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Law SR, Mathes F, Paten AM, Alexandre PA, Regmi R, Reid C, Safarchi A, Shaktivesh S, Wang Y, Wilson A, Rice SA, Gupta VVSR. Life at the borderlands: microbiomes of interfaces critical to One Health. FEMS Microbiol Rev 2024; 48:fuae008. [PMID: 38425054 PMCID: PMC10977922 DOI: 10.1093/femsre/fuae008] [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: 07/26/2023] [Revised: 02/12/2024] [Accepted: 02/27/2024] [Indexed: 03/02/2024] Open
Abstract
Microbiomes are foundational components of the environment that provide essential services relating to food security, carbon sequestration, human health, and the overall well-being of ecosystems. Microbiota exert their effects primarily through complex interactions at interfaces with their plant, animal, and human hosts, as well as within the soil environment. This review aims to explore the ecological, evolutionary, and molecular processes governing the establishment and function of microbiome-host relationships, specifically at interfaces critical to One Health-a transdisciplinary framework that recognizes that the health outcomes of people, animals, plants, and the environment are tightly interconnected. Within the context of One Health, the core principles underpinning microbiome assembly will be discussed in detail, including biofilm formation, microbial recruitment strategies, mechanisms of microbial attachment, community succession, and the effect these processes have on host function and health. Finally, this review will catalogue recent advances in microbiology and microbial ecology methods that can be used to profile microbial interfaces, with particular attention to multi-omic, advanced imaging, and modelling approaches. These technologies are essential for delineating the general and specific principles governing microbiome assembly and functions, mapping microbial interconnectivity across varying spatial and temporal scales, and for the establishment of predictive frameworks that will guide the development of targeted microbiome-interventions to deliver One Health outcomes.
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Affiliation(s)
- Simon R Law
- CSIRO MOSH-Future Science Platform, Australia
- CSIRO Agriculture and Food, Canberra, ACT 2601, Australia
| | - Falko Mathes
- CSIRO MOSH-Future Science Platform, Australia
- CSIRO Environment, Floreat, WA 6014, Australia
| | - Amy M Paten
- CSIRO MOSH-Future Science Platform, Australia
- CSIRO Environment, Canberra, ACT 2601, Australia
| | - Pamela A Alexandre
- CSIRO MOSH-Future Science Platform, Australia
- CSIRO Agriculture and Food, St Lucia, Qld 4072, Australia
| | - Roshan Regmi
- CSIRO MOSH-Future Science Platform, Australia
- CSIRO Agriculture and Food, Urrbrae, SA 5064, Australia
| | - Cameron Reid
- CSIRO MOSH-Future Science Platform, Australia
- CSIRO Environment, Urrbrae, SA 5064, Australia
| | - Azadeh Safarchi
- CSIRO MOSH-Future Science Platform, Australia
- CSIRO Health and Biosecurity, Westmead, NSW 2145, Australia
| | - Shaktivesh Shaktivesh
- CSIRO MOSH-Future Science Platform, Australia
- CSIRO Data 61, Clayton, Vic 3168, Australia
| | - Yanan Wang
- CSIRO MOSH-Future Science Platform, Australia
- CSIRO Health and Biosecurity, Adelaide SA 5000, Australia
| | - Annaleise Wilson
- CSIRO MOSH-Future Science Platform, Australia
- CSIRO Health and Biosecurity, Geelong, Vic 3220, Australia
| | - Scott A Rice
- CSIRO MOSH-Future Science Platform, Australia
- CSIRO Agriculture, and Food, Westmead, NSW 2145, Australia
| | - Vadakattu V S R Gupta
- CSIRO MOSH-Future Science Platform, Australia
- CSIRO Agriculture and Food, Urrbrae, SA 5064, Australia
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Hassan FU, Liu C, Mehboob M, Bilal RM, Arain MA, Siddique F, Chen F, Li Y, Zhang J, Shi P, Lv B, Lin Q. Potential of dietary hemp and cannabinoids to modulate immune response to enhance health and performance in animals: opportunities and challenges. Front Immunol 2023; 14:1285052. [PMID: 38111585 PMCID: PMC10726122 DOI: 10.3389/fimmu.2023.1285052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 11/17/2023] [Indexed: 12/20/2023] Open
Abstract
Cannabinoids are a group of bioactive compounds abundantly present in Cannabis sativa plant. The active components of cannabis with therapeutic potential are known as cannabinoids. Cannabinoids are divided into three groups: plant-derived cannabinoids (phytocannabinoids), endogenous cannabinoids (endocannabinoids), and synthetic cannabinoids. These compounds play a crucial role in the regulation various physiological processes including the immune modulation by interacting with the endocannabinoid system (A complex cell-signaling system). Cannabinoid receptor type 1 (CB1) stimulates the binding of orexigenic peptides and inhibits the attachment of anorexigenic proteins to hypothalamic neurons in mammals, increasing food intake. Digestibility is unaffected by the presence of any cannabinoids in hemp stubble. Endogenous cannabinoids are also important for the peripheral control of lipid processing in adipose tissue, in addition to their role in the hypothalamus regulation of food intake. Regardless of the kind of synaptic connection or the length of the transmission, endocannabinoids play a crucial role in inhibiting synaptic transmission through a number of mechanisms. Cannabidiol (CBD) mainly influences redox equilibrium through intrinsic mechanisms. Useful effects of cannabinoids in animals have been mentioned e.g., for disorders of the cardiovascular system, pain treatment, disorders of the respiratory system or metabolic disorders. Dietary supplementation of cannabinoids has shown positive effects on health, growth and production performance of small and large animals. Animal fed diet supplemented with hemp seeds (180 g/day) or hemp seed cake (143 g/kg DM) had achieved batter performance without any detrimental effects. But the higher level of hemp or cannabinoid supplementation suppress immune functions and reduce productive performance. With an emphasis on the poultry and ruminants, this review aims to highlight the properties of cannabinoids and their derivatives as well as their significance as a potential feed additive in their diets to improve the immune status and health performance of animals.
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Affiliation(s)
- Faiz-ul Hassan
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
- Faculty of Animal Production and Technology, Cholistan University of Veterinary and Animal Sciences, Bahawalpur, Pakistan
| | - Chunjie Liu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Maryam Mehboob
- Department of Zoology, Wildlife and Fisheries, University of Agriculture, Faisalabad, Pakistan
| | - Rana Muhammad Bilal
- Faculty of Animal Production and Technology, Cholistan University of Veterinary and Animal Sciences, Bahawalpur, Pakistan
| | - Muhammad Asif Arain
- Faculty of Veterinary and Animal Sciences, Lasbela University of Agriculture, Water and Marine Sciences, Uthal, Balochistan, Pakistan
| | - Faisal Siddique
- Faculty of Animal Production and Technology, Cholistan University of Veterinary and Animal Sciences, Bahawalpur, Pakistan
| | - Fengming Chen
- Hunan Provincial Key Laboratory of the TCM Agricultural Biogenomics, Changsha Medical University, Changsha, China
| | - Yuying Li
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Jingmeng Zhang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Pengjun Shi
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Biguang Lv
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Qian Lin
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
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Xu Y, Zhu M, Feng Y, Xu H. Panax notoginseng-microbiota interactions: From plant cultivation to medicinal application. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2023; 119:154978. [PMID: 37549538 DOI: 10.1016/j.phymed.2023.154978] [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: 04/03/2023] [Revised: 06/25/2023] [Accepted: 07/15/2023] [Indexed: 08/09/2023]
Abstract
BACKGROUND Microbiomes and their host plants are closely linked with each other; for example, the microbiome affects plant growth, fitness, nutrient uptake, stress tolerance and pathogen resistance, whereas the host plant supports the photosynthetically carbon-rich nutrition of the microbiome. The importance of the microbiome in plant‒soil ecosystems is unquestioned and has expanded to influence the medicinal application of some herbal plants via the gut microbiota. PURPOSE Herbal plant-microbiome interactions may provide novel knowledge to enhance the robustness of herbal plant crop performance and medicinal applications, which requires a systematic review and preceding discussion. STUDY DESIGN AND METHODS The interactions between Panax notoginseng and microorganisms (from soil to host) were reviewed from the literature. The terms "Panax notoginseng" and "microbiota" were used in combination with the keywords "microbiota/microbes", "bacteria/bacterium" or "fungi/fungus" or "endophyte", as well as our targeted bioactive phytochemicals, including saponins and ginsenosides. RESULT Our study focuses on the famous medicinal herb Panax notoginseng F. H. Chen and proposes that the microbiota is a crucial participant not only in the cultivation of this herbal plant but also in its medicinal application. We also summarize and discuss how these plant‒microbe co-associations shape the assembly of plant-related microbiomes and produce bioactive phytochemicals, as well as influence beneficial herbal traits, such as herbal plant health and pharmacology. In addition, we also highlight future directions. CONCLUSION The rhizosphere and endophytic microbiome of Panax notoginseng are indirectly or directly involved in plant health, biomass production, and the synthesis/biotransformation of plant secondary metabolites. Harnessing the microbiome to improve the quality of traditional Chinese medicine and improve the value of medicinal plants for human health is highly promising.
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Affiliation(s)
- Yu Xu
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Mengjie Zhu
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Yibin Feng
- School of Chinese Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong.
| | - Hongxi Xu
- Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, PR China.
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Beiralas R, Ozer N, Segev E. Abundant Sulfitobacter marine bacteria protect Emiliania huxleyi algae from pathogenic bacteria. ISME COMMUNICATIONS 2023; 3:100. [PMID: 37740057 PMCID: PMC10517135 DOI: 10.1038/s43705-023-00311-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 09/10/2023] [Accepted: 09/13/2023] [Indexed: 09/24/2023]
Abstract
Emiliania huxleyi is a unicellular micro-alga that forms massive oceanic blooms and plays key roles in global biogeochemical cycles. Mounting studies demonstrate various stimulatory and inhibitory influences that bacteria have on the E. huxleyi physiology. To investigate these algal-bacterial interactions, laboratory co-cultures have been established by us and by others. Owing to these co-cultures, various mechanisms of algal-bacterial interactions have been revealed, many involving bacterial pathogenicity towards algae. However, co-cultures represent a significantly simplified system, lacking the complexity of bacterial communities. In order to investigate bacterial pathogenicity within an ecologically relevant context, it becomes imperative to enhance the microbial complexity of co-culture setups. Phaeobacter inhibens bacteria are known pathogens that cause the death of E. huxleyi algae in laboratory co-culture systems. The bacteria depend on algal exudates for growth, but when algae senesce, bacteria switch to a pathogenic state and induce algal death. Here we investigate whether P. inhibens bacteria can induce algal death in the presence of a complex bacterial community. We show that an E. huxleyi-associated bacterial community protects the alga from the pathogen, although the pathogen occurs within the community. To study how the bacterial community regulates pathogenicity, we reduced the complex bacterial community to a five-member synthetic community (syncom). The syncom is comprised of a single algal host and five isolated bacterial species, which represent major bacterial groups that are naturally associated with E. huxleyi. We discovered that a single bacterial species in the reduced community, Sulfitobacter pontiacus, protects the alga from the pathogen. We further found that algal protection from P. inhibens pathogenicity is a shared trait among several Sulfitobacter species. Algal protection by bacteria might be a common phenomenon with ecological significance, which is overlooked in reduced co-culture systems.
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Affiliation(s)
- Roni Beiralas
- Department of Plant and Environmental Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Noy Ozer
- Department of Plant and Environmental Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Einat Segev
- Department of Plant and Environmental Sciences, The Weizmann Institute of Science, Rehovot, Israel.
