16S rRNA Gene-Based Metagenomic Analysis of Soil Bacterial Diversity in Brazzaville, Republic of the Congo — Oak Academic Publishing
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16S rRNA Gene-Based Metagenomic Analysis of Soil Bacterial Diversity in Brazzaville, Republic of the Congo
Laboratoire de Biologie Cellulaire et Moléculaire (BCM), Faculté des Sciences et Techniques, Université Marien Ngouabi, Brazzaville, Republic of the Congo
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Unité de Recherche en Bioinformatique et Microbiologie Moléculaire, Faculté des Sciences et Techniques, Université Marien Ngouabi, Brazzaville, Republic of the Congo
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Institut National de Recherche en Sciences Exactes et Naturelles (IRSEN), Brazzaville, Republic of the Congo
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Laboratoire de Biologie Cellulaire et Moléculaire (BCM), Faculté des Sciences et Techniques, Université Marien Ngouabi, Brazzaville, Republic of the Congo
,
Unité de Recherche en Bioinformatique et Microbiologie Moléculaire, Faculté des Sciences et Techniques, Université Marien Ngouabi, Brazzaville, Republic of the Congo
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Institut National de Recherche en Sciences Exactes et Naturelles (IRSEN), Brazzaville, Republic of the Congo
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Institut National de Recherche en Sciences Exactes et Naturelles (IRSEN), Brazzaville, Republic of the Congo
1 Laboratoire de Biologie Cellulaire et Moléculaire (BCM), Faculté des Sciences et Techniques, Université Marien Ngouabi, Brazzaville, Republic of the Congo
2 Unité de Recherche en Bioinformatique et Microbiologie Moléculaire, Faculté des Sciences et Techniques, Université Marien Ngouabi, Brazzaville, Republic of the Congo
3 Institut National de Recherche en Sciences Exactes et Naturelles (IRSEN), Brazzaville, Republic of the Congo
4 Laboratoire de Biologie Cellulaire et Moléculaire (BCM), Faculté des Sciences et Techniques, Université Marien Ngouabi, Brazzaville, Republic of the Congo
5 Unité de Recherche en Bioinformatique et Microbiologie Moléculaire, Faculté des Sciences et Techniques, Université Marien Ngouabi, Brazzaville, Republic of the Congo
6 Institut National de Recherche en Sciences Exactes et Naturelles (IRSEN), Brazzaville, Republic of the Congo
7 Institut National de Recherche en Sciences Exactes et Naturelles (IRSEN), Brazzaville, Republic of the Congo
Soil contains a great diversity of microorganisms, among which are bacteria. This study aimed to explore bacterial diversity in soil samples in Brazzaville in the Republic of the Congo. Environmental DNA was extracted. The illumina MiSeq sequencing was held and the diversity indices have been computed. Illumina MiSeq sequencing revealed 21 Phyla, four of which were abundant: Proteobacteria, Acidobacteria, Actinobacteria and Bacteroidetes. Soil microbial communities in the studied samples were phylogenetically diverse but with a stable community structure. 17 classes are represented with relative abundances of Rihzobiales, Bacillales, Actinomycetales and Acidobacteriales. 40 families, the Alphaproteobacteria, the Bacilli and the 12 Actinobacteria. 83 orders among which the Rhizobiales are the most abundant followed by Bacillales and the least abundant followed by the Flavobacteriaceae. Of the 28 genera listed, the Bradyrhizobium is the most dominant in Mw3 and Mw4. 25 listed species, Bradyrhizobium, Bacillus, Actinoplanes, and Candidatu coribacter Acidobacterium are the most abundant species. The Shannon indices of Mw3 and Mw4 are equal, the H’max of Mw4 is greater than the H’max of Mw3. The Simpson index of Mw4 is equal to the Simpson index of Mw3, and the Pielou index (J) of Mw4 is less than the R of Mw3, but very close. This study opens interesting perspectives on the knowledge and exploitation of telluric bacteria in several areas of life.
Ranjard, L., Maron, P.A., Cuny, P., et al. (2017) La microbiologie moléculaire au service du diagnostic environnemental. Étude et Gestion des Sols, 24, 9-31.
