Complete genome sequence and analysis of Alcaligenes faecalis strain Mc250, a new potential plant bioinoculant

Abstract

Here we present and analyze the complete genome of Alcaligenes faecalis strain Mc250 (Mc250), a bacterium isolated from the roots of Mimosa calodendron, an endemic plant growing in ferruginous rupestrian grasslands in Minas Gerais State, Brazil. The genome has 4,159,911 bp and 3,719 predicted protein-coding genes, in a single chromosome. Comparison of the Mc250 genome with 36 other Alcaligenes faecalis genomes revealed that there is considerable gene content variation among these strains, with the core genome representing only 39% of the protein-coding gene repertoire of Mc250. Mc250 encodes a complete denitrification pathway, a network of pathways associated with phenolic compounds degradation, and genes associated with HCN and siderophores synthesis; we also found a repertoire of genes associated with metal internalization and metabolism, sulfate/sulfonate and cysteine metabolism, oxidative stress and DNA repair. These findings reveal the genomic basis for the adaptation of this bacterium to the harsh environmental conditions from where it was isolated. Gene clusters associated with ectoine, terpene, resorcinol, and emulsan biosynthesis that can confer some competitive advantage were also found. Experimental results showed that Mc250 was able to reduce (~60%) the virulence phenotype of the plant pathogen Xanthomonas citri subsp. citri when co-inoculated in Citrus sinensis, and was able to eradicate 98% of juveniles and stabilize the hatching rate of eggs to 4% in two species of agricultural nematodes. These results reveal biotechnological potential for the Mc250 strain and warrant its further investigation as a biocontrol and plant growth-promoting bacterium.

Streptomyces sp. AC04842: Genomic Insights and Functional Expression of Its Latex Clearing Protein Genes (lcp1 and lcp2) When Cultivated With Natural and Vulcanized Rubber as the Sole Carbon Source

“…AC04842 draft genome contained 30 genes related to the chloroaromatic degradation pathway genes ( catA , catF , catI , catJ , and PCAH ) and p-hydroxybenzoate degradation genes ( pobA , HT ) ( Göbel et al, 2002 ). Some soil microbes or plant pathogens are known to have this ability, as plants contain significant levels of natural phenolic compounds essential for reproduction and growth and a defense mechanism against pathogens ( Felestrino et al, 2020 ).…”

Alcaligenes ammonioxydans HO-1 antagonizes Bacillus velezensis via hydroxylamine-triggered population response

“…The HA-negative mutant strain, A. ammonioxydans 2-29, showed no antagonism and reconstituting this mutant with the intact dnfR gene restored the ability to inhibit the growth of V4 cells, indicating that HA was the key molecule in this process. Since other Alcaligenes species are potential candidates in the production of antibacterial substances (Felestrino et al, 2020;Fernandes et al, 2021), it is tempting to speculate that other antagonistic secondary metabolites existed. The degradation of HA beyond ∼24 h of culture, while some antagonism could still be observed beyond this time point suggested that this may be the case especially during the late growth stage of HO-1.…”

“…Many B. velezensis strains gained practical application in promoting plant growth and antagonizing pathogens (Fan et al, 2018). Alcaligenes species are another group of potential PGPR (Yokoyama et al, 2013;Ray et al, 2016;Gong et al, 2019;Lahlali et al, 2020), with distinct biotechnological potential in the pharmaceutical industry and bioremediation of contaminated environments (Ray et al, 2015;Dixit et al, 2020;Felestrino et al, 2020;Onajobi et al, 2020;Zouari et al, 2020;Fernandes et al, 2021).…”

Complete Genome Sequence of Lacticaseibacillus paracasei Strain VHProbi O44, Isolated from Feces from a Healthy Baby

“…For PacBio sequencing, DNA was centrifuged in g-TUBES (Covaris, Woburn, MA) for shearing into fragments. Then, ~10-kb fragments were purified, end repaired, and ligated with SMRTbell sequencing adapters following the manufacturer’s recommendations (PacBio, Menlo Park, CA) ( 4 , 5 ). Next, an insert library was prepared using the SMRTbell Express template preparation kit v2.0 and sequenced in one single-molecule real-time (SMRT) Cell using standard methods.…”