Bacillus pumilus Group Comparative Genomics: Toward Pangenome Features, Diversity, and Marine Environmental Adaptation

Fu, Xiugen; Gong, Li; Liu, Yang; Lai, Qiliang; Li, Guangyu; Shao, Zongze

doi:10.3389/fmicb.2021.571212

Cited by 16 publications

(25 citation statements)

References 117 publications

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“…2B). Due to the several taxonomic misclassifications of strains belonging to the Bacillus pumilus group (as reported here and by others (Espariz et al, 2016;X. Fu et al, 2021;Liu et al, 2013)), it is likely that strain C1 truly belongs to a B. safensis species; however, complete genome of C1 is not available to confirm this hypothesis.…”

Section: C-terminal Residues Differentiate Cynd From B Pumilus and B Safensismentioning

confidence: 57%

“…1A, brown names) contains several strains already characterized as Bacillus altitudinis by different methods (for instance: BA06, ku-bf1, B-388 (X. Fu et al, 2021)) and also 4 strains (TUAT1, MTCB 6033, SH-B11 and C4) previously annotated as Bacillus pumilus. However, our analysis clearly demonstrates that they belong to Bacillus altitudinis and therefore require reclassification (Table S5) as previously suggested (Espariz et al, 2016;X.…”

Section: Bacillus Sp Per-urp-08 Is Classified As Bacillus Safensis Based On Core-genome Comparisonsmentioning

confidence: 99%

“…Fu et al, 2021)) and also 4 strains (TUAT1, MTCB 6033, SH-B11 and C4) previously annotated as Bacillus pumilus. However, our analysis clearly demonstrates that they belong to Bacillus altitudinis and therefore require reclassification (Table S5) as previously suggested (Espariz et al, 2016;X. Fu et al, 2021).…”

Section: Bacillus Sp Per-urp-08 Is Classified As Bacillus Safensis Based On Core-genome Comparisonsmentioning

confidence: 99%

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Isolation of a Bacillus safensis from mine tailings in Peru, genomic characterization and characterization of its cyanide-degrading enzyme CynD

Arevalo

Sifuentes

Portocarrero

et al. 2021

Preprint

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Cyanide is widely used in industry as a potent lixiviant due to its capacity to tightly bind metals. This property imparts cyanide enormous toxicity to all known organisms. Thus, industries that utilize this compound must reduce its concentration in recycled or waste waters. Physical, chemical, and biological treatments have been used for cyanide remediation; however, none of them meet all the desired characteristics: efficiency, low cost and low environmental impact. A better understanding of metabolic pathways and biochemistry of enzymes involved in cyanide degradation is a necessary step to improve cyanide bioremediation efficacy to satisfy the industry requirements. Here, we used several approaches to explore this topic. We have isolated three cyanide-degrading Bacillus strains from water in contact with mine tailings from Lima, Peru, and classified them as Bacillus safensis PER-URP-08, Bacillus licheniformis PER-URP-12, and Bacillus subtilis PER-URP-17 based on 16S rRNA gene sequencing and core genome analyses. Additionally, core genome analyses of 132 publicly available genomes of Bacillus pumilus group including B. safensis and B. altitudinis allowed us to reclassify some strains and identify two strains that did not match with any known species of the Bacillus pumilus group. We searched for possible routes of cyanide-degradation in the genomes of these three strains and identified putative B. licheniformis PER-URP-12 and B. subtilis PER-URP-17 rhodaneses and B. safensis PER-URP-08 cyanide dihydratase (CynD) sequences possibly involved cyanide degradation. We identified characteristic C-terminal residues that differentiate CynD from B. pumilus and B. safensis, and showed that, differently from CynD from B. pumilus C1, recombinant CynD from the Bacillus safensis PER-URP-08 strain remains active up to pH 9 and presents a distinct oligomerization pattern at pH 8 and 9. Moreover, transcripts of B. safensis PER-URP-08 CynD (CynDPER-URP-08) are strongly induced in the presence of cyanide. Our results warrant further investigation of B. safensis PER-URP-08 and CynDPER-URP-08 as potential tools for cyanide-bioremediation.

