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Gilbert JA, Hartmann EM. The indoors microbiome and human health. Nat Rev Microbiol 2024:10.1038/s41579-024-01077-3. [PMID: 39030408 DOI: 10.1038/s41579-024-01077-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/25/2024] [Indexed: 07/21/2024]
Abstract
Indoor environments serve as habitat for humans and are replete with various reservoirs and niches for microorganisms. Microorganisms enter indoor spaces with their human and non-human hosts, as well as via exchange with outdoor sources, such as ventilation and plumbing. Once inside, many microorganisms do not survive, especially on dry, barren surfaces. Even reduced, this microbial biomass has critical implications for the health of human occupants. As urbanization escalates, exploring the intersection of the indoor environment with the human microbiome and health is increasingly vital. The indoor microbiome, a complex ecosystem of microorganisms influenced by human activities and environmental factors, plays a pivotal role in modulating infectious diseases and fostering healthy immune development. Recent advancements in microbiome research shed light on this unique ecological system, highlighting the need for innovative approaches in creating health-promoting living spaces. In this Review, we explore the microbial ecology of built environments - places where humans spend most of their lives - and its implications for immune, endocrine and neurological health. We further propose strategies to harness the indoor microbiome for better health outcomes.
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Affiliation(s)
- Jack A Gilbert
- Department of Paediatrics, University of California San Diego, La Jolla, CA, USA.
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA.
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA.
| | - Erica M Hartmann
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL, USA
- Department of Medicine, Division of Pulmonary Medicine, Northwestern University, Chicago, IL, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
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Lu Y, Duan M, Li Y, Zhang S, Hu X, Liu L. Altitude-associated trends in bacterial communities in ultrahigh-altitude residences. ENVIRONMENT INTERNATIONAL 2024; 185:108503. [PMID: 38377724 DOI: 10.1016/j.envint.2024.108503] [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: 10/22/2023] [Revised: 02/10/2024] [Accepted: 02/12/2024] [Indexed: 02/22/2024]
Abstract
BACKGROUND Indoor bacterial communities may change with altitude because their major contributors, outdoor bacterial communities, vary with altitude. People's health effects from bacteria inhalation exposure can also vary with altitude because human respiratory physiology changes with oxygen content in air. Accordingly, adjusting indoor bacterial communities may help to acclimate newcomers from low-altitude environments to ultrahigh-altitude environments. To lay the groundwork for further research, we aimed to first elucidate the bacterial communities in ultrahigh-altitude residences and the effects of altitude on these communities. We collected 187 environmental samples from residential communities at ultrahigh altitudes of 3811-4651 m in Ngari, China and sequenced bacterial 16S rRNA genes. RESULTS On one hand, when abundant genera in ultrahigh-altitude residences and those reported by previous studies on low-altitude residences were compared, nine genera were shared, whereas other five genera were abundant only at ultrahigh altitudes. On the other hand, when the bacterial communities of residences at different ultrahigh altitudes were further compared, the bacterial composition in indoor surface samples varied significantly with altitude. The relative abundance of five bacterial genera in indoor air samples and 10 genera and three phyla in indoor surface samples varied monotonically with altitude. CONCLUSIONS Altitude may be a long-neglected factor that shapes residential bacterial communities and thus warrants attention.
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Affiliation(s)
- Yiran Lu
- Department of Building Science, Tsinghua University, Beijing 100084, China; Laboratory of Eco-Planning & Green Building, Ministry of Education, Tsinghua University, Beijing 100084, China
| | - Mengjie Duan
- Laboratory of Eco-Planning & Green Building, Ministry of Education, Tsinghua University, Beijing 100084, China; Vanke School of Public Health, Tsinghua University, Beijing 100084, China
| | - Yifan Li
- Department of Building Science, Tsinghua University, Beijing 100084, China; Laboratory of Eco-Planning & Green Building, Ministry of Education, Tsinghua University, Beijing 100084, China
| | - Shengyu Zhang
- Department of Gastroenterology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Xiaomin Hu
- Department of Medical Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Li Liu
- Department of Building Science, Tsinghua University, Beijing 100084, China; Laboratory of Eco-Planning & Green Building, Ministry of Education, Tsinghua University, Beijing 100084, China.
