[보고서]희귀·특산식물의 마이크로바이옴 분석을 통한 환경스트레스 저항 기능 구명 및 소재 발굴

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보고서 정보

주관연구기관

전북대학교
Chonbuk National University

연구책임자

이용훈

참여연구자

나채선

보고서유형

최종보고서

발행국가

대한민국

언어

한국어

발행년월

2023-04

과제시작연도

2022

주관부처

산림청
Korea Forest Service

등록번호

TRKO202300004950

과제고유번호

1405005424

사업명

산림생명자원소재발굴연구

DB 구축일자

2023-08-16

키워드

희귀․특산식물.마이크로바이옴.내생균.식물생육촉진균.환경스트레스.Rare and endemic plant.Microbiome.Endophyte.PGPR.Environmental stress.

표 Physiochemical properties of soils
표 Rarefaction curves for bacterial operational taxonomic units (OTUs) of long-sepal Donggang pasque-flower plant. Rarefaction curves of bulk soil (A, D), rhizosphere (B, E), and endophyte (C, F) in wild and cultivated area, respectively with cut-off value at 97% similarity. The vertical axis indicates the number of OTUs expected after sampling the number of sequences denoted in the horizontal axis
표 Estimated OTU richness and diversity indices in the bulk soil, rhizosphere soil, and roots from plants in cultivated area
표 Richness and diversity of microbial communities between compartments in wild and cultivated area. Richness was estimated by the Chao1 (A), species evenness was represented by Shannon’s index (B), and biodiversity incorporating phylogenetic difference between species was measured through Phylogenetic diversity (C). Red and green represent high and low while horizontal blue bars within boxes represent median. The tops and bottoms of boxes represent 75th and 25th quartiles, respectively. Diversities compared between Bulk soil (Bs), rhizosphere soil (Rs), and Root (Ro) in wild area and cultivated areas
표 Principal coordinates analysis (PCoA) of bacterial communities and UPGMA clustering based on Bray-Curtis dissimilarity index in (A) wild and (B) cultivated areas using all OTUs relative abundances present in all samples. The red box shows the cluster formed exclusively in roots of both wild and cultivated area
표 Comparison of bacterial composition and relative abundance at the phylum taxonomic level in bulk soil (Bs), rhizosphere (Rs), and root (Ro) of long-sepal Donggangpasque-flowerplant collected from native (-W) and cultivated (-C) area. A phylum with relative abundances less than 1% are referred as “Others”
표 Relative abundance (%) of bacterial genera in bulk soil, rhizosphere and roots of Donggang pasque-flower plants in (A) wild and (B) cultivated areas. Bars illustrate the mean relative abundance (>1%) per compartment of each dominant phyla ± standard deviation
표 Comparision of relative abundance of bacteria at genus level. The top 25 relative abundance of bacteria at genus level in bulk soil, rhizosphere, and roots of (A) wild and (B) cultivated habitats. The number of bacterial genus (>1% average relative abundance) that is unique or shared between compartments of (C) wild and (D) cultivated soil
표 Relative abundance of bacterial species in bulk soil, rhizosphere, and roots of long-sepal Donggang pasque-flower plants. The relative abundances (%) were compared between bulk soil, rhizosphere, and root of wild (A) and cultivated (B) habitats
표 Plant growth promoting and antagonistic activities of bacteria selected from rhizosphere and roots of long-sepal Donggang pasque-flower plants
표 Growth promotion of Arabidopsis by treatment of bacterial cells isolated from rhizosphere and endophytic bacteria in long-sepal Donggang pasque-flower plant. A. thaliana ecotype Col-0 seeds were surface sterilized and bacterized by soaking in each bacterial suspension. The bacterized seeds were sown onto 1/2 MS medium and cultured in plant-growth chambers. The photos were taken 10 days after incubation. Note Table 4 for scientific name of each strain