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Guo Q, Zhu Y, Korpelainen H, Niinemets Ü, Li C. How does plant sex alter microbiota assembly in dioecious plants? Trends Microbiol 2023; 31:894-902. [PMID: 37120361 DOI: 10.1016/j.tim.2023.03.014] [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: 02/11/2023] [Revised: 03/17/2023] [Accepted: 03/20/2023] [Indexed: 05/01/2023]
Abstract
Plant microbiota can greatly impact plant growth, defense, and health in different environments. Thus, it might be evolutionarily beneficial for plants to be able to control processes related to microbiota assembly. Dioecious plant species display sexual dimorphism in morphology, physiology, and immunity. These differences imply that male and female individuals might differently regulate their microbiota, but the role of sex in microbiota assembly has been largely neglected so far. Here, we introduce the mechanism of how sex controls microbiota in plants analogically to the sex regulation of gut microbiota in animals, in particular in humans. We argue that plant sex imposes selective pressure on filtering and constructing microbiota in the rhizosphere, phyllosphere, and endosphere along the soil-plant continuum. Since male plants are more resistant than female plants to environmental stresses, we suggest that a male host forms more stable and resistant plant microbiota that cooperate more effectively with the host to resist stresses. Male and female plants can distinguish whether a plant is of the same or different sex, and males can alleviate stress-caused damage in females. The impact of a male host on microbiota would protect female plants from unfavorable environments.
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Affiliation(s)
- Qingxue Guo
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Yuanjing Zhu
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Helena Korpelainen
- Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, P.O. Box 27, FI-00014, Finland
| | - Ülo Niinemets
- Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Kreutzwaldi 1, 51006, Tartu, Estonia
| | - Chunyang Li
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China.
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Jamieson PE, Carbonero F, Stevens JF. Dietary (poly)phenols mitigate inflammatory bowel disease: Therapeutic targets, mechanisms of action, and clinical observations. Curr Res Food Sci 2023; 6:100521. [PMID: 37266414 PMCID: PMC10230173 DOI: 10.1016/j.crfs.2023.100521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 05/14/2023] [Accepted: 05/16/2023] [Indexed: 06/03/2023] Open
Abstract
Inflammatory bowel diseases (IBD), which include Crohn's disease and ulcerative colitis, are a rapidly growing public health concern worldwide. These diseases are heterogeneous at the clinical, immunological, molecular, genetic, and microbial level, but characteristically involve a disrupted immune-microbiome axis. Shortcomings in conventional treatment options warrant the need for novel therapeutic strategies to mitigate these life-long and relapsing disorders of the gastrointestinal tract. Polyphenols, a diverse group of phytochemicals, have gained attention as candidate treatments due to their array of biological effects. Polyphenols exert broad anti-inflammatory and antioxidant effects through the modulation of cellular signaling pathways and transcription factors important in IBD progression. Polyphenols also bidirectionally modulate the gut microbiome, supporting commensals and inhibiting pathogens. One of the primary means by which gut microbiota interface with the host is through the production of metabolites, which are small molecules produced as intermediate or end products of metabolism. There is growing evidence to support that modulation of the gut microbiome by polyphenols restores microbially derived metabolites critical to the maintenance of intestinal homeostasis that are adversely disrupted in IBD. This review aims to define the therapeutic targets of polyphenols that may be important for mitigation of IBD symptoms, as well as to collate evidence for their clinical use from randomized clinical trials.
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Affiliation(s)
- Paige E. Jamieson
- School of Biological and Population Health Sciences, Oregon State University, Corvallis, OR, 97331, USA
- Linus Pauling Institute, Oregon State University, Corvallis, OR, 97331, USA
| | - Franck Carbonero
- Department of Nutrition and Exercise Physiology, Washington State University, Spokane, WA, 99202, USA
| | - Jan F. Stevens
- Linus Pauling Institute, Oregon State University, Corvallis, OR, 97331, USA
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, OR, 97331, USA
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Microbials for Agriculture: Why Do They Call Them Biostimulants When They Mean Probiotics? Microorganisms 2023; 11:microorganisms11010153. [PMID: 36677445 PMCID: PMC9867170 DOI: 10.3390/microorganisms11010153] [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: 11/28/2022] [Revised: 12/28/2022] [Accepted: 01/02/2023] [Indexed: 01/11/2023] Open
Abstract
There is growing interest in using plant-beneficial microorganisms to partially replace chemicals and help reduce the environmental impact of agriculture. Formulated microbial products or inoculants for agriculture contain single strains or a consortium of live microbes, well characterized and biosafe, which can contribute to the growth, health, and development of a plant host. This concept conforms to the definition of probiotics. However, some plant-growth-promoting microorganisms (PGPMs) have been considered a category of biostimulants since some years ago, despite the traditional concept of biostimulants involves substances or materials with no fertilizer value, which in minute amounts promote plant growth. The inclusion of PGPMs together with substances has also involved a significant distortion of the classical concept of biostimulants. Regulations such as the recent EU Fertilizing Products Regulation (EU No. 2019/1009) have incorporated the new definition of biostimulants and included microbials as a subcategory of biostimulants. We discuss that this regulation and the forthcoming European harmonized standards disregard some key features of microbial products, such as the live, true biological nature of their active principles. The factors that determine the complex functional compatibility of plant-microbe associations, and important biosafety issues that concern the intentional release of microbes into the environment, seem to be also ignored. We anticipate that by equating microbials to chemicals, the biological nature of microbial products and their specific requirements will be underestimated, with pernicious consequences for their future development and success.
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Pandey SS, Jain R, Bhardwaj P, Thakur A, Kumari M, Bhushan S, Kumar S. Plant Probiotics – Endophytes pivotal to plant health. Microbiol Res 2022; 263:127148. [DOI: 10.1016/j.micres.2022.127148] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 04/22/2022] [Accepted: 07/26/2022] [Indexed: 12/11/2022]
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Jiang G, Zhang Y, Gan G, Li W, Wan W, Jiang Y, Yang T, Zhang Y, Xu Y, Wang Y, Shen Q, Wei Z, Dini-Andreote F. Exploring rhizo-microbiome transplants as a tool for protective plant-microbiome manipulation. ISME COMMUNICATIONS 2022; 2:10. [PMID: 37938685 PMCID: PMC9723603 DOI: 10.1038/s43705-022-00094-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 01/11/2022] [Accepted: 01/18/2022] [Indexed: 04/20/2023]
Abstract
The development of strategies for effectively manipulating and engineering beneficial plant-associated microbiomes is a major challenge in microbial ecology. In this sense, the efficacy and potential implications of rhizosphere microbiome transplant (RMT) in plant disease management have only scarcely been explored in the literature. Here, we initially investigated potential differences in rhizosphere microbiomes of 12 Solanaceae eggplant varieties and accessed their level of resistance promoted against bacterial wilt disease caused by the pathogen Ralstonia solanacearum, in a 3-year field trial. We elected 6 resistant microbiomes and further tested the broad feasibility of using RMT from these donor varieties to a susceptible model Solanaceae tomato variety MicroTom. Overall, we found the rhizosphere microbiome of resistant varieties to enrich for distinct and specific bacterial taxa, of which some displayed significant associations with the disease suppression. Quantification of the RMT efficacy using source tracking analysis revealed more than 60% of the donor microbial communities to successfully colonize and establish in the rhizosphere of recipient plants. RTM from distinct resistant donors resulted in different levels of wilt disease suppression, reaching up to 47% of reduction in disease incidence. Last, we provide a culture-dependent validation of potential bacterial taxa associated with antagonistic interactions with the pathogen, thus contributing to a better understanding of the potential mechanism associated with the disease suppression. Our study shows RMT from appropriate resistant donors to be a promising tool to effectively modulate protective microbiomes and promote plant health. Together we advocate for future studies aiming at understanding the ecological processes and mechanisms mediating rates of coalescence between donor and recipient microbiomes in the plant rhizosphere.
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Affiliation(s)
- Gaofei Jiang
- Laboratory of Bio-interactions and Crop Health, Jiangsu Provincial Key Laboratory for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Nanjing, China
| | - Yuling Zhang
- Laboratory of Bio-interactions and Crop Health, Jiangsu Provincial Key Laboratory for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Nanjing, China
| | - Guiyun Gan
- Institute of Vegetable Research, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Weiliu Li
- Institute of Vegetable Research, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Wen Wan
- Laboratory of Bio-interactions and Crop Health, Jiangsu Provincial Key Laboratory for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Nanjing, China
| | - Yaqin Jiang
- Institute of Vegetable Research, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Tianjie Yang
- Laboratory of Bio-interactions and Crop Health, Jiangsu Provincial Key Laboratory for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Nanjing, China
| | - Yong Zhang
- College of Resources and Environment, Interdisciplinary Research Center for Agriculture Green Development in Yangtze River Basin, Southwest University, Chongqing, China
| | - Yangchun Xu
- Laboratory of Bio-interactions and Crop Health, Jiangsu Provincial Key Laboratory for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Nanjing, China
| | - Yikui Wang
- Institute of Vegetable Research, Guangxi Academy of Agricultural Sciences, Nanning, China.
| | - Qirong Shen
- Laboratory of Bio-interactions and Crop Health, Jiangsu Provincial Key Laboratory for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Nanjing, China
| | - Zhong Wei
- Laboratory of Bio-interactions and Crop Health, Jiangsu Provincial Key Laboratory for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Nanjing, China.
| | - Francisco Dini-Andreote
- Department of Plant Science & Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
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van Leeuwen HC, Roelofs D, Corver J, Hensbergen P. Phylogenetic analysis of the bacterial Pro-Pro-endopeptidase domain reveals a diverse family including secreted and membrane anchored proteins. CURRENT RESEARCH IN MICROBIAL SCIENCES 2021; 2:100024. [PMID: 34841315 PMCID: PMC8610288 DOI: 10.1016/j.crmicr.2021.100024] [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: 01/29/2021] [Revised: 02/19/2021] [Accepted: 02/21/2021] [Indexed: 11/21/2022] Open
Abstract
Bacterial Pro-Pro-endopeptidase (PPEP) is the latest member of the metalloendopeptidase class (E.C. 3.4.24.89). PPEP homologs are found in two firmicutes orders, clostridiales and bacillales spread over 9 genera and more than 130 species. Some PPEP homologs have acquired additional anchor domains that bind noncovalently to various elements of the bacterial peptidoglycan cell wall. Prototype family members, PPEP-1 and PPEP-2, target bacterial surface adhesion proteins, but homologs could target other extracellular proteins.
Pro-Pro-endopeptidases (PPEP, EC 3.4.24.89) are secreted, zinc metalloproteases that have the unusual capacity to cleave a peptide bond between two prolines, a bond that is generally less sensitive to proteolytic cleavage. Two well studied members of the family are PPEP-1 and PPEP-2, produced by Clostridioides difficile, a human pathogen, and Paenibacillus alvei, a bee secondary invader, respectively. Both proteases seem to be involved in mediating bacterial adhesion by cleaving cell surface anchor proteins on the bacterium itself. By using basic alignment and phylogenetic profiling analysis, this work shows that the complete family of proteins that contain a PPEP domain includes proteins from more than 130 species spread over 9 genera. These analyses also suggest that the PPEP domain spread through horizontal gene transfer events between species within the Firmicutes’ classes Bacilli and Clostridia. Bacterial species containing PPEP homologs are found in diverse habitats, varying from human pathogens and gut microbiota to free-living bacteria, which were isolated from various environments, including extreme conditions such as hot springs, desert soil and salt lakes. The phylogenetic tree reveals the relationships between family members and suggests that smaller subgroups could share cleavage specificity, substrates and functional similarity. Except for PPEP-1 and PPEP-2, no cleavage specificity, specific physiological target, or function has been assigned for any of the other PPEP-family members. Some PPEP proteins have acquired additional domains that recognize and bind noncovalently to various elements of the bacterial peptidoglycan cell-wall, anchoring these PPEPs. Secreted or anchored to the cell-wall surface PPEP proteins seem to perform various functions.