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Section: C-terminal Residues Differentiate Cynd From B Pumilus and B Safensismentioning

confidence: 57%

Section: Bacillus Sp Per-urp-08 Is Classified As Bacillus Safensis Based On Core-genome Comparisonsmentioning

confidence: 99%

Section: Bacillus Sp Per-urp-08 Is Classified As Bacillus Safensis Based On Core-genome Comparisonsmentioning

confidence: 99%

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Isolation of a Bacillus safensis from mine tailings in Peru, genomic characterization and characterization of its cyanide-degrading enzyme CynD

Arevalo

Sifuentes

Portocarrero

et al. 2021

Preprint

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“…Four strains, namely, TUAT1, MTCC B6033, SH-B11, and C4, formed a separate cluster that had less than 95% homology with other strains of B. pumilus . In a previous study, it has been reported that three strains, namely TUAT1, MTCC B6033 and SH-B11 cluster with other B. altitudinis [ 41 ]. Our findings confirm this conclusion and place the C4 strain under B. altitudinis .…”

Section: Resultsmentioning

confidence: 99%

Comparative Genome Analysis of Two Bacillus pumilus Strains Producing High Level of Extracellular Hydrolases

Pudova

Toymentseva

Gogoleva

et al. 2022

Genes

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Whole-genome sequencing of a soil isolate Bacillus pumilus, strain 7P, and its streptomycin-resistant derivative, B. pumilus 3-19, showed genome sizes of 3,609,117 bp and 3,609,444 bp, respectively. Annotation of the genome showed 3794 CDS (3204 with predicted function) and 3746 CDS (3173 with predicted function) in the genome of strains 7P and 3-19, respectively. In the genomes of both strains, the prophage regions Bp1 and Bp2 were identified. These include 52 ORF of prophage proteins in the Bp1 region and 38 prophages ORF in the Bp2 region. Interestingly, more than 50% of Bp1 prophage proteins are similar to the proteins of the phi105 in B. subtilis. The DNA region of Bp2 has 15% similarity to the DNA of the Brevibacillus Jimmer phage. Degradome analysis of the genome of both strains revealed 148 proteases of various classes. These include 60 serine proteases, 48 metalloproteases, 26 cysteine proteases, 4 aspartate proteases, 2 asparagine proteases, 3 threonine proteases, and 2 unclassified proteases. Likewise, three inhibitors of proteolytic enzymes were found. Comparative analysis of variants in the genomes of strains 7P and 3-19 showed the presence of 81 nucleotide variants in the genome 3-19. Among them, the missense mutations in the rpsL, comA, spo0F genes and in the upstream region of the srlR gene were revealed. These nucleotide polymorphisms may have affected the streptomycin resistance and overproduction of extracellular hydrolases of the 3-19 strain. Finally, a plasmid DNA was found in strain 7P, which is lost in its derivative, strain 3-19. This plasmid contains five coding DNA sequencing (CDS), two regulatory proteins and three hypothetical proteins.

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“…nov. Halomonas stenophila Tamlana crocina, sp. nov. 24,74,75 . In seeds of C. armena Novosphingobium was determined.…”

Section: Discussionmentioning

confidence: 99%

Bacterial Seed Endophytes of the Holoparasitic Cistanche Armena and C. Phelypaea (Orobanchaceae) from Saline Habitats: Semi-Deserts vs Flooded Coasts

Petrosyan¹,

Piwowarczyk²,

Ruraż³

et al. 2021

Preprint

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The current study compares the bacterial seed endomicrobiomes of the endemic holoparasitic plant species Cistanche armena and C. phelypaea. Both species thrive in habitats that are saline but with a very different soil water status. The study aims to uncover how environmental conditions influence the diversity of the bacterial communities of seeds of these holoparasites and also highlights the physiological activities, several enzymatic and PGP traits of culturable endophytes that may support the tolerance of their hosts to abiotic stresses. A combination of culture-dependent and molecular techniques was employed for the identification of the seed endomicrobiome (culturable and unculturable). From the seeds of both parasitic plant species closely related strains were isolated. Sixteen phyla, 323 genera and 710 bacterial species were identified, mainly Gram negative, halotolerant bacteria with an environmental origin. Most of the isolates were endospore forming, halotolerant and alkaliphile Bacillus spp. which suggests that the endophytic bacteria of C. armena and C. phelypaea seeds possess traits that are correlated with the natural habitat of their hosts. The Paenibacillus strains from both plant species demonstrate similar biochemical traits. Although the seed endophytic microbiomes of C. armena and C. phelypaea contain a high number of common bacterial taxa, also remarkable differences exist. We demonstrated that the diversity of the bacterial communities is related to the environmental conditions, water status or abiotic stresses.

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Bacillus pumilus Group Comparative Genomics: Toward Pangenome Features, Diversity, and Marine Environmental Adaptation

Cited by 16 publications

References 117 publications

Isolation of a Bacillus safensis from mine tailings in Peru, genomic characterization and characterization of its cyanide-degrading enzyme CynD

Isolation of a Bacillus safensis from mine tailings in Peru, genomic characterization and characterization of its cyanide-degrading enzyme CynD

Comparative Genome Analysis of Two Bacillus pumilus Strains Producing High Level of Extracellular Hydrolases

Bacterial Seed Endophytes of the Holoparasitic Cistanche Armena and C. Phelypaea (Orobanchaceae) from Saline Habitats: Semi-Deserts vs Flooded Coasts

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