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Heinen R, Hannula SE, De Long JR, Huberty M, Jongen R, Kielak A, Steinauer K, Zhu F, Bezemer TM. Plant community composition steers grassland vegetation via soil legacy effects. Ecol Lett 2020; 23:973-982. [PMID: 32266749 PMCID: PMC7318629 DOI: 10.1111/ele.13497] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 01/13/2020] [Accepted: 02/28/2020] [Indexed: 01/14/2023]
Abstract
Soil legacy effects are commonly highlighted as drivers of plant community dynamics and species co-existence. However, experimental evidence for soil legacy effects of conditioning plant communities on responding plant communities under natural conditions is lacking. We conditioned 192 grassland plots using six different plant communities with different ratios of grasses and forbs and for different durations. Soil microbial legacies were evident for soil fungi, but not for soil bacteria, while soil abiotic parameters did not significantly change in response to conditioning. The soil legacies affected the composition of the succeeding vegetation. Plant communities with different ratios of grasses and forbs left soil legacies that negatively affected succeeding plants of the same functional type. We conclude that fungal-mediated soil legacy effects play a significant role in vegetation assembly of natural plant communities.
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Affiliation(s)
- Robin Heinen
- Department of Terrestrial Ecology, Netherlands Institute of Ecology, P.O. Box 50, 6700 AB, Wageningen, The Netherlands.,Institute of Biology, Section Plant Ecology and Phytochemistry, Leiden University, P.O. Box 9505, 2300 RA, Leiden, The Netherlands
| | - S Emilia Hannula
- Department of Terrestrial Ecology, Netherlands Institute of Ecology, P.O. Box 50, 6700 AB, Wageningen, The Netherlands
| | - Jonathan R De Long
- Department of Terrestrial Ecology, Netherlands Institute of Ecology, P.O. Box 50, 6700 AB, Wageningen, The Netherlands
| | - Martine Huberty
- Department of Terrestrial Ecology, Netherlands Institute of Ecology, P.O. Box 50, 6700 AB, Wageningen, The Netherlands.,Institute of Biology, Section Plant Ecology and Phytochemistry, Leiden University, P.O. Box 9505, 2300 RA, Leiden, The Netherlands
| | - Renske Jongen
- Department of Terrestrial Ecology, Netherlands Institute of Ecology, P.O. Box 50, 6700 AB, Wageningen, The Netherlands
| | - Anna Kielak
- Department of Terrestrial Ecology, Netherlands Institute of Ecology, P.O. Box 50, 6700 AB, Wageningen, The Netherlands
| | - Katja Steinauer
- Department of Terrestrial Ecology, Netherlands Institute of Ecology, P.O. Box 50, 6700 AB, Wageningen, The Netherlands
| | - Feng Zhu
- Department of Terrestrial Ecology, Netherlands Institute of Ecology, P.O. Box 50, 6700 AB, Wageningen, The Netherlands.,Key Laboratory of Agricultural Water Resources, Hebei Key Laboratory of Soil Ecology, Center for Agricultural Resources Research, Institute of Genetic and Developmental Biology, The Chinese Academy of Sciences, 286 Huaizhong Road, 050021, Shijiazhuang, Hebei, China
| | - T Martijn Bezemer
- Department of Terrestrial Ecology, Netherlands Institute of Ecology, P.O. Box 50, 6700 AB, Wageningen, The Netherlands.,Institute of Biology, Section Plant Ecology and Phytochemistry, Leiden University, P.O. Box 9505, 2300 RA, Leiden, The Netherlands
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102
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Pineda A, Kaplan I, Hannula SE, Ghanem W, Bezemer TM. Conditioning the soil microbiome through plant-soil feedbacks suppresses an aboveground insect pest. THE NEW PHYTOLOGIST 2020; 226:595-608. [PMID: 31863484 PMCID: PMC7155073 DOI: 10.1111/nph.16385] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2019] [Accepted: 12/04/2019] [Indexed: 05/21/2023]
Abstract
Soils and their microbiomes are now recognized as key components of plant health, but how to steer those microbiomes to obtain their beneficial functions is still unknown. Here, we assess whether plant-soil feedbacks can be applied in a crop system to shape soil microbiomes that suppress herbivorous insects in above-ground tissues. We used four grass and four forb species to condition living soil. Then we inoculated those soil microbiomes into sterilized soil and grew chrysanthemum as a focal plant. We evaluated the soil microbiome in the inocula and after chrysanthemum growth, as well as plant and herbivore parameters. We show that inocula and inoculated soil in which a focal plant had grown harbor remarkably different microbiomes, with the focal plant exerting a strong negative effect on fungi, especially arbuscular mycorrhizal fungi. Soil inoculation consistently induced resistance against the thrips Frankliniella occidentalis, but not against the mite Tetranychus urticae, when compared with sterilized soil. Additionally, plant species shaped distinct microbiomes that had different effects on thrips, chlorogenic acid concentrations in leaves and plant growth. This study provides a proof-of-concept that the plant-soil feedback concept can be applied to steer soil microbiomes with the goal of inducing resistance above ground against herbivorous insects.
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Affiliation(s)
- Ana Pineda
- Department of Terrestrial EcologyNetherlands Institute of Ecology (NIOO‐KNAW)Wageningen6700 ABthe Netherlands
| | - Ian Kaplan
- Department of Terrestrial EcologyNetherlands Institute of Ecology (NIOO‐KNAW)Wageningen6700 ABthe Netherlands
- Department of EntomologyPurdue UniversityWest LafayetteIN47907USA
| | - S. Emilia Hannula
- Department of Terrestrial EcologyNetherlands Institute of Ecology (NIOO‐KNAW)Wageningen6700 ABthe Netherlands
| | - Wadih Ghanem
- Department of Terrestrial EcologyNetherlands Institute of Ecology (NIOO‐KNAW)Wageningen6700 ABthe Netherlands
- Department of EntomologyPurdue UniversityWest LafayetteIN47907USA
| | - T. Martijn Bezemer
- Department of Terrestrial EcologyNetherlands Institute of Ecology (NIOO‐KNAW)Wageningen6700 ABthe Netherlands
- Institute of BiologySection Plant Ecology and PhytochemistryLeiden UniversityLeiden2300 RAthe Netherlands
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103
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Zafeiropoulos H, Viet HQ, Vasileiadou K, Potirakis A, Arvanitidis C, Topalis P, Pavloudi C, Pafilis E. PEMA: a flexible Pipeline for Environmental DNA Metabarcoding Analysis of the 16S/18S ribosomal RNA, ITS, and COI marker genes. Gigascience 2020; 9:giaa022. [PMID: 32161947 PMCID: PMC7066391 DOI: 10.1093/gigascience/giaa022] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 01/05/2020] [Accepted: 02/14/2020] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND Environmental DNA and metabarcoding allow the identification of a mixture of species and launch a new era in bio- and eco-assessment. Many steps are required to obtain taxonomically assigned matrices from raw data. For most of these, a plethora of tools are available; each tool's execution parameters need to be tailored to reflect each experiment's idiosyncrasy. Adding to this complexity, the computation capacity of high-performance computing systems is frequently required for such analyses. To address the difficulties, bioinformatic pipelines need to combine state-of-the art technologies and algorithms with an easy to get-set-use framework, allowing researchers to tune each study. Software containerization technologies ease the sharing and running of software packages across operating systems; thus, they strongly facilitate pipeline development and usage. Likewise programming languages specialized for big data pipelines incorporate features like roll-back checkpoints and on-demand partial pipeline execution. FINDINGS PEMA is a containerized assembly of key metabarcoding analysis tools that requires low effort in setting up, running, and customizing to researchers' needs. Based on third-party tools, PEMA performs read pre-processing, (molecular) operational taxonomic unit clustering, amplicon sequence variant inference, and taxonomy assignment for 16S and 18S ribosomal RNA, as well as ITS and COI marker gene data. Owing to its simplified parameterization and checkpoint support, PEMA allows users to explore alternative algorithms for specific steps of the pipeline without the need of a complete re-execution. PEMA was evaluated against both mock communities and previously published datasets and achieved results of comparable quality. CONCLUSIONS A high-performance computing-based approach was used to develop PEMA; however, it can be used in personal computers as well. PEMA's time-efficient performance and good results will allow it to be used for accurate environmental DNA metabarcoding analysis, thus enhancing the applicability of next-generation biodiversity assessment studies.
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Affiliation(s)
- Haris Zafeiropoulos
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR), Former U.S. Base of Gournes P.O. Box 2214, 71003, Heraklion, Crete, Greece
- Department of Biology, University of Crete, Voutes University Campus, Heraklion, Greece
| | - Ha Quoc Viet
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR), Former U.S. Base of Gournes P.O. Box 2214, 71003, Heraklion, Crete, Greece
| | - Katerina Vasileiadou
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR), Former U.S. Base of Gournes P.O. Box 2214, 71003, Heraklion, Crete, Greece
- Charles University, Department of Ecology, Faculty of Science, Viničná 7, CZ-12844, Prague, Czech Republic
| | - Antonis Potirakis
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR), Former U.S. Base of Gournes P.O. Box 2214, 71003, Heraklion, Crete, Greece
| | - Christos Arvanitidis
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR), Former U.S. Base of Gournes P.O. Box 2214, 71003, Heraklion, Crete, Greece
- LifeWatch ERIC, Plaza España SN, SECTOR II-III 41013, Seville, Spain
| | - Pantelis Topalis
- Institute of Molecular Biology and Biotechnology (IMBB), Foundation for Research and Technology (FORTH), Foundation for Research and Technology – Hellas, N. Plastira 100, GR-70013, Heraklion, Crete, Greece
| | - Christina Pavloudi
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR), Former U.S. Base of Gournes P.O. Box 2214, 71003, Heraklion, Crete, Greece
| | - Evangelos Pafilis
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR), Former U.S. Base of Gournes P.O. Box 2214, 71003, Heraklion, Crete, Greece
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104
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Abstract
The aim of this work was to study the fungal colonization of a new winery over time, specifically for Saccharomyces cerevisiae. Therefore, we analyzed the flora present before the arrival of the first harvest on the floor, the walls and the equipment of this new winery by Illumina MiSeq. The genus Saccharomyces (≤0.3%) was detected on floor and equipment but the presence of S. cerevisiae species was not reported. Wild S. cerevisiae strains were isolated from a ‘Pied de Cuve’ used during the first vintage to ensure the alcoholic fermentation (AF). Among 25 isolates belonging to this species, 17 different strains were identified highlighting a great intraspecific diversity. S. cerevisiae strains were also isolated from different vats throughout the spontaneous fermentations during the first vintage. The following year, some of these strains were isolated again during AF. Some of them (four) were found in the winery equipment before the arrival of the third harvest suggesting a potential colonization by these strains. To better understand what promotes the yeast colonization of the winery’s environment, the ability to form a biofilm on solid surfaces for eight colonizing or non-colonizing strains was studied. This capacity, different according to the strains, could partly explain the colonization observed for certain strains.
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105
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Garrido-Benavent I, Pérez-Ortega S, Durán J, Ascaso C, Pointing SB, Rodríguez-Cielos R, Navarro F, de los Ríos A. Differential Colonization and Succession of Microbial Communities in Rock and Soil Substrates on a Maritime Antarctic Glacier Forefield. Front Microbiol 2020; 11:126. [PMID: 32117148 PMCID: PMC7018881 DOI: 10.3389/fmicb.2020.00126] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 01/20/2020] [Indexed: 12/20/2022] Open
Abstract
Glacier forefields provide a unique chronosequence to assess microbial or plant colonization and ecological succession on previously uncolonized substrates. Patterns of microbial succession in soils of alpine and subpolar glacier forefields are well documented but those affecting high polar systems, including moraine rocks, remain largely unexplored. In this study, we examine succession patterns in pioneering bacterial, fungal and algal communities developing on moraine rocks and soil at the Hurd Glacier forefield (Livingston Island, Antarctica). Over time, changes were produced in the microbial community structure of rocks and soils (ice-free for different lengths of time), which differed between both substrates across the entire chronosequence, especially for bacteria and fungi. In addition, fungal and bacterial communities showed more compositional consistency in soils than rocks, suggesting community assembly in each niche could be controlled by processes operating at different temporal and spatial scales. Microscopy revealed a patchy distribution of epilithic and endolithic lithobionts, and increasing endolithic colonization and microbial community complexity along the chronosequence. We conclude that, within relatively short time intervals, primary succession processes at polar latitudes involve significant and distinct changes in edaphic and lithic microbial communities associated with soil development and cryptogamic colonization.
