scholarly journals Diversity of the Bacterial Microbiome Associated With the Endosphere and Rhizosphere of Different Cassava (Manihot esculenta Crantz) Genotypes

2021 ◽  
Vol 12 ◽  
Author(s):  
Jingwen Ha ◽  
Yu Gao ◽  
Rui Zhang ◽  
Ke Li ◽  
Yijie Zhang ◽  
...  
Keyword(s):  
Bacterial Communities ◽  
Rhizosphere Soil ◽  
Hierarchical Cluster ◽  
Plant Growth And Development ◽  
Manihot Esculenta Crantz ◽  
Tuberous Roots ◽  
Rdna Sequencing ◽  
Microbial Community Structures ◽  
Bacterial Microbiome ◽  
Tuber Roots

Root-associated microbial communities play important roles in plant growth and development. However, little attention has been paid to the microbial community structures associated with cassava, which is a staple food for approximately 800 million people worldwide. Here, we studied the diversity and structure of tuber endosphere and rhizosphere bacterial communities in fourteen cassava genotypes: SC5, SC8, SC9, SC205, KU50, R72, XL1, FX01, SC16, 4612, 587, 045, S0061, and 1110. The results of bacterial 16S rDNA sequencing showed that the richness and diversity of bacteria in the rhizosphere were higher than those in the tuber endosphere across the 14 cassava genotypes. After sequencing, 21 phyla and 310 genera were identified in the tuberous roots, and 36 phyla and 906 genera were identified in the rhizosphere soils. The dominant phylum across all tuber samples was Firmicutes, and the dominant phyla across all rhizosphere samples were Actinobacteria, Proteobacteria, and Acidobacteria. The numbers of core bacterial taxa within the tuber endospheres and the rhizospheres of all cassava genotypes were 11 and 236, respectively. Principal coordinate analysis and hierarchical cluster analysis demonstrated significant differences in the compositions of rhizosphere soil microbiota associated with the different cassava genotypes. Furthermore, we investigated the metabolic changes in tuber roots of three genotypes, KU50, SC205, and SC9. The result showed that the abundances of Firmicutes, Proteobacteria, and Actinobacteria in tuber samples were positively correlated with organic acids and lipids and negatively correlated with vitamins and cofactors. These results strongly indicate that there are clear differences in the structure and diversity of the bacterial communities associated with different cassava genotypes.

scholarly journals Influence of Manure Application on the Soil Bacterial Microbiome in Integrated Crop-Livestock Farms in Maryland

2021 ◽  
Vol 9 (12) ◽  
pp. 2586
Author(s):  
Mengfei Peng ◽  
Zajeba Tabashsum ◽  
Patricia Millner ◽  
Salina Parveen ◽  
Debabrata Biswas
Keyword(s):  
Bacterial Communities ◽  
The United States ◽  
Shared Environment ◽  
Agricultural System ◽  
Manure Application ◽  
Soil Bacterial Communities ◽  
Rdna Sequencing ◽  
Bacterial Microbiome ◽  
Livestock Farms ◽  
Soil Bacterial

As a traditional agricultural system, integrated crop-livestock farms (ICLFs) involve the production of animals and crops in a shared environment. The ICLFs in the mid-Atlantic region of the United States practice sustainable manure aging or composting processes to provide an on-farm source of soil amendment for use as natural fertilizer and soil conditioner for crop production. However, crop fertilization by soil incorporation of aged manure or compost may introduce different microbes and alter the soil microbial community. The aim of this study was to characterize the influence of aged or composted manure application on the diversity of soil bacterial community in ICLFs. Soil samples from six ICLFs in Maryland were collected before (pre-crop) and during the season (2020–2021) and used to analyze soil bacterial microbiome by 16S rDNA sequencing. Results showed that both phylum- and genus-level alterations of soil bacterial communities were associated with amendment of aged or composted manure. Particularly, Proteobacteria and Actinobacteria were enriched, while Acidobacteria, Bacteroidetes, Planctomycetes, Firmicutes, and Chloroflexi were reduced after manure product application. Meanwhile, the relative abundance of Bacillus was decreased, while two zoonotic pathogens, Salmonella and Listeria, were enriched by manure amendments. Overall, animal manure amendment of soil increased the phylogenetic diversity, but reduced the richness and evenness of the soil bacterial communities. Although manure composting management in ICLFs benefits agricultural sustainable production, the amendments altered the soil bacterial communities and were associated with the finding of two major zoonotic bacterial pathogens, which raises the possibility of their potential transfer to fresh horticultural produce crops that may be produced on the manured soils and then subsequently consumed without cooking.

