Metagenomic Insights and Genomic Analysis of Phosphogypsum and Its Associated Plant Endophytic Microbiomes Reveals Valuable Actors for Waste Bioremediation

Abstract

The phosphogypsum (PG) endogenous bacterial community and endophytic bacterial communities of four plants growing in phosphogypsum-contaminated sites, Suaeda fruticosa (SF), Suaeda mollis (SM), Mesembryanthmum nodiflorum (MN) and Arthrocnemum indicum (AI) were investigated by amplicon sequencing. Results highlight a more diverse community of phosphogypsum than plants associated endophytic communities. Additionally, the bacterial culturable communities of phosphogypsum and associated plant endophytes were isolated and their plant-growth promotion capabilities, bioremediation potential and stress tolerance studied. Most of plant endophytes were endowed with plant growth-promoting (PGP) activities and phosphogypsum communities and associated plants endophytes proved highly resistant to salt, metal and antibiotic stress. They also proved very active in bioremediation of phosphogypsum and other organic and inorganic environmental pollutants. Genome sequencing of five members of the phosphogypsum endogenous community showed that they belong to the recently described species Bacillus albus (BA). Genome mining of BA allowed the description of pollutant degradation and stress tolerance mechanisms. Prevalence of this tool box in the core, accessory and unique genome allowed to conclude that accessory and unique genomes are critical for the dynamics of strain acquisition of bioremediation abilities. Additionally, secondary metabolites (SM) active in bioremediation such as petrobactin have been characterized. Taken together, our results reveal hidden untapped valuable bacterial actors for waste remediation.

Mitigation of NaCl Stress in Wheat by Rhizosphere Engineering Using Salt Habitat Adapted PGPR Halotolerant Bacteria

“…Development of the halo zone surrounding the colony was considered as a positive indication of the considered protease or chitinase activity. For cellulase and amylase development of clear halos around the colonies after addition of 1% iodine solution, respectively, was considered as a positive indication of cellulase or amylase activity [3,11,12].…”

“…Bacterial cultures grown in Tryptic Soy Broth were spotted or streaked in the same plate with a distance of 4 cm from the test fungus and incubated at 28 ± 2 • C for 5 to 6 days. The diameter of the inhibition zone against test fungi was measured and the percentage of inhibition relative to the control (without bacteria) was evaluated [11].…”

“…Amplification and sequencing were performed as previously. Phylogenetic analyses were performed according to Mefteh et al [11].…”

“…Rhizosphere engineering through the use of plant growth-promoting rhizobacteria is a valuable strategy that allows crop tolerance to salinity and subsequent promotion of plant productivity and yield under saline condition [3,4,9]. Plant growth-promoting bacteria (PGPB) stimulate plant growth [10] with two different lifestyles: free-living soil bacteria associated with the root surface of many different plant species referred to as plant growth-promoting rhizobacteria (PGPR) [4,11,12] and those that live inside host plant tissues [3,4,13]. Stimulation of plant growth by PGPB would be provided either through indirect or direct mechanisms [10].…”

Draft Genome Sequence of Bacillus albus Strain IB84, Isolated from Mexican Soil

“…The average nucleotide identity (ANI) of the whole genome determined during the GenBank submission process ( 9 ) showed 97.907% identity with the type genome of Bacillus albus ; this and the sequence identities of rRNA 16S, gyrB , groEL , and xre genes suggest that this isolate belongs to the Bacillus albus species ( 10 ). This species has been described recently as having an important salt tolerance and the ability to degrade poultry waste processing industrial (PWPI) effluent ( 10 , 11 ). The IB84 whole-genome analysis revealed sequences associated with assimilation and detoxification of nitrogen and arsenate compounds, as well as salt tolerance, antibiotic resistance, and oxidative stress genes.…”