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Affiliation(s)
- Isaac Garrido-Benavent
- Departamento de Biogeoquímica y Ecología Microbiana, Museo Nacional de Ciencias Naturales, CSIC, Madrid, Spain
| | | | - Jorge Durán
- Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - Carmen Ascaso
- Departamento de Biogeoquímica y Ecología Microbiana, Museo Nacional de Ciencias Naturales, CSIC, Madrid, Spain
| | - Stephen B. Pointing
- Yale-NUS College, National University of Singapore, Singapore, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Ricardo Rodríguez-Cielos
- ETSI de Telecomunicación, Departamento de Señales, Sistemas y Radiocomunicaciones, Universidad Politécnica de Madrid, Madrid, Spain
| | - Francisco Navarro
- ETSI de Telecomunicación, Departamento de Matemática Aplicada a las TIC, Universidad Politécnica de Madrid, Madrid, Spain
| | - Asunción de los Ríos
- Departamento de Biogeoquímica y Ecología Microbiana, Museo Nacional de Ciencias Naturales, CSIC, Madrid, Spain
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106
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Fadiji AE, Babalola OO. Metagenomics methods for the study of plant-associated microbial communities: A review. J Microbiol Methods 2020; 170:105860. [PMID: 32027927 DOI: 10.1016/j.mimet.2020.105860] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 01/31/2020] [Accepted: 02/02/2020] [Indexed: 12/20/2022]
Abstract
Plant microbiota have different effects on the plant which can be beneficial or pathogenic. In this study, we concentrated on beneficial microbes associated with plants using endophytic microbes as a case study. Detailed knowledge of the microbial diversity, abundance, composition, functional genes patterns, and metabolic pathways at genome level could assist in understanding the contributions of microbial community towards plant growth and health. Recently, the study of microbial community has improved greatly with the discovery of next-generation sequencing and bioinformatics technologies. Analysis of next generation sequencing data and a proper computational method plays a key role in examining microbial metagenome. This review presents the general metagenomics and computational methods used in processing plant associated metagenomes with concentration on endophytes. This includes 1) introduction of plant-associated microbiota and the factors driving their diversity. 2) plant metagenome focusing on DNA extraction, verification and quality control. 3) metagenomics methods used in community analysis of endophytes focusing on maize plant and, 4) computational methods used in the study of endophytic microbiomes. Limitations and future prospects of metagenomics and computational methods for the analysis of plant-associated metagenome (endophytic metagenome) were also discussed with the aim of fostering its development. We conclude that there is need to adopt advanced genomic features such as k-mers of random size, which do not depend on annotation and can represent other sequence alternatives.
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Affiliation(s)
- Ayomide Emmanuel Fadiji
- Food Security and Safety Niche, Faculty of Natural and Agricultural Sciences, North-West University, Private Mail Bag X2046, Mmabatho, South Africa
| | - Olubukola Oluranti Babalola
- Food Security and Safety Niche, Faculty of Natural and Agricultural Sciences, North-West University, Private Mail Bag X2046, Mmabatho, South Africa.
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107
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Bradley CW, Lee FF, Rankin SC, Kalan LR, Horwinski J, Morris DO, Grice EA, Cain CL. The otic microbiota and mycobiota in a referral population of dogs in eastern USA with otitis externa. Vet Dermatol 2020; 31:225-e49. [PMID: 31960536 DOI: 10.1111/vde.12826] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/21/2019] [Indexed: 12/14/2022]
Abstract
BACKGROUND Canine otitis externa (OE) is a common inflammatory disease that is frequently complicated by secondary bacterial and/or yeast infections. The otic microbial population is more complex than appreciated by cytological methods and aerobic culture alone. HYPOTHESIS/OBJECTIVES Differences in bacterial and fungal populations of the external ear canal will correlate with specific cytological and culture-based definitions of bacterial and Malassezia otitis. ANIMALS Forty client-owned dogs; 30 with OE and 10 with healthy ears. METHODS AND MATERIALS Prospective study comparing cytological samples, aerobic bacterial cultures and culture-independent sequencing-based analyses of the external ear canal. Subjects with OE included 10 dogs with only cocci [≥25/high power field (HPF)] on cytological evaluation and culture of Staphylococcus spp.; 10 dogs with rods (≥25/HPF) and exclusive culture of Pseudomonas aeruginosa; 10 dogs with only yeast on cytological results morphologically compatible with Malassezia spp. (≥5/HPF). RESULTS Staphylococcus was the most abundant taxa across all groups. Ears cytologically positive for cocci had decreased diversity, and all types of OE were associated with decreased fungal diversity compared to controls. CONCLUSIONS AND CLINICAL IMPORTANCE Cytological and culture-based assessment of the ear canal is not predictive of the diverse microbiota of the ear canal in cases of Pseudomonas or Malassezia otitis. Less abundant bacterial taxa in cases of staphylococcal OE are worth scrutiny for future biological therapy.
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Affiliation(s)
- Charles W Bradley
- Departments of Pathobiology, University of Pennsylvania, 3900 Delancey St, Philadelphia, PA, 19104, USA
| | - Fiona F Lee
- Clinical Sciences and Advanced Medicine, School of Veterinary Medicine, University of Pennsylvania, 3900 Delancey St, Philadelphia, PA, 19104, USA
| | - Shelley C Rankin
- Departments of Pathobiology, University of Pennsylvania, 3900 Delancey St, Philadelphia, PA, 19104, USA
| | - Lindsay R Kalan
- Dermatology, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Blvd, Philadelphia, PA, 19104, USA
| | - Joseph Horwinski
- Dermatology, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Blvd, Philadelphia, PA, 19104, USA
| | - Daniel O Morris
- Clinical Sciences and Advanced Medicine, School of Veterinary Medicine, University of Pennsylvania, 3900 Delancey St, Philadelphia, PA, 19104, USA
| | - Elizabeth A Grice
- Dermatology, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Blvd, Philadelphia, PA, 19104, USA
| | - Christine L Cain
- Clinical Sciences and Advanced Medicine, School of Veterinary Medicine, University of Pennsylvania, 3900 Delancey St, Philadelphia, PA, 19104, USA
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108
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Nilsson RH, Anslan S, Bahram M, Wurzbacher C, Baldrian P, Tedersoo L. Mycobiome diversity: high-throughput sequencing and identification of fungi. Nat Rev Microbiol 2020; 17:95-109. [PMID: 30442909 DOI: 10.1038/s41579-018-0116-y] [Citation(s) in RCA: 404] [Impact Index Per Article: 101.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Fungi are major ecological players in both terrestrial and aquatic environments by cycling organic matter and channelling nutrients across trophic levels. High-throughput sequencing (HTS) studies of fungal communities are redrawing the map of the fungal kingdom by hinting at its enormous - and largely uncharted - taxonomic and functional diversity. However, HTS approaches come with a range of pitfalls and potential biases, cautioning against unwary application and interpretation of HTS technologies and results. In this Review, we provide an overview and practical recommendations for aspects of HTS studies ranging from sampling and laboratory practices to data processing and analysis. We also discuss upcoming trends and techniques in the field and summarize recent and noteworthy results from HTS studies targeting fungal communities and guilds. Our Review highlights the need for reproducibility and public data availability in the study of fungal communities. If the associated challenges and conceptual barriers are overcome, HTS offers immense possibilities in mycology and elsewhere.
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Affiliation(s)
- R Henrik Nilsson
- Gothenburg Global Biodiversity Centre, Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden.
| | - Sten Anslan
- Zoological Institute, Braunschweig University of Technology, Braunschweig, Germany
| | - Mohammad Bahram
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Christian Wurzbacher
- Chair of Urban Water Systems Engineering, Technical University of Munich, Garching, Germany
| | - Petr Baldrian
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Praha, Czech Republic
| | - Leho Tedersoo
- Natural History Museum of Tartu University, Tartu, Estonia
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109
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Sanjar F, Weaver AJ, Peacock TJ, Nguyen JQ, Brandenburg KS, Leung KP. Temporal shifts in the mycobiome structure and network architecture associated with a rat (Rattus norvegicus) deep partial-thickness cutaneous burn. Med Mycol 2020; 58:107-117. [PMID: 31041451 PMCID: PMC6939685 DOI: 10.1093/mmy/myz030] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 02/01/2019] [Accepted: 03/11/2019] [Indexed: 12/22/2022] Open
Abstract
With a diverse physiological interface to colonize, mammalian skin is the first line of defense against pathogen invasion and harbors a consortium of microbes integral in maintenance of epithelial barrier function and disease prevention. While the dynamic roles of skin bacterial residents are expansively studied, contributions of fungal constituents, the mycobiome, are largely overlooked. As a result, their influence during skin injury, such as disruption of skin integrity in burn injury and impairment of host immune defense system, is not clearly delineated. Burn patients experience a high risk of developing hard-to-treat fungal infections in comparison to other hospitalized patients. To discern the changes in the mycobiome profile and network assembly during cutaneous burn-injury, a rat scald burn model was used to survey the mycobiome in healthy (n = 30) (sham-burned) and burned (n = 24) skin over an 11-day period. The healthy skin demonstrated inter-animal heterogeneity over time, while the burned skin mycobiome transitioned toward a temporally stabile community with declining inter-animal variation starting at day 3 post-burn injury. Driven primarily by a significant increase in relative abundance of Candida, fungal species richness and abundance of the burned skin decreased, especially in days 7 and 11 post-burn. The network architecture of rat skin mycobiome displayed community reorganization toward increased network fragility and decreased stability compared to the healthy rat skin fungal network. This study provides the first account of the dynamic diversity observed in the rat skin mycobiome composition, structure, and network assembly associated with postcutaneous burn injury.
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Affiliation(s)
- Fatemeh Sanjar
- Dental and Craniofacial Trauma Research and Tissue Regeneration Directorate, US Army Institute of Surgical Research, JBSA Fort Sam Houston, Texas, USA
| | - Alan J Weaver
- Dental and Craniofacial Trauma Research and Tissue Regeneration Directorate, US Army Institute of Surgical Research, JBSA Fort Sam Houston, Texas, USA
| | - Trent J Peacock
- Office of Research Compliance, Mississippi State University, Mississippi, USA
| | - Jesse Q Nguyen
- Dental and Craniofacial Trauma Research and Tissue Regeneration Directorate, US Army Institute of Surgical Research, JBSA Fort Sam Houston, Texas, USA
| | - Kenneth S Brandenburg
- Dental and Craniofacial Trauma Research and Tissue Regeneration Directorate, US Army Institute of Surgical Research, JBSA Fort Sam Houston, Texas, USA
| | - Kai P Leung
- Dental and Craniofacial Trauma Research and Tissue Regeneration Directorate, US Army Institute of Surgical Research, JBSA Fort Sam Houston, Texas, USA
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110
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Hannula SE, Ma HK, Pérez-Jaramillo JE, Pineda A, Bezemer TM. Structure and ecological function of the soil microbiome affecting plant-soil feedbacks in the presence of a soil-borne pathogen. Environ Microbiol 2019; 22:660-676. [PMID: 31788934 PMCID: PMC7027455 DOI: 10.1111/1462-2920.14882] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 11/22/2019] [Accepted: 11/28/2019] [Indexed: 11/30/2022]
Abstract
Interactions between plants and soil microbes are important for plant growth and resistance. Through plant–soil‐feedbacks, growth of a plant is influenced by the previous plant that was growing in the same soil. We performed a plant–soil feedback study with 37 grass, forb and legume species, to condition the soil and then tested the effects of plant‐induced changes in soil microbiomes on the growth of the commercially important cut‐flower Chrysanthemum in presence and absence of a pathogen. We analysed the fungal and bacterial communities in these soils using next‐generation sequencing and examined their relationship with plant growth in inoculated soils with or without the root pathogen, Pythium ultimum. We show that a large part of the soil microbiome is plant species‐specific while a smaller part is conserved at the plant family level. We further identified clusters of plant species creating plant growth promoting microbiomes that suppress concomitantly plant pathogens. Especially soil inocula with higher relative abundances of arbuscular mycorrhizal fungi caused positive effects on the Chrysanthemum growth when exposed to the pathogen. We conclude that plants differ greatly in how they influence the soil microbiome and that plant growth and protection against pathogens is associated with a complex soil microbial community.
