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Lee SY, Roh E, Kim SG, Kong HG. Competition for nutrient niches within the apple blossom microbiota antagonizes the initiation of fire blight infection. THE NEW PHYTOLOGIST 2024. [PMID: 39031531 DOI: 10.1111/nph.19971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Accepted: 06/26/2024] [Indexed: 07/22/2024]
Abstract
Changes in the plant microbiota composition are intimately associated with the health of the plant, but factors controlling the microbial community in flowers are poorly understood. In this study, we used apple flowers and fire blight as a model system to investigate the effects of floral microbiota and microbial competition on disease development and suppression. To compare changes in microbial flora with the RNA expression patterns of plants, the flower samples were collected in three different flowering stages (Bud, Popcorn, and Full-bloom). Using advanced sequencing technology, we analyzed the data and conducted both in vitro and in vivo experiments to validate our findings. Our results show that the Erwinia amylovora use arabinogalactan, which is secreted on the flowers, for early colonization of apple flowers. Pantoea agglomerans was more competitive for arabinogalactan than E. amylovora. Additionally, P. agglomerans suppressed the expression of virulence factors of E. amylovora by using arabinose, which is a major component of arabinogalactan, which induces virulence gene expression. The present data provide new insights into developing control strategies for diverse plant diseases, including fire blight, by highlighting the importance of nutrients in disease development or suppression.
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Affiliation(s)
- Seung Yeup Lee
- Crop Protection Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju-gun, 55365, Korea
| | - Eunjung Roh
- Crop Protection Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju-gun, 55365, Korea
| | - Sang Guen Kim
- Department of Biological Sciences, Kyonggi University, Suwon-si, 16227, Korea
| | - Hyun Gi Kong
- Crop Protection Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju-gun, 55365, Korea
- College of Agriculture, Life and Environment Sciences, Chungbuk National University, Cheongju-si, 28644, Korea
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2
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Jorquera MA, Acuña JJ, Huerta N, Bai J, Zhang L, Xiao R, Sadowsky MJ. Multiple antibiotic resistance and herbicide catabolic profiles of bacteria isolated from Lake Villarrica surface sediments (Chile). ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 358:124538. [PMID: 39002747 DOI: 10.1016/j.envpol.2024.124538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 07/09/2024] [Accepted: 07/10/2024] [Indexed: 07/15/2024]
Abstract
Antibiotics and herbicides are contaminants of emerging concern in aquatic environments. Lake Villarrica is a relevant freshwater body in Chile and was recently designated a 'saturated nutrient zone'. Here, we investigated the occurrence of multiple antibiotic resistance (MAR) and herbicide catabolic profiles among bacteria present in the surface sediments of Lake Villarrica. The occurrence of antibiotic-resistant genes (ARGs; blaTEM, catA and tetM) and herbicide-catabolic genes (HCGs; phnJ and atzA) was investigated by qPCR. Subsequently, the presence of culturable bacteria with multiple resistance to amoxicillin (AMX), chloramphenicol (CHL) and oxytetracycline (OXT) was studied. Forty-six culturable MAR (AMX + CHL + OXT) strains were isolated and characterized with respect to their resistance to 11 antibiotics by using a disc diffusion assay and testing their ability to use herbicides as a nutrient source. qPCR analyses revealed that ARGs and HCGs were present in all sediment samples (101 to 103 gene copies g-1), with significant (P ≤ 0.05) higher values in sites near Villarrica city and cattle pastures. The plate method was used to recover MAR isolates from sediment (103-106 CFU g-1), and most of the 46 isolates also showed resistance to oxacillin (100%), cefotaxime (83%), erythromycin (96%) and vancomycin (93%). Additionally, 54 and 57% of the MAR isolates were able to grow on agar supplemented (50 mg L-1) with atrazine and glyphosate as nutrient sources, respectively. Most of the MAR isolates were taxonomically close to Pseudomonas (76.1%) and Pantoea (17.4%), particularly those isolated from urbanized sites (Pucón city). This study shows the presence of MAR bacteria with herbicide catabolic activity in sediments, which is valuable for conservation strategies and risk assessments of Lake Villarrica. However, major integrative studies on sediments as reservoirs or on the fate of MAR strains and traces of antibiotics and herbicides as a result of anthropic pressure are still needed.
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Affiliation(s)
- Milko A Jorquera
- Laboratorio de Ecología Microbiana Aplicada (EMALAB), Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Temuco, Chile; Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Ave. Francisco Salazar, 01145, Temuco, Chile.
| | - Jacquelinne J Acuña
- Laboratorio de Ecología Microbiana Aplicada (EMALAB), Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Temuco, Chile; Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Ave. Francisco Salazar, 01145, Temuco, Chile; Millennium Institute Center for Genome Regulation (MI-CGR), Valenzuela Puelma 10207, La Reina, 7800003, Chile
| | - Nicole Huerta
- Laboratorio de Ecología Microbiana Aplicada (EMALAB), Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Temuco, Chile
| | - Junhong Bai
- School of Environment, Beijing Normal University, 19, Xinjiekouwaida Street, Haidian District, Beijing, 100875, China
| | - Ling Zhang
- School of Environment, Beijing Normal University, 19, Xinjiekouwaida Street, Haidian District, Beijing, 100875, China
| | - Rong Xiao
- College of Environment & Safety Engineering, FuZhou University, Fuzhou, China
| | - Michael J Sadowsky
- College of Agriculture, Food, and Environmental Sciences, University of Minnesota, St. Paul, Minnesota, 55108, USA
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3
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Sivaprakasam N, Vaithiyanathan S, Gandhi K, Narayanan S, Kavitha PS, Rajasekaran R, Muthurajan R. Metagenomics approaches in unveiling the dynamics of Plant Growth-Promoting Microorganisms (PGPM) vis-à-vis Phytophthora sp. suppression in various crop ecological systems. Res Microbiol 2024:104217. [PMID: 38857835 DOI: 10.1016/j.resmic.2024.104217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 05/02/2024] [Accepted: 06/04/2024] [Indexed: 06/12/2024]
Abstract
Phytophthora species are destructive pathogens causing yield losses in different ecological systems, such as potato, black pepper, pepper, avocado, citrus, and tobacco. The diversity of plant growth-promoting microorganisms (PGPM) plays a crucial role in disease suppression. Knowledge of metagenomics approaches is essential for assessing the dynamics of PGPM and Phytophthora species across various ecosystems, facilitating effective management strategies for better crop protection. This review discusses the dynamic interplay between PGPM and Phytophthora sp. using metagenomics approaches that sheds light on the potential of PGPM strains tailored to specific crop ecosystems to bolster pathogen suppressiveness.
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Affiliation(s)
- Navarasu Sivaprakasam
- Department of Plant Pathology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | | | - Karthikeyan Gandhi
- Department of Plant Pathology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | - Swarnakumari Narayanan
- Department of Nematology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | - P S Kavitha
- School of Post Graduate Studies, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | - Raghu Rajasekaran
- Centre for Plant Molecular Biology & Biotechnology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | - Raveendran Muthurajan
- Centre for Plant Molecular Biology & Biotechnology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
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4
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Hassani MA, Cui Z, LaReau J, Huntley RB, Steven B, Zeng Q. Inter-species interactions between two bacterial flower commensals and a floral pathogen reduce disease incidence and alter pathogen activity. mBio 2024; 15:e0021324. [PMID: 38376185 PMCID: PMC10936193 DOI: 10.1128/mbio.00213-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Accepted: 01/30/2024] [Indexed: 02/21/2024] Open
Abstract
Flowers are colonized by a diverse community of microorganisms that can alter plant health and interact with floral pathogens. Erwinia amylovora is a flower-inhabiting bacterium and a pathogen that infects different plant species, including Malus × domestica (apple). Previously, we showed that the co-inoculation of two bacterial strains, members of the genera Pseudomonas and Pantoea, isolated from apple flowers, reduced disease incidence caused by this floral pathogen. Here, we decipher the ecological interactions between the two flower-associated bacteria and E. amylovora in field experimentation and in vitro co-cultures. The two flower commensal strains did not competitively exclude E. amylovora from the stigma habitat, as both bacteria and the pathogen co-existed on the stigma of apple flowers and in vitro. This suggests that plant protection might be mediated by other mechanisms than competitive niche exclusion. Using a synthetic stigma exudation medium, ternary co-culture of the bacterial strains led to a substantial alteration of gene expression in both the pathogen and the two microbiota members. Importantly, the gene expression profiles for the ternary co-culture were not just additive from binary co-cultures, suggesting that some functions only emerged in multipartite co-culture. Additionally, the ternary co-culture of the strains resulted in a stronger acidification of the growth milieu than mono- or binary co-cultures, pointing to another emergent property of co-inoculation. Our study emphasizes the critical role of emergent properties mediated by inter-species interactions within the plant holobiont and their potential impact on plant health and pathogen behavior. IMPORTANCE Fire blight, caused by Erwinia amylovora, is one of the most important plant diseases of pome fruits. Previous work largely suggested plant microbiota commensals suppressed disease by antagonizing pathogen growth. However, inter-species interactions of multiple flower commensals and their influence on pathogen activity and behavior have not been well studied. Here, we show that co-inoculating two bacterial strains that naturally colonize the apple flowers reduces disease incidence. We further demonstrate that the interactions between these two microbiota commensals and the floral pathogen led to the emergence of new gene expression patterns and a strong alteration of the external pH, factors that may modify the pathogen's behavior. Our findings emphasize the critical role of emergent properties mediated by inter-species interactions between plant microbiota and plant pathogens and their impact on plant health.
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Affiliation(s)
- M. Amine Hassani
- Department of Plant Pathology and Ecology, The Connecticut Agricultural Experiment Station, New Haven, Connecticut, USA
| | - Zhouqi Cui
- Department of Plant Pathology and Ecology, The Connecticut Agricultural Experiment Station, New Haven, Connecticut, USA
| | - Jacquelyn LaReau
- Department of Environmental Science and Forestry, The Connecticut Agricultural Experiment Station, New Haven, Connecticut, USA
| | - Regan B. Huntley
- Department of Plant Pathology and Ecology, The Connecticut Agricultural Experiment Station, New Haven, Connecticut, USA
| | - Blaire Steven
- Department of Environmental Science and Forestry, The Connecticut Agricultural Experiment Station, New Haven, Connecticut, USA
| | - Quan Zeng
- Department of Plant Pathology and Ecology, The Connecticut Agricultural Experiment Station, New Haven, Connecticut, USA
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5
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Rering CC, Rudolph AB, Li QB, Read QD, Muñoz PR, Ternest JJ, Hunter CT. A quantitative survey of the blueberry (Vaccinium spp.) culturable nectar microbiome: variation between cultivars, locations, and farm management approaches. FEMS Microbiol Ecol 2024; 100:fiae020. [PMID: 38366934 PMCID: PMC10903978 DOI: 10.1093/femsec/fiae020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 01/25/2024] [Accepted: 02/15/2024] [Indexed: 02/19/2024] Open
Abstract
Microbes in floral nectar can impact both their host plants and floral visitors, yet little is known about the nectar microbiome of most pollinator-dependent crops. In this study, we examined the abundance and composition of the fungi and bacteria inhabiting Vaccinium spp. nectar, as well as nectar volume and sugar concentrations. We compared wild V. myrsinites with two field-grown V. corymbosum cultivars collected from two organic and two conventional farms. Differences in nectar traits and microbiomes were identified between V. corymbosum cultivars but not Vaccinium species. The microbiome of cultivated plants also varied greatly between farms, whereas management regime had only subtle effects, with higher fungal populations detected under organic management. Nectars were hexose-dominant, and high cell densities were correlated with reduced nectar sugar concentrations. Bacteria were more common than fungi in blueberry nectar, although both were frequently detected and co-occurred more often than would be predicted by chance. "Cosmopolitan" blueberry nectar microbes that were isolated in all plants, including Rosenbergiella sp. and Symmetrospora symmetrica, were identified. This study provides the first systematic report of the blueberry nectar microbiome, which may have important implications for pollinator and crop health.
