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Predicting the biotechnological potential of bacteria isolated from Antarctic soils, including the rhizosphere of vascular plants

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Abstract

Although there is great interest in cultivable Antarctic microorganisms for potential biotechnology applications, little is known about the microbial diversity and the metabolic potential of samples from Antarctic environments. Two hundred and fifty bacterial isolates were obtained from Antarctic soil and from rhizosphere samples of the Antarctic plants Colobanthus quitensis and Deschampsia antarctica. The samples were screened using amplified ribosomal DNA restriction analysis (ARDRA) and identified by 16S rRNA sequencing. Their metabolic potential was predicted in silico using the Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUS) tool. Additionally, the strains were screened for the production of amylases, proteases, cellulases and chitinases at 4, 12 and 25 °C. The bacterial isolates obtained were classified into the phyla Proteobacteria, Arthrobacter, Firmicutes and Bacteroidetes. The species belonging to the genus Pseudomonas were predominant in all the soil and rhizosphere samples. Twenty-one different Operational Taxonomic Units (OTUs) were detected, and the functional profile of each OTU indicated that most of the predicted genes were related to metabolic functions. Among the OTUs, one affiliated with the genus Rhodococcus sp. (OTU 7) and one affiliated with the genus Rhizobium sp. (OTU 18) showed the largest numbers of predicted genes for amino acid and carbohydrate metabolism and for xenobiotics. The traditional enzyme screening indicated that only proteases were produced by all the bacterial isolates and that the bacterial isolates with greatest predicted metabolic potential (OTUs 7 and 18) also presented the greatest diversity of enzyme production. The results suggested that gene prediction might reflect, at some level, the real metabolic plasticity of the microorganisms and provide a tool for screening promising biotechnological strains, including strains producing multiple enzymes.

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Fig. 1

Adapted from Simões and colleagues (2004)

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References

  • Alnahdi HS (2012) Isolation and screening of extracellular proteases produced by new Isolated Bacillus sp. J Appl Pharm Sci 2:071–074. doi:10.7324/JAPS.2012.2915

    Google Scholar 

  • Antranikian G, Vorgias CE, Bertoldo C (2005) Extreme environments as a resource for microorganisms and novel biocatalysts. Adv Biochem Engin Biotechnol 96:219–262. doi:10.1007/b135786

    CAS  Google Scholar 

  • APHA (1992) Standard methods for the examination of water and wastewater, 18th edn American Public Health Association, Washington, DC

    Google Scholar 

  • Bairagi A, Ghosh KS, Sen SK, Ray AK (2002) Enzyme producing bacterial flora isolated from fish digestive tracts. Aquacult Int 10:109–121. doi:10.1023/A:1021355406412

    Article  CAS  Google Scholar 

  • Bozal N, Montes MJ, Mercadé E (2007) Pseudomonas guineae sp. nov., a novel psychrotolerant bacterium from an Antarctic environment. Int J Syst Evol Micr 57:2609–2612. doi:10.1099/ijs.0.65141-0

    Article  CAS  Google Scholar 

  • Brizzio S, Turchetti B, De García V, Libkind D, Buzzini P, Van Broock M (2007) Extracellular enzymatic activities of basidiomycetous yeasts isolated from glacial and subglacial waters of northwest Patagonia (Argentina). Can J Microbiol 53:519–525. doi:10.1139/W07-010

    Article  CAS  PubMed  Google Scholar 

  • Carrión O, Miñana-Galbis D, Montes MJ, Mercadé E (2011) Pseudomonas deceptionensis sp. nov., a psychrotolerant bacterium from the Antarctic. Int J Syst Evol Micr 61:2401–2405. doi:10.1099/ijs.0.024919-0

    Article  Google Scholar 

  • Chong CW, Pearce DA, Convey P, Yew WC, Tan IKP (2012) Patterns in the distribution of soil bacterial 16S rRNA gene sequences from different regions of Antarctica. Geoderma 181–182:45–55. doi:10.1016/j.geoderma.2012.02.017

    Article  Google Scholar 

  • Cole JR, Wang Q, Cardenas E, Fish J, Chai B, Farris RJ, Kulam-Syed-Mohideen AS, McGarrell DM, Marsh T, Garrity GM, Tiedje JM (2009) The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res 37:141–145. doi:10.1093/nar/gkn879

    Article  Google Scholar 

  • Curry CH, McCarthy JS, Darragh HM, Wake RA, Churchill SE, Robins AM, Lowen RJ (2005) Identification of an agent suitable for disinfecting boots of visitors to the Antarctic. Polar Rec 41:39–45. doi:10.1017/S0032247404003961

    Article  Google Scholar 

  • D’Amico S, Collins T, Marx JC, Feller G, Gerday C (2006) Psychrophilic microorganisms: challenges for life. EMBO Rep 7:385–389. doi:10.1038/sj.embor.7400662