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Affiliation(s)
- Hans C van Leeuwen
- Department of CBRN Protection, Netherlands Organization for Applied Scientific Research TNO, Lange Kleiweg 137, 2288 GJ Rijswijk, the Netherlands
| | - Dick Roelofs
- KeyGene, Agro Business Park 90, 6708 PW Wageningen, the Netherlands
| | - Jeroen Corver
- Department of Medical Microbiology, Leiden University Medical Center, Albinusdreef 2, PO Box 9600, 2300 RC Leiden, the Netherlands
| | - Paul Hensbergen
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Albinusdreef 2, PO Box 9600, 2300 RC Leiden, the Netherlands
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Willing CE, Pierroz G, Guzman A, Anderegg LDL, Gao C, Coleman-Derr D, Taylor JW, Bruns TD, Dawson TE. Keep your friends close: Host compartmentalisation of microbial communities facilitates decoupling from effects of habitat fragmentation. Ecol Lett 2021; 24:2674-2686. [PMID: 34523223 DOI: 10.1111/ele.13886] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 08/25/2021] [Accepted: 08/30/2021] [Indexed: 11/28/2022]
Abstract
Root-associated fungal communities modify the climatic niches and even the competitive ability of their hosts, yet how the different components of the root microbiome are modified by habitat loss remains a key knowledge gap. Using principles of landscape ecology, we tested how free-living versus host-associated microbes differ in their response to landscape heterogeneity. Further, we explore how compartmentalisation of microbes into specialised root structures filters for key fungal symbionts. Our study demonstrates that free-living fungal community structure correlates with landscape heterogeneity, but that host-associated fungal communities depart from these patterns. Specifically, biotic filtering in roots, especially via compartmentalisation within specialised root structures, decouples the biogeographic patterns of host-associated fungal communities from the soil community. In this way, even as habitat loss and fragmentation threaten fungal diversity in the soils, plant hosts exert biotic controls to ensure associations with critical mutualists, helping to preserve the root mycobiome.
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Affiliation(s)
- Claire E Willing
- Department of Environmental Science, Policy and Management, UC Berkeley, Berkeley, California, USA
| | - Grady Pierroz
- Department of Plant and Microbial Biology, UC Berkeley, Berkeley, California, USA.,Plant Gene Expression Center, USDA-ARS, Albany, California, USA
| | - Aidee Guzman
- Department of Environmental Science, Policy and Management, UC Berkeley, Berkeley, California, USA
| | - Leander D L Anderegg
- Department of Integrative Biology, UC Berkeley, Berkeley, California, USA.,Department of Ecology, Evolution & Marine Biology, UC Santa Barbara, Santa Barbara, California, USA
| | - Cheng Gao
- Department of Plant and Microbial Biology, UC Berkeley, Berkeley, California, USA.,State Key Laboratory of Mycology, Chinese Academy of Sciences, Beijing, China
| | - Devin Coleman-Derr
- Department of Plant and Microbial Biology, UC Berkeley, Berkeley, California, USA.,Plant Gene Expression Center, USDA-ARS, Albany, California, USA
| | - John W Taylor
- Department of Plant and Microbial Biology, UC Berkeley, Berkeley, California, USA
| | - Tom D Bruns
- Department of Environmental Science, Policy and Management, UC Berkeley, Berkeley, California, USA.,Department of Plant and Microbial Biology, UC Berkeley, Berkeley, California, USA
| | - Todd E Dawson
- Department of Environmental Science, Policy and Management, UC Berkeley, Berkeley, California, USA.,Department of Integrative Biology, UC Berkeley, Berkeley, California, USA
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12
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Samaddar S, Karp DS, Schmidt R, Devarajan N, McGarvey JA, Pires AFA, Scow K. Role of soil in the regulation of human and plant pathogens: soils' contributions to people. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200179. [PMID: 34365819 DOI: 10.1098/rstb.2020.0179] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Soil and soil biodiversity play critical roles in Nature's Contributions to People (NCP) # 10, defined as Nature's ability to regulate direct detrimental effects on humans, and on human-important plants and animals, through the control or regulation of particular organisms considered to be harmful. We provide an overview of pathogens in soil, focusing on human and crop pathogens, and discuss general strategies, and examples, of how soils' extraordinarily diverse microbial communities regulate soil-borne pathogens. We review the ecological principles underpinning the regulation of soil pathogens, as well as relationships between pathogen suppression and soil health. Mechanisms and specific examples are presented of how soil and soil biota are involved in regulating pathogens of humans and plants. We evaluate how specific agricultural management practices can either promote or interfere with soil's ability to regulate pathogens. Finally, we conclude with how integrating soil, plant, animal and human health through a 'One Health' framework could lead to more integrated, efficient and multifunctional strategies for regulating detrimental organisms and processes. This article is part of the theme issue 'The role of soils in delivering Nature's Contributions to People'.
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Affiliation(s)
- Sandipan Samaddar
- Department of Land, Air and Water Resources, University of California, Davis, Davis, CA, USA
| | - Daniel S Karp
- Department of Wildlife, Fish, and Conservation Biology, University of California, Davis, Davis, CA, USA
| | - Radomir Schmidt
- Department of Land, Air and Water Resources, University of California, Davis, Davis, CA, USA
| | - Naresh Devarajan
- Department of Wildlife, Fish, and Conservation Biology, University of California, Davis, Davis, CA, USA
| | - Jeffery A McGarvey
- Agricultural Research Service, US Department of Agriculture, Albany, CA, USA
| | - Alda F A Pires
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, USA
| | - Kate Scow
- Department of Land, Air and Water Resources, University of California, Davis, Davis, CA, USA
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13
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Martínez‐Romero E, Aguirre‐Noyola JL, Bustamante‐Brito R, González‐Román P, Hernández‐Oaxaca D, Higareda‐Alvear V, Montes‐Carreto LM, Martínez‐Romero JC, Rosenblueth M, Servín‐Garcidueñas LE. We and herbivores eat endophytes. Microb Biotechnol 2021; 14:1282-1299. [PMID: 33320440 PMCID: PMC8313258 DOI: 10.1111/1751-7915.13688] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 10/06/2020] [Accepted: 10/07/2020] [Indexed: 12/16/2022] Open
Abstract
Health depends on the diet and a vegetal diet promotes health by providing fibres, vitamins and diverse metabolites. Remarkably, plants may also provide microbes. Fungi and bacteria that reside inside plant tissues (endophytes) seem better protected to survive digestion; thus, we investigated the reported evidence on the endophytic origin of some members of the gut microbiota in animals such as panda, koala, rabbits and tortoises and several herbivore insects. Data examined here showed that some members of the herbivore gut microbiota are common plant microbes, which derived to become stable microbiota in some cases. Endophytes may contribute to plant fibre or antimetabolite degradation and synthesis of metabolites with the plethora of enzymatic activities that they display; some may have practical applications, for example, Lactobacillus plantarum found in the intestinal tract, plants and in fermented food is used as a probiotic that may defend animals against bacterial and viral infections as other endophytic-enteric bacteria do. Clostridium that is an endophyte and a gut bacterium has remarkable capabilities to degrade cellulose by having cellulosomes that may be considered the most efficient nanomachines. Cellulose degradation is a challenge in animal digestion and for biofuel production. Other endophytic-enteric bacteria may have cellulases, pectinases, xylanases, tannases, proteases, nitrogenases and other enzymatic capabilities that may be attractive for biotechnological developments, indeed many endophytes are used to promote plant growth. Here, a cycle of endophytic-enteric-soil-endophytic microbes is proposed which has relevance for health and comprises the fate of animal faeces as natural microbial inoculants for plants that constitute bacterial sources for animal guts.
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Affiliation(s)
| | | | | | - Pilar González‐Román
- Programa de Ecología GenómicaCentro de Ciencias GenómicasUNAMCuernavacaMorelosMexico
| | | | | | | | | | - Mónica Rosenblueth
- Programa de Ecología GenómicaCentro de Ciencias GenómicasUNAMCuernavacaMorelosMexico
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14
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Improvement of Soil Microbial Diversity through Sustainable Agricultural Practices and Its Evaluation by -Omics Approaches: A Perspective for the Environment, Food Quality and Human Safety. Microorganisms 2021; 9:microorganisms9071400. [PMID: 34203506 PMCID: PMC8308033 DOI: 10.3390/microorganisms9071400] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 06/24/2021] [Accepted: 06/25/2021] [Indexed: 01/02/2023] Open
Abstract
Soil is one of the key elements for supporting life on Earth. It delivers multiple ecosystem services, which are provided by soil processes and functions performed by soil biodiversity. In particular, soil microbiome is one of the fundamental components in the sustainment of plant biomass production and plant health. Both targeted and untargeted management of soil microbial communities appear to be promising in the sustainable improvement of food crop yield, its nutritional quality and safety. –Omics approaches, which allow the assessment of microbial phylogenetic diversity and functional information, have increasingly been used in recent years to study changes in soil microbial diversity caused by agronomic practices and environmental factors. The application of these high-throughput technologies to the study of soil microbial diversity, plant health and the quality of derived raw materials will help strengthen the link between soil well-being, food quality, food safety and human health.
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15
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Li J, Li C, Wang M, Wang L, Liu X, Gao C, Ren L, Luo Y. Gut Structure and Microbial Communities in Sirex noctilio (Hymenoptera: Siricidae) and Their Predicted Contribution to Larval Nutrition. Front Microbiol 2021; 12:641141. [PMID: 33897646 PMCID: PMC8060704 DOI: 10.3389/fmicb.2021.641141] [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: 12/13/2020] [Accepted: 03/15/2021] [Indexed: 12/25/2022] Open
Abstract
The European woodwasp, Sirex noctilio Fabricius, is a major invasive quarantine pest that attacks and kills pine trees outside of its native range. Insect gut structure and gut microbiota play crucial roles in various life activities. Despite a few reports in nutrition and survival, an extensive study on the S. noctilio larval gut microbiome is lacking. We studied the gut structure using a stereo microscope and used high throughput sequencing of the bacterial 16S rRNA genes and fungal internal transcribed spacer 2 (ITS2) regions to investigate gut microbiota in different developmental stages of S. noctilio, including larvae, adults, and larval frass. We used PICRUSt2 to predict the functional profiles. The larval gut was thin and thread-like from the oral cavity to the anus, carrying few xylem particles in the crop. Pseudomonas, Ralstonia, and Burkholderia s.l were the dominant bacteria in the guts of larvae, adults, and frass, respectively. Even though Pseudomonas was the most abundant among all bacteria, Zoogloea, Ruminobacter, and Nitrosospira, which might be involved in degrading organic matter and fixing nitrogen occurred exclusively in the larval gut indicating their possible role in the growth and development of larvae in pine tree xylem. Fungal communities did not change significantly across different developmental stages or the frass. Amylostereum was dominant in the woodwasp’s larval gut. Functional prediction of bacterial and fungal communities revealed that they may encod enzymes involved in degrading lignocellulose and fixing nitrogen. Ours is the first study that compares gut microbial communities present in S. noctilio larvae, adults, and frass. This study could provide an understanding of larval nutrient acquisition in nutrient-deficient host xylem to some extent. Our study may unlock novel strategies for the development of pest management approaches based on interfering with the gut microbiota and restricting their role in larval survival and development.
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Affiliation(s)
- Jiale Li
- Beijing Key Laboratory for Forest Pest Control, Beijing Forestry University, Beijing, China
| | - Chengcheng Li
- Beijing Key Laboratory for Forest Pest Control, Beijing Forestry University, Beijing, China
| | - Ming Wang
- Beijing Key Laboratory for Forest Pest Control, Beijing Forestry University, Beijing, China
| | - Lixiang Wang
- Beijing Key Laboratory for Forest Pest Control, Beijing Forestry University, Beijing, China
| | - Xiaobo Liu
- Beijing Key Laboratory for Forest Pest Control, Beijing Forestry University, Beijing, China
| | - Chenglong Gao
- Beijing Key Laboratory for Forest Pest Control, Beijing Forestry University, Beijing, China
| | - Lili Ren
- Beijing Key Laboratory for Forest Pest Control, Beijing Forestry University, Beijing, China.,Sino-France Joint Laboratory for Invasive Forest Pests in Eurasia, Beijing Forestry University, Beijing, China
| | - Youqing Luo
- Beijing Key Laboratory for Forest Pest Control, Beijing Forestry University, Beijing, China.,Sino-France Joint Laboratory for Invasive Forest Pests in Eurasia, Beijing Forestry University, Beijing, China
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16
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Middleton H, Yergeau É, Monard C, Combier JP, El Amrani A. Rhizospheric Plant-Microbe Interactions: miRNAs as a Key Mediator. TRENDS IN PLANT SCIENCE 2021; 26:132-141. [PMID: 33036916 DOI: 10.1016/j.tplants.2020.09.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 09/03/2020] [Accepted: 09/04/2020] [Indexed: 05/20/2023]
Abstract
The importance of microorganisms in plant development, nutrition, and stress resistance is unquestioned and has led to a more holistic approach of plant-microbe interactions, under the holobiont concept. The structure of the plant microbiota is often described as host driven, especially in the rhizosphere, where microbial communities are shaped by diverse rhizodeposits. Gradually, this anthropogenic vision is fading and being replaced by the idea that plants and microorganisms co-shape the plant microbiota. Through coevolution, plants and microbes have developed cross-kingdom communication channels. Here, we propose that miRNAs are crucial mediators of plant-microbe interactions and microbiota shaping in the rhizosphere. Moreover, we suggest, as an alternative to generally unsuccessful strategies based on microbial inoculants, miRNAs as a promising tool for novel holobiont engineering.
