The structures of LPS from both mutants were elucidated using nuclear magnetic resonance spectroscopy and mass spectrometry. The capped core of the wapR mutant was found to be truncated and lacked α-1,3-l-Rha. In contrast, uncapped core OS from the migA mutant lacked α-1,6-l-Rha. These results provide evidence that WapR is the α-1,3-rhamnosyltransferase, while MigA is the α-1,6-rhamnosyltransferase.

Influence of Plant Growth Promoting Rhizobium on Growth of Pigeon Pea [Cajanus cajan (L.) Millsp.] 

2021 ◽  
Author(s):  
H.A. Harshitha ◽  
Geeta Goudar
Keyword(s):  
Plant Growth ◽  
Growth Parameters ◽  
Functional Characterization ◽  
Pigeon Pea ◽  
Iaa Production ◽  
Northern District ◽  
Plant Growth Promoting ◽  
Growth Promoting ◽  
Biological Nitrogen

Background: Symbiotic nitrogen fixation plays a major role in the production of million tons of total biological nitrogen. The Rhizobium not only fixes the nitrogen but also produces plant growth promoting hormones. In this view, the present study was undertaken to characterize the native Rhizobium isolates for their functional properties and evaluate on pigeon pea for their plant growth promotional activities. Methods: The present investigation was carried out during the year 2018-19 at UAS, Dharwad. Five of the native isolates obtained from Northern district of Karnataka were subjected for functional characterization using standard methods. The isolates were also tested for their plant growth promotional activities.Result: The IAA production in the isolates was ranged from 20.50 to 22.85 mg IAA/ml of broth and GA production from 13.40 to 14.51 mg/25ml of broth. ACC deamination activity in the isolates was ranged from 57.50 to 75.5 nmoles of α-ketobutyrate/mg/h of broth. All the isolates exhibited their ability to solubilize P and Zn. Out of ten isolates, four isolates exhibited potential to inhibit mycelial growth of Fusarium oxysporum f. sp. udum and per cent inhibition was ranged from 48.75 to 73.75. All the isolates were found to be positive for siderophore and HCN production. The isolate AMVPR98 performed better with respect to all the growth parameters of pigeon pea. Molecular characterization of isolate AMVPR98 revealed 99% similarity with Rhizobium pusense strain AB3.

scholarly journals Functional Characterization of WaaL, a Ligase Associated with Linking O-Antigen Polysaccharide to the Core of Pseudomonas aeruginosa Lipopolysaccharide

2005 ◽  
Vol 187 (9) ◽  
pp. 3002-3012 ◽  
Author(s):  
Priyanka D. Abeyrathne ◽  
Craig Daniels ◽  
Karen K. H. Poon ◽  
Mauricia J. Matewish ◽  
Joseph S. Lam
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Lipid A ◽  
Functional Characterization ◽  
Wild Type ◽  
The Core ◽  
O Antigen ◽  
Repeat Units ◽  
Cytoplasmic Face ◽  
O Antigens

ABSTRACT The O antigen of Pseudomonas aeruginosa B-band lipopolysaccharide is synthesized by assembling O-antigen-repeat units at the cytoplasmic face of the inner membrane by nonprocessive glycosyltransferases, followed by polymerization on the periplasmic face. The completed chains are covalently attached to lipid A core by the O-antigen ligase, WaaL. In P. aeruginosa the process of ligating these O-antigen molecules to lipid A core is not clearly defined, and an O-antigen ligase has not been identified until this study. Using the sequence of waaL from Salmonella enterica as a template in a BLAST search, a putative waaL gene was identified in the P. aeruginosa genome. The candidate gene was amplified and cloned, and a chromosomal knockout of PAO1 waaL was generated. Lipopolysaccharide (LPS) from this mutant is devoid of B-band O-polysaccharides and semirough (SR-LPS, or core-plus-one O-antigen). The mutant PAO1waaL is also deficient in the production of A-band polysaccharide, a homopolymer of d-rhamnose. Complementation of the mutant with pPAJL4 containing waaL restored the production of both A-band and B-band O antigens as well as SR-LPS, indicating that the knockout was nonpolar and waaL is required for the attachment of O-antigen repeat units to the core. Mutation of waaL in PAO1 and PA14, respectively, could be complemented with waaL from either strain to restore wild-type LPS production. The waaL mutation also drastically affected the swimming and twitching motilities of the bacteria. These results demonstrate that waaL in P. aeruginosa encodes a functional O-antigen ligase that is important for cell wall integrity and motility of the bacteria.

scholarly journals A Plant snoRNP Complex Containing snoRNAs, Fibrillarin, and Nucleolin-Like Proteins Is Competent for both rRNA Gene Binding and Pre-rRNA Processing In Vitro

2004 ◽  
Vol 24 (16) ◽  
pp. 7284-7297 ◽  
Author(s):  
Julio Sáez-Vasquez ◽  
David Caparros-Ruiz ◽  
Fredy Barneche ◽  
Manuel Echeverría
Keyword(s):  
Cleavage Site ◽  
Functional Characterization ◽  
Binding Activity ◽  
Rrna Gene ◽  
External Transcribed Spacer ◽  
Associated Proteins ◽  
Primary Cleavage

ABSTRACT In eukaryotes the primary cleavage of the precursor rRNA (pre-rRNA) occurs in the 5′ external transcribed spacer (5′ETS). In Saccharomyces cerevisiae and animals this cleavage depends on a conserved U3 small nucleolar ribonucleoprotein particle (snoRNP), including fibrillarin, and on other transiently associated proteins such as nucleolin. This large complex can be visualized by electron microscopy bound to the nascent pre-rRNA soon after initiation of transcription. Our group previously described a radish rRNA gene binding activity, NF D, that specifically binds to a cluster of conserved motifs preceding the primary cleavage site in the 5′ETS of crucifer plants including radish, cauliflower, and Arabidopsis thaliana (D. Caparros-Ruiz, S. Lahmy, S. Piersanti, and M. Echeverria, Eur. J. Biochem. 247:981-989, 1997). Here we report the purification and functional characterization of NF D from cauliflower inflorescences. Remarkably NF D also binds to 5′ETS RNA and accurately cleaves it at the primary cleavage site mapped in vivo. NF D is a multiprotein factor of 600 kDa that dissociates into smaller complexes. Two polypeptides of NF D identified by microsequencing are homologues of nucleolin and fibrillarin. The conserved U3 and U14 snoRNAs associated with fibrillarin and required for early pre-rRNA cleavages are also found in NF D. Based on this it is proposed that NF D is a processing complex that assembles on the rDNA prior to its interaction with the nascent pre-rRNA.

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