Gardi, C., Montanarella, L., Arrouays, D., Bispo, A., Lemanceau, P., Mulder, C., Ranjard, L., Rombke, L., Rutger, M. and Menta, C. (2009) Soil Biodiversity Monitoring in Europe: Ongoing Activities and Challenges. European Journal of Soil Science, 60, 807-819. https://doi.org/10.1111/j.1365-2389.2009.01177.x
Barberán, A., et al. (2014) Why Are Some Microbes More Ubiquitous than Others? Predicting the Habitat Breadth of Soil Bacteria. Ecology Letters, 17, 794-802. https://doi.org/10.1111/ele.12282
Hendershot, J.N., Read, Q.D., Henning, J.A., Sanders, N.J. and Classen, A.T. (2017) Consistently Inconsistent Drivers of Microbial Diversity and Abundance at Macroecological Scales. Ecology, 98, 1757-1763. https://doi.org/10.1002/ecy.1829
Pester, M., Maixner, F., Berry, D., Rattei, T., Koch, H., Lücker, S., Nowka, B., Richter, A., Spieck, E. and Lebedeva, E. (2014) NxrB Encoding the Beta Subunit of Nitrite Oxidoreductase as Functional and Phylogenetic Marker for Nitrite-Oxidizing Nitrospira. Environmental Microbiology, 16, 3055-3071. https://doi.org/10.1111/1462-2920.12300
Janssen, P.H. (2006) Identifying the Dominant Soil Bacterial Taxa in Libraries of 16S rRNA and 16S rRNA Genes. Applied and Environmental Microbiology, 72, 1719-1728. https://doi.org/10.1128/AEM.72.3.1719-1728.2006
Lozupone, C.A. and Knight, R. (2007) Global Patterns in Bacterial Diversity. Proceedings of the National Academy of Sciences of the United States of America, 104, 11436-11440. https://doi.org/10.1073/pnas.0611525104
Lin, C., Li, X. and Jin, H. (2015) Soil Degradation Characteristics of Food-Plain Wetlands in Yellow River Source Zone. Chinese Agricultural Science Bulletin, 31, 243-249.
Khan, K.S., Mack, R., Castillo, X., Kaiser, M. and Joergensena, R.G. (2016) Microbial Biomass, Fungal and Bacterial Residues, and Their Relationships to the Soil Organic Matter C/N/P/S Ratios. Geoderma, 271, 115-123. https://doi.org/10.1016/j.geoderma.2016.02.019
Bastida, F., Zsolnay, A., Hernández, T. and García, C. (2008) Past, Present and Future of Soil Quality Indices: A Biological Perspective. Geoderma, 147, 159-171. https://doi.org/10.1016/j.geoderma.2008.08.007
Gyaneshwar, P., Kumar, G.N., Parekh, L.J. and Poole, P.S. (2002) Role of Soil Microorganisms in Improving P Nutrition of Plants. Plant Soil, 245, 83-93. https://doi.org/10.1023/A:1020663916259
Berg, G. (2009) Plant—Microbe Interactions Promoting Plant Growth and Health: Perspectives for Controlled Use of Microorganisms in Agriculture. Applied Microbiology and Biotechnology, 84, 11-18. https://doi.org/10.1007/s00253-009-2092-7
Xu, X., Stern, A., Liu, Z., Kan, B. and Zhu, J. (2010) Virulence Regulator AphB Enhances toxR Transcription in Vibrio cholerae. BMC Microbiology, 10, Article No. 3. https://doi.org/10.1186/1471-2180-10-3
Kumar, S. and Tuteja, U. (2009) Detection of Virulence-Associated Genes in Clinical Isolates of Bacillus anthracis by Multiplex PCR and DNA Probes. Journal of Microbiology and Biotechnology, 19, 1475-1481. https://doi.org/10.4014/jmb.0902.101
Hanniffy, S.B., Pelaez, C., Martinez-Bartolome, M.A., Requena, T. and Martinez-Cuesta, M.C. (2009) Key Enzymes Involved in Methionine Catabolism by Cheese Lactic Acid Bacteria. International Journal of Food Microbiology, 135, 223-230. https://doi.org/10.1016/j.ijfoodmicro.2009.08.009