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Artigas Ramírez MD, Agake SI, Maeda M, Kojima K, Ohkama-Ohtsu N, Yokoyama T. Diversity of Fast-Growth Spore-Forming Microbes and Their Activity as Plant Partners. Microorganisms 2023; 11:microorganisms11020232. [PMID: 36838197 PMCID: PMC9961442 DOI: 10.3390/microorganisms11020232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/15/2023] [Accepted: 01/16/2023] [Indexed: 01/18/2023] Open
Abstract
Biofertilizers are agricultural materials capable of reducing the usage amounts of chemical fertilizers. Spore-forming microorganisms (SFM) could be used for plant growth promotion or to improve plant health. Until now, biofertilizers based on SFM have been applied for rice and other crops. In this study, we isolated and characterized SFM, which were colonized on the Oryza sativa L. roots. SFM were analyzed regarding the short-term effects of biofertilization on the nursery growths. Analysis was performed without nitrogen or any inorganic fertilizer and was divided into two groups, including bacteria and fungi. SF-bacteria were dominated by the Firmicutes group, including species from Viridibacillus, Lysinibacillus, Solibacillus, Paenibacillus, Priestia, and mainly Bacillus (50%). The fungi group was classified as Mucoromycota, Basidiomycota, and mainly Ascomycota (80%), with a predominance of Penicillium and Trichoderma species. In plant performance in comparison with B. pumilus TUAT1, some bacteria and fungus isolates significantly improved the early growth of rice, based on 48 h inoculum with 107 CFU mL-1. Furthermore, several SFM showed positive physiological responses under abiotic stress or with limited nutrients such as phosphorous (P). Moreover, the metabolic fingerprint was obtained. The biofertilizer based on SFM could significantly reduce the application of the inorganic fertilizer and improve the lodging resistances of rice, interactively enhancing better plant health and crop production.
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Affiliation(s)
- María Daniela Artigas Ramírez
- Iriomote Station, Tropical Biosphere Research Center, University of the Ryukyus, 870 Uehara, Yaeyama, Taketomi, Okinawa 907-1541, Japan
- Institute of Global Innovation Research, Tokyo University of Agriculture and Technology (TUAT), Saiwai-cho 3-5-8, Fuchu, Tokyo 183-8538, Japan
| | - Shin-ichiro Agake
- Institute of Global Innovation Research, Tokyo University of Agriculture and Technology (TUAT), Saiwai-cho 3-5-8, Fuchu, Tokyo 183-8538, Japan
| | - Masumi Maeda
- Institute of Agriculture, Tokyo University of Agriculture and Technology (TUAT), Harumi-cho 3-8-8, Fuchu, Tokyo 183-8538, Japan
| | - Katsuhiro Kojima
- Faculty of Agriculture, Tokyo University of Agriculture and Technology (TUAT), Saiwai-cho 3-5-8, Fuchu, Tokyo 183-8538, Japan
| | - Naoko Ohkama-Ohtsu
- Institute of Global Innovation Research, Tokyo University of Agriculture and Technology (TUAT), Saiwai-cho 3-5-8, Fuchu, Tokyo 183-8538, Japan
- Institute of Agriculture, Tokyo University of Agriculture and Technology (TUAT), Harumi-cho 3-8-8, Fuchu, Tokyo 183-8538, Japan
| | - Tadashi Yokoyama
- Institute of Agriculture, Tokyo University of Agriculture and Technology (TUAT), Harumi-cho 3-8-8, Fuchu, Tokyo 183-8538, Japan
- Faculty of Food and Agricultural Science, Fukushima University, Kanayagawa 1, Fukushima 960-1296, Japan
- Correspondence: ; Tel.: +81-24-548-8420
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Mhuireach GÁ, Fahimipour AK, Vandegrift R, Muscarella ME, Hickey R, Bateman AC, Van Den Wymelenberg KG, Bohannan BJM. Temporary establishment of bacteria from indoor plant leaves and soil on human skin. ENVIRONMENTAL MICROBIOME 2022; 17:61. [PMID: 36572917 PMCID: PMC9793532 DOI: 10.1186/s40793-022-00457-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 12/15/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Plants are found in a large percentage of indoor environments, yet the potential for bacteria associated with indoor plant leaves and soil to colonize human skin remains unclear. We report results of experiments in a controlled climate chamber to characterize bacterial communities inhabiting the substrates and leaves of five indoor plant species, and quantify microbial transfer dynamics and residence times on human skin following simulated touch contact events. Controlled bacterial propagule transfer events with soil and leaf donors were applied to the arms of human occupants and repeatedly measured over a 24-h period using 16S rRNA gene amplicon sequencing. RESULTS Substrate samples had greater biomass and alpha diversity compared to leaves and baseline skin bacterial communities, as well as dissimilar taxonomic compositions. Despite these differences in donor community diversity and biomass, we observed repeatable patterns in the dynamics of transfer events. Recipient human skin bacterial communities increased in alpha diversity and became more similar to donor communities, an effect which, for soil contact only, persisted for at least 24 h. Washing with soap and water effectively returned communities to their pre-perturbed state, although some abundant soil taxa resisted removal through washing. CONCLUSIONS This study represents an initial characterization of bacterial relationships between humans and indoor plants, which represent a potentially valuable element of biodiversity in the built environment. Although environmental microbiota are unlikely to permanently colonize skin following a single contact event, repeated or continuous exposures to indoor biodiversity may be increasingly relevant for the functioning and diversity of the human microbiome as urbanization continues.
