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Microbial Ecology

, Volume 78, Issue 4, pp 885–894 | Cite as

Diversity and Distribution of Bacteria Producing Known Secondary Metabolites

  • Jadranka Nappi
  • Erika Soldi
  • Suhelen EganEmail author
Environmental Microbiology

Abstract

There is an increasing interest in the utilisation of marine bioactive compounds as novel biopharmaceuticals and agrichemicals; however, little is known about the environmental distribution for many of these molecules. Here, we aimed to elucidate the environmental distribution and to detect the biosynthetic gene clusters in environmental samples of four bioactive compounds, namely violacein, tropodithietic acid (TDA), tambjamine and the antibacterial protein AlpP. Our database analyses revealed high bacterial diversity for AlpP and violacein producers, while TDA-producing bacteria were mostly associated with marine surfaces and all belonged to the roseobacter group. In contrast, the tambjamine cluster was only found in the genomes of two Pseudoalteromonas species and in one terrestrial species belonging to the Cupriavidus genus. Using a PCR-based screen of different marine samples, we detected TDA and violacein genes associated with the microbiome of Ulva and Protohyale niger and tambjamine genes associated with Nodilittorina unifasciata; however, alpP was not detected. These results highlight the variable distribution of the genes encoding these four bioactive compounds, including their detection from the surface of multiple marine eukaryotic hosts. Determining the natural distribution of these gene clusters will help to understand the ecological importance of these metabolites and the bacteria that produce them.

Keywords

Marine bioactive compounds Surface-associated bacteria Antibiotic-producing bacteria (APB) Violacein Tropodithietic acid (TDA) Tambjamine AlpP 

Notes

Acknowledgements

The authors thank Torsten Thomas and members of the CMB group for feedback on the manuscript.

Funding

This work was supported by an Australian Research Council (ARC) Future Fellowship awarded to Suhelen Egan (grant number: FT130100828).

Compliance with Ethical Standards

Conflict of Interest

The authors declare that they have no conflict of interest.

Supplementary material

248_2019_1380_MOESM1_ESM.docx (2 mb)
ESM 1 (DOCX 2032 kb)

