Co-occurrence and patterns of phosphate solubilizing, salt and metal tolerant and antibiotic-resistant bacteria in diverse soils

Rathore, Parikshita; Joy, Sherina Sara; Yadav, Radheshyam; Ramakrishna, Wusirika

doi:10.1007/s13205-021-02904-7

Cited by 4 publications

(3 citation statements)

References 63 publications

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“…decreased. These changes in metabolic functions associated with plant growth [61] may also regulate the growth and development of G. elata Bl. f. glauca [62].…”

Section: Discussionmentioning

confidence: 99%

An exploration of mechanism of high quality and yield of Gastrodia elata Bl. f. glauca by the isolation, identification and evaluation of Armillaria

Gao

et al. 2022

BMC Plant Biol

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Background Gastrodia elata Bl. f. glauca, a perennial herb of G.elata Bl. in Orchidaceae, is one of the most valuable traditional Chinese medicines. G. elata Bl. is a chlorophyll-free myco-heterotrophic plant, which must rely on the symbiotic growth of Armillaria, but not all Armillaria strains can play the symbiotic role. Additionally, Armillaria is easy to degenerate after multiple generations, and the compatibility between the strains from other areas and G. elata Bl. f. glauca in Changbai Mountain is unstable. Therefore, it is incredibly significant to isolate, identify and screen the symbiotic Armillaria suitable for the growth of G. elata Bl. f. glauca in Changbai Mountain, and to explore the mechanism by which Armillaria improves the production performance of G. elata Bl. f. glauca. Results Firstly, G. elata Bl. f. glauca tubers, and rhizomorphs and fruiting bodies of Armillaria were used for the isolation and identification of Armillaria. Five Armillaria isolates were obtained in our laboratory and named: JMG, JMA, JMB, JMC and JMD. Secondly, Armillaria was selected based on the yield and the effective component content of G. elata Bl. f. glauca. It was concluded that the yield and quality of G. elata Bl. f. glauca co-planted with JMG is the highest. Finally, the mechanism of its high quality and yield was explored by investigating the effects of different Armillaria strains on the soil, its nutrition element contents and the soil microbial diversity around G. elata Bl. f. glauca in Changbai Mountain. Conclusions Compared with commercial strains, JMG significantly increased the content of Na, Al, Si, Mn, Fe, Zn, Rb and the absorption of C, Na, Mg, Ca, Cr, Cu, Zn and Rb in G. elata Bl. f. glauca; it improved the composition, diversity and metabolic functions of soil microbial communities around G. elata Bl. f. glauca at phylum, class and genus levels; it markedly increased the relative abundance of bacteria such as Chthoniobacter and Armillaria in the dominant populations, and enhanced such functions as Cell motility, amino acid metabolism and Lipid metabolism; it dramatically decreased the relative abundance of Bryobacter and other fungi in the dominant populations, and reduced such functions as microbial energy metabolism, translation and carbohydrate metabolism. This is the main reason why excellent Armillaria strains promote the high quality and yield of G. elata Bl. f. glauca in Changbai Mountain.

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“…decreased. These changes in metabolic functions associated with plant growth [61] may also regulate the growth and development of G. elata Bl. f. glauca [62].…”

Section: Discussionmentioning

confidence: 99%

An exploration of mechanism of high quality and yield of Gastrodia elata Bl. f. glauca by the isolation, identification and evaluation of Armillaria

Gao

et al. 2022

BMC Plant Biol

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“…Approximately 83.33% of the MAGs obtained by Megahit, 86.95% by MetaSpades, and 90.47% by IDBA-UD contained both salt homeostasis and heavy metal tolerance capacity. Some of the earlier studies also reported the coexistence of these properties, improving the environmental fitness and the survivability chances of the microorganisms in highly saline habitats ( 48 ).…”

Section: Discussionmentioning

confidence: 91%

Metagenomic assembled genomes indicated the potential application of hypersaline microbiome for plant growth promotion and stress alleviation in salinized soils

