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. 2020 Sep 17;9(38):e00222-20. doi: 10.1128/MRA.00222-20

Complete Genome Sequences of 47 Environmental Isolates of Escherichia coli

Georgia Breckell a,✉, Olin K Silander a
Editor: David Raskob
PMCID: PMC7498420  PMID: 32943554

Escherichia coli is commonly considered a host-associated bacterium. However, there is evidence that some strains occupy environmental (non-host-associated) niches. Here, we report the complete genomes of 47 Escherichia coli environmental isolates. These will be useful for understanding the dynamics of plasmids, phages, and other repetitive genetic elements.

ABSTRACT

Escherichia coli is commonly considered a host-associated bacterium. However, there is evidence that some strains occupy environmental (non-host-associated) niches. Here, we report the complete genomes of 47 Escherichia coli environmental isolates. These will be useful for understanding the dynamics of plasmids, phages, and other repetitive genetic elements.

ANNOUNCEMENT

Escherichia coli has historically been considered a host-associated bacterium, although recent evidence suggests that many strains may persist and grow in the environment, and in some cases this may be the primary niche (1–4). E. coli is also well known for its prolific horizontal gene transfer (3, 5). To understand the rates of gene transfer, especially of mobile genetic elements (which are often repetitive in nature), complete genomes are required. To achieve this, we carried out whole-genome sequencing and assembly for 47 environmental strains of E. coli isolated from the shore of the St. Louis River in Minnesota, near Lake Superior (6).

We grew all strains in LB medium and isolated genomic DNA using either the Promega Wizard kit or phenol-chloroform extraction (7). All strains were sequenced using both the Oxford Nanopore Technologies (ONT) and Illumina sequencing platforms. Illumina data were obtained from MicrobesNG with in-house quality control (adapter trimming with Trimmomatic v0.30, with a sliding window quality score cutoff value of Q15) using DNA extracted with the Promega Wizard kit. We prepared ONT sequencing libraries using the rapid barcoding kit (SQK-RBK004) and ran all libraries on R9.4 flow cells, multiplexing between 6 and 12 strains on each flow cell. We performed base calling using Guppy v2.3.7. We obtained at least 250 Mbp of sequence data for all strains except one (Table 1), with a median of 1,002 Mbp per strain (interquartile range [IQR], 670 Mbp to 1,296 Mbp). For all strains with more than 500 Mbp of sequence data, we used Filtlong v0.2.0 (https://github.com/rrwick/Filtlong) to retain only 500 Mbp in total, prioritizing read quality over length with the following parameters: min length set to 1,000, mean q weight set to 10, and split set to 500. The filtered read sets had a median read N50 value of 17.4 kbp (IQR, 13.4 kbp to 20.5 kbp). We also obtained at least 30-fold coverage of 2 × 250-bp paired-end Illumina reads for each genome.

TABLE 1.

