Sweet Sorghum Genotypes Tolerant and Sensitive to Nitrogen Stress Select Distinct Root Endosphere and Rhizosphere Bacterial Communities

Lopes, Lucas Dantas; Chai, Yen Ning; Marsh, Ellen L.; Rajewski, J. F.; Dweikat, İsmail; Schachtman, Daniel P.

doi:10.3390/microorganisms9061329

Cited by 13 publications

(10 citation statements)

References 86 publications

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“…These results were corroborated by our analysis of amplicon sequences from 2016, as well as metagenomes assembled from both 2016 and 2017 samples that showed a significant increase in nitrogen-fixing genes under low nitrogen (Supplementary Figure 6). Similar patterns have been identified in other studies of the sorghum rhizosphere (Yu et al 2011, Hara et al 2019, Lopes et al 2021, Wu et al 2021. Interestingly, this nitrogen-fixing guild seems to be preceded by other putatively plantgrowth promoting taxa, such as Massilia and Bacillus (clusters 12 and 17), whose abundances were also higher under low nitrogen.…”

Section: Real Data Analysissupporting

confidence: 85%

Poisson hurdle model-based method for clustering microbiome features

et al. 2022

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Motivation High-throughput sequencing technologies have greatly facilitated microbiome research and have generated a large volume of microbiome data with the potential to answer key questions regarding microbiome assembly, structure, and function. Cluster analysis aims to group features that behave similarly across treatments, and such grouping helps highlight the functional relationships among features and may provide biological insights into microbiome networks. However, clustering microbiome data is challenging due to the sparsity and high-dimensionality. Results We propose a model-based clustering method based on Poisson hurdle models for sparse microbiome count data. We describe an expectation-maximization algorithm and a modified version using simulated annealing to conduct the cluster analysis. Moreover, we provide algorithms for initialization and choosing the number of clusters. Simulation results demonstrate that our proposed methods provide better clustering results than alternative methods under a variety of settings. We also apply the proposed method to a sorghum rhizosphere microbiome dataset that results in interesting biological findings. Availability R package is freely available for download at https://cran.r-project.org/package=PHclust. Supplementary information Supplementary Materials are available at Bioinformatics online.

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Section: Real Data Analysissupporting

confidence: 85%

Poisson hurdle model-based method for clustering microbiome features

et al. 2022

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“…A recent study reported that the genus Streptomyces was enriched in the root endosphere of a nitrogen stress-tolerant sweet sorghum line under low-nitrogen eld growth (Lopes et al, 2021). In this study, not only the genus Streptomyces predominated the bacterial microbiota in the maturing roots of N778, but OTU434 and OTU1304 were also particularly enriched in the maturing root sample of N778 when compared to the control sorghum line TP60 (Table S7).…”

Section: Discussionmentioning

confidence: 49%

Root-inhabiting bacterial microbiota of the perennial sweet sorghum cultivar at the maturing stage under cold stress

Lü

Cao

Fazal

et al. 2022

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The bacterial microbiota inhabiting the endosphere and rhizoplane play numerous important functions in improving plant growth. The mutualistic interaction between sweet sorghum and soil bacteria has drawn increasing attention. However, the bacterial microbiota inhabiting the roots of sweet sorghum’s perennial analog have rarely been characterized. Here, the root-inhabiting bacterial microbiota of the perennial sweet sorghum cultivar NaPBS778 (N778 simply) and its control TP60 were discovered at the flowering and maturing stages under field growth by high-throughput amplicon sequencing of the 16S rRNA gene via Illumina MiSeq. Almost all alpha diversity indices of aerial and primary root samples of N778 were not significantly different from those of TP60 at the maturing stage, except for the observed species (Sobs) and phylogenetic diversity indices. Next, the beta diversity of aerial and primary root samples showed no significant differences between N778 and its control TP60 at the maturing stage. Moreover, the bacterial microbiota in N778 aerial and primary roots was not only predominated by Proteobacteria, Actinobacteria, and Bacteroidetes at the phylum level but was also strikingly distinct from the bacterial microbiota in rhizosphere soil at the genus level. Additionally, the root samples of N778 at the maturing stage were considerably enriched with OTU1262, OTU434, OTU1304, and OTU836, which belonged to the genera Pseudarthrobacter, Streptomyces, and an unclassified genus of the family Oxalobacteraceae, respectively. Our findings imply that the perennial sweet sorghum cultivar N778 may recruit not only potentially cold-tolerant but also plant growth-promoting and nitrogen stress-tolerant bacterial taxa into roots at the maturing stage.

