The complete genome sequence of Hafnia alvei A23BA; a potential antibiotic-producing rhizobacterium

Abstract

Objectives The urgent need for novel antibiotics cannot be overemphasized. Hafnia alvei A23BA was isolated from plant rhizosphere as part of an effort to recover novel antibiotic-producing bacterial strains from soil samples. The genome of the isolate was sequenced to facilitate mining for potential antibiotic-encoding biosynthetic gene clusters and to gain insights into how these gene clusters could be activated. Data description Here, we report the complete genome sequence of H. alvei A23BA obtained from the hybrid assembly of Illumina HiSeq and GridION reads. The genome, consisting of a circular chromosome and a circular plasmid, is 4.77 Mb in size with a GC content of 48.77%. The assembly is 99.5% complete with genomic features including 4,217 CDSs, 125 RNAs, and 30 pseudogenes. Thiopeptide, beta-lactone, siderophore, and homoserine lactone biosynthetic gene clusters were also identified. Other gene clusters of interest include those associated with bioremediation, biocontrol, and plant growth promotion- all of which are reported for H. alvei for the first time. This dataset serves to expedite the exploration of the biosynthetic and metabolic potentials of the species. Furthermore, being the first published genome sequence of a soil isolate, this dataset enriches the comparative genomics study of H. alvei strains.

The Molecular Weaponry Produced by the Bacterium Hafnia alvei in Foods

“…Genomes from the sequenced environmental and pathogenic H. alvei strains contain genes for quorum sensing, mobility and biofilm formation [ 4 , 5 , 30 ]. The production of several enzymatic activities in H. alvei is under the control of quorum-sensing (Q-S) mechanisms [ 31 ], which also occur in other bacteria [ 32 ].…”

“…Additionally, in the work of Awolope and coworkers [ 4 ], interesting siderophores were identified in the genome of an H. alveus strain isolated from the rhizosphere of a garden plant, which could be used as Trojan horses to facilitate the action of some antibiotics against resistant bacteria [ 91 , 92 , 93 ]. Interestingly, some H. alvei strains isolated from the gut microbiota of rainbow trout Oncorhynchus mykiss showed antagonistic activity to both Gram-negative pathogens ( Aeromonas hydrophila , Salmonella enterica , and Escherichia coli ) and Gram-positive pathogens ( Listeria monocytogenes ).…”

“…Hafnia alvei is a Gram-negative bacillus that belongs to a family recently proposed as Hafniaceae , within the order Enterobacterales [ 1 , 2 ]. H. alvei occurs in many natural environments such as rivers and fish farms, as well as in polluted waters and sewage [ 3 , 4 ]. This bacterium is also common in the digestive tract of many animal [ 5 ].…”

Genome Insights into the Plant Growth-Promoting bacterium Saccharibacillus brassicae ATSA2T

“…After 30 min of incubation at room temperature, the concentration of IAA was quanti ed colorimetrically by measuring the optical density at 530 nm (Asghar et al, 2002) using a spectrophotometer (Optizen POP). Bacterial IAA production was estimated against a standard curve (Ahmad et al, 2005) using commercial IAA (Sigma-Aldrich) at different concentrations (0,10,20,30,40,50, and 60 µg/mL). This experiment was performed in independent triplicates.…”

The Gram-Negative Bacilli Isolated from Caves—Sphingomonas paucimobilis and Hafnia alvei and a Review of Their Involvement in Human Infections

“…The need for the discovery of new antibiotics has galvanized researchers to focus on microorganisms that resist antibiotics [ 6 ]. A recent report of the complete genome of the Hafnia alvei A23BA isolated from plant rhizosphere demonstrates that environmental strains could advance the discovery of antibiotic-producing environmental strains [ 7 ].…”