scholarly journals Unlocking a high bacterial diversity in the coralloid root microbiome from the cycad genusDioon

2018 ◽  
Author(s):  
Pablo de Jesús Suárez-Moo ◽  
Andrew P. Vovides ◽  
M. Patrick Griffith ◽  
Francisco Barona-Gómez ◽  
Angélica Cibrián-Jaramillo
Keyword(s):  
Bacterial Diversity ◽  
Natural Populations ◽  
Amplicon Sequencing ◽  
Botanical Garden ◽  
Taxonomic Composition ◽  
Rrna Gene ◽  
Biological Interactions ◽  
Plant Growth Promoting ◽  
Coralloid Roots ◽  
Root Microbiome

AbstractCycads are among the few plants that have developed specialized roots to host nitrogen-fixing bacteria. We describe the bacterial diversity of the coralloid roots from sevenDioonspecies and their surrounding rhizosphere and soil. Using 16S rRNA gene amplicon sequencing, we found that all coralloid roots are inhabited by a broad diversity of bacterial groups, including cyanobacteria and Rhizobiales among the most abundant groups. The diversity and composition of the endophytes are similar in the six Mexican species ofDioonthat we evaluated, suggesting a recent divergence ofDioonpopulations and/or similar plant-driven restrictions in maintaining the coralloid root microbiome. Botanical garden samples and natural populations have a similar taxonomic composition, although the beta diversity differed between these populations. The rhizosphere surrounding the coralloid root serves as a reservoir and source of mostly diazotroph and plant growth-promoting groups that colonize the coralloid endosphere. In the case of cyanobacteria, the endosphere is enriched withNostocspp andCalothrixspp that are closely related to previously reported symbiont genera in cycads and other early divergent plants. The data reported here provide an in-depth taxonomic characterization of the bacterial community associated with coralloid root microbiome. The functional aspects of the endophytes, their biological interactions, and their evolutionary history are the next research step in this recently discovered diversity within the cycad coralloid root microbiome.

scholarly journals Metagenomic, Metabolomic, and Functional Evaluation of Kimchi Broth Treated with Light-Emitting Diodes (LEDs)

Metabolites ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 472
Author(s):  
Yeong-Ji Oh ◽  
Ye-Rin Park ◽  
Jungil Hong ◽  
Do-Yup Lee
Keyword(s):  
Amplicon Sequencing ◽  
Taxonomic Composition ◽  
Metabolic Phenotype ◽  
Rrna Gene ◽  
Functional Evaluation ◽  
Initial Condition ◽  
Microbial Composition ◽  
Light Emitting ◽  
Blue Led ◽  
Red Led

The light-emitting diode (LED) has been widely used in the food industry, and its application has been focused on microbial sterilization, specifically using blue-LED. The investigation has been recently extended to characterize the biotic and abiotic (photodynamic) effects of different wavelengths. Here, we investigated LED effects on kimchi fermentation. Kimchi broths were treated with three different colored-LEDs (red, green, and blue) or kept in the dark as a control. Multiomics was applied to evaluate the microbial taxonomic composition using 16S rRNA gene amplicon sequencing, and the metabolomic profiles were determined using liquid chromatography–Orbitrap mass spectrometry. Cell viability was tested to determine the potential cytotoxicity of the LED-treated kimchi broths. First, the amplicon sequencing data showed substantial changes in taxonomic composition at the family and genus levels according to incubation (initial condition vs. all other groups). The differences among the treated groups (red-LED (RLED), green-LED (GLED), blue-LED (BLED), and dark condition) were marginal. The relative abundance of Weissella was decreased in all treated groups compared to that of the initial condition, which coincided with the decreased composition of Lactobacillus. Compositional changes were relatively high in the GLED group. Subsequent metabolomic analysis indicated a unique metabolic phenotype instigated by different LED treatments, which led to the identification of the LED treatment-specific and common compounds (e.g., luteolin, 6-methylquinoline, 2-hydroxycinnamic acid, and 9-HODE). These results indicate that different LED wavelengths induce characteristic alterations in the microbial composition and metabolomic content, which may have applications in food processing and storage with the aim of improving nutritional quality and the safety of food.

