scholarly journals Soil Microbial Composition and Structure Allow Assessment of Biological Product Effectiveness and Crop Yield Prediction

2021 ◽  
Author(s):  
Nabeel Imam ◽  
Ignacio Belda ◽  
Adrian J. Duehl ◽  
James R. Doroghazi ◽  
Daniel E. Almonacid ◽  
...  
Keyword(s):  
Microbial Community ◽  
Crop Yield ◽  
Bacterial Communities ◽  
Bacillus Amyloliquefaciens ◽  
Rhizosphere Soil ◽  
Microbial Composition ◽  
Microbiome Composition ◽  
Microbial Inoculant ◽  
Composition And Structure ◽  
Taxonomic Groups

ABSTRACTUnderstanding the effectiveness and potential mechanism of action of agricultural biological products under different soil profiles and crops will allow more precise product recommendations based on local conditions and will ultimately result in increased crop yield. This study aimed to use bulk and rhizosphere soil’s microbial composition and structure to evaluate the effect of a Bacillus amyloliquefaciens strain QST713 inoculant on potatoes, and to explore its relationship with crop yield. We implemented NGS and bioinformatics approaches to assess the bacterial and fungal biodiversity in 185 soil samples, distributed over four different time points -from planting to harvest -from three different geographical regions in the United States.In addition to variety, phenological stage of the potato plant and geography being important factors defining the microbiome composition and structure, the microbial inoculant applied as a treatment also had a significant effect. However, treatment preserved the native communities without causing a detectable long-lasting effect on the alpha- and beta-diversity patterns after harvest. Specific taxonomic groups, and most interestingly the structure of the fungal and bacterial communities (measured using co-occurrence and co-exclusion networks), changed after inoculation. Additionally, using information about the application of the microbial inoculant and considering microbiome composition and structure data we were able to train a Random Forest model to estimate if a bulk or rhizosphere soil sample came from a low or high yield block with relatively high accuracy, concluding that the structure of fungal communities is a better estimator of potato yield than the structure of bacterial communities.IMPORTANCEThe manuscript’s results reinforce the notion that each crop variety on each location recruits a unique microbial community and that these communities are modulated by the vegetative growth stage of the plant. Moreover, inoculation of a Bacillus amyloliquefaciens strain QST713-based product on potatoes also changed specific taxonomic groups and, most interestingly, the structure of local fungal and bacterial networks in bulk and rhizosphere soil. The data obtained, coming from in-field assays performed in three different geographical locations, allowed training a predictive model to estimate the yield of a certain block, identifying microbiome variables -especially those related to microbial community structure- with a higher predictive power than the variety and geography of the block. The methods described here can be replicated to fit new models predicting yield in any other crop, and to evaluate the effect of any Ag-input product in the composition and structure of the soil microbiome.

scholarly journals Bacterial Composition and Diversity Associated with Rhizosphere of the Chinese Medicinal Herb Dendrobium

2020 ◽  
Author(s):  
Yingdan Yuan ◽  
Mengting Zu ◽  
Lei Liu ◽  
Xiaomei Song
Keyword(s):  
Microbial Community ◽  
Environmental Factor ◽  
Bacterial Communities ◽  
Soil Microorganisms ◽  
Rhizosphere Soil ◽  
Available Phosphorus ◽  
Maturity Stage ◽  
Bacterial Phyla ◽  
Rhizosphere Microorganisms ◽  
Rhizosphere Microbial Community

Abstract Background: Dendrobium is a precious herbal belongs to Orchid and widely used as health care traditional Chinese medicine in Asia. Although orchids are mycorrhizal plants, most researches still focus on endophytes, and there is still large unknown in rhizosphere microorganisms. In order to investigate the rhizosphere microbial community of different Dendrobium species during the maturity stage, we used high-throughput sequencing to analyze microbial community in rhizosphere soil during maturity stage of three kinds of Dendrobium species.Results: In our study, a total of 240,320 sequences and 11,179 OTUs were obtained from these three Dendrobium species. According to the analysis of OTU annotation results, different Dendrobium rhizosphere soil bacteria include 2 kingdoms, 63 phyla, 72 classes, 159 orders, 309 families, 850 genera and 663 species. Among all sequences, the dominant bacterial phyla (relative abundance > 1%) were Proteobacteria, Actinobacteria, Bacteroidetes, Acidobacteria, Firmicutes, Verrucomicrobia, Planctomycetes, Chloroflexi, Gemmatimonadetes. We analyzed the environmental factors of the growth of Dendrobium and found that the environmental factor that affects the rhizosphere soil microorganisms of Dendrobium is the soil factor. Among them, soil factors most closely related to the influence of Dendrobium rhizosphere soil microorganisms include total nitrogen, available phosphorus, ammonium nitrogen and pH value.Conclusions: We found that the rhizosphere bacterial communities of the three kinds of Dendrobium have significant differences, and the main species of rhizosphere microorganisms of Dendrobium are concentrated in the Proteobacteria, Actinobacteria, Bacteroidetes. Moreover, the smaller the level of bacterial, the greater the difference among Dendrobium species. Soil is the most important environmental factor affecting the bacterial communities in the rhizosphere soil of Dendrobium. These results fill the gap in the rhizosphere microbial community of Dendrobium and provide a theoretical basis for the subsequent mining of microbial functions and the study of biological fertilizers.

