|
1
|
Kenya E, Kinyanjui G, Kipnyargis A, Kinyua F, Mwangi M, Khamis F, Mwirichia R. Amplicon-based assessment of bacterial diversity and community structure in three tropical forest soils in Kenya. Heliyon 2022; 8:e11577. [PMID: 36411924 PMCID: PMC9674510 DOI: 10.1016/j.heliyon.2022.e11577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 07/14/2022] [Accepted: 11/07/2022] [Indexed: 11/16/2022] Open
Abstract
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.
Collapse
Affiliation(s)
- Eucharia Kenya
- Department of Biological Sciences, University of Embu, P. O. Box 6-60100, Embu, Kenya
| | - Grace Kinyanjui
- Department of Biological Sciences, University of Embu, P. O. Box 6-60100, Embu, Kenya
| | - Alex Kipnyargis
- Department of Biological Sciences, University of Embu, P. O. Box 6-60100, Embu, Kenya
| | - Franklin Kinyua
- Department of Biological Sciences, University of Embu, P. O. Box 6-60100, Embu, Kenya
| | - Mary Mwangi
- Department of Biochemistry and Biotechnology, Kenyatta University, P. O. Box 43844-00100, Nairobi, Kenya
| | - Fathiya Khamis
- International Centre of Insect Physiology and Ecology (ICIPE), P. O. Box 30772-00100, Nairobi, Kenya
| | - Romano Mwirichia
- Department of Biological Sciences, University of Embu, P. O. Box 6-60100, Embu, Kenya
- Corresponding author.
| |
Collapse
|
|
2
|
Native or Exotic: A Bibliographical Review of the Debate on Ecological Science Methodologies: Valuable Lessons for Urban Green Space Design. LAND 2022. [DOI: 10.3390/land11081201] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Knowledge from ecological sciences is an important reference for landscape design as Urban Green Spaces (UGS) play a critical role in the ecological protection of cities. There is an ongoing debate among ecologists on the value of exotic vegetation to ecosystem resilience and integrity, with authors arguing that in order for ecosystems to survive in future climates, exotic species with similar conditions in their current range must be considered. Others deem biodiversity vital for ecosystem functions and services, stating that most biodiversity losses are man-induced and should be addressed through the enhancement of native communities. Through a literature review, we confronted the arguments used in this debate, with the aim of conducting a comprehensive analysis of the potential of exotic and native vegetation in different aspects of the vegetation’s performance. The outcomes are important for the assessment of vegetation assemblages within UGS projects. Despite the strong arguments regarding their performative and adaptive capacity, we conclude that exotics pose significant ecological risks and have multiple negative impacts on ecosystem processes. Natives not only present high adaptive capacity, but also provide additional benefits for biodiversity, ecosystem integrity, and for people. In a broader framework, the literature demonstrates a preference for the use of native species in most situations.
Collapse
|
|
3
|
Li Y, Wang Y, Shen C, Xu L, Yi S, Zhao Y, Zuo W, Gu C, Shan Y, Bai Y. Structural and Predicted Functional Diversities of Bacterial Microbiome in Response to Sewage Sludge Amendment in Coastal Mudflat Soil. BIOLOGY 2021; 10:biology10121302. [PMID: 34943217 PMCID: PMC8698727 DOI: 10.3390/biology10121302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 12/04/2021] [Accepted: 12/06/2021] [Indexed: 11/16/2022]
Abstract
The study investigated the influence of sewage sludge application at rates of 0 (CK), 30 (ST), 75 (MT), and 150 (HT) t ha−1 to mudflats on bacterial community diversity and predicted functions using amplicon-based sequencing. Soils under sewage sludge treatments, especially the HT treatment, exhibited lower pH, salinity and higher nutrient contents (C, N, and P). Moreover, restructured bacterial communities with significantly higher diversities and distinct core and unique microbiomes were observed in all sewage sludge-amended soils as compared to the control. Specifically, core bacterial families, such as Hyphomicrobiaceae, Cytophagaceae, Pirellulaceae Microbacteriaceae, and Phyllobacteriaceae, were significantly enriched in sewage sludge-amended soils. In addition, sewage sludge amendment significantly improved predicted functional diversities of core microbiomes, with significantly higher accumulative relative abundances of functions related to carbon and nitrogen cycling processes compared to the unamended treatment. Correlation analyses showed that modified soil physicochemical properties were conducive for the improvement of diversities of bacterial communities and predicted functionalities. These outcomes demonstrated that sewage sludge amendment not only alleviated saline–sodic and nutrient deficiency conditions, but also restructured bacterial communities with higher diversities and versatile functions, which may be particularly important for the fertility formation and development of mudflat soils.