scholarly journals A Plant Growth-Promoting Microbial Soil Amendment Dynamically Alters the Strawberry Root Bacterial Microbiome

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Siwen Deng ◽  
Heidi M.-L. Wipf ◽  
Grady Pierroz ◽  
Ted K. Raab ◽  
Rajnish Khanna ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Soil Amendment ◽  
Bacterial Community Composition ◽  
Illumina Miseq ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Bacterial Microbiome ◽  
Plant Growth Promoting ◽  
Miseq Platform ◽  
Soil Rhizosphere

AbstractDespite growing interest in utilizing microbial-based methods for improving crop growth, much work still remains in elucidating how beneficial plant-microbe associations are established, and what role soil amendments play in shaping these interactions. Here, we describe a set of experiments that test the effect of a commercially available soil amendment, VESTA, on the soil and strawberry (Fragaria x ananassa Monterey) root bacterial microbiome. The bacterial communities of the soil, rhizosphere, and root from amendment-treated and untreated fields were profiled at four time points across the strawberry growing season using 16S rRNA gene amplicon sequencing on the Illumina MiSeq platform. In all sample types, bacterial community composition and relative abundance were significantly altered with amendment application. Importantly, time point effects on composition are more pronounced in the root and rhizosphere, suggesting an interaction between plant development and treatment effect. Surprisingly, there was slight overlap between the taxa within the amendment and those enriched in plant and soil following treatment, suggesting that VESTA may act to rewire existing networks of organisms through an, as of yet, uncharacterized mechanism. These findings demonstrate that a commercial microbial soil amendment can impact the bacterial community structure of both roots and the surrounding environment.

scholarly journals Effect of Geography and Captivity on Scat Bacterial Communities in the Imperiled Channel Island Fox

2021 ◽  
Author(s):  
Nicole E Adams ◽  
Madeleine A Becker ◽  
Suzanne Edmands
Keyword(s):  
Bacterial Diversity ◽  
Bacterial Communities ◽  
Captive Breeding ◽  
Interdisciplinary Approach ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Sample Collection ◽  
Channel Island ◽  
Island Fox ◽  
Urocyon Littoralis

Abstract Background With developing understanding that host-associated microbiota play significant roles in individual health and fitness, taking an interdisciplinary approach combining microbiome research with conservation science is increasingly favored. Here we establish the scat microbiome of the imperiled Channel Island fox (Urocyon littoralis) and look at the effects of geography and captivity on the variation in bacterial communities. Results Using high throughput 16S rRNA gene amplicon sequencing, we discovered distinct bacterial communities in each island fox subspecies. Weight, timing of the sample collection, and sex contributed to the geographic patterns. We uncovered significant taxonomic differences and an overall decrease in bacterial diversity in captive versus wild foxes. Conclusions Understanding the drivers of microbial variation in this system provides a valuable lens through which to evaluate the health and conservation of these genetically depauperate foxes. The island-specific bacterial community baselines established in this study can make monitoring island fox health easier and understanding the implications of inter-island translocation clearer. The decrease in bacterial diversity within captive foxes could lead to losses in the functional services normally provided by commensal microbes and suggests that zoos and captive breeding programs would benefit from maintaining microbial diversity.

scholarly journals Changes in the Bacterial Diversity of Human Milk during Late Lactation Period (Weeks 21 to 48)

Foods ◽  
2020 ◽  
Vol 9 (9) ◽  
pp. 1184
Author(s):  
Wendy Marin-Gómez ◽  
Mᵃ José Grande ◽  
Rubén Pérez-Pulido ◽  
Antonio Galvez ◽  
Rosario Lucas
Keyword(s):  
Bacterial Diversity ◽  
Single Mother ◽  
Variable Region ◽  
Sampling Period ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Sequencing Analysis ◽  
Lactation Period ◽  
Relative Abundances ◽  
The 16S Rrna Gene

