Diversity Analysis of an Extremely Acidic Soil in a Layer of Coal Mine Detected the Occurrence of Rare Actinobacteria

Authors

  • Megga Ratnasari PIKOLI Department of Biology, Faculty of Science and Technology, Universitas Islam Negeri Syarif Hidayatullah Jakarta, Ciputat, Tangerang Selatan, Indonesia http://orcid.org/0000-0003-3607-5074
  • Irawan SUGORO Center for Application of Technology of Isotope and Radiation, Badan Tenaga Nuklir Nasional, Jakarta Selatan, Indonesia
  • Suharti SUHARTI Department of Chemistry, Faculty of Science and Computation, Universitas Pertamina, Simprug, Jakarta Selatan, Indonesia

DOI:

https://doi.org/10.48048/wjst.2020.4380

Keywords:

Acidic soil, Actinobacteria, Biodiversity, Clay soil, Coal mine

Abstract

Studies that explore the diversity of microorganisms in unusual (extreme) environments have become more common. Our research aims to predict the diversity of bacteria that inhabit an extreme environment, a coal mine’s soil with pH of 2.93. Soil samples were collected from the soil at a depth of 12 meters from the surface, which is a clay layer adjacent to a coal seam in Tanjung Enim, South Sumatera, Indonesia. A culture-independent method, the polymerase chain reaction based denaturing gradient gel electrophoresis, was used to amplify the 16S rRNA gene to detect the viable-but-unculturable bacteria. Results showed that some OTUs that have never been found in the coal environment and which have phylogenetic relationships to the rare actinobacteria Actinomadura, Actinoallomurus, Actinospica, Streptacidiphilus, Aciditerrimonas, and Ferrimicrobium. Accordingly, the highly acidic soil in the coal mine is a source of rare actinobacteria that can be explored further to obtain bioactive compounds for the benefit of biotechnology.

Downloads

Download data is not yet available.

Metrics

Metrics Loading ...

References

V Torsvik and L Øvreås. Microbial diversity and function in soil: From genes to ecosystems. Curr. Opin. Microbiol. 2002; 5, 240-5.

D Cowan, Q Meyer, W Stafford, S Muyanga, R Cameron and P Wittwer. Metagenomic gene discovery: Past, present and future. Trends Biotechnol. 2005; 23, 321-9.

PD Schloss and J Handelsman. Toward a census of bacteria in soil. PLoS Comput. Biol. 2006; 2, 786-93.

R Berlemont, D Pipers, M Delsaute, F Angiono, G Feller, M Galleni and P Power. Exploring the Antarctic soil metagenome as a source of novel cold-adapted enzymes and genetic mobile elements. Rev. Argent. Microbiol. 2011; 43, 94-103.

JK Vester, MA Glaring and P Stougaard. Discovery of novel enzymes with industrial potential from a cold and alkaline environment by a combination of functional metagenomics and culturing. Microb. Cell Fact. 2014; 13, 72.

P Shrivastava, R Kumar and MS Yandigeri. In vitro biocontrol activity of halotolerant Streptomyces aureofaciens K20: A potent antagonist against Macrophomina phaseolina (Tassi) Goid, Saudi. J. Biol. Sci. 2015; 24, 192-9.

MR Pikoli, P Aditiawati, DI Astuti and Akhmaloka. Bacterial diversity in subbituminous coal and soil from coal mine of South Sumatra, Indonesia. Int. J. Integr. Biol. 2013; 14, 96-103.

AS Azman, I Othman, SS Velu, KG Chan and LH Lee. Mangrove rare actinobacteria: Taxonomy, natural compound, and discovery of bioactivity. Front. Microbiol. 2015; 6, 1-15.

X Guo, N Liu, X Li, Y Ding, F Shang, Y Gao, J Ruan and Y Huang. Red soils harbor diverse culturable actinomycetes that are promising sources of novel secondary metabolites. Appl. Environ. Microbiol. 2015; 81, 3086-103.

