Identification and screening of enzymatic abilities of Ktedonobacteria from forest soil of Cisolok Geothermal Area, Indonesia

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MAZYTHA KINANTI RACHMANIA
FITRIA NINGSIH
DHIAN CHITRA AYU FITRIA SARI
YURIZA ESHANANDA
YASUTERU SAKAI
SHUHEI YABE
AKIRA YOKOTA
WELLYZAR SJAMSURIDZAL

Abstract

Abstract. Rachmania MK, Ningsih F, Sari DCAF, Eshananda Y, Sakai Y, Yabe S, Yokota A, Sjamsuridzal W. 2022. Identification and screening of enzymatic abilities of Ktedonobacteria from forest soil of Cisolok Geothermal Area, Indonesia. Biodiversitas 23: 4686-4695. This study aimed to provide information on culturable Ktedonobacteria from forest soil in the Cisolok geothermal area and their potential as enzyme producers. Twelve ktedonobacterial isolates were obtained from this study and identified based on full-sequence of the 16S rRNA gene. Seventeen isolates (including five isolates from previous studies) were used for enzymatic screening and phylogenetic analyses. Screening of amylolytic (0.5% soluble starch) and cellulolytic (0.5% carboxymethylcellulose) (CMC) activities from ktedonobacterial isolates was performed on a ten-fold diluted R2A agar medium, and were incubated at 30 °C for 21 days. The EzBioCloud search revealed that all isolates showed low sequence similarities with Dictyobacter aurantiacus S-27T (97.82 to 98.18%) as their closest related species. The phylogenetic tree showed that all isolates belong to the genus Dictyobacter (family Dictyobacteraceae of the class Ktedonobacteria). All isolates formed a monophyletic group and were placed as the sister clade to D. aurantiacus, as supported by a very strong bootstrap value (99%). Screening of amylolytic and cellulolytic abilities showed that most isolates (88.23%) were able to degrade both 0.5% starch and 0.5% CMC as substrates. This study revealed the presence of Ktedonobacteria with amylolytic and cellulolytic abilities in the forest soil of Cisolok geothermal area.

