Community structure and abundance of ACC deaminase containing bacteria in soils with 16S-PICRUSt2 inference or direct acdS gene sequencing

Manter, Daniel K.; Hamm, Alison; Deel, Heather L.

doi:10.1016/j.mimet.2023.106740

Cited by 7 publications

(6 citation statements)

References 65 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…It is also interesting to note that the majority of the genera belonged to the phylum proteobacteria followed by actinobacteria. Occurrence of ACCD gene has been reported in diverse taxa but predominatnce in the phyla proteobacteria, actinobacteria and rmicutes has been reported (Manter et al 2023;Nascimento et al 2014). Our ndings are consistent with the above reports and suggest the wide prevalence of ACCD protein in the rice rhizosphere.…”

Section: Discussionmentioning

confidence: 99%

“…The structural genes encoding ACCD from several bacteria have been identi ed as acdS genes (Nascimento et al 2014;Singh et al 2015). acdS are GC rich and highly polymorphic, genetic diversity analysis is problematic (Bouffaud et al 2018;Manter et al 2023;Nascimento et al 2014). However, a degenerate primer pair has been synthesized to amplify a 113 bp region designated as the ACCD domain region (ACCD-DR) which has well conserved region suitable for genetic analysis (Jin et al 2016).…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Clone-based sequencing and NGS of plant growth-promoting genes from metagenomic DNA of rice rhizosphere show marked diversity

Kumar¹,

Kumar

2023

Preprint

View full text Add to dashboard Cite

Backgrounds and AimsAn attempt has been made to assess the distribution and diversity of important plant growth-promoting genes from the metagenomic DNA of rice rhizosphere soil. Methods A novel multiplex polymerase chain reaction was developed for the amplification of three important genes namely nifH, pqqC and accd-DR simultaneously from the metagenomic DNA. Next generation sequencing was employed for the sequencing of above genes for the assessment of diversity. Results Ninety six nifH clones from the metagenomic DNA of rice rhizosphere were selected which belonged to 15 groups on the basis of RFLP. Sequencing of the representative 15 clones showed higher level of similarity with the uncultured bacteria. Similarly, 12 clones of pqqC were selected, majority of the clones showed similarity with both uncultured and cultured bacteria. NGS of nifH showed fourteen types of genera with varying number of OTUs, the dominant genus identified as Halorhodospira (7.38%). pqqC and accd-DRshowed seven types of genera with varying number of OTUs. The highest abundance of Pseudomonas sp. (48.73%) was noted in pqqC and accd-DR showed the abundance of Acidovorax sp. (58.28%). Conclusions Altogether, findings of this study suggest marked diversity in nifH, pqqC and accd-DRgenes in rice rhizosphere. It would be desirable to apply both clone-based sequencing and NGS for the analysis of total bacterial community and plant growth promoting genes from the metagenome of any habitat.

show abstract

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Clone-based sequencing and NGS of plant growth-promoting genes from metagenomic DNA of rice rhizosphere show marked diversity

Kumar¹,

Kumar

2023

Preprint

View full text Add to dashboard Cite

show abstract

“…To assess predive functions of rhizosphere bacteria in unfertilized soil, data from PICRUSt2 was explored. PICRUSt2 accurately and significantly correlates gene abundances with those values produced from gene-specific primers, such as those for the acdS gene 82 . However, these functions that are linked to bacteria are solely predictive 42 .…”

Section: Methodsmentioning

confidence: 99%

Tomato domestication rather than subsequent breeding events reduces microbial associations related to phosphorus recovery

Dixon,

Afkairin,

Davis

et al. 2024

Sci Rep

Self Cite

View full text Add to dashboard Cite

Legacy phosphorus (P) is a reservoir of sparingly available P, and its recovery could enhance sustainable use of nonrenewable mineral fertilizers. Domestication has affected P acquisition, but it is unknown if subsequent breeding efforts, like the Green Revolution (GR), had a similar effect. We examined how domestication and breeding events altered P acquisition by growing wild, traditional (pre-GR), and modern (post-GR) tomato in soil with legacy P but low bioavailable P. Wild tomatoes, particularly accession LA0716 (Solanum pennellii), heavily cultured rhizosphere P solubilizers, suggesting reliance on microbial associations to acquire P. Wild tomato also had a greater abundance of other putatively beneficial bacteria, including those that produce chelating agents and antibiotic compounds. Although wild tomatoes had a high abundance of these P solubilizers, they had lower relative biomass and greater P stress factor than traditional or modern tomato. Compared to wild tomato, domesticated tomato was more tolerant to P deficiency, and both cultivated groups had a similar rhizosphere bacterial community composition. Ultimately, this study suggests that while domestication changed tomato P recovery by reducing microbial associations, subsequent breeding processes have not further impacted microbial P acquisition mechanisms. Selecting microbial P-related traits that diminished with domestication may therefore increase legacy P solubilization.

show abstract

“…First, we used the python script place_seqs.py with EPA-NG to add the query sequences to the default PICRUSt2 prokaryotic 16S rRNA phylogenetic tree. Second, we used the python script hsp.py with the castor R package to predict the number of 16S rRNA and functional gene copies per genome [ 31 ].…”

Section: Methodsmentioning

confidence: 99%

“…This analysis compared the total abundances between the unfertilized treatment and the fertilized treatment for all OTUs that shared 99% genetic distance. To further elucidate the differences in the whole bacterial community structure, a distance-based redundancy analysis (db-RDA) was run [ 31 ].…”

Section: Methodsmentioning

confidence: 99%

Harnessing Phosphorous (P) Fertilizer-Insensitive Bacteria to Enhance Rhizosphere P Bioavailability in Legumes

Afkairin,

Dixon,

Buchanan

et al. 2024

Microorganisms

Self Cite

View full text Add to dashboard Cite

Phosphorous (P) is widely used in agriculture; yet, P fertilizers are a nonrenewable resource. Thus, mechanisms to improve soil P bioavailability need to be found. Legumes are efficient in P acquisition and, therefore, could be used to develop new technologies to improve soil P bioavailability. Here, we studied different species and varieties of legumes and their rhizosphere microbiome responses to low-P stress. Some varieties of common beans, cowpeas, and peas displayed a similar biomass with and without P fertilization. The rhizosphere microbiome of those varieties grown without P was composed of unique microbes displaying different levels of P solubilization and mineralization. When those varieties were amended with P, some of the microbes involved in P solubilization and mineralization decreased in abundance, but other microbes were insensitive to P fertilization. The microbes that decreased in abundance upon P fertilization belonged to groups that are commonly used as biofertilizers such as Pseudomonas and Azospirillum. The microbes that were not affected by P fertilization constitute unique species involved in P mineralization such as Arenimonas daejeonensis, Hyphomicrobium hollandicum, Paenibacillus oenotherae, and Microlunatus speluncae. These P-insensitive microbes could be used to optimize P utilization and drive future sustainable agricultural practices to reduce human dependency on a nonrenewable resource.

show abstract

Community structure and abundance of ACC deaminase containing bacteria in soils with 16S-PICRUSt2 inference or direct acdS gene sequencing

Cited by 7 publications

References 65 publications

Clone-based sequencing and NGS of plant growth-promoting genes from metagenomic DNA of rice rhizosphere show marked diversity

Clone-based sequencing and NGS of plant growth-promoting genes from metagenomic DNA of rice rhizosphere show marked diversity

Tomato domestication rather than subsequent breeding events reduces microbial associations related to phosphorus recovery

Harnessing Phosphorous (P) Fertilizer-Insensitive Bacteria to Enhance Rhizosphere P Bioavailability in Legumes

Contact Info

Product

Resources

About