Pub Date : 2023-12-01DOI: 10.1094/pbiomes-06-23-0046-r
Sasha-Lee Gush, Pedro Lebre, T. A. Coutinho, Donald Arthur Cowan, J. E. van der Waals
The fungus Rhizoctonia solani AG 3-PT is a devastating pathogen causing several diseases on potatoes in South Africa and globally. The removal of various fungicides from the market and strict regulations on the use of synthetic chemicals makes disease management difficult. Therefore alternative, environmentally safe control measures are being considered, such as the use of biocontrol agents (BCAs). BCAs are an attractive alternative for improving plant and soil health of economically important crops. To identify key microbial indicators of disease suppression against R. solani AG 3-PT, a greenhouse pot trial experiment was conducted using soil from a potato-growing region in KwaZulu-Natal, South Africa. High-throughput sequencing of fungal ITS and bacterial 16S rRNA was used to characterize the fungal and bacterial community composition in the soil, respectively, with and without artificial inoculation with R. solani AG 3-PT. Results indicated that the pathogen caused dysbiosis in the potato soil microbiome, leading to a shift in the fungal and bacterial community composition. Differentially abundant microbial taxa in R. solaniAG 3-PT inoculated soils suggest a promising potential for disease-suppressive activity. Network analysis also confirmed the presence of key taxa involved in the microbial community shifts, which could support their role in the suppression of R. solani AG 3-PT. The identification of key microbial indicators against Rhizoctonia diseases can contribute to the development of environmentally sustainable potato production systems, which are particularly important considering the implementation of the European Green Deal.
真菌solanrhizoctonia ag3 - pt是一种破坏性病原体，在南非和全球马铃薯上引起几种疾病。各种杀菌剂从市场上撤下以及对合成化学品使用的严格规定使疾病管理变得困难。因此，正在考虑使用生物防治剂(bca)等环境安全的替代控制措施。bca是改善重要经济作物植物和土壤健康的一种有吸引力的替代方法。利用南非夸祖鲁-纳塔尔省一个马铃薯种植区的土壤，进行了温室盆栽试验，以确定对番茄枯萎病(R. solani AG 3-PT)的关键微生物指标。利用真菌ITS和细菌16S rRNA的高通量测序，分别表征了人工接种和未接种茄茄菌AG 3-PT后土壤中真菌和细菌的群落组成。结果表明，病原菌引起马铃薯土壤微生物群落失调，导致真菌和细菌群落组成发生变化。3-PT接种后土壤微生物类群丰富程度的差异表明其具有良好的抑菌活性。网络分析还证实了参与微生物群落转移的关键类群的存在，这可能支持它们在抑制茄茄菌AG 3-PT中的作用。确定防治根丝核菌病的关键微生物指标有助于开发环境可持续的马铃薯生产系统，考虑到《欧洲绿色协议》的实施，这一点尤为重要。
{"title":"Disentangling shifts in the soil microbiome of potatoes infected with Rhizoctonia solani AG 3-PT in search of potential biocontrol agents","authors":"Sasha-Lee Gush, Pedro Lebre, T. A. Coutinho, Donald Arthur Cowan, J. E. van der Waals","doi":"10.1094/pbiomes-06-23-0046-r","DOIUrl":"https://doi.org/10.1094/pbiomes-06-23-0046-r","url":null,"abstract":"The fungus Rhizoctonia solani AG 3-PT is a devastating pathogen causing several diseases on potatoes in South Africa and globally. The removal of various fungicides from the market and strict regulations on the use of synthetic chemicals makes disease management difficult. Therefore alternative, environmentally safe control measures are being considered, such as the use of biocontrol agents (BCAs). BCAs are an attractive alternative for improving plant and soil health of economically important crops. To identify key microbial indicators of disease suppression against R. solani AG 3-PT, a greenhouse pot trial experiment was conducted using soil from a potato-growing region in KwaZulu-Natal, South Africa. High-throughput sequencing of fungal ITS and bacterial 16S rRNA was used to characterize the fungal and bacterial community composition in the soil, respectively, with and without artificial inoculation with R. solani AG 3-PT. Results indicated that the pathogen caused dysbiosis in the potato soil microbiome, leading to a shift in the fungal and bacterial community composition. Differentially abundant microbial taxa in R. solaniAG 3-PT inoculated soils suggest a promising potential for disease-suppressive activity. Network analysis also confirmed the presence of key taxa involved in the microbial community shifts, which could support their role in the suppression of R. solani AG 3-PT. The identification of key microbial indicators against Rhizoctonia diseases can contribute to the development of environmentally sustainable potato production systems, which are particularly important considering the implementation of the European Green Deal.","PeriodicalId":48504,"journal":{"name":"Phytobiomes Journal","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138614422","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-11-28DOI: 10.1094/pbiomes-05-23-0031-r
C. De Tender, M. Vandecasteele, S. Ommeslag, Noémie De Zutter, Ellen Vandenbussche, A. Haegeman, K. Audenaert, Leilei Li, Bart Vandecasteele, Floris Voorthuijzen, Kristof Maenhout, Stien Beirinckx, Rosita Barneveldt, Sofie Goormachtig, J. Debode
Chitin has proven to be a valuable alternative for mineral fertilizers in growing media. We recently hypothesized that chitin might work as a biostimulant, attracting plant growth promoting microbes to the rhizosphere. Especially Mortierellales increase massively in abundance by chitin application and might have a profound role in chitin-mediated plant growth promotion. We isolated four strains of this order, classified as Linnemannia elongata, from chitin-enriched growing medium and the lettuce rhizosphere. The isolates induced a consistent increase in shoot and root fresh weight and increased chlorophyll content of Arabidopsis thaliana in vitro as measured by multispectral imaging. By studying the isolate’s genomes, we postulate that this growth promotion is induced through auxin production and/or translocation of Ca to the plant. The synergy between chitin and L. elongata was demonstrated by (1) the chitinase activity and chitin degradation potential of all isolates and (2) the positive effect of chitin and L. elongata seed coating on germination of A. thaliana seeds as compared to L. elongata seed coating without chitin. We conclude that chitin-related growth promotion is depending on the activation of the microbial community, with L. elongata as a key species.
