African Journal of
Microbiology Research

  • Abbreviation: Afr. J. Microbiol. Res.
  • Language: English
  • ISSN: 1996-0808
  • DOI: 10.5897/AJMR
  • Start Year: 2007
  • Published Articles: 5233

Full Length Research Paper

Molecular identification of bacterial isolates from the rhizospheres of four mangrove species in Kenya

Edith M. Muwawa
  • Edith M. Muwawa
  • Department of Biological Sciences, School of Pure and Applied Sciences, Pwani University, P. O. Box 195-80108 Kilifi, Kenya.
  • Google Scholar
Huxley M. Makonde
  • Huxley M. Makonde
  • Department of Pure and Applied Sciences, Technical University of Mombasa, P. O. Box 90420-80100, Mombasa, Kenya.
  • Google Scholar
Joyce M. Jefwa
  • Joyce M. Jefwa
  • Departement of Biological Sciences, School of Pure and Applied Sciences, Pwani University, P. O. Box 195, 80108 Kilifi, Kenya.
  • Google Scholar
James H. P. Kahindi
  • James H. P. Kahindi
  • Departement of Biological Sciences, School of Pure and Applied Sciences, Pwani University, P. O. Box 195, 80108 Kilifi, Kenya.
  • Google Scholar
Damase P. Khasa
  • Damase P. Khasa
  • Centre for Forest Research and Institute for Systems and Integrative Biology, Université Laval, 1030 Avenue de la Médecine, Québec, QC, G1V0A6, Canada.
  • Google Scholar


  •  Received: 27 July 2020
  •  Accepted: 14 September 2020
  •  Published: 30 September 2020

References

Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990). Basic local alignment search tool. Journal of Molecular Biology 215(3):403-410.
Crossref

 

Anna PSAR, Bruno FRdeO, Renan de SS, Igor DAR, Ariana AR, Danns PB, Matheus MV, José DGV (2018). Isolation and characterization of phenol degrading Bacillus species from Southeast Brazilian mangrove sediment. African Journal of Microbiology Research 12(46):1032-1038.
Crossref

 
 

Ashelford KE, Chuzhanova NA, Fry JC, Jones AJ, Weightman AJ (2006). New screening software shows that most recent large 16S rRNA gene clone libraries contain chimeras. Applied and Environmental Microbiology 72(9):5734-5741.
Crossref

 
 

Azman AS, Othman I, Velu SS, Chan KG, Lee LH (2015). Mangrove rare actinobacteria: Taxonomy, natural compound, and discovery of bioactivity. Frontiers in Microbiology 6:1-15.
Crossref

 
 

Barka EA, Vatsa P, Sanchez L, Gaveau-vaillant N, Jacquard C, Klenk H, Clément C, Ouhdouch Y, Wezel P (2016). Taxonomy, Physiology, and Natural Products of Actinobacteria. Microbiology and Molecular Biology Reviews 80(1):1-44.
Crossref

 
 

Behera BC, Parida S, Dutta SK, Thatoi HN (2014a). Isolation and Identification of Cellulose Degrading Bacteria from Mangrove Soil of Mahanadi River Delta and Their Cellulase Production Ability. American Journal of Microbiological Research 2(1):41-46.
Crossref

 
 

Behera BC, Patra M, Dutta SK, Thatoi HN (2014b). Isolation and Characterization of Sulphur Oxidising Bacteria from Mangrove Soil of Mahanadi River Delta and Their Sulphur Oxidising Ability. Journal of Applied and Environmental Microbiology 2(1):1-5.
Crossref

 
 

Bergey DH, Holt JG (1994). Bergey's manual of determinative bacteriology. 

