scholarly journals N-cycling microbiome recruitment differences between modern and wild Zea mays

2021 ◽  
Author(s):  
Alonso Favela ◽  
Martin O. Bohn ◽  
Angela Kent
Keyword(s):  
High Throughput Sequencing ◽  
Gene Diversity ◽  
Taxonomic Composition ◽  
N Cycling ◽  
Cycling Gene ◽  
Modern Maize ◽  
Functional Gene Diversity ◽  
Maize Domestication ◽  
Gene Richness ◽  
Species Richness And Abundance

Rewilding modern agricultural cultivars by reintroducing beneficial ancestral traits is a proposed approach to improve sustainability of modern agricultural systems. In this study, we compared recruitment of the rhizosphere microbiome among modern inbred maize and wild teosinte to assess whether potentially beneficial plant microbiome traits have been lost through maize domestication and modern breeding. To do this, we surveyed the bacterial and fungal communities along with nitrogen cycling functional groups in the rhizosphere of 6 modern domesticated maize genotypes and ancestral wild teosinte genotypes, while controlling for environmental conditions and starting soil inoculum. Using a combination of high-throughput sequencing and quantitative PCR, we found that the rhizosphere microbiomes of modern inbred and wild teosinte differed substantially in taxonomic composition, species richness, and abundance of N-cycling functional genes. Furthermore, the modern vs wild designation explained 27% of the variation in the prokaryotic microbiome, 62% of the variation in N-cycling gene richness, and 66% of N-cycling gene abundance. Surprisingly, we found that modern inbred genotypes hosted microbial communities with higher taxonomic and functional gene diversity within their microbiomes compared to ancestral genotypes. These results imply that modern maize and wild maize differ in their interaction with N-cycling microorganisms in the rhizosphere and that genetic variation exists within Zea to potentially ‘rewild’ microbiome-associated traits (i.e., exudation, root phenotypes, etc.).

scholarly journals 16S rRNA gene and 18S rRNA gene diversity in microbial mat communities in meltwater ponds on the McMurdo Ice Shelf, Antarctica

Polar Biology ◽  
2021 ◽  
Author(s):  
Eleanor E. Jackson ◽  
Ian Hawes ◽  
Anne D. Jungblut
Keyword(s):  
16S Rrna ◽  
18S Rrna ◽  
High Throughput Sequencing ◽  
Microbial Mats ◽  
Gene Diversity ◽  
Salinity Gradient ◽  
18S Rrna Gene ◽  
Rrna Gene ◽  
Ice Shelf ◽  
The Impact

AbstractThe undulating ice of the McMurdo Ice Shelf, Southern Victoria Land, supports one of the largest networks of ice-based, multiyear meltwater pond habitats in Antarctica, where microbial mats are abundant and contribute most of the biomass and biodiversity. We used 16S rRNA and 18S rRNA gene high-throughput sequencing to compare variance of the community structure in microbial mats within and between ponds with different salinities and pH. Proteobacteria and Cyanobacteria were the most abundant phyla, and composition at OTU level was highly specific for the meltwater ponds with strong community sorting along the salinity gradient. Our study provides the first detailed evaluation of eukaryote communities for the McMurdo Ice Shelf using the 18S rRNA gene. They were dominated by Ochrophyta, Chlorophyta and Ciliophora, consistent with previous microscopic analyses, but many OTUs belonging to less well-described heterotrophic protists from Antarctic ice shelves were also identified including Amoebozoa, Rhizaria and Labyrinthulea. Comparison of 16S and 18S rRNA gene communities showed that the Eukaryotes had lower richness and greater similarity between ponds in comparison with Bacteria and Archaea communities on the McMurdo Ice shelf. While there was a weak correlation between community dissimilarity and geographic distance, the congruity of microbial assemblages within ponds, especially for Bacteria and Archaea, implies strong habitat filtering in ice shelf meltwater pond ecosystems, especially due to salinity. These findings help to understand processes that are important in sustaining biodiversity and the impact of climate change on ice-based aquatic habitats in Antarctica.