甲壳素已被证明是生长介质中矿物肥料的重要替代品。我们最近推测，几丁质可以作为一种生物刺激剂，吸引促进植物生长的微生物进入根瘤层。特别是毛霉属（Mortierellales）微生物的数量会随着几丁质的施用而大量增加，并可能在几丁质介导的植物生长促进过程中发挥重要作用。我们从富含几丁质的生长介质和莴苣根瘤菌层中分离出了四株该菌纲的菌株，它们被归类为Linnemannia elongata。通过多光谱成像测量，这些分离菌株在体外诱导拟南芥的芽和根鲜重持续增加，叶绿素含量也有所增加。通过研究分离物的基因组，我们推测这种生长促进作用是通过产生辅助素和/或将 Ca 转化到植物体内而诱导的。甲壳素与纤毛虫之间的协同作用体现在：（1）所有分离物的甲壳素酶活性和甲壳素降解潜力；（2）与不含甲壳素的纤毛虫种子包衣相比，甲壳素和纤毛虫种子包衣对黄连木种子萌发的积极影响。我们的结论是，与几丁质相关的生长促进作用取决于微生物群落的激活，而长叶菌是其中的关键物种。
{"title":"Linnemannia elongata: a key species in chitin-based plant growth promotion","authors":"C. De Tender, M. Vandecasteele, S. Ommeslag, Noémie De Zutter, Ellen Vandenbussche, A. Haegeman, K. Audenaert, Leilei Li, Bart Vandecasteele, Floris Voorthuijzen, Kristof Maenhout, Stien Beirinckx, Rosita Barneveldt, Sofie Goormachtig, J. Debode","doi":"10.1094/pbiomes-05-23-0031-r","DOIUrl":"https://doi.org/10.1094/pbiomes-05-23-0031-r","url":null,"abstract":"Chitin has proven to be a valuable alternative for mineral fertilizers in growing media. We recently hypothesized that chitin might work as a biostimulant, attracting plant growth promoting microbes to the rhizosphere. Especially Mortierellales increase massively in abundance by chitin application and might have a profound role in chitin-mediated plant growth promotion. We isolated four strains of this order, classified as Linnemannia elongata, from chitin-enriched growing medium and the lettuce rhizosphere. The isolates induced a consistent increase in shoot and root fresh weight and increased chlorophyll content of Arabidopsis thaliana in vitro as measured by multispectral imaging. By studying the isolate’s genomes, we postulate that this growth promotion is induced through auxin production and/or translocation of Ca to the plant. The synergy between chitin and L. elongata was demonstrated by (1) the chitinase activity and chitin degradation potential of all isolates and (2) the positive effect of chitin and L. elongata seed coating on germination of A. thaliana seeds as compared to L. elongata seed coating without chitin. We conclude that chitin-related growth promotion is depending on the activation of the microbial community, with L. elongata as a key species.","PeriodicalId":48504,"journal":{"name":"Phytobiomes Journal","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2023-11-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139221887","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-11-21DOI: 10.1094/pbiomes-10-23-0104-r
A. Bultreys, I. Gheysen
Outbreaks in Europe have raised concerns about poinsettia bacterial canker caused by Curtobacterium flaccumfaciens pv. poinsettiae described in the USA. Using a semi-selective medium containing aztreonam and fosfomycin and selection during isolation based on MALDI-TOF MS spectra, 424 Curtobacterium strains were isolated from Belgian poinsettias of African and European origin. Different populations coexisted: 130 strains were identified as C. flaccumfaciens with scores ≥2.0, but 294 with scores <2.0 or as another Curtobacterium. MALDI-TOF MS libraries constructed using similar medium and extraction procedure and a pathogenicity test on poinsettia were used to screen collections from poinsettia and wheat, a possible alternative host, for C. f. pv. poinsettiae. The concatenated recA-gyrB partial sequences showed that 114 poinsettia or wheat strains belonged to different Curtobacterium species. Eighty-eight nonpathogenic strains and four U.S. strains from litter were intermingled with bean pathogenic C. f. pv. flaccumfaciens strains in the three genetic groups of C. flaccumfaciens, but lacked their pathogenicity markers. Four new European recA-gyrB sequatypes of C. f. pv. poinsettiae, obtained from symptomatic and asymptomatic poinsettias, were distinguished from three American sequatypes. Six sequatypes were pathogenic in tests, belonged to genetic groups related to two different genomospecies, and possessed a plasmid. Sequencing of six plasmids revealed three related plasmids containing proteases and a polygalacturonase found only in strains pathogenic in pathogenicity tests and specifically identified by polygalacturonase-based PCR and LAMP assays. Similarities between plant and litter Curtobacterium and the role of plasmids in pathogenicity and punctual transmissions of pathogenicity among heterogeneous C. flaccumfaciens are suggested.
