Diversity of bacteria associated with corn roots inoculated with Canadian woodland soils, and description of Pseudomonas aylmerense sp. nov.

Tchagang, Caetanie F.; Xu, Ran; Overy, David P.; Blackwell, Barbara A.; Chabot, Denise; Hubbard, Keith; Doumbou, Cyr Lézin; Bromfield, E. S. P.; Tambong, James T.

doi:10.1016/j.heliyon.2018.e00761

“…Since pseudomonads are a complex group, differentiation and characterization at the species level is highly important to avoid taxonomic inconsistencies. The characterization of new species has increased over the years due to advanced tools for species delineation, new sequencing methods and knowledge derived from studies on microbial communities [4, 5]. Initially, bacterial taxonomy was based only on phenotypic assays based on several biochemical reactions [6, 7].…”

Section: Full-textmentioning

confidence: 99%

Pseudomonas californiensis sp. nov. and Pseudomonas quasicaspiana sp. nov., isolated from ornamental crops in California

Carvalho

¹

,

Albu

²

,

Timilsina

³

et al. 2022

International Journal of Systematic and Evolutionary Microbiology

1

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Five bacterial strains were isolated from symptomatic leaves of Achillea millefolium, Delphinium sp. and Hydrangea sp. in California. Colonies isolated on King’s medium B (KMB) appeared white, mucoid and round, similar to Pseudomonas species. Phylogenetic analyses based on 16S rRNA, rpoB, rpoD and gyrB genes placed the bacteria into three distinct groups within Pseudomonas that were most closely related to Pseudomonas viridiflava , Pseudomonas cichorii or Pseudomonas caspiana . To further characterize the strains, phenotypic analyses and the following tests were performed: fatty acid methyl ester composition, LOPAT, fluorescence on KMB, Biolog assay, and transmission electron microscopy. Finally, whole genome sequencing of the strains was conducted, and the sequences were compared with reference genomes of Pseudomonas species based on average nucleotide identity (ANI). The first group, which consists of three strains isolated from delphinium, hydrangea and achillea, had 95.6–96.9 % pairwise ANI between each other; the second group consists of two strains isolated from delphinium that had 100 % pairwise ANI. Although comparisons of the two groups with publicly available genomes revealed closest relationships with P. viridiflava (91.6 %), P. caspiana (88.3 %) and P. asturiensis (86.7 %), ANI values were less than 95 % compared to all validly published pseudomonads. Combining genomic and phenotypic data, we conclude that these strains represent two new species and the names proposed are Pseudomonas quasicaspiana sp. nov. (type strain DSMZ 11 30 42T=LMG 32 434T) for the strains isolated from delphinium, achillea and hydrangea and Pseudomonas californiensis sp. nov. (DSMZ 11 30 43T=LMG 32 432T) for the two strains isolated from delphinium. The specific epithets quasicaspiana and californiensis were selected based on the close phylogenetic relationship of strains with P. caspiana and on the geographic location of isolation, respectively.

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“…Spesies tertentu seperti E. stewartii dapat menyebabkan penyakit pada tanaman jagung (Nimtz et al, 1996). Pada tanah K2 lebih banyak ditemukan Pseudomonas (7/15) yang termasuk ke dalam Proteobacteria (Janse, 2005) yang dapat berasosiasi dengan perakaran tanaman (Tchagang et al, 2018). Pada tanah K3 banyak ditemukan Coryneform (6/17) yang merupakan bakteri gram positif dari Actinobacteria (Janse, 2005) dan banyak dimanfaatkan dalam industri (Hermann, 2003 Hasil indeks keseragaman (E) pada keempat jenis tanah, didapatkan nilai sebesar 0,882; 0,815; 0,898, dan 0,952 pada tanah O1, K1, K2, dan K3 secara berurutan.…”

Section: Analisis Dataunclassified

Pengaruh Fungisida Terhadap Keanekaragaman Bakteri Tanah Di Kota Batu

Khulillah

¹

,

Abadi²,

Aini³

2019

JTSL

0

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Environmentally friendly and conventional cultivation systems that are selected and used by farmers can directly or indirectly affect microbes in the soil. Microbial population diversity can be used as a sensitive parameter to soil quality. Bacterial populations are a determining factor in ecosystems that are important because of biological and biogeochemical cycles, and heterotrophic activities. This study suggests looking at environmentally friendly (O1) and conventional (K1, K2, K3) soil bacteria on soil planted with sweet maize and function of bacteria in ecosystems. The results of this study that diversity on environmentally friendly was higher than conventional soil. The value was 1,775; while those of the conventional lands 1, 2 and 3 were 1,587; 1,245 and 1,320. In O1 soil, the most common genus was Agrobacterium and bacteria which were only found in environmentally friendly soils were Bacillus and Clostridium. Bacteria found such as O1F and O1G which were related to B. paramycoides could be used as biological agents against Cercospora leaf spot disease, B. megaterium could bind nitrate to the rhizosphere and dissolve phosphate in the soil, and B. aryabhattai which was potential as biological fertilizers and bioremediation.

