P = >0.05 (NS) P = <0.01 ** P = <0.01 **
P = <0.001*** P = <0.001 *** P = <0.001 ***
P = >0.05 (NS) P = >0.05 (NS) P = <0.001 ***
P = <0.001*** P = <0.05 * P = <0.01 **
P = <0.001*** P = <0.001 *** P = <0.001 ***
P = <0.01** P = <0.001 ***
125 Figure 7.1The nutrient analysis metadata collected for the 16 bulk soil samples from the four locations; C (Cambridge), H (Havelock North), P (Palmerston North), and B (Burnham). An analysis of variance model was applied to indicate the significantly different soil nutrient variables. Significance was judged based on the p-value codes ( ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ NS (>0.005))
126 Figure 7.2 Rarefaction curve based on the number of reads vs the number of bacterial ASVs for the 78 ryegrass samples, used to analyse the minimum number of reads necessary to adequately sample the variation. Each sample was rarefied to an even sequencing depth (12000 reads) for alpha diversity analysis.
Figure 7.3 Rarefaction curve based on the number of reads vs the number of fungal ASVs for the 62 ryegrass samples, used to analyse the minimum number of reads necessary to adequately sample the variation. Each sample was rarefied to an even sequencing depth (7500 reads) for alpha diversity analysis. The refraction curves show that the top 5 samples may demonstrate a small amount of un-sampled diversity; however, this will include no more than 1-20 fungal ASVs.
127 Table 7.1 The nematode analysis data for the four ryegrass bulk soil reps from the four site locations, B (Burnham), P (Palmerston North), H (Havelock North) and C (Cambridge).
Site B B B B M M M M H H H H C C C C
Total nemas (per 100 g dry soil)
4996 7698 6937 4424 1772 1448 684 2352 3906 6281 3284 3244 8018 5859 12328 12998 Meloidogyne
(per 100 g dry soil)
0 0 0 0 36 76 0 46 0 0 0 0 0 36 224 17
Heterodera (per 100 g dry soil)
0 0 0 0 0 0 0 0 0 0 0 0 0 0 94 17
Pratylenchus (per 100 g dry soil)
193 582 1392 649 188 439 36 291 206 241 150 469 1024 455 337 244 Paratylenchus
(per 100 g dry soil)
3964 5508 3405 2040 16 20 15 0 829 4264 1206 988 389 697 4359 1466 Helicotylenchus
(per 100 g dry soil)
0 0 0 0 57 15 10 5 0 0 0 0 0 14 19 0
128 Table 7.2 The core bacterial ASVs with their associated taxonomical classification for the five microbiome habitats. Bacterial ASVs were considered core if found across at least 90% of samples within a microbiome category at a relative abundance of higher than 0.001. Note: that the shoot endosphere microbiome area did not demonstrate any bacterial ASVs considered as core.
Microbiome Category
ASV Phylum Class Order Family Genus
Bulk soil 10 Firmicutes Bacilli Bacillales Bacillaceae Bacillus
21 Proteobacteria Alphaproteobacteria Rhizobiales Xanthobacteraceae Bradyrhizobium 22 Proteobacteria Alphaproteobacteria Rhizobiales Xanthobacteraceae Bradyrhizobium
24 Firmicutes Bacilli Bacillales Bacillaceae Bacillus
29 Firmicutes Bacilli Bacillales Bacillaceae Bacillus
36 Actinobacteriota Actinobacteria Streptomycetales Streptomycetaceae Streptomyces 38 Actinobacteriota Actinobacteria Catenulisporales Catenulisporaceae Catenulispora 45 Proteobacteria Alphaproteobacteria Rhizobiales Xanthobacteraceae Bradyrhizobium 50 Actinobacteriota Actinobacteria Propionibacteriales Nocardioidaceae Nocardioides 81 Actinobacteriota Actinobacteria Frankiales Acidothermaceae Acidothermus 86 Actinobacteriota Actinobacteria Micrococcales Intrasporangiaceae Terrabacter 145 Actinobacteriota Thermoleophilia Gaiellales uncultured uncultured_ge 147 Actinobacteriota Thermoleophilia Gaiellales uncultured uncultured_ge 164 Proteobacteria Alphaproteobacteria Rhizobiales Xanthobacteraceae uncultured 165 Actinobacteriota Actinobacteria Micrococcales Micrococcaceae Arthrobacter 222 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas 276 Actinobacteriota Thermoleophilia Gaiellales uncultured uncultured_ge 304 Proteobacteria Alphaproteobacteria Rhizobiales Xanthobacteraceae uncultured 395 Actinobacteriota Acidimicrobiia IMCC26256 IMCC26256_fa IMCC26256_ge 430 Actinobacteriota Acidimicrobiia
