Open access
Environmental Microbiology
Announcement
22 December 2023

Five draft genome assemblies from Bacillaceae isolated from a degraded wetland environment

ABSTRACT

We isolated five Bacillaceae from a degraded wetland environment and sequenced their genomes using Illumina NextSeq. Here, we report draft genome sequences of Bacillus velezensus-SC119, Priestia megaterium strain SC120, Bacillus zhangzhouensis strain SC123, Bacillus pumilis strain SC124, and Bacillus idriensis strain SC127. The genomes range between 3,657,353 and 5,772,725 bp with % GC between 37.62% and 46.38%.

ANNOUNCEMENT

Wetland environments play critical roles in the terrestrial carbon and water cycles, and microbial communities are key players in ecosystem function (1). Endospore-forming bacteria in the Bacillaceae family are metabolically and genomically diverse soil heterotrophs that influence plant health and nutrient cycling, and produce diverse natural products that influence bacterial and non-bacterial species in their environment (2).
We collected two 30-mL soil samples on 19 January 2023 from 42°43′7″N, 73°45′01.4″W. One was highly hydrated and within a patch of invasive common reeds (Phragmites sp.), and the other was near the base of an Eastern cottonwood tree (Populus deltoides). Bacillus pumilis strain SC124 was isolated from the soil from near the tree, while Bacillus velezensis strain SC119, Priestia megaterium strain SC120, Bacillus zhangzhouensis strain SC123, and Bacillus idriensis strain SC127 were isolated from the marshy soil (Table 1). Unique bacterial strains were isolated as described previously by boiling 100- to 400-μL soil subsamples for 10 minutes in 1-mL water, and suspended cells were spread by swab on Tryptic soy agar (TSA) + 5% sheep blood and incubated for 24 hours at 37°C (3). All strains grew and remained viable at temperatures between 22°C and 37°C. After colony purification and basic characterization, genomic DNA was isolated and sequenced as described previously (3) using a Promega DNA wizard kit from cultures grown for approximately 3 hours at 37°C in tryptic soy broth, and libraries were prepared and sequenced as 151-bp paired-end reads using an Illumina NextSeq 2000 instrument by SeqCenter, which prepared libraries using the Illumina DNA Prep kit and IDT 10-bp UDI indices (Pittsburgh, PA). Demultiplexing, quality control, and adapter trimming were performed with bcl-convert v.3.9.3 (Illumina). Sequence reads were imported into the KBase environment for analysis, with each genome analysis occurring in parallel in its own narrative (46). Read quality was checked with FastQC v.0.11.09; reads were trimmed with Trimmomatic v.0.36, assembled de novo using SPAdes v.3.15.3, and annotated using RASTtk v.1.073 and Prokka v.1.14.5; probable species identities were determined using both GTDB-Tk v.1.7.0 and TYGS, which were in agreement in all cases; and metabolic predictions were made using DRAM v.0.1.2 (720). Default parameters were used when running all programs.
TABLE 1
TABLE 1 Summary of genome statistics and access
StrainSC119SC120SC123SC124SC127
SpeciesBacillus velezensisPriestia megateriumBacillus zhangzhouensisBacillus pumilusBacillus idriensis
Number of reads7,568,0648,044,8386,292,5166,681,4926,671,362
Number of contigs2327222115
Total length (bp)3,947,2385,772,7253,657,3533,837,3274,483,053
N50578,9874,216,129339,228824,075675,715
% GC46.3837.6241.4341.3341.01
Predicted genes (Prokka via Kbase)3,8756,0103,7133,9814,498
Predicted genes (GenBank)3,9086,0133,7223,9634,492
KBase narrativehttps://kbase.us/n/139243/37/https://kbase.us/n/139247/20/https://kbase.us/n/139245/53/https://kbase.us/n/139244/41/https://kbase.us/n/139250/65/
SRA accessionSAMN37195270SAMN37195271SAMN37195272SAMN37195273SAMN37195274
GenBank accessionJAVIKC000000000JAVIKB000000000JAVIKA000000000JAVIJZ000000000JAVIJY000000000
Surprisingly, despite strain isolation from boiled soil samples and genes necessary for endospore formation, isolates showed dramatic differences in sporulation following 24-hour 37°C incubation on Difco Sporulation Medium (DSM), 0.8% Difco nutrient broth, 0.1% KCl, 0.0012% MgSO4, 1% agar, and pH 7.6) plates (21); B. velezensis strain SC119 achieved high sporulation efficiency, measured by outgrowth of boiled and unboiled serial dilutions, while B. idriensis strain SC127 did not detectably sporulate. These strains and their genomes provide additional insights into the genetic basis for phenotypic variation between closely related species (Table 1).

