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Table 3 The most abundant taxa within investigated oilseed rape seed microbiomes

From: The structure of the Brassica napus seed microbiome is cultivar-dependent and affects the interactions of symbionts and pathogens

Taxaa

Avatarb

Sherpab

Traviatab

Putative functionc

Co-occurrenced

Cyanobacteria ML635J-21_

0.101 ± 0.026a

0.114 ± 0.073a

0.078 ± 0.041a

Beneficial

No

Ralstonia*

0.131 ± 0.014 b

0.038 ± 0.020a

0.046 ± 0.024a

Pathogen

Yes

Acetobacteraceae_

0.030 ± 0.007a

0.057 ± 0.025a

0.058 ± 0.021a

Beneficial

Yes

Bacillus

0.033 ± 0.015a

0.048 ± 0.012a

0.041 ± 0.008a

Beneficial

Yes

Sphingomonas

0.029 ± 0.004a

0.035 ± 0.004ab

0.044 ± 0.010b

Beneficial

Yes

Salmonella/ E. coli*

0.033 ± 0.008a

0.025 ± 0.005a

0.027 ± 0.008a

Pathogen

No

Methylobacterium

0.023 ± 0.004a

0.026 ± 0.007a

0.033 ± 0.010a

Methanotroph

No

Burkholderia

0.044 ± 0.006 b

0.015 ± 0.005a

0.016 ± 0.007a

Beneficial

Yes

Methylocystaceae_

0.019 ± 0.009a

0.021 ± 0.005a

0.026 ± 0.007a

Methanotroph

No

Rhizobiaceae

0.014 ± 0.001a

0.031 ± 0.022a

0.020 ± 0.006a

Beneficial

No

Acidobacteria_iii-1-15_

0.013 ± 0.002 a

0.026 ± 0.003b

0.025 ± 0.001b

Unknown

No

Comamonadaceae_

0.032 ± 0.004 b

0.011 ± 0.003a

0.015 ± 0.005a

Unknown

Yes

Xanthomonadaceae_

0.022 ± 0.002a

0.015 ± 0.002a

0.015 ± 0.004a

Beneficial and pathogen

Yes

Bradyrhizobiaceae_

0.024 ± 0.004 b

0.008 ± 0.003a

0.010 ± 0.003a

Beneficial

Yes

Pseudomonas

0.010 ± 0.000 a

0.014 ± 0.001b

0.016 ± 0.002b

Beneficial

No

Rubellimicrobium

0.009 ± 0.001a

0.015 ± 0.005a

0.015 ± 0.005a

Unknown

No

Burkholderiaceae_

0.023 ± 0.003 b

0.006 ± 0.003a

0.012 ± 0.007a

Beneficial

Yes

Mesorhizobium

0.021 ± 0.002 b

0.006 ± 0.001a

0.008 ± 0.001a

Beneficial

Yes

Erwinia

0.009 ± 0.000a

0.01 ± 0.003ab

0.014 ± 0.002b

Pathogen

No

  1. aThe OTU designation was performed at genus level where possible. The taxa for which no genus levels were assigned were named as the lowest known taxonomy followed by “_”. For the taxa labeled with asterisks, a manual BLAST was performed on the representative sequence of the most abundant OTUs. The assignment was based on the highest scores with at least 99% identity. In cases where several taxa with the same score appeared, both identifications were stated
  2. bThe relative abundance of the 20 most abundant (median among the cultivars and repetitions) taxa. The taxa that were significantly different (p < 0.05, according to a Tukey-HSD t test) in one of the cultivars when compared to the two others are highlighted in italics. Values designated with the same letters were not significantly different (p < 0.05) according to a Tukey-HSD t test
  3. cThe putative functions of some known strains of the taxa
  4. dThe involvement of the taxa in the statistically significant (p < 4 × 10−4; q < 4 × 10−4) co-occurrence patterns as shown by network analysis is labeled as “yes”, otherwise “no”. Please refer to the Fig. 5