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References
Acosta-Martínez V, Dowd SE, Bell CW, Lascano R, Booker JD, Zobeck TM, Upchurch DR. 2010. Microbial community composition as affected by dryland cropping systems and tillage in a semiarid sandy soil. Diversity 2 (6): 910-931.
Brodie EL, DeSantis TZ, Joyner DC, Baek SM, Larsen JT, Andersen GL, Hazen TC, Richardson PM, Herman DJ, Tokunaga TK, Wan JM, Firestone MK. 2006. Application of a high-density oligonucleotide microarray approach to study bacterial population dynamics during uranium reduction and reoxidation. Appl. Environ. Microbiol 72 (9): 6288-6298.
Cavaletti L, Monciardini P, Bamonte R, Schumann P, Rohde M, Sosio M, Donadio S. 2006. New lineage of filamentous, spore-forming, gram-positive bacteria from soil. Appl. Environ. Microbiol 72 (6): 4360-4369.
Effendi Y, Aini N, Pambudi A, Sasaerila HY. 2020. Metagenomics analysis of soil microbial communities in plant agroforestry system rubber tree (Hevea brasiliensis)–Ganyong (Canna sp.). IOP Conf Ser: Earth Environ Sci 468: 012045.
Eshananda Y, Ningsih F, Sakai Y, Yokota A, Yabe S, Sjamsuridzal W. 2020. Isolation and identification of rare actinomycete-like bacteria from soil-based on 16S ribosomal RNA gene sequences. J Phys: Conf Ser. 1524: 012062.
Felsenstein J. 1981. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17 (6): 368-376.
Felsenstein J. 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39 (4): 783-791.
Gopinath SC, Anbu P, Arshad MM, Lakshmipriya T, Voon CH, Hashim U, Chinni SV. 2017. Biotechnological processes in microbial amylase production. Biomed Res Int 2017: 1272193.
Herdianita NR, Mandradewi W. 2010. Evolution of Cisolok–Cisukarame Geothermal System, West Java–Indonesia, based on its surface manifestation. Proceedings World Geothermal Congress.
Igarashi Y, Yamamoto K, Ueno C, Yamada N, Saito K, Takahashi K, Enomoto M, Kuwahara S, Tashiro E, Imoto M, Xiaohanyao Y, Zhou T, Harunari E, Oku N. 2019. Ktedonoketone and 2’-oxosattabacin, benzenoid metabolites from a thermophilic bacterium Thermosporothrix hazakensis in the phylum Chloroflexi. J Antibiot Res 72 (9): 653-660.
Kimura M. 1980. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16 (2): 111-120.
King CE, King GM. 2014. Description of Thermogemmatispora carboxidivorans sp. nov., a carbon-monoxide-oxidizing member of the class Ktedonobacteria isolated from a geothermally heated biofilm, and analysis of carbon monoxide oxidation by members of the class Ktedonobacteria. Int J Syst Evol Microbiol 64 (4): 1244-1251.
Lane D. 1991. 16S/23S rRNA sequencing. In: Stackebrandt E, Goodfellow M. Nucleic Acid Techniques in Bacterial Systematics. John Wiley and Sons, New York.
Littlechild JA. 2015. Enzymes from extreme environments and their industrial applications. Front Bioeng Biotechnol 3: 161.
Mezzasoma A, Coleine C, Sannino C, Selbmann L. 2022. Endolithic bacterial diversity in lichen-dominated communities is shaped by sun exposure in McMurdo Dry Valleys, Antarctica. Microb Ecol 83 (2): 328-339.
Park JS, Kagaya N, Hashimoto J, Izumikawa M, Yabe S, Shin-ya K, Nishiyama M, Kuzuyama, T. 2014. Identification and biosynthesis of new Acyloins from the thermophilic bacterium Thermosporothrix hazakensis SK20-1T. Chembiochem 15 (4): 527-532.
Rachmania MK, Ningsih F, Sakai Y, Yabe S, Yokota A, Sjamsuridzal W. 2020. Isolation and identification of Ktedonobacteria using 16S rRNA gene sequences data. IOP Conf Ser: Earth Environ Sci 439: 012031.
Rzhetsky A, Nei M. 1992. A simple method for estimating and testing minimum-evolution trees. Mol Biol Evol 9 (5): 945-967.
Saitou N, Nei M. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Molecular Biology and Evolution 4 (4): 406-425.
Satyanarayana T, Littlechild J, Kawarabayasi Y. 2013. Thermophilic Microbes in Environmental and Industrial Biotechnology: Biotechnology of Thermophiles, 2nd ed. Springer, New York.
Stott MB, Crowe MA, Mountain BW, Smirnova AV, Hou S, Alam M, Dunfield PF. 2008. Isolation of novel bacteria, including a candidate division, from geothermal soils in New Zealand. Environ Microbiol 10 (8): 2030-2041.
Sumartha AGA, Kurniawan I, Wiradinata R, Nandaliarasyad N, Pratama HB, Prabata TW. 2020. Updating the Conceptual Model of Cisolok-Cisukarame Geothermal field, West Java, Indonesia. IOP Conf Ser: Earth Environ Sci 417: 012025.