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Affiliation(s)
- Caitlin C Rering
- Chemistry Research Unit, Center for Medical, Agricultural and Veterinary Entomology, Agricultural Research Service, United States Department of Agriculture, 1700 SW 23rd Dr, Gainesville, FL 32608, United States
| | - Arthur B Rudolph
- Chemistry Research Unit, Center for Medical, Agricultural and Veterinary Entomology, Agricultural Research Service, United States Department of Agriculture, 1700 SW 23rd Dr, Gainesville, FL 32608, United States
| | - Qin-Bao Li
- Chemistry Research Unit, Center for Medical, Agricultural and Veterinary Entomology, Agricultural Research Service, United States Department of Agriculture, 1700 SW 23rd Dr, Gainesville, FL 32608, United States
| | - Quentin D Read
- Agricultural Research Service, Southeast Area, United States Department of Agriculture, 840 Oval Drive, Raleigh, NC 27606, United States
| | - Patricio R Muñoz
- Horticultural Sciences Department, University of Florida, 2550 Hull Rd, Gainesville, FL 32611, United States
| | - John J Ternest
- Department of Entomology and Nematology, University of Florida, 1881 Natural Area Dr, Gainesville, FL 32611, United States
| | - Charles T Hunter
- Chemistry Research Unit, Center for Medical, Agricultural and Veterinary Entomology, Agricultural Research Service, United States Department of Agriculture, 1700 SW 23rd Dr, Gainesville, FL 32608, United States
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Blakney AJC, St-Arnaud M, Hijri M. Does soil history decline in influencing the structure of bacterial communities of Brassica napus host plants across different growth stages? ISME COMMUNICATIONS 2024; 4:ycae019. [PMID: 38500702 PMCID: PMC10944699 DOI: 10.1093/ismeco/ycae019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 01/24/2024] [Accepted: 01/29/2024] [Indexed: 03/20/2024]
Abstract
Soil history has been shown to condition future rhizosphere microbial communities. However, previous experiments have also illustrated that mature, adult plants can "re-write," or mask, different soil histories through host plant-soil community feedbacks. This leaves a knowledge gap concerning how soil history influences bacterial community structure across different growth stages. Thus, here we tested the hypothesis that previously established soil histories will decrease in influencing the structure of Brassica napus bacterial communities over the growing season. We used an on-going agricultural field experiment to establish three different soil histories, plots of monocrop canola (B. napus), or rotations of wheat-canola, or pea-barley-canola. During the following season, we repeatedly sampled the surrounding bulk soil, rhizosphere, and roots of the B. napus hosts at different growth stages-the initial seeding conditions, seedling, rosette, bolting, and flower-from all three soil history plots. We compared composition and diversity of the B. napus soil bacterial communities, as estimated using 16S rRNA gene metabarcoding, to identify any changes associated with soil history and growth stages. We found that soil history remained significant across each growth stage in structuring the bacterial bulk soil and rhizosphere communities, but not the bacterial root communities. This suggests that the host plant's capacity to "re-write" different soil histories may be quite limited as key components that constitute the soil history's identity remain present, such that the previously established soil history continues to impact the bacterial rhizosphere communities, but not the root communities. For agriculture, this highlights how previously established soil histories persist and may have important long-term consequences on future plant-microbe communities, including bacteria.
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Affiliation(s)
- Andrew J C Blakney
- Institut de recherche en biologie végétale, Département de Sciences Biologiques, Université de Montréal and Jardin botanique de Montréal, Montréal, Québec, H1X 2B2, Canada
- Present address: Department of Physical and Environmental Sciences, University of Toronto, Scarborough, Ontario, M1C 1A4, Canada
| | - Marc St-Arnaud
- Institut de recherche en biologie végétale, Département de Sciences Biologiques, Université de Montréal and Jardin botanique de Montréal, Montréal, Québec, H1X 2B2, Canada
| | - Mohamed Hijri
- Institut de recherche en biologie végétale, Département de Sciences Biologiques, Université de Montréal and Jardin botanique de Montréal, Montréal, Québec, H1X 2B2, Canada
- African Genome Center, Mohammed VI Polytechnic University (UM6P), Lot 660, Hay Moulay Rachid, Ben Guerir 43150, Morocco
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Ruraż K, Przemieniecki SW, Błaszak M, Czarnomska SD, Ochmian I, Piwowarczyk R. Stigmas of holoparasitic Phelipanche arenaria (Orobanchaceae) - a suitable ephemeric flower habitat for development unique microbiome. BMC PLANT BIOLOGY 2023; 23:486. [PMID: 37821804 PMCID: PMC10566107 DOI: 10.1186/s12870-023-04488-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 09/26/2023] [Indexed: 10/13/2023]
Abstract
BACKGROUND Microbial communities have occasionally been observed in part of the ephemeric reproductive structure of floral stigmas, but their prevalence, phylogenetic diversity and ecological roles are understudied. This report describes the first study of bacterial and fungal communities in immature and mature stigma tissue of the endangered holoparasitic plant Phelipanche arenaria. Culture-dependent methods coupled with next-generation sequencing indicated that a small surface of the flower stigma was an unexpectedly rich and diverse microhabitat for colonization of microbial. We also compared the enzymatic activity of the bacterial communities between immature and mature stigmas samples. RESULTS Using high-throughput sequencing methods, we identified and classified 39 to over 51 OTUs per sample for bacterial OTUs represented by Pantoea agglomerans and P. ananatis, comprising 50.6%, followed by Pseudomonas, Luteibacter spp., Sphingomonas spp. with 17% of total frequency. The bacterial profile of immature stigmas of P. arenaria contained unique microorganisms (21 of the most numerous OTUs) that were not confirmed in mature stigmas. However, the enzymatic activity of bacteria in mature stigmas of P. arenaria showed more activity than observed in immature stigmas. In the fungal profile, we recorded even 80 OTUs in mature stigmas, consisting of Capnodiales 45.03% of the total abundance with 28.27% of frequency was created by Alternaria eichhorniae (10.55%), Mycosphaerella tassiana (9.69%), and Aureobasidium pullulans (8.03%). Additionally, numerous putative plant growth-promoting bacteria, fungal pathogens and pathogen-antagonistic yeasts were also detected. CONCLUSIONS Our study uncovered that P. arenaria stigmas host diverse bacterial and fungal communities. These microorganisms are well known and have been described as beneficial for biotechnological and environmental applications (e.g., production of different enzymes and antimicrobial compounds). This research provided valuable insight into the parasitic plant-microbe interactions.
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Affiliation(s)
- Karolina Ruraż
- Center for Research and Conservation of Biodiversity, Department of Environmental Biology, Institute of Biology, Jan Kochanowski University, Uniwersytecka 7, 25-406, Kielce, Poland
| | - Sebastian Wojciech Przemieniecki
- Department of Entomology, Phytopathology and Molecular Diagnostics, University of Warmia and Mazury in Olsztyn, Prawocheńskiego 17, 10-720 Olsztyn, Poland
| | - Magdalena Błaszak
- Department of Bioengineering, West Pomeranian University of Technology in Szczecin, Słowackiego 17, 71-434 Szczecin, Poland
| | - Sylwia Dagmara Czarnomska
- Museum and Institute of Zoology, Polish Academy of Sciences, Nadwiślańska 108, 80-680 Gdańsk, Poland
| | - Ireneusz Ochmian
- Department of Horticulture, West Pomeranian University of Technology in Szczecin, Słowackiego 17, 71-434 Szczecin, Poland
| | - Renata Piwowarczyk
- Center for Research and Conservation of Biodiversity, Department of Environmental Biology, Institute of Biology, Jan Kochanowski University, Uniwersytecka 7, 25-406, Kielce, Poland
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Campos MA, Zhang Q, Acuña JJ, Rilling JI, Ruiz T, Carrazana E, Reyno C, Hollenback A, Gray K, Jaisi DP, Ogram A, Bai J, Zhang L, Xiao R, Elias M, Sadowsky MJ, Hu J, Jorquera MA. Structure and Functional Properties of Bacterial Communities in Surface Sediments of the Recently Declared Nutrient-Saturated Lake Villarrica in Southern Chile. MICROBIAL ECOLOGY 2023; 86:1513-1533. [PMID: 36752910 DOI: 10.1007/s00248-023-02173-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 01/12/2023] [Indexed: 06/18/2023]
Abstract
Lake Villarrica, one of Chile's main freshwater water bodies, was recently declared a nutrient-saturated lake due to increased phosphorus (P) and nitrogen (N) levels. Although a decontamination plan based on environmental parameters is being established, it does not consider microbial parameters. Here, we conducted high-throughput DNA sequencing and quantitative polymerase chain reaction (qPCR) analyses to reveal the structure and functional properties of bacterial communities in surface sediments collected from sites with contrasting anthropogenic pressures in Lake Villarrica. Alpha diversity revealed an elevated bacterial richness and diversity in the more anthropogenized sediments. The phylum Proteobacteria, Bacteroidetes, Acidobacteria, and Actinobacteria dominated the community. The principal coordinate analysis (PCoA) and redundancy analysis (RDA) showed significant differences in bacterial communities of sampling sites. Predicted functional analysis showed that N cycling functions (e.g., nitrification and denitrification) were significant. The microbial co-occurrence networks analysis suggested Chitinophagaceae, Caldilineaceae, Planctomycetaceae, and Phycisphaerae families as keystone taxa. Bacterial functional genes related to P (phoC, phoD, and phoX) and N (nifH and nosZ) cycling were detected in all samples by qPCR. In addition, an RDA related to N and P cycling revealed that physicochemical properties and functional genes were positively correlated with several nitrite-oxidizing, ammonia-oxidizing, and N-fixing bacterial genera. Finally, denitrifying gene (nosZ) was the most significant factor influencing the topological characteristics of co-occurrence networks and bacterial interactions. Our results represent one of a few approaches to elucidate the structure and role of bacterial communities in Chilean lake sediments, which might be helpful in conservation and decontamination plans.
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Affiliation(s)
- Marco A Campos
- Laboratorio de Ecología Microbiana Aplicada (EMALAB), Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Ave. Francisco Salazar, 01145, Temuco, Chile
- Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Ave. Francisco Salazar, 01145, Temuco, Chile
| | - Qian Zhang
- The BioTechnology Institute, University of Minnesota, 140 Gortner Lab, 1479 Gortner Ave., St Paul, MN, 55108-6106, USA
- Fujian Provincial Key Laboratory for Coastal Ecology and Environmental Studies, College of the Environment and Ecology, Xiamen University, Xiamen, 361100, People's Republic of China
| | - Jacquelinne J Acuña
- Laboratorio de Ecología Microbiana Aplicada (EMALAB), Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Ave. Francisco Salazar, 01145, Temuco, Chile
- Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Ave. Francisco Salazar, 01145, Temuco, Chile
| | - Joaquin I Rilling
- Laboratorio de Ecología Microbiana Aplicada (EMALAB), Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Ave. Francisco Salazar, 01145, Temuco, Chile
- Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Ave. Francisco Salazar, 01145, Temuco, Chile
| | - Tay Ruiz
- Laboratorio de Ecología Microbiana Aplicada (EMALAB), Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Ave. Francisco Salazar, 01145, Temuco, Chile
- Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Ave. Francisco Salazar, 01145, Temuco, Chile
- Doctorado en Ciencias de Recursos Naturales, Universidad de La Frontera, Ave. Francisco Salazar, 01145, Temuco, Chile
| | - Elizabeth Carrazana
- Laboratorio de Ecología Microbiana Aplicada (EMALAB), Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Ave. Francisco Salazar, 01145, Temuco, Chile
- Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Ave. Francisco Salazar, 01145, Temuco, Chile
- Doctorado en Ciencias mención Biología Celular y Molecular Aplicada, Universidad de La Frontera, Ave. Francisco Salazar, 01145, Temuco, Chile
| | - Cristóbal Reyno
- Laboratorio de Ecología Microbiana Aplicada (EMALAB), Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Ave. Francisco Salazar, 01145, Temuco, Chile
- Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Ave. Francisco Salazar, 01145, Temuco, Chile
- Doctorado en Ciencias mención Biología Celular y Molecular Aplicada, Universidad de La Frontera, Ave. Francisco Salazar, 01145, Temuco, Chile
| | - Anthony Hollenback
- Department of Plant and Soil Sciences, University of Delaware, Newark, DE, 19716, USA
| | - Katelyn Gray
- Department of Plant and Soil Sciences, University of Delaware, Newark, DE, 19716, USA
| | - Deb P Jaisi
- Department of Plant and Soil Sciences, University of Delaware, Newark, DE, 19716, USA
| | - Andrew Ogram
- Soil and Water Sciences Department, University of Florida, PO Box 110290, Gainesville, FL, 32608-32611, USA
| | - Junhong Bai
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, 100875, China
| | - Ling Zhang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, 100875, China
| | - Rong Xiao
- College of Environment and Safety Engineering, Fuzhou University, Fuzhou, 350108, China
| | - Mikael Elias
- The BioTechnology Institute, University of Minnesota, 140 Gortner Lab, 1479 Gortner Ave., St Paul, MN, 55108-6106, USA
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 140 Gortner Lab, 1479 Gortner Ave., St Paul, MN, 55108-6106, USA
| | - Michael J Sadowsky
- The BioTechnology Institute, University of Minnesota, 140 Gortner Lab, 1479 Gortner Ave., St Paul, MN, 55108-6106, USA
| | - Jingming Hu
- College of the Environment & Ecology, Xiamen University, Xiamen, 361100, People's Republic of China
| | - Milko A Jorquera
- Laboratorio de Ecología Microbiana Aplicada (EMALAB), Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Ave. Francisco Salazar, 01145, Temuco, Chile.
- Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Ave. Francisco Salazar, 01145, Temuco, Chile.
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9
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Ai D, Chen L, Xie J, Cheng L, Zhang F, Luan Y, Li Y, Hou S, Sun F, Xia LC. Identifying local associations in biological time series: algorithms, statistical significance, and applications. Brief Bioinform 2023; 24:bbad390. [PMID: 37930023 DOI: 10.1093/bib/bbad390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 08/21/2023] [Accepted: 09/14/2023] [Indexed: 11/07/2023] Open
Abstract
Local associations refer to spatial-temporal correlations that emerge from the biological realm, such as time-dependent gene co-expression or seasonal interactions between microbes. One can reveal the intricate dynamics and inherent interactions of biological systems by examining the biological time series data for these associations. To accomplish this goal, local similarity analysis algorithms and statistical methods that facilitate the local alignment of time series and assess the significance of the resulting alignments have been developed. Although these algorithms were initially devised for gene expression analysis from microarrays, they have been adapted and accelerated for multi-omics next generation sequencing datasets, achieving high scientific impact. In this review, we present an overview of the historical developments and recent advances for local similarity analysis algorithms, their statistical properties, and real applications in analyzing biological time series data. The benchmark data and analysis scripts used in this review are freely available at http://github.com/labxscut/lsareview.