 
 

Brupbacher RH, Bonner WP, Sedberry JRJ (1968). Analytical methods and procedures used in the soil testing laboratory: 15. View

 
 

Bull AT, Ward AC, Goodfellow M (2000). Search and Discovery Strategies for Biotechnology: The Paradigm Shift. Microbiology and Molecular Biology Reviews 64(3):573-606.
Crossref

 
 

Clarridge JE (2004). Impact of 16S rRNA Gene Sequence Analysis for Identification of Bacteria on Clinical Microbiology and Infectious Diseases. Clinical Microbiology Reviews 17(4):840-862.
Crossref

 
 

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 Research 37(1):141-145.
Crossref

 
 

Conlan S, Kong HH, Segre JA (2012). Species-Level Analysis of DNA Sequence Data from the NIH Human Microbiome Project. PLoS ONE 7(10).
Crossref

 
 

Dahdouh-Guebas F, Van Pottelbergh I, Kairo JG, Cannicci S, Koedam N (2004). Human-impacted mangroves in Gazi (Kenya): Predicting future vegetation based on retrospective remote sensing, social surveys, and tree distribution. Marine Ecology Progress Series 272:77-92.
Crossref

 
 

de Mendiburu F (2020). agricolae: Statistical Procedures for Agricultural Research. R package version 1.3-2.

 
 

Dissanayake N, Chandrasekara U (2014). Effects of Mangrove Zonation and the Physicochemical Parameters of Soil on the Distribution of Macrobenthic Fauna in Kadolkele Mangrove Forest, a Tropical Mangrove Forest in Sri Lanka. Advances in Ecology, pp. 1-13.
Crossref

 
 

Felsenstein J (1985). Confidence Limits on Phylogenies: An Approach Using the Bootstrap. Evolution 39(4):783.
Crossref

 
 

Fettweis JM, Serrano MG, Sheth NU, Mayer CM, Glascock AL, Brooks JP, Jefferson KK, Buck GA (2012). Species-level classification of the vaginal microbiome. BMC Genomics 13(8):1-9.
Crossref

 
 

Giannopoulos G, Lee DY, Neubauer SC, Brown BL, Franklin RB (2019). A simple and effective sampler to collect undisturbed cores from tidal marshes.
Crossref

 
 

Goessens A, Satyanarayana B, Van Der Stocken T, Zuniga MQ, Mohd-Lokman H, Sulong I, Dahdouh-Guebas F (2014). Is Matang Mangrove Forest in Malaysia sustainably rejuvenating after more than a century of conservation and harvesting management? PLoS ONE 9:8.
Crossref

 
 

Haldar S, Nazareth SW (2018). Taxonomic diversity of bacteria from mangrove sediments of Goa: metagenomic and functional analysis. 3 Biotech 8:436-446.
Crossref

 
 

Holguin G, Vazquez P, Bashan Y (2001). The role of sediment microorganisms in the productivity, conservation, and rehabilitation of mangrove ecosystems: An overview. Biology and Fertility of Soils 33(4):265-278.
Crossref

 
 

Jenoh EM, De Villiers EP, De Villiers SM, Okoth S, Jefwa J, Kioko E, Kaimenyi D, Hendrickx M, Dahdouh-Guebas F, Koedam N (2019). Infestation mechanisms of two woodborer species in the mangrove Sonneratia alba J. Smith in Kenya and co-occurring endophytic fungi. PLoS ONE 14(10):1-20.
Crossref

 
 

Jenoh EM, Robert EMR, Lehmann I, Kioko E, Bosire JO, Ngisiange N, Dahdouh-Guebas F, Koedam N (2016). Wide ranging insect infestation of the pioneer mangrove Sonneratia alba by two insect species along the Kenyan coast. PLoS ONE 11(5):1-15.
Crossref

 
 

Josiah OK, Huxley MM, Hamadi IB, Anne TWM, Jun U (2018). Phylogenetic diversity of prokaryotes on the snow-cover of Lewis glacier in Mount Kenya. African Journal of Microbiology Research 12(24):574-579.
Crossref

 
 