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“…(Gram-positive) were from the soil. Despite being widely distributed and abundant in the soil and/or rhizosphere of various crops, the genera Chitinophaga (Chung et al, 2012;Li et al, 2014;Chiniquy et al, 2021) and Caulobacter (Gao et al, 2018;Lopes et al, 2021a) are rarely tested for their plant growth-promoting abilities. Compared to these two genera, the genus Terrabacter has also been detected in many plant species, including maize (Dohrmann et al, 2013), sorghum (Lopes et al, 2021a), and napa cabbage (Bhattacharyya et al, 2018), but in very low abundance and is understudied.…”

Section: Introductionmentioning

confidence: 99%

“…Despite being widely distributed and abundant in the soil and/or rhizosphere of various crops, the genera Chitinophaga (Chung et al, 2012;Li et al, 2014;Chiniquy et al, 2021) and Caulobacter (Gao et al, 2018;Lopes et al, 2021a) are rarely tested for their plant growth-promoting abilities. Compared to these two genera, the genus Terrabacter has also been detected in many plant species, including maize (Dohrmann et al, 2013), sorghum (Lopes et al, 2021a), and napa cabbage (Bhattacharyya et al, 2018), but in very low abundance and is understudied. Therefore, we sought to determine whether these bacteria could promote plant growth and their host colonization efficiency with different inoculation methods since they are phylogenetically distinct and exhibit different cell wall structure.…”

Section: Introductionmentioning

confidence: 99%

Assessment of Bacterial Inoculant Delivery Methods for Cereal Crops

2022

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Despite growing evidence that plant growth-promoting bacteria can be used to improve crop vigor, a comparison of the different methods of delivery to determine which is optimal has not been published. An optimal inoculation method ensures that the inoculant colonizes the host plant so that its potential for plant growth-promotion is fully evaluated. The objective of this study was to compare the efficacy of three seed coating methods, seedling priming, and soil drench for delivering three bacterial inoculants to the sorghum rhizosphere and root endosphere. The methods were compared across multiple time points under axenic conditions and colonization efficiency was determined by quantitative polymerase chain reaction (qPCR). Two seed coating methods were also assessed in the field to test the reproducibility of the greenhouse results under non-sterile conditions. In the greenhouse seed coating methods were more successful in delivering the Gram-positive inoculant (Terrabacter sp.) while better colonization from the Gram-negative bacteria (Chitinophaga pinensis and Caulobacter rhizosphaerae) was observed with seedling priming and soil drench. This suggested that Gram-positive bacteria may be more suitable for the seed coating methods possibly because of their thick peptidoglycan cell wall. We also demonstrated that prolonged seed coating for 12 h could effectively enhance the colonization of C. pinensis, an endophytic bacterium, but not the rhizosphere colonizing C. rhizosphaerae. In the field only a small amount of inoculant was detected in the rhizosphere. This comparison demonstrates the importance of using the appropriate inoculation method for testing different types of bacteria for their plant growth-promotion potential.

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Sweet Sorghum Genotypes Tolerant and Sensitive to Nitrogen Stress Select Distinct Root Endosphere and Rhizosphere Bacterial Communities

Cited by 13 publications

References 86 publications

Poisson hurdle model-based method for clustering microbiome features

Poisson hurdle model-based method for clustering microbiome features

Root-inhabiting bacterial microbiota of the perennial sweet sorghum cultivar at the maturing stage under cold stress

Assessment of Bacterial Inoculant Delivery Methods for Cereal Crops

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