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Nature Ecology & Evolution May 2018The growth and survival of organisms often depend on interactions between them. In many cases, these interactions are positive and caused by a cooperative modification...
The growth and survival of organisms often depend on interactions between them. In many cases, these interactions are positive and caused by a cooperative modification of the environment. Examples are the cooperative breakdown of complex nutrients in microbes or the construction of elaborate architectures in social insects, in which the individual profits from the collective actions of her peers. However, organisms can similarly display negative interactions by changing the environment in ways that are detrimental for them, for example by resource depletion or the production of toxic byproducts. Here we find an extreme type of negative interactions, in which Paenibacillus sp. bacteria modify the environmental pH to such a degree that it leads to a rapid extinction of the whole population, a phenomenon that we call ecological suicide. Modification of the pH is more pronounced at higher population densities, and thus ecological suicide is more likely to occur with increasing bacterial density. Correspondingly, promoting bacterial growth can drive populations extinct whereas inhibiting bacterial growth by the addition of harmful substances-such as antibiotics-can rescue them. Moreover, ecological suicide can cause oscillatory dynamics, even in single-species populations. We found ecological suicide in a wide variety of microbes, suggesting that it could have an important role in microbial ecology and evolution.
Topics: Environment; Hydrogen-Ion Concentration; Microbial Interactions; Paenibacillus; Population Dynamics
PubMed: 29662223
DOI: 10.1038/s41559-018-0535-1 -
Microbial Cell Factories Feb 2016Nitrogen fixation has been established in protokaryotic model Escherichia coli by transferring a minimal nif gene cluster composed of 9 genes (nifB, nifH, nifD, nifK,...
BACKGROUND
Nitrogen fixation has been established in protokaryotic model Escherichia coli by transferring a minimal nif gene cluster composed of 9 genes (nifB, nifH, nifD, nifK, nifE, nifN, nifX, hesA and nifV) from Paenibacillus sp. WLY78. However, the nitrogenase activity in the recombinant E. coli 78-7 is only 10 % of that observed in wild-type Paenibacillus. Thus, it is necessary to increase nitrogenase activity through synthetic biology.
RESULTS
In order to increase nitrogenase activity in heterologous host, a total of 28 selected genes from Paenibacillus sp. WLY78 and Klebsiella oxytoca were placed under the control of Paenibacillus nif promoter in two different vectors and then they are separately or combinationally transferred to the recombinant E. coli 78-7. Our results demonstrate that Paenibacillus suf operon (Fe-S cluster assembly) and the potential electron transport genes pfoAB, fldA and fer can increase nitrogenase activity. Also, K. oxytoca nifSU (Fe-S cluster assembly) and nifFJ (electron transport specific for nitrogenase) can increase nitrogenase activity. Especially, the combined assembly of the potential Paenibacillus electron transporter genes (pfoABfldA) with K. oxytoca nifSU recovers 50.1 % of wild-type (Paenibacillus) activity. However, K. oxytoca nifWZM and nifQ can not increase activity.
CONCLUSION
The combined assembly of the potential Paenibacillus electron transporter genes (pfoABfldA) with K. oxytoca nifSU recovers 50.1 % of wild-type (Paenibacillus) activity in the recombinant E. coli 78-7. Our results will provide valuable insights for the enhancement of nitrogenase activity in heterogeneous host and will provide guidance for engineering cereal plants with minimal nif genes.
