Draft genome sequence data of heavy metal-resistant Morganella morganii WA01/MUTU, a silver nanoparticle (AgNP) synthesising bacterium

Morganella morganii WA01/MUTU is a heavy metal tolerant strain capable of producing silver nanoparticles (AgNPs) from AgNO3. Here we present the draft genome sequence of M. morganii WA01/MUTU isolated from a water sample collected in Nakhon Pathom province, Thailand. The draft genome was sequenced on the Illumina NextSeq 550 sequencer. The genome consisted of 34 contigs with a total size of 3,991,804 bp, an N50 value of 364,423 bp and a GC content of 50.93%. The digital DNA-DNA hybridisation (dDDH) between WA01/MUTU and Morganella morganii (NBRC 3848) was 83.9%, identifying the strain as Morganella morganii. The data presented here can be used in comparative genomics to identify gene clusters involved in AgNP biosynthesis and secondary metabolite production. The draft genome sequence data was deposited at NCBI under Bioproject accession number PRJNA493966.

a b s t r a c t Morganella morganii WA01/MUTU is a heavy metal tolerant strain capable of producing silver nanoparticles (AgNPs) from AgNO 3 .Here we present the draft genome sequence of M. morganii WA01/MUTU isolated from a water sample collected in Nakhon Pathom province, Thailand.The draft genome was sequenced on the Illumina NextSeq 550 sequencer.The genome consisted of 34 contigs with a total size of 3,991,804 bp, an N50 value of 364,423 bp and a GC content of 50.93%.The digital DNA-DNA hybridisation (dDDH) between WA01/MUTU and Morganella morganii (NBRC 3848) was 83.9%, identifying the strain as Morganella morganii .The data presented here can be used in comparative genomics to identify gene clusters involved in AgNP biosynthesis and secondary metabolite production.The draft genome sequence data was deposited at NCBI under Bioproject accession number PRJNA493966.
© 2023 The Author(s

Value of the Data
• The draft genome sequence of M. morganii WA01/MUTU may be useful for comparative genomic studies with other Morganella species.• Elucidation of the genome sequence of M. morganii WA01/MUTU may help to characterise the genes involved in AgNP biosynthesis.• Elucidation of the genome sequence of M. morganii WA01/MUTU may help in the discovery of novel gene clusters encoding bioactive compounds.

Data Description
Morganella morganii is Gram-negative, facultatively anaerobic [1] and motile with peritrichous flagella [2] .Cells of M. morganii are short, straight rods and do not produce pigment or capsules [3] .Growth of M. morganii occurs between 4 °C and 45 °C on nutrient agar and colonies are smooth, transparent with an entire edge [3] .Some species of the genus Morganella are capable of synthesising metal nanoparticles in the aqueous phase [ 4 , 5 ].Furthermore, there is a strong correlation between the ability of different bacterial strains to synthesise metal nanoparticles and the heavy metal resistance mechanism [6] .These biosynthesised NPs have potential use in several medical applications, including antibacterial and drug delivery [ 7 , 8 ].The minimum inhibitory concentration (MIC) of strain WA01/MUTU against CdCl 2 was 3.2 mM.The silver nanoparticles (AgNPs) produced by WA01/MUTU have a spherical shape with a diameter of approximately 15-20 nm.Therefore, we analysed the whole genome sequence of M. morganii WA01/MUTU to obtain insight into possible genes that involved in NP synthesis and to extend our knowledge of secondary metabolite production.
The draft genome sequence of strain WA01/MUTU (accession number JAVJNK0 0 0 0 0 0 0 0 0) is available at the National Center for Biotechnology Information (NCBI) under the BioProject number PRJNA493966 and the BioSample number SAMN37308709 ( Table 1 ).Raw reads were deposited in the NCBI Sequence Read Archive (SRA) database (SRR25935570) ( Table 1 ).Here we present data on the draft genome sequence of M. morganii WA01/MUTU ( Fig. 1 ), including its potential secondary metabolite biosynthesis.The draft genome of strain WA01/MUTU consists of 34 contigs with a total length of 3,991,804 base pairs.The N50 was 364,423 bp and the GC content was 50.93% ( Table 1 ).The CheckM reported 100% completeness with an estimated contamination of less than 1% for the WA01/MUTU draft genome sequence.The bacterial strain WA01/MUTU was affiliated to Morganella morganii (NBRC 3848) with a digital DNA-DNA hybridisation (dDDH) value of 83.9% [9] .The phylogenomic tree of the strain WA01/MUTU and closely related strains is shown in Fig. 2 .A cluster of nitrate reductase genes, which play an important role in AgNP biosynthesis [10] , was observed in the draft genome sequence of strain WA01/MUTU.The genome mining study revealed three potential secondary metabolic gene clusters, including betalactone, thiopeptide and arylpolyene, were observed within three regions with varying percentages of similarity.The highest cluster similarity was 84% for arylpolyene (APE), corresponding to bacterial pigment production [11] .We believe that the draft genome sequence will facilitate the characterisation of genes involved in the biosynthesis of AgNPs and secondary metabolites in M. morganii WA01/MUTU.