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Affiliation(s)
- S Emilia Hannula
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands
| | - Hai-Kun Ma
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands.,Institute of Biology, Section Plant Ecology and Phytochemistry, Leiden University, P.O. Box 9505, 2300 RA, Leiden, The Netherlands
| | - Juan E Pérez-Jaramillo
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands
| | - Ana Pineda
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands
| | - T Martijn Bezemer
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands.,Institute of Biology, Section Plant Ecology and Phytochemistry, Leiden University, P.O. Box 9505, 2300 RA, Leiden, The Netherlands
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111
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Time after Time: Temporal Variation in the Effects of Grass and Forb Species on Soil Bacterial and Fungal Communities. mBio 2019; 10:mBio.02635-19. [PMID: 31848279 PMCID: PMC6918080 DOI: 10.1128/mbio.02635-19] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Our findings highlight how soil fungal and bacterial communities respond to time, season, and plant species identity. We found that succession shapes the soil bacterial community, while plant species and the type of plant species that grows in the soil drive the assembly of soil fungal communities. Future research on the effects of plants on soil microbes should take into consideration the relative roles of both time and plant growth on creating soil legacies that impact future plants growing in the soil. Understanding the temporal (in)stability of microbial communities in soils will be crucial for predicting soil microbial composition and functioning, especially as plant species compositions will shift with global climatic changes and land-use alterations. As fungal and bacterial communities respond to different environmental cues, our study also highlights that the selection of study organisms to answer specific ecological questions is not trivial and that the timing of sampling can greatly affect the conclusions made from these studies. Microorganisms are found everywhere and have critical roles in most ecosystems, but compared to plants and animals, little is known about their temporal dynamics. Here, we investigated the temporal stability of bacterial and fungal communities in the soil and how their temporal variation varies between grasses and forb species. We established 30 outdoor mesocosms consisting of six plant monocultures and followed microbial communities for an entire year in these soils. We demonstrate that bacterial communities vary greatly over time and that turnover plays an important role in shaping microbial communities. We further show that bacterial communities rapidly shift from one state to another and that this is related to changes in the relative contribution of certain taxa rather than to extinction. Fungal soil communities are more stable over time, and a large part of the variation can be explained by plant species and by whether they are grasses or forbs. Our findings show that the soil bacterial community is shaped by time, while plant group and plant species-specific effects drive soil fungal communities. This has important implications for plant-soil research and highlights that temporal dynamics of soil communities cannot be ignored in studies on plant-soil feedback and microbial community composition and function.
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Vanegas J, Muñoz-García A, Pérez-Parra KA, Figueroa-Galvis I, Mestanza O, Polanía J. Effect of salinity on fungal diversity in the rhizosphere of the halophyte Avicennia germinans from a semi-arid mangrove. FUNGAL ECOL 2019. [DOI: 10.1016/j.funeco.2019.07.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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113
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Gavito ME, Leyva-Morales R, Vega-Peña EV, Arita H, Jairus T, Vasar M, Öpik M. Local-scale spatial diversity patterns of ectomycorrhizal fungal communities in a subtropical pine-oak forest. FUNGAL ECOL 2019. [DOI: 10.1016/j.funeco.2019.08.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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114
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Bergsveinson J, Perry BJ, Simpson GL, Yost CK, Schutzman RJ, Hall BD, Cameron ADS. Spatial analysis of a hydrocarbon waste-remediating landfarm demonstrates influence of management practices on bacterial and fungal community structure. Microb Biotechnol 2019; 12:1199-1209. [PMID: 30927344 PMCID: PMC6801160 DOI: 10.1111/1751-7915.13397] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 02/15/2019] [Accepted: 02/21/2019] [Indexed: 11/27/2022] Open
Abstract
Cultivation of dedicated soil plots called 'landfarms' is an effective technology for bioremediation of hydrocarbon waste generated by various industrial practices. To understand the influence of soil conditions on landfarm microbial communities, analysis of bacterial and fungal community structure using next-generation sequencing at different sections and depths was performed across a hydrocarbon-waste landfarm in Regina, Saskatchewan, Canada. While a core set of hydrocarbon-associated bacterial and fungal taxa are present throughout the landfarm, unique bacterial and fungal operational taxonomic units are differentially abundant at sections within the landfarm, which correlate with differences in soil physiochemical properties and management practices. Increased frequency of waste application resulted in strong positive correlations between bacterial community assemblages and elevated amounts of oil, grease and F3 - F4 hydrocarbon fractions. In areas of standing water and lower application of hydrocarbon, microbial community structure correlated with soil pH, trace nutrients and metals. Overall, diversity and structure of bacterial communities remain relatively stable across the landfarm, while in contrast, fungal community structure appears more responsive to soil oxygen conditions. Results are consistent with the hypothesis that years of bioremediation activity have shaped microbial communities; however, several management practices can be undertaken to increase efficiency of remediation, including the removal of standing water and soil tilling across the landfarm.
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Affiliation(s)
- Jordyn Bergsveinson
- Department of BiologyUniversity of ReginaReginaSKCanada
- Institute for Microbial Systems and SocietyUniversity of ReginaReginaSKCanada
| | - Benjamin J. Perry
- Department of BiologyUniversity of ReginaReginaSKCanada
- Present address:
Department of Microbiology and ImmunologyUniversity of OtagoDunedinNew Zealand
| | - Gavin L. Simpson
- Department of BiologyUniversity of ReginaReginaSKCanada
- Institute of Environmental Change and SocietyUniversity of ReginaReginaSKCanada
| | - Christopher K. Yost
- Department of BiologyUniversity of ReginaReginaSKCanada
- Institute for Microbial Systems and SocietyUniversity of ReginaReginaSKCanada
| | | | - Britt D. Hall
- Department of BiologyUniversity of ReginaReginaSKCanada
| | - Andrew D. S. Cameron
- Department of BiologyUniversity of ReginaReginaSKCanada
- Institute for Microbial Systems and SocietyUniversity of ReginaReginaSKCanada
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Lucaciu R, Pelikan C, Gerner SM, Zioutis C, Köstlbacher S, Marx H, Herbold CW, Schmidt H, Rattei T. A Bioinformatics Guide to Plant Microbiome Analysis. FRONTIERS IN PLANT SCIENCE 2019; 10:1313. [PMID: 31708944 PMCID: PMC6819368 DOI: 10.3389/fpls.2019.01313] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 09/20/2019] [Indexed: 05/18/2023]
Abstract
Recent evidence for intimate relationship of plants with their microbiota shows that plants host individual and diverse microbial communities that are essential for their survival. Understanding their relatedness using genome-based and high-throughput techniques remains a hot topic in microbiome research. Molecular analysis of the plant holobiont necessitates the application of specific sampling and preparatory steps that also consider sources of unwanted information, such as soil, co-amplified plant organelles, human DNA, and other contaminations. Here, we review state-of-the-art and present practical guidelines regarding experimental and computational aspects to be considered in molecular plant-microbiome studies. We discuss sequencing and "omics" techniques with a focus on the requirements needed to adapt these methods to individual research approaches. The choice of primers and sequence databases is of utmost importance for amplicon sequencing, while the assembly and binning of shotgun metagenomic sequences is crucial to obtain quality data. We discuss specific bioinformatic workflows to overcome the limitation of genome database resources and for covering large eukaryotic genomes such as fungi. In transcriptomics, it is necessary to account for the separation of host mRNA or dual-RNAseq data. Metaproteomics approaches provide a snapshot of the protein abundances within a plant tissue which requires the knowledge of complete and well-annotated plant genomes, as well as microbial genomes. Metabolomics offers a powerful tool to detect and quantify small molecules and molecular changes at the plant-bacteria interface if the necessary requirements with regard to (secondary) metabolite databases are considered. We highlight data integration and complementarity which should help to widen our understanding of the interactions among individual players of the plant holobiont in the future.
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Affiliation(s)
| | | | | | | | | | | | | | - Hannes Schmidt
- Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Thomas Rattei
- Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
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Radchenko ЕЕ, Abdullaev RA, Alpatieva NV, Putina OV, Gasich EL. Alternaria leaf blight of clusterbean. Vavilovskii Zhurnal Genet Selektsii 2019. [DOI: 10.18699/vj19.536] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Affiliation(s)
- Е. Е. Radchenko
- Federal Research Center the N.I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR)
| | - R. A. Abdullaev
- Federal Research Center the N.I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR)
| | - N. V. Alpatieva
- Federal Research Center the N.I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR)
| | - O. V. Putina
- Krymsk Experiment Breeding Station – Branch of Federal Research Center the N.I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR)
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117
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Bioinformatics matters: The accuracy of plant and soil fungal community data is highly dependent on the metabarcoding pipeline. FUNGAL ECOL 2019. [DOI: 10.1016/j.funeco.2019.03.005] [Citation(s) in RCA: 103] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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118
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The needle mycobiome of Picea glauca – A dynamic system reflecting surrounding environment and tree phenological traits. FUNGAL ECOL 2019. [DOI: 10.1016/j.funeco.2019.05.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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119
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Gene-diet interactions associated with complex trait variation in an advanced intercross outbred mouse line. Nat Commun 2019; 10:4097. [PMID: 31506438 PMCID: PMC6736984 DOI: 10.1038/s41467-019-11952-w] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 08/13/2019] [Indexed: 12/12/2022] Open
Abstract
Phenotypic variation of quantitative traits is orchestrated by a complex interplay between the environment (e.g. diet) and genetics. However, the impact of gene-environment interactions on phenotypic traits mostly remains elusive. To address this, we feed 1154 mice of an autoimmunity-prone intercross line (AIL) three different diets. We find that diet substantially contributes to the variability of complex traits and unmasks additional genetic susceptibility quantitative trait loci (QTL). By performing whole-genome sequencing of the AIL founder strains, we resolve these QTLs to few or single candidate genes. To address whether diet can also modulate genetic predisposition towards a given trait, we set NZM2410/J mice on similar dietary regimens as AIL mice. Our data suggest that diet modifies genetic susceptibility to lupus and shifts intestinal bacterial and fungal community composition, which precedes clinical disease manifestation. Collectively, our study underlines the importance of including environmental factors in genetic association studies. Complex traits associate with genetic variation and environment and their interaction. Here, the authors study the influence of different diets on trait variability in 1154 outbred mice from an advanced intercross line and find gene-diet interactions associated with spontaneous autoimmunity development in these animals.
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120
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Shigyo N, Umeki K, Hirao T. Seasonal Dynamics of Soil Fungal and Bacterial Communities in Cool-Temperate Montane Forests. Front Microbiol 2019; 10:1944. [PMID: 31507559 PMCID: PMC6716449 DOI: 10.3389/fmicb.2019.01944] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 08/07/2019] [Indexed: 02/01/2023] Open
Abstract
Both fungal and bacterial communities in soils play key roles in driving forest ecosystem processes across multiple time scales, but how seasonal changes in environmental factors shape these microbial communities is not well understood. Here, we aimed to evaluate the importance of seasons, elevation, and soil depth in determining soil fungal and bacterial communities, given the influence of climate conditions, soil properties and plant traits. In this study, seasonal patterns of diversity and abundance did not synchronize between fungi and bacteria, where soil fertility explained the diversity and abundance of soil fungi but soil water content explained those of soil bacteria. Model-based clustering showed that seasonal changes in both abundant and rare taxonomic groups were different between soil fungi and bacteria. The cluster represented by ectomycorrhizal genus Lactarius was a dominant group across soil fungal communities and fluctuated seasonally. For soil bacteria, the clusters composed of dominant genera were seasonally stable but varied greatly depending on elevation and soil depth. Seasonally changing clusters of soil bacteria (e.g., Nitrospira and Pelosinus) were not dominant groups and were related to plant phenology. These findings suggest that the contribution of seasonal changes in climate conditions, soil fertility, and plant phenology to microbial communities might be equal to or greater than the effects of spatial heterogeneity of those factors. Our study identifies aboveground-belowground components as key factors explaining how microbial communities change during a year in forest soils at mid-to-high latitudes.