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Affiliation(s)
- Dongmei Ai
- School of Mathematics and Physics, University of Science and Technology Beijing, Beijing 100083, China
| | - Lulu Chen
- School of Mathematics and Physics, University of Science and Technology Beijing, Beijing 100083, China
| | - Jiemin Xie
- Department of Statistics and Financial Mathematics, School of Mathematics, South China University of Technology, Guangzhou 510641, China
| | - Longwei Cheng
- School of Mathematics and Physics, University of Science and Technology Beijing, Beijing 100083, China
| | - Fang Zhang
- Shenwan Hongyuan Securities Co. Ltd., Shanghai 200031, China
| | - Yihui Luan
- School of Mathematics, Shandong University, Jinan 250100, China
| | - Yang Li
- Department of Statistics and Financial Mathematics, School of Mathematics, South China University of Technology, Guangzhou 510641, China
| | - Shengwei Hou
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Fengzhu Sun
- Department of Quantitative and Computational Biology, University of Southern California, California, 90007, USA
| | - Li Charlie Xia
- Department of Statistics and Financial Mathematics, School of Mathematics, South China University of Technology, Guangzhou 510641, China
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10
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Verhaegen M, Bergot T, Liebana E, Stancanelli G, Streissl F, Mingeot-Leclercq MP, Mahillon J, Bragard C. On the use of antibiotics to control plant pathogenic bacteria: a genetic and genomic perspective. Front Microbiol 2023; 14:1221478. [PMID: 37440885 PMCID: PMC10333595 DOI: 10.3389/fmicb.2023.1221478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 06/08/2023] [Indexed: 07/15/2023] Open
Abstract
Despite growing attention, antibiotics (such as streptomycin, oxytetracycline or kasugamycin) are still used worldwide for the control of major bacterial plant diseases. This raises concerns on their potential, yet unknown impact on antibiotic and multidrug resistances and the spread of their genetic determinants among bacterial pathogens. Antibiotic resistance genes (ARGs) have been identified in plant pathogenic bacteria (PPB), with streptomycin resistance genes being the most commonly reported. Therefore, the contribution of mobile genetic elements (MGEs) to their spread among PPB, as well as their ability to transfer to other bacteria, need to be further explored. The only well-documented example of ARGs vector in PPB, Tn5393 and its highly similar variants (carrying streptomycin resistance genes), is concerning because of its presence outside PPB, in Salmonella enterica and Klebsiella pneumoniae, two major human pathogens. Although its structure among PPB is still relatively simple, in human- and animal-associated bacteria, Tn5393 has evolved into complex associations with other MGEs and ARGs. This review sheds light on ARGs and MGEs associated with PPB, but also investigates the potential role of antibiotic use in resistance selection in plant-associated bacteria.
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Affiliation(s)
- Marie Verhaegen
- Laboratory of Food and Environmental Microbiology, Earth and Life Institute, Catholic University of Louvain (UCLouvain), Louvain-la-Neuve, Belgium
| | - Thomas Bergot
- Laboratory of Food and Environmental Microbiology, Earth and Life Institute, Catholic University of Louvain (UCLouvain), Louvain-la-Neuve, Belgium
| | | | | | | | - Marie-Paule Mingeot-Leclercq
- Cellular and Molecular Pharmacology Unit, Louvain Drug Research Institute, UCLouvain, Woluwe-Saint-Lambert, Belgium
| | - Jacques Mahillon
- Laboratory of Food and Environmental Microbiology, Earth and Life Institute, Catholic University of Louvain (UCLouvain), Louvain-la-Neuve, Belgium
| | - Claude Bragard
- Plant Health Laboratory, Earth and Life Institute, UCLouvain, Louvain-la-Neuve, Belgium
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11
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Han Y, Du J. A comparative study of the effect of bacteria and yeasts communities on inoculated and spontaneously fermented apple cider. Food Microbiol 2023; 111:104195. [PMID: 36681399 DOI: 10.1016/j.fm.2022.104195] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 10/26/2022] [Accepted: 11/24/2022] [Indexed: 11/27/2022]
Abstract
Understanding bacteria and yeasts communities can reduce unpredictable changes of apple cider. In this study, apple juice inoculated with Saccharomyces cerevisiae WET 136 and fermented spontaneously were compared, the relationships of bacteria, yeasts, organic acids, and volatiles were analyzed. Results showed that microbial diversity affected the fermentation, organic acids and volatiles in apple ciders. In the first four spontaneous fermentation days, LAB (lactic acid bacteria) multiplied and reached 7.89 lg CFU/mL, and then triggered malolactic fermentation (MLF), leading to malic acid decreased by 3880.52 mg/L and lactic acid increased by 4787.55 mg/L. The citric, succinic and fumaric acids content was 2171.14, 701.51 and 8.06 mg/L lower than that in inoculated cider, respectively. Although the yeasts multiplied during spontaneous fermentation, it did not reach 7.50 lg CFU/mL until the 5th day, which led to a long lag period, as well as later and lower production of acetaldehyde and higher alcohols. The inoculated yeast inhibited LAB, acetic acid bacteria, Rahnella, and non-Saccharomyces. Yeasts were the key to produce citric acid, acetaldehyde and 3-methyl-1-butanol in apple cider; while bacteria were closely related to the formation of lactic acid, acetic acid and ethyl acetate. It suggested that low higher alcohols and acetaldehyde can be realized by selecting yeasts, and Leuconostoc pseudomesenteroides can work as candidate to reduce L-malic and citric acids in apple cider.
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Affiliation(s)
- Yingying Han
- College of Food Science and Engineering, Shandong Agricultural University, Tai'an, 271018, China
| | - Jinhua Du
- College of Food Science and Engineering, Shandong Agricultural University, Tai'an, 271018, China.
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12
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Ruraż K, Przemieniecki SW, Piwowarczyk R. Interspecies and temporal dynamics of bacterial and fungal microbiomes of pistil stigmas in flowers in holoparasitic plants of the Orobanche series Alsaticae (Orobanchaceae). Sci Rep 2023; 13:6749. [PMID: 37185962 PMCID: PMC10130099 DOI: 10.1038/s41598-023-33676-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 04/17/2023] [Indexed: 05/17/2023] Open
Abstract
Little is known about the microbiomes of flower parts, and even less information is available regarding these microorganisms' colonization of specific niches in parasitic plants. We investigate the temporal interspecies dynamics of the parasitic plants microbiome of flower stigmas in two stages of development: immature stigmas in flower buds and mature stigmas in opened flowers. We compared two related holoparasitic Orobanche species from localities approximately 90 km apart and characterize their bacterial and fungal communities using 16S rRNA gene and ITS sequences, respectively. We identified from 127 to over 228 OTUs per sample for fungi, sequences belonging to genera: Aureobasidium, Cladosporium, Malassezia, Mycosphaerella, and Pleosporales, constituting approximately 53% of the community in total. In the bacterial profile, we recorded 40 to over 68 OTUs per sample consisting of Enterobacteriaceae, and genera Cellulosimicrobium, Pantoea, and Pseudomonas spp., with an approximately 75% frequency. In microbial communities, higher numbers of OTUs colonizing mature stigmas were recorded than in immature. This implies that the dynamics and concurrence of microbial communities were different between O. alsatica and O. bartlingii and underwent significant changes during flower development. To the best of our knowledge, is the first study of the interspecies and temporal dynamics of the bacterial and fungal microbiomes of pistil stigmas in flowers.
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Affiliation(s)
- Karolina Ruraż
- Center for Research and Conservation of Biodiversity, Department of Environmental Biology, Institute of Biology, Jan Kochanowski University, Uniwersytecka 7, 25-406, Kielce, Poland.
| | - Sebastian Wojciech Przemieniecki
- Department of Entomology, Phytopathology and Molecular Diagnostics, University of Warmia and Mazury in Olsztyn, Prawocheńskiego 17, 10-720, Olsztyn, Poland
| | - Renata Piwowarczyk
- Center for Research and Conservation of Biodiversity, Department of Environmental Biology, Institute of Biology, Jan Kochanowski University, Uniwersytecka 7, 25-406, Kielce, Poland
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13
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Kardish MR, Stachowicz JJ. Local environment drives rapid shifts in composition and phylogenetic clustering of seagrass microbiomes. Sci Rep 2023; 13:3673. [PMID: 36871071 PMCID: PMC9985655 DOI: 10.1038/s41598-023-30194-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 02/17/2023] [Indexed: 03/06/2023] Open
Abstract
Plant microbiomes depend on environmental conditions, stochasticity, host species, and genotype identity. Eelgrass (Zostera marina) is a unique system for plant-microbe interactions as a marine angiosperm growing in a physiologically-challenging environment with anoxic sediment, periodic exposure to air at low tide, and fluctuations in water clarity and flow. We tested the influence of host origin versus environment on eelgrass microbiome composition by transplanting 768 plants among four sites within Bodega Harbor, CA. Over three months following transplantation, we sampled microbial communities monthly on leaves and roots and sequenced the V4-V5 region of the 16S rRNA gene to assess community composition. The main driver of leaf and root microbiome composition was destination site; more modest effects of host origin site did not last longer than one month. Community phylogenetic analyses suggested that environmental filtering structures these communities, but the strength and nature of this filtering varies among sites and over time and roots and leaves show opposing gradients in clustering along a temperature gradient. We demonstrate that local environmental differences create rapid shifts in associated microbial community composition with potential functional implications for rapid host acclimation under shifting environmental conditions.
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Affiliation(s)
- Melissa R Kardish
- Department of Evolution and Ecology, University of California, One Shields Avenue, Davis, CA, 95616, USA. .,Center for Population Biology, University of California, One Shields Avenue, Davis, CA, 95616, USA.
| | - John J Stachowicz
- Department of Evolution and Ecology, University of California, One Shields Avenue, Davis, CA, 95616, USA.,Center for Population Biology, University of California, One Shields Avenue, Davis, CA, 95616, USA
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14
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Larrouy JL, Dhami MK, Jones EE, Ridgway HJ. Physiological stage drives fungal community dynamics and diversity in Leptospermum scoparium (mānuka) flowers. Environ Microbiol 2023; 25:766-771. [PMID: 36562630 DOI: 10.1111/1462-2920.16324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 12/20/2022] [Indexed: 12/24/2022]
Abstract
Flowers are an important niche for microbes, and microbes in turn influence plant fitness. As flower morphology and biology change rapidly over time, dynamic niches for microbes are formed and lost. Floral physiology at each life stage can therefore influence arrival, persistence and loss of microbial species; however, this remains little understood despite its potential consequences for host reproductive success. Through internal transcribed spacer 1 (ITS1) community profiling, we characterized the effect of transitioning through five floral stages of mānuka (Leptospermum scoparium), from immature bud to spent flower, and subsequent allocation to seed, on the flower-inhabiting fungal community. We found nectar-consuming yeasts from Aureobasidium and Vishniacozyma genera and functionally diverse filamentous fungi from the Cladosporium genus dominated the anthosphere. The candidate core microbiota persisted across this dynamic niche despite high microbial turnover, as observed in shifts in community composition and diversity as flowers matured and senesced. The results demonstrated that floral stages are strong drivers of anthosphere fungal community assembly and dynamics. This study represents the first detailed exploration of fungi through floral development, building on fundamental knowledge in microbial ecology of healthy flowers.
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Affiliation(s)
- Justine L Larrouy
- Department of Pest-management and Conservation, Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln, Christchurch, New Zealand
| | - Manpreet K Dhami
- Biocontrol & Molecular Ecology, Manaaki Whenua Landcare Research, Lincoln, New Zealand
| | - Eirian E Jones
- Department of Pest-management and Conservation, Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln, Christchurch, New Zealand
| | - Hayley J Ridgway
- Department of Pest-management and Conservation, Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln, Christchurch, New Zealand
- The New Zealand Institute for Plant and Food Research Limited, Lincoln, New Zealand
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15
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Colazza S, Peri E, Cusumano A. Chemical Ecology of Floral Resources in Conservation Biological Control. ANNUAL REVIEW OF ENTOMOLOGY 2023; 68:13-29. [PMID: 36130040 DOI: 10.1146/annurev-ento-120220-124357] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Conservation biological control aims to enhance populations of natural enemies of insect pests in crop habitats, typically by intentional provision of flowering plants as food resources. Ideally, these flowering plants should be inherently attractive to natural enemies to ensure that they are frequently visited. We review the chemical ecology of floral resources in a conservation biological control context, with a focus on insect parasitoids. We highlight the role of floral volatiles as semiochemicals that attract parasitoids to the food resources. The discovery that nectar-inhabiting microbes can be hidden players in mediating parasitoid responses to flowering plants has highlighted the complexity of the interactions between plants and parasitoids. Furthermore, because food webs in agroecosystems do not generally stop at the third trophic level, we also consider responses of hyperparasitoids to floral resources. We thus provide an overview of floral compounds as semiochemicals from a multitrophic perspective, and we focus on the remaining questions that need to be addressed to move the field forward.