표 Growth stimulating and antimicrobial activities of bacterial strains isolated from rhizosphere and root of long-sepal Donggang pasque-flower plant. Siderophore production (A) was assessed from Pseudomonas fluorescens strains EnD56 and EnD210 (from upper to low panel) by a change in the color of CAS medium from blue to orange. Protease activity (B) by strain Bacillus subtilis EnD14 and P. fluorescens EnD56 was determined using skim milk agar medium based on clear zone around colonies. Phosphate solubilization (C) by strain B. subtilis EnD14 and P. fluorescens EnD56 was determined using Pikovskaya's agar medium by induction of clear zone around the colonies. Antagonistic activity of B. subtilis EnD-14 (D) against fungal pathogen Botrytis cinerea and bacterial pathogen Xanthomonas oryzae pv. oryzae. Antifungal and antibacterial activity of P. fluorescens EnD56 (E) against Pyricularia oryzae and Xanthomonas axonopodis pv. glycines, respectively
표 Seed germination of Pasque flower plants. The mycelial plugs were inoculated in the center WA and seeds were sown around the fungal isolate. (A) Front view of plates-showing fungus engulfing the seeds (B) Back view of plates-showing germinated radicles (C) Seeds and germinated seedlings
표 Sampling sites and Ulleung-sanmaneul plant investigated. The endemic plants collected from native habitats and cultivated field located (red dot) in Ulleung island, Gyeongsangbuk-do (A, Ba, C) and a medicinal herb experiment station, Jinan-gun, Jeollabuk-do (Bb, D), respectively
표 Rarefaction curves for bacterial operational taxonomic units (OTUs) of Ulleung-sanmaneul plant. Rarefaction curves of bulk soil and rhizosphere (A), and endophyte (B) in wild and cultivated area, respectively with cut-off value at 97% similarity. The vertical axis indicates the number of OTUs expected after sampling the number of sequences denoted in the horizontal axis
표 Estimated OTU richness and diversity indices in the bulk soil, rhizosphere soil, and roots from plants in wild area
표 Estimated OTU richness and diversity indices in the bulk soil, rhizosphere soil, and roots from plants in cultivated area
표 Comparison of richness and diversity of microbial communities between compartments in wild and cultivated area. Richness was estimated by the Chao1 (A), species evenness was represented by Shannon’s index (B) and biodiversity incorporating phylogenetic difference between species was measured through Phylogenetic diversity (C). Red and green represent high and low while horizontal blue bars within boxes represent median. The tops and bottoms of boxes represent 75th and 25th quartiles, respectively. Boxes with same letter do not differ significantly. Diversities compared between Bulk soil (Bs), rhizosphere soil (Rs), and Root (Ro) in wild area and cultivated areas
표 Principal coordinates analysis (PCoA) of bacterial microbiota (A) and UPGMA clustering based on Bray-Curtis dissimilarity in (B) wild and (C) cultivated areas using relative abundances of all OTUs at species level. The red box shows the cluster formed exclusively in roots of both wild and cultivated habitats
표 Comparative analysis of bacterial composition and relative abundance at the phylum taxonomic level in bulk soil (Bs), rhizosphere soil (Rs), and root (Ro) of Ulleung-sanmaneul plants collected from wild and cultivated area. Phyla with relative abundances more than 1% in at least one compartment were selected and compared. Phyla with relative abundances less than 1% were referred as “ETC”
표 Comparison of relative abundance of bacteria at genus level in bulk soil, rhizosphere, and root of Ulleung-sanmaneul plants. The bacterial genera with at least 1% relative abundance in each compartment of wild (A) and cultivated (B) habitats were selected for comparison