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Affiliation(s)
- Nobuhiko Shigyo
- The University of Tokyo Chichibu Forest, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Chichibu, Japan
| | - Kiyoshi Umeki
- Graduate School of Horticulture, Chiba University, Matsudo, Japan
| | - Toshihide Hirao
- The University of Tokyo Chichibu Forest, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Chichibu, Japan
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121
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Heeger F, Wurzbacher C, Bourne EC, Mazzoni CJ, Monaghan MT. Combining the 5.8S and ITS2 to improve classification of fungi. Methods Ecol Evol 2019. [DOI: 10.1111/2041-210x.13266] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Felix Heeger
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB) Berlin Germany
- Berlin Center for Genomics in Biodiversity Research Berlin Germany
| | - Christian Wurzbacher
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB) Berlin Germany
- Berlin Center for Genomics in Biodiversity Research Berlin Germany
- Chair of Urban Water Systems Engineering Technical University of Munich Garching Germany
| | - Elizabeth C. Bourne
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB) Berlin Germany
- Berlin Center for Genomics in Biodiversity Research Berlin Germany
| | - Camila J. Mazzoni
- Berlin Center for Genomics in Biodiversity Research Berlin Germany
- Department of Evolutionary Genetics Leibniz Institute of Zoo‐ and Wildlife Research (IZW) Berlin Germany
| | - Michael T. Monaghan
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB) Berlin Germany
- Berlin Center for Genomics in Biodiversity Research Berlin Germany
- Institut für Biologie Freie Universität Berlin Berlin Germany
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122
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Liu L, She X, Qian Y, Li Y, Tao Y, Che Z, Liu G, Rao Y. Effect of different fermenting containers on the deterioration of Sichuan pickle. Lebensm Wiss Technol 2019. [DOI: 10.1016/j.lwt.2019.05.024] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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123
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A meta-barcoding analysis of soil mycobiota of the upper Andean Colombian agro-environment. Sci Rep 2019; 9:10085. [PMID: 31300737 PMCID: PMC6625999 DOI: 10.1038/s41598-019-46485-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 06/17/2019] [Indexed: 11/23/2022] Open
Abstract
Colombia is a country for which one of the highest biodiversity rates is reported, and one of the first in the tropical areas where an effort was made to gather information on indigenous fungi. Nevertheless, mycological data are still scarce and discontinuous, above all on soil fungi. The present study wanted to contribute to unveil the large soil fungal biodiversity in the upper Andean Colombian agro-ecosystems. The studied area is located in the department of Boyacà, considered with a notable economical value, partly devoted to subsistence agriculture. More than 150 described species were revealed in this study, belonging to 5 phyla with Ascomycota representing the dominant taxon. Basidiomycota and Zygomycota are also well represented, dominated by species of the genus Sebacina and Mortierella respectively, mainly distributed in the semi-natural plots (woodland and grassland). Most of the species are reported as first records for Colombia. Some of them are particularly interesting for their conservation significance such as Geoglossum fallax, which is the dominant species in the unimproved grassland plot. The bootstrap-based clustering analysis showed a different distribution of the species in orchards and non-cultivated areas as a possible response of the fungal community to different use of soil in the agro-environment.
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124
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Exploring the impact of Helicobacter pylori on gut microbiome composition. PLoS One 2019; 14:e0218274. [PMID: 31211818 PMCID: PMC6581275 DOI: 10.1371/journal.pone.0218274] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 05/29/2019] [Indexed: 02/07/2023] Open
Abstract
Helicobacter pylori (H. pylori) is known to colonize gastric mucosa, induce inflammation, and alter gastric microbiota resulting in a spectrum of gastric diseases. Likewise, changes in gut microbiota have recently been linked with various metabolic and inflammatory diseases. While extensive number of studies were published examining the relationship between H. pylori and gastric microbiota, little is known about the impact of H. pylori on downstream gut microbiota. In this study, we performed 16 S rRNA and ITS2-based microbial profiling analysis of 60 stool samples from adult individuals. Remarkably, the gut microbiota of H. pylori infected individuals was shown to be increased of members belonging to Succinivibrio, Coriobacteriaceae, Enterococcaceae, and Rikenellaceae. Moreover, gut microbiota of H. pylori infected individuals was shown to have increased abundance of Candida glabrata and other unclassified Fungi. These results links possible role for H. pylori-associated changes in the gut microbiota in intestinal mucosal barrier disruption and early stage colorectal carcinoma deployment. Altogether, the identified differences in bacterial and fungal composition provides important information that may eventually lead to the development of novel biomarkers and more effective management strategies.
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125
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Mueller KD, Zhang H, Serrano CR, Billmyre RB, Huh EY, Wiemann P, Keller NP, Wang Y, Heitman J, Lee SC. Gastrointestinal microbiota alteration induced by Mucor circinelloides in a murine model. J Microbiol 2019; 57:509-520. [PMID: 31012059 PMCID: PMC6737537 DOI: 10.1007/s12275-019-8682-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 01/10/2019] [Accepted: 01/15/2019] [Indexed: 12/12/2022]
Abstract
Mucor circinelloides is a pathogenic fungus and etiologic agent of mucormycosis. In 2013, cases of gastrointestinal illness after yogurt consumption were reported to the US FDA, and the producer found that its products were contaminated with Mucor. A previous study found that the Mucor strain isolated from an open contaminated yogurt exhibited virulence in a murine systemic infection model and showed that this strain is capable of surviving passage through the gastrointestinal tract of mice. In this study, we isolated another Mucor strain from an unopened yogurt that is closely related but distinct from the first Mucor strain and subsequently examined if Mucor alters the gut microbiota in a murine host model. DNA extracted from a ten-day course of stool samples was used to analyze the microbiota in the gastrointestinal tracts of mice exposed via ingestion of Mucor spores. The bacterial 16S rRNA gene and fungal ITS1 sequences obtained were used to identify taxa of each kingdom. Linear regressions revealed that there are changes in bacterial and fungal abundance in the gastrointestinal tracts of mice which ingested Mucor. Furthermore, we found an increased abundance of the bacterial genus Bacteroides and a decreased abundance of the bacteria Akkermansia muciniphila in the gastrointestinal tracts of exposed mice. Measurements of abundances show shifts in relative levels of multiple bacterial and fungal taxa between mouse groups. These findings suggest that exposure of the gastrointestinal tract to Mucor can alter the microbiota and, more importantly, illustrate an interaction between the intestinal mycobiota and bacteriota. In addition, Mucor was able to induce increased permeability in epithelial cell monolayers in vitro, which might be indicative of unstable intestinal barriers. Understanding how the gut microbiota is shaped is important to understand the basis of potential methods of treatment for gastrointestinal illness. How the gut microbiota changes in response to exposure, even by pathogens not considered to be causative agents of food-borne illness, may be important to how commercial food producers prevent and respond to contamination of products aimed at the public. This study provides evidence that the fungal microbiota, though understudied, may play an important role in diseases of the human gut.
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Affiliation(s)
- Katherine D Mueller
- South Texas Center for Emerging Infectious Diseases (STCEID), Department of Biology, The University of Texas at San Antonio, San Antonio, TX, USA
| | - Hao Zhang
- South Texas Center for Emerging Infectious Diseases (STCEID), Department of Biology, The University of Texas at San Antonio, San Antonio, TX, USA
| | - Christian R Serrano
- South Texas Center for Emerging Infectious Diseases (STCEID), Department of Biology, The University of Texas at San Antonio, San Antonio, TX, USA
| | - R Blake Billmyre
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, USA
| | - Eun Young Huh
- South Texas Center for Emerging Infectious Diseases (STCEID), Department of Biology, The University of Texas at San Antonio, San Antonio, TX, USA
| | - Philipp Wiemann
- Department of Medical Microbiology and Immunology, University of Wisconsin at Madison, Madison, WI, USA
| | - Nancy P Keller
- Department of Medical Microbiology and Immunology, University of Wisconsin at Madison, Madison, WI, USA
| | - Yufeng Wang
- South Texas Center for Emerging Infectious Diseases (STCEID), Department of Biology, The University of Texas at San Antonio, San Antonio, TX, USA
| | - Joseph Heitman
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, USA
| | - Soo Chan Lee
- South Texas Center for Emerging Infectious Diseases (STCEID), Department of Biology, The University of Texas at San Antonio, San Antonio, TX, USA.
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Luis P, Vallon L, Tran FH, Hugoni M, Tran-Van V, Mavingui P, Minard G, Moro CV. Aedes albopictus mosquitoes host a locally structured mycobiota with evidence of reduced fungal diversity in invasive populations. FUNGAL ECOL 2019. [DOI: 10.1016/j.funeco.2019.02.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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127
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McGinniss JE, Imai I, Simon-Soro A, Brown MC, Knecht VR, Frye L, Ravindran PM, Dothard MI, Wadell DA, Sohn MB, Li H, Christie JD, Diamond JM, Haas AR, Lanfranco AR, DiBardino DM, Bushman FD, Collman RG. Molecular analysis of the endobronchial stent microbial biofilm reveals bacterial communities that associate with stent material and frequent fungal constituents. PLoS One 2019; 14:e0217306. [PMID: 31141557 PMCID: PMC6541290 DOI: 10.1371/journal.pone.0217306] [Citation(s) in RCA: 15] [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: 12/12/2018] [Accepted: 05/08/2019] [Indexed: 12/19/2022] Open
Abstract
Endobronchial stents are increasingly used to treat airway complications in multiple conditions including lung transplantation but little is known about the biofilms that form on these devices. We applied deep sequencing to profile luminal biofilms of 46 endobronchial stents removed from 20 subjects primarily with lung transplantation-associated airway compromise. Microbial communities were analyzed by bacterial 16S rRNA and fungal ITS marker gene sequencing. Corynebacterium was the most common bacterial taxa across biofilm communities. Clustering analysis revealed three bacterial biofilm types: one low diversity and dominated by Corynebacterium; another was polymicrobial and characterized by Staphylococcus; and the third was polymicrobial and associated with Pseudomonas, Streptococcus, and Prevotella. Biofilm type was significantly correlated with stent material: covered metal with the Staphylococcus-type biofilm, silicone with the Corynebacterium-dominated biofilm, and uncovered metal with the polymicrobial biofilm. Subjects with sequential stents had frequent transitions between community types. Fungal analysis found Candida was most prevalent, Aspergillus was common and highly enriched in two of three stents associated with airway anastomotic dehiscence, and fungal taxa not typically considered pathogens were highly enriched in some stents. Thus, molecular analysis revealed a complex and dynamic endobronchial stent biofilm with three bacterial types that associate with stent material, a central role for Corynebacterium, and that both expected and unexpected fungi inhabit this unique niche. The current work provides a foundation for studies to investigate the relationship between stent biofilm composition and clinical outcomes, mechanisms of biofilm establishment, and strategies for improved stent technology and use in airway compromise.