Genome statistics for all 47 assemblies

Strain IDa Sample date (yr-mo-day) Location No. of Illumina reads ONT extraction methodb Total ONT sequence size (bp) No. of ONT reads ONT read N50 (bp) Filtered ONT read N50(bp)c Chromosome length (bp)d Circular chromosomee Genome length (bp)f Total no. of contigs rRNA orientationg Read accession no. Assembly accession no.
SC468 2005-8-15 Upshore 1,288,488 Phenol-CHCl3 1,402,515,335 34,337 7,164 14,815 4,426,017 Yes 4,426,017 1 Standard SAMEA6595239 GCA_902825195
SC457 2005-8-15 Upshore 603,943 Phenol-CHCl3 465,520,117 51,693 9,209 10,280 4,555,909 Yes 4,555,909 1 Standard SAMEA6595235 GCA_902810185
SC455 2005-8-15 Upshore 819,314 Phenol-CHCl3 1,033,029,654 30,634 10,560 17,536 4,655,420 Yes 4,655,420 1 Standard SAMEA6595233 GCA_902810345
SC434 2005-8-15 Waterline 618,526 Phenol-CHCl3 849,800,865 33,880 10,113 16,056 4,658,197 Yes 4,658,197 1 Standard SAMEA6595225 GCA_902810315
SC477 2005-9-19 Surface water 1,045,031 Phenol-CHCl3 843,013,946 44,613 7,856 12,549 4,658,510 Yes 4,658,510 1 Standard SAMEA6595243 GCA_902810395
SC316 2005-6-15 Surface water 3,409,700 Promega 43,287,859 39,445 11,807 13,365 4,663,327 Yes 4,681,204 3 Standard SAMEA6595204 GCA_902809975
SC467 2005-8-15 Upshore 922,562 Phenol-CHCl3 1,003,216,478 38,336 8,521 13,963 4,715,938 Yes 4,715,938 1 Standard SAMEA6595238 GCA_902825205
SC423 2005-8-15 Sediment 849,233 Phenol-CHCl3 274,260,727 18,522 16,188 18,066 4,716,885 Yes 4,716,885 1 Standard SAMEA6595220 GCA_902810325
SC465 2005-8-15 Upshore 1,577,380 Promega and phenol-CHCl3 1,386,503,691 35,047 9,489 15,195 4,722,586 Yes 4,785,019 2 Standard SAMEA6595237 GCA_902810145
SC452 2005-8-15 Upshore 417,390 Phenol-CHCl3 2,207,184,721 16,959 11,909 30,889 4,723,951 Yes 4,755,166 2 Standard SAMEA6595230 GCA_902810195
SC431 2005-8-15 Waterline 722,122 Phenol-CHCl3 1,774,332,186 25,144 3,326 21,138 4,727,732 Yes 4,866,254 2 Standard SAMEA6595223 GCA_902810235
SC475 2005-9-19 Surface water 413,920 Phenol-CHCl3 907,422,842 36,085 8,263 14,996 4,729,401 Yes 4,729,401 1 Standard SAMEA6595241 GCA_902810385
SC492 2005-9-19 Surface water 544,889 Phenol-CHCl3 718,894,150 30,095 13,767 18,501 4,736,913 Yes 4,736,913 1 Standard SAMEA6595248 GCA_902810375
SC480 2005-9-19 Surface water 614,748 Phenol-CHCl3 1,009,767,146 25,686 12,892 20,491 4,741,504 Yes 4,741,504 1 Standard SAMEA6595245 GCA_902810405
SC476 2005-9-19 Surface water 661,043 Promega and phenol-CHCl3 1,467,536,905 33,435 6,509 15,758 4,747,946 Yes 4,747,946 1 Standard SAMEA6595242 GCA_902810415
SC479 2005-9-19 Surface water 483,518 Phenol-CHCl3 468,589,667 41,638 11,800 13,367 4,762,128 Yes 4,913,012 3 Standard SAMEA6595244 GCA_902810125
SC392 2005-8-24 Upshore 870,803 Promega 366,289,283 44,990 8,646 9,714 4,770,015 Yes 4,783,281 2 Standard SAMEA6595208 GCA_902810015
SC312 2005-6-15 Surface water 3,582,617 Promega 678,059,117 32,708 13,222 17,765 4,775,485 Yes 4,878,778 3 Standard SAMEA6595203 GCA_902810065
SC386 2005-8-18 Upshore 1,917,879 Promega 989,915,389 4,259 7,170 12,507 4,778,381 Yes 5,088,094 5 Standard SAMEA6595207 GCA_902810055
SC456 2005-8-15 Upshore 350,577 Phenol-CHCl3 120,521,609 14,793 8,716 9,946 4,790,285 Yes 4,885,342 2 Standard SAMEA6595234 GCA_902810135
SC487 2005-9-19 Surface water 1,289,213 Phenol-CHCl3 651,178,805 34,634 13,099 17,546 4,794,586 Yes 4,794,586 1 Standard SAMEA6595246 GCA_902810365
SC433 2005-8-15 Waterline 566,913 Phenol-CHCl3 660,660,048 25,781 17,312 23,362 4,797,429 Yes 4,961,214 2 Standard SAMEA6595224 GCA_902810215
SC429 2005-8-15 Waterline 1,110,243 Promega and phenol-CHCl3 1,081,882,331 28,668 9,271 18,780 4,797,468 Yes 4,961,244 2 Standard SAMEA6595221 GCA_902810175