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“…The presence of members of this genus in a variety of niches might be indicative of their potential ecological roles. While some members of the fluorescent pseudomonads are plant pathogens, most are reported to play significant roles in agricultural and environmental sustainability, as xenobiotic-degraders, plant growth promoters and biological pesticides [4–9]. These attributes coupled with their ubiquitous nature make this bacterial genus an ecologically interesting group.…”

Section: Introductionmentioning

confidence: 99%

“…The cultivable bacterial communities of the Canadian woodland are poorly documented [4]. Tchagang et al .…”

Section: Introductionmentioning

confidence: 99%

“…Over 500 validly and non-validly described species have been documented [1]. Pseudomonas species are ubiquitous, complex and versatile bacteria with the ability to colonize diverse ecological niches such as rhizosphere, soils, water as well as organisms (plants, animal and humans) [2–4]. The presence of members of this genus in a variety of niches might be indicative of their potential ecological roles.…”

Section: Introductionmentioning

confidence: 99%

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Pseudomonas quebecensis sp. nov., a bacterium isolated from root-zone soil of a native legume, Amphicarpaea bracteata (L.) Fernald, in Quebec, Canada

Tambong,

Xu,

Chi

et al. 2023

International Journal of Systematic and Evolutionary Microbiology

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Four bacterial strains (S1Bt3, S1Bt7, S1Bt30 and S1Bt42T) isolated from soil collected from the rhizosphere of a native legume, Amphicarpaea bracteata, were investigated using a polyphasic approach. Colonies were fluorescent, white-yellowish, circular and convex with regular margins on King’s B medium. Cells were Gram-reaction-negative, aerobic, non-spore-forming rods. Oxidase- and catalase-positive. The optimal growth temperature of the strains was 37 °C. Phylogenetic analysis of the 16S rRNA gene sequences placed the strains within the genus Pseudomonas . Analysis of the 16S rRNA-rpoD-gyrB concatenated sequences clustered the strains and well separated from Pseudomonas rhodesiae CIP 104664T and Pseudomonas grimontii CFM 97-514T with the type strains of the closest species. Phylogenomic analysis of 92 up-to-date bacterial core gene and matrix-assisted laser desorption/ionization-time-of-flight MS biotyper data confirmed the distinct clustering pattern of these four strains. Digital DNA–DNA hybridization (41.7 %–31.2 %) and average nucleotide identity (91.1 %–87.0 %) values relative to closest validly published Pseudomonas species were below the species delineation thresholds of 70 and 96 %, respectively. Fatty acid composition results validated the taxonomic position of the novel strains in the genus Pseudomonas . Phenotypic characteristics from carbon utilization tests differentiated the novel strains from closely related Pseudomonas species. In silico prediction of secondary metabolite biosynthesis gene clusters in the whole-genome sequences of the four strains revealed the presence of 11 clusters involved in the production of siderophore, redox-cofactor, betalactone, terpene, arylpolyene and nonribosomal peptides. Based on phenotypic and genotypic data, strains S1Bt3, S1Bt7, S1Bt30 and S1Bt42T represent a novel species for which the name Pseudomonas quebecensis sp. nov. is proposed. The type strain is S1Bt42T (=DOAB 746T=LMG 32141T=CECT 30251T). The genomic DNA G+C content is 60.95 mol%.

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Diversity of bacteria associated with corn roots inoculated with Canadian woodland soils, and description of Pseudomonas aylmerense sp. nov.

Cited by 17 publications

References 52 publications

Pseudomonas californiensis sp. nov. and Pseudomonas quasicaspiana sp. nov., isolated from ornamental crops in California

Pseudomonas californiensis sp. nov. and Pseudomonas quasicaspiana sp. nov., isolated from ornamental crops in California

Pengaruh Fungisida Terhadap Keanekaragaman Bakteri Tanah Di Kota Batu

Pseudomonas quebecensis sp. nov., a bacterium isolated from root-zone soil of a native legume, Amphicarpaea bracteata (L.) Fernald, in Quebec, Canada

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