Application of targeted metagenomics to explore abundance and diversity of CO2-fixing bacterial community using cbbL gene from the rhizosphere of Arachis hypogaea

Gene ◽  
2012 ◽  
Vol 506 (1) ◽  
pp. 18-24 ◽  
Author(s):  
Basit Yousuf ◽  
Jitendra Keshri ◽  
Avinash Mishra ◽  
Bhavanath Jha
Keyword(s):  
Bacterial Community ◽  
Arachis Hypogaea ◽  
Cbbl Gene ◽  
Abundance And Diversity

scholarly journals Comparison of the bacterial abundance and diversity in the Leptocybe invasa Fisher & La Salle (Hymenoptera: Eulophidae) between both sexes

2019 ◽  
Author(s):  
Chunhui Guo ◽  
Xin Peng ◽  
Xialin Zheng ◽  
Xiaoyun Wang ◽  
Ruirui Wang ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Illumina Miseq ◽  
Invasive Pest ◽  
Operational Taxonomic Units ◽  
Adult Females ◽  
Comprehensive Comparison ◽  
Leptocybe Invasa ◽  
Sex Regulation ◽  
Abundance And Diversity ◽  
Dominant Bacteria

Background. Insects harbor a myriad of microorganisms, many of which can affect the sex ratio and manipulate the reproduction of the host. Leptocybe invasa is an invasive pest that causes serious damage to eucalyptus plantations, and both female-biased sex ratios and thelytokous parthenogenesis in L. invasa contribute to the rapid invasion and fast growth of the population. However, the interior bacterial composition and abundance of L. invasa and the differences between both sexes remain unclear. Results. The Illumina MiSeq platform was used to compare the composition of the bacterial community in adult females and males by sequencing with variation in the V3-V4 region of the 16S ribosomal DNA gene. The results showed that 1320 operational taxonomic units (OTUs) were obtained in total. These OTUs were annotated into 24 phyla, 71 classes, 130 orders, 245 families and 501 genera. At the genus level, the dominant bacteria in females and males was Rickettsia and Rhizobium, respectively. Conclusion. The bacteria living in L. invasa adult females and males had high diversity. There were differences in the bacterial community in L. invasa between both sexes, and the bacterial diversity in male adults was more abundant than that in female adults. This study presents a comprehensive comparison of bacterial communities living in L. invasa between sexes, which plays a significant role in reproductive strategy, sex regulation and the invasive mechanism of L. invasa and provides a basis for follow-up studies on the coevolution and interaction between L. invasa and its predominant bacteria.

Difference of microbiome and antibiotic resistome between earthworm gut and soil deciphered by a continental-scale survey

2020 ◽  
Author(s):  
Yong-Guan Zhu ◽  
Dong Zhu ◽  
Manuel Delgado-Baquerizo ◽  
Jian-Qiang Su ◽  
Jing Ding ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Bacterial Community ◽  
Field Experiments ◽  
Arable Land ◽  
Spatial Distance ◽  
Continental Scale ◽  
Earthworm Gut ◽  
Abundance And Diversity ◽  
Term Field

Abstract Background Earthworms are globally distributed and quite capable of redistributing compounds, as well as bacteria and antibiotic resistance genes (ARGs) throughout the soil profile. The spread of medically relevant ARGs in soils has become an emerging environmental and health issue globally. However, our understanding on earthworm gut microbiome and antibiotic resistome is still lacking, especially at the large scale, and little is known about the role of earthworm in the dispersal of ARGs. Methods We conducted a continental-scale survey, including samples (earthworm gut and soil) from 28 provinces across China, from both natural and agricultural ecosystems (arable land: 35 sites and forested land: 16 sites). The 16S rRNA amplicon sequencing and high throughput quantitative PCR were used to characterize the microbiome and antibiotic resistome, respectively. We further explored potential mechanisms behind changes in the abundance and diversity of ARGs in the earthworm gut. Then, the microcosm experiments and long-term field experiments with or without earthworms were employed to test the potential for earthworms to reduce the abundance of ARGs in soils. Results The diversity and structure of bacterial community were observably different between the earthworm gut and soil. Firmicutes (35.7%) and Proteobacteria (34.8%) were the dominant phyla in all earthworm gut samples. A significant correlation between bacterial community dissimilarity and spatial distance was identified in the earthworm gut. The earthworm gut consistently had a lower diversity and abundance of ARGs than in the surrounding soil. We further revealed that the change of ARGs in the earthworm gut was likely a consequence of the reduction in the abundance of mobile genetic elements and dominant bacterial phylotypes that are the likely hosts of ARGs. The microcosm study and long-term field experiments provided the experimental evidence that the presence of earthworms reduced the abundance and diversity of ARGs in soils. Conclusions Our findings highlight that earthworm gut and soil present the distinct microbiome and resistome at the continental scale, and earthworms may play an important role in the continental-scale mitigation of antibiotic resistance.

scholarly journals Dynamic Succession of Soil Bacterial Community during Continuous Cropping of Peanut (Arachis hypogaea L.)