S Naorungrote and W Chunglok. Actinomycetes producing anti-methicillin resistant Staphylococcus aureus from soil samples in Nakhon Si Thammarat. Walailak J. Sci. Tech. 2011; 8, 131-8.

DB Xu, WW Ye, Y Han, ZX Deng and K Hong.Natural products from mangrove actinomycetes. Mar. Drugs. 2014; 12, 2590-613.

L Katz and RH Baltz. Natural product discovery: past, present, and future. J. Ind. Microbiol. Biotechnol. 2016; 43, 155-76.

A Chroňáková, V Krištůfek, M Tichý and D Elhottová. Biodiversity of streptomycetes isolated from a succession sequence at a post-mining site and their evidence in Miocene lacustrine sediment. Microbiol. Res. 2010; 165, 594-608.

L Procópio, VM Alvarez, DA Jurelevicius, L Hansen, SJ Sørensen, JS Cardoso, M Pádula, AC Leitão, L Seldin and JD van Elsas. Insight from the draft genome of Dietzia cinnamea P4 reveals mechanisms of survival in complex tropical soil habitats and biotechnology potential. Antonie van Leeuwenhoek, Int. J. Gen. Mol. Microbiol. 2012; 101, 289-302.

G Cuesta, A Soler, JL Alonso, MA Ruvira, T Lucena, DR Arahal and M Goodfellow. Pseudonocardia hispaniensis sp. nov., a novel actinomycete isolated from industrial wastewater activated sludge. Antonie Van Leeuwenhoek 2013; 103,135-42.

A Shade, CS Hogan, AK Klimowicz, M Linske, PS Mcmanus and J Handelsman. Culturing captures members of the soil rare biosphere. Environ. Microbiol. 2012; 14, 2247-52.

FOP Stefani, TH Bell, C Marchand, IE De La Providencia, A El Yassimi, M St-Arnaud and M Hijri. Culture-dependent and -independent methods capture different microbial community fractions in hydrocarbon-contaminated soils. PloS One 2015; 10, 1-16.

VHT Pham and J Kim. Cultivation of unculturable soil bacteria. Trends Biotechnol. 2012; 30, 475-84.

L Cocolin, V Alessandria, P Dolci, R Gorra and K Rantsiou. Culture independent methods to assess the diversity and dynamics of microbiota during food fermentation. Int. J. Food Microbiol. 2013; 167, 29-43.

J Zhou, MA Bruns and JM Tiedje. DNA recovery from soils of diverse composition. Appl. Environ. Microbiol. 1996; 62, 316-22.

A Schmalenberger, F Schwieger and CC Tebbe. Effect of primers hybridizing to different evolutionarily conserved regions of the small-subunit rRNA gene in PCR-based microbial community analyses and genetic profiling. Appl. Environ. Microbiol. 2001; 67, 3557-63.

CA Schneider, WS Rasband and KW Eliceiri. NIH Image to ImageJ: 25 years of image analysis, Nat. Meth. 2012; 9, 671-75.

N Fromin, J Hamelin, S Tarnawski, D Roesti, N Forestier, F Gillet, M Aragno and P Rossi. Minireview Statistical analysis of denaturing gel electrophoresis (DGGE) fingerprinting patterns, Environ. Microbiol. 2007; 4, 634-43.

ES Wright, LS Yilmaz and DR Noguera. DECIPHER, a search-based approach to chimera identification for 16S rRNA sequences. Appl. Environ. Microbiol. 2012; 78,717-25.

K Tamura, G Stecher, D Peterson, A Filipski and S Kumar. MEGA6: Molecular evolutionary genetics analysis version 6.0. Mol. Biol. Evol. 2013; 30, 2725-9.

BC Stöver and KF Müller. TreeGraph 2: Combining and visualizing evidence from different phylogenetic analyses. BMC Bioinform. 2010; 11, 7.