SC430 2005-8-15 Waterline 2,171,974 Promega and phenol-CHCl3 1,749,627,499 27,343 7,478 19,159 4,797,499 Yes 4,961,283 2 Standard SAMEA6595222 GCA_902810205
SC397 2005-8-15 Surface water 1,485,195 Promega 1,001,724,414 28,040 13,643 19,677 4,858,696 No 5,067,247 3 Standard SAMEA6595209 GCA_902809965
SC411 2005-8-15 Surface water 565,996 Phenol-CHCl3 1,360,250,706 25,134 11,224 20,582 4,859,344 Yes 5,068,109 3 Standard SAMEA6595216 GCA_902810035
SC419 2005-8-15 Sediment 793,357 Phenol-CHCl3 1,421,369,578 35,942 6,732 14,684 4,859,796 Yes 4,916,116 2 Standard SAMEA6595218 GCA_902810255
SC364 2005-7-27 Surface water 9,348,468 Promega 1,077,384,666 26,426 13,126 20,928 4,860,085 Yes 5,063,812 2 Standard SAMEA6595205 GCA_902810045
SC453 2005-8-15 Upshore 522,987 Promega and phenol-CHCl3 1,231,172,695 50,059 7,010 11,072 4,863,138 No 5,308,239 4 Standard SAMEA6595231 GCA_902810175
SC307 2005-6-15 Surface water 2,670,106 Promega 1,216,450,680 26,661 10,595 19,865 4,892,106 Yes 5,221,106 5 Standard SAMEA6596823 GCA_902809955
SC400 2005-8-15 Surface water 9,809,258 Promega 1,138,079,055 21,521 16,543 25,690 4,924,724 Yes 5,065,688 2 Standard SAMEA6595210 GCA_902809905
SC489 2005-9-19 Surface water 779,700 Phenol-CHCl3 530,260,839 73,424 5,806 7,779 4,929,025 No 5,008,168 4 Standard SAMEA6595247 GCA_902810115
SC469 2005-9-19 Surface water 399,522 Phenol-CHCl3 723,447,743 40,512 9,772 13,766 4,940,057 Yes 5,129,818 3 Standard SAMEA6595240 GCA_902810165
SC402 2005-8-15 Surface water 3,305,579 Promega 1,103,528,651 25,927 14,104 20,875 4,944,324 Yes 5,085,287 2 Standard SAMEA6595211 GCA_902810085
SC406 2005-8-15 Surface water 700,028 Promega and phenol-CHCl3 2,471,779,990 25,820 8,152 19,613 4,958,102 Yes 4,958,102 1 Standard SAMEA6595213 GCA_902810285
SC454 2005-8-15 Upshore 1,653,791 Phenol-CHCl3 1,010,953,794 43,107 7,741 13,039 4,982,834 Yes 4,988,386 2 Alternative SAMEA6595232 GCA_902810105
SC441 2005-8-15 Waterline 738,159 Phenol-CHCl3 988,454,259 46,048 6,225 11,435 4,986,040 Yes 5,022,479 2 Alternative SAMEA6595226 GCA_902810245
SC446 2005-8-15 Waterline 1,037,860 Phenol-CHCl3 451,143,119 35,499 13,071 14,580 4,986,746 Yes 4,997,068 2 Alternative SAMEA6595229 GCA_902810265
SC445 2005-8-15 Waterline 490,093 Phenol-CHCl3 260,701,609 14,322 19,183 21,437 4,987,469 Yes 5,033,261 2 Alternative SAMEA6595228 GCA_902810225
SC443 2005-8-15 Waterline 841,953 Phenol-CHCl3 1,027,640,114 31,687 9,897 17,265 4,999,711 No 5,021,047 2 Alternative SAMEA6595227 GCA_902810185
SC410 2005-8-15 Surface water 436,740 Phenol-CHCl3 981,338,093 25,375 10,873 22,404 5,001,654 Yes 5,008,324 2 Standard SAMEA6595215 GCA_902809925
SC422 2005-8-15 Sediment 514,475 Phenol-CHCl3 611,712,027 98,763 4,900 5,623 5,003,951 Yes 5,003,951 1 Standard SAMEA6595219 GCA_902810275
SC464 2005-8-15 Upshore 874,611 Promega and phenol-CHCl3 3,086,301,299 18,303 8,993 27,897 5,023,622 Yes 5,137,983 2 Standard SAMEA6595236 GCA_902810155
SC407 2005-8-15 Surface water 1,260,500 Promega and phenol-CHCl3 2,703,637,269 24,419 7,660 20,853 5,088,866 Yes 5,088,866 1 Standard SAMEA6595214 GCA_902810295
SC403 2005-8-15 Surface water 1,257,142 Promega 765,980,798 33,276 12,830 17,205 5,089,116 Yes 5,145,436 2 Standard SAMEA6595212 GCA_902809945
SC368 2005-7-31 Surface water 4,766,180 Promega 910,447,798 48,174 6,454 11,026 5,101,998 Yes 5,101,998 1 Standard SAMEA6595206 GCA_902810305
SC418 2005-8-15 Sediment 665,222 Promega and phenol-CHCl3 2,677,454,945 24,282 7,752 21,140 5,222,289 Yes 5,222,289 1 Standard SAMEA6595217 GCA_902810335
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a