Lucy, M., Reed, E. and Glick, B.R. (2004) Applications of Free Living Plant Growth-Promoting Rhizobacteria. Antonie van Leeuwenhoek, 86, 1-25. https://doi.org/10.1023/B:ANTO.0000024903.10757.6e
Lugtenberg, B. and Kamilova, F. (2009) Plant-Growth-Promoting Rhizobacteria. Annual Review of Microbiology, 63, 541-556. https://doi.org/10.1146/annurev.micro.62.081307.162918
Wong, S.L. (1995) Advances in the Use of Bacillus subtilis for the Expression and Secretion of Heterologous Proteins. Current Opinion in Biotechnology, 6, 517-522. https://doi.org/10.1016/0958-1669(95)80085-9
Zhou, Q.F., Li, M.Y. and Li, C.W. (2009) Cloning and Expression of a Novel Insulin-Releasing Peptide, Brevinin-2GU from Escherichia coli. Journal of Bioscience and Bioengineering, 107, 460-463. https://doi.org/10.1016/j.jbiosc.2008.12.011
Demain, A.L. (1999) Pharmaceutically Active Secondary Metabolites of Microorganisms. Applied Microbiology and Biotechnology, 52, 455-463. https://doi.org/10.1007/s002530051546
Rappe, M.S. and Giovannoni, S.J. (2003) The Uncultured Microbial Majority. Annual Review of Microbiology, 57, 369-394. https://doi.org/10.1146/annurev.micro.57.030502.090759
McHardy, A.C. and Rigoutsos, I. (2007) What’s in the Mix: Phylogenetic Classification of Metagenome Sequence Samples. Current Opinion in Microbiology, 10, 499-503. https://doi.org/10.1016/j.mib.2007.08.004
Lawrence, J.G. (1999) Gene Transfer, Speciation, and the Evolution of Bacterial Genomes. Current Opinion in Microbiology, 2, 519-523. https://doi.org/10.1016/S1369-5274(99)00010-7
Ding, G.C., Piceno, Y.M., Heuer, H., Weinert, N., Dohrmann, A.B., Carrillo, A., Andersen, G.L., Castellanos, T., Tebbe, C.C. and Smalla, K. (2013) Changes of Soil Bacterial Diversity as a Consequence of Agricultural Land Use in a Semi-Arid Ecosystem. PLOS ONE, 8, e59497. https://doi.org/10.1371/journal.pone.0059497
Lagerlöf, J., Adolfsson, L., Börjesson, G., Ehlers, K., Vinyoles, G.P. and Sundh, I. (2014) Land-Use Intensification and Agroforestry in the Kenyan Highland: Impacts on Soil Microbial Community Composition and Functional Capacity. Applied Soil Ecology, 82, 93-99. https://doi.org/10.1016/j.apsoil.2014.05.015
Sun, R., Zhang, X.X., Guo, X., Wang, D. and Chu, H. (2015) Bacterial Diversity in Soils Subjected to Long-Term Chemical Fertilization Can Be More Stably Maintained with the Addition of Livestock Manure than Wheat Straw. Soil Biology and Biochemistry, 88, 9-18. https://doi.org/10.1016/j.soilbio.2015.05.007
Coolon, J.D., Jones, K.L., Todd, T.C., Blair, J.M. and Herman, M.A. (2013) Long-Term Nitrogen Amendment Alters the Diversity and Assemblage of Soil Bacterial Communities in Tallgrass Prairie. PLOS ONE, 8, e67884. https://doi.org/10.1371/journal.pone.0067884
He, Z.L., Xu, M.Y., et al. (2010) Metagenomic Analysis Reveals Amarked Divergence in the Structure of Belowground Microbial Communities at Elevated CO2. Ecology Letters, 13, 564-575. https://doi.org/10.1111/j.1461-0248.2010.01453.x