Elevation trend in bacterial functional gene diversity decouples from taxonomic diversity

CATENA ◽  
2021 ◽  
Vol 199 ◽  
pp. 105099
Author(s):  
Dorsaf Kerfahi ◽  
Ke Dong ◽  
Ying Yang ◽  
Hyoki Kim ◽  
Koichi Takahashi ◽  
...  
Keyword(s):  
Gene Diversity ◽  
Taxonomic Diversity ◽  
Functional Gene ◽  
Functional Gene Diversity

Amazing grass: developmental genetics of maize domestication

2005 ◽  
Vol 33 (6) ◽  
pp. 1502-1506 ◽  
Author(s):  
E. Vollbrecht ◽  
B. Sigmon
Keyword(s):  
Reverse Genetics ◽  
Population Genomics ◽  
Evolutionary Developmental Biology ◽  
Developmental Genetics ◽  
Crop Domestication ◽  
Modern Maize ◽  
Signatures Of Selection ◽  
Maize Domestication ◽  
Plant Form ◽  
Evo Devo

Crop plants were domesticated by prehistoric farmers through artificial selection to provide a means of feeding the human population. This article discusses the developmental genetics of crop domestication and improvement, including the historical framework and recent approaches in maize and other grasses. In many cases, selecting for a plant form that correlates with productivity involves controlling meristem activity. In the domestication of modern maize from its progenitor Zea mays ssp. parviglumis, QTL (quantitative trait loci) mapping, genetics and population genomics approaches have identified several genes that contain signatures of selection. Only a few genes involved in the derivation of the highly productive maize ear have been identified, including teosinte glume architecture1 and ramosa1. Future prospects hinge on forward and reverse genetics, as well as on other approaches from the developing discipline of evo-devo (evolutionary developmental biology).

Metagenomics of Marine Actinomycetes: From Functional Gene Diversity to Biodiscovery

Marine OMICS ◽  
2016 ◽  
pp. 165-186 ◽  
Author(s):  
Sergey B. Zotchev ◽  
Olga N. Sekurova ◽  
D. İpek Kurtböke
Keyword(s):  
Gene Diversity ◽  
Functional Gene ◽  
Marine Actinomycetes ◽  
Functional Gene Diversity

scholarly journals Gcd Gene Diversity of Quinoprotein Glucose Dehydrogenase in the Sediment of Sancha Lake and Its Response to the Environment

2018 ◽  
Vol 16 (1) ◽  
pp. 1 ◽  
Author(s):  
Yong Li ◽  
Jianqiang Zhang ◽  
Zhiliang Gong ◽  
Wenlai Xu ◽  
Zishen Mou
Keyword(s):  
Correlation Analysis ◽  
High Throughput Sequencing ◽  
Gene Diversity ◽  
Pearson Correlation ◽  
Glucose Dehydrogenase ◽  
Sampling Site ◽  
Soluble Phosphate ◽  
High Genetic Diversity ◽  
Alpha And Beta Diversity ◽  
Insoluble Phosphate

