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 Microbiome Analysis Reveals Diversity and Function of Mollicutes Associated with the Eastern Oyster, Crassostrea virginica

mSphere ◽  
2021 ◽  
Vol 6 (3) ◽  
Author(s):  
Zachary T. Pimentel ◽  
Keith Dufault-Thompson ◽  
Kayla T. Russo ◽  
Abigail K. Scro ◽  
Roxanna M. Smolowitz ◽  
...  
Keyword(s):  
Functional Analysis ◽  
Crassostrea Virginica ◽  
Marine Invertebrates ◽  
Eastern Oyster ◽  
High Variability ◽  
Metabolic Reconstruction ◽  
High Prevalence ◽  
Adult Oyster ◽  
Genome Scale

ABSTRACT Marine invertebrate microbiomes play important roles in diverse host and ecological processes. However, a mechanistic understanding of host-microbe interactions is currently available for a small number 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-based amplicon profiling, shotgun metagenomics, and genome-scale metabolic reconstruction. Relatively high variability of the microbiome was observed across individual oysters and among different tissue types. Specifically, a significantly higher alpha diversity was observed in the inner shell than in the gut, gill, mantle, and pallial fluid samples, and a distinct microbiome composition was revealed in the gut compared to other tissues examined in this study. 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 compared to closely related genomes of Mollicutes isolates, indicating distinct mechanisms of carbon and energy acquisition by the oyster-associated Mollicutes. A systematic reanalysis of public eastern oyster-derived microbiome data revealed a high prevalence of the Mollicutes among adult oyster guts and a significantly lower relative abundance of the Mollicutes in oyster larvae and adult oyster biodeposits. IMPORTANCE Despite their biological and ecological significance, a mechanistic characterization of microbiome function is frequently missing from many nonmodel marine invertebrates. As an initial step toward filling this gap for the eastern oyster, Crassostrea virginica, this study provides an integrated taxonomic and functional analysis of the oyster microbiome using samples from a coastal salt pond in August 2017. The study identified high variability of the microbiome across tissue types and among individual oysters, with some dominant taxa showing higher relative abundance in specific tissues. A high prevalence of Mollicutes in the adult oyster gut was revealed by comparative analysis of the gut, biodeposit, and larva microbiomes. Phylogenomic analysis and metabolic reconstruction suggested the oyster-associated Mollicutes is closely related but functionally distinct from Mollicutes isolated from other marine invertebrates. To the best of our knowledge, this study represents the first metagenomics-derived functional inference of Mollicutes in the eastern oyster microbiome.

scholarly journals Physicochemical and Techno-Functional Characterization of Native Corn Reintroduced in the Andean Zone of Jujuy, Argentina

Proceedings ◽  
2020 ◽  
Vol 53 (1) ◽  
pp. 7
Author(s):  
María Alejandra Giménez ◽  
Cristina Noemí Segundo ◽  
Manuel Oscar Lobo ◽  
Norma Cristina Sammán
Keyword(s):  
Principal Component Analysis ◽  
Functional Properties ◽  
Food Industry ◽  
Functional Characterization ◽  
Principal Component ◽  
Component Analysis ◽  
High Variability ◽  
Pca Analysis

The chemical and techno-functional properties of nine maize races from the Andean zone of Jujuy, Argentina, in the process of reintroduction, were determined. Principal component analysis (PCA) was applied to establish the differences between them. The breeds studied showed high variability in their chemical and techno-functional properties, which would indicate that their applications in the food industry will also be differentiated. The PCA analysis allowed us to group them into four groups, and the Capia Marron and Culli races showed unique properties, mainly in the formation of gels.

Characterization of microsatellite loci in the eastern oyster, Crassostrea virginica

2000 ◽  
Vol 9 (12) ◽  
pp. 2216-2218 ◽  
Author(s):  
Bonnie L. Brown ◽  
Dean E. Franklin ◽  
Patrick M. Gaffney ◽  
Min Hong ◽  
Dan Dendanto ◽  
...  
Keyword(s):  
Crassostrea Virginica ◽  
Microsatellite Loci ◽  
Eastern Oyster

Characterization of hemocytes from different body fluids of the eastern oyster Crassostrea virginica

2017 ◽  
Vol 71 ◽  
pp. 372-379 ◽  
Author(s):  
Yuk-Ting Lau ◽  
Lauren Sussman ◽  
Emmanuelle Pales Espinosa ◽  
Selma Katalay ◽  
Bassem Allam
Keyword(s):  
Crassostrea Virginica ◽  
Eastern Oyster ◽  
Body Fluids

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.

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.

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