Strain identification (ID) and sampling information were taken from reference 6. Strains are sorted by chromosome length.

b

Phenol-CHCl3 indicates that phenol-chloroform extraction was used; Promega indicates that the Promega Wizard DNA extraction kit was used.

c

Filtered read N50 indicates the N50 value after Filtlong (https://github.com/rrwick/filtlong) was used to retain only 500 Mbp from each strain.

d

Chromosome length indicates the length of the longest contig, assumed to be the chromosome.

e

Circular chromosome indicates whether the chromosome is a single circular contig.

f

Genome length indicates the sum of the lengths of all contigs.

g

rRNA orientation indicates the orientation of the seven ribosomal operons in E. coli, as assessed by socru (11).

We used the long-read assembler Flye v2.4.2 (8) for genome assembly. We polished the assemblies using four rounds of long-read polishing with Pilon v1.23 (9), followed by two rounds of short-read polishing with Racon v1.3.2 with the following parameter changes: gap penalty increased to −8, match score increased to 8, and mismatch score increased to −6 (10). The contigs were left as linear if not circularized by Flye, with no reorientation. We confirmed the structural accuracy of each genome using socru v2.1.7 (11) to assess the order and orientation of the seven rRNA operons (Table 1). In all cases, the rRNA operons were found in standard or known orientations, supporting the structural accuracy of these genomes. All software was run using default parameters, unless otherwise specified.

The genomes range in length from 4.4 Mbp to 5.2 Mbp. Under the assumption that any nonchromosomal contigs are plasmids, 17 isolates contained no plasmids (i.e., only one chromosomal contig), 21 isolates contained a single plasmid, and 10 isolates contained multiple plasmids (Table 1). The 47 complete genomes produced in this study provide a resource for insight into environmental adaptation and the genome dynamics of repetitive mobile genetic elements in E. coli.

Data availability.

The complete sequences and reads for these isolates have been deposited in the ENA database, and the accession numbers are listed in Table 1.

ACKNOWLEDGMENTS

We thank Nikki Freed for assistance with ONT sequencing.

Illumina genome sequences were provided by MicrobesNG, which is supported by the Biotechnology and Biological Sciences Research Council (grant BB/L024209/1). This work was supported by a Marsden Grant (grant MAU1703) to O.K.S. The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

REFERENCES

  • 1.Luo C, Walk ST, Gordon DM, Feldgarden M, Tiedje JM, Konstantinidis KT. 2011. Genome sequencing of environmental Escherichia coli expands understanding of the ecology and speciation of the model bacterial species. Proc Natl Acad Sci U S A 108:7200–7205. doi: 10.1073/pnas.1015622108. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 2.Méric G, Kemsley EK, Falush D, Saggers EJ, Lucchini S. 2013. Phylogenetic distribution of traits associated with plant colonization in Escherichia coli. Environ Microbiol 15:487–501. doi: 10.1111/j.1462-2920.2012.02852.x. [DOI] [PubMed] [Google Scholar]
  • 3.Touchon M, Perrin A, de Sousa JAM, Vangchhia B, Burn S, O’Brien CL, Denamur E, Gordon D, Rocha EPC. 2020. Phylogenetic background and habitat drive the genetic diversification of Escherichia coli. PLoS Genet 16:e1008866. doi: 10.1371/journal.pgen.1008866. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 4.NandaKafle G, Huegen T, Potgieter SC, Steenkamp E, Venter SN, Brözel VS. 2020. Niche preference of Escherichia coli in a peri-urban pond ecosystem. bioRxiv 2020.01.30.926667. doi: 10.1101/2020.01.30.926667. [DOI] [PMC free article] [PubMed]
  • 5.Guttman DS, Dykhuizen DE. 1994. Clonal divergence in Escherichia coli as a result of recombination, not mutation. Science 266:1380–1383. doi: 10.1126/science.7973728. [DOI] [PubMed] [Google Scholar]
  • 6.Ishii S, Ksoll WB, Hicks RE, Sadowsky MJ. 2006. Presence and growth of naturalized Escherichia coli in temperate soils from Lake Superior watersheds. Appl Environ Microbiol 72:612–621. doi: 10.1128/AEM.72.1.612-621.2006. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 7.Quick J. 2018. Ultra-long read sequencing protocol for RAD004 V.(mrxc57n). protocols.io doi: 10.17504/protocols.io.mrxc57n. [DOI]
  • 8.Kolmogorov M, Yuan J, Lin Y, Pevzner PA. 2019. Assembly of long, error-prone reads using repeat graphs. Nat Biotechnol 37:540–546. doi: 10.1038/s41587-019-0072-8. [DOI] [PubMed] [Google Scholar]
  • 9.Walker BJ, Abeel T, Shea T, Priest M, Abouelliel A, Sakthikumar S, Cuomo CA, Zeng Q, Wortman J, Young SK, Earl AM. 2014. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS One 9:e112963. doi: 10.1371/journal.pone.0112963. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 10.Vaser R, Sović I, Nagarajan N, Šikić M. 2017. Fast and accurate de novo genome assembly from long uncorrected reads. Genome Res 27:737–746. doi: 10.1101/gr.214270.116. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 11.Page AJ, Ainsworth EV, Langridge GC. 2020. socru: typing of genome-level order and orientation around ribosomal operons in bacteria. Microb Genom 6. doi: 10.1099/mgen.0.000396. [DOI] [PMC free article] [PubMed] [Google Scholar]

Associated Data

This section collects any data citations, data availability statements, or supplementary materials included in this article.

Data Availability Statement

The complete sequences and reads for these isolates have been deposited in the ENA database, and the accession numbers are listed in Table 1.

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