Bacterial isolation
Strain WA01/MUTU was isolated from a water sample collected in Nakhon Pathom, Thailand (N 13º 43 55.518 , E 100º 11 15.373 ).For screening experiment, the water sample was spread on Luria-Betani (LB) agar containing 0.4 mM CdCl 2 and incubated at 37 °C for 18 h.The 0.4 mM cadmium (Cd) resistant strains were isolated by cross-streaking on LB agar plates and incubated at 37 °C for 18 h.For the heavy metal tolerance test, the resistant strains were tested against 2-fold concentrations of CdCl 2 (ranging from 0.1-3.2mM) on LB agar.A single colony of strain WA01/MUTU at the minimum inhibitory concentration (MIC) of CdCl 2 was grown in LB broth overnight at 37 °C with shaking at 250 rpm.The ability of strain WA01/MUTU to synthesise extracellular silver nanoparticles (AgNPs) was observed by treatment with 5 mM AgNO 3 and incubation for 20 h at 37 °C with shaking at 180 rpm.The characteristic of AgNPs produced by strain WA01/MUTU was determined by ultraviolet-visible (UV-Vis) spectroscopy (Shimadzu, Japan), and surface plasmon resonance (SRP) at 350-530 nm was used to determine the characteristic peak of AgNPs.In addition, the morphology and size of AgNPs were determined by transmission electron microscopy (JOEL, Japan).

Genomic DNA (gDNA) preparation
High quality gDNA from the strain WA01/MUTU was obtained from overnight cultures using the Quick-DNA HMW MagBead Kit (Zymo, USA).The concentration of gDNA was determined using NanoDrop spectrophotometry (Thermo Scientific, USA).

Taxonomic identification of the strain
Genome quality assessment was performed using CheckM v1.1.2with default parameters [16] .Digital DNA-DNA hybridisation (dDDH) and a phylogenomic tree based on the whole genome sequence of WA01/MUTU and closely related strains were performed using the Type (Strain) Genome Server (TYGS) [9] .

Genome annotation and sequence analysis
Genome annotation was performed using the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) with default parameters [17] , and genome mining for potential secondary metabolites was performed using antiSMASH v7.0.1 with default parameters [18] .

Limitations
The use of next-generation sequencing techniques generates vast quantities of data.However, de novo genome assemblies resulting from this data often display significant deficiencies in completeness.The current assemblies possess shortcomings that render them vulnerable to annotation errors, particularly regarding the imprecise estimation of genes that could possibly exist in the draft genome of WA01/MUTU.

Ethics Statement
This work does not involve human subjects, animal experiments, or any data collected from social media platforms.

Fig. 1 .Fig. 2 .
Fig. 1.Genome map of M. morganii WA01/MUTU.The map consists of blue arrows indicating CDSs, grey arrows indicating contigs, green peaks representing GC skew + , purple peaks representing GC skew-, and black peaks representing GC content.(For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.) ). Published by Elsevier Inc.This is an open access article under the CC BY license ( http://creativecommons.org/licenses/by/4.0/ )

Table 1
Genomic features and assembly statistics for M. morganii WA01/MUTU.