欧洲爆发的一品红细菌性腐烂病引起了人们对美国描述的由 Curtobacterium flaccumfaciens pv. poinsettiae 引起的一品红细菌性腐烂病的关注。使用含有阿曲霉素和磷霉素的半选择性培养基，并在分离过程中根据 MALDI-TOF MS 图谱进行筛选，从原产于非洲和欧洲的比利时一品红中分离出 424 株杆菌。不同的种群共存：130 株菌株被鉴定为 C. flaccumfaciens（得分≥2.0），但 294 株菌株得分＜2.0，或被鉴定为另一种杆菌。利用类似的培养基和提取程序构建的 MALDI-TOF MS 文库以及对一品红的致病性测试，从一品红和小麦（可能的替代宿主）中筛选出了 C. f. pv. poinsettiae。重组的 recA-gyrB 部分序列显示，114 株一品红或小麦菌株属于不同的鼠李属杆菌。在 C. flaccumfaciens 的三个基因组中，有 88 株非致病性菌株和 4 株来自垃圾的美国菌株与豆类致病性 C. f. pv. flaccumfaciens 菌株混杂在一起，但缺乏其致病性标记。从有症状和无症状的一品红中获得的四种新的欧洲 poinsettiae C. f. pv. 的 recA-gyrB 序列型与三种美国序列型区分开来。六个序列型在试验中具有致病性，属于与两个不同基因组相关的基因群，并具有一个质粒。六个质粒的测序结果显示，三个相关质粒含有蛋白酶和一种聚半乳糖醛酸酶，只有在致病性试验中致病的菌株中才能发现，并通过基于聚半乳糖醛酸酶的聚合酶链式反应（PCR）和聚合酶链式反应（LAMP）测定法进行了特异性鉴定。这表明植物和枯落物绵毛杆菌之间存在相似性，质粒在致病性和异源绵毛杆菌之间的致病性传递中起着重要作用。
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Pub Date : 2023-11-17DOI: 10.1094/pbiomes-09-23-0090-r
N. Kuzmanović, J. Nesme, Jacqueline Wolf, Meina Neumann-Schaal, Jörn Petersen, G. Fernandez-Gnecco, Cathrin Sproeer, B. Bunk, Joerg Overmann, S. J. Sørensen, Elke Idczak, K. Smalla
Tumorigenic agrobacteria are widespread plant pathogens causing crown gall and cane gall diseases on various agricultural crops. These pathogens genetically transform its host plant and thus form an ecological niche (galls), in which specific metabolites (i.e., opines) are produced. Opines provide the pathogen with multiple competitive advantages, but they can also be utilized by other bacteria colonizing galls. To gain a thorough understanding of disease processes and ecology, it is necessary to consider the pathogen in the context of its microbial environment within the diseased plant (i.e., the pathobiome). Therefore, in this study, we investigated the bacterial pathobiome associated with aerial crown gall tumors (gallobiome) on rhododendron. For this purpose, combination of cultivation-dependent and -independent approaches were applied, which also involved development of a novel amplicon sequencing approach targeting the recA housekeeping gene. The 16S rRNA and recA gene amplicon sequencing clearly indicated that Rhizobium rhododendri and the group of Agrobacterium spp., primarily belonging to the so-called “rubi” clade were the dominant members of bacterial microbiota in rhododendron galls. While the tumor-inducing (Ti) plasmid-harboring R. rhododendri strains are causative agents of crown gall disease, Agrobacterium spp. strains isolated in this study were nonpathogenic and carried genes for the catabolism of opines, enabling these bacteria to efficiently colonize tumor tissue. Taken together, our results clearly showed that the tumorigenic R. rhododendri and nonpathogenic opine-catabolizing Agrobacterium spp. were the key players within the bacterial microbiota associated with aerial crown gall tumors on rhododendron.