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Affiliation(s)
- John E. McGinniss
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Ize Imai
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Aurea Simon-Soro
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Melanie C. Brown
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Vincent R. Knecht
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Laura Frye
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Priyanka M. Ravindran
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Marisol I. Dothard
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Dylan A. Wadell
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Michael B. Sohn
- Department of Epidemiology, Biostatistics and Informatics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Hongzhe Li
- Department of Epidemiology, Biostatistics and Informatics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Jason D. Christie
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Department of Epidemiology, Biostatistics and Informatics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Joshua M. Diamond
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Andrew R. Haas
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Anthony R. Lanfranco
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - David M. DiBardino
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Frederic D. Bushman
- Department of Microbiology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- * E-mail: (RGC); (FDB)
| | - Ronald G. Collman
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Department of Microbiology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- * E-mail: (RGC); (FDB)
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Foliar-feeding insects acquire microbiomes from the soil rather than the host plant. Nat Commun 2019; 10:1254. [PMID: 30890706 PMCID: PMC6425034 DOI: 10.1038/s41467-019-09284-w] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 03/01/2019] [Indexed: 12/13/2022] Open
Abstract
Microbiomes of soils and plants are linked, but how this affects microbiomes of aboveground herbivorous insects is unknown. We first generated plant-conditioned soils in field plots, then reared leaf-feeding caterpillars on dandelion grown in these soils, and then assessed whether the microbiomes of the caterpillars were attributed to the conditioned soil microbiomes or the dandelion microbiome. Microbiomes of caterpillars kept on intact plants differed from those of caterpillars fed detached leaves collected from plants growing in the same soil. Microbiomes of caterpillars reared on detached leaves were relatively simple and resembled leaf microbiomes, while those of caterpillars from intact plants were more diverse and resembled soil microbiomes. Plant-mediated changes in soil microbiomes were not reflected in the phytobiome but were detected in caterpillar microbiomes, however, only when kept on intact plants. Our results imply that insect microbiomes depend on soil microbiomes, and that effects of plants on soil microbiomes can be transmitted to aboveground insects feeding later on other plants. Leaf-feeding insect microbiomes could be influenced by the soil, the plant, or a product of the two. Here, the authors conduct a series of experiments to show that an herbivorous insect predominantly acquires its microbiome from the soil rather than the plant, and that these insect microbiomes reflect soil legacies of earlier growing plants.
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Sha SP, Suryavanshi MV, Tamang JP. Mycobiome Diversity in Traditionally Prepared Starters for Alcoholic Beverages in India by High-Throughput Sequencing Method. Front Microbiol 2019; 10:348. [PMID: 30891011 PMCID: PMC6411702 DOI: 10.3389/fmicb.2019.00348] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2018] [Accepted: 02/11/2019] [Indexed: 12/13/2022] Open
Abstract
Chowan, dawdim, humao, hamei, khekhrii, and phut are sun-dried starters used for preparation of alcoholic beverages in North East regions of India. We attempted to profile the mycobiome community in these starters by high-throughput sequencing (HTS) method. All fungal populations were found to be restricted to Ascomycota (67-99%), Zygomycota (0.7-29%), Basidiomycota (0.03-7%), and Chytridiomycota (0.0003%). We found 45 core operational taxonomic units (OTUs) which were universally present and were further weighed to 41 genera level and 22 species level taxonomy. A total number of 594 fungal species were detected by HTS including common species (224), unique species (133) and rare-species (237) in samples of starters. Unique species were recorded in phut (40 species), khekhrii (28), hamei (23), dawdim (21), chowan (13), and humao (8), respectively. Most of the fungal families were found to correlate to a type of nutritional mode and growth morphologies of the community, where saprotrophic mode of mold species were more dominant, whereas morphotypes were more dominant in yeast species.
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Affiliation(s)
| | | | - Jyoti Prakash Tamang
- DAICENTRE (DBT-AIST International Centre for Translational and Environmental Research) and Bioinformatics Centre, Department of Microbiology, School of Life Sciences, Sikkim University, Gangtok, India
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Vu D, Groenewald M, de Vries M, Gehrmann T, Stielow B, Eberhardt U, Al-Hatmi A, Groenewald J, Cardinali G, Houbraken J, Boekhout T, Crous P, Robert V, Verkley G. Large-scale generation and analysis of filamentous fungal DNA barcodes boosts coverage for kingdom fungi and reveals thresholds for fungal species and higher taxon delimitation. Stud Mycol 2019; 92:135-154. [PMID: 29955203 PMCID: PMC6020082 DOI: 10.1016/j.simyco.2018.05.001] [Citation(s) in RCA: 433] [Impact Index Per Article: 86.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Species identification lies at the heart of biodiversity studies that has in recent years favoured DNA-based approaches. Microbial Biological Resource Centres are a rich source for diverse and high-quality reference materials in microbiology, and yet the strains preserved in these biobanks have been exploited only on a limited scale to generate DNA barcodes. As part of a project funded in the Netherlands to barcode specimens of major national biobanks, sequences of two nuclear ribosomal genetic markers, the Internal Transcribed Spaces and 5.8S gene (ITS) and the D1/D2 domain of the 26S Large Subunit (LSU), were generated as DNA barcode data for ca. 100 000 fungal strains originally assigned to ca. 17 000 species in the CBS fungal biobank maintained at the Westerdijk Fungal Biodiversity Institute, Utrecht. Using more than 24 000 DNA barcode sequences of 12 000 ex-type and manually validated filamentous fungal strains of 7 300 accepted species, the optimal identity thresholds to discriminate filamentous fungal species were predicted as 99.6 % for ITS and 99.8 % for LSU. We showed that 17 % and 18 % of the species could not be discriminated by the ITS and LSU genetic markers, respectively. Among them, ∼8 % were indistinguishable using both genetic markers. ITS has been shown to outperform LSU in filamentous fungal species discrimination with a probability of correct identification of 82 % vs. 77.6 %, and a clustering quality value of 84 % vs. 77.7 %. At higher taxonomic classifications, LSU has been shown to have a better discriminatory power than ITS. With a clustering quality value of 80 %, LSU outperformed ITS in identifying filamentous fungi at the ordinal level. At the generic level, the clustering quality values produced by both genetic markers were low, indicating the necessity for taxonomic revisions at genus level and, likely, for applying more conserved genetic markers or even whole genomes. The taxonomic thresholds predicted for filamentous fungal identification at the genus, family, order and class levels were 94.3 %, 88.5 %, 81.2 % and 80.9 % based on ITS barcodes, and 98.2 %, 96.2 %, 94.7 % and 92.7 % based on LSU barcodes. The DNA barcodes used in this study have been deposited to GenBank and will also be publicly available at the Westerdijk Institute's website as reference sequences for fungal identification, marking an unprecedented data release event in global fungal barcoding efforts to date.
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Affiliation(s)
- D. Vu
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - M. Groenewald
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - M. de Vries
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - T. Gehrmann
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - B. Stielow
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - U. Eberhardt
- Staatliches Museum f. Naturkunde Stuttgart, Abt. Botanik, Rosenstein 1, D-70191 Stuttgart, Germany
| | - A. Al-Hatmi
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - J.Z. Groenewald
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - G. Cardinali
- University of Perugia, Dept. of Pharmaceutical Sciences, Via Borgo 20 Giugno 74, I 06121 Perugia, Italy
| | - J. Houbraken
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - T. Boekhout
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, The Netherlands
| | - P.W. Crous
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Wageningen University and Research Centre (WUR), Laboratory of Phytopathology, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
- Department of Genetics, Biochemistry and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0028, South Africa
| | - V. Robert
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - G.J.M. Verkley
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
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Drott MT, Debenport T, Higgins SA, Buckley DH, Milgroom MG. Fitness Cost of Aflatoxin Production in Aspergillus flavus When Competing with Soil Microbes Could Maintain Balancing Selection. mBio 2019; 10:e02782-18. [PMID: 30782658 PMCID: PMC6381279 DOI: 10.1128/mbio.02782-18] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Accepted: 01/08/2019] [Indexed: 02/08/2023] Open
Abstract
Selective forces that maintain the polymorphism for aflatoxigenic and nonaflatoxigenic individuals of Aspergillus flavus are largely unknown. As soils are widely considered the natural habitat of A. flavus, we hypothesized that aflatoxin production would confer a fitness advantage in the soil environment. To test this hypothesis, we used A. flavus DNA quantified by quantitative PCR (qPCR) as a proxy for fitness of aflatoxigenic and nonaflatoxigenic field isolates grown in soil microcosms. Contrary to predictions, aflatoxigenic isolates had significantly lower fitness than did nonaflatoxigenic isolates in natural soils across three temperatures (25, 37, and 42°C). The addition of aflatoxin to soils (500 ng/g) had no effect on the growth of A. flavus Amplicon sequencing showed that neither the aflatoxin-producing ability of the fungus nor the addition of aflatoxin had a significant effect on the composition of fungal or bacterial communities in soil. We argue that the fitness disadvantage of aflatoxigenic isolates is most likely explained by the metabolic cost of producing aflatoxin. Coupled with a previous report of a selective advantage of aflatoxin production in the presence of some insects, our findings give an ecological explanation for balancing selection resulting in persistent polymorphisms in aflatoxin production.IMPORTANCE Aflatoxin, produced by the fungus Aspergillus flavus, is an extremely potent hepatotoxin that causes acute toxicosis and cancer, and it incurs hundreds of millions of dollars annually in agricultural losses. Despite the importance of this toxin to humans, it has remained unclear what the fungus gains by producing aflatoxin. In fact, not all strains of A. flavus produce aflatoxin. Previous work has shown an advantage to producing aflatoxin in the presence of some insects. Our current work demonstrates the first evidence of a disadvantage to A. flavus in producing aflatoxin when competing with soil microbes. Together, these opposing evolutionary forces could explain the persistence of both aflatoxigenic and nonaflatoxigenic strains through evolutionary time.
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Affiliation(s)
- Milton T Drott
- School of Integrative Plant Science, Plant Pathology and Plant-Microbe Biology Section, Cornell University, Ithaca, New York, USA
| | - Tracy Debenport
- School of Integrative Plant Science, Plant Pathology and Plant-Microbe Biology Section, Cornell University, Ithaca, New York, USA
| | - Steven A Higgins
- School of Integrative Plant Science, Soil and Crop Sciences Section, Cornell University, Ithaca, New York, USA
| | - Daniel H Buckley
- School of Integrative Plant Science, Soil and Crop Sciences Section, Cornell University, Ithaca, New York, USA
| | - Michael G Milgroom
- School of Integrative Plant Science, Plant Pathology and Plant-Microbe Biology Section, Cornell University, Ithaca, New York, USA
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Changes in the Rumen Microbiota of Cows in Response to Dietary Supplementation with Nitrate, Linseed, and Saponin Alone or in Combination. Appl Environ Microbiol 2019; 85:AEM.02657-18. [PMID: 30504215 DOI: 10.1128/aem.02657-18] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Accepted: 11/21/2018] [Indexed: 01/21/2023] Open
Abstract
Dietary supplementation with linseed, saponins, and nitrate is a promising methane mitigation strategy in ruminant production. Here, we aimed to assess the effects of these additives on the rumen microbiota in order to understand underlying microbial mechanisms of methane abatement. Two 2-by-2 factorial design studies were conducted simultaneously, which also allowed us to make a broad-based assessment of microbial responses. Eight nonlactating cows were fed diets supplemented with linseed or saponin in order to decrease hydrogen production and nitrate to affect hydrogen consumption; also, combinations of linseed plus nitrate or saponin plus nitrate were used to explore the interaction between dietary treatments. Previous work assessed effects on methane and fermentation patterns. Rumen microbes were studied by sequencing 18S and 16S rRNA genes and ITS1 amplicons. Methanogen activity was monitored by following changes in mcrA transcript abundance. Nitrate fed alone or in combination in both studies dramatically affected the composition and structure of rumen microbiota, although impacts were more evident in one of the studies. Linseed moderately modified only bacterial community structure. Indicator operational taxonomic unit (OTU) analysis revealed that both linseed and nitrate reduced the relative abundance of hydrogen-producing Ruminococcaceae Linseed increased the proportion of bacteria known to reduce succinate to propionate, whereas nitrate supplementation increased nitrate-reducing bacteria and decreased the metabolic activity of rumen methanogens. Saponins had no effect on the microbiota. Inconsistency found between the two studies with nitrate supplementation could be explained by changes in microbial ecosystem functioning rather than changes in microbial community structure.IMPORTANCE This study aimed at identifying the microbial mechanisms of enteric methane mitigation when linseed, nitrate, and saponins were fed to nonlactating cows alone or in a combination. Hydrogen is a limiting factor in rumen methanogenesis. We hypothesized that linseed and saponins would affect hydrogen producers and nitrate would affect hydrogen consumption, leading to reduced methane production in the rumen. Contrary to what was predicted, both linseed and nitrate had a deleterious effect on hydrogen producers; linseed also redirected hydrogen consumption toward propionate production, whereas nitrate stimulated the growth of nitrate-reducing and, hence, hydrogen-consuming bacterial taxa. This novel knowledge of microbial mechanisms involved in rumen methanogenesis provides insights for the development and optimization of methane mitigation strategies.
