Characterization of Bacterial and Fungal Communities in Soils under Different Farming Systems. The Cacao Plantation in Sulawesi Island—Indonesia
The cacao plantations in Sulawesi Island, Indonesia are responsible for a great part of the local economy; however, their soils still need to be deeply explored. Our study focused on evaluation of the microbial communities in cacao soils according to their location and applied management system. Four soil samples were taken from six cacao farms under two kinds of systems (conventional and organic). 16S and ITS rDNA amplicon sequencing analyses of soils were also performed to identify bacteria and fungi, respectively, whereby their relative abundance and diversity were determined. In general view, the bacterial and fungal communities were affected by management system at the local and general levels. Bacterial analyses indicated that the number of operational taxonomic units and bacterial diversity were higher under the organic system in Kulawi, Palolo, and Poso farms. The composition and biodiversity of fungi were clearly different between organic and conventional systems and between different places (coastal and inland). The effect of agricultural management was observed in each location individually and in general.
Keywords:agricultural management amplicon sequencing location microbial diversity
We would like to thank the cacao farmers in Sulawesi, Indonesia, for allowing us to sample in their areas. We would also like to thank the students at Tadulako University who assisted us with sampling and analysis. Finally, we are thankful to Dr. Geleta Dugassa Markaof Universidade Federal de Vicosa, Brasil, for the constructive comments of this manuscript. This project was supported by the bilateral cooperation program between JSPS (Japan) and DHGE (Indonesia), and another grant of International collaboration.
- 2.A. H. C. van Bruggen, M. He, V. V. Zelenev, V. M. Semenov, A. M., Semenov, E. V. Semenova, T. V. Kuznetsova, A. K. Khozaeva, A. M. Kuznetsov, and M. V. Semenov, “Relationships between greenhouse gas emissions and cultivable bacterial populations in conventional, organic and long-term grass plots as affected by environmental variables and disturbances,” Soil Biol. Biochem. 114, 145–159 (2017).CrossRefGoogle Scholar
- 3.A. M. Semenov, I. A. Bubnov, V. M. Semenov, E. V. Semenova, V. V. Zelenev, and N. A. Semenova, “Daily dynamics of bacterial numbers, CO2 emissions from soil and relationships between their wavelike fluctuations and succession of the microbial community,” Eurasian Soil Sci. 46, 869–884 (2013).CrossRefGoogle Scholar
- 4.A. Orgiazzi, V. Bianciotto, P. Bonfante, S. Daghino, S. Ghignone, A. Lazzari, E. Lumini, A. Mello, C. Napoli, S. Perotto, A. Vizzini, S. Bagella, C. Murat, and M. Girlanda, “454 pyrosequencing analysis of fungal assemblages from geographically distant, disparate soils reveals spatial patterning and a core mycobiome,” Diversity 5, 73–98 (2013).CrossRefGoogle Scholar
- 6.C. Will, A. Thurmer, A. Wollherr, H. Nacke, N. Herold, M. Schrumpf, J. Gutknecht, T. Wubet, F. Buscot, and R. Daniel, “Horizon-specific bacterial community composition of German grassland soils, as revealed by pyrosequencing-based analysis of 16S rRNA genes,” Appl. Environ. Microbiol. 76, 6751–6759 (2010).CrossRefGoogle Scholar
- 7.D. N. Chavarria, C. Pérez-Brandan, D. L. Serri, J. M. Meriles, S. B. Restovich, A. E. Andriulo, L. Jacquelin, and S. Vargas-Gil, “Response of soil microbial communities to agroecological versus conventional systems of extensive agriculture,” Agric. Ecosyst. Environ. 264, 1–8 (2018).CrossRefGoogle Scholar
- 9.FAO, Food Agriculture Organization, GeoNetwork. http://www.fao.org/geonetwork/srv/en/main.home.Google Scholar
- 19.L. M. H. Kilowasid, T. S. Syamsudin, E. Sulystiawati, and F. X. Susilo, “Structure of soil food web in smallholder cocoa plantation, South Konawe district, Southeast Sulawesi, Indonesia,” Agrivita, J. Agric. Sci. 36, 33–47 (2014).Google Scholar
- 22.M. He, W. Ma, V. V. Zelenev, A. K. Khodzaeva, A. M. Kuznetsov, A. M. Semenov, V. M. Semenov, W. Blok, and A. H. C. van Bruggen, “Short-term dynamics of greenhouse gas emissions and cultivable bacterial populations in response to induced and natural disturbances in organically and conventionally managed soils,” Appl. Soil Ecol. 119, 294–306 (2017).CrossRefGoogle Scholar
- 27.S. Dequiedt, N. P. A. Saby, M. Lelievre, C. Jolivet, J. Thioulouse, B. Toutain, D. Arrouays, A. Bispo, P. Lemanceau, and L. Ranjard, “Biogeographical patterns of soil molecular microbial biomass as influenced by soil characteristics and management,” Global Ecol. Biogeogr. 20, 641 (2011).CrossRefGoogle Scholar