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Enagbonma BJ, Fadiji AE, Babalola OO. Anthropogenic fertilization influences a shift in barley rhizosphere microbial communities. PeerJ 2024; 12:e17303. [PMID: 39006020 PMCID: PMC11246026 DOI: 10.7717/peerj.17303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 04/04/2024] [Indexed: 07/16/2024] Open
Abstract
Background Anthropogenic mediations contribute a significant role in stimulating positive reactions in soil-plant interactions; however, methodical reports on how anthropogenic activities impact soil microorganism-induced properties and soil health are still inadequate. In this study, we evaluated the influence of anthropogenic fertilization of farmland soil on barley rhizosphere microbial community structure and diversity, and the significant impacts on agro-ecosystem productivity. This will help validate the premise that soil amendment with prolonged synthetic fertilizers can lead to a significant reduction in bacterial abundance and diversity, while soils amended with organic fertilizers elicit the succession of the native soil microbial community and favor the growth of copiotrophic bacteria. Methods The total metagenomic DNA was extracted from soils obtained from the barley rhizosphere under chemical fertilization (CB), organic fertilization (OB), and bulk soil (NB). Subsequently, these samples were sequenced using an amplicon-based sequencing approach, and the raw sequence dataset was examined using a metagenomic rast server (MG-RAST). Results Our findings showed that all environments (CB, OB, and NB) shared numerous soil bacterial phyla but with different compositions. However, Bacteroidetes, Proteobacteria, and Actinobacteria predominated in the barley rhizosphere under chemical fertilization, organic fertilization, and bulk soils, respectively. Alpha and beta diversity analysis showed that the diversity of bacteria under organic barley rhizosphere was significantly higher and more evenly distributed than bacteria under chemical fertilization and bulk soil. Conclusion Understanding the impact of conventional and organic fertilizers on the structure, composition, and diversity of the rhizosphere microbiome will assist in soil engineering to enhance microbial diversity in the agroecosystem.
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Affiliation(s)
- Ben Jesuorsemwen Enagbonma
- Food Security and Safety Focus Area, Faculty of Natural and Agricultural Sciences, North-West University, Mmabatho, North-West Province, South Africa
| | - Ayomide Emmanuel Fadiji
- Food Security and Safety Focus Area, Faculty of Natural and Agricultural Sciences, North-West University, Mmabatho, North-West Province, South Africa
| | - Olubukola Oluranti Babalola
- Food Security and Safety Focus Area, Faculty of Natural and Agricultural Sciences, North-West University, Mmabatho, North-West Province, South Africa
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Mason ARG, Cavagnaro TR, Guerin GR, Lowe AJ. Soil Bacterial Assemblage Across a Production Landscape: Agriculture Increases Diversity While Revegetation Recovers Community Composition. MICROBIAL ECOLOGY 2023; 85:1098-1112. [PMID: 36763113 PMCID: PMC10156840 DOI: 10.1007/s00248-023-02178-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 01/17/2023] [Indexed: 05/04/2023]
Abstract
Aboveground ecological impacts associated with agricultural land use change are evident as natural plant communities are replaced with managed production systems. These impacts have been extensively studied, unlike those belowground, which remain poorly understood. Soil bacteria are good candidates to monitor belowground ecological dynamics due to their prevalence within the soil system and ability to survive under harsh and changing conditions. Here, we use soil physicochemical assessment and 16S rRNA gene sequencing to investigate the soil physical and bacterial assemblage changes across a mixed-use agricultural landscape. We assess soil from remnant vegetation (Eucalyptus mallee), new and old vineyards, old pasture, and recently revegetated areas. Elevated concentrations of nitrogen (NO3-) and plant-available (Colwell) phosphorus were identified in the managed vineyard systems, highlighting the impact of agricultural inputs on soil nutrition. Alpha diversity comparison revealed a significant difference between the remnant mallee vegetation and the vineyard systems, with vineyards supporting highest bacterial diversity. Bacterial community composition of recently revegetated areas was similar to remnant vegetation systems, suggesting that bacterial communities can respond quickly to aboveground changes, and that actions taken to restore native plant communities may also act to recover natural microbial communities, with implications for soil and plant health. Findings here suggest that agriculture may disrupt the correlation between above- and belowground diversities by altering the natural processes that otherwise govern this relationship (e.g. disturbance, plant production, diversity of inputs), leading to the promotion of belowground microbial diversity in agricultural systems.
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Affiliation(s)
- A R G Mason
- School of Agriculture, Food & Wine, The University of Adelaide, Adelaide, Australia.
| | - T R Cavagnaro
- School of Agriculture, Food & Wine, The University of Adelaide, Adelaide, Australia
| | - G R Guerin
- School of Biological Sciences, The University of Adelaide, Adelaide, Australia
| | - A J Lowe
- School of Biological Sciences, The University of Adelaide, Adelaide, Australia
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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.
