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

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Abstract

Soil is a treasure chest for beneficial bacteria with applications in diverse fields, which include agriculture, rhizoremediation, and medicine. Metagenomic analysis of four soil samples identified Proteobacteria as the dominant phylum (32–52%) followed by the phylum Acidobacteria (11–21% in three out of four soils). Bacteria that were prevalent at the highest level belong to the genus Kaistobacter (8–19%). PICRUSt analysis predicted KEGG functional pathways associated with the metagenomes of the four soils. The identified pathways could be attributed to metal tolerance, antibiotic resistance and plant growth promotion. The prevalence of phosphate solubilizing bacteria (PSB) was investigated in four soil samples, ranging from 26 to 59% of the total culturable bacteria. The abundance of salt-tolerant and metal-tolerant bacteria showed considerable variation ranging from 1 to 62% and 4–69%, respectively. In comparison, the soil with the maximum prevalence of temperature-tolerant and antibiotic-resistant bacteria was close 30%. In this study, the common pattern observed was that PSB were the most abundant in all types of soils compared to other traits. Conversely, most of the isolates, which are salt-tolerant, copper-tolerant, and ampicillin-resistant, showed phosphate solubilization activity. The sequencing of the partial 16S-rRNA gene revealed that PSB belonged to Bacillus genera.

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Abbreviations

PSB:

Phosphate solubilizing bacteria

STB:

Salt-tolerant bacteria

MTB:

Metal-tolerant bacteria

ARB:

Antibiotic-resistant bacteria

PGPB:

Plant growth-promoting bacteria

ICP-MS:

Inductively coupled plasma mass spectrometry

NGS:

Next-generation sequencing

MSA:

Multiple sequence alignment

BIC:

Bayesian information criterion

ML:

Maximum-likelihood

MRGs:

Metal resistance genes

ARGs:

Antibiotic-resistance genes

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Authors and Affiliations

  1. Department of Biochemistry, Central University of Punjab, Bathinda, Punjab, India

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

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  1. Parikshita Rathore
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Correspondence to Wusirika Ramakrishna.

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Supplementary Information

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13205_2021_2904_MOESM1_ESM.pptx

Supplementary file1 (PPTX 829 KB) Fig. S1. Map showing areas in Punjab and Mizoram from where soil samples were collected. White colored dot in Punjab map is the site from where Ramsara soil was collected, blue colored dot is the site from where rice and cotton field samples were collected and white dot in Mizoram map is the site from where Aizawl sample was collected. Maps were downloaded from https://gramener.com/indiamap/

Supplementary file2 (PPTX 62 KB) Fig. S2. Experimental design for screening of soil samples.

13205_2021_2904_MOESM3_ESM.pptx

Supplementary file3 (PPTX 84 KB) Fig. S3. Rarefaction plot for four samples of V3-V4 region at a depth of 2,00,000. The number of sequences per sample are shown on x-axis versus nember of observed species on y-axis. The samples have been colored by their respective names.

13205_2021_2904_MOESM4_ESM.pptx

Supplementary file4 (PPTX 538 KB) Fig. S4. Maximum likelihood (ML) phylogram based on 16S rRNA gene sequences using the TN92+G model of molecular evolution in MEGA X. Numbers near nodes represent the ML bootstrap proportion. Bootstrapping was performed with 1000 replicates. The sequences of soil bacteria that are part of the current study are in bold. This phylogram is rooted with Pseudomonas aeruginosa (LN874213) sequence as an outgroup. Scale bar is given on the bottom.

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Rathore, P., Joy, S.S., Yadav, R. et al. Co-occurrence and patterns of phosphate solubilizing, salt and metal tolerant and antibiotic-resistant bacteria in diverse soils. 3 Biotech 11, 356 (2021). https://doi.org/10.1007/s13205-021-02904-7

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