scholarly journals Microsporidian Infection in Mosquitoes (Culicidae) Is Associated with Gut Microbiome Composition and Predicted Gut Microbiome Functional Content

2021 ◽  
Author(s):  
Artur Trzebny ◽  
Anna Slodkowicz-Kowalska ◽  
Johanna Björkroth ◽  
Miroslawa Dabert
Keyword(s):  
16S Rrna ◽  
Gut Microbiota ◽  
Gut Microbiome ◽  
Bacterial Communities ◽  
Bacterial Species ◽  
Rrna Gene ◽  
Microbial Composition ◽  
Microbiome Composition ◽  
Microsporidian Infection ◽  
Functional Content

AbstractThe animal gut microbiota consist of many different microorganisms, mainly bacteria, but archaea, fungi, protozoans, and viruses may also be present. This complex and dynamic community of microorganisms may change during parasitic infection. In the present study, we investigated the effect of the presence of microsporidians on the composition of the mosquito gut microbiota and linked some microbiome taxa and functionalities to infections caused by these parasites. We characterised bacterial communities of 188 mosquito females, of which 108 were positive for microsporidian DNA. To assess how bacterial communities change during microsporidian infection, microbiome structures were identified using 16S rRNA microbial profiling. In total, we identified 46 families and four higher taxa, of which Comamonadaceae, Enterobacteriaceae, Flavobacteriaceae and Pseudomonadaceae were the most abundant mosquito-associated bacterial families. Our data suggest that the mosquito gut microbial composition varies among host species. In addition, we found a correlation between the microbiome composition and the presence of microsporidians. The prediction of metagenome functional content from the 16S rRNA gene sequencing suggests that microsporidian infection is characterised by some bacterial species capable of specific metabolic functions, especially the biosynthesis of ansamycins and vancomycin antibiotics and the pentose phosphate pathway. Moreover, we detected a positive correlation between the presence of microsporidian DNA and bacteria belonging to Spiroplasmataceae and Leuconostocaceae, each represented by a single species, Spiroplasma sp. PL03 and Weissella cf. viridescens, respectively. Additionally, W. cf. viridescens was observed only in microsporidian-infected mosquitoes. More extensive research, including intensive and varied host sampling, as well as determination of metabolic activities based on quantitative methods, should be carried out to confirm our results.

scholarly journals Spatial Diversity in Bacterial Communities across Barren and Vegetated, Native and Invasive, Coastal Dune Microhabitats

Diversity ◽  
2021 ◽  
Vol 13 (11) ◽  
pp. 525
Author(s):  
Brianna L. Boss ◽  
Bianca R. Charbonneau ◽  
Javier A. Izquierdo
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Community Composition ◽  
Plant Species ◽  
Bacterial Communities ◽  
Environmental Gradients ◽  
Microbial Community Composition ◽  
Soil Microbial Communities ◽  
Spatial Diversity ◽  
Microbial Composition

The microbial community composition of coastal dunes can vary across environmental gradients, with the potential to impact erosion and deposition processes. In coastal foredunes, invasive plant species establishment can create and alter environmental gradients, thereby altering microbial communities and other ecogeomorphic processes with implications for storm response and management and conservation efforts. However, the mechanisms of these processes are poorly understood. To understand how changing microbial communities can alter these ecogeomorphic dynamics, one must first understand how soil microbial communities vary as a result of invasion. Towards this goal, bacterial communities were assessed spatially along foredune microhabitats, specifically in barren foredune toe and blowout microhabitats and in surrounding vegetated monocultures of native Ammophila breviligulata and invasive Carex kobomugi. Across dune microhabitats, microbial composition was more dissimilar in barren dune toe and blowout microhabitats than among the two plant species, but it did not appear that it would favor the establishment of one plant species over the other. However, the subtle differences between the microbial community composition of two species could ultimately aid in the success of the invasive species by reducing the proportions of bacterial genera associated exclusively with A. breviligulata. These results suggest that arrival time may be crucial in fostering microbiomes that would further the continued establishment and spread of either plant species.