致瘤农杆菌是一种广泛存在的植物病原体，可导致多种农作物的冠瘿和蔗瘿病。这些病原体会对寄主植物进行基因改造，从而形成一个生态位（虫瘿），并在其中产生特定的代谢产物（即蛋白烯）。蛋白烯为病原体提供了多种竞争优势，但它们也可被定殖在虫瘿中的其他细菌所利用。为了全面了解病害过程和生态学，有必要结合病害植物体内的微生物环境（即病原生物群）来考虑病原体。因此，在本研究中，我们调查了与杜鹃花气生冠瘿瘤相关的细菌病原生物群（gallobiome）。为此，我们结合了依赖培养和不依赖培养的方法，还开发了一种以 recA 管家基因为目标的新型扩增子测序方法。16S rRNA 和 recA 基因扩增片段测序结果清楚地表明，根瘤根瘤菌和农杆菌属（主要属于所谓的 "rubi "支系）是杜鹃花虫瘿中细菌微生物群的主要成员。虽然携带肿瘤诱导（Ti）质粒的 R. rhododendri 菌株是冠瘿病的致病菌，但本研究中分离到的农杆菌属菌株是非致病菌，并携带蛋白鸦片分解基因，使这些细菌能够有效地定植于肿瘤组织中。总之，我们的研究结果清楚地表明，致瘤的 R. rhododendri 和非致病的分解阿片的农杆菌属是杜鹃花气生冠瘿瘤相关细菌微生物群中的关键角色。
{"title":"Deciphering the key players within the bacterial microbiota associated with aerial crown gall tumors on rhododendron: Insights into the gallobiome","authors":"N. Kuzmanović, J. Nesme, Jacqueline Wolf, Meina Neumann-Schaal, Jörn Petersen, G. Fernandez-Gnecco, Cathrin Sproeer, B. Bunk, Joerg Overmann, S. J. Sørensen, Elke Idczak, K. Smalla","doi":"10.1094/pbiomes-09-23-0090-r","DOIUrl":"https://doi.org/10.1094/pbiomes-09-23-0090-r","url":null,"abstract":"Tumorigenic agrobacteria are widespread plant pathogens causing crown gall and cane gall diseases on various agricultural crops. These pathogens genetically transform its host plant and thus form an ecological niche (galls), in which specific metabolites (i.e., opines) are produced. Opines provide the pathogen with multiple competitive advantages, but they can also be utilized by other bacteria colonizing galls. To gain a thorough understanding of disease processes and ecology, it is necessary to consider the pathogen in the context of its microbial environment within the diseased plant (i.e., the pathobiome). Therefore, in this study, we investigated the bacterial pathobiome associated with aerial crown gall tumors (gallobiome) on rhododendron. For this purpose, combination of cultivation-dependent and -independent approaches were applied, which also involved development of a novel amplicon sequencing approach targeting the recA housekeeping gene. The 16S rRNA and recA gene amplicon sequencing clearly indicated that Rhizobium rhododendri and the group of Agrobacterium spp., primarily belonging to the so-called “rubi” clade were the dominant members of bacterial microbiota in rhododendron galls. While the tumor-inducing (Ti) plasmid-harboring R. rhododendri strains are causative agents of crown gall disease, Agrobacterium spp. strains isolated in this study were nonpathogenic and carried genes for the catabolism of opines, enabling these bacteria to efficiently colonize tumor tissue. Taken together, our results clearly showed that the tumorigenic R. rhododendri and nonpathogenic opine-catabolizing Agrobacterium spp. were the key players within the bacterial microbiota associated with aerial crown gall tumors on rhododendron.","PeriodicalId":48504,"journal":{"name":"Phytobiomes Journal","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2023-11-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139264974","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-11-07DOI: 10.1094/pbiomes-08-23-0077-r
Catarina Leal, Ales Eichmeier, Katerina Stuskova, Josep Armengol, Rebeca Bujanda, Florence Fontaine, Patricia Trotel-Aziz, David Gramaje
With a reduction on available chemical treatments, there is an increased interest on biological control of grapevine trunk diseases. Few studies have investigated the impact of introducing beneficial microorganisms in rhizosphere, on the indigenous soil existent microbiome. In this study, we explored the effect of two biological control agents, Trichoderma atroviride SC1 (commercial product Vintec® from Certis Belchim, Ta SC1) and Bacillus subtilis PTA-271 (Bs PTA-271), on the grapevine rhizosphere bacterial and fungal microbiome, and on plant defense expression, using High-Throughput Amplicon Sequencing and qPCR, respectively. Additionally, we quantified both Ta SC1 and Bs PTA-271 in rhizosphere overtime using digital droplet PCR. The fungal microbiome was more affected by factors such as soil type, BCA treatment, and sampling time than bacterial microbiome. Specifically, Ta SC1 application produced negative impacts on fungal diversity, while applications of BCAs did not affect bacterial diversity. Interestingly, the survival and establishment of both BCAs showed opposite trends depending on the soil type, indicating that the physicochemical properties of soils have a role on BCA establishment. Fungal co-occurrence networks were less complex than bacterial networks, but highly impacted by Ta SC1 application. Soils treated with Ta SC1, presented more complex and stable co-occurrence networks, with a higher number of positive correlations. Induced grapevine defenses also differed according to the soil, being more affected by BCA inoculation on sandy soil.
