The Rhizobial Microbiome from the Tropical Savannah Zones in Northern Côte d’Ivoire
Abstract
:1. Introduction
2. Materials and Methods
2.1. The Study Area
2.2. Soil Sampling
2.3. Analysis of Soil Physicochemical Properties
2.4. DNA Extraction, PCR, MiSeq Sequencing, and Sequence Data Analysis
2.5. Statistical and Diversity Index Analyses
2.6. In Silico Evaluation of the 16S rRNA Gene V-Regions Discriminatory Power for Rhizobia
3. Results
3.1. Physico-Chemical Properties of Soil Samples
3.2. Sequence Data and Taxonomic Affiliation
3.3. Relative Abundance of Rhizobia Taxa per Soil Sample
3.4. Richness and Diversity Indices
3.5. In Silico Evaluation of 16S rDNA V-Regions Discriminatory Power for Rhizobia
4. Discussion
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Soil ID | GPS Location | Location (Province/City/Region) | Environment |
---|---|---|---|
CI11 | N08°58′52.1”, W003°10′50.1” | Kokpingué/Bouna/Bounkani | Natural wooded grassland soils (Acacia spp.) |
CI13 | N09°41′49.9”, W003°17′43.9” | Doropo/Bouna/Bounkani | Natural wooded grassland soils (Parkia biglobosa) |
CI14 | N10°04′54.6”, W005°24′41.0” | Ouangolo/Ouangolo/Tchologo | Rice field, Native Forest & natural grassland soils |
CI17 | N09°13′11.1”, W005°35′22.0” | Kalogokaha/Korhogo/Poro | Cashew field soils |
CI18 | N08°52′12.5”, W005°22′08.0” | Kanawolo/Niakara/Hambol | Cashew field and natural grassland soils (Loudetia spp.) |
CI20 | N08°05′38.2”, W005°05′01.3” | Katiola/Katiola/Hambol | Maize & cassava fields and natural grassland soils |
CI44 | N09°03′41.5”, W007°35′20.8” | Bako/Odienné/Denguélé | Cashew field and woodeed savanna soils |
No. | Genus | Number of Species 3 | Number of Nod+/ Fix+ species 4 | Genus Type Species | Genome Accession | 16S rRNA Gene Full Size (bp) 6 | Symbiotic Capacity of the Genus Type Species |
---|---|---|---|---|---|---|---|
1 | Allorhizobium | 8 | 1 | Allorhizobium undicola ORS 992T | NZ_JHXQ01000045 | 1482 | Nod+/Fix+ [73] |
2 | Aminobacter | 7 | 1 | Aminobacter aminovorans DSM 7048T | NZ_SLZO01000023 | 1484 | unknown [74] |
3 | Azorhizobium | 3 | 2 | Azorhizobium caulinodans ORS 571T | AP009384 | 1482 | Nod+/Fix+ [75] |
4 | Bradyrhizobium | 57 | 55 | Bradyrhizobium japonicum USDA 6T | NC_017249 | 1488 | Nod+/Fix+ [23] |
5 | Cupriavidus 1 | 18 | 2 | Cupriavidus necator N-1T | CNE_1c16970 | 1531 | Nod−7 [76] |
6 | Devosia | 26 | 1 | Devosia riboflavina IFO13584T | NZ_JQGC01000043 | 1481 | nod/fix genes were not detected [77] |
7 | Ensifer | 20 | 16 | Ensifer adhaerens Casida AT | NZ_CP015880 | 1484 | Nod−, nod genes were not detected [78] |
8 | Mesorhizobium | 56 | 45 | Mesorhizobium loti DSM 2626T | NZ_QGGH01000001 | 1484 | Nod+/Fix+ [79,80] |
9 | Methylobacterium | 45 | 1 | Methylobacterium organophilum DSM 760T | NZ_QEKZ01000068 | 1482 | unknown [81] |
10 | Microvirga | 17 | 5 | Microvirga subterranea DSM 14364T | NZ_QQBB01000028 | 1486 | unknown [82] |
11 | Neorhizobium | 4 | 4 | Neorhizobium galegae HAMBI 540T | HG938353 | 1480 | Nod+/Fix+ [83,84] |
12 | Ochrobactrum 2 | 17 | 2 | Ochrobactrum anthropi ATCC 49188T | NC_009667 | 1482 | non-symbiotic bacterium [85,86] |
13 | Paraburkholderia 1 | 73 | 16 | Paraburkholderia graminis PHS1 5 | GCF_003330785 | 1532 | unknown [87,88] |
14 | Pararhizobium | 6 | 2 | Pararhizobium giardinii H152T | NZ_KB902704 | 1484 | Nod+/Fix+ [89,90] |