Rhizosphere 10 Firmicutes Bacilli Bacillales Bacillaceae Bacillus
21 Proteobacteria Alphaproteobacteria Rhizobiales Xanthobacteraceae Bradyrhizobium 22 Proteobacteria Alphaproteobacteria Rhizobiales Xanthobacteraceae Bradyrhizobium
24 Firmicutes Bacilli Bacillales Bacillaceae Bacillus
32 Actinobacteriota Actinobacteria Streptomycetales Streptomycetaceae Streptomyces 33 Actinobacteriota Actinobacteria Micrococcales Microbacteriaceae Schumannella
129 35 Actinobacteriota Actinobacteria Propionibacteriales Nocardioidaceae Nocardioides
38 Actinobacteriota Actinobacteria Catenulisporales Catenulisporaceae Catenulispora 45 Proteobacteria Alphaproteobacteria Rhizobiales Xanthobacteraceae Bradyrhizobium 50 Actinobacteriota Actinobacteria Propionibacteriales Nocardioidaceae Nocardioides 81 Actinobacteriota Actinobacteria Frankiales Acidothermaceae Acidothermus 86 Actinobacteriota Actinobacteria Micrococcales Intrasporangiaceae Terrabacter 90 Actinobacteriota Actinobacteria Frankiales Nakamurellaceae Nakamurella 104 Actinobacteriota Actinobacteria Corynebacteriales Mycobacteriaceae Mycobacterium 108 Actinobacteriota Actinobacteria Micrococcales Intrasporangiaceae Lapillicoccus 114 Actinobacteriota Actinobacteria Corynebacteriales Mycobacteriaceae Mycobacterium 140 Actinobacteriota Thermoleophilia Solirubrobacterales Solirubrobacteracea
e
Conexibacter 147 Actinobacteriota Thermoleophilia Gaiellales uncultured uncultured_ge 159 Actinobacteriota Acidimicrobiia IMCC26256 IMCC26256_fa IMCC26256_ge 164 Proteobacteria Alphaproteobacteria Rhizobiales Xanthobacteraceae uncultured 165 Actinobacteriota Actinobacteria Micrococcales Micrococcaceae Arthrobacter 174 Actinobacteriota Actinobacteria Propionibacteriales Nocardioidaceae Marmoricola 175 Actinobacteriota Thermoleophilia Solirubrobacterales Solirubrobacteracea
e
Solirubrobacter Root
Endosphere
7 Proteobacteria Gammaproteobacteria Xanthomonadales Xanthomonadaceae Xanthomonas
10 Firmicutes Bacilli Bacillales Bacillaceae Bacillus
14 Actinobacteriota Actinobacteria Pseudonocardiales Pseudonocardiaceae Amycolatopsis 21 Proteobacteria Alphaproteobacteria Rhizobiales Xanthobacteraceae Bradyrhizobium 22 Proteobacteria Alphaproteobacteria Rhizobiales Xanthobacteraceae Bradyrhizobium 32 Actinobacteriota Actinobacteria Streptomycetales Streptomycetaceae Streptomyces 33 Actinobacteriota Actinobacteria Micrococcales Microbacteriaceae Schumannella 36 Actinobacteriota Actinobacteria Streptomycetales Streptomycetaceae Streptomyces 45 Proteobacteria Alphaproteobacteria Rhizobiales Xanthobacteraceae Bradyrhizobium 50 Actinobacteriota Actinobacteria Propionibacteriales Nocardioidaceae Nocardioides 66 Actinobacteriota Actinobacteria Propionibacteriales Nocardioidaceae Aeromicrobium 69 Actinobacteriota Actinobacteria Streptomycetales Streptomycetaceae Streptomyces 80 Proteobacteria Gammaproteobacteria Burkholderiales Comamonadaceae uncultured
130 87 Proteobacteria Gammaproteobacteria Xanthomonadales Rhodanobacteraceae Rhodanobacter
144 Proteobacteria Gammaproteobacteria Burkholderiales Comamonadaceae Rhizobacter 176 Actinobacteriota Actinobacteria Streptomycetales Streptomycetaceae Streptomyces 193 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Phyllosphere 6 Actinobacteriota Actinobacteria Micrococcales Microbacteriaceae Curtobacterium