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Affiliation(s)
- Stefano Colazza
- Department of Agricultural, Food, and Forest Sciences, University of Palermo, Palermo, Italy; , ,
| | - Ezio Peri
- Department of Agricultural, Food, and Forest Sciences, University of Palermo, Palermo, Italy; , ,
| | - Antonino Cusumano
- Department of Agricultural, Food, and Forest Sciences, University of Palermo, Palermo, Italy; , ,
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16
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Hietaranta E, Juottonen H, Kytöviita MM. Honeybees affect floral microbiome composition in a central food source for wild pollinators in boreal ecosystems. Oecologia 2023; 201:59-72. [PMID: 36434466 DOI: 10.1007/s00442-022-05285-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 11/07/2022] [Indexed: 11/26/2022]
Abstract
Basic knowledge on dispersal of microbes in pollinator networks is essential for plant, insect, and microbial ecology. Thorough understanding of the ecological consequences of honeybee farming on these complex plant-pollinator-microbe interactions is a prerequisite for sustainable honeybee keeping. Most research on plant-pollinator-microbe interactions have focused on temperate agricultural systems. Therefore, information on a wild plant that is a seasonal bottleneck for pollinators in cold climate such as Salix phylicifolia is of specific importance. We investigated how floral visitation by insects influences the community structure of bacteria and fungi in Salix phylicifolia inflorescences under natural conditions. Insect visitors were experimentally excluded with net bags. We analyzed the microbiome and measured pollen removal in open and bagged inflorescences in sites where honeybees were foraging and in sites without honeybees. Site and plant individual explained most of the variation in floral microbial communities. Insect visitation and honeybees had a smaller but significant effect on the community composition of microbes. Honeybees had a specific effect on the inflorescence microbiome and, e.g., increased the relative abundance of operational taxonomic units (OTUs) from the bacterial order Lactobacillales. Site had a significant effect on the amount of pollen removed from inflorescences but this was not due to honeybees. Insect visitors increased bacterial and especially fungal OTU richness in the inflorescences. Pollinator visits explained 38% variation in fungal richness, but only 10% in bacterial richness. Our work shows that honeybee farming affects the floral microbiome in a wild plant in rural boreal ecosystems.
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Affiliation(s)
- Elsi Hietaranta
- Department of Biological and Environmental Science, University of Jyväskylä, P.O. Box 35, 40014, Jyväskylä, Finland.
| | - Heli Juottonen
- Department of Biological and Environmental Science, University of Jyväskylä, P.O. Box 35, 40014, Jyväskylä, Finland
| | - Minna-Maarit Kytöviita
- Department of Biological and Environmental Science, University of Jyväskylä, P.O. Box 35, 40014, Jyväskylä, Finland
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17
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Tran HT, Nguyen HM, Nguyen TMH, Chang C, Huang WL, Huang CL, Chiang TY. Microbial Communities Along 2,3,7,8-tetrachlorodibenzodioxin Concentration Gradient in Soils Polluted with Agent Orange Based on Metagenomic Analyses. MICROBIAL ECOLOGY 2023; 85:197-208. [PMID: 35034142 DOI: 10.1007/s00248-021-01953-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 12/21/2021] [Indexed: 06/14/2023]
Abstract
The 2,3,7,8-tetrachlorodibenzodioxin (TCDD), a contaminant in Agent Orange released during the US-Vietnam War, led to a severe environmental crisis. Approximately, 50 years have passed since the end of this war, and vegetation has gradually recovered from the pollution. Soil bacterial communities were investigated by 16S metagenomics in habitats with different vegetation physiognomies in Central Vietnam, namely, forests (S0), barren land (S1), grassland (S2), and developing woods (S3). Vegetation complexity was negatively associated with TCDD concentrations, revealing the reasoning behind the utilization of vegetation physiognomy as an indicator for ecological succession along the gradient of pollutants. Stark changes in bacterial composition were detected between S0 and S1, with an increase in Firmicutes and a decrease in Acidobacteria and Bacteroidetes. Notably, dioxin digesters Arthrobacter, Rhodococcus, Comamonadaceae, and Bacialles were detected in highly contaminated soil (S1). Along the TCDD gradients, following the dioxin decay from S1 to S2, the abundance of Firmicutes and Actinobacteria decreased, while that of Acidobacteria increased; slight changes occurred at the phylum level from S2 to S3. Although metagenomics analyses disclosed a trend toward bacterial communities before contamination with vegetation recovery, non-metric multidimensional scaling analysis unveiled a new trajectory deviating from the native state. Recovery of the bacterial community may have been hindered, as indicated by lower bacterial diversity in S3 compared to S0 due to a significant loss of bacterial taxa and recruitment of fewer colonizers. The results indicate that dioxins significantly altered the soil microbiomes into a state of disorder with a deviating trajectory in restoration.
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Affiliation(s)
- Huyen-Trang Tran
- Department of Biology, Vinh University, Vinh, Nghe An, 461010, Vietnam
| | - Hung-Minh Nguyen
- Center for responding to climate change, Department of Climate Change, Ministry of Natural Resources and Environment, Hanoi, 125000, Vietnam
| | - Thi-Minh-Hue Nguyen
- Analytical laboratory for Environment, Dioxin and Toxins, Northern Center for Environmental Monitoring, Vietnam Environment Administration, Hanoi, 115000, Vietnam
| | - Chieh Chang
- Department of Life Sciences, National Cheng Kung University, Tainan, 70101, Taiwan
| | - Wei-Ling Huang
- Department of Life Sciences, National Cheng Kung University, Tainan, 70101, Taiwan
| | - Chao-Li Huang
- Institute of Tropical Plant Sciences and Microbiology, National Cheng Kung University, Tainan, 70101, Taiwan.
| | - Tzen-Yuh Chiang
- Department of Life Sciences, National Cheng Kung University, Tainan, 70101, Taiwan.
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18
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Bhatt K, Suyal DC, Kumar S, Singh K, Goswami P. New insights into engineered plant-microbe interactions for pesticide removal. CHEMOSPHERE 2022; 309:136635. [PMID: 36183882 DOI: 10.1016/j.chemosphere.2022.136635] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 09/21/2022] [Accepted: 09/25/2022] [Indexed: 06/16/2023]
Abstract
Over the past decades, rapid industrialization along with the overutilization of organic pollutants/pesticides has altered the environmental circumstances. Moreover, various anthropogenic, xenobiotics and natural activities also affected plants, soil, and human health, in both direct and indirect ways. To counter this, several conventional methods are currently practiced, but are uneconomical, noxious, and is yet inefficient for large-scale application. Plant-microbe interactions are mediated naturally in an ecosystem and are practiced in several areas. Plant growth promoting rhizobacteria (PGPR) possess certain attributes affecting plant and soil consequently performing decontamination activity via a direct and indirect mechanism. PGPR also harbors indispensable genes stimulating the mineralization of several organic and inorganic compounds. This makes microbes potential candidates for contributing to sustainably remediating the harmful pesticide contaminants. There is a limited piece of information about the plant-microbe interaction pertaining predict and understand the overall interaction concerning a sustainable environment. Therefore, this review focuses on the plant-microbe interaction in the rhizosphere and inside the plant's tissues, along with the utilization augmenting the crop productivity, reduction in plant stress along with decontamination of pesticides/organic pollutants in soil for sustainable environmental management.
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Affiliation(s)
- Kalpana Bhatt
- Department of Food Science, Purdue University, West Lafayette, IN, 47907, USA.
| | - Deep Chandra Suyal
- Department of Microbiology, Akal College of Basic Sciences, Eternal University, Baru Sahib, Sirmour, Himachal Pradesh, India.
| | - Saurabh Kumar
- ICAR-Research Complex for Eastern Region, Patna, 800014, Bihar, India
| | - Kuldeep Singh
- Department of Microbiology, Chaudhary Charan Singh Haryana Agricultural University, Hisar, 125004, India
| | - Priya Goswami
- Department of Biotechnology, Mangalayatan University, Uttar Pradesh, India
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19
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Micro"bee"ota: Honey Bee Normal Microbiota as a Part of Superorganism. Microorganisms 2022; 10:microorganisms10122359. [PMID: 36557612 PMCID: PMC9785237 DOI: 10.3390/microorganisms10122359] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 11/17/2022] [Accepted: 11/28/2022] [Indexed: 12/02/2022] Open
Abstract
Honey bees are model organisms for microbiota research. Gut microbiomes are very interesting for surveys due to their simple structure and relationship with hive production. Long-term studies reveal the gut microbiota patterns of various hive members, as well as the functions, sources, and interactions of the majority of its bacteria. But the fungal non-pathogenic part of gut microbiota is almost unexplored, likewise some other related microbiota. Honey bees, as superorganisms, interact with their own microorganisms, the microbial communities of food stores, hive surfaces, and other environments. Understanding microbiota diversity, its transition ways, and hive niche colonization control are necessary for understanding any separate microbiota niche because of their interplay. The long coevolution of bees with the microorganisms populating these niches makes these systems co-dependent, integrated, and stable. Interaction with the environment, hive, and other bees determines caste lifestyle as well as individual microbiota. In this article, we bring together studies on the microbiota of the western honey bee. We show a possible relationship between caste determination and microbiota composition. And what is primary: caste differentiation or microbiota composition?
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20
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Scherer BP, Mast A. Red Mangrove Propagule Bacterial Communities Vary With Geographic, But Not Genetic Distance. MICROBIAL ECOLOGY 2022:10.1007/s00248-022-02147-w. [PMID: 36441249 DOI: 10.1007/s00248-022-02147-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 11/12/2022] [Indexed: 06/16/2023]
Abstract
Bacterial communities associated with plant propagules remain understudied, despite the opportunities that propagules represent as dispersal vectors for bacteria to new sites. These communities may be the product of a combination of environmental influence and inheritance from parent to offspring. The relative role of these mechanisms could have significant implications for our understanding of plant-microbe interactions. We studied the correlates of microbiome community similarities across an invasion front of red mangroves (Rhizophora mangle L.) in Florida, where the species is expanding northward. We collected georeferenced propagule samples from 110 individuals of red mangroves across 11 populations in Florida and used 16S rRNA gene (iTag) sequencing to describe their bacterial communities. We found no core community of bacterial amplicon sequence variants (ASVs) across the Florida range of red mangroves, though there were some ASVs shared among individuals within most populations. Populations differed significantly as measured by Bray-Curtis dissimilarity, but not Unifrac distance. We generated data from 6 microsatellite loci from 60 individuals across 9 of the 11 populations. Geographic distance was correlated with beta diversity, but genetic distance was not. We conclude that red mangrove propagule bacterial communities are likely influenced more by local environmental acquisition than by inheritance.
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Affiliation(s)
- Brendan P Scherer
- Department of Biological Science, Florida State University, King Life Sciences Building, 319 Stadium Drive, Tallahassee, Fl, 32304, USA.
| | - Austin Mast
- Department of Biological Science, Florida State University, King Life Sciences Building, 319 Stadium Drive, Tallahassee, Fl, 32304, USA
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21
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Antoszewski M, Mierek-Adamska A, Dąbrowska GB. The Importance of Microorganisms for Sustainable Agriculture-A Review. Metabolites 2022; 12:1100. [PMID: 36422239 PMCID: PMC9694901 DOI: 10.3390/metabo12111100] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/04/2022] [Accepted: 11/08/2022] [Indexed: 08/27/2023] Open
Abstract
In the face of climate change, progressive degradation of the environment, including agricultural land negatively affecting plant growth and development, endangers plant productivity. Seeking efficient and sustainable agricultural techniques to replace agricultural chemicals is one of the most important challenges nowadays. The use of plant growth-promoting microorganisms is among the most promising approaches; however, molecular mechanisms underneath plant-microbe interactions are still poorly understood. In this review, we summarized the knowledge on plant-microbe interactions, highlighting the role of microbial and plant proteins and metabolites in the formation of symbiotic relationships. This review covers rhizosphere and phyllosphere microbiomes, the role of root exudates in plant-microorganism interactions, the functioning of the plant's immune system during the plant-microorganism interactions. We also emphasized the possible role of the stringent response and the evolutionarily conserved mechanism during the established interaction between plants and microorganisms. As a case study, we discussed fungi belonging to the genus Trichoderma. Our review aims to summarize the existing knowledge about plant-microorganism interactions and to highlight molecular pathways that need further investigation.
