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Amplicon-based assessment of bacterial diversity and community structure in three tropical forest soils in Kenya
Forest soils provide a multitude of habitats for diverse communities of bacteria. In this study, we selected three tropical forests in Kenya to determine the diversity and community structure of soil bacteria inhabiting these regions. Kakamega and Irangi are rainforests, whereas Gazi Bay harbors man...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Elsevier
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9674510/ https://www.ncbi.nlm.nih.gov/pubmed/36411924 http://dx.doi.org/10.1016/j.heliyon.2022.e11577 |
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author | Kenya, Eucharia Kinyanjui, Grace Kipnyargis, Alex Kinyua, Franklin Mwangi, Mary Khamis, Fathiya Mwirichia, Romano |
author_facet | Kenya, Eucharia Kinyanjui, Grace Kipnyargis, Alex Kinyua, Franklin Mwangi, Mary Khamis, Fathiya Mwirichia, Romano |
author_sort | Kenya, Eucharia |
collection | PubMed |
description | Forest soils provide a multitude of habitats for diverse communities of bacteria. In this study, we selected three tropical forests in Kenya to determine the diversity and community structure of soil bacteria inhabiting these regions. Kakamega and Irangi are rainforests, whereas Gazi Bay harbors mangrove forests. The three natural forests occupy different altitudinal zones and differ in their environmental characteristics. Soil samples were collected from a total of 12 sites and soil physicochemical parameters for each sampling site were analyzed. We used an amplicon-based Illumina high-throughput sequencing approach. Total community DNA was extracted from individual samples using the phenol-chloroform method. The 16S ribosomal RNA gene segment spanning the V4 region was amplified using the Illumina MiSeq platform. Diversity indices, rarefaction curves, hierarchical clustering, principal component analysis (PCA), and non-metric multidimensional scaling (NMDS) analyses were performed in R software. A total of 13,410 OTUs were observed at 97% sequence similarity. Bacterial communities were dominated by Proteobacteria, Bacteroidetes, Firmicutes, Actinobacteria, and Acidobacteria in both rainforest and mangrove sampling sites. Alpha diversity indices and species richness were higher in Kakamega and Irangi rainforests compared to mangroves in Gazi Bay. The composition of bacterial communities within and between the three forests was also significantly differentiated (R = 0.559, p = 0.007). Clustering in both PCA and NMDS plots showed that each sampling site had a distinct bacterial community profile. The NMDS analysis also indicated that soil EC, sodium, sulfur, magnesium, boron, and manganese contributed significantly to the observed variation in the bacterial community structure. Overall, this study demonstrated the presence of diverse taxa and heterogeneous community structures of soil bacteria inhabiting three tropical forests of Kenya. Our results also indicated that variation in soil chemical parameters was the major driver of the observed bacterial diversity and community structure in these forests. |
format | Online Article Text |
id | pubmed-9674510 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Elsevier |
record_format | MEDLINE/PubMed |
spelling | pubmed-96745102022-11-20 Amplicon-based assessment of bacterial diversity and community structure in three tropical forest soils in Kenya Kenya, Eucharia Kinyanjui, Grace Kipnyargis, Alex Kinyua, Franklin Mwangi, Mary Khamis, Fathiya Mwirichia, Romano Heliyon Research Article Forest soils provide a multitude of habitats for diverse communities of bacteria. In this study, we selected three tropical forests in Kenya to determine the diversity and community structure of soil bacteria inhabiting these regions. Kakamega and Irangi are rainforests, whereas Gazi Bay harbors mangrove forests. The three natural forests occupy different altitudinal zones and differ in their environmental characteristics. Soil samples were collected from a total of 12 sites and soil physicochemical parameters for each sampling site were analyzed. We used an amplicon-based Illumina high-throughput sequencing approach. Total community DNA was extracted from individual samples using the phenol-chloroform method. The 16S ribosomal RNA gene segment spanning the V4 region was amplified using the Illumina MiSeq platform. Diversity indices, rarefaction curves, hierarchical clustering, principal component analysis (PCA), and non-metric multidimensional scaling (NMDS) analyses were performed in R software. A total of 13,410 OTUs were observed at 97% sequence similarity. Bacterial communities were dominated by Proteobacteria, Bacteroidetes, Firmicutes, Actinobacteria, and Acidobacteria in both rainforest and mangrove sampling sites. Alpha diversity indices and species richness were higher in Kakamega and Irangi rainforests compared to mangroves in Gazi Bay. The composition of bacterial communities within and between the three forests was also significantly differentiated (R = 0.559, p = 0.007). Clustering in both PCA and NMDS plots showed that each sampling site had a distinct bacterial community profile. The NMDS analysis also indicated that soil EC, sodium, sulfur, magnesium, boron, and manganese contributed significantly to the observed variation in the bacterial community structure. Overall, this study demonstrated the presence of diverse taxa and heterogeneous community structures of soil bacteria inhabiting three tropical forests of Kenya. Our results also indicated that variation in soil chemical parameters was the major driver of the observed bacterial diversity and community structure in these forests. Elsevier 2022-11-15 /pmc/articles/PMC9674510/ /pubmed/36411924 http://dx.doi.org/10.1016/j.heliyon.2022.e11577 Text en © 2022 The Author(s) https://creativecommons.org/licenses/by-nc-nd/4.0/This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/). |
spellingShingle | Research Article Kenya, Eucharia Kinyanjui, Grace Kipnyargis, Alex Kinyua, Franklin Mwangi, Mary Khamis, Fathiya Mwirichia, Romano Amplicon-based assessment of bacterial diversity and community structure in three tropical forest soils in Kenya |
title | Amplicon-based assessment of bacterial diversity and community structure in three tropical forest soils in Kenya |
title_full | Amplicon-based assessment of bacterial diversity and community structure in three tropical forest soils in Kenya |
title_fullStr | Amplicon-based assessment of bacterial diversity and community structure in three tropical forest soils in Kenya |
title_full_unstemmed | Amplicon-based assessment of bacterial diversity and community structure in three tropical forest soils in Kenya |
title_short | Amplicon-based assessment of bacterial diversity and community structure in three tropical forest soils in Kenya |
title_sort | amplicon-based assessment of bacterial diversity and community structure in three tropical forest soils in kenya |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9674510/ https://www.ncbi.nlm.nih.gov/pubmed/36411924 http://dx.doi.org/10.1016/j.heliyon.2022.e11577 |
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