EMS Brito, HA Piñón-Castillo, R Guyoneaud, CA Caretta, JF Gutiérrez-Corona, R Duran, GE Reyna-López, GV Nevárez-Moorillón, A Fahy and M Goñi-Urriza. Bacterial biodiversity from anthropogenic extreme environments: A hyper-alkaline and hyper-saline industrial residue contaminated by chromium and iron. Appl. Microbiol. Biotechnol. 2013; 97, 369-78.

J Liu, ZS Hua, LX Chen, JL Kuang, SJ Li, WS Shu and LN Huang. Correlating microbial diversity patterns with geochemistry in an extreme and heterogeneous environment of mine tailings. Appl. Environ. Microbiol. 2014; 80, 3677-86.

CJ Duan and JX Feng. Mining metagenomes for novel cellulase genes. Biotechnol. Lett. 2010; 32, 1765-75.

S Pandey, S Singh, AN Yadav, L Nain and AK Saxena. Phylogenetic diversity and characterization of novel and efficient cellulase producing bacterial isolates from various extreme environments. Biosci. Biotechnol. Biochem. 2013; 77, 1474-80.

Z Hong, W Chen, X Rong, P Cai, K Dai and Q Huang. The effect of extracellular polymeric substances on the adhesion of bacteria to clay minerals and goethite. Chem. Geol. 2013; 360-361, 118-25.

NV Potekhina, AS Shashkov and IB Naumova. The cell wall of Actinomadura madura contains poly(galactosyl-1C2-glycerol phosphate) and poly-(3-O-methylgalactosyl-1C2-glycerol phosphate). Microbiologiya (Moscow) 1996; 65, 522-6.

M Diao, E Taran, S Mahler and AV Nguyen. A concise review of nanoscopic aspects of bioleaching bacteria-mineral interactions. Adv. Colloid Interface Sci. 2014; 212, 45-63.

D Jiang, Q Huang, P Cai, X Rong and W Chen. Adsorption of Pseudomonas putida on clay minerals and iron oxide. Colloids Surfaces B Biointerfaces 2007; 54, 217-21.

IL Maier and RM Pepper. Earth Environments. In: CP Maier, RM Pepper and IL Gerba (Eds.). Environmental Microbiology. Academic Press, London, 2009, p. 57-81.

Ö Ínceošlu, EF Hoogwout, P Hill and JDV Elsas. Effect of DNA extraction method on the apparent microbial diversity of soil. Appl. Environ. Microbiol. 2010; 76, 3378-82.

HF Santos, FL Carmo, DCA Leite, HE Jesus, PDC Maalouf, CI Almeida, AU Soriano, D Altomari, L Suhett, V Vólaro, E Valoni, M Francisco, J Vieira, R Rocha, BL Sardinha, LB Mendes, RR João, B Lacava, RF Jesus, GV Sebastian, A Pessoa, JD van Elsas, RP Rezende, DO Pires, G Duarte, CB Castro, ASI Rosado and RS Peixoto. Comparison of different protocols for the extraction of microbial DNA from reef corals. Brazilian J. Microbiol. 2012; 43, 517-27.

RW Muirhead, RP Collins and PJ Bremer. Interaction of Escherichia coli and soil particles in runoff. Appl. Environ. Microbiol. 2006; 72, 3406-11.

NK Dhand, JALML Toribio and RJ Whittington. Adsorption of Mycobacterium avium subsp. paratuberculosis to soil particles. Appl. Environ. Microbiol. 2009; 75, 5581-5.

Z Hong, X Rong, P Cai, K Dai, W Liang, W Chen and Q Huang. Initial adhesion of Bacillus subtilis on soil minerals as related to their surface properties. Eur. J. Soil Sci. 2012; 63, 457-66.

L Ranjard, F Poly, J Combrisson, A Richaume, F Gourbière, J Thioulouse and S Nazaret. Heterogeneous cell density and genetic structure of bacterial pools associated with various soil microenvironments as determined by enumeration and DNA fingerprinting approach (RISA). Microb Ecol. 2000; 39, 263-72.