{"title":"Biocontrol agents establishment and their impact on rhizosphere microbiome and induced grapevine defenses is highly soil-dependent","authors":"Catarina Leal, Ales Eichmeier, Katerina Stuskova, Josep Armengol, Rebeca Bujanda, Florence Fontaine, Patricia Trotel-Aziz, David Gramaje","doi":"10.1094/pbiomes-08-23-0077-r","DOIUrl":"https://doi.org/10.1094/pbiomes-08-23-0077-r","url":null,"abstract":"With a reduction on available chemical treatments, there is an increased interest on biological control of grapevine trunk diseases. Few studies have investigated the impact of introducing beneficial microorganisms in rhizosphere, on the indigenous soil existent microbiome. In this study, we explored the effect of two biological control agents, Trichoderma atroviride SC1 (commercial product Vintec® from Certis Belchim, Ta SC1) and Bacillus subtilis PTA-271 (Bs PTA-271), on the grapevine rhizosphere bacterial and fungal microbiome, and on plant defense expression, using High-Throughput Amplicon Sequencing and qPCR, respectively. Additionally, we quantified both Ta SC1 and Bs PTA-271 in rhizosphere overtime using digital droplet PCR. The fungal microbiome was more affected by factors such as soil type, BCA treatment, and sampling time than bacterial microbiome. Specifically, Ta SC1 application produced negative impacts on fungal diversity, while applications of BCAs did not affect bacterial diversity. Interestingly, the survival and establishment of both BCAs showed opposite trends depending on the soil type, indicating that the physicochemical properties of soils have a role on BCA establishment. Fungal co-occurrence networks were less complex than bacterial networks, but highly impacted by Ta SC1 application. Soils treated with Ta SC1, presented more complex and stable co-occurrence networks, with a higher number of positive correlations. Induced grapevine defenses also differed according to the soil, being more affected by BCA inoculation on sandy soil.","PeriodicalId":48504,"journal":{"name":"Phytobiomes Journal","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-11-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135475178","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-10-23DOI: 10.1094/pbiomes-05-23-0038-r
Chunyan Guo, An Yang, Wen-Hao Zhang
Elucidating the plant-microbiome network is of importance in understanding species coexistence of natural ecosystems. Phyllosphere, which is the aerial parts of terrestrial plants, is inhabited by diverse microbes. However, few studies have focused on phyllosphere microbiome and plant-microbiome network in temperate grasslands. In this study, we explored the diversity, community structure, and network architecture of phyllosphere bacteria and fungi in 19 plant species native to the temperate grassland in Inner Mongolia, China. We obtained 3,313 and 758 phyllosphere bacterial and fungal OTUs, and found that the bacterial community was dominated by Proteobacteria, Actinobacteriota and Firmicutes. The fungal community was dominated by Ascomycota and Basidiomycota. Plant identity exerted significant impacts on α-diversities of both bacterial and fungal communities. The composition of bacterial and fungal communities differed among plant species. Plant identity had a greater effect on fungal than on bacterial communities. Both bacterial and fungal network structures were characterized by specialized and modular, lowly connected and no nested properties. The plant-fungal network had a high level of specification, modularity, antinestedness and connectance compared to the plant-bacterial network. Our results suggest more intimate relationships between plants and phyllosphere fungi than between plants and phyllosphere bacteria, and that the phyllosphere fungal community is more resistant to environmental disturbance than the phyllosphere bacterial community in the temperate grassland ecosystem. These findings may contribute to our understanding of the mechanisms by which species coexist and community stabilizes in the grassland ecosystems.
{"title":"Host identity determines the bacterial and fungal community and network structures in the phyllosphere of plant species in a temperate steppe","authors":"Chunyan Guo, An Yang, Wen-Hao Zhang","doi":"10.1094/pbiomes-05-23-0038-r","DOIUrl":"https://doi.org/10.1094/pbiomes-05-23-0038-r","url":null,"abstract":"Elucidating the plant-microbiome network is of importance in understanding species coexistence of natural ecosystems. Phyllosphere, which is the aerial parts of terrestrial plants, is inhabited by diverse microbes. However, few studies have focused on phyllosphere microbiome and plant-microbiome network in temperate grasslands. In this study, we explored the diversity, community structure, and network architecture of phyllosphere bacteria and fungi in 19 plant species native to the temperate grassland in Inner Mongolia, China. We obtained 3,313 and 758 phyllosphere bacterial and fungal OTUs, and found that the bacterial community was dominated by Proteobacteria, Actinobacteriota and Firmicutes. The fungal community was dominated by Ascomycota and Basidiomycota. Plant identity exerted significant impacts on α-diversities of both bacterial and fungal communities. The composition of bacterial and fungal communities differed among plant species. Plant identity had a greater effect on fungal than on bacterial communities. Both bacterial and fungal network structures were characterized by specialized and modular, lowly connected and no nested properties. The plant-fungal network had a high level of specification, modularity, antinestedness and connectance compared to the plant-bacterial network. Our results suggest more intimate relationships between plants and phyllosphere fungi than between plants and phyllosphere bacteria, and that the phyllosphere fungal community is more resistant to environmental disturbance than the phyllosphere bacterial community in the temperate grassland ecosystem. These findings may contribute to our understanding of the mechanisms by which species coexist and community stabilizes in the grassland ecosystems.","PeriodicalId":48504,"journal":{"name":"Phytobiomes Journal","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-10-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135366713","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-10-19DOI: 10.1094/pbiomes-06-23-0049-r