References

  1. 1.
    Luna GM (2015) Biotechnological potential of marine microbes. In: Kim S-K (ed) Springer handbook of marine biotechnology. Springer Berlin Heidelberg, Berlin, pp 651–661.  https://doi.org/10.1007/978-3-642-53971-8_26pp CrossRefGoogle Scholar
  2. 2.
    Egan S, Holmström C, Kjelleberg S (2001) Pseudoalteromonas ulvae sp. nov., a bacterium with antifouling activities isolated from the surface of a marine alga. Int J Syst Evol Microbiol 51:1499–1504PubMedGoogle Scholar
  3. 3.
    Uzair B, Menaa F, Khan BA, Mohammad FV, Ahmad VU, Djeribi R, Menaa B (2018) Isolation, purification, structural elucidation and antimicrobial activities of kocumarin, a novel antibiotic isolated from actinobacterium Kocuria marina CMG S2 associated with the brown seaweed Pelvetia canaliculata. Microbiol Res 206:186–197PubMedGoogle Scholar
  4. 4.
    Burke C, Thomas T, Egan S, Kjelleberg S (2007) The use of functional genomics for the identification of a gene cluster encoding for the biosynthesis of an antifungal tambjamine in the marine bacterium Pseudoalteromonas tunicata. Environ Microbiol 9:814–818PubMedGoogle Scholar
  5. 5.
    Kim W, Hendricks GL, Lee K, Mylonakis E (2017) An update on the use of C. elegans for preclinical drug discovery: screening and identifying anti-infective drugs. Expert Opin Drug Discovery 12:625–633Google Scholar
  6. 6.
    Suleria HAR, Gobe G, Masci P, Osborne SA (2016) Marine bioactive compounds and health promoting perspectives; innovation pathways for drug discovery. Trends Food Sci Technol 50:44–55Google Scholar
  7. 7.
    Crawford AD, Jaspars M, De Pascale D, Andersen JH, Reyes F, Ianora A (2016) The marine biodiscovery pipeline and ocean medicines of tomorrow. J Mar Biol Assoc U K 96:151–158Google Scholar
  8. 8.
    Amos GC, Borsetto C, Laskaris P, Krsek M, Berry AE, Newsham KK, Calvo-Bado L, Pearce DA, Vallin C, Wellington EM (2015) Designing and implementing an assay for the detection of rare and divergent NRPS and PKS clones in European, Antarctic and Cuban soils. PLoS One 10:e0138327PubMedPubMedCentralGoogle Scholar
  9. 9.
    Charlop-Powers Z, Owen JG, Reddy BVB, Ternei MA, Guimarães DO, de Frias UA, Pupo MT, Seepe P, Feng Z, Brady SF (2015) Global biogeographic sampling of bacterial secondary metabolism. Elife 4Google Scholar
  10. 10.
    Ayuso-Sacido A, Genilloud O (2005) New PCR primers for the screening of NRPS and PKS-I systems in actinomycetes: detection and distribution of these biosynthetic gene sequences in major taxonomic groups. Microb Ecol 49:10–24PubMedGoogle Scholar
  11. 11.
    James SG, Holmström C, Kjelleberg S (1996) Purification and characterization of a novel antibacterial protein from the marine bacterium D2. Appl Environ Microbiol 62:2783–2788PubMedPubMedCentralGoogle Scholar
  12. 12.
    Skovhus TL, Holmström C, Kjelleberg S, Dahllöf I (2007) Molecular investigation of the distribution, abundance and diversity of the genus Pseudoalteromonas in marine samples. FEMS Microbiol Ecol 61:348–361PubMedGoogle Scholar
  13. 13.
    Ballestriero F, Daim M, Penesyan A, Nappi J, Schleheck D, Bazzicalupo P, Di Schiavi E, Egan S (2014) Antinematode activity of violacein and the role of the insulin/IGF-1 pathway in controlling violacein sensitivity in Caenorhabditis elegans. PLoS One 9:e109201PubMedPubMedCentralGoogle Scholar
  14. 14.
    Wu Y-H, Cheng H, Xu L, Jin X-B, Wang C-S, Xu X-W (2017) Physiological and genomic features of a novel violacein-producing bacterium isolated from surface seawater. PLoS One 12:e0179997PubMedPubMedCentralGoogle Scholar
