1
|
Matteoli FP, Silva AMM, de Araújo VLVP, Feiler HP, Cardoso EJBN. Organic farming promotes the abundance of fungi keystone taxa in bacteria-fungi interkingdom networks. World J Microbiol Biotechnol 2024; 40:119. [PMID: 38429532 DOI: 10.1007/s11274-024-03926-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 02/14/2024] [Indexed: 03/03/2024]
Abstract
Soil bacteria-fungi interactions are essential in the biogeochemical cycles of several nutrients, making these microbes major players in agroecosystems. While the impact of the farming system on microbial community composition has been extensively reported in the literature, whether sustainable farming approaches can promote associations between bacteria and fungi is still unclear. To study this, we employed 16S, ITS, and 18S DNA sequencing to uncover how microbial interactions were affected by conventional and organic farming systems on maize crops. The Bray-Curtis index revealed that bacterial, fungal, and arbuscular mycorrhizal fungi communities were significantly different between the two farming systems. Several taxa known to thrive in healthy soils, such as Nitrosophaerales, Orbiliales, and Glomus were more abundant in the organic farming system. Constrained ordination revealed that the organic farming system microbial community was significantly correlated with the β-glucosidase activity, whereas the conventional farming system microbial community significantly correlated with soil pH. Both conventional and organic co-occurrence interkingdom networks exhibited a parallel node count, however, the former had a higher number of edges, thus being denser than the latter. Despite the similar amount of fungal nodes in the co-occurrence networks, the organic farming system co-occurrence network exhibited more than 3-fold the proportion of fungal taxa as keystone nodes than the conventional co-occurrence network. The genera Bionectria, Cercophora, Geastrum, Penicillium, Preussia, Metarhizium, Myceliophthora, and Rhizophlyctis were among the fungal keystone nodes of the organic farming system network. Altogether, our results uncover that beyond differences in microbial community composition between the two farming systems, fungal keystone nodes are far more relevant in the organic farming system, thus suggesting that bacteria-fungi interactions are more frequent in organic farming systems, promoting a more functional microbial community.
Collapse
Affiliation(s)
- Filipe Pereira Matteoli
- Laboratory of Microbial Bioinformatics, Department of Biological Sciences, Faculty of Sciences, São Paulo State University, Bauru, Brazil.
| | - Antonio M M Silva
- Department of Soil Sciences, University of São Paulo, "Luiz de Queiroz" College of Agriculture, Piracicaba, Brazil
| | - Victor L V P de Araújo
- Department of Soil Sciences, University of São Paulo, "Luiz de Queiroz" College of Agriculture, Piracicaba, Brazil
| | - Henrique P Feiler
- Department of Soil Sciences, University of São Paulo, "Luiz de Queiroz" College of Agriculture, Piracicaba, Brazil
| | - Elke J B N Cardoso
- Department of Soil Sciences, University of São Paulo, "Luiz de Queiroz" College of Agriculture, Piracicaba, Brazil
| |
Collapse
|
2
|
Huang X, Zheng Y, Li P, Cui J, Sui P, Chen Y, Gao W. Organic management increases beneficial microorganisms and promotes the stability of microecological networks in tea plantation soil. Front Microbiol 2023; 14:1237842. [PMID: 37795307 PMCID: PMC10546928 DOI: 10.3389/fmicb.2023.1237842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 08/21/2023] [Indexed: 10/06/2023] Open
Abstract
Introduction Organic agriculture is highly regarded by people for its commitment to health, ecology, care, and fairness. The soil microbial community responds quickly to environmental changes and is a good indicator for evaluating soil microecology. Therefore, from the perspective of soil microbial communities, elucidating the impact of organic management on soil microecology in tea plantations has great significance for improving local tea plantation systems. Methods The study collected bulk soil from organic management (OM) and conventional management (CM) tea plantations in Pu'er City, a major tea-producing area in China, and analyzed their species diversity, structural composition, and co-occurrence networks using metagenomics technology. Results Compared with CM, the diversity index (Shannon) and evenness index (Heip) of soil fungi increased by 7.38% and 84.2% in OM tea plantations, respectively. The relative abundance of microorganisms related to the nitrogen cycle increased. Specifically, there was a significant increase in Rhodobiales, a 2-fold increase in Nitrospirae, and approximately 1.95 and 2.03 times increases in unclassified genera within Betaproteobacteria and Deltaproteobacteria, respectively. The relative abundance of plant residue degradation species, Gemmatimonadetes, Ascomycota, and Basidiomycota, increased by 2.8, 1, and 1.4 times, respectively. The OM was conducive to the establishment of collaborative relationships among bacterial species and increased the diversity and complexity of species relationships in fungal communities. The network stability of soil ecosystems was promoted. The organic tea plantations' keystone taxa contained mycorrhizal fungi (Pezoloma_ericae, Rhizophagus_irregularis, Rhizophagus_clarus), as well as species involved in soil nitrogen metabolism (Acidobacteria_bacterium, Acidobacteriia_bacterium_AA117, Sphingomonas_sp._URHD0007, Enhydrobacter_aerosaccus), pathogen (Erysiphe_pulchra), and parasites (Paramycosporidium saccamoeba). The partial least squares method (PLS-SEM) indicated that OM affected N-NH4 + negatively, increasing the abundance of fungi, and thereby positively affecting the Shannon index. Conclusion In brief, reasonable organic management can improve the diversity of soil microorganisms, increase the relative abundance of beneficial bacteria in tea plantation soil, and promote the stability of the soil microbial ecological network.