    Article  PubMed  PubMed Central  Google Scholar 

  • Fan J, Li L, Han J, Ming H, Li J, Na G, Chen J (2013) Diversity and structure of bacterial communities in Fildes Peninsula, King George Island. Polar Biol 36:1385–1399. doi:10.1007/s00300-013-1358-9

    Article  Google Scholar 

  • Feller G, Gerday C (2003) Psychrophilic enzymes: hot topics in cold adaptation. Nat Rev Microbiol 1:200–208. doi:10.1038/nrmicro773

    Article  CAS  PubMed  Google Scholar 

  • García-Echauri SA, Gidekel M, Gutiérrez-Moraga A, Santos L, De León-Rodríguez A (2011) Isolation and phylogenetic classification of culturable psychrophilic prokaryotes from the Collins glacier in the Antarctica. Folia Microbiol 56:209–214. doi:10.1007/s12223-011-0038-9

    Article  Google Scholar 

  • Gascuel O, Steel M (2006) Neighbor-joining revealed. Mol Biol Evol 23:1997–2000. doi:10.1093/molbev/msl072

    Article  CAS  PubMed  Google Scholar 

  • Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl Acid S 41:95–98

    CAS  Google Scholar 

  • Hedges JI, Stern JH (1984) Carbon and nitrogen determinations of carbonate-containing solids. Limnol Oceanogr 29:657–663. doi:10.4319/lo.1984.29.3.0657

    Article  CAS  Google Scholar 

  • Helmke E, Weyland H (2004) Psychrophilic versus psychrotolerant bacteria-occurrence and significance in polar and temperate marine habitats. Cel. Mol Biol 50:553–561. doi:10.1170/T545

    CAS  Google Scholar 

  • Jiménez DJ, Dini-Andreote F, Van Elsas JD (2014) Metataxonomic profiling and prediction of functional behaviour of wheat straw degrading microbial consortia. Biotechnol Biofuels 7:1–17. doi:10.1186/1754-6834-7-92

    Article  Google Scholar 

  • Joshi S, Satyanarayana, T (2013) Biotechnology of cold-active proteases. Biology 2:755–783. doi:10.3390/biology2020755

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Jukes TH, Cantor CR (1969) Evolution of protein molecules. In: Munro HN (ed) Mammalian protein metabolism. Academic Press, New York, pp 21–132

    Chapter  Google Scholar 

  • Lane DJ (1991) Nucleic acid techniques in bacterial systematics. In: Stackebrandt E, Goodfellow M (eds) 16S/23 S rRNA sequencing. Wiley, New York, pp 115–175

    Google Scholar 

  • Langille MGI, Zaneveld J, Caporaso JG, McDonald D, Knights D, Reyes JA, Clemente JC, Burkepile DE, Vega Thurber RL, Knight R, Beiko RG, Huttenhower C (2013) Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nat Biotechnol 31:814–821. doi:10.1038/nbt.2676

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Liu HX, Rocha CS, Dandekar S, Wan YJ (2016) Functional analysis of the relationship between intestinal microbiota and the expression of hepatic genes and pathways during the course of liver regeneration. J Hepatol 64:641–650. doi:10.1016/j.jhep.2015.09.022

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Manivasagan P, Sivakumar K, Gnanam S, Venkatesan J, Kim SK (2014) Production, biochemical characterization and detergents application of keratinase from the marine Actinobacterium actinoalloteichus sp. MA-32. J Surfactants Deterg 17:669–682. doi:10.1007/s11743-013-1519-4

    Article  CAS  Google Scholar 

  • Marx JC, Collins T, D’Amico S, Feller G, Gerday C (2007) Cold-adapted enzymes from marine Antarctic microorganisms. Mar Biotechnol 9:293–304. doi:10.1007/s10126-006-6103-8

    Article  CAS  PubMed  Google Scholar 

  • Murthy N, Bleakley B (2012) Simplified method of preparing colloidal chitin used for screening of chitinase-producing microorganisms. The internet. J Microbiol 10:1–5

    Google Scholar 

  • Nadkarni RA (1984) Applications of microwave oven sample dissolution in analysis. Anal Chem 56:2233–2237. doi:10.1021/ac00276a056

    Article  CAS  Google Scholar 

  • Pan Q, Wang F, Zhang Y, Cai M, He J, Yang H (2013) Denaturing gradient gel electrophoresis fingerprinting of soil bacteria in the vicinity of the Chinese Great Wall Station, King George Island, Antarctica. J Environ Sci 25:16491655. doi:10.1016/S1001-0742(12)60229-0

    Google Scholar 

  • Pant G, Prakash A, Pavani JVP, Bera S, Deviram GVNS, Kumar A, Panchpuri M RG (2015) Production, optimization and partial purification of protease from Bacillus subtilis. J Taibah Univ Sci 9:50–55. doi:10.1016/j.jtusci.2014.04.010

    Article  Google Scholar 

  • Riffenburgh B (1998) Impacts on the Antarctic environment: tourism vs government programmes. Polar Rec 34:193–196. doi:10.1017/S0032247400025651