Breast milk from a single mother was collected during a 28-week lactation period. Bacterial diversity was studied by amplicon sequencing analysis of the V3-V4 variable region of the 16S rRNA gene. Firmicutes and Proteobacteria were the main phyla detected in the milk samples, followed by Actinobacteria and Bacteroidetes. The proportion of Firmicutes to Proteobacteria changed considerably depending on the sampling week. A total of 411 genera or higher taxons were detected in the set of samples. Genus Streptococcus was detected during the 28-week sampling period, at relative abundances between 2.0% and 68.8%, and it was the most abundant group in 14 of the samples. Carnobacterium and Lactobacillus had low relative abundances. At the genus level, bacterial diversity changed considerably at certain weeks within the studied period. The weeks or periods with lowest relative abundance of Streptococcus had more diverse bacterial compositions including genera belonging to Proteobacteria that were poorly represented in the rest of the samples.

scholarly journals Microbacterium azadirachtae sp. nov., a plant-growth-promoting actinobacterium isolated from the rhizoplane of neem seedlings

2010 ◽  
Vol 60 (7) ◽  
pp. 1687-1692 ◽  
Author(s):  
Munusamy Madhaiyan ◽  
Selvaraj Poonguzhali ◽  
Jung-Sook Lee ◽  
Keun-Chul Lee ◽  
Venkatakrishnan Sivaraj Saravanan ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Genetic Characterization ◽  
Novel Species ◽  
Botanical Garden ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Light Yellow ◽  
Plant Growth Promoting ◽  
Growth Promoting ◽  
Close Relatives

Microbacterium strain AI-S262T was isolated from the rhizoplane of neem seedlings in the Botanical garden of Tamilnadu Agricultural University, Coimbatore, India, and subjected to phenotypic, chemotaxonomic and genetic characterization. Cells of this strain were Gram-stain-positive, motile, non-spore-forming, short rods and formed light-yellow-pigmented colonies on nutrient agar. Strain AI-S262T contained MK-12 and MK-13 as the main respiratory quinones, anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0 as the predominant fatty acids, peptidoglycan-type B2β with glycolyl residues, and had a DNA G+C content of 69.5 mol%. A phylogenetic analysis based on 16S rRNA gene sequences showed 98.0–98.6 % pair-wise similarity with respect to close relatives in the genus Microbacterium. DNA–DNA hybridization experiments revealed a low level of DNA–DNA relatedness (less than 39%) between strain AI-S262T and its closest relatives. Data from DNA–DNA hybridization and phenotypic analyses supported the conclusion that strain AI-S262T represents a novel species in the genus Microbacterium, for which the name Microbacterium azadirachtae sp. nov. is proposed. The type strain is AI-S262T (=JCM 15681T =LMG 24772T =KCTC 19668T).

scholarly journals Seasonal and ontogenetic variation of skin microbial communities and relationships to natural disease dynamics in declining amphibians

2015 ◽  
Vol 2 (7) ◽  
pp. 140377 ◽  
Author(s):  
Ana V. Longo ◽  
Anna E. Savage ◽  
Ian Hewson ◽  
Kelly R. Zamudio
Keyword(s):  
Bacterial Diversity ◽  
Batrachochytrium Dendrobatidis ◽  
Developmental Stages ◽  
Pathogenic Fungus ◽  
Natural Populations ◽  
Amplicon Sequencing ◽  
Protective Role ◽  
Skin Microbiome ◽  
Skin Bacteria

Recently, microbiologists have focused on characterizing the probiotic role of skin bacteria for amphibians threatened by the fungal disease chytridiomycosis. However, the specific characteristics of microbial diversity required to maintain health or trigger disease are still not well understood in natural populations. We hypothesized that seasonal and developmental transitions affecting susceptibility to chytridiomycosis could also alter the stability of microbial assemblages. To test our hypothesis, we examined patterns of skin bacterial diversity in two species of declining amphibians ( Lithobates yavapaiensis and Eleutherodactylus coqui ) affected by the pathogenic fungus Batrachochytrium dendrobatidis ( Bd ). We focused on two important transitions that affect Bd susceptibility: ontogenetic (from juvenile to adult) shifts in E. coqui and seasonal (from summer to winter) shifts in  L. yavapaiensis . We used a combination of community-fingerprinting analyses and 16S rRNA amplicon sequencing to quantify changes in bacterial diversity and assemblage composition between seasons and developmental stages, and to investigate the relationship between bacterial diversity and pathogen load. We found that winter-sampled frogs and juveniles, two states associated with increased Bd susceptibility, exhibited higher diversity compared with summer-sampled frogs and adult individuals. Our findings also revealed that hosts harbouring higher bacterial diversity carried lower Bd infections, providing support for the protective role of bacterial communities. Ongoing work to understand skin microbiome resilience after pathogen disturbance has the potential to identify key taxa involved in disease resistance.