  15. 15.
    Penesyan A, Tebben J, Lee M, Thomas T, Kjelleberg S, Harder T, Egan S (2011) Identification of the antibacterial compound produced by the marine epiphytic bacterium Pseudovibrio sp. D323 and related sponge-associated bacteria. Mar Drugs 9:1391–1402PubMedPubMedCentralGoogle Scholar
  16. 16.
    Harrington C, Reen FJ, Mooij MJ, Stewart FA, Chabot J-B, Guerra AF, Glöckner FO, Nielsen KF, Gram L, Dobson AD (2014) Characterisation of non-autoinducing tropodithietic acid (TDA) production from marine sponge Pseudovibrio species. Mar Drugs 12:5960–5978PubMedPubMedCentralGoogle Scholar
  17. 17.
    Durán N, Justo GZ, Durán M, Brocchi M, Cordi L, Tasic L, Castro GR, Nakazato G (2016) Advances in Chromobacterium violaceum and properties of violacein-its main secondary metabolite: a review. Biotechnol Adv 34:1030–1045PubMedGoogle Scholar
  18. 18.
    Durán N, Menck CF (2001) Chromobacterium violaceum: a review of pharmacological and industiral perspectives. Crit Rev Microbiol 27:201–222PubMedGoogle Scholar
  19. 19.
    Ballantine J, Beer R, Crutchley D, Dodd G, Palmer D (1958) The synthesis of violacein and related compounds. Royal Soc Chemestry Thomas Graham House, Science Park, pp 232–233Google Scholar
  20. 20.
    Balibar CJ, Walsh CT (2006) In vitro biosynthesis of violacein from L-tryptophan by the enzymes VioA-E from Chromobacterium violaceum. Biochemistry 45:15444–15457PubMedGoogle Scholar
  21. 21.
    Geng H, Bruhn JB, Nielsen KF, Gram L, Belas R (2008) Genetic dissection of tropodithietic acid biosynthesis by marine roseobacters. Appl Environ Microbiol 74:1535–1545PubMedPubMedCentralGoogle Scholar
  22. 22.
    Berger M, Neumann A, Schulz S, Simon M, Brinkhoff T (2011) Tropodithietic acid production in Phaeobacter gallaeciensis is regulated by N-acyl homoserine lactone-mediated quorum sensing. J Bacteriol 193:6576–6585PubMedPubMedCentralGoogle Scholar
  23. 23.
    Bruhn JB, Nielsen KF, Hjelm M, Hansen M, Bresciani J, Schulz S, Gram L (2005) Ecology, inhibitory activity, and morphogenesis of a marine antagonistic bacterium belonging to the Roseobacter clade. Appl Environ Microbiol 71:7263–7270PubMedPubMedCentralGoogle Scholar
  24. 24.
    Brinkhoff T, Bach G, Heidorn T, Liang L, Schlingloff A, Simon M (2004) Antibiotic production by a Roseobacter clade-affiliated species from the German Wadden Sea and its antagonistic effects on indigenous isolates. Appl Environ Microbiol 70:2560–2565PubMedPubMedCentralGoogle Scholar
  25. 25.
    Porsby CH, Nielsen KF, Gram L (2008) Phaeobacter and Ruegeria species of the Roseobacter clade colonize separate niches in a Danish turbot (Scophthalmus maximus)-rearing farm and antagonize Vibrio anguillarum under different growth conditions. Appl Environ Microbiol 74:7356–7364PubMedPubMedCentralGoogle Scholar
  26. 26.
    Gram L, Melchiorsen J, Bruhn JB (2010) Antibacterial activity of marine culturable bacteria collected from a global sampling of ocean surface waters and surface swabs of marine organisms. Mar Biotechnol 12:439–451PubMedGoogle Scholar
  27. 27.
    Thole S, Kalhoefer D, Voget S, Berger M, Engelhardt T, Liesegang H, Wollherr A, Kjelleberg S, Daniel R, Simon M (2012) Phaeobacter gallaeciensis genomes from globally opposite locations reveal high similarity of adaptation to surface life. ISME J 6:2229–2244PubMedPubMedCentralGoogle Scholar
  28. 28.
    Tanigaki K, Sato T, Tanaka Y, Ochi T, Nishikawa A, Nagai K, Kawashima H, Ohkuma S (2002) BE18591 as a new H+/Cl− symport ionophore that inhibits immunoproliferation and gastritis. FEBS Lett 524:37–42PubMedGoogle Scholar
