Phytobiomes Journal最新文献

The Tomato’s Tale: Exploring taxonomy, biogeography, domestication and microbiome for enhanced resilience 番茄的故事：探索分类学、生物地理学、驯化和微生物组以增强复原力

IF 4.4 3区生物学

Phytobiomes Journal Pub Date : 2023-12-11 DOI: 10.1094/pbiomes-09-23-0091-mf

Stalin W. Sarango Flores, Viviane Cordovez, B. Oyserman, N. Stopnisek, J. Raaijmakers, Pieter Van 't Hof

{"title":"The Tomato’s Tale: Exploring taxonomy, biogeography, domestication and microbiome for enhanced resilience","authors":"Stalin W. Sarango Flores, Viviane Cordovez, B. Oyserman, N. Stopnisek, J. Raaijmakers, Pieter Van 't Hof","doi":"10.1094/pbiomes-09-23-0091-mf","DOIUrl":"https://doi.org/10.1094/pbiomes-09-23-0091-mf","url":null,"abstract":"Plant domestication and breeding not only resulted in multiple phenotypic changes, but also impacted agricultural ecosystems where our current crops are cultivated. Most crops to date rely on the extensive use of fertilizers and pesticides to support crop growth and health. To minimize the environmental impact of these management practices, the plant microbiome got renewed attention as a large, yet untapped resource of microorganisms with beneficial effects on plant growth and health. In the past decade, it has become evident that the microbiome of plants plays a key role in nutrient acquisition, plant development and tolerance to diverse abiotic and biotic stresses. Here we review past and present knowledge of the microbiome of tomato as a model for unraveling the functional potential of plant microbiomes, the impact of domestication and the underlying genetics of microbiome assembly and activity. We also provide perspectives on how this knowledge can be adopted to enhance crop productivity and strengthen the sustainability of agricultural management practices.","PeriodicalId":48504,"journal":{"name":"Phytobiomes Journal","volume":"53 8","pages":""},"PeriodicalIF":4.4,"publicationDate":"2023-12-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139010418","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}

引用次数: 0

Disentangling shifts in the soil microbiome of potatoes infected with Rhizoctonia solani AG 3-PT in search of potential biocontrol agents 厘清感染根瘤菌 AG 3-PT 的马铃薯土壤微生物组的变化，寻找潜在的生物控制剂

IF 4.4 3区生物学

Phytobiomes Journal Pub Date : 2023-12-01 DOI: 10.1094/pbiomes-06-23-0046-r

Sasha-Lee Gush, Pedro Lebre, T. A. Coutinho, Donald Arthur Cowan, J. E. van der Waals

{"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":" 22","pages":""},"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}

引用次数: 0

Linnemannia elongata: a key species in chitin-based plant growth promotion Linnemannia elongata：以几丁质为基础促进植物生长的关键物种

IF 4.4 3区生物学

Phytobiomes Journal Pub Date : 2023-11-28 DOI: 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

{"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":"1 1","pages":""},"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}

引用次数: 0

High diversity of Curtobacterium flaccumfaciens in poinsettia and detection of three pathogenicity plasmids for identification of C. f. pv. poinsettiae 一品红中 Curtobacterium flaccumfaciens 的高度多样性和用于鉴定 C. f. pv. poinsettiae 的三个致病性质粒的检测

IF 4.4 3区生物学

Phytobiomes Journal Pub Date : 2023-11-21 DOI: 10.1094/pbiomes-10-23-0104-r

A. Bultreys, I. Gheysen

{"title":"High diversity of Curtobacterium flaccumfaciens in poinsettia and detection of three pathogenicity plasmids for identification of C. f. pv. poinsettiae","authors":"A. Bultreys, I. Gheysen","doi":"10.1094/pbiomes-10-23-0104-r","DOIUrl":"https://doi.org/10.1094/pbiomes-10-23-0104-r","url":null,"abstract":"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.","PeriodicalId":48504,"journal":{"name":"Phytobiomes Journal","volume":"2 1 1","pages":""},"PeriodicalIF":4.4,"publicationDate":"2023-11-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139251636","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}

引用次数: 0

Deciphering the key players within the bacterial microbiota associated with aerial crown gall tumors on rhododendron: Insights into the gallobiome 破译与杜鹃花气冠瘿瘤相关的细菌微生物群中的关键角色：洞察瘿生物群

IF 4.4 3区生物学

Phytobiomes Journal Pub Date : 2023-11-17 DOI: 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

{"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":"78 1","pages":""},"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}

引用次数: 0

Biocontrol agents establishment and their impact on rhizosphere microbiome and induced grapevine defenses is highly soil-dependent 生物防治剂的建立及其对根际微生物群和诱导葡萄植株防御的影响是高度依赖土壤的

3区生物学

Phytobiomes Journal Pub Date : 2023-11-07 DOI: 10.1094/pbiomes-08-23-0077-r

Catarina Leal, Ales Eichmeier, Katerina Stuskova, Josep Armengol, Rebeca Bujanda, Florence Fontaine, Patricia Trotel-Aziz, David Gramaje

{"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":"323 2","pages":"0"},"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}

引用次数: 0

Host identity determines the bacterial and fungal community and network structures in the phyllosphere of plant species in a temperate steppe 寄主身份决定了温带草原植物种层圈内的细菌和真菌群落及网络结构

3区生物学

Phytobiomes Journal Pub Date : 2023-10-23 DOI: 10.1094/pbiomes-05-23-0038-r

Chunyan Guo, An Yang, Wen-Hao Zhang

{"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":"11 1","pages":"0"},"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}

引用次数: 0

Rapid restructuring of rhizosphere and endospheric fungal communities with drought in multiple lines of domesticated sunflower 多系驯化向日葵根际和内层真菌群落在干旱条件下的快速重组

3区生物学

Phytobiomes Journal Pub Date : 2023-10-19 DOI: 10.1094/pbiomes-06-23-0049-r

Shawn Brown, Jennifer Mandel

{"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":"1 1","pages":"0"},"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}

引用次数: 0

Potato soil core microbiomes are regionally variable across the continental US 马铃薯土壤核心微生物群在美国大陆是区域可变的

3区生物学

Phytobiomes Journal Pub Date : 2023-10-19 DOI: 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

{"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":"24 1","pages":"0"},"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}

引用次数: 0

Impact of inoculation practices on microbiota assembly and community stability in a fabricated ecosystem 接种措施对人工生态系统中微生物群聚集和群落稳定性的影响

3区生物学

Phytobiomes Journal Pub Date : 2023-10-19 DOI: 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

{"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":"30 1","pages":"0"},"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}

引用次数: 0