Quinoprotein glucose dehydrogenase (GDH) is the most important enzyme of inorganic phosphorus-dissolving metabolism, catalyzing the oxidation of glucose to gluconic acid. The insoluble phosphate in the sediment is converted into soluble phosphate, facilitating mass reproduction of algae. Therefore, studying the diversity of gcd genes which encode GDH is beneficial to reveal the microbial group that has a significant influence on the eutrophication of water. Taking the eutrophic Sancha Lake sediments as the research object, we acquired samples from six sites in the spring and autumn. A total of 219,778 high-quality sequences were obtained by DNA extraction of microbial groups in sediments, PCR amplification of the gcd gene, and high-throughput sequencing. Six phyla, nine classes, 15 orders, 29 families, 46 genera, and 610 operational taxonomic units (OTUs) were determined, suggesting the high genetic diversity of gcd. Gcd genes came mainly from the genera of Rhizobium (1.63–77.99%), Ensifer (0.13–56.95%), Shinella (0.32–25.49%), and Sinorhizobium (0.16–11.88%) in the phylum of Proteobacteria (25.10–98.85%). The abundance of these dominant gcd-harboring bacteria was higher in the spring than in autumn, suggesting that they have an important effect on the eutrophication of the Sancha Lake. The alpha and beta diversity of gcd genes presented spatial and temporal differences due to different sampling site types and sampling seasons. Pearson correlation analysis and canonical correlation analysis (CCA) showed that the diversity and abundance of gcd genes were significantly correlated with environmental factors such as dissolved oxygen (DO), phosphorus hydrochloride (HCl–P), and dissolved total phosphorus (DTP). OTU composition was significantly correlated with DO, total organic carbon (TOC), and DTP. GDH encoded by gcd genes transformed insoluble phosphate into dissolved phosphate, resulting in the eutrophication of Sancha Lake. The results suggest that gcd genes encoding GDH may play an important role in lake eutrophication.

scholarly journals Evolutionary and functional genomics of DNA methylation in maize domestication and improvement

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Gen Xu ◽  
Jing Lyu ◽  
Qing Li ◽  
Han Liu ◽  
Dafang Wang ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Direct Selection ◽  
Whole Genome ◽  
Evolutionary Forces ◽  
Weak Evidence ◽  
Modern Maize ◽  
Genome Bisulfite Sequencing ◽  
Maize Domestication ◽  
Chromatin Feature

Abstract DNA methylation is a ubiquitous chromatin feature, present in 25% of cytosines in the maize genome, but variation and evolution of the methylation landscape during maize domestication remain largely unknown. Here, we leverage whole-genome sequencing (WGS) and whole-genome bisulfite sequencing (WGBS) data on populations of modern maize, landrace, and teosinte (Zea mays ssp. parviglumis) to estimate epimutation rates and selection coefficients. We find weak evidence for direct selection on DNA methylation in any context, but thousands of differentially methylated regions (DMRs) are identified population-wide that are correlated with recent selection. For two trait-associated DMRs, vgt1-DMR and tb1-DMR, HiChIP data indicate that the interactive loops between DMRs and respective downstream genes are present in B73, a modern maize line, but absent in teosinte. Our results enable a better understanding of the evolutionary forces acting on patterns of DNA methylation and suggest a role of methylation variation in adaptive evolution.

Temporal dynamics in the taxonomic and functional profile of the Sphagnum-associated fungi (mycobiomes) in a Sphagnum farming field site in Northwestern Germany

2020 ◽  
Vol 96 (11) ◽  
Author(s):  
Mathilde Borg Dahl ◽  
Matthias Krebs ◽  
Martin Unterseher ◽  
Tim Urich ◽  
Greta Gaudig
Keyword(s):  
Fungal Community ◽  
Plant Pathogens ◽  
High Throughput Sequencing ◽  
Temporal Dynamics ◽  
Environmental Parameters ◽  
Taxonomic Composition ◽  
Raw Material ◽  
Negative Consequences ◽  
Field Site ◽  
Community Profile

ABSTRACT The drainage of peatlands for their agricultural use leads to huge emissions of greenhouse gases. One sustainable alternative is the cultivation of peat mosses after rewetting (‘Sphagnum farming’). Environmental parameters of such artificial systems may differ from those of natural Sphagnum ecosystems which host a rich fungal community. We studied the fungal community at a 4 ha Sphagnum farming field site in Northwestern Germany and compared it with that of natural Sphagnum ecosystems. Additionally, we asked if any fungi occur with potentially negative consequences for the commercial production and/or use of Sphagnum biomass. Samples were collected every 3 months within 1 year. High-throughput sequencing of the fungal ITS2 barcode was used to obtain a comprehensive community profile of the fungi. The dominant taxa in the fungal community of the Sphagnum farming field site were all commonly reported from natural Sphagnum ecosystems. While the taxonomic composition showed clear differences between seasons, a stable functional community profile was identified across seasons. Additionally, nutrient supply seems to affect composition of fungal community. Despite a rather high abundance of bryophyte parasites, and the occurrence of both Sphagnum-species-specific and general plant pathogens, their impact on the productivity and usage of Sphagnum biomass as raw material for growing media was considered to be low.

