Tropical soils are a reservoir for fluorescent Pseudomonas spp. biodiversity
Lucas Dantas Lopes
Department of Soil Science, “Luiz de Queiroz” College of Agriculture, University of São Paulo, Piracicaba, SP, Brazil
Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
Search for more papers by this authorEdward W. Davis II
Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
Molecular and Cellular Biology Program, Oregon State University, Corvallis, OR 97331, USA
Search for more papers by this authorMichele de C. Pereira e Silva
Department of Soil Science, “Luiz de Queiroz” College of Agriculture, University of São Paulo, Piracicaba, SP, Brazil
Search for more papers by this authorAlexandra J. Weisberg
Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
Search for more papers by this authorLuana Bresciani
Department of Soil Science, “Luiz de Queiroz” College of Agriculture, University of São Paulo, Piracicaba, SP, Brazil
Search for more papers by this authorJeff H. Chang
Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
Molecular and Cellular Biology Program, Oregon State University, Corvallis, OR 97331, USA
Search for more papers by this authorJoyce E. Loper
Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
Molecular and Cellular Biology Program, Oregon State University, Corvallis, OR 97331, USA
Search for more papers by this authorCorresponding Author
Fernando D. Andreote
Department of Soil Science, “Luiz de Queiroz” College of Agriculture, University of São Paulo, Piracicaba, SP, Brazil
For correspondence. E-mail [email protected]; Tel. +55(19)34172123; Fax (19) 3417-2100/3417-2110.Search for more papers by this authorLucas Dantas Lopes
Department of Soil Science, “Luiz de Queiroz” College of Agriculture, University of São Paulo, Piracicaba, SP, Brazil
Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
Search for more papers by this authorEdward W. Davis II
Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
Molecular and Cellular Biology Program, Oregon State University, Corvallis, OR 97331, USA
Search for more papers by this authorMichele de C. Pereira e Silva
Department of Soil Science, “Luiz de Queiroz” College of Agriculture, University of São Paulo, Piracicaba, SP, Brazil
Search for more papers by this authorAlexandra J. Weisberg
Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
Search for more papers by this authorLuana Bresciani
Department of Soil Science, “Luiz de Queiroz” College of Agriculture, University of São Paulo, Piracicaba, SP, Brazil
Search for more papers by this authorJeff H. Chang
Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
Molecular and Cellular Biology Program, Oregon State University, Corvallis, OR 97331, USA
Search for more papers by this authorJoyce E. Loper
Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
Molecular and Cellular Biology Program, Oregon State University, Corvallis, OR 97331, USA
Search for more papers by this authorCorresponding Author
Fernando D. Andreote
Department of Soil Science, “Luiz de Queiroz” College of Agriculture, University of São Paulo, Piracicaba, SP, Brazil
For correspondence. E-mail [email protected]; Tel. +55(19)34172123; Fax (19) 3417-2100/3417-2110.Search for more papers by this authorSummary
Fluorescent Pseudomonas spp. are widely studied for their beneficial activities to plants. To explore the genetic diversity of Pseudomonas spp. in tropical regions, we collected 76 isolates from a Brazilian soil. Genomes were sequenced and compared to known strains, mostly collected from temperate regions. Phylogenetic analyses classified the isolates in the P. fluorescens (57) and P. putida (19) groups. Among the isolates in the P. fluorescens group, most (37) were classified in the P. koreensis subgroup and two in the P. jessenii subgroup. The remaining 18 isolates fell into two phylogenetic subclades distinct from currently recognized P. fluorescens subgroups, and probably represent new subgroups. Consistent with their phylogenetic distance from described subgroups, the genome sequences of strains in these subclades are asyntenous to the genome sequences of members of their neighbour subgroups. The tropical isolates have several functional genes also present in known fluorescent Pseudomonas spp. strains. However, members of the new subclades share exclusive genes not detected in other subgroups, pointing to the potential for novel functions. Additionally, we identified 12 potential new species among the 76 isolates from the tropical soil. The unexplored diversity found in the tropical soil is possibly related to biogeographical patterns.
Supporting Information
Additional Supporting Information may be found in the online version of this article at the publisher's web-site:
| Filename | Description |
|---|---|
| emi13957-sup-0001-suppinfo1.tif6.7 MB |
Fig. S1. Non-metric Multidimensional Scaling (NMDS) using the Bray-Curtis similarity index for ordination of samples (isolates and references) according to the ANI values. Black dots are the reference strains; blue dots are isolates in the P. koreensis subgroup; purple dots are isolates in the P. jessenii subgroup; red dots are isolates in the P. putida group; and grey dots are isolates in the new subclades X and Y. |
| emi13957-sup-0002-suppinfo2.tif13.4 MB |
Fig. S2. Synteny analyses performed by multiple genome alignments using the mauve software. Different colours in the genome sequences correspond to genome regions with high percentage alignment. Lines indicate rearranged regions and show their position in the compared genomes. The origin of replication is approximately in the middle of each genome sequence, based on the reference genome sequences used to reorder the contigs of the other assemblies analysed, that is, A) isolate R12 (∼2962 Mbp) for the comparison inside the subclade X; and B) isolate R26 (∼3148 Mbp) for the comparison inside the subclade Y. |
| emi13957-sup-0003-suppinfo3.pdf222.1 KB |
Table S1. Accession numbers of the 76 genome sequences available in the Genbank/DDBJ/ENA databases. |
| emi13957-sup-0004-suppinfo4.pdf98.4 KB |
Table S2. Main quality parameters of genome assemblies output. |
| emi13957-sup-0005-suppinfo5.pdf144.9 KB |
Table S3. BLAST searches for the set of genes related to important functions performed by known P. fluorescens strains. Functions were considered present in a genome only if the complete set of genes were found with high similarity and identity hits in the tBLASTn. Abbreviations: DAPG, 2,4-diacetylphloroglucinol; GABA, Gamma-aminobutyric acid; IAA, indole acetic acid (iaaMH); Tcc4 and Tcc5, toxin complex clusters; AprA, exoprotease; T2SS, type 2 secretion system; T3SS, type 3 secretion system; T6SS, type VI secretion system. Toxin complex clusters and secretion systems are designated according to Loper and colleagues (2012). |
Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
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