표 Comparison of relative abundance of bacteria at genus level in bulk soil, rhizosphere, and root of Ulleung-sanmaneul plants. The bacterial genera with more than 1% relative abundance in each compartment of wild (A) and cultivated (B) habitats were selected for comparison. The Venn diagrams show unique or shared genera of bacterial microbiota with relative abundance above 0.1% in each compartment of wild (C) and cultivated (D) areas. Among the species with relative abundance >1% in roots of wild and cultivated plants, Pseudomonas fulva was common with similar abundance in both the roots
표 Relative abundance of bacterial species within the roots of Ulleung-sanmaneul plants. The bacterial species with relative abundance >1% in roots were compared between wild (A) and cultivated (B) habitats
표 Comparative analysis of endophytic bacterial composition at the phylum taxonomic level in bulb (Bu) and root (Ro) of plants collected from wild and cultivated area. Relative abundance of phyla >1% in each compartment was compared
표 Comparison of relative abundance of bacteria at genus level root and bulb of Ulleung-sanmaneul plants
표 Growth promotion of Arabidopsis by treatment of various cell concentration of Pseudoxanthomonas sp. JBCE485 and Variovorax paradoxus JBCE486. Seeds of Arabidopsis thaliana Col-0 were treated with 1×106, 107 and 108 cfu/ml bacterial suspension of each bacterium and grown on half-strength MS medium. The photos were taken 14 days after treatment
표 Growth of Arabidopsis by treatment of Pseudoxanthomonas sp. JBCE485 and Variovorax paradoxus JBCE486. Seeds of Arabidopsis thaliana Col-0 were treated with 107 cfu/ml cells of each bacterium and combination of JBCE485 and JBCE486. Seeds were grown on (A) half-strength MS medium and (B) 1/2 MS medium amended with 100 mM NaCl. The growth performance was analyzed by measuring the root length, number of lateral roots, and fresh weight of plants. The data are represented as mean±standard deviation
표 Stress alleviation of Arabidopsis by treatment of Pseudoxanthomonas sp. JBCE485 and Variovorax paradoxus JBCE486. Seeds of Arabidopsis thaliana Col-0 were treated with 107 cfu/ml cells of each bacterium and combination of JBCE485 and JBCE486. Seeds were grown on (A) half-strength MS medium and (B) half-strength MS medium amended with 100 mM NaCl
표 The effect of Pseudoxanthomonas sp. JBCE485 and Variovorax paradoxus JBCE486 on the growth of chive under salt stress conditions. Seeds of chive were treated with 1 × 107 cfu/ml cells of each bacterium JBCE485 and JBCE486, and their mixture. Seeds were grown on horticultural nursery soil soaked with tap water (A) with or (B) without 175 mM NaCl. (soil/water, 2:1 v/v). The left Y-axis indicate shoot height (cm) and root length (cm), and right Y-axis indicate fresh weight of plants (g). The growth was recorded at 4 weeks and 6 weeks after cultivation in soil without or with salt, respectively. The data are represented as mean±standard deviation and bars with same letter do not differ significantly at P=0.05
표 Stress alleviation of chive by treatment of Pseudoxanthomonas sp. JBCE485 and Variovorax paradoxus JBCE486. Seeds were surface sterilized and treated with 1×107 cfu/ml cells of individual and combination of JBCE485 and JBCE486. Seeds were grown on normal horticultural soil soaked with tap water (A) with or (B) without 175 mM NaCl. Representative photos of plants were taken after 4 weeks and 6 weeks of treatment in soil without or with salt, respectively
표 Compatibility between Pseudoxanthomonas sp. JBCE485 and Variovorax paradoxus JBCE486. (A) Both strains were streaked perpendicularly as indicated in the photo. (B) One strain was mixed with LB media and another strain was inoculated on the paper disk. Growth inhibition or inhibition zone was photographed 3 days after incubation