Topics: Electron Transport; Escherichia coli; Genes, Bacterial; Iron-Sulfur Proteins; Klebsiella; Multigene Family; Nitrogenase; Paenibacillus; Recombination, Genetic; Synthetic Biology
PubMed: 26897628
DOI: 10.1186/s12934-016-0442-6 -
Applied Microbiology and Biotechnology Sep 2016The gram-positive bacterium Paenibacillus larvae is the etiological agent of American Foulbrood of honey bees, a notifiable disease in many countries. Hence, P. larvae... (Review)
Review
The gram-positive bacterium Paenibacillus larvae is the etiological agent of American Foulbrood of honey bees, a notifiable disease in many countries. Hence, P. larvae can be considered as an entomopathogen of considerable relevance in veterinary medicine. P. larvae is a highly specialized pathogen with only one established host, the honey bee larva. No other natural environment supporting germination and proliferation of P. larvae is known. Over the last decade, tremendous progress in the understanding of P. larvae and its interactions with honey bee larvae at a molecular level has been made. In this review, we will present the recent highlights and developments in P. larvae research and discuss the impact of some of the findings in a broader context to demonstrate what we can learn from studying "exotic" pathogens.
Topics: Animals; Bacterial Toxins; Bees; Host Specificity; Host-Pathogen Interactions; Larva; Paenibacillus larvae
PubMed: 27394713
DOI: 10.1007/s00253-016-7716-0 -
International Journal of Systematic and... Jul 2018A Gram-stain-positive, aerobic, motile with peritrichous flagella, rod-shaped bacterium, designated CFH S0170, was isolated from a soil sample collected from Catba...
A Gram-stain-positive, aerobic, motile with peritrichous flagella, rod-shaped bacterium, designated CFH S0170, was isolated from a soil sample collected from Catba island in Ha Long Bay, Hai Phong City, Vietnam. Comparison of the 16S rRNA gene sequences showed that strain CFH S0170 belonged to the genus Paenibacillus and showed closest relationship with Paenibacillus vulneris CCUG 53270 (98.1 % similarity). Phylogenetic analysis demonstrated that the novel candidate formed a coherent branch with P. vulneris CCUG 53270 and Paenibacillus yunnanensis YN2. Furthermore, the novel strain shared 87.2 % rpoB gene sequence similarity with P. vulneris CCUG 53270. Growth of strain CFH S0170 occurred at 10-40 °C, pH 6.0-8.0 and with 0-2.0 % (w/v) NaCl. Strain CFH S0170 contained mannose, glucose and rhamnose as the major whole-cell sugars. The cell-wall peptidoglycan contained meso-diaminopimelic acid, glutamic acid, lysine and aspartic acid. The polar lipid profile contained diphosphatidylglycerol, phosphatidylethanolamine, glycolipids and phospholipids. The dominant cellular fatty acids included anteiso-C15 : 0 and C15 : 0. The genomic DNA G+C content was 50.9 mol%. On the basis of phenotypic, chemotaxonomic and phylogenetic analysis, strain CFH S0170 is affiliated to the genus Paenibacillus, but could be distinguished from other valid species of this genus. It is concluded that strain CFH S0170 should be considered to represent a novel species of the genus Paenibacillus, for which the name Paenibacillus esterisolvens sp. nov. is proposed. The type strain is CFH S0170 (=KCTC 33624=BCRC 80802).
Topics: Bacterial Typing Techniques; Base Composition; Cell Wall; DNA, Bacterial; Diaminopimelic Acid; Fatty Acids; Genes, Bacterial; Glycolipids; Nucleic Acid Hybridization; Paenibacillus; Peptidoglycan; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil Microbiology; Vietnam
PubMed: 29701575
DOI: 10.1099/ijsem.0.002754 -
International Journal of Systematic and... Sep 2021A Gram-stain-positive and motile bacterial strain, designated IB182363, was isolated from surface seawater of the South China Sea. Cells grew at pH 5.0-9.5 (optimum, pH...