15 | Phyllobacterium | 12 | 3 | Phyllobacterium myrsinacearum DSM 5892T | NZ_SHLH01000013 | 1484 | Nod− [91] |
16 | Rhizobium | 91 | 48 | Rhizobium leguminosarum USDA 2370T | GCA_003058385 | 1480 | Nod+/Fix+ [27] |
17 | Shinella | 8 | 1 | Shinella granuli DSM 18401T | NZ_SLVX01000061 | 1484 | unknown [92] |
18 | Trinickia 1 | 7 | 1 | Trinickia symbiotica JPY-345T | NZ_PTIR01000049 | 1530 | Nod+/Fix+ [76] |
16S rDNA V-region 1 | Forward Name 2 | Forward Sequence (5′ to 3′) | Reverse Name | Reverse Sequence (5′ to 3′) | Size (bp) Variation Among Rhizobia 3 | Size variation OnceEdited (Primers Deleted) | Total Positions in the Final Dataset Aligned 4 |
---|---|---|---|---|---|---|---|
V1-V9 | 27F | AGAGTTTGATCMTGGCTCAG | 1492Rmod | TACGGYTACCTTGTTAYGACTT | 1445–1497 | 1403–1455 | 1486 |
V1-V2 | 27F | AGAGTTTGATCMTGGCTCAG | 337R | CYIACTGCTGCCTCCCGTAG | 320–350 | 280–310 | 325 |
V1-V3 | 27F | AGAGTTTGATCMTGGCTCAG | 534R | ATTACCGCGGCTGCTGG | 468–523 | 431–486 | 501 |
V3-V4 | 341F | CCTACGGGNGGCWGCAG | 805R | GACTACHVGGGTATCTAATCC | 440–465 | 402–427 | 427 |
V3-V5 | 341F | CCTACGGGNGGCWGCAG | 926Rb | CCGTCAATTYMTTTRAGT | 560–585 | 525–550 | 550 |
V4 | 515F | GTGCCAGCMGCCGCGGTAA | 806R | GGACTACHVGGGTWTCTAAT | 292 | 253 | 253 |
V4-V5 | 515F–Y | GTGYCAGCMGCCGCGGTAA | 909–928R | CCCCGYCAATTCMTTTRAGT | 413 | 374 | 374 |
V5-V7 | 799F | AACMGGATTAGATACCCKG | 1193R | ACGTCATCCCCACCTTCC | 409–417 | 372–380 | 385 |
V6-V9 | 928F | TAAAACTYAAAKGAATTGACGGGG | 1492Rmod | TACGGYTACCTTGTTAYGACTT | 605–612 | 560-567 | 576 |
V7-V9 | 1100F | YAACGAGCGCAACCC | 1492Rmod | TACGGYTACCTTGTTAYGACTT | 408–415 | 371-378 | 380 |
Bray–Curtis Distance | CI11 | CI13 | CI14 | CI17 | CI18 | CI20 |
---|---|---|---|---|---|---|
CI13 | 0.30 | - | - | - | - | - |
CI14 | 0.33 | 0.40 | - | - | - | - |
CI17 | 0.65 | 0.58 | 0.67 | - | - | - |
CI18 | 0.46 | 0.46 | 0.51 | 0.41 | - | - |
CI20 | 0.52 | 0.49 | 0.58 | 0.39 | 0.38 | - |
CI44 | 0.40 | 0.37 | 0.43 | 0.41 | 0.29 | 0.34 |
Jaccard Distance | CI11 | CI13 | CI14 | CI17 | CI18 | CI20 |
---|---|---|---|---|---|---|
CI13 | 0.53 | - | - | - | - | - |
CI14 | 0.61 | 0.64 | - | - | - | - |
CI17 | 0.82 | 0.74 | 0.79 | - | - | - |
CI18 | 0.75 | 0.70 | 0.77 | 0.61 | - | - |
CI20 | 0.67 | 0.69 | 0.70 | 0.70 | 0.67 | - |
CI44 | 0.62 | 0.54 | 0.63 | 0.63 | 0.62 | 0.52 |
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Gnangui, S.L.E.; Fossou, R.K.; Ebou, A.; Amon, C.E.R.; Koua, D.K.; Kouadjo, C.G.Z.; Cowan, D.A.; Zézé, A. The Rhizobial Microbiome from the Tropical Savannah Zones in Northern Côte d’Ivoire. Microorganisms 2021, 9, 1842. https://doi.org/10.3390/microorganisms9091842
Gnangui SLE, Fossou RK, Ebou A, Amon CER, Koua DK, Kouadjo CGZ, Cowan DA, Zézé A. The Rhizobial Microbiome from the Tropical Savannah Zones in Northern Côte d’Ivoire. Microorganisms. 2021; 9(9):1842. https://doi.org/10.3390/microorganisms9091842
Chicago/Turabian StyleGnangui, Sara Laetitia Elphège, Romain Kouakou Fossou, Anicet Ebou, Chiguié Estelle Raïssa Amon, Dominique Kadio Koua, Claude Ghislaine Zaka Kouadjo, Don A. Cowan, and Adolphe Zézé. 2021. "The Rhizobial Microbiome from the Tropical Savannah Zones in Northern Côte d’Ivoire" Microorganisms 9, no. 9: 1842. https://doi.org/10.3390/microorganisms9091842