Collapse
Affiliation(s)
- Xinhui Huang
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Yuting Zheng
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Panfeng Li
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Jixiao Cui
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Peng Sui
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Yuanquan Chen
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Wangsheng Gao
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| |
Collapse
|
3
|
Onyango LA, Ngonga FA, Karanja EN, Kuja JO, Boga HI, Cowan DA, Mwangi KW, Maghenda MW, Marinho Lebre PBN, Kambura AK. The soil microbiomes of forest ecosystems in Kenya: their diversity and environmental drivers. Sci Rep 2023; 13:7156. [PMID: 37130890 PMCID: PMC10154314 DOI: 10.1038/s41598-023-33993-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 04/21/2023] [Indexed: 05/04/2023] Open
Abstract
Soil microbiomes in forest ecosystems act as both nutrient sources and sinks through a range of processes including organic matter decomposition, nutrient cycling, and humic compound incorporation into the soil. Most forest soil microbial diversity studies have been performed in the northern hemisphere, and very little has been done in forests within African continent. This study examined the composition, diversity and distribution of prokaryotes in Kenyan forests top soils using amplicon sequencing of V4-V5 hypervariable region of the 16S rRNA gene. Additionally, soil physicochemical characteristics were measured to identify abiotic drivers of prokaryotic distribution. Different forest soils were found to have statistically distinct microbiome compositions, with Proteobacteria and Crenarchaeota taxa being the most differentially abundant across regions within bacterial and archaeal phyla, respectively. Key bacterial community drivers included pH, Ca, K, Fe, and total N while archaeal diversity was shaped by Na, pH, Ca, total P and total N. To contextualize the prokaryote diversity of Kenyan forest soils on a global scale, the sample set was compared to amplicon data obtained from forest biomes across the globe; displaying them to harbor distinct microbiomes with an over-representation of uncultured taxa such as TK-10 and Ellin6067 genera.
Collapse
Affiliation(s)
- Lorine Akinyi Onyango
- Department of Biochemistry, Jomo Kenyatta University of Agriculture and Technology, P. O. Box 62000-00200, Nairobi, Kenya
| | - Florence Atieno Ngonga
- Department of Biochemistry, Jomo Kenyatta University of Agriculture and Technology, P. O. Box 62000-00200, Nairobi, Kenya
| | - Edward Nderitu Karanja
- International Centre for Insect Physiology and Ecology, P.O. Box 30772-00100, Nairobi, Kenya
| | - Josiah Ochieng' Kuja
- Department of Botany, Jomo Kenyatta University of Agriculture and Technology, P. O. Box 62000-00200, Nairobi, Kenya
| | - Hamadi Iddi Boga
- School of Agriculture, Earth and Environmental Sciences, Taita Taveta University, P. O. Box 635-80300, Voi, Kenya
| | - Don A Cowan
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | | | - Marianne Wughanga Maghenda
- School of Agriculture, Earth and Environmental Sciences, Taita Taveta University, P. O. Box 635-80300, Voi, Kenya
| | - Pedro Bixirao Neto Marinho Lebre
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Anne Kelly Kambura
- School of Agriculture, Earth and Environmental Sciences, Taita Taveta University, P. O. Box 635-80300, Voi, Kenya.