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Affiliation(s)
- Gwynne Á Mhuireach
- Biology and the Built Environment Center, University of Oregon, Eugene, OR, USA.
| | - Ashkaan K Fahimipour
- Biology and the Built Environment Center, University of Oregon, Eugene, OR, USA
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA
- Department of Biological Sciences, Florida Atlantic University, Boca Raton, FL, USA
| | - Roo Vandegrift
- Biology and the Built Environment Center, University of Oregon, Eugene, OR, USA
- United States Department of Agriculture, APHIS, PPQ, Miami, FL, USA
| | - Mario E Muscarella
- Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, AK, USA
| | - Roxana Hickey
- Biology and the Built Environment Center, University of Oregon, Eugene, OR, USA
| | - Ashley C Bateman
- Biology and the Built Environment Center, University of Oregon, Eugene, OR, USA
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Adi Wicaksono W, Reisenhofer-Graber T, Erschen S, Kusstatscher P, Berg C, Krause R, Cernava T, Berg G. Phyllosphere-associated microbiota in built environment: Do they have the potential to antagonize human pathogens? J Adv Res 2022; 43:109-121. [PMID: 36585101 PMCID: PMC9811327 DOI: 10.1016/j.jare.2022.02.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 02/01/2022] [Accepted: 02/09/2022] [Indexed: 02/06/2023] Open
Abstract
INTRODUCTION The plant microbiota is known to protect its host against invasion by plant pathogens. Recent studies have indicated that the microbiota of indoor plants is transmitted to the local built environment where it might fulfill yet unexplored functions. A better understanding of the interplay of such microbial communities with human pathogens might provide novel cues related to natural inhibition of them. OBJECTIVE We studied the plant microbiota of two model indoor plants, Musa acuminata and Chlorophytum comosum, and their effect on human pathogens. The main objective was to identify mechanisms by which the microbiota of indoor plants inhibits human-pathogenic bacteria. METHODS Microbial communities and functioning were investigated using a comprehensive set of experiments and methods combining amplicon and shotgun metagenomic analyses with results from interaction assays. RESULTS A diverse microbial community was found to be present on Musa and Chlorophytum grown in different indoor environments; the datasets comprised 1066 bacterial, 1261 fungal, and 358 archaeal ASVs. Bacterial communities were specific for each plant species, whereas fungal and archaeal communities were primarily shaped by the built environment. Sphingomonas and Bacillus were found to be prevalent components of a ubiquitous core microbiome in the two model plants; they are well-known for antagonistic activity towards plant pathogens. Interaction assays indicated that they can also antagonize opportunistic human pathogens. Moreover, the native plant microbiomes harbored a broad spectrum of biosynthetic gene clusters, and in parallel, a variety of antimicrobial resistance genes. By conducting comparative metagenomic analyses between plants and abiotic surfaces, we found that the phyllosphere microbiota harbors features that are clearly distinguishable from the surrounding abiotic surfaces. CONCLUSIONS Naturally occurring phyllosphere bacteria can potentially act as a protective shield against opportunistic human pathogens. This knowledge and the underlying mechanisms can provide an important basis to establish a healthy microbiome in built environments.
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Affiliation(s)
- Wisnu Adi Wicaksono
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria.
| | | | - Sabine Erschen
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria.
| | - Peter Kusstatscher
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria.
| | - Christian Berg
- Institute of Plant Sciences, Karl-Franzens-University, Graz, Austria.
| | - Robert Krause
- Department of Internal Medicine, Medical University of Graz, Graz, Austria; BioTechMed Graz, Inter-university Cooperation Platform, Graz, Austria.
| | - Tomislav Cernava
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria; BioTechMed Graz, Inter-university Cooperation Platform, Graz, Austria.