  29. 29.
    Egan S, James S, Holmström C, Kjelleberg S (2002) Correlation between pigmentation and antifouling compounds produced by Pseudoalteromonas tunicata. Environ Microbiol 4:433–442PubMedGoogle Scholar
  30. 30.
    Franks A, Haywood P, Holmström C, Egan S, Kjelleberg S, Kumar N (2005) Isolation and structure elucidation of a novel yellow pigment from the marine bacterium Pseudoalteromonas tunicata. Molecules 10:1286–1291PubMedPubMedCentralGoogle Scholar
  31. 31.
    Williamson NR, Simonsen HT, Ahmed RA, Goldet G, Slater H, Woodley L, Leeper FJ, Salmond GP (2005) Biosynthesis of the red antibiotic, prodigiosin, in Serratia: identification of a novel 2-methyl-3-n-amyl-pyrrole (MAP) assembly pathway, definition of the terminal condensing enzyme, and implications for undecylprodigiosin biosynthesis in Streptomyces. Mol Microbiol 56:971–989PubMedGoogle Scholar
  32. 32.
    Cerdeño AM, Bibb MJ, Challis GL (2001) Analysis of the prodiginine biosynthesis gene cluster of Streptomyces coelicolor A3 (2): new mechanisms for chain initiation and termination in modular multienzymes. Chem Biol 8:817–829PubMedGoogle Scholar
  33. 33.
    Markowitz VM, Chen IMA, Palaniappan K, Chu K, Szeto E, Grechkin Y, Ratner A, Jacob B, Huang J, Williams P, Huntemann M, Anderson I, Mavromatis K, Ivanova NN, Kyrpides NC (2012) IMG: the integrated microbial genomes database and comparative analysis system. Nucleic Acids Res 40:D115–D122.  https://doi.org/10.1093/nar/gkr1044 CrossRefPubMedGoogle Scholar
  34. 34.
    Parks DH, Chuvochina M, Waite DW, Rinke C, Skarshewski A, Chaumeil P-A, Hugenholtz P (2018) A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life. Nat BiotechnolGoogle Scholar
  35. 35.
    Coordinators NR (2016) Database resources of the national center for biotechnology information. Nucleic Acids Res 44:D7Google Scholar
  36. 36.
    Boeckmann B, Bairoch A, Apweiler R, Blatter M-C, Estreicher A, Gasteiger E, Martin MJ, Michoud K, O’donovan C, Phan I (2003) The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res 31:365–370PubMedPubMedCentralGoogle Scholar
  37. 37.
    Rost B (1999) Twilight zone of protein sequence alignments. Protein Eng 12:85–94PubMedGoogle Scholar
  38. 38.
    Coustau C, Gourbal B, Duval D, Yoshino T, Adema C, Mitta G (2015) Advances in gastropod immunity from the study of the interaction between the snail Biomphalaria glabrata and its parasites: a review of research progress over the last decade. Fish Shellfish Immunol 46:5–16PubMedGoogle Scholar
  39. 39.
    Lokmer A, Wegner KM (2015) Hemolymph microbiome of Pacific oysters in response to temperature, temperature stress and infection. ISME J 9:670–682PubMedGoogle Scholar
  40. 40.
    Kumar V, Zozaya-Valdes E, Kjelleberg S, Thomas T, Egan S (2016) Multiple opportunistic pathogens can cause a bleaching disease in the red seaweed Delisea pulchra. Environ Microbiol 18:3962–3975PubMedGoogle Scholar
  41. 41.
    Kessler RW, Weiss A, Kuegler S, Hermes C, Wichard T Macroalgal-bacterial interactions: role of dimethylsulfoniopropionate in microbial gardening by Ulva (Chlorophyta). Mol Ecol 2017, 27(8):1808–1819PubMedGoogle Scholar
  42. 42.
    Offret C, Rochard V, Laguerre H, Mounier J, Huchette S, Brillet B, Le Chevalier P, Fleury Y (2018) Protective efficacy of a Pseudoalteromonas strain in European abalone, Haliotis tuberculata, infected with Vibrio harveyi ORM4. Probiotics Antimicrobial Proteins:1–9Google Scholar