Kambura AK, Mwirichia RK, Kasili RW, Karanja EN, Makonde HM, Boga HI (2016a). Bacteria and Archaea diversity within the hot springs of Lake Magadi and Little Magadi in Kenya. BMC Microbiology 16(1):1-12.
Crossref

 
 

Kambura AK, Romano KM, Remmy WK, Edward NK, Huxley MM, Hamadi IB (2016b). Diversity of fungi in sediments and water sampled from the hot springs of Lake Magadi and Little Magadi in Kenya. African Journal of Microbiology Research 10(10):330-338.
Crossref

 
 

Kathiresan K, Selvam MM (2006). Evaluation of beneficial bacteria from mangrove soil. Botanica Marina 49(1):86-88.
Crossref

 
 

Kawaka F, H, Dida M, Opala P, Ombori O, Maingi J, Muoma J (2018). Genetic diversity of symbiotic bacteria nodulating common bean (Phaseolus vulgaris) in western Kenya. PLoS ONE 13(11):1-13.
Crossref

 
 

Krüger C, Kohout P, Janoušková M, Püschel D, Frouz J, Rydlová J (2017). Plant communities rather than soil properties structure arbuscular mycorrhizal fungal communities along primary succession on a mine spoil. Frontiers in Microbiology 8:1-1.
Crossref

 
 

Kumar S, Stecher G, Li M, Knyaz C, Tamura K (2018). MEGA X: Molecular evolutionary genetics analysis across computing platforms. Molecular Biology and Evolution 35(6):1547-1549.
Crossref

 
 

Kunasundari B, Naresh S, Che Zakaria NZ (2017). Isolation and characterization of cellulase producing bacteria from tropical mangrove soil. ACM International Conference Proceeding Series Part F131935(9):34-37.
Crossref

 
 

Kurniawan A, Prihanto AA, Sari SP, Febriyanti D, Kurniawan A, Sambah AB, Asriani E (2018). Isolation and Identification of cellulolytic bacteria from mangrove sediment in Bangka Island. IOP Conference Series: Earth and Environmental Science 137(1):0-6.
Crossref

 
 

Ladeira SA, Cruz E, Delatorre AB, Barbosa JB, Martins MLL (2015). Cellulase production by thermophilic Bacillus sp. SMIA-2 and its detergent compatibility. Electronic Journal of Biotechnology 18(2):110-115.
Crossref

 
 

Lang'at JKS (2008). Variability of mangrove forests along the Kenyan coast. 

 
 

Lee L, Zainal N, Azman A, Eng S, Goh B, Yin W, Mutalib NA, Chan K (2014). Diversity and Antimicrobial Activities of Actinobacteria Isolated from Tropical Mangrove Sediments in Malaysia. Hindawi: 1-14.
Crossref

 
 

Makonde HM, Mwirichia R, Osiemo Z, Boga HI, Klenk HP (2015). 454 Pyrosequencing-based assessment of bacterial diversity and community structure in termite guts, mounds and surrounding soils. SpringerPlus 4(1):471.

 
 

Maldonado LA, Stach JEM, Pathom-Aree W, Ward AC, Bull AT, Goodfellow M (2005). Diversity of cultivable actinobacteria in geographically widespread marine sediments. International Journal of General and Molecular Microbiology 87(1):11-18.
Crossref

 
 

Malek NA, Jalal A, Chowdhury K, Zainuddin Z (2014). Selective Isolation of Actinomycetes from Mangrove Forest of Pahang, Malaysia. International Conference on Agriculture, Biology and Environmental Sciences 14:9-13.