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133
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Doña J, Proctor H, Serrano D, Johnson KP, Oploo AO, Huguet‐Tapia JC, Ascunce MS, Jovani R. Feather mites play a role in cleaning host feathers: New insights from DNA metabarcoding and microscopy. Mol Ecol 2019; 28:203-218. [PMID: 29726053 PMCID: PMC6905397 DOI: 10.1111/mec.14581] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2017] [Revised: 02/15/2018] [Accepted: 03/21/2018] [Indexed: 12/31/2022]
Abstract
Parasites and other symbionts are crucial components of ecosystems, regulating host populations and supporting food webs. However, most symbiont systems, especially those involving commensals and mutualists, are relatively poorly understood. In this study, we have investigated the nature of the symbiotic relationship between birds and their most abundant and diverse ectosymbionts: the vane-dwelling feather mites. For this purpose, we studied the diet of feather mites using two complementary methods. First, we used light microscopy to examine the gut contents of 1,300 individual feather mites representing 100 mite genera (18 families) from 190 bird species belonging to 72 families and 19 orders. Second, we used high-throughput sequencing (HTS) and DNA metabarcoding to determine gut contents from 1,833 individual mites of 18 species inhabiting 18 bird species. Results showed fungi and potentially bacteria as the main food resources for feather mites (apart from potential bird uropygial gland oil). Diatoms and plant matter appeared as rare food resources for feather mites. Importantly, we did not find any evidence of feather mites feeding upon bird resources (e.g., blood, skin) other than potentially uropygial gland oil. In addition, we found a high prevalence of both keratinophilic and pathogenic fungal taxa in the feather mite species examined. Altogether, our results shed light on the long-standing question of the nature of the relationship between birds and their vane-dwelling feather mites, supporting previous evidence for a commensalistic-mutualistic role of feather mites, which are revealed as likely fungivore-microbivore-detritivore symbionts of bird feathers.
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Affiliation(s)
- Jorge Doña
- Department of Evolutionary EcologyEstación Biológica de Doñana (EBD‐CSIC)SevillaSpain
| | - Heather Proctor
- Department of Biological SciencesUniversity of AlbertaEdmontonABCanada
| | - David Serrano
- Department of Conservation BiologyEstación Biológica de Doñana (EBD‐CSIC)SevillaSpain
| | - Kevin P. Johnson
- Illinois Natural History SurveyPrairie Research InstituteUniversity of Illinois at Urbana‐ChampaignChampaignIllinois
| | | | | | - Marina S. Ascunce
- Department of Plant PathologyUniversity of FloridaGainesvilleFlorida
- Emerging Pathogens InstituteUniversity of FloridaGainesvilleFlorida
| | - Roger Jovani
- Department of Evolutionary EcologyEstación Biológica de Doñana (EBD‐CSIC)SevillaSpain
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134
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Mason CJ, Campbell AM, Scully ED, Hoover K. Bacterial and Fungal Midgut Community Dynamics and Transfer Between Mother and Brood in the Asian Longhorned Beetle (Anoplophora glabripennis), an Invasive Xylophage. MICROBIAL ECOLOGY 2019; 77:230-242. [PMID: 29948017 DOI: 10.1007/s00248-018-1205-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 05/14/2018] [Indexed: 05/09/2023]
Abstract
Microbial symbionts play pivotal roles in the ecology and physiology of insects feeding in woody plants. Both eukaryotic and bacterial members occur in these systems where they facilitate digestive and nutrient provisioning. The larval gut of the Asian longhorned beetle (Anoplophora glabripennis) is associated with a microbial consortium that fulfills these metabolic roles. While members of the community vary in presence and abundance among individuals from different hosts, A. glabripennis is consistently associated with a fungus in the Fusarium solani species complex (FSSC). We used amplicon sequencing, taxon-specific PCR, culturing, and imaging to determine how bacterial and fungal communities differ between life stages and possible modes of symbiont transfer. The bacterial and fungal communities of adult guts were more diverse than those from larvae and eggs. The communities of larvae and eggs were more similar to those from oviposition sites than from adult female guts. FSSC isolates were not detected in the reproductive tissues of adult females, but were consistently detected on egg surfaces after oviposition and in frass. These results demonstrate that frass can serve as a vehicle of transmission of a subset for the beetle gut microbiota. Vertically transmitted symbionts are often beneficial to their host, warranting subsequent functional studies.
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Affiliation(s)
- Charles J Mason
- Department of Entomology and Center for Chemical Ecology, The Pennsylvania State University, University Park, State College, PA, 16823, USA.
| | - Alexander M Campbell
- Department of Entomology and Center for Chemical Ecology, The Pennsylvania State University, University Park, State College, PA, 16823, USA
| | - Erin D Scully
- Stored Product Insect and Engineering Research Unit, USDA, Agricultural Research Service, Center for Grain and Animal Health Research, Manhattan, KS, 66502, USA
| | - Kelli Hoover
- Department of Entomology and Center for Chemical Ecology, The Pennsylvania State University, University Park, State College, PA, 16823, USA
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Abstract
Helicobacter pylori (H. pylori) is known to colonize gastric mucosa, induce inflammation, and alter gastric microbiota resulting in a spectrum of gastric diseases. Likewise, changes in gut microbiota have recently been linked with various metabolic and inflammatory diseases. While extensive number of studies were published examining the relationship between H. pylori and gastric microbiota, little is known about the impact of H. pylori on downstream gut microbiota. In this study, we performed 16 S rRNA and ITS2-based microbial profiling analysis of 60 stool samples from adult individuals. Remarkably, the gut microbiota of H. pylori infected individuals was shown to be increased of members belonging to Succinivibrio, Coriobacteriaceae, Enterococcaceae, and Rikenellaceae. Moreover, gut microbiota of H. pylori infected individuals was shown to have increased abundance of Candida glabrata and other unclassified Fungi. These results links possible role for H. pylori-associated changes in the gut microbiota in intestinal mucosal barrier disruption and early stage colorectal carcinoma deployment. Altogether, the identified differences in bacterial and fungal composition provides important information that may eventually lead to the development of novel biomarkers and more effective management strategies.
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136
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Hellequin E, Monard C, Quaiser A, Henriot M, Klarzynski O, Binet F. Specific recruitment of soil bacteria and fungi decomposers following a biostimulant application increased crop residues mineralization. PLoS One 2018; 13:e0209089. [PMID: 30596675 PMCID: PMC6312294 DOI: 10.1371/journal.pone.0209089] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 11/29/2018] [Indexed: 12/31/2022] Open
Abstract
Agriculture is undergoing important changes in order to meet sustainable soil management with respect to biodiversity (namely agroecology). Within this context, alternative solutions to mineral fertilizers such as agricultural biostimulants are thus promoted and being developed. The mechanisms by which some soil biostimulants sustain soil biological functioning and indirectly increase crop yields are still unknown. Our goal in the present study was to demonstrate if and to what extent the application of a soil biostimulant affects the soil heterotrophic microbial communities that are involved in organic matter decomposition and carbon mineralization. We hypothesized that the addition of a biostimulant results in changes in the composition and in the biomass of soil microbial communities. This in turn increases the mineralization of the organic matter derived from crop residues. We performed soil microcosm experiments with the addition of crop residues and a biostimulant, and we monitored the organic carbon (orgC) mineralization and the microbial biomass, along with the microbial community composition by sequencing 16S rRNA gene and ITS amplicons. The addition of a soil biostimulant caused a pH neutralizing effect and simultaneous enhancement of the orgC mineralization of crop residues (+ 400 μg orgC g-1 dry soil) and microbial biomass (+ 60 μg orgC g-1 dry soil) that were linked to changes in the soil microbial communities. Our findings suggest that the soil carbon mineralization enhancement in the presence of the biostimulant was supported by the specific recruitment of soil bacteria and fungi. Whereas archaea remained stable, several operational taxonomic units (OTUs) of indigenous soil bacteria and fungi were enriched and affiliated with known microbial decomposers such as Cytophagaceae, Phaselicystis sp., Verrucomicrobia, Pseudomonas sp., Ramicandelaber sp., and Mortierella sp., resulting in lower soil microbial richness and diversity.
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Affiliation(s)
- Eve Hellequin
- University of Rennes, CNRS, ECOBIO [(Ecosystèmes, biodiversité, évolution)]—UMR 6553, Rennes, France
- BIO3G Company, Merdrignac, France
- * E-mail: (EH); (FB)
| | - Cécile Monard
- University of Rennes, CNRS, ECOBIO [(Ecosystèmes, biodiversité, évolution)]—UMR 6553, Rennes, France
| | - Achim Quaiser
- University of Rennes, CNRS, ECOBIO [(Ecosystèmes, biodiversité, évolution)]—UMR 6553, Rennes, France
| | | | | | - Françoise Binet
- University of Rennes, CNRS, ECOBIO [(Ecosystèmes, biodiversité, évolution)]—UMR 6553, Rennes, France
- * E-mail: (EH); (FB)
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137
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The Interior Surfaces of Wooden Barrels Are an Additional Microbial Inoculation Source for Lambic Beer Production. Appl Environ Microbiol 2018; 85:AEM.02226-18. [PMID: 30389768 DOI: 10.1128/aem.02226-18] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 10/11/2018] [Indexed: 11/20/2022] Open
Abstract
Traditional lambic beer production takes place through wort inoculation with environmental air and fermentation and maturation in wooden barrels. These wooden casks or foeders are possible additional inoculation sources of microorganisms for lambic worts. To date, however, these lambic barrels have been examined only with culture-dependent techniques, thereby missing a portion of the microorganisms present. Moreover, the effects of the cleaning procedures (involving high-pressure water and/or fumigation) and the barrel type on the microbial community structures of the interior surfaces of wooden lambic barrels were unclear. The culture-dependent plating and culture-independent amplicon sequencing of swab samples obtained from the interior surfaces of different wooden casks and foeders used for traditional lambic beer production in Belgium revealed that the microbial compositions of these surfaces differed statistically throughout the barrel-cleaning procedures applied. At the end of the cleaning procedures, amplicon sequencing still detected fermentation- and maturation-related microorganisms, although only a few colonies were still detectable using culture-dependent methods. It is possible that some of the surviving microorganisms were missed due to the presence of many of these cells in a viable but not culturable state and/or engrained deeper in the wood. These surviving microorganisms could act as an additional inoculation source, besides brewery air and brewery equipment, thereby helping to establish a stable microbial community in the wort to diminish batch-to-batch variations in fermentation profiles. Furthermore, the microbial compositions of the interior barrel surfaces differed statistically based on the barrel type, possibly reflecting different characteristics of the lambic barrels in terms of age, wood thickness, and wood porosity.IMPORTANCE Although the coolship step is generally regarded as the main contributor to the spontaneous inoculation by environmental air of fresh worts for lambic beer production, it is known that microorganisms often associate with specific surfaces present in a brewery. However, knowledge about the association of microorganisms with the interior surfaces of wooden lambic barrels is limited. To clarify the role of casks and foeders as additional microbial inoculation sources, it was important to determine the influence of the barrel characteristics and the cleaning procedures on the microbial communities of the interior barrel surfaces. Moreover, this helped to elucidate the complex spontaneous lambic beer fermentation and maturation process. It will allow further optimization of the lambic beer production process, as well as the wooden-barrel-cleaning procedures applied.
