Microbial Diversity of Saline Environments
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Díaz‑Cárdenas et al. AMB Expr (2017) 7:223 https://doi.org/10.1186/s13568-017-0527-6 ORIGINAL ARTICLE Open Access Microbial diversity of saline environments: searching for cytotoxic activities Carolina Díaz‑Cárdenas1, Angela Cantillo2, Laura Yinneth Rojas3, Tito Sandoval3, Susana Fiorentino3, Jorge Robles4, Freddy A. Ramos5, María Mercedes Zambrano2 and Sandra Baena1* Abstract In order to select halophilic microorganisms as a source of compounds with cytotoxic activities, a total of 135 bacte‑ rial strains were isolated from water and sediment samples collected from the Zipaquirá salt mine in the Colombian Andes. We determined the cytotoxic efects of 100 crude extracts from 54 selected organisms on the adherent murine mammary cell carcinoma 4T1 and human mammary adenocarcinoma MCF-7 cell lines. These extracts were obtained from strains of Isoptericola, Ornithinimicrobium, Janibacter, Nesterenkonia, Alkalibacterium, Bacillus, Halomonas, Chromohalobacter, Shewanella, Salipiger, Martellela, Oceanibaculum, Caenispirillum and Labrenzia. The extracts of 23 1 strains showed an IC50 of less than 100 μg mL− . They were subsequently analyzed by LC/MS allowing dereplication of 20 compounds. The cytotoxic efect was related to a complex mixture of diketopiperazines present in many of the extracts analyzed. The greatest cytotoxic activity against both of the evaluated cell lines was obtained from the 1 chloroform extract of Labrenzia aggregata USBA 371 which had an IC50 < 6 μg mL− . Other extracts with high levels 1 of cytotoxic activity were obtained from Bacillus sp. (IC50 < 50 μg mL− ) which contained several compounds such as macrolactin L and A, 7-O-succinoylmacrolactin F and iturin. Shewanella chilikensis USBA 344 also showed high levels 1 of cytotoxic activity against both cell lines in the crude extract: an IC50 < 15 μg mL− against the 4T1 cell line and an 1 1 IC50 < 68 μg mL− against the MCF-7 cell line. Nesterenkonia sandarakina CG 35, which has an IC50 of 118 µg mL− against 4T1, is a producer of diketopiperazines and 1-acetyl-β-carboline. Also, Ornithinimicrobium kibberense CG 24, 1 which has IC50 < 50 μg mL− , was a producer of diketopiperazines and lagunamycin. Our study demonstrates that these saline environments are habitats of halophilic and halotolerant bacteria that have previously unreported cyto‑ toxic activity. Keywords: Phylogenetic diversity, Halophilic bacteria, Cytotoxic activity, Secondary metabolism Introduction their potentially promising applications. Tey are sources Saline environments are usually defned as those con- of compatible solutes, stable enzymes (DNAses, lipases, taining salt concentrations similar to seawater (~ 3.5% amylases and proteases), bacteriorhodopsin, polymers, (w/v) total dissolved salts) whereas hypersaline environ- β-carotene and other organic substances of interest ments contain higher salt concentrations and these envi- (Chen et al. 2010; Oren 2010; Braña et al. 2015; da Silva ronments are largely used for the study of the microbial et al. 2015). diversity and ecology (Ventosa et al. 2014). Halophiles Tese microorganisms have been also considered as a have attracted the interests of researchers because of potential source of bioactive compounds. Several anti- their adaptability to a wide range of salinities as well as tumor and antimicrobial substances have already been isolated from moderately and extremely halophilic microorganisms including archaeal proteinaceous anti- *Correspondence: [email protected] microbials (i.e. halocins) that have been isolated from 1 Unidad de Saneamiento y Biotecnología Ambiental, Departamento de Biología, Pontifcia Universidad Javeriana, POB 56710, Bogotá DC, several extremely halophilic archaea such as Natrinema Colombia sp. (Karthikeyan et al. 2013) and Haloferax mediterranei Full list of author information is available at the end of the article © The Author(s) 2017. This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. Díaz‑Cárdenas et al. AMB Expr (2017) 7:223 Page 2 of 16 2− −1 (O’Connor and Shand 2002). Other examples are pig- (SO3 mg L ) was performed using standard methods ments such as prodigiosin isolated from Vibrio spp., (APHA/AWWA/WEF 2012). that exhibit antimicrobial activity (Gallardo et al. 2016). Lipopeptides, polyketides, terpenes, macrolac- Strains tins from diverse microorganisms such as Saccharo- Both halophilic microorganisms isolated from Zipaquirá thrix sp., Nocardiopsis sp., and Bacillus spp. (Gan et al. salt mine and other previously isolated strains were used 2015; Son et al. 2016; Kim et al. 2017) and diketopip- for screening in this study. Tese previously isolated erazines (DKPs) from