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Affiliation(s)
| | - Agnieszka Mierek-Adamska
- Department of Genetics, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University, Lwowska 1, 87-100 Toruń, Poland
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22
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Dynamic Fluctuation and Niche Differentiation of Fungal Pathogens Infecting Bell Pepper Plants. Appl Environ Microbiol 2022; 88:e0100322. [PMID: 36036572 PMCID: PMC9499033 DOI: 10.1128/aem.01003-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The plant microbiome is shaped by plant development and microbial interaction. Fungal pathogens infecting bell pepper plants may fluctuate across the growing seasons. Dynamic fluctuation of the microbiome and fungal pathogens in bell pepper plants is poorly understood, and the origin of fungal pathogens causing fruit rot and leaf wilt has been barely investigated. In this study, we used amplicon sequencing (i.e., 16S rRNA and internal transcribed spacer [ITS] sequencing) to explore the compositional variations of the microbiome in bell pepper plants and studied the fluctuation of fungal pathogens across the growing seasons. Co-occurrence network analysis was applied to track the origin and dissemination route of fungal pathogens that infected bell pepper plants. ITS and 16S rRNA sequencing analyses demonstrated that fungal pathogens infecting fruits and leaves probably belonged to the Penicillium, Cladosporium, Fusarium, and unclassified_Sclerotiniaceae genera rather than one specific genus. The dominant fungal pathogens were different, along with the development of bell pepper plants. Both plant development and fungal pathogens shaped microbial communities in bell pepper plants across the growing seasons. Fungal pathogens decreased species richness and diversity of fungal communities in fungus-infected fruit and leaf tissues but not the uninfected stem tissues. Bacterial metabolic functions of xenobiotics increased in fungus-infected leaves at a mature developmental stage. Competitive interaction was present between fungal and bacterial communities in leaves. Co-occurrence network analysis revealed that the origins of fungal pathogens included the greenhouse, packing house, and storage room. Niche differentiation of microbes was discovered among these locations. IMPORTANCE Bell peppers are widely consumed worldwide. Fungal pathogen infections of bell peppers lead to enormous economic loss. To control fungal pathogens and increase economic benefit, it is essential to investigate the shifting patterns of the microbiome and fungal pathogens in bell pepper plants across the growing seasons. In this study, bell pepper plant diseases observed in fruits and leaves were caused by different fungal pathogens. Fungal pathogens originated from the greenhouse, packing house, and storage room, and niche differentiation existed among microbes. This study improves the understanding of dynamic fluctuation and source of fungal pathogens infecting bell pepper plants in the farming system. It also facilitates precise management of fungal pathogens in the greenhouse.
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Yuan AE, Shou W. Data-driven causal analysis of observational biological time series. eLife 2022; 11:72518. [PMID: 35983746 PMCID: PMC9391047 DOI: 10.7554/elife.72518] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 01/23/2022] [Indexed: 11/28/2022] Open
Abstract
Complex systems are challenging to understand, especially when they defy manipulative experiments for practical or ethical reasons. Several fields have developed parallel approaches to infer causal relations from observational time series. Yet, these methods are easy to misunderstand and often controversial. Here, we provide an accessible and critical review of three statistical causal discovery approaches (pairwise correlation, Granger causality, and state space reconstruction), using examples inspired by ecological processes. For each approach, we ask what it tests for, what causal statement it might imply, and when it could lead us astray. We devise new ways of visualizing key concepts, describe some novel pathologies of existing methods, and point out how so-called ‘model-free’ causality tests are not assumption-free. We hope that our synthesis will facilitate thoughtful application of methods, promote communication across different fields, and encourage explicit statements of assumptions. A video walkthrough is available (Video 1 or https://youtu.be/AlV0ttQrjK8).
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Affiliation(s)
- Alex Eric Yuan
- Molecular and Cellular Biology PhD program, University of Washington, Seattle, United States.,Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, United States
| | - Wenying Shou
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
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24
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Burgess EC, Schaeffer RN. The Floral Microbiome and Its Management in Agroecosystems: A Perspective. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:9819-9825. [PMID: 35917340 DOI: 10.1021/acs.jafc.2c02037] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Disease management is critical to ensuring healthy crop yields and is often targeted at flowers because of their susceptibility to pathogens and direct link to reproduction. Many disease management strategies are unsustainable however because of the potential for pathogens to evolve resistance, or nontarget effects on beneficial insects. Manipulating the floral microbiome holds some promise as a sustainable alternative to chemical means of disease control. In this perspective, we discuss the current state of research concerning floral microbiome assembly and management in agroecosystems as well as future directions aimed at improving the sustainability of disease control and insect-mediated ecosystem services.
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Affiliation(s)
- Emily C Burgess
- Department of Biology, Utah State University, Logan, Utah 84322, United States
| | - Robert N Schaeffer
- Department of Biology, Utah State University, Logan, Utah 84322, United States
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25
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López-García E, Benítez-Cabello A, Martín-Arranz V, Garrido-Fernández A, Jiménez-Díaz R, Arroyo-López FN. Optimisation of working parameters for lactic acid bacteria and yeast recovery from table olive biofilms, preserving fruit integrity and reducing chloroplast recovery. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2022.113787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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26
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Vermote L, Verce M, Mozzi F, De Vuyst L, Weckx S. Microbiomes Associated With the Surfaces of Northern Argentinian Fruits Show a Wide Species Diversity. Front Microbiol 2022; 13:872281. [PMID: 35898900 PMCID: PMC9309516 DOI: 10.3389/fmicb.2022.872281] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 06/23/2022] [Indexed: 11/13/2022] Open
Abstract
The fiber, vitamin, and antioxidant contents of fruits contribute to a balanced human diet. In countries such as Argentina, several tropical fruits are witnessing a high yield in the harvest season, with a resulting surplus. Fruit fermentation using autochthonous starter cultures can provide a solution for food waste. However, limited knowledge exists about the microbiota present on the surfaces of fruits and the preceding flowers. In the present exploratory study, the microbiomes associated with the surfaces of tropical fruits from Northern Argentina, such as white guava, passion fruit and papaya were investigated using a shotgun metagenomic sequencing approach. Hereto, one sample composed of 14 white guava fruits, two samples of passion fruits with each two to three fruits representing the almost ripe and ripe stage of maturity, four samples of papaya with each two to three fruits representing the unripe, almost ripe, and ripe stage of maturity were processed, as well as a sample of closed and a sample of open Japanese medlar flowers. A considerable heterogeneity was found in the composition of the fruits’ surface microbiota at the genus and species level. While bacteria dominated the microbiota of the fruits and flowers, a small number of the metagenomic sequence reads corresponded with yeasts and filamentous fungi. A minimal abundance of bacterial species critical in lactic acid and acetic acid fermentations was found. A considerable fraction of the metagenomic sequence reads from the fruits’ surface microbiomes remained unidentified, which suggested that intrinsic species are to be sequenced or discovered.
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Affiliation(s)
- Louise Vermote
- Faculty of Sciences and Bioengineering Sciences, Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Vrije Universiteit Brussel, Brussels, Belgium
| | - Marko Verce
- Faculty of Sciences and Bioengineering Sciences, Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Vrije Universiteit Brussel, Brussels, Belgium
| | - Fernanda Mozzi
- Technology and Development Laboratory, Centro de Referencia para Lactobacilos (CERELA)-CONICET, San Miguel de Tucumán, Argentina
| | - Luc De Vuyst
- Faculty of Sciences and Bioengineering Sciences, Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Vrije Universiteit Brussel, Brussels, Belgium
| | - Stefan Weckx
- Faculty of Sciences and Bioengineering Sciences, Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Vrije Universiteit Brussel, Brussels, Belgium
- *Correspondence: Stefan Weckx,
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Francioli D, Cid G, Hajirezaei MR, Kolb S. Leaf bacterial microbiota response to flooding is controlled by plant phenology in wheat (Triticum aestivum L.). Sci Rep 2022; 12:11197. [PMID: 35778470 PMCID: PMC9249782 DOI: 10.1038/s41598-022-15133-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 06/20/2022] [Indexed: 11/09/2022] Open
Abstract
Leaf microbiota mediates foliar functional traits, influences plant fitness, and contributes to various ecosystem functions, including nutrient and water cycling. Plant phenology and harsh environmental conditions have been described as the main determinants of leaf microbiota assembly. How climate change may modulate the leaf microbiota is unresolved and thus, we have a limited understanding on how environmental stresses associated with climate change driven weather events affect composition and functions of the microbes inhabiting the phyllosphere. Thus, we conducted a pot experiment to determine the effects of flooding stress on the wheat leaf microbiota. Since plant phenology might be an important factor in the response to hydrological stress, flooding was induced at different plant growth stages (tillering, booting and flowering). Using a metabarcoding approach, we monitored the response of leaf bacteria to flooding, while key soil and plant traits were measured to correlate physiological plant and edaphic factor changes with shifts in the bacterial leaf microbiota assembly. In our study, plant growth stage represented the main driver in leaf microbiota composition, as early and late plants showed distinct bacterial communities. Overall, flooding had a differential effect on leaf microbiota dynamics depending at which developmental stage it was induced, as a more pronounced disruption in community assembly was observed in younger plants.
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Affiliation(s)
- Davide Francioli
- Microbial Biogeochemistry, Research Area Landscape Functioning, Leibniz Center for Agricultural Landscape Research E.V. (ZALF), Müncheberg, Germany.
| | - Geeisy Cid
- Department of Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Mohammad-Reza Hajirezaei
- Department of Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Steffen Kolb
- Microbial Biogeochemistry, Research Area Landscape Functioning, Leibniz Center for Agricultural Landscape Research E.V. (ZALF), Müncheberg, Germany.,Thaer Institute, Faculty of Life Sciences, Humboldt University of Berlin, Berlin, Germany
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Abdelfattah A, Tack AJM, Wasserman B, Liu J, Berg G, Norelli J, Droby S, Wisniewski M. Evidence for host-microbiome co-evolution in apple. THE NEW PHYTOLOGIST 2022; 234:2088-2100. [PMID: 34823272 PMCID: PMC9299473 DOI: 10.1111/nph.17820] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 10/18/2021] [Indexed: 05/07/2023]
Abstract
Plants evolved in association with a diverse community of microorganisms. The effect of plant phylogeny and domestication on host-microbiome co-evolutionary dynamics are poorly understood. Here we examined the effect of domestication and plant lineage on the composition of the endophytic microbiome of 11 Malus species, representing three major groups: domesticated apple (M. domestica), wild apple progenitors, and wild Malus species. The endophytic community of M. domestica and its wild progenitors showed higher microbial diversity and abundance than wild Malus species. Heirloom and modern cultivars harbored a distinct community composition, though the difference was not significant. A community-wide Bayesian model revealed that the endophytic microbiome of domesticated apple is an admixture of its wild progenitors, with clear evidence for microbiome introgression, especially for the bacterial community. We observed a significant correlation between the evolutionary distance of Malus species and their microbiome. This study supports co-evolution between Malus species and their microbiome during domestication. This finding has major implications for future breeding programs and our understanding of the evolution of plants and their microbiomes.
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Affiliation(s)
- Ahmed Abdelfattah
- Institute of Environmental BiotechnologyGraz University of TechnologyPetersgasse 12Graz8010Austria
- Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB)Max‐Eyth Allee 10014469PotsdamGermany
| | - Ayco J. M. Tack
- Department of Ecology, Environment and Plant SciencesStockholm UniversitySvante Arrhenius väg 20AStockholmSE‐106 91Sweden
| | - Birgit Wasserman
- Institute of Environmental BiotechnologyGraz University of TechnologyPetersgasse 12Graz8010Austria
| | - Jia Liu
- Chongqing Key Laboratory of Economic Plant BiotechnologyCollege of Landscape Architecture and Life SciencesChongqing University of Arts and SciencesYongchuanChongquing402160China
| | - Gabriele Berg
- Institute of Environmental BiotechnologyGraz University of TechnologyPetersgasse 12Graz8010Austria
- Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB)Max‐Eyth Allee 10014469PotsdamGermany
- Institute for Biochemistry and BiologyUniversity of Postdam14476Potsdam OT GolmGermany
| | - John Norelli
- Appalachian Fruit Research StationUnited States Department of Agriculture – Agricultural Research ServiceKearneysvilleWV25430USA
| | - Samir Droby
- Department of Postharvest ScienceAgricultural Research OrganizationThe Volcani InstitutePO Box 15159Rishon LeZion7505101Israel
| | - Michael Wisniewski
- Department of Biological SciencesVirginia Polytechnic Institute and State University220 Ag Quad LnBlacksburgVA24061USA
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29
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Mawarda PC, Lakke SL, Dirk van Elsas J, Salles JF. Temporal dynamics of the soil bacterial community following Bacillus invasion. iScience 2022; 25:104185. [PMID: 35479409 PMCID: PMC9035691 DOI: 10.1016/j.isci.2022.104185] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 03/21/2022] [Accepted: 03/28/2022] [Indexed: 01/04/2023] Open
Abstract
Microbial inoculants are constantly introduced into the soil as the deployment of sustainable agricultural practices increases. These introductions might induce soil native communities’ dynamics, influencing their assembly process. We followed the impact and successional trajectories of native soil communities of different diversity levels to the invasion by Bacillus mycoides M2E15 (BM) and B. pumilus ECOB02 (BP). Whereas the impact was more substantial when the invader survived (BM), the transient presence of BP also exerted tangible effects on soil bacterial diversity. Community assembly analyses revealed that deterministic processes primarily drove community turnover. This selection acted stronger in highly diverse communities invaded by BM than in those invaded by BP. We showed that resident bacterial communities exhibit patterns of secondary succession following invasions, even if the latter are unsuccessful. Furthermore, the intensification of biotic interactions in more diverse communities might strengthen the deterministic selection upon invasion in communities with higher diversity. Microbial invaders altered soil bacterial diversity regardless of their survival The impact was more pronounced when the invader was established Deterministic selection primarily drove community turnover following invasion The dynamic of invaded community showed pattern of secondary succession
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Olimi E, Kusstatscher P, Wicaksono WA, Abdelfattah A, Cernava T, Berg G. Insights into the microbiome assembly during different growth stages and storage of strawberry plants. ENVIRONMENTAL MICROBIOME 2022; 17:21. [PMID: 35484554 PMCID: PMC9052558 DOI: 10.1186/s40793-022-00415-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 04/17/2022] [Indexed: 05/11/2023]
Abstract
BACKGROUND Microbiome assembly was identified as an important factor for plant growth and health, but this process is largely unknown, especially for the fruit microbiome. Therefore, we analyzed strawberry plants of two cultivars by focusing on microbiome tracking during the different growth stages and storage using amplicon sequencing, qPCR, and microscopic approaches. RESULTS Strawberry plants carried a highly diverse microbiome, therein the bacterial families Sphingomonadaceae (25%), Pseudomonadaceae (17%), and Burkholderiaceae (11%); and the fungal family Mycosphaerella (45%) were most abundant. All compartments were colonized by high number of bacteria and fungi (107-1010 marker gene copies per g fresh weight), and were characterized by high microbial diversity (6049 and 1501 ASVs); both were higher for the belowground samples than in the phyllosphere. Compartment type was the main driver of microbial diversity, structure, and abundance (bacterial: 45%; fungal: 61%) when compared to the cultivar (1.6%; 2.2%). Microbiome assembly was strongly divided for belowground habitats and the phyllosphere; only a low proportion of the microbiome was transferred from soil via the rhizosphere to the phyllosphere. During fruit development, we observed the highest rates of microbial transfer from leaves and flowers to ripe fruits, where most of the bacteria occured inside the pulp. In postharvest fruits, microbial diversity decreased while the overall abundance increased. Developing postharvest decay caused by Botrytis cinerea decreased the diversity as well, and induced a reduction of potentially beneficial taxa. CONCLUSION Our findings provide insights into microbiome assembly in strawberry plants and highlight the importance of microbe transfer during fruit development and storage with potential implications for food health and safety.