Collapse
Affiliation(s)
- Yunlong Li
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou 225127, China; (Y.L.); (Y.W.); (C.S.); (L.X.); (S.Y.); (Y.Z.); (W.Z.); (Y.S.)
| | - Yimin Wang
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou 225127, China; (Y.L.); (Y.W.); (C.S.); (L.X.); (S.Y.); (Y.Z.); (W.Z.); (Y.S.)
| | - Chao Shen
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou 225127, China; (Y.L.); (Y.W.); (C.S.); (L.X.); (S.Y.); (Y.Z.); (W.Z.); (Y.S.)
| | - Lu Xu
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou 225127, China; (Y.L.); (Y.W.); (C.S.); (L.X.); (S.Y.); (Y.Z.); (W.Z.); (Y.S.)
| | - Siqiang Yi
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou 225127, China; (Y.L.); (Y.W.); (C.S.); (L.X.); (S.Y.); (Y.Z.); (W.Z.); (Y.S.)
| | - Yilin Zhao
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou 225127, China; (Y.L.); (Y.W.); (C.S.); (L.X.); (S.Y.); (Y.Z.); (W.Z.); (Y.S.)
| | - Wengang Zuo
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou 225127, China; (Y.L.); (Y.W.); (C.S.); (L.X.); (S.Y.); (Y.Z.); (W.Z.); (Y.S.)
| | - Chuanhui Gu
- Environmental Research Center, Duke Kunshan University, Kunshan 215316, China;
| | - Yuhua Shan
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou 225127, China; (Y.L.); (Y.W.); (C.S.); (L.X.); (S.Y.); (Y.Z.); (W.Z.); (Y.S.)
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing 210095, China
| | - Yanchao Bai
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou 225127, China; (Y.L.); (Y.W.); (C.S.); (L.X.); (S.Y.); (Y.Z.); (W.Z.); (Y.S.)
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing 210095, China
- Correspondence:
| |
Collapse
|
|
4
|
Pan Y, Kang P, Hu J, Song N. Bacterial community demonstrates stronger network connectivity than fungal community in desert-grassland salt marsh. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 798:149118. [PMID: 34332392 DOI: 10.1016/j.scitotenv.2021.149118] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 07/12/2021] [Accepted: 07/14/2021] [Indexed: 06/13/2023]
Abstract
The diversity of soil bacterial and fungal communities is closely related to the soil characteristics and vegetation types in salt marsh ecosystems, but the biogeographic patterns and driving factors in desert-grassland salt marsh (DGSM) are still unclear. In this study, we divided sample plots according to the dominant species in Jiantan Lake wetland of a typical DGSM in Northwestern China. The effects of different environmental factors and halophytes on the structure of soil bacterial and fungal communities were investigated using soil physicochemical characterization and high-throughput sequencing analysis. The diversity of bacterial communities in bulk soil and three dominant halophytes (Kalidium cuspidatum, Nitraria tangutorum and Sophora alopecuroides) were the main factors affecting soil physicochemical properties and halophyte vegetation coverage. Proteobacteria, Bacteroides and Gemmatimonadetes had the highest abundance in bulk soil and the lowest in Sophora alopecuroides sample soil; the opposite was true for Acidobacteria and Chloroflexi. The abundance of Ascomycota in bulk soil and Sophora alopecuroides sample soil was higher than Kalidium cuspidatum and Nitraria tangutorum sample soils, whereas the Mortierellomycota was the highest in Nitraria tangutorum sample soil. Co-occurrence network analysis showed that halophyte cover increased the connectivity and complexity of the bacterial-fungal interaction network, and the halophytic shrub sample soil had a more stable network relationship than the halophytic herb soil. The key taxa of each plot were identified through network relationships. It was found that the keystone taxa of Proteobacteria, Firmicutes, Ascomycota and Chytridiomycota played important roles in maintaining community functions, and most of them were not significantly influenced by soil physicochemical properties. The results of this study provide new insights for a deeper understanding of the halophytes that drive the multifunctionality and stability of soil ecosystems in DGSM.
Collapse
Affiliation(s)
- Yaqing Pan
- College of Agriculture, Ningxia University, Yinchuan 750021, Ningxia, China; Breeding Base for State Key Laboratory of Land Degradation and Ecological Restoration of Northwest China, Yinchuan 750021, Ningxia, China; Key Laboratory for Restoration and Reconstruction of Degraded Ecosystems in Northwest China, Ministry of Education, Ningxia University, Yinchuan 750021, China
| | - Peng Kang
- College of Biological Sciences and Engineering, North Minzu University, Yinchuan 750021, China; Ningxia Key Laboratory for the Development and Application of Microbial Resources in Extreme Environments, North Minzu University, Yinchuan 750021, China
| | - Jinpeng Hu
- College of Biological Sciences and Engineering, North Minzu University, Yinchuan 750021, China
| | - Naiping Song
- College of Agriculture, Ningxia University, Yinchuan 750021, Ningxia, China; Breeding Base for State Key Laboratory of Land Degradation and Ecological Restoration of Northwest China, Yinchuan 750021, Ningxia, China; Key Laboratory for Restoration and Reconstruction of Degraded Ecosystems in Northwest China, Ministry of Education, Ningxia University, Yinchuan 750021, China.
| |
Collapse
|