Swofford DL, Berlocher SH. 1987. Inferring evolutionary trees from gene frequency data under the principle of maximum parsimony. Syst Biol 36 (3): 293-325.
Tamura K, Stecher G, Kumar S. 2021. MEGA11: molecular evolutionary genetics analysis version 11. Mol Biol Evol 38 (7): 3022-3027.
Tomazini A, Higasi P, Manzine LR, Stott M, Sparling R, Levin DB, Polikarpov I. 2019. A novel thermostable GH5 ?-xylosidase from Thermogemmatispora sp. T81. New biotechnology 53: 57-64.
Wang CM, Zheng Y, Sakai Y, Toyoda A, Minakuchi Y, Abe K, Yokota A, Yabe S. 2019. Tengunoibacter tsumagoiensis gen. nov., sp. nov., Dictyobacter kobayashii sp. nov., Dictyobacter alpinus sp. nov., and description of Dictyobacteraceae fam. nov. within the order Ktedonobacterales isolated from Tengu-no-mugimeshi, a soil-like granular mass of micro-organisms, and emended descriptions of the genera Ktedonobacter and Dictyobacter. Int J Syst Evol Microbiol 69 (7): 1910-1918.
Yabe S, Aiba Y, Sakai Y, Hazaka M, Yokota A. 2010a. A life cycle of branched aerial mycelium-and multiple budding spore-forming bacterium Thermosporothrix hazakensis belonging to the phylum Chloroflexi. J Gen Appl Microbiol 56 (2): 137-141.
Yabe S, Aiba Y, Sakai Y, Hazaka M, Yokota A. 2010b. Thermosporothrix hazakensis gen. nov., sp. nov., isolated from compost, description of Thermosporotrichaceae fam. nov. within the class Ktedonobacteria Cavaletti et al. 2007 and emended description of the class Ktedonobacteria. Int J Syst Evol Microbiol 60 (8): 1794-1801.
Yabe S, Sakai Y, Abe K, Yokota A, Také A, Matsumoto A, Sugiharto A, Susilowati D, Hamada M, Nara K, Sudiana IM, Otsuka S. 2017. Dictyobacter aurantiacus gen. nov., sp. nov., a member of the family Ktedonobacteraceae, isolated from soil, and emended description of the genus Thermosporothrix. Int J Syst Evol Microbiol 67 (8): 2615-2621.
Yabe S, Sakai Y, Abe K, Yokota A. 2017a. Diversity of Ktedonobacteria with actinomycetes-like morphology in terrestrial environments. Microbes Environ ME16144.
Yabe S, Sakai Y, Hazaka M, Fitrianingsih, Oetari A, Sjamsuridzal W, Yokota A. 2017. The attractive features of “Ktedonobacteria” in Indonesia and their potential as microbial resources. Paper Proceedings Scholar Summit 2017. Universitas Indonesia, Depok: 400-404.
Yabe S, Sakai Y, Yokota A. 2016. Thermosporothrix narukonensis sp. nov., belonging to the class Ktedonobacteria, isolated from fallen leaves on geothermal soil, and emended description of the genus Thermosporothrix. Int J Syst Evol Microbiol 66 (6): 2152-2157.
Yabe S, Zheng Y, Wang CM, Sakai Y, Abe K, Yokota A, Donadio S, Cavaletti L, Monciardini P. 2021. Reticulibacter mediterranei gen. nov., sp. nov., within the new family Reticulibacteraceae fam. nov., and Ktedonospora formicarum gen. nov., sp. nov., Ktedonobacter robiniae sp. nov., Dictyobacter formicarum sp. nov. and Dictyobacter arantiisoli sp. nov., belonging to the class Ktedonobacteria. Int J Syst Evol Microbiol 71 (7): 004883.
Yan B, Guo X, Liu M, Huang Y. 2020. Ktedonosporobacter rubrisoli gen. nov., sp. nov., a novel representative of the class Ktedonobacteria, isolated from red soil, and proposal of Ktedonosporobacteraceae fam. nov. Int J Syst Evol Microbiol 70 (2): 1015-1025.
Yoon SH, Ha SM, Kwon S, Lim J, Kim Y, Seo H, Chun J. 2017. Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Intl J Syst Evol Microbiol 67 (5): 1613.
Zheng Y, Maruoka M, Nanatani K, Hidaka M, Abe N, Kaneko J, Sakai Y, Abe K, Yokota A, Yabe S. 2021. High cellulolytic potential of the Ktedonobacteria lineage revealed by genome-wide analysis of CAZymes. J Biosci Bioeng 131 (6): 622-630.
Zheng Y, Saitou A, Wang CM, Toyoda A, Minakuchi Y, Sekiguchi Y, Ueda K, Takano H, Sakai Y, Abe K, Yokota A, Yabe S. 2019a. Genome features and secondary metabolites biosynthetic potential of the class Ktedonobacteria. Front Microbiol 10, 893.
Zheng Y, Wang CM, Sakai Y, Abe K, Yokota A, Yabe S. 2019b. Thermogemmatispora aurantia sp. nov. and Thermogemmatispora argillosa sp. nov., within the class Ktedonobacteria, and emended description of the genus Thermogemmatispora. Intl J Syst Evol Microbiol 69 (6): 1744-1750.
Zheng Y, Wang CM, Sakai Y, Abe K, Yokota A, Yabe S. 2020. Dictyobacter vulcani sp. nov., belonging to the class Ktedonobacteria, isolated from soil of the Mt Zao volcano. Intl J Syst Evol Microbiol 70 (3): 1805-1813.

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