 
 

Matthijs S, Tack J, van Speybroeck D, Koedam N (1999). Mangrove species zonation and soil redox state, sulphide concentration and salinity in Gazi Bay (Kenya), a preliminary study. Mangroves and Salt Marshes 3(4):243-249.
Crossref

 
 

Mendes R, Garbeva P, Raaijmakers JM (2013). The rhizosphere microbiome: Significance of plant beneficial, plant pathogenic, and human pathogenic microorganisms. FEMS Microbiology Reviews 37(5):634-663.
Crossref

 
 

Mo K, Huang H, Bao S, Hu Y (2020). Bacillus caeni sp. Nov., isolated from mangrove sediment. International Journal of Systematic and Evolutionary Microbiology 70(3):1503-1507.
Crossref

 
 

Mohamed MOS, Neukermans G, Kairo JG, Dahdouh-Guebas F, Koedam N (2009). Mangrove forests in a peri-urban setting: The case of Mombasa (Kenya). Wetlands Ecology and Management 17(3):243-255.
Crossref

 
 

Mohan YSYVJ, Sirisha B, Prathyusha K, Rao P (2014). Isolation, Screening and Characterization of Actinomycetes from Marine Sediments for their Potential to Produce Antifungal Agents. International Journal of Life Sciences, Biotechnology and Pharmaceutical Research 3(4):131-137.

 
 

Muhonja CN, Magoma G, Imbuga M, Makonde HM (2018a). Molecular characterization of Low-Density Polyethene (LDPE) degrading bacteria and fungi from Dandora dumpsite, Nairobi, Kenya. International Journal of Microbiology. Article ID 4167845.
Crossref

 
 

Muhonja CN, Makonde H, Magoma G, Imbuga M (2018b). Biodegradability of polyethylene by bacteria and fungi from Dandora dumpsite Nairobi-Kenya. PLoS ONE 13(7):1-17.
Crossref

 
 

Muwawa EM, Nancy LMB, Zipporah LO, Hamadi IB, Huxley MM (2016). Isolation and characterization of some gut microbial symbionts from fungus-cultivating termites (Macrotermes and Odontotermes spp.). African Journal of Microbiology Research 10(26):994-1004.
Crossref

 
 

Naik G, Shukla S, Kumar MS (2013). Isolation and Characterization of Actinomycetes Isolates for Production of Antimicrobial Compounds. Journal of Microbiology and Biotechnology Research 3(5):33-36.

 
 

Naresh S, Kunasundari B, Gunny AAN, Teoh YP, Shuit SH, Ng QH, Hoo PY (2019). Isolation and partial characterisation of thermophilic cellulolytic bacteria from north Malaysian tropical mangrove soil. Tropical Life Sciences Research 30(1):123-147.

 
 

Ntabo RM, Nyamache AK, Lwande W, Kabii J, Nonoh J (2018). Enzymatic Activity of Endophytic Bacterial Isolates from Selected Mangrove Plants in Kenya. The Open Microbiology Journal 12(1):354-363.
Crossref

 
 

Priya E, Thenmozhi R, Nagasathya A, Thajuddin N, Muralitharan G (2014). Diversity of Actinobacteria in Mangrove Ecosystem of Muthupet, India. International Research Journal of Environment Sciences 3(4):13-17.

 
 

Pruesse E, Quast C, Knittel K, Fuchs BM, Ludwig W, Peplies J, Glöckner FO (2007). SILVA: A comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Research 35(21):7188-7196.
Crossref

 
 

Pupin B, Nahas E (2014). Microbial populations and activities of mangrove, restinga and Atlantic forest soils from Cardoso Island, Brazil. Journal of Applied Microbiology 116(4):851-864.
Crossref

 
 

Rasigraf O, Helmond NAGM, van Frank J, Lenstra WK, Egger M, Slomp C.P, Jetten MSM (2019). Metagenomic analysis reveals large potential for carbon, nitrogen and sulfur cycling in coastal methanic sediments of the Bothnian Sea. BioRxiv-Pre-Print: 553131.
Crossref

 
 

Saitou N, Nei M (1987). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Molecular Biology and Evolution 4(4):406-425.

 
 

Salano OA, Huxley MM, Remmy WK, Hamadi IB (2018). Isolation and characterization of fungi from a hot-spring on the shores of Lake Bogoria, Kenya. Journal of Yeast and Fungal Research 9(1):1-13.
Crossref

 
 

Salano OA, Makonde HM, Kasili RW, Wangai LN, Nawiri MP, Boga HI (2017). Diversity and distribution of fungal communities within the hot springs of soda lakes in the Kenyan rift valley. African Journal of Microbiology Research 11(19):764-775.