16S rRNA gene amplicon sequencing reveals dominance of Actinobacteria in Rhodnius pallescens compared to Triatoma maculata midgut microbiota in natural populations of vector insects from Colombia

Acta Tropica ◽  
2018 ◽  
Vol 178 ◽  
pp. 327-332 ◽  
Author(s):  
Luisa M. Montoya-Porras ◽  
Triana-Chavez Omar ◽  
Juan F. Alzate ◽  
Claudia X. Moreno-Herrera ◽  
Gloria E. Cadavid-Restrepo
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Natural Populations ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Rhodnius Pallescens

scholarly journals The evolution of realized niches within freshwater Synechococcus

2019 ◽  
Author(s):  
Nicolas Tromas ◽  
Zofia E. Taranu ◽  
Mathieu Castelli ◽  
Juliana S. M. Pimentel ◽  
Daniel A. Pereira ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Environmental Parameters ◽  
Amplicon Sequencing ◽  
Fundamental Question ◽  
Rrna Gene ◽  
Biological Interactions ◽  
Sequencing Data ◽  
Evolutionary Time ◽  
Genus Level

SummaryUnderstanding how ecological traits have changed over evolutionary time is a fundamental question in biology. Specifically, the extent to which more closely-related organisms share similar ecological preferences due to phylogenetic conservation – or if they are forced apart by competition – is still debated. Here we explored the co-occurrence patterns of freshwater cyanobacteria at the sub-genus level to investigate whether more closely-related taxa share more similar niches, and to what extent these niches were defined by abiotic or biotic variables. We used deep 16S rRNA gene amplicon sequencing and measured several abiotic environmental parameters (nutrients, temperature, etc.) in water samples collected over time and space in Furnas Reservoir, Brazil. We found that relatively more closely-related Synechococcus (in the continuous range of 93-100% nucleotide identity in 16S) had an increased tendency to co-occur with one another (i.e. had similar realized niches). This tendency could not be easily explained by shared preferences for measured abiotic niche dimensions. Thus, commonly measured abiotic parameters might not be sufficient to characterize, nor to predict community assembly or dynamics. Rather, co-occurrence between Synechococcus and the surrounding community (whether or not they represent true biological interactions) may be a more sensitive measure of realized niches. Overall, our results suggest that realized niches are phylogenetically conserved, at least at the sub-genus level and at the resolution of the 16S marker. Determining how these results generalize to other genera and at finer genetic resolution merits further investigation.Originality-Significance StatementWe address a fundamental question in ecology and evolution: how do niche preferences change over evolutionary time? Using time-series analysis of 16S rRNA gene amplicon sequencing data, we develop an approach to highlight the importance of biotic factors in defining realized niches, and show how niche preferences change proportionally with the 16S gene molecular clock within the genus Synechococcus. Ours is also one of few studies on the ecology of freshwater Synechococcus, adding significantly to our knowledge about this abundant and widespread lineage of Cyanobacteria.

scholarly journals Identification and Differentiation of Pseudomonas Species in Field Samples Using an rpoD Amplicon Sequencing Methodology

mSystems ◽  
2021 ◽  
Author(s):  
Jonas Greve Lauritsen ◽  
Morten Lindqvist Hansen ◽  
Pernille Kjersgaard Bech ◽  
Lars Jelsbak ◽  
Lone Gram ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Content Type ◽  
Field Samples ◽  
Plant Growth Promoting ◽  
Growth Promoting ◽  
Rrna Gene Sequencing ◽  
Specific Species

A high-throughput sequencing-based method for profiling of Pseudomonas species in soil microbiomes was developed and identified more species than 16S rRNA gene sequencing or cultivation. Pseudomonas species are used as biocontrol organisms and plant growth-promoting agents, and the method will allow tracing of specific species of Pseudomonas as well as enable screening of environmental samples for further isolation and exploitation.

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