Shawn Brown, Jennifer Mandel
Plant-associated mycobiomes can influence important host plant traits including those related to disease, nutrient acquisition, phenology, stress tolerance, and productivity. Disentangling the complex multifaceted relationships between host plants and their associated mycobiomes is a critical first step for generating improvements in environmental sustainability and/or plant productivity. Despite decades of work on these plant-fungal interactions, consequences of and mechanisms controlling these interactions are not well resolved, especially in the face of environmental stress such as drought. Moreover, plant differential genotypic responses under stress and associated mycobiome assembly dynamics are likely important in structuring communities but have been less well-studied. We conducted a controlled drought stress experiment by manipulating water treatment in a diverse set of cultivated sunflower lines with different inherent drought resistance levels to evaluate how sunflower host genotypes and drought interacts to affect belowground fungal mycobiomes at the rhizospheric and endospheric levels. Our results demonstrated that fungal community structure was driven by watering treatment, plant genotype, treatment by genotype interactions, genotype by plant compartment interactions and treatment by genotype by compartment interactions. Additionally, our analyses demonstrated the relative abundance of plant pathogens and arbuscular mycorrhizal fungi increased with host genetic variation, or heterozygosity, levels. Our study provides evidence for drought and genotypic drivers of belowground sunflower-fungi interactions and offers a framework for leveraging these interactions to further understand how mycobiome community structure can improve plant productivity under stress.
{"title":"Rapid restructuring of rhizosphere and endospheric fungal communities with drought in multiple lines of domesticated sunflower","authors":"Shawn Brown, Jennifer Mandel","doi":"10.1094/pbiomes-06-23-0049-r","DOIUrl":"https://doi.org/10.1094/pbiomes-06-23-0049-r","url":null,"abstract":"Plant-associated mycobiomes can influence important host plant traits including those related to disease, nutrient acquisition, phenology, stress tolerance, and productivity. Disentangling the complex multifaceted relationships between host plants and their associated mycobiomes is a critical first step for generating improvements in environmental sustainability and/or plant productivity. Despite decades of work on these plant-fungal interactions, consequences of and mechanisms controlling these interactions are not well resolved, especially in the face of environmental stress such as drought. Moreover, plant differential genotypic responses under stress and associated mycobiome assembly dynamics are likely important in structuring communities but have been less well-studied. We conducted a controlled drought stress experiment by manipulating water treatment in a diverse set of cultivated sunflower lines with different inherent drought resistance levels to evaluate how sunflower host genotypes and drought interacts to affect belowground fungal mycobiomes at the rhizospheric and endospheric levels. Our results demonstrated that fungal community structure was driven by watering treatment, plant genotype, treatment by genotype interactions, genotype by plant compartment interactions and treatment by genotype by compartment interactions. Additionally, our analyses demonstrated the relative abundance of plant pathogens and arbuscular mycorrhizal fungi increased with host genetic variation, or heterozygosity, levels. Our study provides evidence for drought and genotypic drivers of belowground sunflower-fungi interactions and offers a framework for leveraging these interactions to further understand how mycobiome community structure can improve plant productivity under stress.","PeriodicalId":48504,"journal":{"name":"Phytobiomes Journal","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-10-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135728888","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-10-19DOI: 10.1094/pbiomes-07-23-0060-r
Scott Klasek, James Crants, Touqeer Abbas, Katherine A. Ashley, Marian Bolton, Madelyn Celovsky, Neil Gudmestead, Jianjun Hao, Jorge Ibarra Caballero, Courtney Jahn, Gilbert Kamgan Nkuekam, Richard Lankau, Robert Larkin, Eglantina Lopez Echartea, Jeff S. Miller, Amber Moore, Julie Sherman Pasche, Matthew Ruark, Brenda K. Schroeder, Shan Shan, Victoria Skillman, Ali Srour, Anna Stasko, Kurt Steinke, Jane E. Stewart, Mike Thornton, Kimberly Zitnick-Anderson, Kenneth Frost, Carl Rosen, Linda Kinkel
Soil microbiomes play crucial roles in pathogen suppression, nutrient mobilization, and maintenance of plant health. Their complexity and variability across spatial and temporal scales provide challenges for identifying common targets–microbial taxa or assemblages–for management in agricultural systems. To understand how microbiomes in potato production soils vary across growing regions and identify commonly distributed taxa among them, we compiled a continental-scale bacterial and eukaryotic amplicon dataset of over 1300 communities with corresponding edaphic measurements from nine US field sites. Field site explained most of the variance across bacterial and eukaryotic (predominantly fungal) communities, while pH, organic matter, and NPK concentrations also varied with community structure. Bacterial and eukaryotic potato soil microbiomes show consistent phylum-level composition across locations at the continental scale, with regional-scale differences evident among genera and amplicon sequence variants (ASVs). Core community analysis identified 606 bacterial and 74 eukaryotic ASVs that were present, but unequally distributed, across all nine field sites. Many of these core ASVs belong to common soil genera, such as Bacillus and Mortierella, which may reveal functional potential involved in maintaining soil health across regionally variable soil systems.