A Gram-stain-positive and motile bacterial strain, designated IB182363, was isolated from surface seawater of the South China Sea. Cells grew at pH 5.0-9.5 (optimum, pH 7.0-8.0), 20-40 °C (optimum, 30 °C) and with 1-8 % (w/v) NaCl (optimum, 2-4 %). On the basis of 16S rRNA gene sequence analysis, strain IB182363 was affiliated to the genus and the closest phylogenetically related species was DSM18677 with 96.9 % sequence similarity. The values of whole genome average nucleotide identity analysis and digital DNA-DNA hybridization between the isolate and the closely related type strains were less than 86.3 and 25.6 %, respectively. Chemotaxonomic analysis revealed that strain IB182363 possessed -diaminopimelic acid in the cell-wall peptidoglycan and contained menaquinone MK-7 as the predominant isoprenoid quinone. The major cellular fatty acids were anteiso-C, C and iso-C. The polar lipids comprised phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, one unidentified glycolipid, two unidentified aminolipids, two unidentified phospholipids and four unidentified aminophospholipids. The genomic DNA G+C content was 54.5 mol%. On the basis of the above results, strain IB182363 represents a novel species of the genus , for which we propose the name sp. nov. with the type strain IB182363 (=MCCC 1K04630=JCM 34214).
Topics: Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Paenibacillus; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Seawater; Sequence Analysis, DNA
PubMed: 34559622
DOI: 10.1099/ijsem.0.005024 -
Microbial Biotechnology Jul 2017Recent studies indicated that the production of secondary metabolites by soil bacteria can be triggered by interspecific interactions. However, little is known to date...
Recent studies indicated that the production of secondary metabolites by soil bacteria can be triggered by interspecific interactions. However, little is known to date about interspecific interactions between Gram-positive and Gram-negative bacteria. In this study, we aimed to understand how the interspecific interaction between the Gram-positive Paenibacillus sp. AD87 and the Gram-negative Burkholderia sp. AD24 affects the fitness, gene expression and the production of soluble and volatile secondary metabolites of both bacteria. To obtain better insight into this interaction, transcriptome and metabolome analyses were performed. Our results revealed that the interaction between the two bacteria affected their fitness, gene expression and the production of secondary metabolites. During interaction, the growth of Paenibacillus was not affected, whereas the growth of Burkholderia was inhibited at 48 and 72 h. Transcriptome analysis revealed that the interaction between Burkholderia and Paenibacillus caused significant transcriptional changes in both bacteria as compared to the monocultures. The metabolomic analysis revealed that the interaction increased the production of specific volatile and soluble antimicrobial compounds such as 2,5-bis(1-methylethyl)-pyrazine and an unknown Pederin-like compound. The pyrazine volatile compound produced by Paenibacillus was subjected to bioassays and showed strong inhibitory activity against Burkholderia and a range of plant and human pathogens. Moreover, strong additive antimicrobial effects were observed when soluble extracts from the interacting bacteria were combined with the pure 2,5-bis(1-methylethyl)-pyrazine. The results obtained in this study highlight the importance to explore bacterial interspecific interactions to discover novel secondary metabolites and to perform simultaneously metabolomics of both, soluble and volatile compounds.
Topics: Anti-Bacterial Agents; Antibiosis; Biological Products; Burkholderia; Gene Expression Profiling; Humans; Metabolomics; Paenibacillus; Secondary Metabolism; Volatile Organic Compounds
PubMed: 28557379
DOI: 10.1111/1751-7915.12735 -
Journal of Applied Microbiology Aug 2022Biodesulfurization of fossil fuels is a promising technology for deep desulfurization. Previously, we have shown that Paenibacillus strains 32O-W and 32O-Y can...
AIMS
Biodesulfurization of fossil fuels is a promising technology for deep desulfurization. Previously, we have shown that Paenibacillus strains 32O-W and 32O-Y can desulfurize dibenzothiophene (DBT) and DBT sulfone (DBTS) effectively. In this work, improvements in DBT and DBTS desulfurization by these strains were investigated through immobilization and nanoparticle coating of cells.
