scholarly journals The Rhizosphere Bacterial Communities Differ Among Domesticated Maize Landraces – An Experimental Confirmation

2022 ◽  
Author(s):  
Mads Lund ◽  
Jacob Agerbo Rasmussen ◽  
Jazmin Ramos-Madrigal ◽  
M. Thomas Pius Gilbert ◽  
Christopher James Barnes
Keyword(s):  
Bacterial Communities ◽  
Environmental Gradients ◽  
Genotypic Variation ◽  
Single Species ◽  
Genomic Variation ◽  
Genotypic Differences ◽  
Limited Sampling ◽  
Maize Landraces ◽  
Controlled Environments ◽  
Rhizosphere Bacterial Communities

The plant-associated microbiome has been shown to vary considerably between species and across environmental gradients. The effects of genomic variation on the microbiome within single species are less clearly understood, with results often confounded by the larger effects of climatic and edaphic variation. In this study, the effect of genomic variation on the rhizosphere bacterial communities of maize was investigated by comparing different genotypes grown within controlled environments. Rhizosphere bacterial communities were profiled by metabarcoding the universal bacterial 16S rRNA v3-v4 region. Initially, plants from the inbred B73 line and the Ancho - More 10 landrace were grown for 12-weeks and compared. The experiment was then repeated with an additional four Mexican landraces (Apachito - Chih 172, Tehua - Chis 204, Serrano - Pueb 180 and Hairnoso de Ocho) that were grown alongside additional B73 and Ancho - More 10 genotypes. In both experiments there were significant genotypic differences in the rhizosphere bacteria. Additionally, the bacterial communities were significantly correlated with genomic distance between genotypes, with the more closely related landraces being more similar in rhizosphere bacterial communities. Despite limited sampling numbers, here we confirm that genomic variation in maize landraces is associated with differences in the rhizosphere bacterial communities. Further studies that go beyond correlations to identify the mechanisms that determine the genotypic variation of the rhizosphere microbiome are required.

scholarly journals Variation of rhizosphere bacterial community diversity in the desert ephemeral plant Ferula sinkiangensis across environmental gradients

2020 ◽  
Author(s):  
Zhang Tao ◽  
Dang Han Li ◽  
Wang Zhong Ke ◽  
Lv Xin Hua ◽  
Zhuang Li
Keyword(s):  
Bacterial Community ◽  
Bacterial Communities ◽  
Bacterial Community Structure ◽  
Environmental Gradients ◽  
Soil Depth ◽  
Community Diversity ◽  
Slope Position ◽  
Rhizosphere Bacterial Community ◽  
Ferula Sinkiangensis ◽  
Rhizosphere Bacterial Communities

Abstract Background Ferula sinkiangensis is a desert short-lived medicinal plant, and its number is rapidly decreasing. Rhizosphere microbial community plays an important role in regulating global biogeochemical cycle, plant growth and adaptability. However, the Ferula sinkiangensis bacterial community and the processes that drive its assembly remain unclear. Results In this study, based on Illumina HiSeq high-throughput sequencing, we explored the diversity, structure and composition of Ferula sinkiangensis rhizosphere bacterial communities at different slope positions (upper, middle and bottom) and soil depths (0-10 cm, 10-25 cm, 25-40 cm) and their correlation with soil physicochemical properties. Actinobacteria (22.7%), Proteobacteria (18.6%), Acidobacteria (14.0%), Gemmatimonadetes (10.1%), Cyanobacteria (7.9%), Bacteroidetes (6.9%), Planctomycetes (3.9%), Verrucomicrobia (3.5%), Firmicutes (3.4%) and Chloroflexi (3.2%) were the dominant bacterial phyla in Ferula sinkiangensis rhizosphere soil. Variance analysis showed that the diversity and abundance of rhizosphere bacterial community in Ferula sinkiangensis were significantly different at various slope positions and soil depths. Specifically, the diversity of bacterial community was significantly higher at the top than the bottom of the slope, and the diversity and richness of bacterial community were significantly greater in the 0-10cm than the 25-40cm soil layer. Linear discriminant effect size (LEfSe) analysis showed the specific phyla and genera of bacteria affected by slope position and soil depth. For example, Planctomycetes, Sphingomonas , Rubrobacter and Adhaeribacter by slope position and significant impact on soil depth. In addition, distance-based redundancy analysis (db-RDA) and variance analysis showed that soil physicochemical factors jointly explained 29.81% of variation in Ferula sinkiangensis rhizosphere bacterial community structure. There was a significant positive correlation between available phosphorus（AP）and the diversity of Ferula sinkiangensis rhizosphere bacterial community ( p < 0.01), whereas pH largely explained the variation of Ferula sinkiangensis rhizosphere bacterial community structure (5.58%, p < 0.01), followed by altitude (5.53%), total salt (TS, 5.21%) and total phosphorus (TP, 4.90%). Conclusion Our results revealed the heterogeneity and variation trends of Ferula sinkiangensis rhizosphere bacterial community diversity and abundance on a fine spatial scale (slope position and depth) and shed new light on the mechanisms of coevolution and interaction between Ferula sinkiangensis and their rhizosphere bacterial communities across environmental gradients.