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Affiliation(s)
- Harriet Middleton
- University of Rennes 1, CNRS/UMR 6553/OSUR, Ecosystems - Biodiversity - Evolution, 35042 Rennes Cedex, France.
| | - Étienne Yergeau
- Institut National de la Recherche Scientifique, Centre Armand-Frappier Santé Biotechnologie, Laval, H7V 1B7, Canada
| | - Cécile Monard
- University of Rennes 1, CNRS/UMR 6553/OSUR, Ecosystems - Biodiversity - Evolution, 35042 Rennes Cedex, France
| | - Jean-Philippe Combier
- Laboratoire de Recherche en Sciences Vegetales, UMR 5546, UPS, CNRS, Auzeville-Tolosane 31320, France
| | - Abdelhak El Amrani
- University of Rennes 1, CNRS/UMR 6553/OSUR, Ecosystems - Biodiversity - Evolution, 35042 Rennes Cedex, France
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17
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Eichmann R, Richards L, Schäfer P. Hormones as go-betweens in plant microbiome assembly. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 105:518-541. [PMID: 33332645 PMCID: PMC8629125 DOI: 10.1111/tpj.15135] [Citation(s) in RCA: 71] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 12/10/2020] [Accepted: 12/11/2020] [Indexed: 05/04/2023]
Abstract
The interaction of plants with complex microbial communities is the result of co-evolution over millions of years and contributed to plant transition and adaptation to land. The ability of plants to be an essential part of complex and highly dynamic ecosystems is dependent on their interaction with diverse microbial communities. Plant microbiota can support, and even enable, the diverse functions of plants and are crucial in sustaining plant fitness under often rapidly changing environments. The composition and diversity of microbiota differs between plant and soil compartments. It indicates that microbial communities in these compartments are not static but are adjusted by the environment as well as inter-microbial and plant-microbe communication. Hormones take a crucial role in contributing to the assembly of plant microbiomes, and plants and microbes often employ the same hormones with completely different intentions. Here, the function of hormones as go-betweens between plants and microbes to influence the shape of plant microbial communities is discussed. The versatility of plant and microbe-derived hormones essentially contributes to the creation of habitats that are the origin of diversity and, thus, multifunctionality of plants, their microbiota and ultimately ecosystems.
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Affiliation(s)
- Ruth Eichmann
- Institute of Molecular BotanyUlm UniversityUlm89069Germany
| | - Luke Richards
- School of Life SciencesUniversity of WarwickCoventryCV4 7ALUK
| | - Patrick Schäfer
- Institute of Molecular BotanyUlm UniversityUlm89069Germany
- School of Life SciencesUniversity of WarwickCoventryCV4 7ALUK
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18
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Pessione E. The Russian Doll Model: How Bacteria Shape Successful and Sustainable Inter-Kingdom Relationships. Front Microbiol 2020; 11:573759. [PMID: 33193180 PMCID: PMC7606975 DOI: 10.3389/fmicb.2020.573759] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 08/31/2020] [Indexed: 12/20/2022] Open
Abstract
Successful inter-kingdom relationships are based upon a dynamic balance between defense and cooperation. A certain degree of competition is necessary to guarantee life spread and development. On the other hand, cooperation is a powerful tool to ensure a long lasting adaptation to changing environmental conditions and to support evolution to a higher level of complexity. Bacteria can interact with their (true or potential) parasites (i.e., phages) and with their multicellular hosts. In these model interactions, bacteria learnt how to cope with their inner and outer host, transforming dangerous signals into opportunities and modulating responses in order to achieve an agreement that is beneficial for the overall participants, thus giving rise to a more complex "organism" or ecosystem. In this review, particular attention will be addressed to underline the minimal energy expenditure required for these successful interactions [e.g., moonlighting proteins, post-translational modifications (PTMs), and multitasking signals] and the systemic vision of these processes and ways of life in which the system proves to be more than the sum of the single components. Using an inside-out perspective, I will examine the possibility of multilevel interactions, in which viruses help bacteria to cope with the animal host and bacteria support the human immune system to counteract viral infection in a circular vision. In this sophisticated network, bacteria represent the precious link that insures system stability with relative low energy expenditure.
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Affiliation(s)
- Enrica Pessione
- Department of Life Sciences and Systems Biology, School of Nature Sciences, Università degli Studi di Torino, Turin, Italy
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19
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Willing CE, Pierroz G, Coleman-Derr D, Dawson TE. The generalizability of water-deficit on bacterial community composition; Site-specific water-availability predicts the bacterial community associated with coast redwood roots. Mol Ecol 2020; 29:4721-4734. [PMID: 33000868 DOI: 10.1111/mec.15666] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 09/18/2020] [Accepted: 09/21/2020] [Indexed: 12/01/2022]
Abstract
Experimental drought has been shown to delay the development of the root microbiome and increase the relative abundance of Actinobacteria, however, the generalizability of these findings to natural systems or other diverse plant hosts remains unknown. Bacterial cell wall thickness and growth morphology (e.g., filamentous or unicellular) have been proposed as traits that may mediate bacterial responses to environmental drivers. Leveraging a natural gradient of water-availability across the coast redwood (Sequoia sempervirens) range, we tested three hypotheses: (a) that site-specific water-availability is an important predictor of bacterial community composition for redwood roots and rhizosphere soils; (b) that there is relative enrichment of Actinobacteria and other monoderm bacterial groups within the redwood microbiome in response to drier conditions; and (c) that bacterial growth morphology is an important predictor of bacteria response to water-availability, where filamentous taxa will become more dominant at drier sites compared to unicellular bacteria. We find that both α- and β-diversity of redwood bacterial communities is partially explained by water-availability and that Actinobacterial enrichment is a conserved response of land plants to water-deficit. Further, we highlight how the trend of Actinobacterial enrichment in the redwood system is largely driven by the Actinomycetales. We propose bacterial growth morphology (filamentous vs. unicellular) as an additional mechanism behind the increase in Actinomycetales with increasing aridity. A trait-based approach including cell-wall thickness and growth morphology may explain the distribution of bacterial taxa across environmental gradients and help to predict patterns of bacterial community composition for a wide range of host plants.
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Affiliation(s)
- Claire E Willing
- Department of Environmental Science, Policy and Management, UC Berkeley, Berkeley, CA, USA
| | - Grady Pierroz
- Department of Plant and Microbial Biology, UC Berkeley, Berkeley, CA, USA.,Plant Gene Expression Center, USDA-ARS, Albany, CA, USA
| | - Devin Coleman-Derr
- Department of Plant and Microbial Biology, UC Berkeley, Berkeley, CA, USA.,Plant Gene Expression Center, USDA-ARS, Albany, CA, USA
| | - Todd E Dawson
- Department of Environmental Science, Policy and Management, UC Berkeley, Berkeley, CA, USA.,Department of Integrative Biology, UC Berkeley, Berkeley, CA, USA
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20
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The Role of Rhizosphere Bacteriophages in Plant Health. Trends Microbiol 2020; 28:709-718. [DOI: 10.1016/j.tim.2020.04.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 03/11/2020] [Accepted: 04/02/2020] [Indexed: 12/12/2022]
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21
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Martínez-Romero E, Aguirre-Noyola JL, Taco-Taype N, Martínez-Romero J, Zuñiga-Dávila D. Plant microbiota modified by plant domestication. Syst Appl Microbiol 2020; 43:126106. [PMID: 32847781 DOI: 10.1016/j.syapm.2020.126106] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 06/19/2020] [Accepted: 06/20/2020] [Indexed: 12/19/2022]
Abstract
Human life became largely dependent on agricultural products after distinct crop-domestication events occurred around 10,000 years ago in different geographical sites. Domestication selected suitable plants for human agricultural practices with unexpected consequences on plant microbiota, which has notable effects on plant growth and health. Among other traits, domestication has changed root architecture, exudation, or defense responses that could have modified plant microbiota. Here we present the comparison of reported data on the microbiota from widely consumed cereals and legumes and their ancestors showing that different bacteria were found in domesticated and wild plant microbiomes in some cases. Considering the large variability in plant microbiota, adequate sampling efforts and function-based approaches are needed to further support differences between the microbiota from wild and domesticated plants. The study of wild plant microbiomes could provide a valuable resource of unexploited beneficial bacteria for crops.
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Affiliation(s)
| | | | - Nataly Taco-Taype
- Laboratorio de Ecología Microbiana, Departamento de Biología, Facultad de Ciencias, Universidad Nacional Agraria La Molina, Lima, Peru
| | | | - Doris Zuñiga-Dávila
- Laboratorio de Ecología Microbiana, Departamento de Biología, Facultad de Ciencias, Universidad Nacional Agraria La Molina, Lima, Peru
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22
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Tosi M, Gaiero J, Linton N, Mafa-Attoye T, Castillo A, Dunfield K. Bacterial Endophytes: Diversity, Functional Importance, and Potential for Manipulation. ACTA ACUST UNITED AC 2020. [DOI: 10.1007/978-981-15-6125-2_1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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23
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Lathe R, St Clair D. From conifers to cognition: Microbes, brain and behavior. GENES BRAIN AND BEHAVIOR 2020; 19:e12680. [PMID: 32515128 DOI: 10.1111/gbb.12680] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Revised: 05/12/2020] [Accepted: 05/29/2020] [Indexed: 12/25/2022]
Abstract
A diversity of bacteria, protozoans and viruses ("endozoites") were recently uncovered within healthy tissues including the human brain. By contrast, it was already recognized a century ago that healthy plants tissues contain abundant endogenous microbes ("endophytes"). Taking endophytes as an informative precedent, we overview the nature, prevalence, and role of endozoites in mammalian tissues, centrally focusing on the brain, concluding that endozoites are ubiquitous in diverse tissues. These passengers often remain subclinical, but they are not silent. We address their routes of entry, mechanisms of persistence, tissue specificity, and potential to cause long-term behavioral changes and/or immunosuppression in mammals, where rabies virus is the exemplar. We extend the discussion to Herpesviridae, Coronaviridae, and Toxoplasma, as well as to diverse bacteria and yeasts, and debate the advantages and disadvantages that endozoite infection might afford to the host and to the ecosystem. We provide a clinical perspective in which endozoites are implicated in neurodegenerative disease, anxiety/depression, and schizophrenia. We conclude that endozoites are instrumental in the delicate balance between health and disease, including age-related brain disease, and that endozoites have played an important role in the evolution of brain function and human behavior.
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Affiliation(s)
- Richard Lathe
- Division of Infection Medicine, University of Edinburgh Medical School, Edinburgh, UK
| | - David St Clair
- Institute of Medical Sciences, School of Medicine, University of Aberdeen, Aberdeen, UK
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24
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de Vries FT, Griffiths RI, Knight CG, Nicolitch O, Williams A. Harnessing rhizosphere microbiomes for drought-resilient crop production. Science 2020; 368:270-274. [PMID: 32299947 DOI: 10.1126/science.aaz5192] [Citation(s) in RCA: 273] [Impact Index Per Article: 68.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Root-associated microbes can improve plant growth, and they offer the potential to increase crop resilience to future drought. Although our understanding of the complex feedbacks between plant and microbial responses to drought is advancing, most of our knowledge comes from non-crop plants in controlled experiments. We propose that future research efforts should attempt to quantify relationships between plant and microbial traits, explicitly focus on food crops, and include longer-term experiments under field conditions. Overall, we highlight the need for improved mechanistic understanding of the complex feedbacks between plants and microbes during, and particularly after, drought. This requires integrating ecology with plant, microbiome, and molecular approaches and is central to making crop production more resilient to our future climate.