  43. 43.
    Holmström C, Kjelleberg S (1999) Marine Pseudoalteromonas species are associated with higher organisms and produce biologically active extracellular agents. FEMS Microbiol Ecol 30:285–293PubMedGoogle Scholar
  44. 44.
    Thomas T, Evans FF, Schleheck D, Mai-Prochnow A, Burke C, Penesyan A, Dalisay DS, Stelzer-Braid S, Saunders N, Johnson J (2008) Analysis of the Pseudoalteromonas tunicata genome reveals properties of a surface-associated life style in the marine environment. PLoS One 3:e3252PubMedPubMedCentralGoogle Scholar
  45. 45.
    Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673–4680PubMedPubMedCentralGoogle Scholar
  46. 46.
    Untergasser A, Cutcutache I, Koressaar T, Ye J, Faircloth BC, Remm M, Rozen SG (2012) Primer3—new capabilities and interfaces. Nucleic Acids Res 40:e115–e115.  https://doi.org/10.1093/nar/gks596 CrossRefPubMedPubMedCentralGoogle Scholar
  47. 47.
    Dayhoff M, Schwartz R, Orcutt B Matrices for detecting distant relationship. Atlas of Protein Sequences 1979, pp 353–358Google Scholar
  48. 48.
    Sambrook J, Russell DW (2001) Molecular cloning: a laboratory manual3rd edn. Coldspring-Harbour Laboratory Press, UKGoogle Scholar
  49. 49.
    Timmermans ML, Paudel YP, Ross AC (2017) Investigating the biosynthesis of natural products from marine proteobacteria: a survey of molecules and strategies. Mar Drugs 15:235PubMedCentralGoogle Scholar
  50. 50.
    Kumar S, Stecher G, Tamura K (2016) MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 33:1870–1874PubMedPubMedCentralGoogle Scholar
  51. 51.
    Freese HM, Sikorski J, Bunk B, Scheuner C, Meier-Kolthoff JP, Spröer C, Gram L, Overmann J (2017) Trajectories and drivers of genome evolution in surface-associated marine Phaeobacter. Genome Biol Evol 9:3297–3311PubMedPubMedCentralGoogle Scholar
  52. 52.
    Raina J-B, Tapiolas D, Motti CA, Foret S, Seemann T, Tebben J, Willis BL, Bourne DG (2016) Isolation of an antimicrobial compound produced by bacteria associated with reef-building corals. PeerJ 4:e2275PubMedPubMedCentralGoogle Scholar
  53. 53.
    Sonnenschein EC, Nielsen KF, D'Alvise P, Porsby CH, Melchiorsen J, Heilmann J, Kalatzis PG, López-Pérez M, Bunk B, Spröer C (2017) Global occurrence and heterogeneity of the Roseobacter-clade species Ruegeria mobilis. ISME J 11:569–583PubMedGoogle Scholar
  54. 54.
    Bentzon-Tilia M, Gram L (2017) Biotechnological applications of the Roseobacter clade. Bioprospecting. Springer, pp 137–166Google Scholar
  55. 55.
    Wilson MZ, Wang R, Gitai Z, Seyedsayamdost MR (2016) Mode of action and resistance studies unveil new roles for tropodithietic acid as an anticancer agent and the γ-glutamyl cycle as a proton sink. Proc Natl Acad Sci U S A 113:1630–1635PubMedPubMedCentralGoogle Scholar
  56. 56.
    Williamson NR, Fineran PC, Leeper FJ, Salmond GP (2006) The biosynthesis and regulation of bacterial prodiginines. Nat Rev Microbiol 4:887–899PubMedGoogle Scholar
  57. 57.
    Nakajima S, Kojiri K, Suda H (1993) A new antitumor substance, BE-18591, produced by a streptomycete. I. Fermentation, isolation, physico-chemical and biological properties. J Antibiot 46:1894–1896PubMedGoogle Scholar
  58. 58.
    Jensen PR, Williams PG, Oh D-C, Zeigler L, Fenical W (2007) Species-specific secondary metabolite production in marine actinomycetes of the genus Salinispora. Appl Environ Microbiol 73:1146–1152PubMedGoogle Scholar
  59. 59.
    Slot JC, Rokas A (2011) Horizontal transfer of a large and highly toxic secondary metabolic gene cluster between fungi. Curr Biol 21:134–139PubMedGoogle Scholar