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Affiliation(s)
- Expedito Olimi
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - Peter Kusstatscher
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - Wisnu Adi Wicaksono
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - Ahmed Abdelfattah
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
- Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Potsdam, Germany
| | - Tomislav Cernava
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
- Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Potsdam, Germany
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
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Bacterial Succession and Community Dynamics of the Emerging Leaf Phyllosphere in Spring. Microbiol Spectr 2022; 10:e0242021. [PMID: 35234496 PMCID: PMC8941926 DOI: 10.1128/spectrum.02420-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Every year, deciduous trees shed their leaves, and when new leaves emerge next spring, they establish a characteristic bacterial leaf community. In this exploratory study, we assessed the bacterial phyllosphere (aboveground plant surfaces) of eight London plane trees (Platanus × acerifolia) in Antwerp and Milan by sampling weekly during leaf emergence and expansion. We sampled the surfaces of different tree compartments: leaves, leaf buds, branches, and trunk, for up to 6 weeks. Phyllosphere community composition was most strongly determined by tree compartment. Only the communities on the emerging leaves showed changing dynamics over time. The rate of change in the leaf phyllosphere composition, expressed as the beta dissimilarity between consecutive time points, was very high following leaf emergence, with decreasing speed over time, indicating that these communities stabilize over time. We also identified cooccurring groups of bacteria associated with potential stages of ecological succession on the leaves and accordingly named them general cluster, early cluster, middle cluster, and late cluster. Taxa of the general cluster were not only more abundant than the others on leaves, but they were also widespread on other tree compartments. The late cluster was most pronounced in trees surrounded by trafficked urban land use. This study mainly generates hypotheses on the ecological succession on the emerging leaves of deciduous trees in urban environments and contributes to understanding the development of the tree leaf phyllosphere in spring. IMPORTANCE Improving our understanding of phyllosphere ecology is key in successfully applying bacterial biological agents or modulating the leaf microbiome in order to achieve valuable ecosystem services, such as plant protection, plant growth, air purification, and developing a healthy human immune system. Modulation of the phyllosphere microbiome in the field works only with variable success. To improve the impact of our applications in the field, a better understanding of the ecological principles governing phyllosphere dynamics is required. This exploratory study demonstrates how the combination of different analyses of a chronosequence of bacterial communities can provide new ecological insights. With a limited number of sampled trees, we demonstrated different indications of ecological succession of bacterial communities in the leaves and observed a potential impact of intensely trafficked land use becoming apparent in the leaf bacterial communities approximately 3 weeks after leaf emergence, consisting of a separate stage in community development.
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Longa CMO, Antonielli L, Bozza E, Sicher C, Pertot I, Perazzolli M. Plant organ and sampling time point determine the taxonomic structure of microbial communities associated to apple plants in the orchard environment. Microbiol Res 2022; 258:126991. [DOI: 10.1016/j.micres.2022.126991] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 01/07/2022] [Accepted: 02/14/2022] [Indexed: 01/04/2023]
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Heminger AR, Belden LK, Barney JN, Badgley BD, Haak DC. Horsenettle ( Solanum carolinense) fruit bacterial communities are not variable across fine spatial scales. PeerJ 2021; 9:e12359. [PMID: 34820171 PMCID: PMC8582302 DOI: 10.7717/peerj.12359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 09/30/2021] [Indexed: 11/20/2022] Open
Abstract
Fruit house microbial communities that are unique from the rest of the plant. While symbiotic microbial communities complete important functions for their hosts, the fruit microbiome is often understudied compared to other plant organs. Fruits are reproductive tissues that house, protect, and facilitate the dispersal of seeds, and thus they are directly tied to plant fitness. Fruit microbial communities may, therefore, also impact plant fitness. In this study, we assessed how bacterial communities associated with fruit of Solanum carolinense, a native herbaceous perennial weed, vary at fine spatial scales (<0.5 km). A majority of the studies conducted on plant microbial communities have been done at large spatial scales and have observed microbial community variation across these large spatial scales. However, both the environment and pollinators play a role in shaping plant microbial communities and likely have impacts on the plant microbiome at fine scales. We collected fruit samples from eight sampling locations, ranging from 2 to 450 m apart, and assessed the fruit bacterial communities using 16S rRNA gene amplicon sequencing. Overall, we found no differences in observed richness or microbial community composition among sampling locations. Bacterial community structure of fruits collected near one another were not more different than those that were farther apart at the scales we examined. These fine spatial scales are important to obligate out-crossing plant species such as S. carolinense because they are ecologically relevant to pollinators. Thus, our results could imply that pollinators serve to homogenize fruit bacterial communities across these smaller scales.
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Affiliation(s)
- Ariel R Heminger
- School of Plant and Environmental Sciences, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, United States of America.,Global Change Center, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, United States of America
| | - Lisa K Belden
- Global Change Center, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, United States of America.,Department of Biological Sciences, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, United States of America
| | - Jacob N Barney
- School of Plant and Environmental Sciences, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, United States of America.,Global Change Center, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, United States of America
| | - Brian D Badgley
- School of Plant and Environmental Sciences, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, United States of America.,Global Change Center, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, United States of America
| | - David C Haak
- School of Plant and Environmental Sciences, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, United States of America.,Global Change Center, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, United States of America
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Mango Endophyte and Epiphyte Microbiome Composition during Fruit Development and Post-Harvest Stages. HORTICULTURAE 2021. [DOI: 10.3390/horticulturae7110495] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The influence of the development stage and post-harvest handling on the microbial composition of mango fruit plays a central role in fruit health. Hence, the composition of fungal and bacterial microbiota on the anthoplane, fructoplane, stems and stem-end pulp of mango during fruit development and post-harvest handling were determined using next-generation sequencing of the internal transcribed spacer and 16S rRNA regions. At full bloom, the inflorescence had the richest fungal and bacterial communities. The young developing fruit exhibited lower fungal richness and diversities in comparison to the intermediate and fully developed fruit stages on the fructoplane. At the post-harvest stage, lower fungal and bacterial diversities were observed following prochloraz treatment both on the fructoplane and stem-end pulp. Ascomycota (52.8%) and Basidiomycota (43.2%) were the most dominant fungal phyla, while Penicillium, Botryosphaeria, Alternaria and Mucor were detected as the known post-harvest decay-causing fungal genera. The Cyanobacteria (35.6%), Firmicutes (26.1%) and Proteobacteria (23.1%) were the most dominant bacterial phyla. Changes in the presence of Bacillus subtilis following post-harvest interventions such as prochloraz suggested a non-target effect of the fungicide. The present study, therefore, provides the primary baseline data on mango fungal and bacterial diversity and composition, which can be foundational in the development of effective disease (stem-end rot) management strategies.
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Capacity of soil bacteria to reach the phyllosphere and convergence of floral communities despite soil microbiota variation. Proc Natl Acad Sci U S A 2021; 118:2100150118. [PMID: 34620708 PMCID: PMC8521660 DOI: 10.1073/pnas.2100150118] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/31/2021] [Indexed: 11/30/2022] Open
Abstract
The role of flowers as environmental filters for bacterial communities and the provenance of bacteria in the phyllosphere are currently poorly understood. We experimentally tested the effect of induced variation in soil communities on the microbiota of plant organs. We identified soil-derived bacteria in the phyllosphere and show a strong convergence of floral communities with an enrichment of members of the Burkholderiaceae family. This finding highlights a potential role of the flower in shaping the interaction between plants and a bacterial family known to harbor both plant pathogens and growth-promoting strains. Because the flower involves host–symbiont feedback, the selection of specific bacteria by the reproductive organs of angiosperms could be relevant for the modulation of fruit and seed production. Leaves and flowers are colonized by diverse bacteria that impact plant fitness and evolution. Although the structure of these microbial communities is becoming well-characterized, various aspects of their environmental origin and selection by plants remain uncertain, such as the relative proportion of soilborne bacteria in phyllosphere communities. Here, to address this issue and to provide experimental support for bacteria being filtered by flowers, we conducted common-garden experiments outside and under gnotobiotic conditions. We grew Arabidopsis thaliana in a soil substitute and added two microbial communities from natural soils. We estimated that at least 25% of the phyllosphere bacteria collected from the plants grown in the open environment were also detected in the controlled conditions, in which bacteria could reach leaves and flowers only from the soil. These taxa represented more than 40% of the communities based on amplicon sequencing. Unsupervised hierarchical clustering approaches supported the convergence of all floral microbiota, and 24 of the 28 bacteria responsible for this pattern belonged to the Burkholderiaceae family, which includes known plant pathogens and plant growth-promoting members. We anticipate that our study will foster future investigations regarding the routes used by soil microbes to reach leaves and flowers, the ubiquity of the environmental filtering of Burkholderiaceae across plant species and environments, and the potential functional effects of the accumulation of these bacteria in the reproductive organs of flowering plants.
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Tarquinio F, Attlan O, Vanderklift MA, Berry O, Bissett A. Distinct Endophytic Bacterial Communities Inhabiting Seagrass Seeds. Front Microbiol 2021; 12:703014. [PMID: 34621247 PMCID: PMC8491609 DOI: 10.3389/fmicb.2021.703014] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 07/12/2021] [Indexed: 11/13/2022] Open
Abstract
Seagrasses are marine angiosperms that can live completely or partially submerged in water and perform a variety of significant ecosystem services. Like terrestrial angiosperms, seagrasses can reproduce sexually and, the pollinated female flower develop into fruits and seeds, which represent a critical stage in the life of plants. Seed microbiomes include endophytic microorganisms that in terrestrial plants can affect seed germination and seedling health through phytohormone production, enhanced nutrient availability and defence against pathogens. However, the characteristics and origins of the seagrass seed microbiomes is unknown. Here, we examined the endophytic bacterial community of six microenvironments (flowers, fruits, and seeds, together with leaves, roots, and rhizospheric sediment) of the seagrass Halophila ovalis collected from the Swan Estuary, in southwestern Australia. An amplicon sequencing approach (16S rRNA) was used to characterize the diversity and composition of H. ovalis bacterial microbiomes and identify core microbiome bacteria that were conserved across microenvironments. Distinct communities of bacteria were observed within specific seagrass microenvironments, including the reproductive tissues (flowers, fruits, and seeds). In particular, bacteria previously associated with plant growth promoting characteristics were mainly found within reproductive tissues. Seagrass seed-borne bacteria that exhibit growth promoting traits, the ability to fix nitrogen and anti-pathogenic potential activity, may play a pivotal role in seed survival, as is common for terrestrial plants. We present the endophytic community of the seagrass seeds as foundation for the identification of potential beneficial bacteria and their selection in order to improve seagrass restoration.