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Affiliation(s)
- Franciska T de Vries
- Department of Earth and Environmental Sciences, University of Manchester, Manchester M13 9PT, UK. .,Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, 1090 GE Amsterdam, Netherlands
| | | | - Christopher G Knight
- Department of Earth and Environmental Sciences, University of Manchester, Manchester M13 9PT, UK
| | - Oceane Nicolitch
- Department of Earth and Environmental Sciences, University of Manchester, Manchester M13 9PT, UK
| | - Alex Williams
- Department of Earth and Environmental Sciences, University of Manchester, Manchester M13 9PT, UK
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25
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Fenner K, Screpanti C, Renold P, Rouchdi M, Vogler B, Rich S. Comparison of Small Molecule Biotransformation Half-Lives between Activated Sludge and Soil: Opportunities for Read-Across? ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:3148-3158. [PMID: 32062976 DOI: 10.1021/acs.est.9b05104] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Compartment-specific degradation half-lives are essential pieces of information in the regulatory risk assessment of synthetic chemicals. However, their measurement according to regulatory testing guidelines is laborious and costly. Despite the obvious ecological and economic benefits of knowing environmental degradability as early as possible, its consideration in the early phases of rational chemical design is therefore challenging. Here, we explore the possibility to use half-lives determined in highly time- and work-efficient biotransformation experiments with activated sludge and mixtures of chemicals to predict soil half-lives from regulatory simulation studies. We experimentally determined half-lives for 52 structurally diverse agrochemical active ingredients in batch reactors with three concentrations of the same activated sludge. We then developed bi- and multivariate models for predicting half-lives in soil by regressing the experimentally determined half-lives in activated sludge against average soil half-lives of the same chemicals extracted from regulatory data. The models differed in how we accounted for sorption-related bioavailability differences in soil and activated sludge. The best-performing models exhibited good coefficients of determination (R2 of around 0.8) and low average errors (<factor of 3 in half-life predictions) and were robust in cross-validation. From a practical perspective, these results suggest that it may indeed be possible to read across from half-lives determined in highly efficient biotransformation experiments in activated sludge to soil half-lives, which are obtained from much more work- and resource-intense regulatory studies, and that these predictions are clearly superior to predictions based on the output of BIOWIN, a publicly available quantitative structure-biodegradation relationship (QSBR) model. From a theoretical perspective, these results suggest that soil and activated sludge microbial communities, although certainly different in terms of taxonomic composition, may be functionally similar with respect to the enzymatic transformation of environmentally relevant concentrations of a diverse range of chemical compounds.
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Affiliation(s)
- Kathrin Fenner
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
- Institute of Biogeochemistry and Pollutant Dynamics, ETH Zürich, 8092 Zürich, Switzerland
- Department of Chemistry, University of Zürich, 8057 Zürich, Switzerland
| | - Claudio Screpanti
- Chemical Research, Syngenta Crop Protection AG, Schaffhauserstrasse 101, CH-4332 Stein, Switzerland
| | - Peter Renold
- Chemical Research, Syngenta Crop Protection AG, Schaffhauserstrasse 101, CH-4332 Stein, Switzerland
| | - Marwa Rouchdi
- Chemical Research, Syngenta Crop Protection AG, Schaffhauserstrasse 101, CH-4332 Stein, Switzerland
| | - Bernadette Vogler
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
| | - Stephanie Rich
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
- Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
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Taghinasab M, Jabaji S. Cannabis Microbiome and the Role of Endophytes in Modulating the Production of Secondary Metabolites: An Overview. Microorganisms 2020; 8:E355. [PMID: 32131457 PMCID: PMC7143057 DOI: 10.3390/microorganisms8030355] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 02/26/2020] [Accepted: 02/28/2020] [Indexed: 12/19/2022] Open
Abstract
Plants, including cannabis (Cannabis sativa subsp. sativa), host distinct beneficial microbial communities on and inside their tissues and organs, including seeds. They contribute to plant growth, facilitating mineral nutrient uptake, inducing defence resistance against pathogens, and modulating the production of plant secondary metabolites. Understanding the microbial partnerships with cannabis has the potential to affect the agricultural practices by improving plant fitness and the yield of cannabinoids. Little is known about this beneficial cannabis-microbe partnership, and the complex relationship between the endogenous microbes associated with various tissues of the plant, and the role that cannabis may play in supporting or enhancing them. This review will consider cannabis microbiota studies and the effects of endophytes on the elicitation of secondary metabolite production in cannabis plants. The review aims to shed light on the importance of the cannabis microbiome and how cannabinoid compound concentrations can be stimulated through symbiotic and/or mutualistic relationships with endophytes.
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Affiliation(s)
| | - Suha Jabaji
- Plant Science Department, Faculty of Agricultural and Environmental Sciences, MacDonald Campus of McGill University, QC H9X 3V9, Canada;
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Krishna SBN, Dubey A, Malla MA, Kothari R, Upadhyay CP, Adam JK, Kumar A. Integrating Microbiome Network: Establishing Linkages Between Plants, Microbes and Human Health. Open Microbiol J 2019. [DOI: 10.2174/1874285801913020330] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The trillions of microbes that colonize and live around us govern the health of both plants and animals through a cascade of direct and indirect mechanisms. Understanding of this enormous and largely untapped microbial diversity has been the focus of microbial research from the past few decades or so. Amidst the advancements in sequencing technologies, significant progress has been made to taxonomically and functionally catalogue these microbes and also to establish their exact role in the health and disease state. In comparison to the human microbiome, plants are also surrounded by a vast diversity of microbes that form complex ecological communities that affect plant growth and health through collective metabolic activities and interactions. This plant microbiome has a substantial influence on human health and environment via its passage through the nasal route and digestive tract and is responsible for changing our gut microbiome. This review primarily focused on the advances and challenges in microbiome research at the interface of plant and human, and role of microbiome at different compartments of the body’s ecosystems along with their correlation to health and diseases. This review also highlighted the potential therapies in modulating the gut microbiota and technologies for studying the microbiome.
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The Xylella fastidiosa-Resistant Olive Cultivar "Leccino" Has Stable Endophytic Microbiota during the Olive Quick Decline Syndrome (OQDS). Pathogens 2019; 9:pathogens9010035. [PMID: 31906093 PMCID: PMC7168594 DOI: 10.3390/pathogens9010035] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 12/20/2019] [Accepted: 12/23/2019] [Indexed: 12/26/2022] Open
Abstract
Xylella fastidiosa is a highly virulent pathogen that causes Olive Quick Decline Syndrome (OQDS), which is currently devastating olive plantations in the Salento region (Apulia, Southern Italy). We explored the microbiome associated with X. fastidiosa-infected (Xf-infected) and -uninfected (Xf-uninfected) olive trees in Salento, to assess the level of dysbiosis and to get first insights into the potential role of microbial endophytes in protecting the host from the disease. The resistant cultivar “Leccino” was compared to the susceptible cultivar “Cellina di Nardò”, in order to identify microbial taxa and parameters potentially involved in resistance mechanisms. Metabarcoding of 16S rRNA genes and fungal ITS2 was used to characterize both total and endophytic microbiota in olive branches and leaves. “Cellina di Nardò” showed a drastic dysbiosis after X. fastidiosa infection, while “Leccino” (both infected and uninfected) maintained a similar microbiota. The genus Pseudomonas dominated all “Leccino” and Xf-uninfected “Cellina di Nardò” trees, whereas Ammoniphilus prevailed in Xf-infected “Cellina di Nardò”. Diversity of microbiota in Xf-uninfected “Leccino” was higher than in Xf-uninfected “Cellina di Nardò”. Several bacterial taxa specifically associated with “Leccino” showed potential interactions with X. fastidiosa. The maintenance of a healthy microbiota with higher diversity and the presence of cultivar-specific microbes might support the resistance of “Leccino” to X. fastidiosa. Such beneficial bacteria might be isolated in the future for biological treatment of the OQDS.
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Does Soil Contribute to the Human Gut Microbiome? Microorganisms 2019; 7:microorganisms7090287. [PMID: 31450753 PMCID: PMC6780873 DOI: 10.3390/microorganisms7090287] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 08/19/2019] [Accepted: 08/20/2019] [Indexed: 12/13/2022] Open
Abstract
Soil and the human gut contain approximately the same number of active microorganisms, while human gut microbiome diversity is only 10% that of soil biodiversity and has decreased dramatically with the modern lifestyle. We tracked relationships between the soil microbiome and the human intestinal microbiome. We propose a novel environmental microbiome hypothesis, which implies that a close linkage between the soil microbiome and the human intestinal microbiome has evolved during evolution and is still developing. From hunter-gatherers to an urbanized society, the human gut has lost alpha diversity. Interestingly, beta diversity has increased, meaning that people in urban areas have more differentiated individual microbiomes. On top of little contact with soil and feces, hygienic measures, antibiotics and a low fiber diet of processed food have led to a loss of beneficial microbes. At the same time, loss of soil biodiversity is observed in many rural areas. The increasing use of agrochemicals, low plant biodiversity and rigorous soil management practices have a negative effect on the biodiversity of crop epiphytes and endophytes. These developments concur with an increase in lifestyle diseases related to the human intestinal microbiome. We point out the interference with the microbial cycle of urban human environments versus pre-industrial rural environments. In order to correct these interferences, it may be useful to adopt a different perspective and to consider the human intestinal microbiome as well as the soil/root microbiome as 'superorganisms' which, by close contact, replenish each other with inoculants, genes and growth-sustaining molecules.
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Bustamante-Brito R, Vera-Ponce de León A, Rosenblueth M, Martínez-Romero JC, Martínez-Romero E. Metatranscriptomic Analysis of the Bacterial Symbiont Dactylopiibacterium carminicum from the Carmine Cochineal Dactylopius coccus (Hemiptera: Coccoidea: Dactylopiidae). Life (Basel) 2019; 9:life9010004. [PMID: 30609847 PMCID: PMC6463064 DOI: 10.3390/life9010004] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 12/14/2018] [Accepted: 12/25/2018] [Indexed: 11/16/2022] Open
Abstract
The scale insect Dactylopius coccus produces high amounts of carminic acid, which has historically been used as a pigment by pre-Hispanic American cultures. Nowadays carmine is found in food, cosmetics, and textiles. Metagenomic approaches revealed that Dactylopius spp. cochineals contain two Wolbachia strains, a betaproteobacterium named Candidatus Dactylopiibacterium carminicum and Spiroplasma, in addition to different fungi. We describe here a transcriptomic analysis indicating that Dactylopiibacterium is metabolically active inside the insect host, and estimate that there are over twice as many Dactylopiibacterium cells in the hemolymph than in the gut, with even fewer in the ovary. Albeit scarce, the transcripts in the ovaries support the presence of Dactylopiibacterium in this tissue and a vertical mode of transmission. In the cochineal, Dactylopiibacterium may catabolize plant polysaccharides, and be active in carbon and nitrogen provisioning through its degradative activity and by fixing nitrogen. In most insects, nitrogen-fixing bacteria are found in the gut, but in this study they are shown to occur in the hemolymph, probably delivering essential amino acids and riboflavin to the host from nitrogen substrates derived from nitrogen fixation.
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Affiliation(s)
- Rafael Bustamante-Brito
- Center for Genomic Sciences, Universidad Nacional Autónoma de México, UNAM, Cuernavaca, Morelos C.P. 62210, Mexico.
| | - Arturo Vera-Ponce de León
- Center for Genomic Sciences, Universidad Nacional Autónoma de México, UNAM, Cuernavaca, Morelos C.P. 62210, Mexico.