{"title":"Potato soil core microbiomes are regionally variable across the continental US","authors":"Scott Klasek, James Crants, Touqeer Abbas, Katherine A. Ashley, Marian Bolton, Madelyn Celovsky, Neil Gudmestead, Jianjun Hao, Jorge Ibarra Caballero, Courtney Jahn, Gilbert Kamgan Nkuekam, Richard Lankau, Robert Larkin, Eglantina Lopez Echartea, Jeff S. Miller, Amber Moore, Julie Sherman Pasche, Matthew Ruark, Brenda K. Schroeder, Shan Shan, Victoria Skillman, Ali Srour, Anna Stasko, Kurt Steinke, Jane E. Stewart, Mike Thornton, Kimberly Zitnick-Anderson, Kenneth Frost, Carl Rosen, Linda Kinkel","doi":"10.1094/pbiomes-07-23-0060-r","DOIUrl":"https://doi.org/10.1094/pbiomes-07-23-0060-r","url":null,"abstract":"Soil microbiomes play crucial roles in pathogen suppression, nutrient mobilization, and maintenance of plant health. Their complexity and variability across spatial and temporal scales provide challenges for identifying common targets–microbial taxa or assemblages–for management in agricultural systems. To understand how microbiomes in potato production soils vary across growing regions and identify commonly distributed taxa among them, we compiled a continental-scale bacterial and eukaryotic amplicon dataset of over 1300 communities with corresponding edaphic measurements from nine US field sites. Field site explained most of the variance across bacterial and eukaryotic (predominantly fungal) communities, while pH, organic matter, and NPK concentrations also varied with community structure. Bacterial and eukaryotic potato soil microbiomes show consistent phylum-level composition across locations at the continental scale, with regional-scale differences evident among genera and amplicon sequence variants (ASVs). Core community analysis identified 606 bacterial and 74 eukaryotic ASVs that were present, but unequally distributed, across all nine field sites. Many of these core ASVs belong to common soil genera, such as Bacillus and Mortierella, which may reveal functional potential involved in maintaining soil health across regionally variable soil systems.","PeriodicalId":48504,"journal":{"name":"Phytobiomes Journal","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-10-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135728645","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-10-19DOI: 10.1094/pbiomes-06-23-0050-r
Hsiao-Han Lin, Marta Torres, Catharine A. Adams, Peter F. Andeer, Trenton K. Owens, Kateryna Zhalnina, Lauren K. Jabusch, Hans K. Carlson, Jennifer Kuehl, Adam M. Deutschbauer, Trent Northen, N. Louise Glass, Jenny C. Mortimer
Studying plant-microbe-soil interactions is challenging due to their high complexity and variability in natural ecosystems. While fabricated ecosystems provide opportunities to recapitulate aspects of these systems in reduced complexity and controlled environments, inoculation can be a significant source of variation. To tackle this, we evaluated how different bacteria inoculation practices and plant harvesting time points affect the reproducibility of a microbial synthetic community (SynCom) in association with the model grass Brachypodium distachyon. We tested three microbial inoculation practices: seed inoculation, transplant inoculation, and seedling inoculation; and two harvesting points: early (14-day-old plants) and late (21 days post-inoculation). We grew our plants and bacterial strains in sterile devices (EcoFABs) and characterized the microbial community from root, rhizosphere, and sand using 16S ribosomal RNA gene sequencing. The results showed that inoculation practices significantly affected the rhizosphere microbial community only when harvesting at an early time point but not at the late stage. As the SynCom showed a persistent association with B. distachyon at 21 days post-inoculation regardless of inoculation practices, we assessed the reproducibility of each inoculation method and found that transplant inoculation showed the highest reproducibility. Moreover, plant biomass was not adversely affected by transplant inoculation treatment. We concluded that bacteria inoculation while transplanting coupled with a later harvesting time point gives the most reproducible microbial community in the EcoFAB-B. distachyon-SynCom fabricated ecosystem and recommend this method as a standardized protocol for use with fabricated ecosystem experimental systems.