표 Characteristics related with plant growth promoting activities of Pseudoxanthomonas sp. JBCE485 and Variovorax paradoxus JBCE486
표 Population dynamics of Pseudoxanthomonas sp. JBCE485 and Variovorax paradoxus JBCE486 cells on chive roots. Seeds were treated with individual and combined cell suspension (1×107 cfu/ml) of JBCE485 and JBCE486 and sown in horticultural soil. (A) Each bacterial population on root surface at 7, 14, 21 and 28 days after treatment. All tissues below soil surface at 7 days after growth and roots at 14, 21 and 28 days after growth were collected and cells per g tissues were estimated by serial dilution plating on LB medium containing rifampicin (25 μg/ml) and tetracycline (25 μg/ml) for JBCE485 and JBCE486, respectively. (B) Each bacterial population inside of roots. Surface sterilized roots were macerated in buffer and plated on LB media. (C) Total population of bacteria residing surface and inside of roots. The experiment was replicated two times with 15 seedlings per replicate. The data are represented as standard deviation of 5 independent biological samples. Bars with same letter(s) do not differ significantly at P=0.05 at each timepoint for respective compartments. * indicate significant difference at P=0.05 of a treatment with respect to niche; NS indicate not significant
표 Circular map of Variovorax paradoxus JBCE486. Marked characteristics are shown from outside to the center; coding sequences (CDS) on forward strand, CDS on reverse strand, tRNA, rRNA, GC content, and GC skew. Region that is not CDS in forward and reverse CDS is described as blank; tRNA is marked in light green; rRNA is marked in red; region with higher value of GC percentage than average is described in exterior light green peak, otherwise, it is described in interior lavender peak and height of the peak describes the difference from the average GC percentage; GC skew determined according to the formula, (G-C)/(G+C) and positive value shows that G is dominant while negative value shows that C is dominant. The exterior light green peak describes the region that has higher G content while interior lavender peak describes the region that higher C content
표 Classification of genes in Variovorax paradoxus JBCE486 into different groups based on their functional roles in the cell
표 Different Pseudomonas species and their genome features
표 Representation of each secondary metabolite biosynthetic gene cluster in the genome of Variovorax paradoxus JBCE486. Red, core biosynthetic genes; pink, additional biosynthetic genes; blue, transport-related genes; green, regulatory genes; and grey, other genes. Biosynthetic gene cluster structure and organization are predicted by antiSMASH6 and confirmed with PRISM3. Abbreviations are as follows: RRE, RRE-element containing cluster; RiPP-like, Other unspecified ribosomally synthesized and post-translationally modified peptide product cluster; NRPS, non-ribosomal peptide synthase; T1PKS, Type I Polyketide synthase
표 Chemical structure of products produced by the biosynthetic gene cluster. The structures of the products were analyzed using PRISM4 for (A) BGC 2, (B) cluster 6, and (C) cluster 8
표 Sampling sites and alpine modest primrose plants. The location of the endemic plant distributed (red circle) in mountain areas of Gyungsangnam-do province, South Korea (A, B) and the plants are mostly collected from between rocks (C, D) at slopes of high mountain at an altitude of 988 m (red circle in Ba). The plants collected from native (E) habitats for the bacterial profiling
표 Physiochemical properties of soils