| |
Collapse
|
4
|
Composition, structure, and functional shifts of prokaryotic communities in response to co-composting of various nitrogenous green feedstocks. BMC Microbiol 2023; 23:50. [PMID: 36859170 PMCID: PMC9979578 DOI: 10.1186/s12866-023-02798-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Accepted: 02/17/2023] [Indexed: 03/03/2023] Open
Abstract
BACKGROUND Thermophilic composting is a promising method of sanitizing pathogens in manure and a source of agriculturally important thermostable enzymes and microorganisms from organic wastes. Despite the extensive studies on compost prokaryotes, shifts in microbial profiles under the influence of various green materials and composting days are still not well understood, considering the complexity of the green material sources. Here, the effect of regimens of green composting material on the diversity, abundance, and metabolic capacity of prokaryotic communities in a thermophilic compost environment was examined. METHODS Total community 16S rRNA was recovered from triplicate compost samples of Lantana-based, Tithonia-based, Grass-based, and mixed (Lantana + Tithonia + Grass)- based at 21, 42, 63, and 84 days of composting. The 16S rRNA was sequenced using the Illumina Miseq platform. Bioinformatics analysis was done using Divisive Amplicon Denoising Algorithm version 2 (DADA2) R version 4.1 and Phylogenetic Investigation of Communities by Reconstruction of Unobserved States version 2 (PICRUSt2) pipelines for community structure and metabolic profiles, respectively. In DADA2, prokaryotic classification was done using the Refseq-ribosomal database project (RDP) and SILVA version 138 databases. RESULTS Our results showed apparent differences in prokaryotic community structure for total diversity and abundance within the four compost regimens and composting days. The study showed that the most prevalent phyla during composting included Acidobacteriota, Actinobacteriota, Bacteroidota, Chloroflexi, and Proteobacteria. Additionally, there were differences in the overall diversity of metabolic pathways but no significant differences among the various compost treatments on major metabolic pathways like carbohydrate biosynthesis, carbohydrate degradation, and nitrogen biosynthesis. CONCLUSION Various sources of green material affect the succession of compost nutrients and prokaryotic communities. The similarity of amounts of nutrients, such as total Nitrogen, at the end of the composting process, despite differences in feedstock material, indicates a significant influence of composting days on the stability of nutrients during composting.
Collapse
|
5
|
Moneda APC, de Carvalho LAL, Teheran-Sierra LG, Funnicelli MIG, Pinheiro DG. Sugarcane cultivation practices modulate rhizosphere microbial community composition and structure. Sci Rep 2022; 12:19174. [PMID: 36357461 PMCID: PMC9649670 DOI: 10.1038/s41598-022-23562-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Accepted: 11/02/2022] [Indexed: 11/12/2022] Open
Abstract
Sugarcane (Saccharum spp.) represents a crop of great economic importance, remarkably relevant in the food industry and energy supply chains from renewable sources. However, its conventional cultivation involves the intensive use of fertilizers, pesticides, and other agrochemical agents whose detrimental effects on the environment are notorious. Alternative systems, such as organic farming, have been presented as an environmentally friendly way of production. Still, the outcomes of different cropping systems on the microbiota associated with sugarcane-whose role in its health and growth is crucial-remain underexplored. Thus, we studied the rhizospheric microbiota of two adjacent sugarcane fields, which differ in terms of the type of farming system. For this, we used the sequencing of taxonomic markers of prokaryotes (gene 16S rRNA, subregions V3-V4) and fungi (Internal transcribed spacer 2) and evaluated the changes caused by the systems. Our results show a well-conserved microbiota composition among farming systems in the highest taxonomic ranks, such as phylum, class, and order. Also, both systems showed very similar alpha diversity indices and shared core taxa with growth-promoting capacities, such as bacteria from the Bacillus and Bradyrhizobium genera and the fungal genus Trichoderma. However, the composition at more specific levels denotes differences, such as the separation of the samples concerning beta diversity and the identification of 74 differentially abundant taxa between the systems. Of these, 60 were fungal taxa, indicating that this microbiota quota is more susceptible to changes caused by farming systems. The analysis of co-occurrence networks also showed the formation of peripheral sub-networks associated with the treatments-especially in fungi-and the presence of keystone taxa in terms of their ability to mediate relationships between other members of microbial communities. Considering that both crop fields used the same cultivar and had almost identical soil properties, we conclude that the observed findings are effects of the activities intrinsic to each system and can contribute to a better understanding of the effects of farming practices on the plant microbiome.
