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Sains Malaysiana
47(2)(2018): 243-251
http://dx.doi.org/10.17576/jsm-2018-4702-05
Bacterial Diversity and
Community Structure of Banana Rhizosphere in Orang Asli Fields and Commercial Plantations
(Kepelbagaian Bakteria dan Struktur Komuniti Rizosfera Pisang di Kebun Orang Asli dan Ladang Komersial)
Jason Yee Neng Lee1,2* & Irene Kit Ping Tan1,2 1Institute of Biological Sciences, Faculty of Science,
University of Malaya, 50603 Kuala Lumpur, Federal Territory, Malaysia 50603 Kuala Lumpur, Federal Territory, Malaysia
Received: 8 January 2017/Accepted: 31 July 2017
ABSTRACT
Bacteria play an important
roles in the soil ecosystem and in the rhizosphere, they are intricately
linked to nutrient content and its accessibility to plants, plant
protection and sometimes pathogenicity. Banana grows well in the
tropics and it is popularly grown in Orang Asli (OA) (indigenous
people) settlements. Banana is also grown in commercial plantations.
In traditional planting practices, the OA do not add pesticide nor
fertilizer to their crops which are planted for self-sustenance
mainly. On the other hand, fertilizer and pesticide are added to
commercial banana plantations to maximise yield. Rhizosphere
bacteria from the banana plant, Pisang Nipah, grown in OA fields
and commercial plantations were identified by clone library construction
of the 16S rRNA gene. This was to determine whether farming practices
influenced the bacterial community in the banana plant rhizosphere.
Acidobacteria,
Proteobacteria and Actinobacteria were found in all
the soil. Other common phyla found in some soil (but not all) were
Nitrospirae,
Firmicutes, Bacteroidetes, Chloroflexi, Verrumicrobia, Gemmatimonadetes
and Cyanobacteria. The bacterial diversity
was a little more diverse in the OA fields than the commercial plantations.
The latter had higher contents of nitrogen, phosphorus and potassium.
These could have exerted selective pressure to reduce the bacterial
diversity in the commercial plantations. Keywords: Bacterial community; banana rhizosphere;
commercial plantations; Orang Asli settlements; 16S cloning
ABSTRAK
Bakteria
memainkan peranan penting di dalam ekosistem tanah dan rizosfera,
sifat bakteria yang dinamik dan kompleks boleh memberi kesan positif
atau negatif kepada tumbuh-tumbuhan. Pokok pisang boleh bertumbuh
dengan baik di kawasan tropika dan juga popular ditanam di penempatan
Orang Asli (OA) dan ladang komersial. OA mengamalkan penanaman tradisi
dan tidak menambahkan racun perosak atau baja kepada tanaman mereka,
terutamanya tanaman yang menghasilkan rezeki kepada mereka. Sebaliknya,
ladang pisang komersial mengamalkan penambahan baja dan racun perosak
untuk memaksimumkan hasil pertanian. Rizosfera bakteria yang dijumpai
pada Pisang Nipah yang ditanam di kebun OA dan ladang komersial
telah dianalisis dengan menggunakan klon gen 16S rRNA. Ini penting
untuk menentukan sama ada amalan pertanian mempengaruhi komuniti
bakteria di dalam rizosfera pokok pisang. Acidobacteria,
Proteobacteria dan Actinobacteria
dijumpai di dalam semua tanah yang dianalisis. Sementara itu, filum
lain yang dijumpai di dalam analisis tanah adalah Nitrospirae,
Firmicutes, Bacteroidetes, Chloroflexi, Verrumicrobia, Gemmatimonadetes
dan Cyanobacteria.
Terdapat lebih banyak jenis bakteria dijumpai di dalam OA berbanding
dengan ladang komersial. Ladang komersial mengandungi lebih banyak
kandungan nitrogen, fosforus dan kalium boleh menyebabkan kekurangan
jenis bakteria di dalam ladang komersial. Kata
kunci: Klon 16S; komuniti bakteria; ladang-ladang komersial; penempatan Orang Asli;
rizosfera pokok pisang
REFERENCES
Abdullah,
M.Y., Hassan, N.M., Mahmood, Z. & Talib, Z. 1999.
