rhizosphere bacteria
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2021 ◽  
Vol 12 ◽  
Author(s):  
Yingwu Shi ◽  
Hongmei Yang ◽  
Ming Chu ◽  
Xinxiang Niu ◽  
Ning Wang ◽  
...  

The plant microbiome is a key determinant of health and productivity. However, it is still difficult to understand the structural composition of the bacterial and fungal microbiomes of diseased and healthy plants, especially the spatial dynamics and phylogenies of endophytic and rhizosphere microbial communities. We studied the differentiation and variability in the rhizosphere and endosphere microbiomes of healthy and diseased cotton from north and south of the Tianshan Mountains using the methods of PCR-based high-throughput sequencing and real-time quantitative PCR. The endophytic and rhizosphere bacterial abundances in the diseased plants were greater than those of healthy plants. The numbers of endophytic and rhizosphere fungi associated with diseased plants were greater than those associated healthy plants (p < 0.05). Endophytic and rhizosphere bacteria did not share common OTUs. The dominant rhizosphere bacteria were Proteobacteria (29.70%), Acidobacteria (23.14%), Gemmatimonadetes (15.17%), Actinobacteria (8.31%), Chloroflexi (7.99%), and Bacteroidetes (5.15%). The dominant rhizosphere fungi were Ascomycota (83.52%), Mortierellomycota (7.67%), Basidiomycota (2.13%), Chytridiomycota (0.39%), and Olpidiomycota (0.08%). The distribution of dominant bacteria in different cotton rhizosphere soils and roots differed, with the dominant bacteria Pseudomonas (15.54%) and Pantoea (9.19%), and the dominant fungi Alternaria (16.15%) and Cephalotrichum (9.10%) being present in the greatest numbers. At sampling points in different ecological regions, the total numbers of cotton endophytic and rhizosphere microbiome OTUs from southern to northern Xinjiang showed an increasing trend. There were significant differences in the composition and diversity of rhizosphere microbes and endophytes during the entire cotton growth period and in representative ecological regions (p < 0.01), whereas rhizosphere microbes and endophytes showed no significant differences among the four growth periods and in representative ecological regions. RB41, H16, Nitrospira, and Sphingomonas play important roles in the microbial ecology of cotton rhizosphere soil. Pseudomonas accounted for a large proportion of the microbes in the cotton rhizosphere soil. This study provides an in-depth understanding of the complex microbial composition and diversity associated with cotton north and south of the Tianshan Mountains.


Author(s):  
Raisa Kabeer ◽  
Sylas V. P. ◽  
Praveen Kumar C. S. ◽  
Thomas A. P. ◽  
Shanthiprabha V. ◽  
...  

PLoS ONE ◽  
2021 ◽  
Vol 16 (11) ◽  
pp. e0259515
Author(s):  
Fating Yin ◽  
Fenghua Zhang ◽  
Haoran Wang

Soil salinity is a serious environmental issue in arid China. Halophytes show extreme salt tolerance and are grow in saline-alkaline environments. There rhizosphere have complex bacterial communities, which mediate a variety of interactions between plants and soil. High-throughput sequencing was used to investigated rhizosphere bacterial community changes under the typical halophyte species in arid China. Three typical halophytes were Leymus chinensis (LC), Puccinellia tenuiflora (PT), Suaeda glauca (SG). The dominant phyla were Proteobacteria, Actinobacteria, Chloroflexi, Gemmatimonadetes, Acidobacteria and Bacteroidetes, Suaeda glauca rhizosphere has stronger enrichment of Nitrospirae and Cyanobacteria. The Ace, Chao and Shannon indices were significantly higher in soils under LC and SG (P<0.05). Functional predictions, based on 16S rRNA gene by PICRUSt, indicated that Energy metabolism, Amino acid metabolism, Carbohydrate metabolism and Fatty acid metabolism are dominant bacterial functions in three halophytes rhizosphere soil. Carbon metabolism, Oxidative phosphorylation, Methane metabolism, Sulfur metabolism and Nitrogen metabolism in SG were significantly higher than that in LC and PT. Regression analysis revealed that rhizosphere soil bacterial community structure is influenced by soil organic matter (SOM) and soil water content (SWC), while soil bacterial community diversity is affected by soil pH. This study contributes to our understanding of the distribution characteristics and metabolic functions under different halophyte rhizosphere bacterial communities, and will provide references for the use of rhizosphere bacteria to regulate the growth of halophytes and ecological restoration of saline soil.


2021 ◽  
Vol 7 (2) ◽  
pp. 61-65
Author(s):  
Dwi Hardestyariki ◽  
Bambang Yudono ◽  
Munawar Munawar

The purpose of this research is to obtain hydrocarbon degrading bacteria that work synergistically in a consortium. Consortium microorganisms is mixture of microbial populations in the form of communities that have mutualistic relationships and doesn’t inhibition the growth of other microbes. In this study, isolates were obtained from the rhizosphere of soil contaminated with petroleum. The isolates obtained were tested for synergism to determine the relationship between bacterial isolates. Synergism testing was carried out using the spread plate method on agar media. The results of this study showed that isolate number one showed antagonistic properties to other bacterial isolates by forming a clear zone around the disc paper. A total of eight bacterial isolates showed the greatest percentage of synergism, namely ≥ 80% so that the eight rhizosphere bacterial isolates could be used as materials for mixed culture.


