6,319
Views
18
CrossRef citations to date
0
Altmetric
Article

Functional profiling of bacterial communities in Lake Tuz using 16S rRNA gene sequences

, ORCID Icon, ORCID Icon, , ORCID Icon, ORCID Icon & ORCID Icon show all
Pages 1-10 | Received 15 Sep 2020, Accepted 17 Oct 2020, Published online: 31 Oct 2020

References

  • Edbeib MF, Wahab RA, Huyop F. Halophiles: biology, adaptation, and their role in decontamination of hypersaline environments. World J Microbiol Biotechnol. 2016;32(8):1–23.
  • Birbir M, Ogan A, Calli B, et al. Enzyme characteristics of extremely halophilic archaeal community in Tuzkoy Salt Mine, Turkey. World J Microbiol Biotechnol. 2004;20(6):613–621.
  • Birbir M, Calli B, Mertoglu B, et al. Extremely halophilic Archaea from Tuz Lake, Turkey, and the adjacent Kaldirim and Kayacik salterns. World J Microbiol Biotechnol. 2007;23(3):309–316.
  • Mutlu MB, Martínez-García M, Santos F, et al. Prokaryotic diversity in Tuz Lake, a hypersaline environment in Inland Turkey. FEMS Microbiol Ecol. 2008;65(3):474–483.
  • Edbeib MF, Wahab RA, Kaya Y, et al. In silico characterization of a novel dehalogenase (DehHX) from the halophile Pseudomonas halophila HX isolated from Tuz Gölü Lake, Turkey: insights into a hypersaline-adapted dehalogenase. Ann Microbiol. 2017;67(5):371–382.
  • Edbeib MF, Aksoy HM, Kaya Y, et al. Haloadaptation: insights from comparative modeling studies between halotolerant and non-halotolerant dehalogenases. J Biomol Struct Dyn. 2020;38(12):3452–3410.
  • Tremblay J, Singh K, Fern A, et al. Primer and platform effects on 16S rRNA tag sequencing. Front Microbiol. 2015;6:771.
  • Klindworth A, Pruesse E, Schweer T, et al. Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies. Nucleic Acids Res. 2013;41(1):e1.
  • Vargas-Albores F, Martínez-Córdova LR, Martínez-Porchas M, et al. Functional metagenomics: a tool to gain knowledge for agronomic and veterinary sciences. Biotechnol Genet Eng Rev. 2019;35(1):69–91.
  • Huse SM, Dethlefsen L, Huber JA, et al. Exploring microbial diversity and taxonomy using SSU rRNA hypervariable tag sequencing. PLoS Genet. 2008;4(11):e1000255.
  • Zaikova E, Goerlitz DS, Tighe SW, et al. Antarctic relic microbial mat community revealed by metagenomics and metatranscriptomics. Front Ecol Evol. 2019;7:1.
  • Narayan NR, Weinmaier T, Laserna-Mendieta EJ, et al. Piphillin predicts metagenomic composition and dynamics from DADA2-corrected 16S rDNA sequences. BMC Genomics. 2020;21(1):56.
  • Mise K, Fujita K, Kunito T, et al. Phosphorus-mineralizing communities reflect nutrient-rich characteristics in Japanese arable Andisols. Microbes Environ. 2018;33(3):282–289.
  • Mallick H, Franzosa EA, McLver LJ, et al. Predictive metabolomic profiling of microbial communities using amplicon or metagenomic sequences. Nat Commun. 2019;10(1):3136.
  • Langille MGI, Zaneveld J, Caporaso JG, et al. Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nat Biotechnol. 2013;31(9):814–821.
  • Muslem WH, Edbeib MF, Aksoy HM, et al. Biodegradation of 3-chloropropionic acid (3-CP) by Bacillus cereus WH2 and its in silico enzyme-substrate docking analysis. J Biomol Struct Dyn. 2020;38(11):3432–3441.
  • Oyewusi HA, Wahab RA, Kaya Y, et al. Alternative bioremediation agents against haloacids, haloacetates and chlorpyrifos using novel halogen-degrading bacterial isolates from the hypersaline lake Tuz. Catalysts. 2020;10(6):651.
  • Heidarrezaei M, Shokravi H, Huyop F, et al. Isolation and characterization of a novel bacterium from the marine environment for trichloroacetic acid bioremediation. Appl Sci. 2020;10(13):4593.
