Exploration of soil bacterial diversity in organic and conventional agriculture fields in Sri Lanka

Data Records

The data in this sampling event resource has been published as a Darwin Core Archive (DwC-A), which is a standardized format for sharing biodiversity data as a set of one or more data tables. The core data table contains 25 records.

1 extension data tables also exist. An extension record supplies extra information about a core record. The number of records in each extension data table is illustrated below.

This IPT archives the data and thus serves as the data repository. The data and resource metadata are available for download in the downloads section. The versions table lists other versions of the resource that have been made publicly available and allows tracking changes made to the resource over time.

Versions

The table below shows only published versions of the resource that are publicly accessible.

How to cite

Researchers should cite this work as follows:

Tissera B, Herath L (2023). Exploration of soil bacterial diversity in organic and conventional agriculture fields in Sri Lanka. Version 1.3. Sri Lanka Institute of Nanotechnology (SLINTEC). Samplingevent dataset. https://cloud.gbif.org/asia/resource?r=soil_bacterial_diversity_in_agroecosystems_in_sri_lanka&v=1.3

Rights

Researchers should respect the following rights statement:

The publisher and rights holder of this work is Sri Lanka Institute of Nanotechnology (SLINTEC). To the extent possible under law, the publisher has waived all rights to these data and has dedicated them to the Public Domain (CC0 1.0). Users may copy, modify, distribute and use the work, including for commercial purposes, without restriction.

GBIF Registration

This resource has been registered with GBIF, and assigned the following GBIF UUID: 7e9d3bc6-bb85-42a5-8826-fe2b27552e2c.  Sri Lanka Institute of Nanotechnology (SLINTEC) publishes this resource, and is itself registered in GBIF as a data publisher endorsed by Participant Node Managers Committee.

Keywords

Sri Lanka; Agroecosystems; Soil biodiversity; eDNA; Sampling-event dataset

Contacts

Geographic Coverage

Asia LK

Temporal Coverage

Project Data

Soil is known to be the reservoir for a vast amount of microorganisms with a prokaryotic diversity that exceeds that of the known catalog of prokaryotes. Soil bacterial diversity is represented by the composition of bacteria and the abundance of its members and is a vital regulator of fundamental ecosystem processes, such as organic matter decomposition and nutrient cycling. Rhizosphere microbial communities play a central role in both plant growth and health and the depletion of soil microbial communities in agroecosystems is a significant course of soil fertility loss. This project aimed to explore the soil bacterial diversity of agroecosystems across the main agroecological zones of Sri Lanka and make it available to the scientific community. Metagenomic sequencing of the V4 region of the bacterial 16S rDNA gene was employed to explore the soil bacterial diversity within the collected samples. This dataset consists of 4,149 different occurrence records which have been georeferenced and classified to their species level. Here we present the first sampling-event dataset consisting of the taxonomy and geographic location of all recorded taxa offering a comprehensive insight into the soil bacterial populations across the diverse agroecosystems of Sri Lanka.

The personnel involved in the project:

Sampling Methods

Soil samples were collected from four different locations in each of the 25 agricultural fields belonging to the main agroecological zones of Sri Lanka. The soil samples were obtained by pushing a 50ml falcon tube to a depth of 20cm into the soil from the natural surface level. The samples were transported to the laboratory in ice boxes and were stored at -20°C until they were used for the extraction of DNA.

Method step description:

1. Soil samples were collected from four different locations in each agricultural field by pushing a 50ml falcon tube to a depth of 20cm into the soil from the natural surface level (Naveed et al., 2016; Wang et al., 2016). The samples were transported to the laboratory in ice boxes. The soil samples from the four different locations in each agricultural field were homogenized to form a composite soil sample, freeze-dried, ball-milled for 30 minutes with 15 metal beads, and passed through a 500μm sieve prior to DNA Extraction. The soil DNA was isolated from 500mg of soil using the HiPurA soil DNA Purification Kit according to the manufacturer’s instructions. DNA extraction was conducted on four 500mg soil samples from each field. The extracted DNA was electrophoresed in 1% agarose gel. The DNA was quantified and its purity was determined using the Spectradrop microplate reader (Yakovleva et al., 2017). The DNA samples that showed a high concentration and purity were pooled and stored at -20 °C until they were used for PCR amplification. The PCR amplification was performed as a two-step program. To amplify the V4 domain of bacterial 16S rDNA for sequencing, PCR amplification was performed using standard forward and reverse primer pair, F515 (GTG CCA GCM GCC GCG GTA A) and R806 (GGA CTA CVS GGG TAT CTA AT) (Zhang et al., 2019). This was the first step of PCR amplification. Next, 3 μL of the PCR product was used as the template for the second step which was performed with barcoded primers. The PCR mixture for both steps contained the Hi-Chrom master mix, forward primer (10X), reverse primer (10X), molecular grade distilled water, and 3μL DNA template in a final volume of 25μL. The amplifications were conducted in a heal force K960 thermal cycler using an initial DNA denaturation step of 94 °C for 1 min, followed by 28 cycles at 94 °C for 30 s, 50 °C for 30 s, 72 °C for 1 min, and a final elongation at 72 °C for 10 min. The PCR products were electrophoresed in 1% agarose gel. The PCR products from the second step were purified using the HiPurA PCR Product Purification Kit, quantified, and their purity was determined using the Spectradrop microplate reader. Finally, the PCR products were sequenced using high-throughput sequencing technology, and the sequence data were used to access the soil bacterial diversity.

Bibliographic Citations

1. Naveed, M., Herath, L., Moldrup, P., Arthur, E., Nicolaisen, M., Norgaard, T., Ferré, T.P.A., de Jonge, L.W., 2016. Spatial variability of microbial richness and diversity and relationships with soil organic carbon, texture and structure across an agricultural field. Applied Soil Ecology 103, 44–55. https://www.sciencedirect.com/science/article/abs/pii/S092913931630066X
2. Wang, Z., Liu, L., Chen, Q., Wen, X., Liao, Y., 2016. Conservation tillage increases soil bacterial diversity in the dryland of Northern China. Agronomy for Sustainable Development 36. https://link.springer.com/article/10.1007/s13593-016-0366-x
3. Yakovleva, A., Plieskatt, J., Jensen, S., Humeida, R., Lang, J., Li, G., Bracci, P., Silver, S. and Bethony, J. (2017) ‘Fit for genomic and proteomic purposes: Sampling the fitness of nucleic acid and protein derivatives from formalin fixed paraffin embedded tissue’ ,PLOS ONE, 12(7), p.e0181756 https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0181756
4. Zhang, Z., Zhang, P., Lin, Q., Cha, Z., Luo, W., 2019. Response of bacterial communities in rubber plantations to different fertilizer treatments. 3 Biotech 9, 293. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6609652/

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