Collapse
Affiliation(s)
- Ana Paula Corrêa Moneda
- grid.410543.70000 0001 2188 478XLaboratory of Bioinformatics, Department of Agricultural, Livestock and Environmental Biotechnology, School of Agricultural and Veterinary Sciences, São Paulo State University (UNESP), Jaboticabal, SP 14884-900 Brazil ,grid.410543.70000 0001 2188 478XGraduate Program in Agricultural and Livestock Microbiology, School of Agricultural and Veterinary Sciences, São Paulo State University (UNESP), Jaboticabal, SP Brazil
| | - Lucas Amoroso Lopes de Carvalho
- grid.410543.70000 0001 2188 478XLaboratory of Bioinformatics, Department of Agricultural, Livestock and Environmental Biotechnology, School of Agricultural and Veterinary Sciences, São Paulo State University (UNESP), Jaboticabal, SP 14884-900 Brazil ,grid.410543.70000 0001 2188 478XGraduate Program in Agricultural and Livestock Microbiology, School of Agricultural and Veterinary Sciences, São Paulo State University (UNESP), Jaboticabal, SP Brazil
| | - Luis Guillermo Teheran-Sierra
- grid.410543.70000 0001 2188 478XLaboratory of Bioinformatics, Department of Agricultural, Livestock and Environmental Biotechnology, School of Agricultural and Veterinary Sciences, São Paulo State University (UNESP), Jaboticabal, SP 14884-900 Brazil ,grid.410543.70000 0001 2188 478XGraduate Program in Agricultural and Livestock Microbiology, School of Agricultural and Veterinary Sciences, São Paulo State University (UNESP), Jaboticabal, SP Brazil
| | - Michelli Inácio Gonçalves Funnicelli
- grid.410543.70000 0001 2188 478XLaboratory of Bioinformatics, Department of Agricultural, Livestock and Environmental Biotechnology, School of Agricultural and Veterinary Sciences, São Paulo State University (UNESP), Jaboticabal, SP 14884-900 Brazil ,grid.410543.70000 0001 2188 478XGraduate Program in Agricultural and Livestock Microbiology, School of Agricultural and Veterinary Sciences, São Paulo State University (UNESP), Jaboticabal, SP Brazil
| | - Daniel Guariz Pinheiro
- grid.410543.70000 0001 2188 478XLaboratory of Bioinformatics, Department of Agricultural, Livestock and Environmental Biotechnology, School of Agricultural and Veterinary Sciences, São Paulo State University (UNESP), Jaboticabal, SP 14884-900 Brazil ,grid.410543.70000 0001 2188 478XGraduate Program in Agricultural and Livestock Microbiology, School of Agricultural and Veterinary Sciences, São Paulo State University (UNESP), Jaboticabal, SP Brazil
| |
Collapse
|
6
|
Muriuki SW, Rengan MS, Budambula NLM. Prokaryotic diversity and potentially pathogenic bacteria in vended foods and environmental samples. ANN MICROBIOL 2021. [DOI: 10.1186/s13213-021-01640-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Abstract
Purpose
Ready-to-eat fast food vending outlets provide a cheap and readily available food. Foodborne diseases have been previously reported in Embu, Kenya, but data on the prokaryotic metagenome in vended foods is scanty. This study aimed to determine the prokaryotic diversity in fruits, vegetable salad, African sausage, chips (potato fries), fried fish, roasted beef (meat), smokies, samosa, soil, and water collected from food vendors and the surrounding environment in Embu Town and Kangaru Market.
Methods
The study used 454 pyrosequencing, Illumina high-throughput sequencing of 16S rRNA gene in the analysis of total community DNA extracted from samples using the phenol-chloroform method. The 16S rRNA gene variable region (V4-V7) of the extracted DNA was amplified and library construction performed. Sequence analysis was done using QIIME2. Hierarchical clustering of samples, diversity indices, rarefaction curves, and Venn diagrams were generated using the R programming language in R software version 3.6.3.
Results
Bacterial operational taxonomic units (OUTs) were distributed in Proteobacteria (52.81%), Firmicutes (31.16%), and Lentisphaerae (0.001%). The OTUs among archaea were Candidatus Nitrososphaera (63.56%) and Nitrososphaera spp. (8.77%). Brucella spp. and Bacillus cereus associated with foodborne diseases were detected. Potential pathogens, Rickettsia spp. in risk group 2 and Brucella spp. in risk group 3, were detected. Uncultured Candidatus Koribacter and Candidatus Solibacter were also detected in the food samples. There was a significant difference in the microbial community structure among the sample types (P<0.1).
Conclusion
The results demonstrated the presence of some prokaryotes that are associated with food spoilage or foodborne diseases in vended foods and environmental samples. This study also detected uncultured prokaryotes. The presence of potential pathogens calls for stringent hygiene measures in food vending operations.
Collapse
|
7
|
How does organic farming shape the soil- and plant-associated microbiota? Symbiosis 2021. [DOI: 10.1007/s13199-021-00767-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
|