Trend in foliar nutrient concentrations and contents and its implication
on leaf area index development and yield in banana cultivar 'berangan'.
In Proceedings of the First National Banana Seminar,
edited by Zakaria, W., Mahmud, T.M.M., Siti, D., Khalijah, M.F.,
Nor Aini & Marziah, M. Awana, Genting, Pahang, Malaysia. pp.
95-105. Aislabie, J. &
Deslippe,
J.R. 2013. Soil microbes and their contribution to soil services.
In Ecosystem
Services in New Zealand - Conditions and Trends, edited
by Dymond, J. Lincoln,
New Zealand: Manaaki Whenua Press. pp. 112-161. Alain,
K. & Querellou, J. 2009. Cultivating the uncultured: Limits,
advances and future challenges. Extremophiles 13: 583-594.
Beauregard, M., Hamel, C. & St-Arnaud, M. 2010. Long-term
phosphorus fertilization impacts soil fungal and bacterial diversity but not AM fungal community in alfalfa. Microbial Ecology 59: 379-389.
Brady, N.C. & Weil, R.R. 1999. The Nature and Properties of Soils. 12th
ed. Upper Saddle River, NJ: Prentice-Hall. p. 881.
Broeckling,
C.D., Broz, A.K., Bergelson, J., Manter, D.K. & Vivanco, J.M. 2008. Root exudates
regulate soil fungal community composition and diversity. Applied and Environmental Microbiology 74: 738-744.
Ceteciogly,
Z., Ince, B.K., Kolukirik, M. & Ince, O. 2009.
Biogeographical distribution and diversity of bacterial and archaeal
communities within highly polluted anoxic marine sediments from the Marmara
Sea. Marine Pollution Bulletin 3: 384-395.
Davis, K.E., Sangwan, P. & Janssen, P.H.
2011. Acidobacteria, Rubrobacteridae and Chloroflexi are abundant among very
slow-growing and mini-colonyforming soil bacteria. Environmental Microbiology 13: 798-805.
de Bruyn, J.M., Nixon, L.T., Fawaz, M.N., Johnson, A.M. & Radosevich, M.
2011. Global biogeography and quantitative seasonal dynamics of
Gemmatimonadetes in soil. Applied and
Environmental Microbiology 77: 6295-6300.
Dong, W.Y., Zhang, X.Y., Dai, X.Q., Fu, X.L., Yang, F.T., Liu, X.Y.,
Sun, X.M., Wen, X.F. & Schaeffer, S.
2014. Changes in soil microbial
community composition in response to fertilization of paddy soils in
subtropical China. Applied Soil Ecology 84: 140-147.
Eilers, K.G., Debenport, S., Anderson, S. & Fierer, N.
2012. Digging deeper to find unique microbial communities: The strong effect of
depth on the structure of bacterial and archaeal communities in soil. Soil Biology and Biochemistry 50: 58-65.
Elisa, C.P.C., Fabyano, A.C.L., Janaina, F.A., Alinne, P.C., Cristine,
C.B., Mercedes, M.C.B., Bertania, F.Q. & Ricardo, H.K. 2014. Soil
Acidobacteria 16S rRNA gene sequences reveal subgroup level differences between
Savanna like Cerrado and Atlantic Forest Brazilian biomes. International Journal of Microbiology 1: 1-12.
Fakruddin, Md. & Khanjada, S.M.
2013. Methods for analyzing diversity of microbial
communities in natural environments. Ceylon Journal of Science 42(1): 19-33.
Faoro,
H., Alves, A.C., Souza, E.M., Rigo, L.U., Cruz, L.M., Al-Janabi, S.M.,
Monteiro, R.A., Baura, V.A. & Pedrosa, F.O. 2010. Influence of soil characteristics
on the diversity of bacteria in the Southern Brazilian Atlantic Forest. Applied
and Environmental Microbiology 76(14): 4744-4749.
Ge, Y., Zhang, J., Yang, M. & He, J. 2008. Long-term
fertilization regimes affect bacterial community structure and diversity of an
agricultural soil in northern China. Journal
of Soil and Sediments 8: 43-50.