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.

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 Effects of shade stress on turfgrasses morphophysiology and rhizosphere soil bacterial communities

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Juanjuan Fu ◽  
Yilan Luo ◽  
Pengyue Sun ◽  
Jinzhu Gao ◽  
Donghao Zhao ◽  
...  
Keyword(s):  
Bacterial Communities ◽  
Rhizosphere Soil ◽  
Soil Bacterial Communities ◽  
Soil Bacterial

Analysis of bacterial communities in rhizosphere soil of healthy and diseased cotton (Gossypium sp.) at different plant growth stages

2010 ◽  
Vol 339 (1-2) ◽  
pp. 447-455 ◽  
Author(s):  
Yan Zhang ◽  
Bing-Hai Du ◽  
Zhi-gang Jin ◽  
Zheng-hua Li ◽  
Hong-ning Song ◽  
...  
Keyword(s):  
Plant Growth ◽  
Bacterial Communities ◽  
Rhizosphere Soil ◽  
Growth Stages ◽  
Plant Growth Stages

Molecular characterization and in situ detection of bacterial communities associated with rhizosphere soil of high altitude native Poaceae from the Andean Puna region

2010 ◽  
Vol 74 (10) ◽  
pp. 1177-1185 ◽  
Author(s):  
Marcela A. Ferrero ◽  
Eugenia Menoyo ◽  
Mónica A. Lugo ◽  
María A. Negritto ◽  
María E. Farías ◽  
...  
Keyword(s):  
High Altitude ◽  
Molecular Characterization ◽  
Bacterial Communities ◽  
Rhizosphere Soil ◽  
In Situ Detection

Analysis of bacterial communities in rhizosphere soil of continuously cropped healthy and diseased konjac

2017 ◽  
Vol 33 (7) ◽  
Author(s):  
Jinping Wu ◽  
Zhenbiao Jiao ◽  
Jie Zhou ◽  
Fengling Guo ◽  
Zili Ding ◽  
...  
Keyword(s):  
Bacterial Communities ◽  
Rhizosphere Soil

scholarly journals Microbiome Analysis of Gut Bacterial Communities of Healthy and Diseased Malaysian Mahseer (Tor tambroides)

2021 ◽  
Author(s):  
Melinda Mei Lin Lau ◽  
Cindy Jia Yung Kho ◽  
LEONARD WHYE KIT LIM ◽  
Siew Chuiang Sia ◽  
Hung Hui Chung ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Bacterial Communities ◽  
Alpha Diversity ◽  
Microbiota Composition ◽  
Petechial Haemorrhage ◽  
Rdna Sequencing ◽  
Degrading Bacteria ◽  
And Function ◽  
Gut Microbial Community ◽  
Gut Microbiota Composition

Aims: The gut microbiota is referred to an extra organ and is ciritical in assisting the host in terms of nutrition and immunity. Environmental stressors could alter gut microbial community and cause gut inflammation. This study aimed to investigate and compare the gut microbiota community between healthy and diseased Tor tambroides. Methodology and results: In this study, such gut microbial alterations were explored using NGS-based 16S rDNA sequencing on the Malaysian mahseer (T. tambroides). Three adult healthy and three diseased adult Malaysian mahseers (showing signs of exophthalmia, coelomic distension and petechial haemorrhage) were obtained from LTT Aquaculture Sdn Bhd. Our results revealed significant differences in microbial diversity, composition and function between both populations of T. tambroides. Alpha diversity analysis depicts lower diversity of gut microbiota composition in diseased T. tambroides as compared to the healthy group. In particular, Enterobacteriaceae, Aeromonas, Bacteroides, Vibrio and Pseudomonas were found within gut microbiota of the diseased fishes. In addition, cellulose-degrading bacteria and protease-producing bacteria were identified from the gut of T. tambroides. Conclusion, significance and impact of study: Thus, our findings emphasised on the association between the alteration in gut microbiota composition and infectious abdominal dropsy (IAD) in T. tambroides. This finding is important to provide basic information for further diagnosis, prevention and treatment of intestinal diseases in fish.

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