ACKNOWLEDGMENTS

The authors gratefully acknowledge support from the National Institutes of Health (R15GM148928-01 to A.L.M.).

REFERENCES

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Information & Contributors

Information

Published In

cover image Microbiology Resource Announcements
Microbiology Resource Announcements
Volume 13Number 215 February 2024
eLocator: e00845-23
Editor: Vanja Klepac-Ceraj, Wellesley College, Wellesley, Massachusetts, USA
PubMed: 38132715

History

Received: 7 September 2023
Accepted: 28 November 2023
Published online: 22 December 2023

Keywords

  1. genomes
  2. Bacillaceae
  3. wetlands

Data Availability

Genome sequences and raw sequencing reads were deposited under BioProject accession number PRJNA862062, Sequence Read Archive accession numbers SAMN37195270, SAMN37195271, SAMN37195272, SAMN37195273, and SAMN37195274 and GenBank genome accession numbers JAVIKC000000000, JAVIKB000000000, JAVIKA000000000, JAVIJZ000000000, and JAVIJY000000000. Analyses are available through KBase narratives https://kbase.us/n/139243/37/, https://kbase.us/n/139247/20/, https://kbase.us/n/139245/53/, https://kbase.us/n/139244/41/, and https://kbase.us/n/139250/65/, and the overview is narrative at https://kbase.us/n/152701/18/.

Contributors

Authors

Department of Biology, Siena College, Loudonville, New York, USA
Author Contributions: Conceptualization, Data curation, Funding acquisition, Methodology, Project administration, Supervision, Writing – original draft, and Writing – review and editing.
Prince Ackaah Asante
Department of Biology, Siena College, Loudonville, New York, USA
Author Contributions: Formal analysis, Investigation, and Validation.
Thomas Anderson
Department of Biology, Siena College, Loudonville, New York, USA
Author Contributions: Formal analysis, Investigation, and Validation.
Kellyanne Cahill
Department of Biology, Siena College, Loudonville, New York, USA
Author Contributions: Formal analysis, Investigation, and Validation.
Delana Cochrane
Department of Biology, Siena College, Loudonville, New York, USA
Author Contributions: Formal analysis, Investigation, and Validation.
Keira Cohen
Department of Biology, Siena College, Loudonville, New York, USA
Author Contributions: Formal analysis, Investigation, and Validation.
Jaylene German
Department of Biology, Siena College, Loudonville, New York, USA
Author Contributions: Formal analysis, Investigation, and Validation.
Christian M. Hrubes
Department of Biology, Siena College, Loudonville, New York, USA
Author Contributions: Formal analysis, Investigation, and Validation.
Isabella LaCroix
Department of Biology, Siena College, Loudonville, New York, USA
Author Contributions: Formal analysis, Investigation, and Validation.
Killian McNamee
Department of Biology, Siena College, Loudonville, New York, USA
Author Contributions: Formal analysis, Investigation, and Validation.
Anna Mossakowski
Department of Biology, Siena College, Loudonville, New York, USA
Author Contributions: Formal analysis, Investigation, and Validation.
Aidan M. Nichter
Department of Biology, Siena College, Loudonville, New York, USA
Author Contributions: Formal analysis, Investigation, and Validation.
Jessica L. Pepe
Department of Biology, Siena College, Loudonville, New York, USA
Author Contributions: Formal analysis, Investigation, and Validation.
Andrew T. Schofield
Department of Biology, Siena College, Loudonville, New York, USA
Author Contributions: Formal analysis, Investigation, and Validation.

Editor

Vanja Klepac-Ceraj
Editor
Wellesley College, Wellesley, Massachusetts, USA

Notes

The authors declare no conflict of interest.

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