- Department of Ecology, Evolution and Organismal Biology, The Ohio State University, Columbus, OH 43210, USA.
| | - Mónica Rosenblueth
- Center for Genomic Sciences, Universidad Nacional Autónoma de México, UNAM, Cuernavaca, Morelos C.P. 62210, Mexico.
| | - Julio César Martínez-Romero
- Center for Genomic Sciences, Universidad Nacional Autónoma de México, UNAM, Cuernavaca, Morelos C.P. 62210, Mexico.
| | - Esperanza Martínez-Romero
- Center for Genomic Sciences, Universidad Nacional Autónoma de México, UNAM, Cuernavaca, Morelos C.P. 62210, Mexico.
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Scholthof KBG, Irigoyen S, Catalan P, Mandadi KK. Brachypodium: A Monocot Grass Model Genus for Plant Biology. THE PLANT CELL 2018; 30:1673-1694. [PMID: 29997238 PMCID: PMC6139682 DOI: 10.1105/tpc.18.00083] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 05/25/2018] [Accepted: 07/11/2018] [Indexed: 05/21/2023]
Abstract
The genus Brachypodium represents a model system that is advancing our knowledge of the biology of grasses, including small grains, in the postgenomics era. The most widely used species, Brachypodium distachyon, is a C3 plant that is distributed worldwide. B. distachyon has a small genome, short life cycle, and small stature and is amenable to genetic transformation. Due to the intensive and thoughtful development of this grass as a model organism, it is well-suited for laboratory and field experimentation. The intent of this review is to introduce this model system genus and describe some key outcomes of nearly a decade of research since the first draft genome sequence of the flagship species, B. distachyon, was completed. We discuss characteristics and features of B. distachyon and its congeners that make the genus a valuable model system for studies in ecology, evolution, genetics, and genomics in the grasses, review current hot topics in Brachypodium research, and highlight the potential for future analysis using this system in the coming years.
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Affiliation(s)
- Karen-Beth G Scholthof
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, Texas 77843
| | - Sonia Irigoyen
- Texas A&M AgriLife Research and Extension Center, Weslaco, Texas 78596
| | - Pilar Catalan
- Universidad de Zaragoza-Escuela Politécnica Superior de Huesca, 22071 Huesca, Spain
- Grupo de Bioquímica, Biofísica y Biología Computacional (BIFI, UNIZAR), Unidad Asociada al CSIC, Zaragoza E-50059, Spain
- Institute of Biology, Tomsk State University, Tomsk 634050, Russia
| | - Kranthi K Mandadi
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, Texas 77843
- Texas A&M AgriLife Research and Extension Center, Weslaco, Texas 78596
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32
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Mohammed WS, Ziganshina EE, Shagimardanova EI, Gogoleva NE, Ziganshin AM. Comparison of intestinal bacterial and fungal communities across various xylophagous beetle larvae (Coleoptera: Cerambycidae). Sci Rep 2018; 8:10073. [PMID: 29968731 PMCID: PMC6030058 DOI: 10.1038/s41598-018-27342-z] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 05/31/2018] [Indexed: 12/27/2022] Open
Abstract
The microbial gut communities associated with various xylophagous beetles offer great potential for different biotechnologies and elaboration of novel pest management strategies. In this research, the intestinal bacterial and fungal communities of various cerambycid larvae, including Acmaeops septentrionis, Acanthocinus aedilis, Callidium coriaceum, Trichoferus campestris and Chlorophorus herbstii, were investigated. The intestinal microbial communities of these Cerambycidae species were mostly represented by members of the bacterial phyla Proteobacteria and Actinobacteria and the fungal phylum Ascomycota. However, the bacterial and fungal communities varied by beetle species and between individual organisms. Furthermore, bacterial communities' metagenomes reconstruction indicated the genes that encode enzymes involved in the lignocellulose degradation (such as peroxidases, alpha-L-fucosidases, beta-xylosidases, beta-mannosidases, endoglucanases, beta-glucosidases and others) and nitrogen fixation (nitrogenases). Most of the predicted genes potentially related to lignocellulose degradation were enriched in the T. campestris, A. aedilis and A. septentrionis larval gut consortia, whereas predicted genes affiliated with the nitrogenase component proteins were enriched in the T. campestris, A. septentrionis and C. herbstii larval gut consortia. Several bacteria and fungi detected in the current work could be involved in the nutrition of beetle larvae.
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Affiliation(s)
- Waleed S Mohammed
- Department of Microbiology, Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan, 420008, Russia
- Department of Biotechnology, Faculty of Agriculture, Al-Azhar University, Cairo, 11651, Egypt
| | - Elvira E Ziganshina
- Department of Microbiology, Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan, 420008, Russia
| | - Elena I Shagimardanova
- Laboratory of Extreme Biology, Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan, 420021, Russia
| | - Natalia E Gogoleva
- Laboratory of Extreme Biology, Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan, 420021, Russia
| | - Ayrat M Ziganshin
- Department of Microbiology, Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan, 420008, Russia.
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Flandroy L, Poutahidis T, Berg G, Clarke G, Dao MC, Decaestecker E, Furman E, Haahtela T, Massart S, Plovier H, Sanz Y, Rook G. The impact of human activities and lifestyles on the interlinked microbiota and health of humans and of ecosystems. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 627:1018-1038. [PMID: 29426121 DOI: 10.1016/j.scitotenv.2018.01.288] [Citation(s) in RCA: 161] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 01/28/2018] [Accepted: 01/28/2018] [Indexed: 05/03/2023]
Abstract
Plants, animals and humans, are colonized by microorganisms (microbiota) and transiently exposed to countless others. The microbiota affects the development and function of essentially all organ systems, and contributes to adaptation and evolution, while protecting against pathogenic microorganisms and toxins. Genetics and lifestyle factors, including diet, antibiotics and other drugs, and exposure to the natural environment, affect the composition of the microbiota, which influences host health through modulation of interrelated physiological systems. These include immune system development and regulation, metabolic and endocrine pathways, brain function and epigenetic modification of the genome. Importantly, parental microbiotas have transgenerational impacts on the health of progeny. Humans, animals and plants share similar relationships with microbes. Research paradigms from humans and other mammals, amphibians, insects, planktonic crustaceans and plants demonstrate the influence of environmental microbial ecosystems on the microbiota and health of organisms, and indicate links between environmental and internal microbial diversity and good health. Therefore, overlapping compositions, and interconnected roles of microbes in human, animal and plant health should be considered within the broader context of terrestrial and aquatic microbial ecosystems that are challenged by the human lifestyle and by agricultural and industrial activities. Here, we propose research priorities and organizational, educational and administrative measures that will help to identify safe microbe-associated health-promoting modalities and practices. In the spirit of an expanding version of "One health" that includes environmental health and its relation to human cultures and habits (EcoHealth), we urge that the lifestyle-microbiota-human health nexus be taken into account in societal decision making.
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Affiliation(s)
- Lucette Flandroy
- Federal Public Service Health, Food Chain Safety and Environment, Belgium
| | - Theofilos Poutahidis
- Laboratory of Pathology, Faculty of Health Sciences, School of Veterinary Medicine, Aristotle University of Thessaloniki, Thessaloniki 54124, Greece
| | - Gabriele Berg
- Environmental Biotechnology, Graz University of Technology, Petersgasse 12, A-8010 Graz, Austria
| | - Gerard Clarke
- Department of Psychiatry and Neurobehavioural Science, APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Maria-Carlota Dao
- ICAN, Institute of Cardiometabolism and Nutrition, Assistance Publique Hôpitaux de Paris, Pitié-Salpêtrière Hospital, Paris, France; INSERM, UMRS U1166 (Eq 6) Nutriomics, Paris 6, France; UPMC, Sorbonne University, Pierre et Marie Curie-Paris 6, France
| | - Ellen Decaestecker
- Aquatic Biology, Department Biology, Science, Engineering & Technology Group, KU Leuven, Campus Kortrijk. E. Sabbelaan 53, B-8500 Kortrijk, Belgium
| | - Eeva Furman
- Finnish Environment Institute (SYKE), Helsinki, Finland
| | - Tari Haahtela
- Skin and Allergy Hospital, Helsinki University Hospital, University of Helsinki, Finland
| | - Sébastien Massart
- Laboratory of Integrated and Urban Phytopathology, TERRA, Gembloux Agro-Bio Tech, University of Liège, Passage des deportes, 2, 5030 Gembloux, Belgium
| | - Hubert Plovier
- Metabolism and Nutrition Research Group, Louvain Drug Research Institute, Université Catholique de Louvain, Brussels, Belgium
| | - Yolanda Sanz
- Microbial Ecology, Nutrition & Health Research Unit, Institute of Agrochemistry and Food Technology, Spanish National Research Council (IATA-CSIC), Valencia, Spain
| | - Graham Rook
- Centre for Clinical Microbiology, Department of Infection, UCL (University College London), London, UK.
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Erland LAE, Shukla MR, Singh AS, Murch SJ, Saxena PK. Melatonin and serotonin: Mediators in the symphony of plant morphogenesis. J Pineal Res 2018; 64. [PMID: 29149453 DOI: 10.1111/jpi.12452] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 10/16/2017] [Indexed: 12/30/2022]
Abstract
Melatonin and serotonin are important signaling and stress mitigating molecules that play important roles across growth and development in plants. Despite many well-documented responses, a systematic investigation of the entire metabolic pathway (tryptophan, tryptamine, and N-acetylserotonin) does not exist, leaving many open questions. The objective of this study was to determine the responses of Hypericum perforatum (L.) to melatonin, serotonin, and their metabolic precursors. Two well-characterized germplasm lines (#4 and 112) created by mutation and a haploid breeding program were compared to wild type to identify specific responses. Germplasm line 4 has lower regenerative and photosynthetic capacity than either wild type or line 112, and there are documented significant differences in the chemistry and physiology of lines 4 and 112. Supplementation of the culture media with tryptophan, tryptamine, N-acetylserotonin, serotonin, or melatonin partially reversed the regenerative recalcitrance and growth impairment of the germplasm lines. Quantification of phytohormones revealed crosstalk between the indoleamines and related phytohormones including cytokinin, salicylic acid, and abscisic acid. We hypothesize that melatonin and serotonin function in coordination with their metabolites in a cascade of phytochemical responses including multiple pathways and phytohormone networks to direct morphogenesis and protect photosynthesis in H. perforatum.
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Affiliation(s)
- Lauren A E Erland
- Department of Plant Agriculture, Gosling Research Institute for Plant Preservation, University of Guelph, Guelph, ON, Canada
| | - Mukund R Shukla
- Department of Plant Agriculture, Gosling Research Institute for Plant Preservation, University of Guelph, Guelph, ON, Canada
| | - Amritpal S Singh
- Summerland Research and Development Centre, Agriculture and Agri-Food Canada, Summerland, BC, Canada
| | - Susan J Murch
- Department of Chemistry, University of British Columbia, Kelowna, BC, Canada
| | - Praveen K Saxena
- Department of Plant Agriculture, Gosling Research Institute for Plant Preservation, University of Guelph, Guelph, ON, Canada
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Orozco-Mosqueda MDC, Rocha-Granados MDC, Glick BR, Santoyo G. Microbiome engineering to improve biocontrol and plant growth-promoting mechanisms. Microbiol Res 2018; 208:25-31. [PMID: 29551209 DOI: 10.1016/j.micres.2018.01.005] [Citation(s) in RCA: 135] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 01/13/2018] [Accepted: 01/20/2018] [Indexed: 12/15/2022]
Abstract
A plant microbiome includes a microbial community that typically interacts extensively with a plant. The plant microbiome can survive either inside or outside of plant tissues, performing various plant beneficial activities including biocontrol of potential phytopathogens and promotion of plant growth. An important part of the plant microbiome includes plant growth-promoting bacteria (PGPB) that commonly reside in the rhizosphere and phyllosphere, and as endophytic bacteria (inside of plant tissues). As new plant microbiome-manipulating strategies have emerged in recent years, we have critically reviewed relevant literature, chiefly from the last decade. We have analysed and compared the rhizosphere, phyllosphere and endosphere as potential ecosystems for manipulation, in order to improve positive interactions with the plant. In addition, many studies on the bioengineering of the endophyte microbiome and its potential impact on the core microbiome were analysed with respect to five different strategies, including host mediated and multi-generation microbiome selection, inoculation into soil and rhizosphere, inoculations into seeds or seedlings, tissue atomisation and direct injection into tissues or wounds. Finally, microbiome engineering presents a feasible strategy to solve multiple agriculture-associated problems in an eco-friendly way.