  60. 60.
    Hakvåg S, Fjærvik E, Klinkenberg G, Borgos SEF, Josefsen KD, Ellingsen TE, Zotchev SB (2009) Violacein-producing Collimonas sp. from the sea surface microlayer of costal waters in Trøndelag, Norway. Mar Drugs 7:576–588PubMedPubMedCentralGoogle Scholar
  61. 61.
    Rao D, Webb JS, Kjelleberg S (2006) Microbial colonization and competition on the marine alga Ulva australis. Appl Environ Microbiol 72:5547–5555PubMedPubMedCentralGoogle Scholar
  62. 62.
    Egan S, James S, Holmström C, Kjelleberg S (2001) Inhibition of algal spore germination by the marine bacterium Pseudoalteromonas tunicata. FEMS Microbiol Ecol 35:67–73PubMedGoogle Scholar
  63. 63.
    Taylor RB, Steinberg PD (2005) Host use by Australasian seaweed mesograzers in relation to feeding preferences of larger grazers. Ecology 86:2955–2967Google Scholar
  64. 64.
    Zhang X, Wu H, Li Z, Li Y, Wang S, Zhu D, Wen X, Li S Effects of dietary supplementation of Ulva pertusa and non-starch polysaccharide enzymes on gut microbiota of Siganus canaliculatus. Chin J Oceanol Limnol 2017:1–12Google Scholar
  65. 65.
    Barbieri E, Paster BJ, Hughes D, Zurek L, Moser DP, Teske A, Sogin ML (2001) Phylogenetic characterization of epibiotic bacteria in the accessory nidamental gland and egg capsules of the squid Loligo pealei (Cephalopoda: Loliginidae). Environ Microbiol 3:151–167PubMedGoogle Scholar
  66. 66.
    Porsby CH, Gram L (2016) Phaeobacter inhibens as biocontrol agent against Vibrio vulnificus in oyster models. Food Microbiol 57:63–70PubMedGoogle Scholar
  67. 67.
    Hjelm M, Riaza A, Formoso F, Melchiorsen J, Gram L (2004) Seasonal incidence of autochthonous antagonistic Roseobacter spp. and Vibrionaceae strains in a turbot larva (Scophthalmus maximus) rearing system. Appl Environ Microbiol 70:7288–7294PubMedPubMedCentralGoogle Scholar
  68. 68.
    Ballestriero F, Nappi J, Zampi G, Bazzicalupo P, Di Schiavi E, Egan S (2016) Caenorhabditis elegans employs innate and learned aversion in response to bacterial toxic metabolites tambjamine and violacein. Sci Rep 6:29284PubMedPubMedCentralGoogle Scholar
  69. 69.
    O’Dwyer K, Blasco-Costa I, Poulin R, Faltýnková A (2014) Four marine digenean parasites of Austrolittorina spp. (Gastropoda: Littorinidae) in New Zealand: morphological and molecular data. Syst Parasitol 89:133–152PubMedGoogle Scholar
  70. 70.
    Ayala-Díaz M, Richardson JM, Anholt BR (2017) Local site differences in survival and parasitism of periwinkles (Littorina sitkana Philippi, 1846). Ecol Evol 7:1021–1029PubMedPubMedCentralGoogle Scholar
  71. 71.
    Curtis L (2002) Ecology of larval trematodes in three marine gastropods. Parasitology 124:43–56Google Scholar
  72. 72.
    Rao D, Webb JS, Kjelleberg S (2005) Competitive interactions in mixed-species biofilms containing the marine bacterium Pseudoalteromonas tunicata. Appl Environ Microbiol 71:1729–1736PubMedPubMedCentralGoogle Scholar
  73. 73.
    Sturtevant D, Lee Y-J, Chapman KD (2016) Matrix assisted laser desorption/ionization-mass spectrometry imaging (MALDI-MSI) for direct visualization of plant metabolites in situ. Curr Opin Biotechnol 37:53–60PubMedGoogle Scholar

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Authors and Affiliations

  1. 1.Centre for Marine Bio-Innovation and School of Biological, Earth and Environmental SciencesThe University of New South Wales SydneySydneyAustralia

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