Streptomyces spp., Bacillus spp. strains were obtained in a previous study from two saline and Nocardiopsis spp. (Raju et al. 2009; Fu et al. 2011; springs in the Central Mountain Range of the Colom- Yonezawa et al. 2011; Gu et al. 2013). Tus, the saline bian Andes and are part of our collection of microorgan- environments could be largely underexplored ecologi- isms (Díaz-Cárdenas and Baena 2015): Oceanibaculum cal niches for the discovery of bioactive metabolites and indicum USBA 36, Caenispirillum bisanense USBA 85, these halophilic microorganisms are potential sources Shewanella chilikensis USBA 344 and Labrenzia aggre- for a broad range of new therapeutic compounds gata USBA 371. All of the strains evaluated for the (Demain 2014). Te current estimate that 90% of the cytotoxic screenings were deposited in the Colección de biosynthetic capacity of microorganisms is yet to be dis- microorganismos de la Pontifcia Universidad Javeriana covered highlights the importance of research in micro- (WDCM857). bial diversity and in the discovery of bioactive principles as keys to unlocking the metabolic potential of microbes Isolation and enrichment of halophilic microorganisms (Walsh and Fischbach 2010). In order to isolate halophilic microorganisms the fol- Te aim of this study was to generate information on lowing media were used. (1) Actinomycete isolation the cytotoxic potential of extracts and compounds pro- agar (per liter of distilled water): 4% (w/v) NaCl, 2.0 g of duced by halophilic and halotolerant organisms isolated sodium caseinate, 0.1 g of asparagine, 4.0 g of sodium from unexplored Colombian rock salt and saline spring propionate, 0.5 g of K2HPO4, 0.1 g of MgSO4·7H2O, 0.1 g environments. Tus, in this study, halophilic microor- of FeSO4, 5.0 g of glycerol and 15 g of agar (Sigma). (2) ganisms were isolated from hypersaline environments at Halophilic medium (HM) (per liter of distilled water): 10 the Zipaquirá salt mine, located in the eastern Andean or 4% (w/v) NaCl, 2.0 g of KCl, 1.0 g of MgSO4, 0.36 g . Mountain range. Tey were then analyzed for their of CaCl2 2H2O, 0.23 g of NaBr, 0.06 g of NaHCO 3, trace capacities to produce cytotoxic compounds under several FeCl3, 10.0 g of yeast extract (Difco), 5.0 g of peptone salt concentrations. (Difco) and 1.0 g of glucose (pH 7.5) (Ventosa Ucero et al. 1982). (3) M63 medium (per liter of distilled water): Materials and methods 13.6 g of KH2PO4, 2 g of (NH 4)2SO4, 0.5 g of FeSO4·7H2O, Zipaquirá salt mine: site description and sampling 0.24 g of MgSO4·7H2O and 4 g of glucose (Takashina Samples of water, sediment, brine and solid (rock salt) et al. 1994). (4) Water from the sampling points fl- were collected in 500 mL sterile glass and plastic bottles tered through 47 mm diameter flters with a pore size of from six sampling points during three sampling events at 0.45 μm (GTTP, Millipore, Billerica, MA, USA) and then the Zipaquirá salt mine in Colombia (5°01′06.18″N and sterilized at 121 °C and 15 psi for 30 min. Tis water was 74°0′13.63″W) at 2656 m.a.s.l. Te samples were used supplemented with 1 ml L−1 of the oligoelement solution to inoculate basal salt medium, to which several carbon SL10 (Widdel et al. 1983) and either 0.1% (w/v) casamino sources were added. Te samples were carefully stored at acids, 10 mM glycerol or 4 mM acetic acid as the carbon 4 °C and transported to the laboratories prior to analysis. source. Te culture medium pH was adjusted to 6.0–7.0 Te samples were used for enrichment on the following with 10% NaOH (w/v) (Merck), to take into account the day. in situ pH at the sampling points. Enrichments were per- For physical–chemical analysis, 5 L of water from each formed by inoculating 1 mL of sample from each of the sampling point were collected. Te temperature and pH six sampling points into tubes containing 5 mL of culture analyses were performed in situ using a Hach pH meter. media and then incubating the tubes at room tempera- 2+ −1 Te analysis of calcium (Ca mg L ), total organic car- ture (22 °C ± 3) in the dark and without agitation until bon (mg L−1), chlorides (Cl− mg L−1), total phospho- growth was observed. Microbial growth was inspected 3− −1 −1 rous (PO4 mg L ), total iron (Fe mg L ), magnesium daily for 2 weeks by light microscopy using a Nikon phase (Mg2+ mg L−1), manganese (Mn2+ mg L−1), nitrates contrast microscope (Nikon i50 Nikon, Melville, NY, −1 −1 (N-NO3 mg L ), ammoniacal nitrogen (N-NH4 mg L ), USA). After confrmation of growth, tenfold serial dilu- potassium (K+ mg L−1), salinity (conductivity mS cm−1), tions were prepared and inoculated into tubes with 5 mL + −1 2− −1 sodium (Na mg L ), sulfate (SO 4 mg L ) and sulftes of culture medium, and the last positive serial dilution Díaz‑Cárdenas et al.