Hani, A., Chantal, J.B., Nadia, G., Rock, C. & Roger, L. 1998. Potential of Rhizobium and Bradyrhizobium species as plant growth promoting rhizobacteria on
non-legumes: Effect on radishes (Raphanus
sativus L.). Plant and Soil 204:
57-67.
Head, M., Saunders, J.R. & Pickup, R.W. 1998. Microbial
evolution, diversity and ecology: A decade of ribosomal RNA analysis of
uncultivated microorganisms. Microbial
Ecology 35: 1-21.
Hirsch,
P.R., Miller, A.J. &
Dennis, P.G. 2013. Do exudates exert more influence on rhizosphere bacteria
community structure than other rhizodeposits? Molecular Microbial Ecology of the Rhizosphere 22: 229-242.
Janda, J.M. & Abbott, S.L. 2007. 16S rRNA gene sequencing
for bacterial identification in the diagnostic laboratory: Pluses, perils, and pitfalls. Journal of Clinical Microbiology 45:
2761-2764.
Kirby,
J.T., Sader, H.S., Walsh, T.R. & Jones, R.N.
2004. Antimicrobial susceptibility and epidemiology of a worldwide collection
of Chryseobacterium spp.: Report from
the SENTRY antimicrobial surveillance program (1997-2001). Journal of Clinical Microbiology 42(1): 445-448.
Lauber, C.L., Hamady, M., Knight, R. & Fierer, N. 2009. Pyrosequencing-based assessment of soil pH as a
predictor of soil bacterial community structure at the continental scale. Applied and Environmental Microbiology 75: 5111-5120.
Lazcano, C., Brandon, M.G., Revilla, P. & Dominguez. J. 2012. Short-term effects of organic and inorganic
fertilizer on soil microbial community structure and function. Biology
and Fertility of Soils 12: 761-767.
Leadbetter,
J.R. 2003. Cultivation of recalcitrant microbes: Cells are alive, well and
revealing their secrets in the 21st century laboratory. Current Opinion in Microbiology 6: 274-281.
Liu,
W.T., Marsh, T.L., Cheng, H. & Forney, L.J.
1997. Characterization of microbial diversity by determining
terminal restriction fragment length polymorphisms of genes encoding 16S rRNA. Applied and Environmental Microbiology 63(11): 4516-4521.
Magurran, A.E. 2004. Measuring Biological Diversity. Oxford: Blackwell Publishing. p.
264.
Memon, N.N., Memon, K.S., Rachel, A.S.A. & Nafees, M. 2010. Status and response to
improved NPK fertilization practices in banana. Pakistan Journal of Botany 42: 2369-2381.
Meng,
F. 2013. The virulence factors of the bacterial wilt pathogen Ralstonia solanacearum. Plant Pathology and Microbiology 4(3):
168.
Mia, M.A.B.,
Shamsuddin, Z.H. & Mahmood, M. 2010. Use of plant growth promoting bacteria
in banana: A new insight for sustainable banana production. International Journal Agricultural and
Biology 12: 459-467.
Moyer,
C.L., Dobbs, F.C. & Karl, D.M. 1993.
Estimation of diversity and community structure through restriction fragment
length polymorphism distribution analysis of bacterial 16S rRNA genes from a
microbial mat at an active, hydrothermal vent system, Loihi Seamount, Hawaii. Applied and Environmental Microbiology 60(3): 871-879.
Nadia,
M.H., Jacques, M.A. & Koebnik, R.
2011. Adhesion mechanisms of plant-pathogenic
Xanthomonadaceae. Advances in
Experimental Medicine and Biology 5: 71-89.
Okano, Y. 2004.
Application of real-time PCR to study effects of ammonium on population size of
ammonia-oxidizing bacteria in soil. Applied and Environmental Microbiology 70: 1008-1016.
Peacock, A. 2001.
Soil microbial community responses to dairy manure or ammonium nitrate
applications. Soil Biology and Biochemistry 33: 1011-1019.
Philippot, L.,
Hallin, S. & Schloter, M. 2007. Ecology of denitrifying bacteria in
agricultural soil. Advances in Agronomy 96: 249-305.
Robinson, J.C.
