Comparative Analyses On The Microbiomes Of Wild Species Fragaria Nilgerrensis And Cultivated Variety Akihime

With the rapid development of China’s strawberry industry,the production of strawberry and cultivated area ranked first in the world,various diseases are becoming more and more numerous in the process of strawberry cultivation.The endophytic and epiphytic bacteria are important sources of disease-resistant,growth-promoting probiotics in the microbiome of Fragaria spp.Therefore,it is particularly important to make sure the distribution characteristics of the microbiome of Fragaria and obtained bacterial resources to carry out the research of growth-promotion and disease prevention mechanisms.At present,there are a few reports about the microbiome of all organs of the Fragaria spp.there will be much work to carry out to target its microbiome.However,we study the compositions and structures of the microbiomes in eight compartments(nonrhizosphere soil,rhizosphere soil,rhizoplane,stem episphere,leaf episphere,root endosphere,stem endosphere,leaf endosphere)of F.nilgerrensis and Akihim by high-throughput amplicon sequencing technology,and analyze the correlation with Soil physicochemical parameters.Meanwhile,the diversity of culturable bacteria from six compartments(rhizoplane,stem episphere,leaf episphere,root endosphere,stem endosphere,leaf endosphere)of F.nilgerrensis and Akihime was also analyzed.The main conclusions of the full text were as follows.1.Research result of the culture-independent method for prokaryotic communities.A total of 26 phyla,60 classes,141 orders,225 families,404 genera,693 species and 1136 OTUs were detected in 24 samples of F.nilgerrensis.Proteobacteria is the dominant phylum in eight compartments.Sphingomonas and Novosphingobium are common genera in eight compartments,the dominant prokaryotic community compositions had significant differences in different compartments at the genus level,and the dominant genera were Sphingomonas,Enterobacter,Sphingomonas,Pantoea,Bradyrhizobium and Pseudomonas.A total of 30 phyla,78 classes,171 orders,261 families,492 genera,815 species and 1461 OTUs were detected in 24 Akihime samples,Proteobacteria is the dominant phylum in eight compartments.Massilia and Sphingomonas are common groups of eight compartments,the dominant prokaryotic community compositions had significant differences in different compartments at the genus level,and the dominant genera were Arthrobacter,Pantoea and Pseudomonas.There were significant differences in the diversity and richness of prokaryotic communities of F.nilgerrensis and Akihime,the genera of Sphingomonas,Pantoea,Candidatus＿Solibacter,RB41,Acinetobacter,Novosphingobium,Pseudomonas,Enterobacter,Streptomyces and so on were the key prokaryotic taxa that affected the differences in the same compartment samples of F.nilgerrensis and Akihime.Two archaea Thermoplasmatota and Crenarchaeota were detected in both samples,and their relative abundance was relatively small.The prokaryotic communities of different compartments of F.nilgerrensis and Akihime were significantly affected by different soil physical and chemical factors.2.Research result of the culture-independent method for fungal communities.A total of 16 phyla,62 classes,169 orders,429 families,1077 genera,1744 species and 4739 OTUs were detected in 24 F.nilgerrensis samples.Ascomycota is dominant phylum in non-rhizosphere soil,rhizosphere soil,rhizoplane,stem episphere and leaf episphere samples.The dominant fungal community compositions have significant difference in different compartments at the genus level,the dominant genera are Cladosporium,Pilidium and Clonostachys.A total of 14 phyla,50 classes,130 orders,298 families,633 genera,934 species and1794 OTUs were detected in 24 Akihime samples,Ascomycota is the dominant phyla in eight compartments.At the genus level,Botrytis,Fusarium and Vishniacozyma were distributed in the non-rhizosphere soil,rhizosphere soil,rhizoplane,stem episphere and leaf episphere samples.There were significant differences in the diversity and richness of fungal communities of F.nilgerrensis and Akihime,the genera of Clonostachys,Podospora,Botrytis,Fusarium,Chaetomium,Apodus,Mortierella,Gibberella,Rhodotorula,Articulospora and Stagonospora were the key fungal taxa that affected the difference in the same compartment samples of F.nilgerrensis and Akihime.The fungal communities of different compartments of F.nilgerrensis and Akihime were significantly affected by different soil physicochemical parameters.3.The ISP5,Gauze’s Medium No.1,R2 A,and plant medium were selected to separate bacteria from the six compartments of F.nilgerrensis and Akihime,A total of 515 strains were isolated from rhizoplane,stem episphere,leaf episphere,root endosphere,stem endosphere,leaf endosphere of F.nilgerrensis,belonging to 55 genera,24 families,14 orders,6 classes of the 3 phyla Proteobacteria(72.04%),Bacteroidetes(24.47%)and Actinobacteria(3.50%);Methylobacterium,Rhizobium,Novosphingobium,and Pseudomonas are common genera in the six compartments.At the genus level,the dominant genus is Rhizobium in rhizoplane sample;the dominant genus is Methylobacterium in the stem and leaf episphere samples;the dominant genus is Rhizobium in root endosphere sample;the dominant genus is Pseudomonas in stem and leaf endosphere samples.A total of495 strains were isolated from rhizoplane,stem episphere,leaf episphere,root endosphere,stem endosphere,leaf endosphere of Akihime,belonging to 61 genera,31 families,18 orders,7 classes of the 4 phyla Proteobacteria(41.62%),Bacteroidetes(4.65%),Firmicutes(3.23%)and Actinobacteria(50.51%),Microbacterium,Streptomyces,Agrobacterium and Pseudomonas are common genera in the six compartments;At the genus level,the dominant genus is Arthrobacte in rhizoplane sample;the dominant genera are Pseudomonas and Methylobacterium in the stem episphere sample;the dominant genus is Microbacterium in leaf episphere and leaf endosphere samples;the dominant genus is Streptomyces in root and stem endosphere samples.Twenty-two potential novel taxa were obtained from F.nilgerrensis,which belonging to the genera of Herbiconiux,Novosphingobium,Asticcacaulis,Pedobacter,Allorhizobium,Mucilaginibacter,Pelomonas,Duganella and Agrobacterium,accounting for 5.27%of the total strains.Seven potential novel taxa were obtained from Akihime,which belonging to the genera of Planctomonas,Chryseobacterium,Flavobacterium and Pseudomonas,accounting for 1.41% of the total strains.4.Comparative study analysis of bacterial communities between culturedependent and culture-independent methods revealed the bacterial communities,which had detected significant differences in two methods.Proteobacteria,Actinobacteria,Bacteroidetes and Firmicutes can be detected by two methods.At the genus level,only 5.69-77.15% of the taxa were isolated from F.nilgerrensis and Akihime samples by using culture-dependent method when compared with culture-independent method.Through the above studies,on the one hand,the diversity of microbial communities and their correlation with soil physicochemical parameters were revealed,the culturable bacteria diversity was also preliminarily analyzed.On the other hand,the present study provides valuable species resources for screening,development and utilization the probiotics of disease-resistant and promote strawberry plants growth.Therefore,the results in this paper have important theoretical and practical significance for sustainable development of strawberry ecological planting and industry.