PLoS ONE ◽  
2014 ◽  
Vol 9 (7) ◽  
pp. e101355 ◽  
Author(s):  
Mingna Chen ◽  
Xiao Li ◽  
Qingli Yang ◽  
Xiaoyuan Chi ◽  
Lijuan Pan ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Arachis Hypogaea ◽  
Soil Bacterial Community ◽  
Continuous Cropping ◽  
Arachis Hypogaea L ◽  
Soil Bacterial

Soil bacterial community abundance and diversity in ice-free areas of Keller Peninsula, Antarctica

2012 ◽  
Vol 61 ◽  
pp. 7-15 ◽  
Author(s):  
Luiz F.W. Roesch ◽  
Roberta R. Fulthorpe ◽  
Antonio B. Pereira ◽  
Clarissa K. Pereira ◽  
Leandro N. Lemos ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Soil Bacterial Community ◽  
Soil Bacterial ◽  
Abundance And Diversity

scholarly journals Impact of Zinc Oxide Nanoparticles Amended Organic Manure on Arachis hypogaea Growth Response and Rhizosphere Bacterial Community

2020 ◽  
pp. 24-35
Author(s):  
Progress Oghenerume ◽  
Samuel Eduok ◽  
Basil Ita ◽  
Ofonime John ◽  
Inemesit Basssy
Keyword(s):  
Zinc Oxide ◽  
Bacterial Community ◽  
Plant Growth ◽  
Oxygen Uptake ◽  
Arachis Hypogaea ◽  
Growth Response ◽  
Oxygen Uptake Rate ◽  
Organic Manure ◽  
Loam Soil ◽  
Rhizosphere Bacterial Community

The effect of zinc oxide nanoparticle-organic manure amended ultisol and loam soils on plant growth response and rhizosphere bacterial community of peanut (Arachis hypogaea) was evaluated using standard methods under greenhouse conditions. Results indicate germination rates ranged between 30 and 100% in the amended soils compared to 50 and 70% in the controls. ZnO nanoparticles exerted concentration-dependent and varying effects on the plant root and shoot lengths, weights, nodules and pod formation in the two soil types. Heterotrophic bacterial counts ranged from 7.21 ± 0.51 to 7.38 ± 0.5 Log10CFUg-1 in the amended ultisol and 6.99 ± 0.55 Log10CFUg-1 in the control with a log reduction to 6.70 ± 0.39 Log10CFUg-1 in 500 mgkg⁻¹ ZnO spiked soil. Counts in the amended loam soil ranged between 6.59 ± 0.48 and 7.22 ± 0.41 Log10CFUg-1 relative to 6.80 ± 0.58 Log10CFUg-1 in the control. ZnO induced concentration-dependent effect on oxygen uptake rate relative to the controls. The organisms were members of the genera Lactobacillus, Pseudomonas, Bacillus, Rhizobium, Xanthobacter, Enterobacter, Citrobacter, Nitrosomonas and Agromyces. ZnO nanoparticle exerted concentration-dependent stimulatory and inhibitory effects on the plant growth response, oxygen uptake rate and induced temporal shifts in soil microbial abundance. It is challenging to generalize a consistent response of the plant or microorganisms because ZnO nanoparticles interacted with A. hypogaea and soil bacterial community in ways that differ in the ultisol and loam soil.

scholarly journals Comparison of the bacterial abundance and diversity in the Leptocybe invasa Fisher & La Salle (Hymenoptera: Eulophidae) between both sexes

2019 ◽  
Author(s):  
Chunhui Guo ◽  
Xin Peng ◽  
Xialin Zheng ◽  
Xiaoyun Wang ◽  
Ruirui Wang ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Illumina Miseq ◽  
Invasive Pest ◽  
Operational Taxonomic Units ◽  
Adult Females ◽  
Comprehensive Comparison ◽  
Leptocybe Invasa ◽  
Sex Regulation ◽  
Abundance And Diversity ◽  
Dominant Bacteria

Background. Insects harbor a myriad of microorganisms, many of which can affect the sex ratio and manipulate the reproduction of the host. Leptocybe invasa is an invasive pest that causes serious damage to eucalyptus plantations, and both female-biased sex ratios and thelytokous parthenogenesis in L. invasa contribute to the rapid invasion and fast growth of the population. However, the interior bacterial composition and abundance of L. invasa and the differences between both sexes remain unclear. Results. The Illumina MiSeq platform was used to compare the composition of the bacterial community in adult females and males by sequencing with variation in the V3-V4 region of the 16S ribosomal DNA gene. The results showed that 1320 operational taxonomic units (OTUs) were obtained in total. These OTUs were annotated into 24 phyla, 71 classes, 130 orders, 245 families and 501 genera. At the genus level, the dominant bacteria in females and males was Rickettsia and Rhizobium, respectively. Conclusion. The bacteria living in L. invasa adult females and males had high diversity. There were differences in the bacterial community in L. invasa between both sexes, and the bacterial diversity in male adults was more abundant than that in female adults. This study presents a comprehensive comparison of bacterial communities living in L. invasa between sexes, which plays a significant role in reproductive strategy, sex regulation and the invasive mechanism of L. invasa and provides a basis for follow-up studies on the coevolution and interaction between L. invasa and its predominant bacteria.