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria; BioTechMed Graz, Inter-university Cooperation Platform, Graz, Austria; Leibniz Institute for Agricultural Engineering and Bioeconomy Potsdam, Potsdam, Germany; Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany.
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Baroja-Fernández E, Almagro G, Sánchez-López ÁM, Bahaji A, Gámez-Arcas S, De Diego N, Dolezal K, Muñoz FJ, Climent Sanz E, Pozueta-Romero J. Enhanced Yield of Pepper Plants Promoted by Soil Application of Volatiles From Cell-Free Fungal Culture Filtrates Is Associated With Activation of the Beneficial Soil Microbiota. FRONTIERS IN PLANT SCIENCE 2021; 12:752653. [PMID: 34745186 PMCID: PMC8566893 DOI: 10.3389/fpls.2021.752653] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 09/30/2021] [Indexed: 06/12/2023]
Abstract
Plants communicate with microorganisms by exchanging chemical signals throughout the phytosphere. Such interactions are important not only for plant productivity and fitness, but also for terrestrial ecosystem functioning. It is known that beneficial microorganisms emit diffusible substances including volatile organic compounds (VOCs) that promote growth. Consistently, soil application of cell-free culture filtrates (CF) of beneficial soil and plant-associated microorganisms enhances plant growth and yield. However, how this treatment acts in plants and whether it alters the resident soil microbiota, are largely unknown. In this work we characterized the responses of pepper (Capsicum annuum L.) plants cultured under both greenhouse and open field conditions and of soil microbiota to soil application of CFs of beneficial and phytopathogenic fungi. To evaluate the contribution of VOCs occurring in the CFs to these responses, we characterized the responses of plants and of soil microbiota to application of distillates (DE) of the fungal CFs. CFs and their respective DEs contained the same potentially biogenic VOCs, and application of these extracts enhanced root growth and fruit yield, and altered the nutritional characteristics of fruits. High-throughput amplicon sequencing of bacterial 16S and fungal ITS rRNA genes of the soil microbiota revealed that the CF and DE treatments altered the microbial community compositions, and led to strong enrichment of the populations of the same beneficial bacterial and fungal taxa. Our findings show that CFs of both beneficial and phytopathogenic fungi can be used as biostimulants, and provide evidence that VOCs occurring in the fungal CFs act as mediators of the plants' responses to soil application of fungal CFs through stimulation of the beneficial soil microbiota.
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Affiliation(s)
| | - Goizeder Almagro
- Instituto de Agrobiotecnología (CSIC/Gobierno de Navarra), Nafarroa, Spain
| | | | - Abdellatif Bahaji
- Instituto de Agrobiotecnología (CSIC/Gobierno de Navarra), Nafarroa, Spain
| | - Samuel Gámez-Arcas
- Instituto de Agrobiotecnología (CSIC/Gobierno de Navarra), Nafarroa, Spain
| | - Nuria De Diego
- Centre of the Region Haná for Biotechnological and Agricultural Research, Czech Advanced Technology and Research Institute, Olomouc, Czechia
| | - Karel Dolezal
- Department of Chemical Biology, Faculty of Science, Palacký University Olomouc, Olomouc, Czechia
- Laboratory of Growth Regulators, Institute of Experimental Botany of the Czech Academy of Sciences, Faculty of Science, Palacký University Olomouc, Olomouc, Czechia
| | | | | | - Javier Pozueta-Romero
- Instituto de Agrobiotecnología (CSIC/Gobierno de Navarra), Nafarroa, Spain
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora” (IHSM-UMA-CSIC) Campus de Teatinos, Málaga, Spain
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Chen Y, Li S, Liu N, He H, Cao X, Lv C, Zhang K, Dai J. Effects of different types of microbial inoculants on available nitrogen and phosphorus, soil microbial community, and wheat growth in high-P soil. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:23036-23047. [PMID: 33438124 DOI: 10.1007/s11356-020-12203-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 12/22/2020] [Indexed: 05/03/2023]
Abstract