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138
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Levy-Booth DJ, Giesbrecht IJW, Kellogg CTE, Heger TJ, D'Amore DV, Keeling PJ, Hallam SJ, Mohn WW. Seasonal and ecohydrological regulation of active microbial populations involved in DOC, CO 2, and CH 4 fluxes in temperate rainforest soil. ISME JOURNAL 2018; 13:950-963. [PMID: 30538276 PMCID: PMC6461783 DOI: 10.1038/s41396-018-0334-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 10/12/2018] [Accepted: 12/03/2018] [Indexed: 11/10/2022]
Abstract
The Pacific coastal temperate rainforest (PCTR) is a global hot-spot for carbon cycling and export. Yet the influence of microorganisms on carbon cycling processes in PCTR soil is poorly characterized. We developed and tested a conceptual model of seasonal microbial carbon cycling in PCTR soil through integration of geochemistry, micro-meteorology, and eukaryotic and prokaryotic ribosomal amplicon (rRNA) sequencing from 216 soil DNA and RNA libraries. Soil moisture and pH increased during the wet season, with significant correlation to net CO2 flux in peat bog and net CH4 flux in bog forest soil. Fungal succession in these sites was characterized by the apparent turnover of Archaeorhizomycetes phylotypes accounting for 41% of ITS libraries. Anaerobic prokaryotes, including Syntrophobacteraceae and Methanomicrobia increased in rRNA libraries during the wet season. Putatively active populations of these phylotypes and their biogeochemical marker genes for sulfate and CH4 cycling, respectively, were positively correlated following rRNA and metatranscriptomic network analysis. The latter phylotype was positively correlated to CH4 fluxes (r = 0.46, p < 0.0001). Phylotype functional assignments were supported by metatranscriptomic analysis. We propose that active microbial populations respond primarily to changes in hydrology, pH, and nutrient availability. The increased microbial carbon export observed over winter may have ramifications for climate-soil feedbacks in the PCTR.
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Affiliation(s)
- David J Levy-Booth
- Department of Microbiology & Immunology, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada.,Hakai Institute, Tula Foundation, Heriot Bay, BC, Canada
| | - Ian J W Giesbrecht
- Hakai Institute, Tula Foundation, Heriot Bay, BC, Canada.,School of Resource and Environmental Management, Simon Fraser University, Burnaby, BC, Canada
| | - Colleen T E Kellogg
- Department of Microbiology & Immunology, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada.,Hakai Institute, Tula Foundation, Heriot Bay, BC, Canada
| | - Thierry J Heger
- The University of Applied Sciences Western Switzerland, CHANGINS, Delémont, Switzerland
| | - David V D'Amore
- U.S. Department of Agriculture, Forest Service, Pacific Northwest Research Station, Juneau, Alaska, USA
| | - Patrick J Keeling
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Steven J Hallam
- Department of Microbiology & Immunology, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada
| | - William W Mohn
- Department of Microbiology & Immunology, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada.
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139
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Hargreaves J, Brickle P, van West P. The fungal ecology of seabird nesting sites in the Falkland Islands indicates a niche for mycoparasites. FUNGAL ECOL 2018. [DOI: 10.1016/j.funeco.2018.08.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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140
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Effects of host species, environmental filtering and forest age on community assembly of ectomycorrhizal fungi in fragmented forests. FUNGAL ECOL 2018. [DOI: 10.1016/j.funeco.2018.08.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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141
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De Roos J, Vandamme P, De Vuyst L. Wort Substrate Consumption and Metabolite Production During Lambic Beer Fermentation and Maturation Explain the Successive Growth of Specific Bacterial and Yeast Species. Front Microbiol 2018; 9:2763. [PMID: 30510547 PMCID: PMC6252343 DOI: 10.3389/fmicb.2018.02763] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 10/29/2018] [Indexed: 12/12/2022] Open
Abstract
The present study combined high-throughput culture-dependent plating and culture-independent amplicon sequencing with a metabolite target analysis to systematically dissect the identity, evolution, and role of the microorganisms, substrates, and metabolites during the four-phase fermentation and maturation process of lambic beer production. This led to the following new insights. The changing physicochemical parameters and substrate and metabolite compositions of the fermenting wort and maturing lambic beer provoked several transitions between microbial species and explained the four-step production process. Manual wort acidification with lactic acid shortened the enterobacterial phase and thus kept biogenic amine formation by enterobacteria present during the early stages of fermentation at a minimum. Growth advantages during the alcoholic fermentation phase caused a transition from the prevalence by Hanseniaspora uvarum and Kazachstania species to that by Saccharomyces cerevisiae and later on Saccharomyces kudriavzevii, due to changing environmental parameters. During the acidification phase, Pediococcus damnosus was prevalent and performed a malolactic fermentation. Acetobacter pasteurianus produced acetic acid and acetoin. Upon maturation, Dekkera species appeared, together with P. damnosus and Pichia membranifaciens, thereby contributing to acetic acid production, depending on the oxygen availability. Moreover, the Dekkera species consumed the acetoin produced by the acetic acid bacteria for redox balancing. The breakdown of maltooligosaccharides seemed to be independent of the occurrence of Dekkera species and started already early in the fermentation process.
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Affiliation(s)
- Jonas De Roos
- Research Group of Industrial Microbiology and Food Biotechnology, Bioengineering Sciences Department, Vrije Universiteit Brussel, Brussels, Belgium
| | - Peter Vandamme
- Laboratory for Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Luc De Vuyst
- Research Group of Industrial Microbiology and Food Biotechnology, Bioengineering Sciences Department, Vrije Universiteit Brussel, Brussels, Belgium
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142
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The Necessity of Multitrophic Approaches in Community Ecology. Trends Ecol Evol 2018; 33:754-764. [DOI: 10.1016/j.tree.2018.07.001] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2017] [Revised: 07/03/2018] [Accepted: 07/04/2018] [Indexed: 11/23/2022]
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143
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Anslan S, Nilsson RH, Wurzbacher C, Baldrian P, Leho Tedersoo, Bahram M. Great differences in performance and outcome of high-throughput sequencing data analysis platforms for fungal metabarcoding. MycoKeys 2018; 39:29-40. [PMID: 30271256 PMCID: PMC6160831 DOI: 10.3897/mycokeys.39.28109] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 08/27/2018] [Indexed: 12/01/2022] Open
Abstract
Along with recent developments in high-throughput sequencing (HTS) technologies and thus fast accumulation of HTS data, there has been a growing need and interest for developing tools for HTS data processing and communication. In particular, a number of bioinformatics tools have been designed for analysing metabarcoding data, each with specific features, assumptions and outputs. To evaluate the potential effect of the application of different bioinformatics workflow on the results, we compared the performance of different analysis platforms on two contrasting high-throughput sequencing data sets. Our analysis revealed that the computation time, quality of error filtering and hence output of specific bioinformatics process largely depends on the platform used. Our results show that none of the bioinformatics workflows appears to perfectly filter out the accumulated errors and generate Operational Taxonomic Units, although PipeCraft, LotuS and PIPITS perform better than QIIME2 and Galaxy for the tested fungal amplicon dataset. We conclude that the output of each platform requires manual validation of the OTUs by examining the taxonomy assignment values.
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Affiliation(s)
- Sten Anslan
- Braunschweig University of Technology, Zoological Institute, Mendelssohnstr. 4, 38106 Braunschweig, Germany
| | - R. Henrik Nilsson
- Gothenburg Global Biodiversity Centre, Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, 405 30 Gothenburg, Sweden
| | | | - Petr Baldrian
- Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 14220 Praha 4, Czech Republic
| | - Leho Tedersoo
- Natural History Museum of Tartu University, 14a Ravila, 50411 Tartu, Estonia
| | - Mohammad Bahram
- Institute of Ecology and Earth Science, Tartu University, 14a Ravila, 50411 Tartu, Estonia
- Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, Uppsala, Sweden
- Department of Ecology, Swedish University of Agricultural Sciences, Ulls väg 16, 756 51 Uppsala, Sweden
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144
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Zuo T, Wong SH, Cheung CP, Lam K, Lui R, Cheung K, Zhang F, Tang W, Ching JYL, Wu JCY, Chan PKS, Sung JJY, Yu J, Chan FKL, Ng SC. Gut fungal dysbiosis correlates with reduced efficacy of fecal microbiota transplantation in Clostridium difficile infection. Nat Commun 2018; 9:3663. [PMID: 30202057 PMCID: PMC6131390 DOI: 10.1038/s41467-018-06103-6] [Citation(s) in RCA: 163] [Impact Index Per Article: 27.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 08/15/2018] [Indexed: 12/26/2022] Open
Abstract
Fecal microbiota transplantation (FMT) is effective in treating recurrent Clostridium difficile infection (CDI). Bacterial colonization in recipients after FMT has been studied, but little is known about the role of the gut fungal community, or mycobiota. Here, we show evidence of gut fungal dysbiosis in CDI, and that donor-derived fungal colonization in recipients is associated with FMT response. CDI is accompanied by over-representation of Candida albicans and decreased fungal diversity, richness, and evenness. Cure after FMT is associated with increased colonization of donor-derived fungal taxa in recipients. Recipients of successful FMT (“responders”) display, after FMT, a high relative abundance of Saccharomyces and Aspergillus, whereas “nonresponders” and individuals treated with antibiotics display a dominant presence of Candida. High abundance of C. albicans in donor stool also correlates with reduced FMT efficacy. Furthermore, C. albicans reduces FMT efficacy in a mouse model of CDI, while antifungal treatment reestablishes its efficacy, supporting a potential causal relationship between gut fungal dysbiosis and FMT outcome. Fecal microbiota transplantation (FMT) is effective in treating recurrent Clostridium difficile infection (CDI). Here, the authors show that the composition of the gut fungal microbiota of donors and recipients, and especially the abundance of Candida, correlates with FMT outcome in CDI patients.
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Affiliation(s)
- Tao Zuo
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China.,Institute of Digestive Disease, State Key Laboratory of Digestive Diseases, LKS Institute of Health Science, The Chinese University of Hong Kong, Hong Kong, China
| | - Sunny H Wong
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China.,Institute of Digestive Disease, State Key Laboratory of Digestive Diseases, LKS Institute of Health Science, The Chinese University of Hong Kong, Hong Kong, China.,Center for Gut Microbiota Research, The Chinese University of Hong Kong, Hong Kong, China
| | - Chun Pan Cheung
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China
| | - Kelvin Lam
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China
| | - Rashid Lui
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China
| | - Kitty Cheung
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China
| | - Fen Zhang
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
| | - Whitney Tang
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China
| | - Jessica Y L Ching
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China
| | - Justin C Y Wu
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China.,Institute of Digestive Disease, State Key Laboratory of Digestive Diseases, LKS Institute of Health Science, The Chinese University of Hong Kong, Hong Kong, China
| | - Paul K S Chan
- Center for Gut Microbiota Research, The Chinese University of Hong Kong, Hong Kong, China.,Department of Microbiology, The Chinese University of Hong Kong, Hong Kong, China
| | - Joseph J Y Sung
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China.,Institute of Digestive Disease, State Key Laboratory of Digestive Diseases, LKS Institute of Health Science, The Chinese University of Hong Kong, Hong Kong, China
| | - Jun Yu
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China.,Institute of Digestive Disease, State Key Laboratory of Digestive Diseases, LKS Institute of Health Science, The Chinese University of Hong Kong, Hong Kong, China.,Center for Gut Microbiota Research, The Chinese University of Hong Kong, Hong Kong, China
| | - Francis K L Chan
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China.,Institute of Digestive Disease, State Key Laboratory of Digestive Diseases, LKS Institute of Health Science, The Chinese University of Hong Kong, Hong Kong, China.,Center for Gut Microbiota Research, The Chinese University of Hong Kong, Hong Kong, China
| | - Siew C Ng
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China. .,Institute of Digestive Disease, State Key Laboratory of Digestive Diseases, LKS Institute of Health Science, The Chinese University of Hong Kong, Hong Kong, China. .,Center for Gut Microbiota Research, The Chinese University of Hong Kong, Hong Kong, China.