{"title":"Impact of inoculation practices on microbiota assembly and community stability in a fabricated ecosystem","authors":"Hsiao-Han Lin, Marta Torres, Catharine A. Adams, Peter F. Andeer, Trenton K. Owens, Kateryna Zhalnina, Lauren K. Jabusch, Hans K. Carlson, Jennifer Kuehl, Adam M. Deutschbauer, Trent Northen, N. Louise Glass, Jenny C. Mortimer","doi":"10.1094/pbiomes-06-23-0050-r","DOIUrl":"https://doi.org/10.1094/pbiomes-06-23-0050-r","url":null,"abstract":"Studying plant-microbe-soil interactions is challenging due to their high complexity and variability in natural ecosystems. While fabricated ecosystems provide opportunities to recapitulate aspects of these systems in reduced complexity and controlled environments, inoculation can be a significant source of variation. To tackle this, we evaluated how different bacteria inoculation practices and plant harvesting time points affect the reproducibility of a microbial synthetic community (SynCom) in association with the model grass Brachypodium distachyon. We tested three microbial inoculation practices: seed inoculation, transplant inoculation, and seedling inoculation; and two harvesting points: early (14-day-old plants) and late (21 days post-inoculation). We grew our plants and bacterial strains in sterile devices (EcoFABs) and characterized the microbial community from root, rhizosphere, and sand using 16S ribosomal RNA gene sequencing. The results showed that inoculation practices significantly affected the rhizosphere microbial community only when harvesting at an early time point but not at the late stage. As the SynCom showed a persistent association with B. distachyon at 21 days post-inoculation regardless of inoculation practices, we assessed the reproducibility of each inoculation method and found that transplant inoculation showed the highest reproducibility. Moreover, plant biomass was not adversely affected by transplant inoculation treatment. We concluded that bacteria inoculation while transplanting coupled with a later harvesting time point gives the most reproducible microbial community in the EcoFAB-B. distachyon-SynCom fabricated ecosystem and recommend this method as a standardized protocol for use with fabricated ecosystem experimental systems.","PeriodicalId":48504,"journal":{"name":"Phytobiomes Journal","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-10-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135729516","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-10-09DOI: 10.1094/pbiomes-05-23-0033-r
Tessa M. Shates, Marco Gebiola, Penglin Sun, Amani Helo, Oaksoe Aung, Jaimie Kenney, Carolyn Malmstrom, Kerry E. Mauck
Plant viruses are ubiquitous throughout plant communities, but research on viral impacts largely focuses on crops. Little is known about how viruses influence wild plants in their native habitats. To address this gap, we examined virus interactions with wild drought-tolerant perennials in California desert natural areas encroached upon by agriculture. We used metagenomics, targeted diagnostics, and phylogenetics to assess virus diversity and clade relationships, and experiments to investigate viral influence on hosts. We focused on three herbaceous perennials (Cucurbita foetidissima, Cucurbita palmata, and Datura wrightii) and tested the hypothesis that these wild species accumulate virus infections typically found in crops and transmitted by polyphagous insects. We predicted that such infections might be retained across seasons and potentially impair plant performance. Virome profiling revealed a rich community of previously-characterized virus species (12 total), with virus community structure varying by site and host species. The dominant viruses in the wild hosts were non-native crop pathogens, including cucurbit aphid-borne yellows virus (CABYV) and cucurbit yellow stunting disorder virus (CYSDV). Targeted testing revealed that CABYV infected as many as 88% of sampled wild Cucurbita individuals, with dual CABYV-CYSDV infections common in natural areas adjacent to desert agriculture. CABYV infections reduced shoot and root production in greenhouse experiments with the two wild Cucurbita species. Phylogenetic analyses suggest that CABYV was introduced to California multiple times from other continents. Our findings provide concerning evidence of ways in which human activities can alter virus pressure on wild plants and potentially contribute to plant decline.
{"title":"Non-native plant viruses prevalent in remnant natural plant communities harm native perennial hosts","authors":"Tessa M. Shates, Marco Gebiola, Penglin Sun, Amani Helo, Oaksoe Aung, Jaimie Kenney, Carolyn Malmstrom, Kerry E. Mauck","doi":"10.1094/pbiomes-05-23-0033-r","DOIUrl":"https://doi.org/10.1094/pbiomes-05-23-0033-r","url":null,"abstract":"Plant viruses are ubiquitous throughout plant communities, but research on viral impacts largely focuses on crops. Little is known about how viruses influence wild plants in their native habitats. To address this gap, we examined virus interactions with wild drought-tolerant perennials in California desert natural areas encroached upon by agriculture. We used metagenomics, targeted diagnostics, and phylogenetics to assess virus diversity and clade relationships, and experiments to investigate viral influence on hosts. We focused on three herbaceous perennials (Cucurbita foetidissima, Cucurbita palmata, and Datura wrightii) and tested the hypothesis that these wild species accumulate virus infections typically found in crops and transmitted by polyphagous insects. We predicted that such infections might be retained across seasons and potentially impair plant performance. Virome profiling revealed a rich community of previously-characterized virus species (12 total), with virus community structure varying by site and host species. The dominant viruses in the wild hosts were non-native crop pathogens, including cucurbit aphid-borne yellows virus (CABYV) and cucurbit yellow stunting disorder virus (CYSDV). Targeted testing revealed that CABYV infected as many as 88% of sampled wild Cucurbita individuals, with dual CABYV-CYSDV infections common in natural areas adjacent to desert agriculture. CABYV infections reduced shoot and root production in greenhouse experiments with the two wild Cucurbita species. Phylogenetic analyses suggest that CABYV was introduced to California multiple times from other continents. Our findings provide concerning evidence of ways in which human activities can alter virus pressure on wild plants and potentially contribute to plant decline.","PeriodicalId":48504,"journal":{"name":"Phytobiomes Journal","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135094768","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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