Irrational application of chemical fertilizers causes soil nutrient imbalance, reduced microbial diversity, soil diseases, and other soil quality problems and is one of the main sources of non-point pollution. The application of microbial inoculant (MI) can improve the soil environment and crop growth to reduce problems caused by irrational application of chemical fertilizers. Field experiments were carried out in high-phosphorus soils to study the effects of the addition of various MIs combined with chemical fertilizers on soil properties, wheat growth, and soil microbial composition and structure. The MIs consisted of one fungal agent: Trichoderma compound agent (TC) and five bacterial agents, namely soil remediation agent (SR), anti-repeat microbial agent (AM), microbial agent (MA), plant growth-promoting rhizobacteria (PG), and biological fertilizer agent (BF). The wheat yield increased by 15.2-33.4% with the addition of MIs, and PG with Bacillus subtilis as the core microorganism had the most obvious effect on increasing the production (p < 0.05). For the entire growth period of wheat, all MIs applied significantly increased the available nitrogen (AN) (p < 0.05) but did not significantly affect the available phosphorus (AP). BF has the best effect on increasing AN in the soil. The 16S rRNA sequencing results indicated that the dominant phyla of soil bacteria were Proteobacteria, Acidobacteria, Bacteroidetes, Actinobacteria, and Verrucomicrobia. The addition of MIs increased the relative abundance of Acidobacteria, Actinobacteria, Chloroflexi and decreased Proteobacteria and Bacteroidetes. The diversity of soil bacterial community (Chao1) was significantly higher in the soil added with TC than that added with BF (p < 0.05). All bacterial agents significantly enriched various genera (p < 0.05), while the fungal agent (TC) did not enrich the genera significantly. pH and AN, but not TP, were closely related to the dominant bacteria phylum in high-P soil. The application of MIs improved AN in soil, increased the wheat yield, and changed the relative abundance of the soil dominant phylum, and these changes were closely related to the type of MIs. The results provide a scientific basis for rational use of different types of MIs in high-P soil.
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Affiliation(s)
- Yihui Chen
- Environment Research Institute, Shandong University, Binhai Road 72, Qingdao, 266237, Shandong, China
| | - Shuangshuang Li
- Environment Research Institute, Shandong University, Binhai Road 72, Qingdao, 266237, Shandong, China
| | - Na Liu
- College of Resource and Environment, Shanxi Agricultural University, Taigu, 030801, China
| | - Huan He
- Environment Research Institute, Shandong University, Binhai Road 72, Qingdao, 266237, Shandong, China
| | - Xiaoyu Cao
- Environment Research Institute, Shandong University, Binhai Road 72, Qingdao, 266237, Shandong, China
| | - Cheng Lv
- Environment Research Institute, Shandong University, Binhai Road 72, Qingdao, 266237, Shandong, China
| | - Ke Zhang
- Environment Research Institute, Shandong University, Binhai Road 72, Qingdao, 266237, Shandong, China
| | - Jiulan Dai
- Environment Research Institute, Shandong University, Binhai Road 72, Qingdao, 266237, Shandong, China.
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Delitte M, Caulier S, Bragard C, Desoignies N. Plant Microbiota Beyond Farming Practices: A Review. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2021. [DOI: 10.3389/fsufs.2021.624203] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Plants have always grown and evolved surrounded by numerous microorganisms that inhabit their environment, later termed microbiota. To enhance food production, humankind has relied on various farming practices such as irrigation, tilling, fertilization, and pest and disease management. Over the past few years, studies have highlighted the impacts of such practices, not only in terms of plant health or yields but also on the microbial communities associated with plants, which have been investigated through microbiome studies. Because some microorganisms exert beneficial traits that improve plant growth and health, understanding how to modulate microbial communities will help in developing smart farming and favor plant growth-promoting (PGP) microorganisms. With tremendous cost cuts in NGS technologies, metagenomic approaches are now affordable and have been widely used to investigate crop-associated microbiomes. Being able to engineer microbial communities in ways that benefit crop health and growth will help decrease the number of chemical inputs required. Against this background, this review explores the impacts of agricultural practices on soil- and plant-associated microbiomes, focusing on plant growth-promoting microorganisms from a metagenomic perspective.