1995. Systems of cultivation and management. In Banana and Plantains, edited by Gowen, S. London: Chapman and Hall.
pp. 15-65.
Rossum, D., Muyotcha, A., Hoop, B., Verseveld, H.W.,
Stouthamer, A.H. & Boogerd, F.C.
1994. Soil acidity in relation to groundnut-Bradyrhizobium symbiotic performance. Plant and Soil 163(2): 165-175.
Rousk, J., Baath, E., Brookes, P.C., Lauber, C.L.,
Lozupone, C., Caporaso, J.G., Knight, R. & Fierer, N. 2010. Soil bacterial
and fungal communities across a pH gradient in an arable soil. International Society for Microbial Ecology4: 1340-1351.
Rovira, A.D. 1991.
Rhizosphere research - 85 years of progress and frustration. In Beltsville
Symposium in Agricultural Research: The Rhizosphere and Plant Growth, edited by Keister, D.L. & Cregan, P.B.
Dordrecht: Kluwer Academic Press. 14: 3-13.
Shannon, C. 1948. A mathematical theory of
communication. The Bell System Technical Journal 27: 379-423.
Shyam, K.R.,
Ganesh, M.I., Rajeswari, R. & Harikrishnan, H. 2011. Utilization of waste
ripe banana, and peels for bioethanol production using Saccharomyces cerevisiae. Journal
of Biosciences 2(2): 67-71.
Simpson, E.H.
1949. Measurement of diversity. Nature 163: 688.
Stark, J.M. & Firestone,
M.K. 1995. Mechanisms for soil moisture effects on activity of nitrifying
bacteria. Applied and Environmental Microbiology 61(1): 218-221.
Surakasi, V.P., Anthony, C.P., Sharma, S., Patole,
M.S. & Shouche, Y.S. 2010. Temporal bacterial diversity
and detection of putative methonotrops in surface mats of Lonar crater lake. Journal of Basic Microbiology 50: 465-474.
Suyal, D.C., Yadav, A., Shouche, Y. & Goel, R. 2015. Bacterial diversity and community
structure of Western Indian Himalayan red kidney bean (Phaseolus vulgaris) rhizosphere as revealed by 16S rRNA gene
sequences. Biologia 70(3): 305-313.
Treseder, K.K.,
2008. Nitrogen additions and microbial biomass: A meta-analysis of ecosystem
studies. Ecology Letters 11: 1111-1120.
Tripathi, B.M.,
Kim, M., Dharmesh, S., Lee, L.C., Ang, L.H., Ainuddin, A.N., Go, R., Rahim,
R.A., Husni, M.H.A., Chun, J. & Adams, J.M. 2012. Tropical soil bacterial
communities in Malaysia: pH dominates in the equatorial tropics too. Microbial Ecology 64: 474-484.
Ward, D.M., Bateson, M.M., Weller, R. & Ruff-Roberts,
A.L. 1992. Ribosomal RNA analysis of
microorganisms as they occur in nature. Advances in Microbial Ecology 12: 219-286.
Whitford,
M.F., Forster, R.J., Beard, C.E., Gong, J. & Teather, R.M. 1998. Phylogenetic
analysis of rumen bacteria by comparative sequence analysis of cloned 16S rRNA
genes. Anaerobe 4: 153-163.
Wong, C., Kiew, R., Argent, G., Set, O., Lee, S.K. & Gan, Y.Y. 2002. Assessment of the validity of the sections in Musa (Musaceae) using AFLP. Annals of Botany 90: 231-238.
van Passel, M.W., Kant, R., Palva, A., Copeland,
A., Lucas, S., Copeland, A., Lucas, S., Lapidus, A., Glavina del Rio, T., Pitluck, S., Goltsman, E., Clum, A., Sun, H., Schmutz, J., Larimer, F.W., Land, M.L., Hauser, L., Kyrpides, N., Mikhailova, N., Richardson, P.P., Janssen, P.H., de Vos, W.M. & Smidt, H. 2011. Genome sequence of the Verrucomicrobium opitutus terrae PB90-1, an abundant inhabitant of
rice paddy soil ecosystems. Journal of Bacteriology 193: 2367-2368.
*Corresponding author; email: jasonleeyeeneng@hotmail.com
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