DB Johnson, P Bacelar-Nicolau, N Okibe, A Thomas and KB Hallberg. Ferrimicrobium acidiphilum gen. nov., sp. nov. and Ferrithrix thermotolerans gen. nov., sp. nov.: Heterotrophic, iron-oxidizing, extremely acidophilic actinobacteria. Int. J. Syst. Evol. Microbiol. 2009; 59, 1082-9.

T Itoh, K Yamanoi, T Kudo, M Ohkuma and T Takashina. Aciditerrimonas ferrireducens gen. nov., sp. nov., an iron-reducing thermoacidophilic actinobacterium isolated from a solfataric field. Int. J. Syst. Evol. Microbiol. 2011; 61, 1281-5.

C Falagán and DB Johnson. Acidibacter ferrireducens gen. nov., sp. nov.: An acidophilic ferric iron-reducing gammaproteobacterium. Extremophiles 2014; 18, 1067-73.

L Cavaletti, P Monciardini, P Schumann, M Rohde, R Bamonte, E Busti, M Sosio and S Donadio. Actinospica robiniae gen. nov., sp. nov. and Actinospica acidiphila sp. nov.: Proposal for Actinospicaceae fam. nov. and Catenulisporinae subord. nov. in the order Actinomycetales. Int. J. Syst. Evol. Microbiol. 2006; 56, 1747-53.

P Golinska, L Ahmed, D Wang and M Goodfellow. Streptacidiphilus durhamensis sp. nov., isolated from a spruce forest soil. Antonie Van Leeuwenhoek 2013; 104, 199-206.

AT Bull. Actinobacteria of the Extremobiosphere. In: K Horikoshi (Ed.). Extremophiles Handbook. Springer, Japan, 2011, p. 1243.

H Muramatsu, R Murakami, ZH Ibrahim, K Murakami, N Shahab and K Nagai Phylogenetic diversity of acidophilic actinomycetes from Malaysia. J. Antibiot. (Tokyo) 2011; 64, 621-4.

T Tamura, Y Ishida, Y Nozawa, M Otoguro and KI Suzuki. Transfer of Actinomadura spadix Nonomura and Ohara 1971 to Actinoallomurus spadix gen. nov., comb. nov., and description of Actinoallomurus amamiensis sp. nov., Actinoallomurus caesius sp. nov., Actinoallomurus coprocola sp. nov., Actinoallomurus fulvus. Int. J. Syst. Evol. Microbiol. 2009; 59, 1867-74.

JY Jiao, L Liu, EM Zhou, DQ Wei, H Ming, WD Xian, CG Yuan, JM Zhong and WJ Li. Actinomadura amylolytica sp. nov. and Actinomadura cellulosilytica sp. nov., isolated from geothermally heated soil. Antonie van Leeuwenhoek, Int. J. Gen. Mol. Microbiol. 2015; 108, 75-83.

M Iorio, SI Maffioli, E Gaspari, R Rossi, P Mauri, M Sosio and S Donadio. Chrolactomycins from the actinomycete actinospica. J. Nat. Prod. 2012; 75, 1991-3.

SH Cho, JH Han, CN Seong and SB Kim. Phylogenetic diversity of acidophilic sporoactinobacteria isolated from various soils. J. Microbiol. 2006; 44, 600-6.

W Nitschke and V Bonnefoy. Energy Acquisition in Low-pH Environments. In: R Quatrini and DB Johnson (Eds.). Acidophiles: Life in Extremely Acidic Environments. Caister Academic Press, Norfolk, UK, 2016, p. 19-48.

UniProt Consortium. UniProt: The universal protein knowledgebase. Nucleic Acids Res. 2018; 46, 2699.

Downloads

Published

2020-06-01

How to Cite

PIKOLI, M. R. ., SUGORO, I., & SUHARTI, S. (2020). Diversity Analysis of an Extremely Acidic Soil in a Layer of Coal Mine Detected the Occurrence of Rare Actinobacteria. Walailak Journal of Science and Technology (WJST), 17(6), 529–542. https://doi.org/10.48048/wjst.2020.4380