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Affiliation(s)
- Flavia Tarquinio
- Oceans and Atmosphere, Indian Ocean Marine Research Centre, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Crawley, WA, Australia.,Environomics Future Science Platform, Indian Ocean Marine Research Centre, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Crawley, WA, Australia
| | - Océane Attlan
- Oceans and Atmosphere, Indian Ocean Marine Research Centre, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Crawley, WA, Australia.,Sciences et Technologies, Université de la Réunion, Saint-Denis, France
| | - Mathew A Vanderklift
- Oceans and Atmosphere, Indian Ocean Marine Research Centre, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Crawley, WA, Australia
| | - Oliver Berry
- Environomics Future Science Platform, Indian Ocean Marine Research Centre, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Crawley, WA, Australia
| | - Andrew Bissett
- Oceans and Atmosphere, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Hobart, TAS, Australia
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37
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Olivieri L, Saville RJ, Gange AC, Xu X. Apple endophyte community in relation to location, scion and rootstock genotypes and susceptibility to European canker. FEMS Microbiol Ecol 2021; 97:fiab131. [PMID: 34601593 PMCID: PMC8497447 DOI: 10.1093/femsec/fiab131] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 09/24/2021] [Indexed: 12/30/2022] Open
Abstract
European apple canker, caused by Neonectria ditissima, is a severe disease of apple. Achieving effective control is difficult with the currently available pesticides. Specific apple endophytes associated with cultivars may partially contribute to the cultivar response to the pathogen and thus could be used for disease management. We sought to determine whether the overall endophyte community differed among cultivars differing in their susceptibility to N. ditissima and to identify specific microbial groups associated with the susceptibility. Using Illumina MiSeq meta-barcoding, we profiled apple tree endophytes in 16 scion-rootstock combinations at two locations and quantified the relative contribution of scion, rootstock and location to the observed variability in the endophyte communities. Endophyte diversity was primarily affected by the orchard location (accounting for 29.4% and 85.9% of the total variation in the PC1 for bacteria and fungi, respectively), followed by the scion genotype (24.3% and 19.5% of PC2), whereas rootstock effects were small (<3% of PC1 and PC2). There were significant differences in the endophyte community between canker-resistant and -susceptible cultivars. Several bacterial and fungal endophyte groups had different relative abundance between susceptible and resistant cultivars. These endophyte groups included putative pathogen antagonists as well as plant pathogens. Their possible ecological roles in the N. ditissima pathosystem are discussed.
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Affiliation(s)
- Leone Olivieri
- NIAB EMR, New Road, East Malling, Kent ME19 6BJ, UK
- Department of Biological Sciences, Royal Holloway, University of London, Egham, Surrey TW20 0EX, UK
| | - Robert J Saville
- NIAB EMR, New Road, East Malling, Kent ME19 6BJ, UK
- Agriculture & Horticulture Development Board, Stoneleigh Park, Kenilworth, Warwickshire CV8 2TL, UK
| | - Alan C Gange
- Department of Biological Sciences, Royal Holloway, University of London, Egham, Surrey TW20 0EX, UK
| | - Xiangming Xu
- NIAB EMR, New Road, East Malling, Kent ME19 6BJ, UK
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38
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O'Brien AM, Ginnan NA, Rebolleda-Gómez M, Wagner MR. Microbial effects on plant phenology and fitness. AMERICAN JOURNAL OF BOTANY 2021; 108:1824-1837. [PMID: 34655479 DOI: 10.1002/ajb2.1743] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 07/07/2021] [Indexed: 06/13/2023]
Abstract
Plant development and the timing of developmental events (phenology) are tightly coupled with plant fitness. A variety of internal and external factors determine the timing and fitness consequences of these life-history transitions. Microbes interact with plants throughout their life history and impact host phenology. This review summarizes current mechanistic and theoretical knowledge surrounding microbe-driven changes in plant phenology. Overall, there are examples of microbes impacting every phenological transition. While most studies have focused on flowering time, microbial effects remain important for host survival and fitness across all phenological phases. Microbe-mediated changes in nutrient acquisition and phytohormone signaling can release plants from stressful conditions and alter plant stress responses inducing shifts in developmental events. The frequency and direction of phenological effects appear to be partly determined by the lifestyle and the underlying nature of a plant-microbe interaction (i.e., mutualistic or pathogenic), in addition to the taxonomic group of the microbe (fungi vs. bacteria). Finally, we highlight biases, gaps in knowledge, and future directions. This biotic source of plasticity for plant adaptation will serve an important role in sustaining plant biodiversity and managing agriculture under the pressures of climate change.
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Affiliation(s)
- Anna M O'Brien
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Nichole A Ginnan
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, USA
| | - María Rebolleda-Gómez
- Department of Ecology and Evolutionary Biology, University of California-Irvine, Irvine, CA, USA
| | - Maggie R Wagner
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, USA
- Kansas Biological Survey and Center for Ecological Research, University of Kansas, Lawrence, KS, USA
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39
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Khwantongyim P, Wansee S, Lu X, Zhang W, Sun G. Variations in the Community Structure of Fungal Microbiota Associated with Apple Fruit Shaped by Fruit Bagging-Based Practice. J Fungi (Basel) 2021; 7:jof7090764. [PMID: 34575802 PMCID: PMC8470174 DOI: 10.3390/jof7090764] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 09/05/2021] [Accepted: 09/13/2021] [Indexed: 11/26/2022] Open
Abstract
The various fungal communities that adhere to apple fruit are influenced by agricultural practices. However, the effects of fruit bagging-based management practice on the fungal microbiota are still unknown, and little is known about the fungal communities of bagged apple fruit. We conducted a study using apple fruit grown in a conventionally managed orchard where pesticide use is an indispensable practice. Fungal communities were collected from the calyx-end and peel tissues of bagged and unbagged fruit and characterized using barcode-type next-generation sequencing. Fruit bagging had a stronger effect on fungal richness, abundance, and diversity of the fungal microbiota in comparison to non-bagging. In addition, bagging also impacted the compositional variation of the fungal communities inhabiting each fruit part. We observed that fruit bagging had a tendency to maintain ecological equilibrium since Ascomycota and Basidiomycota were more distributed in bagged fruit than in unbagged fruit. These fungal communities consist of beneficial fungi rather than potentially harmful fungi. Approximately 50 dominant taxa were detected in bagged fruit, for example, beneficial genera such as Articulospora, Bullera, Cryptococcus, Dioszegia, Erythrobasidium, and Sporobolomyces, as well as pathogenic genera such as Aureobasidium and Taphrina. These results suggested that fruit bagging could significantly increase fungal richness and promote healthy fungal communities, especially the harmless fungal communities, which might be helpful for protecting fruit from the effects of pathogens. This study provides a foundation for understanding the impacts of bagging-based practice on the associated fungal microbiota.
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40
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Kong HG, Ham H, Lee MH, Park DS, Lee YH. Microbial Community Dysbiosis and Functional Gene Content Changes in Apple Flowers due to Fire Blight. THE PLANT PATHOLOGY JOURNAL 2021; 37:404-412. [PMID: 34365752 PMCID: PMC8357563 DOI: 10.5423/ppj.nt.05.2021.0072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 06/02/2021] [Accepted: 06/06/2021] [Indexed: 06/13/2023]
Abstract
Despite the plant microbiota plays an important role in plant health, little is known about the potential interactions of the flower microbiota with pathogens. In this study, we investigated the microbial community of apple blossoms when infected with Erwinia amylovora. The long-read sequencing technology, which significantly increased the genome sequence resolution, thus enabling the characterization of fire blight-induced changes in the flower microbial community. Each sample showed a unique microbial community at the species level. Pantoea agglomerans and P. allii were the most predominant bacteria in healthy flowers, whereas E. amylovora comprised more than 90% of the microbial population in diseased flowers. Furthermore, gene function analysis revealed that glucose and xylose metabolism were enriched in diseased flowers. Overall, our results showed that the microbiome of apple blossoms is rich in specific bacteria, and the nutritional composition of flowers is important for the incidence and spread of bacterial disease.
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Affiliation(s)
- Hyun Gi Kong
- Corresponding author. Phone) +82-63-238-3279, FAX) +82-63-238-3838, E-mail)
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41
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Sauer S, Dlugosch L, Kammerer DR, Stintzing FC, Simon M. The Microbiome of the Medicinal Plants Achillea millefolium L. and Hamamelis virginiana L. Front Microbiol 2021; 12:696398. [PMID: 34354692 PMCID: PMC8329415 DOI: 10.3389/fmicb.2021.696398] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 06/22/2021] [Indexed: 01/19/2023] Open
Abstract
In the recent past many studies investigated the microbiome of plants including several medicinal plants (MP). Microbial communities of the associated soil, rhizosphere and the above-ground organs were included, but there is still limited information on their seasonal development, and in particular simultaneous investigations of different plant organs are lacking. Many studies predominantly addressed either the prokaryotic or fungal microbiome. A distinction of epi- and endophytic communities of above-ground plant organs has rarely been made. Therefore, we conducted a comprehensive investigation of the bacterial and fungal microbiome of the MP Achillea millefolium and studied the epi- and endophytic microbial communities of leaves, flower buds and flowers between spring and summer together with the microbiome of the associated soil at one location. Further, we assessed the core microbiome of Achillea from four different locations at distances up to 250 km in southern Germany and Switzerland. In addition, the bacterial and fungal epi- and endophytic leaf microbiome of the arborescent shrub Hamamelis virginiana and the associated soil was investigated at one location. The results show a generally decreasing diversity of both microbial communities from soil to flower of Achillea. The diversity of the bacterial and fungal endophytic leaf communities of Achillea increased from April to July, whereas that of the epiphytic leaf communities decreased. In contrast, the diversity of the fungal communities of both leaf compartments and that of epiphytic bacteria of Hamamelis increased over time indicating plant-specific differences in the temporal development of microbial communities. Both MPs exhibited distinct microbial communities with plant-specific but also common taxa. The core taxa of Achillea constituted a lower fraction of the total number of taxa than of the total abundance of taxa. The results of our study provide a basis to link interactions of the microbiome with their host plant in relation to the production of bioactive compounds.
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Affiliation(s)
- Simon Sauer
- WALA Heilmittel GmbH, Bad Boll, Germany
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Leon Dlugosch
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | | | | | - Meinhard Simon
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
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42
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Jurburg SD, Bossers A. Age Matters: Community Assembly in the Pig Fecal Microbiome in the First Month of Life. Front Microbiol 2021; 12:564408. [PMID: 33790871 PMCID: PMC8006452 DOI: 10.3389/fmicb.2021.564408] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 02/22/2021] [Indexed: 01/04/2023] Open
Abstract
Despite the wealth of research into strategies for microbiome modulation, studies of microbiome management in pig hosts have found mixed results. A refined understanding of the patterns of microbiome assembly during the host’s early life, when management strategies are most commonly applied, is necessary for the development of successful management practices. Here, we study the development of the pig gut microbial community in a monitoring experiment, sampling the microbiome of pigs in a commercial farm intensively during the first month of life. We found that the community’s taxonomic richness increased linearly with host age. Furthermore, rapid changes across communities occurred in stages, and non-linear patterns in relative abundance were commonly observed among dominant taxa across host age, consistent with primary succession. Our results highlight the importance of understanding the patterns of microbiome assembly during host development, and identify successional stages as windows of opportunity for future research.
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Affiliation(s)
- Stephanie D Jurburg
- German Centre for Integrative Biodiversity Research iDiv (Halle/Jena/Leipzig), Leipzig, Germany.,Department of Infection Biology, Wageningen Bioveterinary Research, Lelystad, Netherlands.,Institute of Biology, Leipzig University, Leipzig, Germany
| | - Alex Bossers
- Department of Infection Biology, Wageningen Bioveterinary Research, Lelystad, Netherlands.,Institute for Risk Assessment Sciences, Utrecht University, Utrecht, Netherlands
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43
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Argüello H, Rodríguez-Gómez IM, Sánchez-Carvajal JM, Pallares FJ, Díaz I, Cabrera-Rubio R, Crispie F, Cotter PD, Mateu E, Martín-Valls G, Carrasco L, Gómez-Laguna J. Porcine reproductive and respiratory syndrome virus impacts on gut microbiome in a strain virulence-dependent fashion. Microb Biotechnol 2021; 15:1007-1016. [PMID: 33656781 PMCID: PMC8913879 DOI: 10.1111/1751-7915.13757] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 12/23/2020] [Accepted: 01/05/2021] [Indexed: 12/24/2022] Open
Abstract
Porcine reproductive and respiratory syndrome (PRRS) is a viral disease defined by reproductive problems, respiratory distress and a negative impact on growth rate and general condition. Virulent PRRS virus (PRRSV) strains have emerged in the last years with evident knowledge gaps in their impact on the host immune response. Thus, the present study examines the impact of acute PRRS virus (PRRSV) infection, with two strains of different virulence, on selected immune parameters and on the gut microbiota composition of infected pigs using 16S rRNA compositional sequencing. Pigs were infected with a low virulent (PRRS_3249) or a virulent (Lena) PRRSV‐1 strain and euthanized at 1, 3, 6, 8 or 13 days post‐inoculation (dpi). Faeces were collected from each animal at the necropsy time‐point. Alpha and beta diversity analyses demonstrated that infection, particularly with the Lena strain, impacted the microbiome composition from 6 dpi onwards. Taxonomic differences revealed that infected pigs had higher abundance of Treponema and Methanobrevibacter (FDR < 0.05). Differences were more considerable for Lena‐ than for PRRS_3249‐infected pigs, showing the impact of strain virulence in the intestinal changes. Lena‐infected pigs had reduced abundancies of anaerobic commensals such as Roseburia, Anaerostipes, Butyricicoccus and Prevotella (P < 0.05). The depletion of these desirable commensals was significantly correlated to infection severity measured by viraemia, clinical signs, lung lesions and immune parameters (IL‐6, IFN‐γ and Hp serum levels). Altogether, the results from this study demonstrate the indirect impact of PRRSV infection on gut microbiome composition in a strain virulence‐dependent fashion and its association with selected immune markers.