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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.
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Microbial Diversity of Temperate Pine and Native Forest Soils Profiled by 16S rRNA Gene Amplicon Sequencing. Microbiol Resour Announc 2021; 10:10/20/e00298-21. [PMID: 34016677 PMCID: PMC8188351 DOI: 10.1128/mra.00298-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Most biodiversity measures indicate an ongoing deterioration due to intensifying anthropogenic pressures even though efforts are being intensified worldwide to conserve biodiversity. Knowledge of the implication of land-use change on soil bacterial communities is essential for ecosystem restoration. Most biodiversity measures indicate an ongoing deterioration due to intensifying anthropogenic pressures even though efforts are being intensified worldwide to conserve biodiversity. Knowledge of the implication of land use change on soil bacterial communities is essential for ecosystem restoration. Here, the effect of the conversion of native forests to temperate pine forests on soil bacterial diversity and community composition was investigated. The diversity and composition of the bacterial communities were affected by land use change across the sites.
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Abstract
Plant rhizobiomes are responsible for major soil processes in the immediate plant environment, but our knowledge of the linkage between below-ground microbiota diversity and plant health is limited. We studied the bacterial and archaeal communities of sunflower rhizosphere organisms by comparing the composition of these communities in bulk soil at three farms in the North West province of South Africa. We evaluated and described a plethora of bacterial and archaeal taxa. Plant rhizobiomes are responsible for major soil processes in the immediate plant environment, but our knowledge of the linkage between below-ground microbiota diversity and plant health is limited. We studied the bacterial and archaeal communities of sunflower rhizosphere organisms by comparing the composition of these communities to bulk soils at three farms in the North West province of South Africa. We evaluated and described a plethora of bacterial and archaeal taxa.
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Ogola HJO, Selvarajan R, Tekere M. Local Geomorphological Gradients and Land Use Patterns Play Key Role on the Soil Bacterial Community Diversity and Dynamics in the Highly Endemic Indigenous Afrotemperate Coastal Scarp Forest Biome. Front Microbiol 2021; 12:592725. [PMID: 33716998 PMCID: PMC7943610 DOI: 10.3389/fmicb.2021.592725] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 01/28/2021] [Indexed: 12/26/2022] Open
Abstract
Southern Afrotemperate forests are small multi-layered and highly fragmented biodiversity rich biomes that support unique flora and fauna endemism. However, little is known about the microbial community and their contribution to these ecosystems. In this study, high throughput sequencing analysis was used to investigate the soil bacterial community structure and function, and understand the effect of local topography/geomorphological formations and land use patterns on a coastal scarp forest. Soil samples were collected from three forest topography sites: upper (steeper gradients, 30-55°; open canopy cover, <30%), mid (less steep, 15-30°; continuous forest canopy, >80%), and lower (flatter gradient, <15°; open canopy cover, 20-65%), and from the adjacent sugarcane farms. Results indicated that forest soils were dominated by members of phyla Proteobacteria (mainly members of α-proteobacteria), Actinobacteria, Acidobacteria, Firmicutes, and Planctomycetes, while Actinobacteria and to a lesser extent β-proteobacteria and γ-proteobacteria dominated SC soils. The core bacterial community clustered by habitat (forest vs. sugarcane farm) and differed significantly between the forest topography sites. The Rhizobiales (genera Variibacter, Bradyrhizobium, and unclassified Rhizobiales) and Rhodospirallales (unclassified Rhodospirillum DA111) were more abundant in forest mid and lower topographies. Steeper forest topography (forest_upper) characterized by the highly leached sandy/stony acidic soils, low in organic nutrients (C and N) and plant densities correlated to significant reduction of bacterial diversity and richness, associating significantly with members of order Burkholderiales (Burkholderia-Paraburkholderia, Delftia, and Massilia) as the key indicator taxa. In contrast, changes in the total nitrogen (TN), soil organic matter (SOM), and high acidity (low pH) significantly influenced bacterial community structure in sugarcane farm soils, with genus Acidothermus (Frankiales) and uncultured Solirubrobacterales YNFP111 were the most abundant indicator taxa. Availability of soil nutrients (TN and SOM) was the strongest driver of metabolic functions related to C fixation and metabolism, N and S cycling; these processes being significantly abundant in forest than sugarcane farm soils. Overall, these results revealed that the local topographical/geomorphological gradients and sugarcane farming affect both soil characteristics and forest vegetation (canopy coverage), that indirectly drives the structure and composition of bacterial communities in scarp forest soils.