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Affiliation(s)
- Ma Del Carmen Orozco-Mosqueda
- Instituto de Investigaciones Químico-Biológicas de la Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Michoacán, Mexico; Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
| | - Ma Del Carmen Rocha-Granados
- Facultad de Agrobiología "Presidente Juárez", Universidad Michoacana de San Nicolás de Hidalgo, Uruapan, Michoacán, Mexico
| | - Bernard R Glick
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
| | - Gustavo Santoyo
- Instituto de Investigaciones Químico-Biológicas de la Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Michoacán, Mexico.
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Auffret MD, Dewhurst RJ, Duthie CA, Rooke JA, John Wallace R, Freeman TC, Stewart R, Watson M, Roehe R. The rumen microbiome as a reservoir of antimicrobial resistance and pathogenicity genes is directly affected by diet in beef cattle. MICROBIOME 2017; 5:159. [PMID: 29228991 PMCID: PMC5725880 DOI: 10.1186/s40168-017-0378-z] [Citation(s) in RCA: 110] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 11/28/2017] [Indexed: 05/08/2023]
Abstract
BACKGROUND The emergence and spread of antimicrobial resistance is the most urgent current threat to human and animal health. An improved understanding of the abundance of antimicrobial resistance genes and genes associated with microbial colonisation and pathogenicity in the animal gut will have a major role in reducing the contribution of animal production to this problem. Here, the influence of diet on the ruminal resistome and abundance of pathogenicity genes was assessed in ruminal digesta samples taken from 50 antibiotic-free beef cattle, comprising four cattle breeds receiving two diets containing different proportions of concentrate. RESULTS Two hundred and four genes associated with antimicrobial resistance (AMR), colonisation, communication or pathogenicity functions were identified from 4966 metagenomic genes using KEGG identification. Both the diversity and abundance of these genes were higher in concentrate-fed animals. Chloramphenicol and microcin resistance genes were dominant in samples from forage-fed animals (P < 0.001), while aminoglycoside and streptomycin resistances were enriched in concentrate-fed animals. The concentrate-based diet also increased the relative abundance of Proteobacteria, which includes many animal and zoonotic pathogens. A high ratio of Proteobacteria to (Firmicutes + Bacteroidetes) was confirmed as a good indicator for rumen dysbiosis, with eight cases all from concentrate-fed animals. Finally, network analysis demonstrated that the resistance/pathogenicity genes are potentially useful as biomarkers for health risk assessment of the ruminal microbiome. CONCLUSIONS Diet has important effects on the complement of AMR genes in the rumen microbial community, with potential implications for human and animal health.
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Affiliation(s)
| | | | | | | | - R. John Wallace
- Rowett Institute, University of Aberdeen, Aberdeen, AB25 2ZD UK
| | - Tom C. Freeman
- Division of Genetics and Genomics, The Roslin Institute and R(D)SVS, University of Edinburgh, Edinburgh, EH25 9RG UK
| | - Robert Stewart
- Edinburgh Genomics, The Roslin Institute and R(D)SVS, University of Edinburgh, Edinburgh, EH25 9RG UK
| | - Mick Watson
- Division of Genetics and Genomics, The Roslin Institute and R(D)SVS, University of Edinburgh, Edinburgh, EH25 9RG UK
- Edinburgh Genomics, The Roslin Institute and R(D)SVS, University of Edinburgh, Edinburgh, EH25 9RG UK
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Shehata HR, Dumigan C, Watts S, Raizada MN. An endophytic microbe from an unusual volcanic swamp corn seeks and inhabits root hair cells to extract rock phosphate. Sci Rep 2017; 7:13479. [PMID: 29044186 PMCID: PMC5647395 DOI: 10.1038/s41598-017-14080-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 10/05/2017] [Indexed: 12/14/2022] Open
Abstract
In the animal microbiome, localization of microbes to specific cell types is well established, but there are few such examples within the plant microbiome which includes endophytes. Endophytes are non-pathogenic microbes that inhabit plants. Root hairs are single cells, equivalent to the nutrient-absorbing intestinal microvilli of animals, used by plants to increase the root surface area for nutrient extraction from soil including phosphorus (P). There has been significant interest in the microbiome of intestinal microvilli but less is known about the root hair microbiome. Here we describe a bacterial endophyte (3F11) from Zea nicaraguensis, a wild corn discovered in a Nicaraguan swamp above rock-P lava flowing from the San Cristobal volcano. Rock-P is insoluble and a major challenge for plants. Following seed coating and germination on insoluble-P, the endophyte colonized epidermal surfaces, ultimately colonizing root hairs intracellularly. The endophyte promoted root hair growth and secreted acids to solubilize rock-P for uptake by a larger root hair surface. The most interesting observation was that a seed-coated endophyte targeted and colonized a critical cell type, root hair cells, consistent with earlier studies. The endophyte maintained its targeting ability in two evolutionary divergent hosts, suggesting that the host recognition machinery is conserved.
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Affiliation(s)
- Hanan R Shehata
- Department of Plant Agriculture, University of Guelph, Guelph, ON, N1G 2W1, Canada
- Department of Microbiology, School of Pharmacy, Mansoura University, Mansoura, Egypt
| | - Christopher Dumigan
- Department of Plant Agriculture, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Sophia Watts
- Department of Plant Agriculture, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Manish N Raizada
- Department of Plant Agriculture, University of Guelph, Guelph, ON, N1G 2W1, Canada.
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Mendes-Soares H, Chia N. Community metabolic modeling approaches to understanding the gut microbiome: Bridging biochemistry and ecology. Free Radic Biol Med 2017; 105:102-109. [PMID: 27989793 PMCID: PMC5401773 DOI: 10.1016/j.freeradbiomed.2016.12.017] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Revised: 11/27/2016] [Accepted: 12/12/2016] [Indexed: 12/27/2022]
Abstract
Interest in the human microbiome is at an all time high. The number of human microbiome studies is growing exponentially, as are reported associations between microbial communities and disease. However, we have not been able to translate the ever-growing amount of microbiome sequence data into better health. To do this, we need a practical means of transforming a disease-associated microbiome into a health-associated microbiome. This will require a framework that can be used to generate predictions about community dynamics within the microbiome under different conditions, predictions that can be tested and validated. In this review, using the gut microbiome to illustrate, we describe two classes of model that are currently being used to generate predictions about microbial community dynamics: ecological models and metabolic models. We outline the strengths and weaknesses of each approach and discuss the insights into the gut microbiome that have emerged from modeling thus far. We then argue that the two approaches can be combined to yield a community metabolic model, which will supply the framework needed to move from high-throughput omics data to testable predictions about how prebiotic, probiotic, and nutritional interventions affect the microbiome. We are confident that with a suitable model, researchers and clinicians will be able to harness the stream of sequence data and begin designing strategies to make targeted alterations to the microbiome and improve health.
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Affiliation(s)
- Helena Mendes-Soares
- Microbiome Program, Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA; Department of Surgery, Mayo Clinic, Rochester, MN 55905, USA
| | - Nicholas Chia
- Microbiome Program, Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA; Department of Surgery, Mayo Clinic, Rochester, MN 55905, USA; Department of Bioengineering and Physiology, College of Medicine, Mayo Clinic, Rochester, MN 55905, USA.
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39
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Müller DB, Vogel C, Bai Y, Vorholt JA. The Plant Microbiota: Systems-Level Insights and Perspectives. Annu Rev Genet 2016; 50:211-234. [DOI: 10.1146/annurev-genet-120215-034952] [Citation(s) in RCA: 408] [Impact Index Per Article: 51.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Daniel B. Müller
- Institute of Microbiology, ETH Zurich, 8093 Zurich, Switzerland;
| | - Christine Vogel
- Institute of Microbiology, ETH Zurich, 8093 Zurich, Switzerland;
| | - Yang Bai
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
- State Key Laboratory of Plant Genomics, National Centre for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Julia A. Vorholt
- Institute of Microbiology, ETH Zurich, 8093 Zurich, Switzerland;
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40
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Müller CA, Obermeier MM, Berg G. Bioprospecting plant-associated microbiomes. J Biotechnol 2016; 235:171-80. [DOI: 10.1016/j.jbiotec.2016.03.033] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Revised: 03/17/2016] [Accepted: 03/21/2016] [Indexed: 10/22/2022]
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41
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Gouda S, Das G, Sen SK, Shin HS, Patra JK. Endophytes: A Treasure House of Bioactive Compounds of Medicinal Importance. Front Microbiol 2016; 7:1538. [PMID: 27746767 PMCID: PMC5041141 DOI: 10.3389/fmicb.2016.01538] [Citation(s) in RCA: 309] [Impact Index Per Article: 38.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 09/14/2016] [Indexed: 01/23/2023] Open
Abstract
Endophytes are an endosymbiotic group of microorganisms that colonize in plants and microbes that can be readily isolated from any microbial or plant growth medium. They act as reservoirs of novel bioactive secondary metabolites, such as alkaloids, phenolic acids, quinones, steroids, saponins, tannins, and terpenoids that serve as a potential candidate for antimicrobial, anti-insect, anticancer and many more properties. While plant sources are being extensively explored for new chemical entities for therapeutic purposes, endophytic microbes also constitute an important source for drug discovery. This review aims to comprehend the contribution and uses of endophytes as an impending source of drugs against various forms of diseases and other possible medicinal use.
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Affiliation(s)
| | - Gitishree Das
- Research Institute of Biotechnology and Medical Converged Science, Dongguk University-Seoul, Goyang South Korea
| | - Sandeep K Sen
- Department of Biotechnology and Medical Engineering, National Institute of Technology Rourkela, Rourkela India
| | - Han-Seung Shin
- Department of Food Science and Biotechnology, Dongguk University-Seoul, Goyang South Korea
| | - Jayanta Kumar Patra
- Research Institute of Biotechnology and Medical Converged Science, Dongguk University-Seoul, Goyang South Korea
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42
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Mitter B, Pfaffenbichler N, Sessitsch A. Plant-microbe partnerships in 2020. Microb Biotechnol 2016; 9:635-40. [PMID: 27418200 PMCID: PMC4993182 DOI: 10.1111/1751-7915.12382] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 06/23/2016] [Indexed: 11/30/2022] Open
Abstract
The plant holobiont comprises the plant and its associated microbiota, which interact with each other and determine holobiont functioning and plant performance. We have started to understand the complexity of the involved microorganisms and their interactions, however, we need more research on plant-microbiome interactions to understand holobiont functioning. By 2020 we expect that our knowledge on these interactions will have considerably increased facilitating crop management practices based on the interactions of the plant holobiont.