9 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas 12 Proteobacteria Alphaproteobacteria Rhizobiales Rhizobiaceae Allorhizobium- Neorhizobium- Pararhizobium- Rhizobium 15 Actinobacteriota Actinobacteria Micrococcales Microbacteriaceae Agreia
20 Actinobacteriota Actinobacteria Micrococcales Microbacteriaceae Microbacterium 27 Actinobacteriota Actinobacteria Corynebacteriales Nocardiaceae Rhodococcus 35 Actinobacteriota Actinobacteria Propionibacteriales Nocardioidaceae Nocardioides 57 Actinobacteriota Actinobacteria Micrococcales Microbacteriaceae Microbacterium 61 Proteobacteria Alphaproteobacteria Rhizobiales Rhizobiaceae Allorhizobium-
Neorhizobium- Pararhizobium- Rhizobium 71 Actinobacteriota Actinobacteria Micrococcales Microbacteriaceae Clavibacter 72 Proteobacteria Gammaproteobacteria Pseudomonadales Pseudomonadaceae Pseudomonas 74 Proteobacteria Gammaproteobacteria Pseudomonadales Pseudomonadaceae Pseudomonas 88 Actinobacteriota Actinobacteria Propionibacteriales Propionibacteriacea
e
Friedmanniella 94 Actinobacteriota Actinobacteria Micrococcales Microbacteriaceae Frigoribacterium 117 Bacteroidota Bacteroidia Flavobacteriales Weeksellaceae Chryseobacterium 119 Actinobacteriota Actinobacteria
131 Table 7.3The core fungal ASVs with their associated taxonomical classification for the five microbiome habitats. Fungal ASVs were considered core if found across at least 90% of samples (within a microbiome category) at a relative abundance of more than 0.001. Note that the shoot endosphere microbiome area did not demonstrate any bacterial ASVs considered core.
Microbiome Category
ASV Domain Phylum Class Order Family Genus
Bulk soil (6)
1 Eukaryota Ascomycota Dothideomycetes Pleosporales Astrosphaeriellaceae Pithomyces
8 Eukaryota Ascomycota Sordariomycetes Hypocreales Nectriaceae Fusarium
10 Eukaryota Ascomycota Sordariomycetes Hypocreales Nectriaceae Fusarium
15 Eukaryota Ascomycota Eurotiomycetes Chaetothyriales Herpotrichiellaceae Exophiala
21 Eukaryota Ascomycota Sordariomycetes Hypocreales Nectriaceae Fusarium
45 Eukaryota Basidiomycota Tremellomycetes Tremellales Trimorphomycetaceae Rhizosphere
(5)
1 Eukaryota Ascomycota Dothideomycetes Pleosporales Astrosphaeriellaceae Pithomyces
8 Eukaryota Ascomycota Sordariomycetes Hypocreales Nectriaceae Fusarium
10 Eukaryota Ascomycota Sordariomycetes Hypocreales Nectriaceae Fusarium
15 Eukaryota Ascomycota Eurotiomycetes Chaetothyriales Herpotrichiellaceae Exophiala
21 Eukaryota Ascomycota Sordariomycetes Hypocreales Nectriaceae Fusarium
Root endosphere (4)
10 Eukaryota Ascomycota Sordariomycetes Hypocreales Nectriaceae Fusarium
11 Eukaryota Ascomycota Sordariomycetes Magnaporthales Magnaporthaceae
15 Eukaryota Ascomycota Eurotiomycetes Chaetothyriales Herpotrichiellaceae Exophiala 88 Eukaryota
Shoot endosphere (10)
1 Eukaryota Ascomycota Dothideomycetes Pleosporales Astrosphaeriellaceae Pithomyces
2 Eukaryota Ascomycota Dothideomycetes Pleosporales Didymellaceae Epicoccum
3 Eukaryota Basidiomycota Tremellomycetes
5 Eukaryota Ascomycota Dothideomycetes Pleosporales Didymellaceae Neoascochyta
8 Eukaryota Ascomycota Sordariomycetes Hypocreales Nectriaceae Fusarium
13 Eukaryota 36 Eukaryota
49 Eukaryota Ascomycota Sordariomycetes Hypocreales Clavicipitaceae Epichloë
68 Eukaryota Ascomycota Eurotiomycetes Eurotiales Aspergillaceae Aspergillus
105 Eukaryota Ascomycota Dothideomycetes
Phyllosphere 1 Eukaryota Ascomycota Dothideomycetes Pleosporales Astrosphaeriellaceae Pithomyces