Isolation of Rhizosphere Bacterial Communities from Soil

BIO-PROTOCOL ◽  
2015 ◽  
Vol 5 (16) ◽  
Author(s):  
Laura White ◽  
Volker Br�zel ◽  
Senthil Subramanian
Keyword(s):  
Bacterial Communities ◽  
Rhizosphere Bacterial Communities

Genotypic Variation in C and N Isotope Discrimination Suggests Local Adaptation of Heart-Leaved Willow

2021 ◽  
Author(s):  
Yi Hu ◽  
Robert D Guy ◽  
Raju Y Soolanayakanahally
Keyword(s):  
Isotopic Composition ◽  
Local Adaptation ◽  
N Uptake ◽  
Genotypic Variation ◽  
Carbon Isotopic Composition ◽  
Genotypic Differences ◽  
Clinal Variation ◽  
Trade Off ◽  
Uptake Efficiency ◽  
N Uptake Efficiency

Abstract Plants acquire multiple resources from the environment and may need to adjust and/or balance their respective resource-use efficiencies to maximize grow and survival, in a locally adaptive manner. In this study, tissue and whole-plant carbon isotopic composition (δ13C) and C/N ratios provided long-term measures of use efficiencies for water (WUE) and nitrogen (NUE), and a nitrogen isotopic composition (δ15N) based mass balance model was used to estimate traits related to N uptake and assimilation in heart-leaved willow (Salix eriocephala Michx.). In an initial common garden experiment consisting of 34 populations, we found population level variation in δ13C, C/N and δ15N, indicating different patterns in WUE, NUE and N uptake and assimilation. Although there was no relationship between foliar δ13C and C/N ratios among populations, there was a significant negative correlation between these measures across all individuals, implying a genetic and/or plastic trade-off between WUE and NUE not associated with local adaptation. To eliminate any environmental effect, we grew a subset of 21 genotypes hydroponically with nitrate as the sole N-source, and detected significant variation in δ13C, δ15N and C/N ratios. Variation in δ15N was mainly due to genotypic differences in the nitrate efflux/influx ratio (E/I) at the root. Both experiments suggested clinal variation in δ15N (and thus N uptake efficiency) with latitude of origin, which may relate to water availability and could contribute to global patterns in ecosystem δ15N. There was a tendency for genotypes with higher WUE to come from more water replete sites with shorter and cooler growing seasons. We found that δ13C, C/N, and E/I were not inter-correlated, suggesting that selection of growth, WUE, NUE and N uptake efficiency can occur without trade-off.

scholarly journals Effect of Two Different Sugarcane Cultivars on Rhizosphere Bacterial Communities of Sugarcane and Soybean Upon Intercropping

2021 ◽  
Vol 11 ◽  
Author(s):  
Yue Liu ◽  
Huichun Yang ◽  
Qi Liu ◽  
Xiaowen Zhao ◽  
Sasa Xie ◽  
...  
Keyword(s):  
Bacterial Communities ◽  
P Uptake ◽  
Organic P ◽  
Inorganic P ◽  
Sugarcane Varieties ◽  
P Mineralization ◽  
Rhizosphere Environment ◽  
Uptake And Transport ◽  
Rhizosphere Bacterial Communities ◽  
Sugarcane Industry