    Article  Google Scholar 

  • Schleif RF, Wensink PC (1981) Practical methods in molecular biology. Springer, New York. doi:10.1007/978-1-4612-5956-5

    Book  Google Scholar 

  • Selbmann L, Zucconi L, Ruisi S, Grube M, Cardinale M, Onofri S (2010) Culturable bacteria associated with Antarctic lichens: affiliation and psychrotolerance. Polar Biol 33:71–83. doi:10.1007/s00300-009-0686-2

    Article  Google Scholar 

  • Simas FNB, Schaefer CEGR, Albuquerque Filho MR, Francelino MR, Fernandes Filho EI, Costa LM (2008) Genesis, properties and classification of Cryosols from Admiralty Bay, Maritime Antarctic. Geoderma 144:116–122. doi:10.1016/j.geoderma.2007.10.019

    Article  CAS  Google Scholar 

  • Simões JC, Arigony Neto J, Bremer UF (2004) O uso de mapas antárticos em publicações. Pesqui Antártica Bras 4:191–197

    Google Scholar 

  • Sunnotel O, Nigam P (2002) Pectinolytic activity of bacteria isolated from soil and two fungal strains during submerged fermentation. World J Microb Biot 18:835–839. doi:10.1023/A:1021209123641

    Article  CAS  Google Scholar 

  • Tamura K, Peterson D, Peterson N, Stecher G, Masatoshi N, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731–2739. doi:10.1093/molbev/msr121

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Teather RM, Wood PJ (1982) Use of Congo red-polysaccharide interactions in enumeration and characterization of cellulolytic bacteria from the bovine rumen. Appl Environ Microb 43:777–780

    CAS  Google Scholar 

  • Teixeira LCRS, Peixoto RS, Cury JC; Sul WJ, Pellizari VH, Tiedje J, Rosado AS (2010) Bacterial diversity in rhizosphere soil from Antarctic vascular plants of Admiralty Bay, Maritime Antarctica. ISME J 4:989–1001. doi:10.1038/ismej.2010.35

    PubMed  Google Scholar 

  • Teixeira LCRS, Yeargeau E, Balieiro FC, Piccolo MC, Peixoto RS, Greer CW, Rosado AS (2013) Plant and bird presence strongly influences the microbial communities in soils of Admiralty Bay, Maritime Antarctica. PLoS One 8:e66109. doi:10.1371/journal.pone.0066109

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tosi S, Kostadinova N, Krumova E, Pashova S, Dishliiska V, Spassova B, Vassilev S, Angelova M (2010) Antioxidant enzyme activity of filamentous fungi isolated from Livingston Island, Maritime Antarctica. Polar Biol 33:1227–1237. doi:10.1007/s00300-010-0812-1

    Article  Google Scholar 

  • Verardo DJ, Froelich PN, McIntyre A (1990) Determination of organic carbon and nitrogen in marine sediments using the Carlo-Erba-Na-1500 analyzer. Deep Sea Res A Oceanogr Res Papers 37:157–165. doi:10.1016/0198-0149(90)90034-S

    Article  CAS  Google Scholar 

  • Wang F, Gai Y, Chen M, Xiao X (2009) Arthrobacter psychrochitiniphilus sp. nov., a psychrotrophic bacterium isolated from Antarctica. Int J Syst Evol Micr 59:2759–2762. doi:10.1099/ijs.0.008912-0

    Article  CAS  Google Scholar 

  • Xiao X, Li M, You Z, Wang F (2007) Bacterial communities inside and in the vicinity of the Chinese Great Wall Station, King George Island, Antarctica. Antarct Sci 19:11–16. doi:10.1017/S095410200700003X

    Article  Google Scholar 

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Acknowledgements

The authors thank the support of the Brazilian Ministries of Science, Technology and Innovation (MCTI), of Environment (MMA), Inter-Ministry Commission for Sea Resources (CIRM) and the Brazilian Navy that supported our research in the Comandante Ferraz Station. We also thank the National Council for Scientific and Technological Development (CNPq), the National Council for the Improvement of Higher Education (CAPES), and the Carlos Chagas Filho Foundation for Research Support of Rio de Janeiro State (FAPERJ) for supporting this work.

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  1. Laboratory of Molecular Microbial Ecology—Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro, Cidade Universitária, CCS, Bloco E, 21.941-590, Rio de Janeiro, Brazil

    Aike Costa da Silva, Caio Tavora Coelho da Costa Rachid, Hugo Emiliano de Jesus, Alexandre Soares Rosado & Raquel Silva Peixoto

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  1. Aike Costa da Silva
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Correspondence to Raquel Silva Peixoto.

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da Silva, A.C., Rachid, C.T.C.d.C., de Jesus, H.E. et al. Predicting the biotechnological potential of bacteria isolated from Antarctic soils, including the rhizosphere of vascular plants. Polar Biol 40, 1393–1407 (2017). https://doi.org/10.1007/s00300-016-2065-0

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