Zhang, W., Chen, L., Zhang, R. and Lin, K.F. (2016) High Throughput Sequencing Analysis of the Joint Effects of BDE209-Pb on Soil Bacterial Community Structure. Journal of Hazardous Materials, 301, 1-7. https://doi.org/10.1016/j.jhazmat.2015.08.037
Zhang, J., Wang, P.C., Tian, H.M., Xiao, Q.Q. and Jiang, H.K. (2019) Pyrosequencing-Based Assessment of Soil Microbial Community Structure and Analysis of Soil Properties with Vegetable Planted at Different Years under Greenhouse Conditions. Soil and Tillage Research, 187, 1-10. https://doi.org/10.1016/j.still.2018.11.008
Acosta-Martínez, V., Dowd, S., Sun, Y. and Allen, V. (2008) Tag-Encoded Pyrosequencing Analysis of Bacterial Diversity in a Single Soil Type as Affected by Management and Land Use. Soil Biology and Biochemistry, 40, 2762-2770. https://doi.org/10.1016/j.soilbio.2008.07.022
Green, J.L., Bohannan, B.J.M. and Whitaker, R.J. (2008) Microbial Biogeography: From Taxonomy to Traits. Science, 320, 1039-1043. https://doi.org/10.1126/science.1153475
Hamady, M., Walker, J.J., Harris, J.K., Gold, N.J. and Knight, R. (2008) Error-Correcting Barcoded Primers for Pyrosequencing Hundreds of Samples in Multiplex. Nature Methods, 5, 235-237. https://doi.org/10.1038/nmeth.1184
Huse, S.M., Dethlefsen, L., Huber, J.A., Welch, D.M., Relman, D.A. and Sogin, M.L. (2008) Exploring Microbial Diversity and Taxonomy Using SSU rRNA Hypervariable Tag Sequencing. PLOS Genetics, 4, e1000255. https://doi.org/10.1371/journal.pgen.1000255
Borneman, J. and Triplett, E.W. (1997) Molecular Microbial Diversity in Soils from Eastern Amazonia: Evidence for Unusual Microorganisms and Microbial Population Shifts Associated with Deforestation. Applied and Environmental Microbiology, 63, 2647-2653. https://doi.org/10.1128/aem.63.7.2647-2653.1997
Cookson, W.R., Osman, M., Marschner, P., Abaye, D.A., Clark, I., Murphy, D.V., Stockdale, E.A. and Watson, C.A. (2007) Controls on Soil Nitrogen Cycling and Microbial Community Composition across Land Use and Incubation Temperature. Soil Biology and Biochemistry, 39, 744-756. https://doi.org/10.1016/j.soilbio.2006.09.022
He, Z.L., Piceno, Y., Deng, Y., et al. (2012) The Phylogenetic Composition and Structure of Soil Microbial Communities Shifts in Response to Elevated Carbon Dioxide. The ISME Journal, 6, 259-272. https://doi.org/10.1038/ismej.2011.99
Hartman, W.H., Richardson, C.J., Vilgalys, R. and Bruland, G.L. (2008) Environmental and Anthropogenic Controls over Bacterial Communities in Wetland Soils. Proceedings of the National Academy of Sciences of the United States of America, 105, 17842-17847. https://doi.org/10.1073/pnas.0808254105
Singh, R.P., Dhania, G., Sharma, A. and Jaiwal, P.K. (2007) Biotechnological Approaches to Improve Phytoremediation Efficiency for Environment Contaminants. In: Singh, S.N. and Tripathi, R.D., Eds., Environmental Bioremediation Technologies, Springer, Berlin, 223-258. https://doi.org/10.1007/978-3-540-34793-4_10
Constancias, F., Saby, N.P.A., Terrat, S., Dequiedt, S., Horrigue, W., Nowak, V., Guillemin, J.P., Biju-Duval, L., Chemidlin Prévost-Bouré, N. and Ranjard, L. (2015) Contrasting Spatial Patterns and Ecological Attributes of Soil Bacterial Taxa across a Landscape. Microbiology Open, 4, 518-531. https://doi.org/10.1002/mbo3.256