scholarly journals Effects of Graphene on Bacterial Community Diversity and Soil Environments of Haplic Cambisols in Northeast China

Forests ◽  
2018 ◽  
Vol 9 (11) ◽  
pp. 677 ◽  
Author(s):  
Jinfeng Song ◽  
Chengwei Duan ◽  
Ying Sang ◽  
Shaoping Wu ◽  
Jiaxin Ru ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Incubation Time ◽  
Metabolic Regulation ◽  
Diversity Index ◽  
Rank Order ◽  
Community Diversity ◽  
Regulation Mechanism ◽  
Bacterial Community Diversity ◽  
Abundance And Diversity ◽  
The Impact

Graphene is the thinnest and toughest two-dimensional nanomaterial yet discovered. However, it inevitably enters the biosphere, where it may pose potential risks to ecosystems. We investigated the impact of applied graphene concentrations on bacterial community diversity, physicochemical properties, and enzyme activities of Haplic Cambisols, the zonal soil of Northeastern China. Soils receiving 0, 10, 100, or 1000 mg kg−1 of graphene were incubated for 7, 15, 30, 60, or 90 days. Adding graphene significantly increased the community richness and diversity index of the bacterial community in Haplic Cambisols, as well as their abundances, but this impact varied with graphene concentration and incubation time. Compared with 0 mg kg−1 of graphene applied, soil bacteria abundance and diversity increased significantly during early stages of incubation (i.e., 7 and 15 days) under different concentrations of graphene, and was inhibited or remained unchanged by a longer incubation time, reaching a minima at 60 days but then following an upward trend. Graphene treatments influenced the bacterial community structure and metabolic function in Haplic Cambisols, and the bacterial community’s metabolic regulation mechanism varied with both incubation time and graphene concentration. The rank order of bacterial similarity in soils treated with graphene was 15 > 7 > 30 > 60 > 90 days. Throughout the incubation periods, except for a few unidentified bacteria, the relative abundances of Proteobacteria and Acidobacteria in the soil samples were the highest, with the number of Pseudomonas of Proteobacteria being particularly large. The rank order of bacterial abundance at the phylum level in Haplic Cambisols was 15 > 7 > 30 > 90 > 60 days. Graphene also influenced bacterial community diversity by affecting several key soil environmental factors, such as organic matter and hydrolytic nitrogen contents, as well as urease and catalase activities.

GERMINACIÓN DE SEMILLAS DE CACAHUATE (Arachis hypogaea L.) UTILIZANDO DIFERENTES DOSIS DE GIBERELINA.

2018 ◽  
Vol 11 (11) ◽  
Author(s):  
S.A. García Muñoz
Keyword(s):  
Arachis Hypogaea ◽  
Arachis Hypogaea L

Objetivo: Evaluar la germinación de cacahuate (Arachis hypogaea L.) mediante el uso de diferentes dosis de ácido giberélico (GA3). Diseño/metodología/aproximación: Se empleó un diseño completamente al azar. Se utilizaron tres tratamientos con 20 repeticiones. Tratamiento 1: 0.05gr/L de ácido giberélico (GA3), Tratamiento 2: 0.10gr/L de ácido giberélico (GA3), Tratamiento 3: 0.15gr/L de ácido giberélico (GA3) y Tratamiento 0: Testigo. Se utilizaron semillas de cacahuate de la variedad Virginia. Los parámetros a evaluar fueron, la altura de plántula, número de hojas, medida de raíz y biomasa.  Las medias fueron comparadas por la prueba de Tukey a un nivel del 5% de confianza. Resultados: Los tratamientos indicaron que el Tratamiento 0 (Testigo) obtuvo un porcentaje de germinación de 85%, siendo mayor que el tratamiento 3 (0.15gr/L de GA3) con un 75% de germinación, sin embargo, el tratamiento 1 (0.05gr/L de GA3) y 2 (0.10gr/L de GA3) presentaron una mejor respuesta al obtener un 95% de germinación cada uno. Limitaciones del estudio/implicaciones: El tratamiento 3 causa efectos negativos en la germinación de la planta. Hallazgos/conclusiones: Es necesario dar seguimiento a la investigación para un mejor control del ambiente y ampliar las dosis de GA3, así como aumentar la velocidad de germinación aplicando 0.15gr/L de GA3.

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