METHODS AND RESULTS
Paenibacillus strains 32O-W and 32O-Y immobilized in alginate gel beads or coated with Fe O magnetite nanoparticles were grown at various concentrations (0.1-2 mmol l ) of DBT or DBTS for 96 h. The production of 2-hydroxybiphenyl (2-HBP) from the 4S pathway biotransformation of DBT or DBTS was measured. The highest amounts of 2-HBP production occurred at concentrations of 0.1 and 0.5 mmol l . Compared to planktonic cultures maximum 2-HBP production increased by 54% for DBT and 90% for DBTS desulfurization with immobilized strains, and 44% for DBT and 66% for DBTS desulfurization by nanoparticle-coated strains.
CONCLUSIONS
Nanoparticle-coated and immobilized cells may be of use in efforts to increase the efficiency of biodesulfurization.
SIGNIFICANCE AND IMPACT OF THE STUDY
Alginate immobilization or nanoparticle coating of bacterial cells may be useful approaches for the enhancement of biodesulfurization for eventual use on an industrial scale.
Topics: Alginates; Nanoparticles; Paenibacillus; Thiophenes
PubMed: 35611623
DOI: 10.1111/jam.15637 -
MSphere Jan 2020is a spore-forming bacterial genus that is frequently isolated from fluid milk and is proposed to play a role in spoilage. To characterize the genetic and phenotypic...
Paenibacillus odorifer, the Predominant Species Isolated from Milk in the United States, Demonstrates Genetic and Phenotypic Conservation of Psychrotolerance but Clade-Associated Differences in Nitrogen Metabolic Pathways.
is a spore-forming bacterial genus that is frequently isolated from fluid milk and is proposed to play a role in spoilage. To characterize the genetic and phenotypic diversity of spp., we first used allelic typing data for a preexisting collection of 1,228 species isolates collected from raw and processed milk, milk products, and dairy environmental sources. Whole-genome sequencing (WGS) and average nucleotide identity by BLAST (ANIb) analyses performed for a subset of 58 isolates representing unique and overrepresented allelic types in the collection revealed that these isolates represent 21 different spp., with being the predominant species. Further genomic characterization of isolates identified two distinct phylogenetic clades, clades A and B, which showed significant overrepresentation of 172 and 164 ortholog clusters and 94 and 52 gene ontology (GO) terms, respectively. While nitrogen fixation genes were found in both clades, multiple genes associated with nitrate and nitrite reduction were overrepresented in clade A isolates; additional phenotypic testing demonstrated that nitrate reduction is specific to isolates in clade A. Hidden Markov models detected 9 to 10 different classes of cold shock-associated genetic elements in all isolates. Phenotypic testing revealed that all isolates tested here can grow in skim milk broth at 6°C, suggesting that psychrotolerance is conserved in Overall, our data suggest that spp. isolated from milk in the United States represent broad genetic diversity, which may provide challenges for targeted-control strategies aimed at reducing fluid milk spoilage. Although species isolates are frequently isolated from pasteurized fluid milk, the link between the genetic diversity and phenotypic characteristics of these isolates was not well understood, especially as some isolated from milk are unable to grow at refrigeration temperatures. Our data demonstrate that spp. isolated from fluid milk represent tremendous interspecies diversity, with being the predominant sp. isolated. Furthermore, genetic and phenotypic data support that is well suited to transition from a soil-dwelling environment, where nitrogen fixation (and other nitrate/nitrite reduction pathways present only in clade A) may facilitate growth, to fluid milk, where its multiple cold shock-associated adaptations enable it to grow at refrigeration temperatures throughout the storage of milk. Therefore, efforts to reduce bacterial contamination of milk will require a systematic approach to reduce contamination of raw milk.