 
 

Sanders CJ, Eyre BD, Santos IR, Machado W, Luiz-silva W, Smoak JM, Breithaupt JL, Ketterer ME, Sanders L, Marotta H, Silva-filho E, Al SET (2014). Impacted Mangrove Wetland. Geophysical Research Letters 41(1):2475-2480.
Crossref

 
 

Sarker A, Haque M, Islam M, Rahman M, Islam M (2015). Isolation and Characterization of a Marine Bacterium from Sundarbans, Bangladesh. British Microbiology Research Journal 6(6):348-357.
Crossref

 
 

Saseeswari A, Kanimozhi G, Panneerselvam A (2016). Bacterial Diversity of Mangrove Soil in Karankadu from East Coast of Tamil Nadu, India. International Journal of Current Microbiology and Applied Sciences 5(4):750-756.
Crossref

 
 

Sengupta S, Pramanik A, Ghosh A, Bhattacharyya M (2015). Antimicrobial activities of actinomycetes isolated from unexplored regions of Sundarbans mangrove ecosystem. BMC Microbiology 15(1):1-16.
Crossref

 
 

Soares-Júnior FL, Dias ACF, Fasanella CC, Taketani RG, Lima AOdeS, Melo IS, Andreote FD (2013). Endo-and exoglucanase activities in bacteria from mangrove sediment. Brazilian Journal of Microbiology 44(3):969-976.
Crossref

 
 

Somanathan H, Mali S, Borges RM, Shilton LA, Altringham JD, Compton SG, Whittaker RJ, Russo SE, Augspurger CK, Nakashima Y, Inoue E, Inoue-Murayama M, Sukor JR, McConkey KR, Prasad S, Corlett RT, Campos-Arceiz A, Brodie JF, Rogers H, Rawat GS (2004). R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing. Oecologia 15:413-448.

 
 

Srinivasan R, Karaoz U, Volegova M, MacKichan J, Kato-Maeda M, Miller S, Nadarajan R, Brodie EL, Lynch SV (2015). Use of 16S rRNA gene for identification of a broad range of clinically relevant bacterial pathogens. PLoS ONE 10(2):1-22.
Crossref

 
 

Tam HT, City CT, Diep CN, City CT (2017). Isolation and Characterization of Bacteria of Mangrove Rhizosphere in the Mekong Delta, Vietnam. International Journal of Innovations in Engineering and Technology 9(1):68-79.
Crossref

 
 

Tamura K, Nei M, Kumar S (2004). Prospects for inferring very large phylogenies by using the neighbor-joining method. Proceedings of the National Academy of Sciences of the United States of America 101(30):11030-11035.
Crossref

 
 

Wang Q, Garrity GM, Tiedje JM, Cole JR (2007). Naïve Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Applied and Environmental Microbiology 73(16):5261-5267.
Crossref

 
 

Wu P, Xiong X, Xu Z, Lu C, Cheng H, Lyu X, Zhang J, He W, Deng W, Lyu Y, Lou Q, Hong Y, Fang H (2016). Bacterial communities in the rhizospheres of three mangrove tree species from Beilun Estuary, China. PLoS ONE 11(10):1-13.
Crossref

 
 

Xu DB, Ye WW, Han Y, Deng ZX, Hong K (2014). Natural products from mangrove actinomycetes. Marine Drugs 12(5):2590-2613.
Crossref

 
 

Zhang Y, Yang Q, Ling J, Van Nostrand JD, Shi Z, Zhou J, Dong J (2017). Diversity and structure of diazotrophic communities in mangrove rhizosphere, revealed by high-throughput sequencing. Frontiers in Microbiology 8(8):1-11.
Crossref