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145
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Malik AA, Puissant J, Buckeridge KM, Goodall T, Jehmlich N, Chowdhury S, Gweon HS, Peyton JM, Mason KE, van Agtmaal M, Blaud A, Clark IM, Whitaker J, Pywell RF, Ostle N, Gleixner G, Griffiths RI. Land use driven change in soil pH affects microbial carbon cycling processes. Nat Commun 2018; 9:3591. [PMID: 30181597 PMCID: PMC6123395 DOI: 10.1038/s41467-018-05980-1] [Citation(s) in RCA: 160] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 08/06/2018] [Indexed: 01/28/2023] Open
Abstract
Soil microorganisms act as gatekeepers for soil–atmosphere carbon exchange by balancing the accumulation and release of soil organic matter. However, poor understanding of the mechanisms responsible hinders the development of effective land management strategies to enhance soil carbon storage. Here we empirically test the link between microbial ecophysiological traits and topsoil carbon content across geographically distributed soils and land use contrasts. We discovered distinct pH controls on microbial mechanisms of carbon accumulation. Land use intensification in low-pH soils that increased the pH above a threshold (~6.2) leads to carbon loss through increased decomposition, following alleviation of acid retardation of microbial growth. However, loss of carbon with intensification in near-neutral pH soils was linked to decreased microbial biomass and reduced growth efficiency that was, in turn, related to trade-offs with stress alleviation and resource acquisition. Thus, less-intensive management practices in near-neutral pH soils have more potential for carbon storage through increased microbial growth efficiency, whereas in acidic soils, microbial growth is a bigger constraint on decomposition rates. Land use intensification could modify microbial activity and thus ecosystem function. Here, Malik et al. sample microbes and carbon-related functions across a land use gradient, demonstrating that microbial biomass and carbon use efficiency are reduced in human-impacted near-neutral pH soils.
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Affiliation(s)
- Ashish A Malik
- Centre for Ecology and Hydrology, Wallingford, OX10 8BB, UK. .,Department of Ecology and Evolutionary Biology, University of California, Irvine, 92697, USA.
| | | | - Kate M Buckeridge
- Lancaster Environment Centre, Lancaster University, Lancaster, LA1 4YQ, UK
| | - Tim Goodall
- Centre for Ecology and Hydrology, Wallingford, OX10 8BB, UK
| | - Nico Jehmlich
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, 04318, Germany
| | - Somak Chowdhury
- Department of Biogeochemical Processes, Max Planck Institute for Biogeochemistry, Jena, 07745, Germany
| | - Hyun Soon Gweon
- Centre for Ecology and Hydrology, Wallingford, OX10 8BB, UK.,School of Biological Sciences, University of Reading, Reading, RG6 6UR, UK
| | - Jodey M Peyton
- Centre for Ecology and Hydrology, Wallingford, OX10 8BB, UK
| | - Kelly E Mason
- Centre for Ecology and Hydrology, Lancaster, LA1 4AP, UK
| | | | - Aimeric Blaud
- Department of Sustainable Agriculture Sciences, Rothamsted Research, Harpenden, AL5 2JQ, UK
| | - Ian M Clark
- Department of Sustainable Agriculture Sciences, Rothamsted Research, Harpenden, AL5 2JQ, UK
| | | | | | - Nick Ostle
- Lancaster Environment Centre, Lancaster University, Lancaster, LA1 4YQ, UK
| | - Gerd Gleixner
- Department of Biogeochemical Processes, Max Planck Institute for Biogeochemistry, Jena, 07745, Germany
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146
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Bergsveinson J, Perry B, Sheedy C, Braul L, Reedyk S, Gossen B, Yost C. Identifying the core bacterial and fungal communities within four agricultural biobeds used for the treatment of pesticide rinsates. J Appl Microbiol 2018; 125:1333-1342. [DOI: 10.1111/jam.14051] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 06/29/2018] [Accepted: 07/13/2018] [Indexed: 11/29/2022]
Affiliation(s)
- J. Bergsveinson
- Department of Biology; University of Regina; Regina SK Canada
| | - B.J. Perry
- Department of Biology; University of Regina; Regina SK Canada
| | - C. Sheedy
- Agriculture and Agri-Food Canada; Lethbridge AB Canada
| | - L. Braul
- Agriculture and Agri-Food Canada; Regina SK Canada
| | - S. Reedyk
- Agriculture and Agri-Food Canada; Edmonton AB Canada
| | - B.D. Gossen
- Agriculture and Agri-Food Canada; Saskatoon SK Canada
| | - C.K. Yost
- Department of Biology; University of Regina; Regina SK Canada
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147
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Soil bacterial networks are less stable under drought than fungal networks. Nat Commun 2018; 9:3033. [PMID: 30072764 PMCID: PMC6072794 DOI: 10.1038/s41467-018-05516-7] [Citation(s) in RCA: 639] [Impact Index Per Article: 106.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 07/11/2018] [Indexed: 12/13/2022] Open
Abstract
Soil microbial communities play a crucial role in ecosystem functioning, but it is unknown how co-occurrence networks within these communities respond to disturbances such as climate extremes. This represents an important knowledge gap because changes in microbial networks could have implications for their functioning and vulnerability to future disturbances. Here, we show in grassland mesocosms that drought promotes destabilising properties in soil bacterial, but not fungal, co-occurrence networks, and that changes in bacterial communities link more strongly to soil functioning during recovery than do changes in fungal communities. Moreover, we reveal that drought has a prolonged effect on bacterial communities and their co-occurrence networks via changes in vegetation composition and resultant reductions in soil moisture. Our results provide new insight in the mechanisms through which drought alters soil microbial communities with potential long-term consequences, including future plant community composition and the ability of aboveground and belowground communities to withstand future disturbances. Drought conditions can alter the composition of soil microbial communities, but the effects of drought on network properties have not been tested. Here, de Vries and colleagues show that co-occurrence networks are destabilised under drought for bacteria but not fungi.
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148
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Kalan L, Grice EA. Fungi in the Wound Microbiome. Adv Wound Care (New Rochelle) 2018; 7:247-255. [PMID: 29984114 DOI: 10.1089/wound.2017.0756] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2017] [Accepted: 10/10/2017] [Indexed: 02/06/2023] Open
Abstract
Significance: Culture-independent methods have revealed the diverse and dynamic bacterial communities that colonize chronic wounds. Only recently have studies begun to examine fungal colonization and interactions with the bacterial component of the microbiome, their relationship with the host, and influence on wound outcomes. Recent Advances: Studies using culture-independent sequencing methods reveal that fungi often go undetected in wounds. Candida spp. and Cladosporidium spp. are the most commonly identified fungi in wounds. The wound environment may promote multispecies biofilm formation between bacteria and fungi in wounds, with implications for pathogenicity, treatment, and outcomes. Critical Issues: Identifying microorganisms that are problematic for healing will require a comprehensive understanding of all members of the polymicrobial wound community, including fungi and bacteria. Improved reference databases and bioinformatics tools for studying fungal communities will stimulate further research into the fungal microbiome. Future Directions: Continued study of polymicrobial wound communities using culture-independent methods will further our understanding of the relationships between microbial bioburden, the host response, and impact on healing, complications, and patient outcomes. Future studies should encompass all types of microbiota, including fungi, and focus on potential multi-kingdom interactions that contribute to pathogenicity, biofilm formation, and poor outcomes.
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Affiliation(s)
- Lindsay Kalan
- Department of Dermatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Elizabeth A. Grice
- Department of Dermatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
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149
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Banchi E, Stankovic D, Fernández-Mendoza F, Gionechetti F, Pallavicini A, Muggia L. ITS2 metabarcoding analysis complements lichen mycobiome diversity data. Mycol Prog 2018; 17:1049-1066. [PMID: 30956650 PMCID: PMC6428334 DOI: 10.1007/s11557-018-1415-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 05/12/2018] [Accepted: 06/04/2018] [Indexed: 01/16/2023]
Abstract
Lichen thalli harbor complex fungal communities (mycobiomes) of species with divergent trophic and ecological strategies. The complexity and diversity of lichen mycobiomes are still largely unknown, despite surveys combining culture-based methods and high-throughput sequencing (HTS). The results of such surveys are strongly influenced by the barcode locus chosen, its sensitivity in discriminating taxa, and the depth to which public sequence repositories cover the phylogenetic spectrum of fungi. Here, we use HTS of the internal transcribed spacer 2 (ITS2) to assess the taxonomic composition and diversity of a well-characterized, alpine rock lichen community that includes thalli symptomatically infected by lichenicolous fungi as well as asymptomatic thalli. Taxa belonging to the order Chaetothyriales are the major components of the observed lichen mycobiomes. We predict sequences representative of lichenicolous fungi characterized morphologically and assess their asymptomatic presence in lichen thalli. We demonstrated the limitations of metabarcoding in fungi and show how the estimation of species diversity widely differs when ITS1 or ITS2 are used as barcode, and particularly biases the detection of Basidiomycota. The complementary analysis of both ITS1 and ITS2 loci is therefore required to reliably estimate the diversity of lichen mycobiomes.
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Affiliation(s)
- Elisa Banchi
- Department of Life Sciences, University of Trieste, Via Giorgieri 10, 34127 Trieste, Italy
| | - David Stankovic
- Department of Life Sciences, University of Trieste, Via Giorgieri 10, 34127 Trieste, Italy
- National Institute of Biology, Marine Biology Station, Fornače 41, 6330 Piran, Slovenia
| | | | - Fabrizia Gionechetti
- Department of Life Sciences, University of Trieste, Via Giorgieri 10, 34127 Trieste, Italy
| | - Alberto Pallavicini
- Department of Life Sciences, University of Trieste, Via Giorgieri 10, 34127 Trieste, Italy
| | - Lucia Muggia
- Department of Life Sciences, University of Trieste, Via Giorgieri 10, 34127 Trieste, Italy
- Institute of Plant Sciences, Karl-Franzens University of Graz, Holteigasse 6, 8010 Graz, Austria
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150
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Thines M, Crous PW, Aime MC, Aoki T, Cai L, Hyde KD, Miller AN, Zhang N, Stadler M. Ten reasons why a sequence-based nomenclature is not useful for fungi anytime soon. IMA Fungus 2018; 9:177-183. [PMID: 30018878 PMCID: PMC6048572 DOI: 10.5598/imafungus.2018.09.01.11] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 05/23/2018] [Indexed: 11/08/2022] Open
Abstract
The large number of species still to be discovered in fungi, together with an exponentially growing number of environmental sequences that cannot be linked to known taxa, has fuelled the idea that it might be necessary to formally name fungi on the basis of sequence data only. Here we object to this idea due to several shortcomings of the approach, ranging from concerns regarding reproducibility and the violation of general scientific principles to ethical issues. We come to the conclusion that sequence-based nomenclature is potentially harmful for mycology as a discipline. Additionally, a classification based on sequences as types is not within reach anytime soon, because there is a lack of consensus regarding common standards due to the fast pace at which sequencing technologies develop.
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Affiliation(s)
- Marco Thines
- Goethe University, Department of Biological Sciences, Institute of Ecology, Evolution and Diversity, Max-von-Laue-Str. 13, D-60483 Frankfurt am Main, Germany
- Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage 25, D-60325 Frankfurt am Main, Germany
| | - Pedro W. Crous
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - M. Catherine Aime
- Department of Botany and Plant Pathology, Purdue University, 915 W. State Street, West Lafayette, IN 47907, USA
| | - Takayuki Aoki
- Genetic Resources Center, National Agriculture and Food Research Organization (NARO), 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
| | - Lei Cai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, NO.1 Beichen West Road, Chaoyang District, Beijing 100101, China
| | - Kevin D. Hyde
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai 57100, Thailand
| | - Andrew N. Miller
- Illinois Natural History Survey, University of Illinois, 1816 South Oak Street, Champaign, IL 61820, USA
| | - Ning Zhang
- Department of Plant Biology, Rutgers University, 59 Dudley Road, Foran Hall 201, New Brunswick, New Jersey 08901, USA
| | - Marc Stadler
- Department of Microbial Drugs, Helmholtz-Zentrum für Infektionsforschung, Inhoffenstrasse 7, D-38124 Braunschweig, Germany
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