Intercropping of soybean and sugarcane is an important strategy to promote sustainable development of the sugarcane industry. In fact, our understanding of the interaction between the rhizosphere and bacterial communities in the intercropping system is still evolving; particularly, the influence of different sugarcane varieties on rhizosphere bacterial communities in the intercropping process with soybean, still needs further research. Here, we evaluated the response of sugarcane varieties ZZ1 and ZZ9 to the root bacterial community during intercropping with soybean. We found that when ZZ9 was intercropped with soybean, the bacterial diversity increased significantly as compared to that when ZZ1 was used. ZZ9 played a major role in changing the bacterial environment of the root system by affecting the diversity of rhizosphere bacteria, forming a rhizosphere environment more conducive to the growth of sugarcane. In addition, our study found that ZZ1 and ZZ9 had differed significantly in their utilization of nutrients. For example, nutrients were affected by different functional genes in processes such as denitrification, P-uptake and transport, inorganic P-solubilization, and organic P-mineralization. These results are significant in terms of providing guidance to the sugarcane industry, particularly for the intercropping of sugarcane and soybean in Guangxi, China.

scholarly journals Rhizosphere Bacteria Exhibit Narrower Environmental Adaptation in Proso Millet Than in Foxtail Millet and Sorghum in Agricultural Fields

2021 ◽  
Author(s):  
Lixin Tian ◽  
Feifei Zhang ◽  
Pengliang Chen ◽  
Panpan Zhang ◽  
Zhijun Gao ◽  
...  
Keyword(s):  
Community Assembly ◽  
Bacterial Communities ◽  
Large Scale ◽  
Foxtail Millet ◽  
Environmental Adaptation ◽  
Rhizosphere Bacteria ◽  
Agricultural Fields ◽  
Proso Millet ◽  
Rhizosphere Community ◽  
Rhizosphere Bacterial Communities

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.

scholarly journals Evolutionary Subdivision of Domestic Chickens: Implications for Local Breeds as Assessed by Phenotype and Genotype in Comparison to Commercial and Fancy Breeds

Agriculture ◽  
2021 ◽  
Vol 11 (10) ◽  
pp. 914
Author(s):  
Tatyana A. Larkina ◽  
Olga Y. Barkova ◽  
Grigoriy K. Peglivanyan ◽  
Olga V. Mitrofanova ◽  
Natalia V. Dementieva ◽  
...  
Keyword(s):  
Egg Production ◽  
Phenotypic Variability ◽  
Genotypic Variation ◽  
Significant Proportion ◽  
Genomic Variation ◽  
Classification Model ◽  
Genotypic Variability ◽  
Marker Assisted Breeding ◽  
Breeding Programs ◽  
Clustering Model

To adjust breeding programs for local, commercial, and fancy breeds, and to implement molecular (marker-assisted) breeding, a proper comprehension of phenotypic and genotypic variation is a sine qua non for breeding progress in animal production. Here, we investigated an evolutionary subdivision of domestic chickens based on their phenotypic and genotypic variability using a wide sample of 49 different breeds/populations. These represent a significant proportion of the global chicken gene pool and all major purposes of breed use (according to their traditional classification model), with many of them being characterized by a synthetic genetic structure and notable admixture. We assessed their phenotypic variability in terms of body weight, body measurements, and egg production. From this, we proposed a phenotypic clustering model (PCM) including six evolutionary lineages of breed formation: egg-type, meat-type, dual purpose (egg-meat and meat-egg), game, fancy, and Bantam. Estimation of genotypic variability was carried out using the analysis of five SNPs, i.e., at the level of genomic variation at the NCAPG-LCORL locus. Based on these data, two generally similar genotypic clustering models (GCM1 and GCM2) were inferred that also had several overlaps with PCM. Further research for SNPs associated with economically important traits can be instrumental in marker-assisted breeding programs.

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