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Affiliation(s)
- Henry Joseph Oduor Ogola
- Department of Environmental Science, University of South Africa, Florida Science Campus, Roodepoort, South Africa
- School of Agricultural and Food Sciences, Jaramogi Oginga Odinga University of Science and Technology, Bondo, Kenya
| | - Ramganesh Selvarajan
- Department of Environmental Science, University of South Africa, Florida Science Campus, Roodepoort, South Africa
| | - Memory Tekere
- Department of Environmental Science, University of South Africa, Florida Science Campus, Roodepoort, South Africa
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Adedeji AA, Babalola OO. Secondary metabolites as plant defensive strategy: a large role for small molecules in the near root region. PLANTA 2020; 252:61. [PMID: 32965531 DOI: 10.1007/s00425-020-03468-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 09/12/2020] [Indexed: 05/20/2023]
Abstract
The roles of plant roots are not merely limited to the provision of mechanical support, nutrients and water, but also include more specific roles, such as the capacity to secrete diverse chemical substances. These metabolites are actively secreted in the near root and play specific and significant functions in plant defense and communication. In this review, we detail the various preventive roles of these powerful substances in the rhizosphere with a perspective as to how plants recruit microbes as a preventive measure against other pathogenic microbes, also, briefly about how the rhizosphere can repel insect pests, and how these chemical substances alter microbial dynamics and enhance symbiotic relationships. We also highlight the need for more research in this area to detail the mode of action and quantification of these compounds in the environment and their roles in some important biological processes in microorganisms and plants.
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Affiliation(s)
- Atilade Adedayo Adedeji
- Food Security and Safety Niche Area, Faculty of Natural and Agricultural Sciences, North-West University, Private Bag X2046, Mmabatho, 2735, South Africa
- Department of Biochemistry and Microbiology, School of Environmental and Biological Sciences, Rutgers University, New Brunswick, NJ, USA
| | - Olubukola Oluranti Babalola
- Food Security and Safety Niche Area, Faculty of Natural and Agricultural Sciences, North-West University, Private Bag X2046, Mmabatho, 2735, South Africa.
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Amoo AE, Enagbonma BJ, Babalola OO. High-throughput sequencing data of soil bacterial communities from Tweefontein indigenous and commercial forests, South Africa. Data Brief 2019; 28:104916. [PMID: 31890783 PMCID: PMC6926133 DOI: 10.1016/j.dib.2019.104916] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 11/22/2019] [Accepted: 11/25/2019] [Indexed: 11/30/2022] Open
Abstract
In this report, the high-throughput sequencing data of soil bacterial communities from indigenous and commercial forests in Tweefontein, South Africa are presented. These data were collected to study the influence of land-use change on soil bacterial diversity and community structure in forests. Illumina Miseq sequencing of 16S rRNA gene amplicon was carried out on soils sampled from Tweefontein commercial (TC) and indigenous (TI) forests in South Africa. The metagenome contained 101,938 sequences with 46,709,377 bp size and 57% G + C content in TI and 91,160 sequences with 41,707,827 bp size and 57% G + C content in TC. Metagenome sequence information are available at NCBI under the Sequence Read Archive (SRA) database with accession numbers SRR8134476 (TI) and SRR8135323 (TC). Taxonomic hits distribution from Metagenomic Rast Server (MG-RAST) analysis of the TI sample revealed the dominance of the phyla Acidobacteria (21.61%), Actinobacteria (18.23%) and Verrucomicrobia (16.78%). Predominant genera were Candidatus Koribacter (12.82%), Candidatus Solibacter (11.74%) and Chthoniobacter (9.36%). MG-RAST assisted analysis of TC sample also detected the dominance of Actinobacteria (23.62%) along with Verrucomicrobia (21.92%) and Acidobacteria (20.74%). Predominant genera were Chthoniobacter (24.94%), Candidatus Solibacter (16.74%) and Candidatus Koribacter (9.39%) which play vital ecological functions in forest ecosystems.
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Affiliation(s)
- Adenike Eunice Amoo
- Food Security and Safety, Faculty of Natural and Agricultural Sciences, North-West University, Private Bag X2046, Mmabatho, 2735, South Africa
| | - Ben Jesuorsemwen Enagbonma
- Food Security and Safety, Faculty of Natural and Agricultural Sciences, North-West University, Private Bag X2046, Mmabatho, 2735, South Africa
| | - Olubukola Oluranti Babalola
- Food Security and Safety, Faculty of Natural and Agricultural Sciences, North-West University, Private Bag X2046, Mmabatho, 2735, South Africa
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