Topics: Animals; Cold-Shock Response; Colony Count, Microbial; Genetic Variation; Markov Chains; Metabolic Networks and Pathways; Milk; Nitrogen; Nitrogen Fixation; Paenibacillus; Phenotype; Phylogeny; Spores, Bacterial; United States; Whole Genome Sequencing
PubMed: 31969477
DOI: 10.1128/mSphere.00739-19 -
Extremophiles : Life Under Extreme... Jan 2017Prior to 2008, all previously studied conventional bacterial flagellar motors appeared to utilize either H or Na as coupling ions. Membrane-embedded stator complexes... (Review)
Review
Prior to 2008, all previously studied conventional bacterial flagellar motors appeared to utilize either H or Na as coupling ions. Membrane-embedded stator complexes support conversion of energy using transmembrane electrochemical ion gradients. The main H-coupled stators, known as MotAB, differ from Na-coupled stators, PomAB of marine bacteria, and MotPS of alkaliphilic Bacillus. However, in 2008, a MotAB-type flagellar motor of alkaliphilic Bacillus clausii KSM-K16 was revealed as an exception with the first dual-function motor. This bacterium was identified as the first bacterium with a single stator-rotor that can utilize both H and Na for ion-coupling at different pH ranges. Subsequently, another exception, a MotPS-type flagellar motor of alkaliphilic Bacillus alcalophilus AV1934, was reported to utilize Na plus K and Rb as coupling ions for flagellar rotation. In addition, the alkaline-tolerant bacterium Paenibacillus sp. TCA20, which can utilize divalent cations such as Ca, Mg, and Sr, was recently isolated from a hot spring in Japan, which contains a high Ca concentration. These findings show that bacterial flagellar motors isolated from unique environments utilize unexpected coupling ions. This suggests that bacteria that grow in different extreme environments adapt to local conditions and evolve their motility machinery.
Topics: Bacillus; Cations, Divalent; Flagellin; Movement; Paenibacillus
PubMed: 27771767
DOI: 10.1007/s00792-016-0886-y -
Archives of Microbiology Apr 2016A Gram-staining-positive, endospore-forming, aerobic, rod-shaped bacterium, designated as DCY97(T), was isolated from ripened Pu'er tea and was identified by using a...
A Gram-staining-positive, endospore-forming, aerobic, rod-shaped bacterium, designated as DCY97(T), was isolated from ripened Pu'er tea and was identified by using a polyphasic approach. 16S rRNA gene sequence analysis showed that strain DCY97(T) was closely related to Paenibacillus dongdonensis KUDC0114(T) (98.0 %), Paenibacillus oceanisediminis L10(T) (97.7 %), and Paenibacillus barcinonensis BP-23(T) (97.2 %). The phenotypic and chemotaxonomic characteristics of strain DCY97(T) matched with the characteristics of members belonging to the genus Paenibacillus. The major identified polar lipids included phosphatidylglycerol, phosphatidylethanolamine, and diphosphatidylglycerol. The predominant quinone was MK-7. The major fatty acids were anteiso-C15:0 (35.1 %), anteiso-C16:0 (19.0 %), and iso-C16:0 (13.9 %). The peptidoglycan cell wall was composed of meso-diaminopimelic acids, alanine, and D-glutamic acid. The genomic DNA G + C content was determined to be 46.7 mol%. The DNA-DNA relatedness between strain DCY97(T) and Paenibacillus dongdonensis KCTC 33221(T), Paenibacillus oceanisediminis KACC 16023(T), Paenibacillus barcinonensis KCTC 13019(T) were 27, 19, and 10 %, respectively. Based on the genotypic, phenotypic, and chemotaxonomic characteristics, strain DCY97(T) is considered as a novel species of the genus Paenibacillus, for which the name Paenibacillus puernese sp. nov. is proposed. The type strain is DCY97(T) (=KCTC 33596(T) = JCM 140369(T)).
Topics: Base Composition; DNA, Bacterial; Diaminopimelic Acid; Fatty Acids; Food Microbiology; Glucosidases; Paenibacillus; Phylogeny; RNA, Ribosomal, 16S; Sequence Homology, Nucleic Acid; Species Specificity
PubMed: 26721586
DOI: 10.1007/s00203-015-1180-6