scholarly journals Effect ofBacillus velezensis JC-K3 on Endophytic Bacterial and Fungal Diversity in Wheat Under Salt Stress

2021 ◽  
Vol 12 ◽  
Author(s):  
Chao Ji ◽  
Xiaohui Wang ◽  
Xin Song ◽  
Qisheng Zhou ◽  
Chaohui Li ◽  
...  
Keyword(s):  
Salt Stress ◽  
Community Structure ◽  
Microbial Community ◽  
Microbial Community Structure ◽  
Bacterial Communities ◽  
Endophytic Bacteria ◽  
Rhizosphere Soil ◽  
Fungal Communities ◽  
Salt Damage ◽  
Bacteria And Fungi

Plant growth-promoting bacteria (PGPB) can effectively reduce salt damage in plants. Currently, there are many studies on the effects of PGPB on the microbial community structure of rhizosphere soil under salt stress, but fewer studies on the community structure of endophytic bacteria and fungi. We propose that inoculation of endophytic bacteria into the rhizosphere of plants can significantly affect the microbial community structure of the plant’s above-ground and underground parts, which may be the cause of the plant’s “Induced Systemic Tolerance.” The isolated endophytes were re-inoculated into the rhizosphere under salinity stress. We found that, compared with the control group, inoculation with endophytic Bacillus velezensis JC-K3 not only increased the accumulation of wheat biomass, but also increased the content of soluble sugar and chlorophyll in wheat, and reduced the absorption of Na in wheat shoots and leaves. The abundance of bacterial communities in shoots and leaves increased and the abundance of fungal communities decreased after inoculation with JC-K3. The fungal community richness of wheat rhizosphere soil was significantly increased. The diversity of bacterial communities in shoots and leaves increased, and the richness of fungal communities decreased. JC-K3 strain improved wheat’s biomass accumulation ability, osmotic adjustment ability, and ion selective absorption ability. In addition, JC-K3 significantly altered the diversity and abundance of endophytic and rhizosphere microorganisms in wheat. PGPB can effectively reduce plant salt damage. At present, there are many studies on the effect of PGPB on the microbial community structure in rhizosphere soil under salt stress, but there are few studies on the community structure changes of endophytic bacteria and fungi in plants.

scholarly journals Local Network Properties of Soil and Rhizosphere Microbial Communities in Potato Plantations Treated with a Biological Product Are Important Predictors of Crop Yield

mSphere ◽  
2021 ◽  
Author(s):  
Nabeel Imam ◽  
Ignacio Belda ◽  
Beatriz García-Jiménez ◽  
Adrian J. Duehl ◽  
James R. Doroghazi ◽  
...  
Keyword(s):  
Microbial Community ◽  
Bacillus Amyloliquefaciens ◽  
Growth Stage ◽  
Local Network ◽  
Biological Product ◽  
Local Networks ◽  
Content Type ◽  
Network Properties ◽  
Taxonomic Groups ◽  
Properties Of Soil

Our results reinforce the notion that each cultivar on each location recruits a unique microbial community and that these communities are modulated by the vegetative growth stage of the plant. Moreover, inoculation of a Bacillus amyloliquefaciens strain QST713-based product on potatoes also changed the abundance of specific taxonomic groups and the structure of local networks in those locations where the product caused an increase in the yield.

scholarly journals Modeling the temporal dynamics of the gut microbial community in adults and infants

2017 ◽  
Author(s):  
Liat Shenhav ◽  
Ori Furman ◽  
Leah Briscoe ◽  
Michael Thompson ◽  
Itzhak Mizrahi ◽  
...  
Keyword(s):  
Time Series ◽  
Microbial Community ◽  
Mixed Model ◽  
Linear Mixed Model ◽  
Temporal Dynamics ◽  
Time Dependent ◽  
Human Gut ◽  
Microbial Composition ◽  
Microbiome Composition ◽  
Time Point