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Affiliation(s)
- Héctor Argüello
- Infectious Diseases and Epidemiology Unit, Department of Animal Health, Faculty of Veterinary Medicine, University of León, León, Spain
| | - Irene Magdalena Rodríguez-Gómez
- Department of Anatomy and Comparative Pathology and Toxicology, Faculty of Veterinary Medicine, University of Córdoba, International Excellence Agrifood Campus 'ceiA3', Córdoba, Spain
| | - Jose María Sánchez-Carvajal
- Department of Anatomy and Comparative Pathology and Toxicology, Faculty of Veterinary Medicine, University of Córdoba, International Excellence Agrifood Campus 'ceiA3', Córdoba, Spain
| | - Francisco José Pallares
- Department of Anatomy and Comparative Pathology, Faculty of Veterinary Medicine, University of Murcia, Mare Nostrum Excellence Campus, Murcia, Spain
| | - Iván Díaz
- IRTA, Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Bellaterra, Spain
| | - Raúl Cabrera-Rubio
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland.,APC Microbiome Ireland, Cork, Ireland
| | - Fiona Crispie
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland.,APC Microbiome Ireland, Cork, Ireland
| | - Paul D Cotter
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland.,APC Microbiome Ireland, Cork, Ireland.,Vistamilk, Fermoy, Co. Cork, Ireland
| | - Enric Mateu
- IRTA, Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Bellaterra, Spain.,Department of Animal Health and Anatomy, Faculty of Veterinary Medicine, Autonomous University of Barcelona, Bellaterra, Spain
| | - Gerard Martín-Valls
- Department of Animal Health and Anatomy, Faculty of Veterinary Medicine, Autonomous University of Barcelona, Bellaterra, Spain
| | - Librado Carrasco
- Department of Anatomy and Comparative Pathology and Toxicology, Faculty of Veterinary Medicine, University of Córdoba, International Excellence Agrifood Campus 'ceiA3', Córdoba, Spain
| | - Jaime Gómez-Laguna
- Department of Anatomy and Comparative Pathology and Toxicology, Faculty of Veterinary Medicine, University of Córdoba, International Excellence Agrifood Campus 'ceiA3', Córdoba, Spain
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44
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Zemenick AT, Vanette RL, Rosenheim JA. Linked networks reveal dual roles of insect dispersal and species sorting for bacterial communities in flowers. OIKOS 2021. [DOI: 10.1111/oik.06818] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Ash T. Zemenick
- Dept of Entomology and Nematology, Univ. of California, Davis Davis CA USA
- Dept of Plant Biology, Michigan State Univ. East Lansing MI USA
| | - Rachel L. Vanette
- Dept of Entomology and Nematology, Univ. of California, Davis Davis CA USA
| | - Jay A. Rosenheim
- Dept of Entomology and Nematology, Univ. of California, Davis Davis CA USA
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45
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Bösch Y, Britt E, Perren S, Naef A, Frey JE, Bühlmann A. Dynamics of the Apple Fruit Microbiome after Harvest and Implications for Fruit Quality. Microorganisms 2021; 9:microorganisms9020272. [PMID: 33525588 PMCID: PMC7912366 DOI: 10.3390/microorganisms9020272] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 01/15/2021] [Accepted: 01/25/2021] [Indexed: 01/04/2023] Open
Abstract
The contribution of the apple microbiome to the production chain of apple was so far largely unknown. Here, we describe the apple fruit microbiome and influences on its composition by parameters such as storage season, storage duration, storage technology, apple variety, and plant protection schemes. A combined culturing and metabarcoding approach revealed significant differences in the abundance, composition, and diversity of the apple fruit microbiome. We showed that relatively few genera contribute a large portion of the microbiome on fruit and that the fruit microbiome changes during the storage season depending on the storage conditions. In addition, we show that the plant protection regime has an influence on the diversity of the fruit microbiome and on the dynamics of pathogenic fungal genera during the storage season. For the genus Neofabraea, the quantitative results from the metabarcoding approach were validated with real-time PCR. In conclusion, we identified key parameters determining the composition and temporal changes of the apple fruit microbiome, and the main abiotic driving factors of microbiome diversity on apple fruit were characterized.
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Affiliation(s)
- Yvonne Bösch
- Competence Division Plants and Plant Products, Agroscope, Müller-Thurgaustr 29, 8820 Wädenswil, Switzerland; (Y.B.); (E.B.); (S.P.); (A.N.)
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Box 7026, 75007 Uppsala, Sweden
| | - Elisabeth Britt
- Competence Division Plants and Plant Products, Agroscope, Müller-Thurgaustr 29, 8820 Wädenswil, Switzerland; (Y.B.); (E.B.); (S.P.); (A.N.)
- Swiss Forest Protection, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Zürcherstrasse 111, 8903 Birmensdorf, Switzerland
| | - Sarah Perren
- Competence Division Plants and Plant Products, Agroscope, Müller-Thurgaustr 29, 8820 Wädenswil, Switzerland; (Y.B.); (E.B.); (S.P.); (A.N.)
| | - Andreas Naef
- Competence Division Plants and Plant Products, Agroscope, Müller-Thurgaustr 29, 8820 Wädenswil, Switzerland; (Y.B.); (E.B.); (S.P.); (A.N.)
| | - Jürg E. Frey
- Competence Division Method Development and Analytics, Agroscope, Müller-Thurgaustr 29, 8820 Wädenswil, Switzerland;
| | - Andreas Bühlmann
- Competence Division Plants and Plant Products, Agroscope, Müller-Thurgaustr 29, 8820 Wädenswil, Switzerland; (Y.B.); (E.B.); (S.P.); (A.N.)
- Correspondence: ; Tel.: +41-584-606-424
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46
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Moroenyane I, Tremblay J, Yergeau É. Temporal and spatial interactions modulate the soybean microbiome. FEMS Microbiol Ecol 2021; 97:fiaa2062. [PMID: 33367840 DOI: 10.1093/femsec/fiaa206] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 10/05/2020] [Indexed: 12/26/2022] Open
Abstract
Managed agricultural ecosystems are unique systems where crops and microbes are intrinsically linked. This study focuses on discerning microbiome successional patterns across all plant organs and tests for evidence of niche differentiation along temporal and spatial axes. Soybean plants were grown in an environmental chamber till seed maturation. Samples from various developmental stages (emergence, growth, flowering and maturation) and compartments (leaf, stem, root and rhizosphere) were collected. Community structure and composition were assessed with 16S rRNA gene and ITS region amplicon sequencing. Overall, the interaction between spatial and temporal dynamics modulated alpha and beta diversity patterns. Time lag analysis on measured diversity indices highlighted a strong temporal dependence of communities. Spatial and temporal interactions influenced the relative abundance of the most abundant genera, whilst random forest predictions reinforced the observed localisation patterns of abundant genera. Overall, our results show that spatial and temporal interactions tend to maintain high levels of biodiversity within the bacterial/archaeal community, whilst in fungal communities OTUs within the same genus tend to have overlapping niches.
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Affiliation(s)
- Itumeleng Moroenyane
- Institut national de la recherche scientifique, Centre Armand-Frappier Santé Biotechnologie, 531 boulevard des Prairies, Laval, Québec, H7V1B7, Canada
| | - Julien Tremblay
- Energy, Mining, and Environment, Natural Resource Council Canada, 6100 avenue Royalmount, Montréal, Québec, H4P 2R2, Canada
| | - Étienne Yergeau
- Institut national de la recherche scientifique, Centre Armand-Frappier Santé Biotechnologie, 531 boulevard des Prairies, Laval, Québec, H7V1B7, Canada
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47
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Hayes RA, Rebolleda‐Gómez M, Butela K, Cabo LF, Cullen N, Kaufmann N, O'Neill S, Ashman T. Spatially explicit depiction of a floral epiphytic bacterial community reveals role for environmental filtering within petals. Microbiologyopen 2021; 10:e1158. [PMID: 33650801 PMCID: PMC7859501 DOI: 10.1002/mbo3.1158] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 12/21/2020] [Accepted: 12/22/2020] [Indexed: 01/04/2023] Open
Abstract
The microbiome of flowers (anthosphere) is an understudied compartment of the plant microbiome. Within the flower, petals represent a heterogeneous environment for microbes in terms of resources and environmental stress. Yet, little is known of drivers of structure and function of the epiphytic microbial community at the within-petal scale. We characterized the petal microbiome in two co-flowering plants that differ in the pattern of ultraviolet (UV) absorption along their petals. Bacterial communities were similar between plant hosts, with only rare phylogenetically distant species contributing to differences. The epiphyte community was highly culturable (75% of families) lending confidence in the spatially explicit isolation and characterization of bacteria. In one host, petals were heterogeneous in UV absorption along their length, and in these, there was a negative relationship between growth rate and position on the petal, as well as lower UV tolerance in strains isolated from the UV-absorbing base than from UV reflecting tip. A similar pattern was not seen in microbes isolated from a second host whose petals had uniform patterning along their length. Across strains, the variation in carbon usage and chemical tolerance followed common phylogenetic patterns. This work highlights the value of petals for spatially explicit explorations of bacteria of the anthosphere.
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Affiliation(s)
- Rebecca A. Hayes
- Department of Biological SciencesUniversity of PittsburghPittsburghPAUSA
| | - Maria Rebolleda‐Gómez
- Department of Biological SciencesUniversity of PittsburghPittsburghPAUSA
- Department of Ecology and Evolutionary BiologyYale UniversityNew HavenCTUSA
| | - Kristen Butela
- Department of Biological SciencesUniversity of PittsburghPittsburghPAUSA
| | - Leah F. Cabo
- Department of Biological SciencesUniversity of PittsburghPittsburghPAUSA
| | - Nevin Cullen
- Department of Biological SciencesUniversity of PittsburghPittsburghPAUSA
| | - Nancy Kaufmann
- Department of Biological SciencesUniversity of PittsburghPittsburghPAUSA
| | - Steffani O'Neill
- Department of Biological SciencesUniversity of PittsburghPittsburghPAUSA
| | - Tia‐Lynn Ashman
- Department of Biological SciencesUniversity of PittsburghPittsburghPAUSA
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48
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Vannette RL. The Floral Microbiome: Plant, Pollinator, and Microbial Perspectives. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2020. [DOI: 10.1146/annurev-ecolsys-011720-013401] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Flowers at times host abundant and specialized communities of bacteria and fungi that influence floral phenotypes and interactions with pollinators. Ecological processes drive variation in microbial abundance and composition at multiple scales, including among plant species, among flower tissues, and among flowers on the same plant. Variation in microbial effects on floral phenotype suggests that microbial metabolites could cue the presence or quality of rewards for pollinators, but most plants are unlikely to rely on microbes for pollinator attraction or reproduction. From a microbial perspective, flowers offer opportunities to disperse between habitats, but microbial species differ in requirements for and benefits received from such dispersal. The extent to which floral microbes shape the evolution of floral traits, influence fitness of floral visitors, and respond to anthropogenic change is unclear. A deeper understanding of these phenomena could illuminate the ecological and evolutionary importance of floral microbiomes and their role in the conservation of plant–pollinator interactions.
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Affiliation(s)
- Rachel L. Vannette
- Department of Entomology and Nematology, University of California, Davis, California 95616, USA
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49
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Floral fungal-bacterial community structure and co-occurrence patterns in four sympatric island plant species. Fungal Biol 2020; 125:49-61. [PMID: 33317776 DOI: 10.1016/j.funbio.2020.10.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 10/06/2020] [Accepted: 10/08/2020] [Indexed: 01/30/2023]
Abstract
Flowers' fungal and bacterial communities can exert great impacts on host plant wellness and reproductive success-both directly and indirectly through species interactions. However, information about community structure and co-occurrence patterns in floral microbiome remains scarce. Here, using culture-independent methods, we investigated fungal and bacterial communities associated with stamens and pistils of four plant species (Scaevola taccada, Ipomoea cairica, Ipomoea pes-caprae, and Mussaenda kwangtungensis) growing together under the same environment conditions in an island located in South China. Plant species identity significantly influenced community composition of floral fungi but not bacteria. Stamen and pistil microbiomes did not differ in community composition, but differed in co-occurrence network topological features. Compared with the stamen network, pistil counterpart had fewer links between bacteria and fungi and showed more modular but less concentrated and connected structure. In addition, degree distribution of microbial network in each host species and each microhabitat (stamen or pistil) followed a significant power-law pattern. These results enhance our understanding in the assembly principles and ecological interactions of floral microbial communities.
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50
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Abstract
Here we show the bacteriome of wasted chewing gums from five different countries and the microbial successions on wasted gums during three months of outdoors exposure. In addition, a collection of bacterial strains from wasted gums was set, and the biodegradation capability of different gum ingredients by the isolates was tested. Our results reveal that the oral microbiota present in gums after being chewed, characterised by the presence of species such as Streptococcus spp. or Corynebacterium spp., evolves in a few weeks to an environmental bacteriome characterised by the presence of Acinetobacter spp., Sphingomonas spp. and Pseudomonas spp. Wasted chewing gums collected worldwide contain a typical sub-aerial biofilm bacteriome, characterised by species such as Sphingomonas spp., Kocuria spp., Deinococcus spp. and Blastococcus spp. Our findings have implications for a wide range of disciplines, including forensics, contagious disease control, or bioremediation of wasted chewing gum residues.
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