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Biostimulant-Treated Seedlings under Sustainable Agriculture: A Global Perspective Facing Climate Change. AGRONOMY-BASEL 2020. [DOI: 10.3390/agronomy11010014] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The primary objectives of modern agriculture includes the environmental sustainability, low production costs, improved plants’ resilience to various biotic and abiotic stresses, and high sowing seed value. Delayed and inconsistent field emergence poses a significant threat in the production of agri-crop, especially during drought and adverse weather conditions. To open new routes of nutrients’ acquisition and revolutionizing the adapted solutions, stewardship plans will be needed to address these questions. One approach is the identification of plant based bioactive molecules capable of altering plant metabolism pathways which may enhance plant performance in a brief period of time and in a cost-effective manner. A biostimulant is a plant material, microorganism, or any other organic compound that not only improves the nutritional aspects, vitality, general health but also enhances the seed quality performance. They may be effectively utilized in both horticultural and cereal crops. The biologically active substances in biostimulant biopreparations are protein hydrolysates (PHs), seaweed extracts, fulvic acids, humic acids, nitrogenous compounds, beneficial bacterial, and fungal agents. In this review, the state of the art and future prospects for biostimulant seedlings are reported and discussed. Biostimulants have been gaining interest as they stimulate crop physiology and biochemistry such as the ratio of leaf photosynthetic pigments (carotenoids and chlorophyll), enhanced antioxidant potential, tremendous root growth, improved nutrient use efficiency (NUE), and reduced fertilizers consumption. Thus, all these properties make the biostimulants fit for internal market operations. Furthermore, a special consideration has been given to the application of biostimulants in intensive agricultural systems that minimize the fertilizers’ usage without affecting quality and yield along with the limits imposed by European Union (EU) regulations.
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Diaz-Garza AM, Fierro-Rivera JI, Pacheco A, Schüßler A, Gradilla-Hernández MS, Senés-Guerrero C. Temporal Dynamics of Rhizobacteria Found in Pequin Pepper, Soybean, and Orange Trees Growing in a Semi-arid Ecosystem. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2020. [DOI: 10.3389/fsufs.2020.602283] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Qu Z, Zhao H, Zhang H, Wang Q, Yao Y, Cheng J, Lin Y, Xie J, Fu Y, Jiang D. Bio-priming with a hypovirulent phytopathogenic fungus enhances the connection and strength of microbial interaction network in rapeseed. NPJ Biofilms Microbiomes 2020; 6:45. [PMID: 33127920 PMCID: PMC7603479 DOI: 10.1038/s41522-020-00157-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 09/23/2020] [Indexed: 12/11/2022] Open
Abstract
Plant disease is one of the most important causes of crop losses worldwide. The effective control of plant disease is related to food security. Sclerotinia stem rot (SSR) caused by Sclerotinia sclerotiorum leads to serious yield losses in rapeseed (Brassica napus) production. Hypovirulent strain DT-8 of S. sclerotiorum, infected with Sclerotinia sclerotiorum hypovirulence-associated DNA virus 1 (SsHADV-1), has the potential to control SSR. In this study, we found rapeseed bio-priming with strain DT-8 could significantly decrease the disease severity of SSR and increase yield in the field. After bio-priming, strain DT-8 could be detected on the aerial part of the rapeseed plant. By 16S rRNA gene and internal transcribed spacer (ITS) sequencing technique, the microbiome on different parts of the SSR lesion on bioprimed and non-bioprimed rapeseed stem was determined. The results indicated that SSR and bio-priming treatment could influence the structure and composition of fungal and bacterial communities. Bio-priming treatment could reduce the total abundance of possible plant pathogens and enhance the connectivity and robustness of the interaction network at the genus level. This might be one of the mechanisms that rapeseed bioprimed with strain DT-8 had excellent tolerance on SSR. It might be another possible mechanism of biocontrol and will provide a theoretical guide for agricultural practical production.
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Affiliation(s)
- Zheng Qu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, China
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, China
| | - Huizhang Zhao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, China
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, China
| | - Hongxiang Zhang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, China
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, China
| | - Qianqian Wang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, China
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, China
| | - Yao Yao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, China
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, China
| | - Jiasen Cheng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, China
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, China
| | - Yang Lin
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, China
| | - Jiatao Xie
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, China
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, China
| | - Yanping Fu
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, China
| | - Daohong Jiang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, China.
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, China.