2021 ◽  
pp. 126917
Author(s):  
Hongxiang Xu ◽  
Fengqiong Yu ◽  
Youwei Zuo ◽  
Yongdong Dai ◽  
Hongping Deng ◽  
...  

2021 ◽  
Vol 886 (1) ◽  
pp. 012003
Author(s):  
Iswanto ◽  
Siti Halimah Larekeng ◽  
Gusmiaty ◽  
Sri Wahyuni Jufri ◽  
Atisa Muslimin ◽  
...  

Abstract Open-pit mining activities cause land degradation; therefore, post-mining land recovery or reclamation is essential. An indicator to rate the success of mine reclamation activities is the diversity of soil microbial populations. Molecular bacteria identification requires prior information about the amplification of universal primers for molecular analysis. This study analyzes the amplification of 16S rRNA primers on rhizosphere bacteria isolates from reclamation and forest areas. The research activities encompassed sample preparation, isolation of bacteria isolates, isolation of DNA isolate, quantitative test, qualitative test, and amplification. The findings showed that pure isolates of rhizosphere bacteria from reclamation and natural forest areas that could be used were five and ten isolates, respectively. One isolate (20%) from the reclamation area and four isolates (40%) from natural forest generated DNA band, which were amplified using 16S rRNA.


2021 ◽  
Author(s):  
Lixin Tian ◽  
Feifei Zhang ◽  
Pengliang Chen ◽  
Panpan Zhang ◽  
Zhijun Gao ◽  
...  

Abstract It is of great ecological significance to understand how the assembly processes of soil microbe communities respond to environmental change. However, the assembly processes of the rhizosphere bacterial communities in three minor grain crops (i.e., foxtail millet, proso millet, and sorghum) across agro-ecosystems are rarely investigated. Here, we investigated the environmental thresholds and phylogenetic signals for ecological preferences of rhizosphere bacterial communities of three minor grain crop taxa across complex environmental gradients to reflect their environmental adaptation. Additionally, we reported environmental factors affecting their community assembly processes based on a large-scale soil survey in agricultural fields across northern China using high-throughput sequencing.. The results demonstrated a narrower range of environmental thresholds and weaker phylogenetic signals for the ecological traits of rhizosphere bacteria in proso millet than in foxtail millet and sorghum fields, while proso millet rhizosphere community was the most phylogenetically clustered. The null model analysis indicated that homogeneous selection belonging to deterministic processes governed the sorghum rhizosphere community, whereas dispersal limitation belonging to stochastic processes was the critical assembly process in the foxtail and proso millet. Mean annual temperature was the decisive factor for adjusting the balance between stochasticity and determinism of the foxtail millet, proso millet, and sorghum rhizosphere communities. A higher temperature resulted in stochasticity in the proso millet and sorghum communities. For the foxtail millet community, the deterministic assembly increased with an increase in temperature. These results contribute to the understanding of root-associated bacterial community assembly processes in agro-ecosystems on a large scale.


PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e12302
Author(s):  
Renyan Duan ◽  
Yuxiang Lin ◽  
Jianing Zhang ◽  
Minyi Huang ◽  
Yihuan Du ◽  
...  

Background Open pit antimony (Sb) mining causes serious soil pollution, and phytoremediation is a low-cost approach to remediate heavy metal contaminated soil. Rhizosphere bacteria play an important role in ecological restoration in mining areas. There is a knowledge gap on how to find suitable rhizosphere microorganisms to improve the phytoremediation effect. Understanding the differences of rhizosphere bacterial diversity in different restoration stages is helpful to find suitable bacteria for ecological restoration. Methods A method of the substitution of “space” for “time” was used to study the effect of natural restoration on rhizosphere bacterial community. According to the dominant vegetation types (herb, shrub, and tree) in the natural restoration area of Sb mining, the early restoration (ER), middle restoration (MR), and later restoration (LR) from the largest Sb mine (Xikuangshan mine) in the world were selected to evaluate the differences in the composition and diversity of rhizosphere bacteria during three natural restoration stages. Each restoration stage had five samples. To determine the relationship between restoration stages and bacterial diversity in the rhizosphere, high throughput sequencing of PCR amplified were used. Results Alpha diversity, as assessed by Chao indices, appeared lowest in ER but this trend was not seen with other diversity metrics, including the Simpson and Shannon. Beta diversity analysis suggested there were differences in rhizobacterial community structure associate with restoration stage. At the phylum level, natural restoration led to a significant increase in the relative abundance of Actinobacteria in the MR, and a significant decrease in the relative abundance of Patescibacteria in the LR. Additionally, Calditrichaeota, Deferribacteres and Epsilonbacteraeota were only found in ER. At the genus level, the relative abundance of RB41 and Haliangium were highest in LR plots, while that of Bacillus and Gaiella were highest in ER plots. Additionally, the Azorhizobium genus was only detected in the ER phase. Overall, our findings suggested that several rhizosphere microbial communities had significant differences among three natural restoration stages (ER, MR, and LR) and the rhizosphere bacterial communities mainly appeared in the early restoration stage can be preferred for remediation of pollution soil in Xikuangshan.


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