Dindhoria,

Kumar,

Bhargava

et al. 2024

mSystems

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Climate change is causing unpredictable seasonal variations globally. Due to the continuously increasing earth’s surface temperature, the rate of water evaporation is enhanced, conceiving a problem of soil salinization, especially in arid and semi-arid regions. The accumulation of salt degrades soil quality, impairs plant growth, and reduces agricultural yields. Salt-tolerant, plant-growth-promoting microorganisms may offer a solution, enhancing crop productivity and soil fertility in salinized areas. In the current study, genome-resolved metagenomic analysis has been performed to investigate the salt-tolerating and plant growth-promoting potential of two hypersaline ecosystems, Sambhar Lake and Drang Mine. The samples were co-assembled independently by Megahit, MetaSpades, and IDBA-UD tools. A total of 67 metagenomic assembled genomes (MAGs) were reconstructed following the binning process, including 15 from Megahit, 26 from MetaSpades, and 26 from IDBA_UD assembly tools. As compared to other assemblers, the MAGs obtained by MetaSpades were of superior quality, with a completeness range of 12.95%–96.56% and a contamination range of 0%–8.65%. The medium and high-quality MAGs from MetaSpades, upon functional annotation, revealed properties such as salt tolerance (91.3%), heavy metal tolerance (95.6%), exopolysaccharide (95.6%), and antioxidant (60.86%) biosynthesis. Several plant growth-promoting attributes, including phosphate solubilization and indole-3-acetic acid (IAA) production, were consistently identified across all obtained MAGs. Conversely, characteristics such as iron acquisition and potassium solubilization were observed in a substantial majority, specifically 91.3%, of the MAGs. The present study indicates that hypersaline microflora can be used as bio-fertilizing agents for agricultural practices in salinized areas by alleviating prevalent stresses. IMPORTANCE The strategic implementation of metagenomic assembled genomes (MAGs) in exploring the properties and harnessing microorganisms from ecosystems like hypersaline niches has transformative potential in agriculture. This approach promises to redefine our comprehension of microbial diversity and its ecosystem roles. Recovery and decoding of MAGs unlock genetic resources, enabling the development of new solutions for agricultural challenges. Enhanced understanding of these microbial communities can lead to more efficient nutrient cycling, pest control, and soil health maintenance. Consequently, traditional agricultural practices can be improved, resulting in increased yields, reduced environmental impacts, and heightened sustainability. MAGs offer a promising avenue for sustainable agriculture, bridging the gap between cutting-edge genomics and practical field applications.

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“…Many of them are known from genomic studies, but most soil microorganisms have not yet been cultivated [1]. The composition of soil bacterial communities is strongly dependent on chemical factors, such as pH, salt content, usable substrates, and humidity [2][3][4]. In addition, noxious substances can suppress the growth of a large number of soil microbes; these substances include pesticides, plant fertilizers and other agrochemicals, and heavy metal ions [5][6][7].…”

Section: Introductionmentioning

confidence: 99%

Three Soil Bacterial Communities from an Archaeological Excavation Site of an Ancient Coal Mine near Bennstedt (Germany) Characterized by 16S r-RNA Sequencing

et al. 2022

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This metagenomics investigation of three closely adjacent sampling sites from an archaeological excavation of a pre-industrial coal mining exploration shaft provides detailed information on the composition of the local soil bacterial communities. The observed significant differences between the samples, reflected in the 16S r-RNA analyses, were consistent with the archaeologically observed situation distinguishing the coal seam, the rapidly deposited bright sediment inside an exploration shaft, and the topsoil sediment. In general, the soils were characterized by a dominance of Proteobacteria, Actinobacteria, Acidobacteria, and Archaea, whereas the coal seam was characterized by the highest proportion of Proteobacteria; the topsoil was characterized by very high proportions of Archaea—in particular, Nitrosotaleaceae—and Acidobacteria, mainly of Subgroup 2. Interestingly, the samples of the fast-deposited bright sediment showed a rank function of OTU abundances with disproportional values in the lower abundance range. This could be interpreted as a reflection of the rapid redeposition of soil material during the refilling of the exploration shaft in the composition of the soil bacterial community. This interpretation is supported by the observation of a comparatively high proportion of reads relating to bacteria known to be alkaliphilic in this soil material. In summary, these investigations confirm that metagenomic analyses of soil material from archaeological excavations can provide valuable information about the local soil bacterial communities and the historical human impacts on them.

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Co-occurrence and patterns of phosphate solubilizing, salt and metal tolerant and antibiotic-resistant bacteria in diverse soils

Cited by 4 publications

References 63 publications

An exploration of mechanism of high quality and yield of Gastrodia elata Bl. f. glauca by the isolation, identification and evaluation of Armillaria

An exploration of mechanism of high quality and yield of Gastrodia elata Bl. f. glauca by the isolation, identification and evaluation of Armillaria

Metagenomic assembled genomes indicated the potential application of hypersaline microbiome for plant growth promotion and stress alleviation in salinized soils

Three Soil Bacterial Communities from an Archaeological Excavation Site of an Ancient Coal Mine near Bennstedt (Germany) Characterized by 16S r-RNA Sequencing

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