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Affiliation(s)
- Birgit Mitter
- Bioresources Unit, Health & Environment Department, AIT Austrian Institute of Technology GmbH, A-3430, Tulln, Austria
| | - Nikolaus Pfaffenbichler
- Bioresources Unit, Health & Environment Department, AIT Austrian Institute of Technology GmbH, A-3430, Tulln, Austria
| | - Angela Sessitsch
- Bioresources Unit, Health & Environment Department, AIT Austrian Institute of Technology GmbH, A-3430, Tulln, Austria
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43
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Sessitsch A, Smalla K, Johnson L, Mitter B. Editorial: Special thematic issue on microbe-assisted crop production. FEMS Microbiol Ecol 2016; 92:fiw167. [PMID: 27495243 DOI: 10.1093/femsec/fiw167] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Affiliation(s)
- Angela Sessitsch
- AIT Austrian Institute of Technology GmbH, Health & Environment Department, Bioresources Unit, Konrad-Lorenz-Straße 24, 3430 Tulln, Austria
| | - Kornelia Smalla
- Julius Kühn-Institut, Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11-12, Braunschweig 38104, Germany
| | - Linda Johnson
- Agresearch Grasslands Research Centre, Forage Improvement, Tennent Drive, Palmerston North 4442, New Zealand
| | - Birgit Mitter
- AIT Austrian Institute of Technology GmbH, Health & Environment Department, Bioresources Unit, Konrad-Lorenz-Straße 24, 3430 Tulln, Austria
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44
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Adam E, Groenenboom AE, Kurm V, Rajewska M, Schmidt R, Tyc O, Weidner S, Berg G, de Boer W, Falcão Salles J. Controlling the Microbiome: Microhabitat Adjustments for Successful Biocontrol Strategies in Soil and Human Gut. Front Microbiol 2016; 7:1079. [PMID: 27468279 PMCID: PMC4942455 DOI: 10.3389/fmicb.2016.01079] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 06/27/2016] [Indexed: 12/22/2022] Open
Affiliation(s)
- Eveline Adam
- Institute of Environmental Biotechnology, Graz University of TechnologyGraz, Austria
| | | | - Viola Kurm
- Department of Terrestrial Ecology, Netherlands Institute of Ecology, The Royal Netherlands Academy of Arts and SciencesWageningen, Netherlands
| | - Magdalena Rajewska
- Laboratory of Biological Plant Protection, Intercollegiate Faculty of Biotechnology, University of Gdańsk and Medical University of GdańskGdańsk, Poland
| | - Ruth Schmidt
- Department of Microbial Ecology, Netherlands Institute of Ecology, The Royal Netherlands Academy of Arts and SciencesWageningen, Netherlands
- Department of Soil Quality, Wageningen University and Research CentreWageningen, Netherlands
| | - Olaf Tyc
- Department of Microbial Ecology, Netherlands Institute of Ecology, The Royal Netherlands Academy of Arts and SciencesWageningen, Netherlands
- Department of Soil Quality, Wageningen University and Research CentreWageningen, Netherlands
| | - Simone Weidner
- Department of Biology, Institute of Environmental Biology, Utrecht UniversityUtrecht, Netherlands
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of TechnologyGraz, Austria
| | - Wietse de Boer
- Department of Microbial Ecology, Netherlands Institute of Ecology, The Royal Netherlands Academy of Arts and SciencesWageningen, Netherlands
- Department of Soil Quality, Wageningen University and Research CentreWageningen, Netherlands
| | - Joana Falcão Salles
- Institute of Evolutionary Life sciences, Groningen UniversityGroningen, Netherlands
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45
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Berg G, Krause R, Mendes R. Cross-Kingdom Similarities in Microbiome Ecology and Biocontrol of Pathogens. Front Microbiol 2015; 6:1311. [PMID: 26635772 PMCID: PMC4658424 DOI: 10.3389/fmicb.2015.01311] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2015] [Accepted: 11/09/2015] [Indexed: 12/13/2022] Open
Affiliation(s)
- Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology and ACIB Austrian Centre of Industrial Biotechnology Graz, Austria
| | - Robert Krause
- Department of Internal Medicine, Medical University of Graz Graz, Austria
| | - Rodrigo Mendes
- Laboratory of Environmental Microbiology, Embrapa Environment Jaguariuna, Brazil
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46
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Hardoim PR, van Overbeek LS, Berg G, Pirttilä AM, Compant S, Campisano A, Döring M, Sessitsch A. The Hidden World within Plants: Ecological and Evolutionary Considerations for Defining Functioning of Microbial Endophytes. Microbiol Mol Biol Rev 2015; 79:293-320. [PMID: 26136581 PMCID: PMC4488371 DOI: 10.1128/mmbr.00050-14] [Citation(s) in RCA: 1058] [Impact Index Per Article: 117.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
All plants are inhabited internally by diverse microbial communities comprising bacterial, archaeal, fungal, and protistic taxa. These microorganisms showing endophytic lifestyles play crucial roles in plant development, growth, fitness, and diversification. The increasing awareness of and information on endophytes provide insight into the complexity of the plant microbiome. The nature of plant-endophyte interactions ranges from mutualism to pathogenicity. This depends on a set of abiotic and biotic factors, including the genotypes of plants and microbes, environmental conditions, and the dynamic network of interactions within the plant biome. In this review, we address the concept of endophytism, considering the latest insights into evolution, plant ecosystem functioning, and multipartite interactions.
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Affiliation(s)
- Pablo R. Hardoim
- Centre of Marine Sciences, University of Algarve, Faro, Portugal
| | | | - Gabriele Berg
- Institute for Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | | | - Stéphane Compant
- Department of Health and Environment, Bioresources Unit, Austrian Institute of Technology GmbH, Tulln, Austria
| | - Andrea Campisano
- Sustainable Agro-Ecosystems and Bioresources Department, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, TN, Italy
| | | | - Angela Sessitsch
- Department of Health and Environment, Bioresources Unit, Austrian Institute of Technology GmbH, Tulln, Austria
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Ogura T, Date Y, Tsuboi Y, Kikuchi J. Metabolic dynamics analysis by massive data integration: application to tsunami-affected field soils in Japan. ACS Chem Biol 2015; 10:1908-15. [PMID: 25997449 DOI: 10.1021/cb500609p] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
A new metabolic dynamics analysis approach has been developed in which massive data sets from time-series of (1)H and (13)C NMR spectra are integrated in combination with microbial variability to characterize the biomass degradation process using field soil microbial communities. On the basis of correlation analyses that revealed relationships between various metabolites and bacteria, we efficiently monitored the metabolic dynamics of saccharides, amino acids, and organic acids, by assessing time-course changes in the microbial and metabolic profiles during biomass degradation. Specific bacteria were found to support specific steps of metabolic pathways in the degradation process of biomass to short chain fatty acids. We evaluated samples from agricultural and abandoned fields contaminated by the tsunami that followed the Great East earthquake in Japan. Metabolic dynamics and activities in the biomass degradation process differed considerably between soil from agricultural and abandoned fields. In particular, production levels of short chain fatty acids, such as acetate and propionate, which were considered to be produced by soil bacteria such as Sedimentibacter sp. and Coprococcus sp., were higher in the soil from agricultural fields than from abandoned fields. Our approach could characterize soil activity based on the metabolic dynamics of microbial communities in the biomass degradation process and should therefore be useful in future investigations of the environmental effects of natural disasters on soils.
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Affiliation(s)
- Tatsuki Ogura
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku,
Yokohama 230-0045, Japan
- Graduate
School of Medical Life Science, Yokohama City University, 1-7-29
Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Yasuhiro Date
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku,
Yokohama 230-0045, Japan
- Graduate
School of Medical Life Science, Yokohama City University, 1-7-29
Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Yuuri Tsuboi
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku,
Yokohama 230-0045, Japan
| | - Jun Kikuchi
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku,
Yokohama 230-0045, Japan
- Graduate
School of Medical Life Science, Yokohama City University, 1-7-29
Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
- Graduate
School of Bioagricultural Sciences, Nagoya University, 1 Furo-cho, Chikusa-ku, Nagoya 464-0810, Japan
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48
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Schnorr SL, Crittenden AN, Venema K, Marlowe FW, Henry AG. Assessing digestibility of Hadza tubers using a dynamic in-vitro model. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2015; 158:371-85. [PMID: 26174414 DOI: 10.1002/ajpa.22805] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Accepted: 06/15/2015] [Indexed: 12/31/2022]
Abstract
OBJECTIVES Bioaccessibility is a useful measure for assessing the biological value of a particular nutrient from food, especially foods such as tubers. The wild tubers exploited by Hadza foragers in Tanzania are of interest because they are nontoxic, consumed raw or briefly roasted, and entail substantial physical barriers to consumers. In this study, we attempted to elucidate the biological value of Hadza tubers by measuring the absorption of glucose through in-vitro digestion. METHODS We quantified digestibility using data from 24 experimental trials on four species of Hadza tuber using a dynamic in-vitro model that replicates digestion in the stomach and small intestine. Analysis of glucose in the input meal and output dialysate revealed the accessible glucose fraction. We also conducted assays for protein, vitamin, and mineral content on whole tubers and meal fractions. RESULTS Bioaccessibility of glucose varies depending on tuber species. Holding effects of chewing constant, brief roasting had negligible effects, but high intraspecific variation precludes interpretive power. Overall, Hadza tubers are very resistant to digestion, with between one- and two-thirds of glucose absorbed on average. Glucose absorption negatively correlated with glucose concentration of the tubers. CONCLUSIONS Roasting may provide other benefits such as ease of peeling and chewing to extract edible parenchymatous tissue. A powerful factor in glucose acquisition is tuber quality, placing emphasis on the skill of the forager. Other nutrient assays yielded unexpectedly high values for protein, iron, and iodine, making tubers potentially valuable resources beyond caloric content.
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Affiliation(s)
- Stephanie L Schnorr
- Plant Foods in Hominin Dietary Ecology Research Group, Max Planck Institute for Evolutionary Anthropology, Leipzig, 04103, Germany
| | - Alyssa N Crittenden
- Metabolism, Anthropometry, and Nutrition Laboratory, Department of Anthropology, University of Nevada, Las Vegas, Nevada, 89154-5003
| | - Koen Venema
- Department of Pharmacokinetics & Human Studies, TNO Healthy Living, Zeist, NL-3704 HE, The Netherlands
| | - Frank W Marlowe
- Division of Biological Anthropology, University of Cambridge, Cambridge, Cb2 1TN, UK
| | - Amanda G Henry
- Plant Foods in Hominin Dietary Ecology Research Group, Max Planck Institute for Evolutionary Anthropology, Leipzig, 04103, Germany
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49
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The Hidden World within Plants: Ecological and Evolutionary Considerations for Defining Functioning of Microbial Endophytes. Microbiol Mol Biol Rev 2015. [PMID: 26136581 DOI: 10.1128/mmbr.00050-14.] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
All plants are inhabited internally by diverse microbial communities comprising bacterial, archaeal, fungal, and protistic taxa. These microorganisms showing endophytic lifestyles play crucial roles in plant development, growth, fitness, and diversification. The increasing awareness of and information on endophytes provide insight into the complexity of the plant microbiome. The nature of plant-endophyte interactions ranges from mutualism to pathogenicity. This depends on a set of abiotic and biotic factors, including the genotypes of plants and microbes, environmental conditions, and the dynamic network of interactions within the plant biome. In this review, we address the concept of endophytism, considering the latest insights into evolution, plant ecosystem functioning, and multipartite interactions.
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50
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Natural environments, ancestral diets, and microbial ecology: is there a modern "paleo-deficit disorder"? Part II. J Physiol Anthropol 2015; 34:9. [PMID: 25889196 PMCID: PMC4353476 DOI: 10.1186/s40101-014-0040-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Accepted: 12/29/2014] [Indexed: 12/19/2022] Open
Abstract
Famed microbiologist René J. Dubos (1901–1982) was an early pioneer in the developmental origins of health and disease (DOHaD) construct. In the 1960s, he conducted groundbreaking research concerning the ways in which early-life experience with nutrition, microbiota, stress, and other environmental variables could influence later-life health outcomes. He recognized the co-evolutionary relationship between microbiota and the human host. Almost 2 decades before the hygiene hypothesis, he suggested that children in developed nations were becoming too sanitized (vs. our ancestral past) and that scientists should determine whether the childhood environment should be “dirtied up in a controlled manner.” He also argued that oft-celebrated growth chart increases via changes in the global food supply and dietary patterns should not be equated to quality of life and mental health. Here in the second part of our review, we reflect the words of Dubos off contemporary research findings in the areas of diet, the gut-brain-axis (microbiota and anxiety and depression) and microbial ecology. Finally, we argue, as Dubos did 40 years ago, that researchers should more closely examine the relevancy of silo-sequestered, reductionist findings in the larger picture of human quality of life. In the context of global climate change and the epidemiological transition, an allergy epidemic and psychosocial stress, our review suggests that discussions of natural environments, urbanization, biodiversity, microbiota, nutrition, and mental health, are often one in the same.
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