AbstractGiven the highly dynamic and complex nature of the human gut microbial community, the ability to identify and predict time-dependent compositional patterns of microbes is crucial to our understanding of the structure and function of this ecosystem. One factor that could affect such time-dependent patterns is microbial interactions, wherein community composition at a given time point affects the microbial composition at a later time point. However, the field has not yet settled on the degree of this effect. Specifically, it has been recently suggested that only a minority of the operational taxonomic units (OTUs) depend on the microbial composition in earlier times. To address the issue of identifying and predicting temporal microbial patterns we developed a new model, MTV-LMM (Microbial Temporal Variability Linear Mixed Model), a linear mixed model for the prediction of the microbial community temporal dynamics based on the community composition at previous time stamps. MTV-LMM can identify time-dependent microbes in time series datasets, which can then be used to analyze the trajectory of the microbiome over time. We evaluated the performance of MTV-LMM on three human microbiome time series datasets, and found that MTV-LMM significantly outperforms all existing methods for microbiome time series modeling. Particularly, we demonstrate that the effect of the microbial composition in previous time points on the abundance levels of an OTU at a later time point is underestimated by a factor of at least 10 when applying previous approaches. Using MTV-LMM, we demonstrate that a considerable proportion of the human gut microbiome, both in infants and adults, has a significant time-dependent component that can be predicted based on microbiome composition in earlier time points. This suggests that microbiome composition at a given time point is a major factor in defining future microbiome composition and that this phenomenon is considerably more common than previously reported for the human gut microbiome.

scholarly journals Degradación de oxalato por bacterias oxalotróficas asociadas a plantas del género Oxalis sp en regiones Andinas del departamento de Nariño, Colombia

2016 ◽  
Vol 18 (1) ◽  
pp. 69
Author(s):  
Roger David Castillo Arteaga ◽  
Edith Mariela Burbano-Rosero ◽  
Iván Darío Otero Ramirez ◽  
Pablo Fernández Izquierdo
Keyword(s):  
Bacillus Subtilis ◽  
Bacillus Cereus ◽  
Bacterial Communities ◽  
Bacillus Amyloliquefaciens ◽  
Rhizosphere Soil ◽  
Acid Soils ◽  
Selective Medium ◽  
Daily Consumption ◽  
Promising Application ◽  
Bacillus Vallismortis

ResumenIntroducción: El ácido oxálico (H2C2O4) y las sales de oxalato son sustancias altamente oxidadas y consideradas tóxicas para algunos sistemas biológicos, incluido el humano, no obstante, pueden ser utilizadas como fuente de carbono y energía por algunas comunidades bacterianas, denominadas oxalotróficas, las cuales por su capacidad metabólica forman parte de la ruta biogeoquímica oxalato-carbonato (OCP, oxalate-carbonate pathway). Objetivo: Aislar y caracterizar bacterias oxalotróficas a partir de plantas del género Oxalis sp., de zonas alto-andina de Nariño- Colombia. Materiales y métodos: Se recolectaron muestras de suelo rizosférico de plantas oxalogénicas que fueron analizadas con parámetros fisicoquímicos y se utilizó un medio selectivo Schlegel para el aislamiento de bacterias oxalotróficas. Resultados: Las bacterias aisladas en medio selectivo Schlegel fueron caracterizadas bioquímicamente como: (Serratia fonticola, Bacillus amyloliquefaciens, Bacillus subtilis, Bacillus vallismortis y Bacillus cereus). Estas especies fueron capaces de degradar oxalato e incrementar el pH producto de la degradación. Conclusión: Este tipo de bacterias pueden ser estudiadas en trabajos complementarios para evaluar su potencial como biofertilizantes y/o alternativas de bioremediación en suelos ácidos. El estudio a pesar de ser indicativo a nivel biológico, puede en un futuro y con base en mayores soportes en investigación, tornarse en una promisoria aplicación para reducir el oxalato de calcio en los alimentos de consumo diario que presentan un renglón de importancia agrícola en la región, potencialmente dañinos para la función renal.AbstractIntroduction: Oxalic acid (H2C2O4) and oxalate salts are highly oxidized substances, which are considered as toxic for some biological systems, including the human being; however, they can be used as a source of carbon and energy for some bacterial communities called oxalotrophic which are part of the so called oxalate-carbonate geochemistry pathway (OCP) due to its metabolic capacity. Objective: The aim of this research was to isolate and characterize oxalotrophic bacteria from plants of the genus Oxalis sp. in the high-andean zone of the department of Nariño, Colombia. Materials and methods: Samples of rhizosphere soil from oxalogenic plants were analyzed with physicochemical parameters and a Schlegel selective medium was used to isolate oxalotrophic bacteria. Results: The isolated bacteria through Schlegel selective medium were identified biochemically as: (Serratia fonticola, Bacillus amyloliquefaciens, Bacillus subtilis, Bacillus vallismortis and Bacillus cereus). The identified species play an important role in the rhizosphere soil, principally for the capacity to increase the pH during oxalate consumption. Conclusion: This type of bacteria can be studied in additional studies to evaluate their potential as bio-fertilizers and/or bioremediation alternatives in acid soils. Despite that the study is indicative at a biological level, it can become a promising application, in the future and with greater support in research, to reduce the calcium oxalate in food of daily consumption which represent an agricultural important line in the region and are potentially harmful to kidney finction.