표 Richness and diversity of microbial communities between compartments in wild and cultivated area. Richness was estimated by the Chao1 (A), species evenness was represented by Shannon’s index (B) and biodiversity incorporating phylogenetic difference between species was measured through Phylogenetic diversity (C). Red and green represent high and low while horizontal blue bars within boxes represent median. The tops and bottoms of boxes represent 75th and 25th quartiles, respectively. Diversities compared between Bulk soil (Bs), rhizosphere soil (Rs), and Root (Ro) in wild area and cultivated areas. The boxes with same letters do not differ significantly at P=0.05
표 Estimated OTU richness and diversity indices in the bulk soil, rhizosphere soil, and roots of alpine modest primrose plants in wild areas
표 Estimated OTU richness and diversity indices in the bulk soil, rhizosphere soil, and roots of alpine modest primrose plants in cultivated areas
표 Principal coordinates analysis (PCoA) of bacterial microbiota (A) and UPGMA clustering based on Bray-Curtis dissimilarity in (B) wild and (C) cultivated areas using relative abundance of all OTUs. The red box shows the cluster formed exclusively by roots of both wild and cultivated plants
표 Comparative analysis of bacterial composition and relative abundance at the phylum taxonomic level in bulk soil (Bs), rhizosphere soil (Rs), and root (Ro) of plants collected from wild and cultivated area. Phyla with relative abundances more than 1% in at least one compartment were selected and compared. Phyla with relative abundances less than 1% were referred as “ETC”
표 Comparison of relative abundance of bacteria at genus level in bulk soil, rhizosphere, and root of alpine modest primrose plants. The bacterial genera with at least 1% relative abundance in each compartment of wild (A) and cultivated (B) habitats were selected for comparison
표 Comparison of relative abundance of bacteria at genus level in bulk soil, rhizosphere, and root of alpine modest primrose plants. The bacterial genera with more than 1% relative abundance in each compartment of wild (A) and cultivated (B) habitats were selected for comparison. The Venn diagrams show unique or shared genera of bacterial microbiota with relative abundance above 1% in each compartment of wild (C) and cultivated (D) areas
표 Comparison of relative abundance of bacteria at genus level in bulk soil, rhizosphere, and root of alpine modest primrose plants. The bacterial genera with at least 1% relative abundance in each compartment of wild and cultivated habitats were selected for comparison
표 Heat map analysis for comparison of bacterial community at species level in respective plant compartments: (A) bulk soil (Bs) and rhizosphere (Rs) and (B) roots (Ro) of alpine modest primrose plants from wild and cultivated habitats
표 The effect of Leifsonia lichenia JBCE310, Chryseobacterium piperi JBCE316 and their combination on the growth of Primula malacoides. Seeds were treated with each bacterium and sown in horticultural soil. The growth performance was analyzed by measuring the shoot and root length, and fresh and dry weight of plants after 10 weeks of sowing. The data are represented as mean±standard deviation and same letters indicate no significant difference at P=0.05
표 The effect Leifsonia lichenia JBCE310, Chryseobacterium piperi JBCE316 and their combination on the germination and growth of Primula malacoides. Seeds were coated with each bacterium and sown in pots with horticultural soil. The germination was recorded at (A) 2 weeks and (B) 5 weeks after sowing. (C) Magnified image of the inset of 5 weeks after sowing and (D) seedlings at 10 weeks after sowing
표 . 측근의 수와 생체중은 균을 혼합하여 처리하였을 경우 각각의 균을 처리한 것에 비해 of Arabidopsis. Seeds of Arabidopsis thaliana Col-0 were treated with 107 cfu/ml bacterial suspension of each bacterium and grown on half-strength MS medium. The growth performance was measured 14-days after treatment. The data are represented as mean±standard deviation and bars with same letter do not differ significantly at P=0.05