Nemergut, D.R., Cleveland, C.C., Wieder, W.R., Washenberger, C.L. and Townsend, A.R. (2010) Plot-Scale Manipulations of Organic Matter Inputs to Soils Correlate with Shifts in Microbial Community Composition in a Lowland Tropical Rain Forest. Soil Biology and Biochemistry, 42, 2153-2160. https://doi.org/10.1016/j.soilbio.2010.08.011
Nedashkovskaya, O.I. and Kim, S.B. (2015) Pontibacter. In: Sneath, P.H.A. and Bergey, D.H., Eds., Bergey’s Manual of Systematics of Archaea and Bacteria, John Wiley & Sons, Hoboken, 1-4. https://doi.org/10.1002/9781118960608.gbm00272
Baldwin, S.A., Khoshnoodi, M., Rezadehbashi, M., et al. (2015) The Microbial Community of a Passive Biochemical Reactor Treating Arsenic, Zinc, and Sulfate Rich Seepage. Frontiers in Bioengineering and Biotechnology, 3, Article 27. https://doi.org/10.3389/fbioe.2015.00027
Ji, Y., Liu, P. and Conrad, R. (2018) Response of Fermenting Bacterial and Methanogenic Archaeal Communities in Paddy Soil to Progressing Rice Straw Degradation. Soil Biology and Biochemistry, 124, 70-80. https://doi.org/10.1016/j.soilbio.2018.05.029
Wang, H., Sheng, Y., He, Y., Wu, J., Jiang, Y., Tam, N. and Zhou, H. (2012) Comparison of the Levels of Bacterial Diversity in Freshwater, Intertidal Wetland, and Marine Sediments by Using Millions of Illumina Tags. Applied and Environmental Microbiology, 78, 8264-8271. https://doi.org/10.1128/AEM.01821-12
Gans, J., Wolinsky, M. and Dunbar, J. (2005) Computational Improvements Reveal Great Bacterial Diversity and High Metal Toxicity in Soil. Science, 309, 1387-1390. https://doi.org/10.1126/science.1112665
Tringe, S.G., von Mering, C., Kobayashi, A., Salamov, A.A., Chen, K., Chang, H.W., Podar, M., Short, J.M., Mathur, E.J., Detter, J.C., Bork, P., Hugenholtz, P. and Rubin, E.M. (2005) Comparative Metagenomics of Microbial Communities. Science, 308, 554-557. https://doi.org/10.1126/science.1107851
Elshahed, M.S., Youssef, N.H., Spain, A.M., Sheik, C., Najar, F.Z., Sukharnikov, L.O., Roe, B.A., Davis, J.P., Schloss, P.D., Bailey, V.L. and Krumholz, L.R. (2008) Novelty and Uniqueness Patterns of Rare Members of the Soil Biosphere. Applied and Environmental Microbiology, 74, 5422-5428. https://doi.org/10.1128/AEM.00410-08
Fulthorpe, R.R., Roesch, L.F.W., Riva, A. and Triplett, E.W. (2008) Distantly Sampled Soils Carry Few Species in Common. The ISME Journal, 2, 901-910. https://doi.org/10.1038/ismej.2008.55
Roesch, L.F.W., Fulthorpe, R.R., Riva, A., Casella, G., Hadwin, A.K.M., Kent, A.D., Daroub, S.H., Camargo, F.A.O., Farmerie, W.G. and Triplett, E.W. (2007) Pyrosequencing Enumerates and Contrasts Soil Microbial Diversity. The ISME Journal, 1, 283-290. https://doi.org/10.1038/ismej.2007.53
Shen, C.C., Xiong, J.B., Zhang, H.Y., Feng, Y.Z., Lin, X.G., Li, X.Y., Liang, W.J. and Chu, H.Y. (2013) Soil pH Drives the Spatial Distribution of Bacterial Communities along Elevation on Changbai Mountain. Soil Biology and Biochemistry, 57, 204-211. https://doi.org/10.1016/j.soilbio.2012.07.013
Lauber, C.L., Hamady, M., Knight, R. and 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. https://doi.org/10.1128/AEM.00335-09