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Xia Y. Correlation and association analyses in microbiome study integrating multiomics in health and disease. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2020; 171:309-491. [PMID: 32475527 DOI: 10.1016/bs.pmbts.2020.04.003] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Correlation and association analyses are one of the most widely used statistical methods in research fields, including microbiome and integrative multiomics studies. Correlation and association have two implications: dependence and co-occurrence. Microbiome data are structured as phylogenetic tree and have several unique characteristics, including high dimensionality, compositionality, sparsity with excess zeros, and heterogeneity. These unique characteristics cause several statistical issues when analyzing microbiome data and integrating multiomics data, such as large p and small n, dependency, overdispersion, and zero-inflation. In microbiome research, on the one hand, classic correlation and association methods are still applied in real studies and used for the development of new methods; on the other hand, new methods have been developed to target statistical issues arising from unique characteristics of microbiome data. Here, we first provide a comprehensive view of classic and newly developed univariate correlation and association-based methods. We discuss the appropriateness and limitations of using classic methods and demonstrate how the newly developed methods mitigate the issues of microbiome data. Second, we emphasize that concepts of correlation and association analyses have been shifted by introducing network analysis, microbe-metabolite interactions, functional analysis, etc. Third, we introduce multivariate correlation and association-based methods, which are organized by the categories of exploratory, interpretive, and discriminatory analyses and classification methods. Fourth, we focus on the hypothesis testing of univariate and multivariate regression-based association methods, including alpha and beta diversities-based, count-based, and relative abundance (or compositional)-based association analyses. We demonstrate the characteristics and limitations of each approaches. Fifth, we introduce two specific microbiome-based methods: phylogenetic tree-based association analysis and testing for survival outcomes. Sixth, we provide an overall view of longitudinal methods in analysis of microbiome and omics data, which cover standard, static, regression-based time series methods, principal trend analysis, and newly developed univariate overdispersed and zero-inflated as well as multivariate distance/kernel-based longitudinal models. Finally, we comment on current association analysis and future direction of association analysis in microbiome and multiomics studies.
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Affiliation(s)
- Yinglin Xia
- Department of Medicine, University of Illinois at Chicago, Chicago, IL, United States.
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Mahnert A, Moissl-Eichinger C, Zojer M, Bogumil D, Mizrahi I, Rattei T, Martinez JL, Berg G. Man-made microbial resistances in built environments. Nat Commun 2019; 10:968. [PMID: 30814504 PMCID: PMC6393488 DOI: 10.1038/s41467-019-08864-0] [Citation(s) in RCA: 114] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 02/01/2019] [Indexed: 11/24/2022] Open
Abstract
Antimicrobial resistance is a serious threat to global public health, but little is known about the effects of microbial control on the microbiota and its associated resistome. Here we compare the microbiota present on surfaces of clinical settings with other built environments. Using state-of-the-art metagenomics approaches and genome and plasmid reconstruction, we show that increased confinement and cleaning is associated with a loss of microbial diversity and a shift from Gram-positive bacteria, such as Actinobacteria and Firmicutes, to Gram-negative such as Proteobacteria. Moreover, the microbiome of highly maintained built environments has a different resistome when compared to other built environments, as well as a higher diversity in resistance genes. Our results highlight that the loss of microbial diversity correlates with an increase in resistance, and the need for implementing strategies to restore bacterial diversity in certain built environments.
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Affiliation(s)
- Alexander Mahnert
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12/I, Graz, 8010, Austria.
| | - Christine Moissl-Eichinger
- Department of Internal Medicine, Medical University Graz, Auenbruggerplatz 2, Graz, 8036, Austria
- BioTechMed Graz, Mozartgasse 12/II, Graz, 8010, Austria
| | - Markus Zojer
- Division of Computational Systems Biology, Department of Microbiology and Ecosystem Science, University of Vienna, Althanstrasse 14, Vienna, 1090, Austria
| | - David Bogumil
- Department of Life Sciences, Faculty of Natural Sciences, Ben-Gurion University of the Negev, Box 653, Beer-Sheva, 84105, Israel
| | - Itzhak Mizrahi
- Department of Life Sciences, Faculty of Natural Sciences, Ben-Gurion University of the Negev, Box 653, Beer-Sheva, 84105, Israel
| | - Thomas Rattei
- Division of Computational Systems Biology, Department of Microbiology and Ecosystem Science, University of Vienna, Althanstrasse 14, Vienna, 1090, Austria
| | - José Luis Martinez
- Centro Nacional de Biotecnologia, CSIC, Calle Darwin 3, Madrid, 28049, Spain
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12/I, Graz, 8010, Austria
- BioTechMed Graz, Mozartgasse 12/II, Graz, 8010, Austria
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