표 The effect Leifsonia lichenia JBCE310 and Chryseobacterium piperi JBCE316 individually and in combination on the growth of Arabidopsis thaliana Col-0. Seeds of Arabidopsis Col-0 were coated with each bacterium or combination and grown on half-strength MS medium. The growth performance was analyzed by measuring the root length, shoot length, number of lateral roots, and fresh weight of 14-day-old plants
표 Compatibility between Leifsonia lichenia JBCE310 and Chryseobacterium piperi JBCE316. Both
표 Mechanisms related with plant growth promotion by Leifsonia lichenia JBCE310, Chryseobacterium piperi JBCE316, and their combination
표 Principal coordinates analysis (PCoA) of bacterial microbiota (A) and UPGMA clustering based on Bray-Curtis dissimilarity (B). Bacterial communities from rhizosphere soil of greenhouse at rooting and juvenile tuber stage (JT), growing and young tuber stage (YT), harvesting and mature tuber stage (MT) were compared using relative abundance of all OTUs
표 Principal coordinates analysis (PCoA) of fungal microbiota (A) and UPGMA clustering based on Bray-Curtis dissimilarity (B). Fungal communities from rhizosphere soil of greenhouse at rooting and juvenile tuber stage (JT), growing and young tuber stage (YT), harvesting and mature tuber stage (MT) were compared using relative abundance of all OTUs.
표 Comparative analysis of bacterial composition and relative abundance at phylum and genus level
표 Effect of bacterialisolate on the Mycenasp.Jinan-1 in the germination of Gastrodiaeletaseeds. eaf extract of Q. acutissimaand 1% soil extract, and a 10μL of the suspension of JBCC3 (1×103 cfu/mL) was dropped on the fungalplug (A) and M. purpureofuscawithout bacteria as control (B). The plates werincubated at 24℃ for 8 weeks after sowing
표 Growth of Mycena sp. mycelia by bacterial isolates. A plug of the fungal mycelia was inoculated in the center of the 50% PDA plate and a 10 μl droplet of bacterial suspension (102 cfu/ml) was dropped onto the fungal plug. Sterile distilled water was used as control. The inoculated plates were cultivated at 25℃ and photos were taken 10 days after incubation. Data represent mean±SD. Bars with same letter do not differ significantly at P=0.05
표 깽깽이풀, 모데미풀, 섬노루귀 자생지 및 종자수집 사진
표 토양 수집지 및 식물체별 자생지, 재배지 거리
표 희귀·특산식물 수집 토양 성분 정보
표 깽깽이풀, 모데미풀 근권 토양 전처리 사진
표 토양 샘플 미생물 순수분리 과정
표 식물체내 Phylum 수준에서의 세균 군집분석 결과
표 깽깽이풀, 모데미풀, 섬노루귀 ASVs 분석에서 각 단계에 대해 제거 및 필터 된 횟수(1차)
표 세 식물의 군집 풍부함 및 다양성(1차) (Community richness & diversity of three plants)
표 판독수가 종/ASV를 식별 가능한지 여부를 위한 Alpha rarefaction graph (Alpha rarefaction graph shows whether the number of reads used in analysis was sufficient in identifying species/ASV.)
표 토양별 ASV(Amplicon Sequence Variant) 그래프(2차)
표 토양별 세균 군집 다양성 그래프(2차)
표 희귀특산 식물 토양 세균 군집분석(Phylum)
표 희귀특산 식물 토양 세균 군집분석(Class)
표 섬노루귀 자생지에 따른 토양 세균 군집 (Phylum)
표 모데미풀 자생지와 재배지에 토양 세균 군집 (Phylum)
표 모데미풀 자생지와 재배지에 토양 세균 군집 (Phylum)
표 깽깽이풀 자생지에 따른 토양 세균 군집 (Phylum)
표 모데미풀 자생지와 재배지에 토양 세균 군집 (Phylum)
표 섬노루귀 자생지 지역별 토양 군집 내 특이적 균주와 특징
표 모데미풀 자생지와 재배지 토양 군집 내 특이적 균주와 특징
표 깽깽이풀 자생지 토양 군집 내 특이적 균주와 특징
표 돌피 종자 미생물 처리
표 미생물 배양액 IAA 함량
표 미생물 배양액 추출물 HPLC

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희귀·특산식물의 마이크로바이옴 분석을 통한 환경스트레스 저항 기능 구명 및 소재 발굴
Analysis of microbiome in rare and endemic plants and development of its use 원문보기

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희귀·특산식물의 마이크로바이옴 분석을 통한 환경스트레스 저항 기능 구명 및 소재 발굴 Analysis of microbiome in rare and endemic plants and development of its use 원문보기

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선택된 텍스트

희귀·특산식물의 마이크로바이옴 분석을 통한 환경스트레스 저항 기능 구명 및 소재 발굴
Analysis of microbiome in rare and endemic plants and development of its use 원문보기

표/그림 (84)

표/그림 (84)