Functional gene diversity and migration timing in reintroduced Chinook salmon

2015 ◽  
Vol 16 (6) ◽  
pp. 1455-1464 ◽  
Author(s):  
Melissa L. Evans ◽  
Samuel J. Shry ◽  
Dave P. Jacobson ◽  
Nicholas M. Sard ◽  
Kathleen G. O’Malley
Keyword(s):  
Chinook Salmon ◽  
Gene Diversity ◽  
Functional Gene ◽  
Migration Timing ◽  
Functional Gene Diversity ◽  
And Migration

scholarly journals New Arsenate Reductase Gene (arrA) PCR Primers for Diversity Assessment and Quantification in Environmental Samples

2016 ◽  
Vol 83 (4) ◽  
Author(s):  
Babur S. Mirza ◽  
Darwin L. Sorensen ◽  
R. Ryan Dupont ◽  
Joan E. McLean
Keyword(s):  
Drinking Water ◽  
Human Health ◽  
High Throughput ◽  
In Silico ◽  
High Throughput Sequencing ◽  
Gene Diversity ◽  
Pcr Primers ◽  
Potential Threat ◽  
Groundwater Samples ◽  
Reductase Gene

ABSTRACT The extent of arsenic contamination in drinking water and its potential threat to human health have resulted in considerable research interest in the microbial species responsible for arsenic reduction. The arsenate reductase gene (arrA), an important component of the microbial arsenate reduction system, has been widely used as a biomarker to study arsenate-reducing microorganisms. A new primer pair was designed and evaluated for quantitative PCR (qPCR) and high-throughput sequencing of the arrA gene, because currently available PCR primers are not suitable for these applications. The primers were evaluated in silico and empirically tested for amplification of arrA genes in clones and for amplification and high-throughput sequencing of arrA genes from soil and groundwater samples. In silico, this primer pair matched (≥90% DNA identity) 86% of arrA gene sequences from GenBank. Empirical evaluation showed successful amplification of arrA gene clones of diverse phylogenetic groups, as well as amplification and high-throughput sequencing of independent soil and groundwater samples without preenrichment, suggesting that these primers are highly specific and can amplify a broad diversity of arrA genes. The arrA gene diversity from soil and groundwater samples from the Cache Valley Basin (CVB) in Utah was greater than anticipated. We observed a significant correlation between arrA gene abundance, quantified through qPCR, and reduced arsenic (AsIII) concentrations in the groundwater samples. Furthermore, we demonstrated that these primers can be useful for studying the diversity of arsenate-reducing microbial communities and the ways in which their relative abundance in groundwater may be associated with different groundwater quality parameters. IMPORTANCE Arsenic is a major drinking water contaminant that threatens the health of millions of people worldwide. The extent of arsenic contamination and its potential threat to human health have resulted in considerable interest in the study of microbial species responsible for the reduction of arsenic, i.e., the conversion of AsV to AsIII. In this study, we developed a new primer pair to evaluate the diversity and abundance of arsenate-reducing microorganisms in soil and groundwater samples from the CVB in Utah. We observed significant arrA gene diversity in the CVB soil and groundwater samples, and arrA gene abundance was significantly correlated with the reduced arsenic (AsIII) concentrations in the groundwater samples. We think that these primers are useful for studying the ecology of arsenate-reducing microorganisms in different environments.

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