scholarly journals Composition and diversity of bacterial communities in the rhizosphere of the Chinese medicinal herb Dendrobium

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Jiajia Zuo ◽  
Mengting Zu ◽  
Lei Liu ◽  
Xiaomei Song ◽  
Yingdan Yuan
Keyword(s):  
Microbial Community ◽  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Rhizosphere Soil ◽  
Maturity Stage ◽  
Chinese Medicinal Herb ◽  
Bacterial Phyla ◽  
Rhizosphere Microorganisms ◽  
The Difference ◽  
Rhizosphere Microbial Community

Abstract Background Dendrobium is a precious herbal that belongs to Orchidaceae and is widely used as health care traditional Chinese medicine in Asia. Although orchids are mycorrhizal plants, most research still focuses on endophytes, and there is still large amount unknown about rhizosphere microorganisms. To investigate the rhizosphere microbial community of different Dendrobium species during the maturity stage, we used high-throughput sequencing to analyze microbial community in rhizosphere soil during the maturity stage of three kinds of Dendrobium species. Results In our study, a total of 240,320 sequences and 11,179 OTUs were obtained from these three Dendrobium species. According to the analysis of OTU annotation results, different Dendrobium rhizosphere soil bacteria include 2 kingdoms, 63 phyla, 72 classes, 159 orders, 309 families, 850 genera and 663 species. Among all sequences, the dominant bacterial phyla (relative abundance > 1%) were Proteobacteria, Actinobacteria, Bacteroidetes, Acidobacteria, Firmicutes, Verrucomicrobia, Planctomycetes, Chloroflexi, and Gemmatimonadetes. And through WGCNA analysis, we found the hub flora was also belong to Acidobacteria, Actinobacteria and Proteobacteria. Conclusions We found that the rhizosphere bacterial communities of the three kinds of Dendrobium have significant differences, and that the main species of rhizosphere microorganisms of Dendrobium are concentrated in the Proteobacteria, Actinobacteria, and Bacteroidetes. Moreover, the smaller the bacterial level, the greater the difference among Dendrobium species. These results fill knowledge gaps in the rhizosphere microbial community of Dendrobium and provide a theoretical basis for the subsequent mining of microbial functions and the study of biological fertilizers.

scholarly journals A Degeneration Gradient of Poplar Trees Contributes to the Taxonomic, Functional, and Resistome Diversity of Bacterial Communities in Rhizosphere Soils

2021 ◽  
Vol 22 (7) ◽  
pp. 3438
Author(s):  
Juan Liu ◽  
Xiangwei He ◽  
Jingya Sun ◽  
Yuchao Ma
Keyword(s):  
Soil Fertility ◽  
Microbial Diversity ◽  
Resistance Genes ◽  
Bacterial Communities ◽  
Rhizosphere Soil ◽  
Antibiotics Resistance ◽  
Plant Growth Promoting Bacteria ◽  
Soil Microbial Diversity ◽  
Antibiotic Target ◽  
And Function

Bacterial communities associated with roots influence the health and nutrition of the host plant. However, the microbiome discrepancy are not well understood under different healthy conditions. Here, we tested the hypothesis that rhizosphere soil microbial diversity and function varies along a degeneration gradient of poplar, with a focus on plant growth promoting bacteria (PGPB) and antibiotic resistance genes. Comprehensive metagenomic analysis including taxonomic investigation, functional detection, and ARG (antibiotics resistance genes) annotation revealed that available potassium (AK) was correlated with microbial diversity and function. We proposed several microbes, Bradyrhizobium, Sphingomonas, Mesorhizobium, Nocardioides, Variovorax, Gemmatimonadetes, Rhizobacter, Pedosphaera, Candidatus Solibacter, Acidobacterium, and Phenylobacterium, as candidates to reflect the soil fertility and the plant health. The highest abundance of multidrug resistance genes and the four mainly microbial resistance mechanisms (antibiotic efflux, antibiotic target protection, antibiotic target alteration, and antibiotic target replacement) in healthy poplar rhizosphere, corroborated the relationship between soil fertility and microbial activity. This result suggested that healthy rhizosphere soil harbored microbes with a higher capacity and had more complex microbial interaction network to promote plant growing and reduce intracellular levels of antibiotics. Our findings suggested a correlation between the plant degeneration gradient and bacterial communities, and provided insight into the role of high-turnover microbial communities as well as potential PGPB as real-time indicators of forestry soil quality, and demonstrated the inner interaction contributed by the bacterial communities.

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