  • Muslem WH, Edbeib MF, Wahab RA, et al. The potential of a novel β-specific dehalogenase from Bacillus cereus WH2 as a bioremediation agent for the removal of β-haloalkanoic acids. Malays J Microbiol. 2017;13(4):298–307.
  • Association APH, Association AWW, Federation WPC, et al. Standard methods for the examination of water and wastewater. Vol. 2. USA: American Public Health Association; University of Illinois at Urbana-Champaign, 1915.
  • Lane DJ. 16S/23S rRNA sequencing. In: Stackebrandt E, Goodfellow M, editors. Nucleic acid techniques in bacterial systematics. New York: Wiley; 1991. p. 115–175.
  • Yoon S-H, Ha S-M, Kwon S, et al. Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol. 2017;67(5):1613–1617.
  • Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30(15):2114–2120.
  • Edgar RC, Haas BJ, Clemente JC, et al. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics. 2011;27(16):2194–2200.
  • Edgar RC. UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nat Methods. 2013;10(10):996–998.
  • Quast C, Pruesse E, Yilmaz P, et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 2013;41(Database issue):D590–D596.
  • Schloss PD, Westcott SL, Ryabin T, et al. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol. 2009;75(23):7537–7541.
  • Douglas GM, Maffei VJ, Zaneveld J, et al. PICRUSt2: an improved and extensible approach for metagenome inference. bioRxiv. 2019;10:672295.
  • Louca S, Doebeli M. Efficient comparative phylogenetics on large trees. Bioinformatics. 2018;34(6):1053–1055.
  • Jacob JH, Hussein EI, Shakhatreh MAK, et al. Microbial community analysis of the hypersaline water of the Dead Sea using high‐throughput amplicon sequencing. MicrobiologyOpen. 2017;6(5):e00500.
  • Wang X, Wang X, Liu M, et al. Bioremediation of marine oil pollution by Brevundimonas diminuta: effect of salinity and nutrients. Desalin Water Treat. 2016;57(42):19768–19768.
  • Tipayno SC, Truu J, Samaddar S, et al. The bacterial community structure and functional profile in the heavy metal contaminated paddy soils, surrounding a nonferrous smelter in South Korea. Ecol Evol. 2018;8(12):6157–6168.
  • Hao B, Wu H, Li W, et al. Periphytic algae mediate interactions between neighbor and target submerged macrophytes along a nutrient gradient. Ecol Indic. 2020;110:105898.
  • Jing Y, Zhang F, He Y, et al. Assessment of spatial and temporal variation of ecological environment quality in Ebinur Lake Wetland National Nature Reserve, Xinjiang, China. Ecol Indic. 2020;110:105874.
  • Edbeib MF, Wahab RA, Huyop F. Characterization of an α-haloalkanoic acid–degrading Pseudomonas aeruginosa MX1 isolated from contaminated seawater. Biorem J. 2016;20(2):89–97.
  • Khosrowabadi E, Huyop F. Screening and characterization of several 2,2-dicholoropropionic acid–degrading bacteria isolated from marine sediment of Danga bay and east coast of Singapore island. Biorem J. 2014;18(1):20–27.
  • Mohanta TK, Mohanta YK, Mohanta N. Role of biotechnology in bioremediation. In: Handbook of Research on Uncovering New Methods for Ecosystem Management Through Bioremediation. Eds. Singh SO, Srivastava K. IGI Global, Pennsylvania, USA. 2015; 399–432.
  • Parte SG, Mohekar AD, Kharat AS. Microbial degradation of pesticide: a review. Afr J Microbiol Res. 2017;11(24):992–1012.
  • Akcay K, Kaya Y. Isolation, characterization and molecular identification of a halotolerant Bacillus megaterium CTBmeg1 able to grow on halogenated compounds. Biotechnol Biotechnol Equip. 2019;33(1):945–953.
  • Nemati M, Edbeib MF, Hamid A, et al. Identification of putative Cof-like hydrolase associated with dehalogenase in Enterobacter cloacae MN1 isolated from the contaminated sea-side area of the Philippines. Malays J Microbiol. 2013;9(3):253–259.